diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 00000000..ab03fb2f --- /dev/null +++ b/.gitattributes @@ -0,0 +1,6 @@ +# Keep the third-party parser separate in reviews and preserve upstream bytes. +src/bin/nlohmann/json.hpp linguist-vendored +src/bin/nlohmann/LICENSE.MIT linguist-vendored -whitespace +gui/vendor/plotly-cartesian.min.js linguist-vendored +gui/vendor/plotly.css linguist-vendored +gui/vendor/plotly-LICENSE.txt linguist-vendored -whitespace diff --git a/.github/workflows/build-wasm.yml b/.github/workflows/build-wasm.yml new file mode 100644 index 00000000..f951d568 --- /dev/null +++ b/.github/workflows/build-wasm.yml @@ -0,0 +1,123 @@ +name: WebAssembly and web interface + +on: + pull_request: + push: + branches: [master] + workflow_dispatch: + +permissions: + contents: read + +jobs: + documentation: + uses: ./.github/workflows/documentation.yml + + build: + runs-on: ubuntu-24.04 + timeout-minutes: 60 + steps: + - uses: actions/checkout@v7 + - uses: emscripten-core/setup-emsdk@v15 + with: + version: '4.0.23' + actions-cache-folder: emsdk-cache + - name: Install native build tools + run: sudo apt-get update && sudo apt-get install --yes autoconf automake libtool pkg-config + - uses: actions/setup-node@v6 + with: + node-version: '24' + - uses: actions/setup-python@v6 + with: + python-version: '3.12' + - name: Test dependency download integrity and cache recovery + run: | + python scripts/wasm/test-downloads.py + python scripts/wasm/test-vienna-release.py + - name: Test input, worker lifecycle and CSV handling + run: npm test --prefix gui + - name: Resolve newest stable ViennaRNA 2.x release and checksum + env: + GITHUB_TOKEN: ${{ github.token }} + run: | + python scripts/wasm/vienna-release.py --latest > "$RUNNER_TEMP/vienna-release.json" + cat "$RUNNER_TEMP/vienna-release.json" + echo "WASM_VIENNA_RELEASE=$RUNNER_TEMP/vienna-release.json" >> "$GITHUB_ENV" + - name: Cross-compile dependencies and IntaRNA + run: bash scripts/wasm/build.sh + - name: Check real WASM predictions against the native reference + run: | + node scripts/wasm/smoke.mjs + node scripts/wasm/smoke-protocol.mjs + - name: Stage the static site and notices + run: bash scripts/wasm/stage.sh + - name: Install browser test tools + run: | + python -m pip install -r scripts/wasm/requirements-browser.txt + python -m playwright install --with-deps chromium firefox + - name: Exercise the browser with real WASM + run: | + python -m http.server 8765 --bind 127.0.0.1 --directory build-wasm > /tmp/intarna-http.log 2>&1 & + server_pid=$! + trap 'kill "$server_pid"' EXIT + for attempt in {1..30}; do + if curl --fail --silent http://127.0.0.1:8765/site/ > /dev/null; then break; fi + sleep 1 + done + python scripts/wasm/test-browser.py http://127.0.0.1:8765/site/ --screenshot build-wasm/browser.png + python scripts/wasm/test-browser.py http://127.0.0.1:8765/site/ --browser firefox + - uses: actions/upload-artifact@v4 + with: + name: intarna-gui + path: build-wasm/site + if-no-files-found: error + + package: + needs: [build, documentation] + runs-on: ubuntu-24.04 + steps: + - uses: actions/download-artifact@v4 + with: + name: intarna-documentation + path: _site + - uses: actions/download-artifact@v4 + with: + name: intarna-gui + path: _site/gui + - name: Verify documentation and browser interface coexist + run: | + test -s _site/index.html + test -s _site/api/index.html + test -s _site/gui/index.html + test -s _site/gui/wasm/intarna.wasm + test -s _site/gui/vendor/plotly-cartesian.min.js + test -s _site/gui/vendor/plotly.css + test -s _site/gui/licenses/Plotly.txt + - uses: actions/upload-artifact@v4 + with: + name: intarna-pages-preview + path: _site + - name: Upload GitHub Pages artifact + if: github.repository == 'BackofenLab/IntaRNA' && github.ref == 'refs/heads/master' && github.event_name != 'pull_request' + uses: actions/upload-pages-artifact@v4 + with: + path: _site + + deploy: + if: github.repository == 'BackofenLab/IntaRNA' && github.ref == 'refs/heads/master' && github.event_name != 'pull_request' + needs: package + runs-on: ubuntu-24.04 + permissions: + pages: write + id-token: write + concurrency: + group: github-pages + cancel-in-progress: false + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + steps: + - uses: actions/configure-pages@v5 + - name: Deploy tested site and existing documentation + id: deployment + uses: actions/deploy-pages@v4 diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 18668a64..b8baddd9 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -4,7 +4,6 @@ on: push: branches: [master] pull_request: - branches: [master] defaults: run: diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index c0b774f4..79a365fa 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -1,10 +1,7 @@ name: Documentation on: - push: - branches: [master] - pull_request: - branches: [master] + workflow_call: workflow_dispatch: permissions: @@ -47,24 +44,9 @@ jobs: test -s _site/index.html test -s _site/doc/figures/icon-up.28.png - - name: Upload documentation for review and deployment - uses: actions/upload-pages-artifact@v4 + - name: Upload documentation for the combined Pages site + uses: actions/upload-artifact@v4 with: + name: intarna-documentation path: _site retention-days: 7 - - deploy: - name: Publish documentation - if: github.repository == 'BackofenLab/IntaRNA' && github.ref == 'refs/heads/master' && github.event_name != 'pull_request' - needs: build - runs-on: ubuntu-24.04 - permissions: - pages: write - id-token: write - environment: - name: github-pages - url: ${{ steps.deployment.outputs.page_url }} - steps: - - name: Deploy GitHub Pages - id: deployment - uses: actions/deploy-pages@v4 diff --git a/.gitignore b/.gitignore index ee819cc0..f09485a9 100644 --- a/.gitignore +++ b/.gitignore @@ -82,3 +82,10 @@ python/intarnapvalue.* /IntaRNA.pc /IntaRNA.exe.stackdump /py-compile + +# Browser build outputs and local test dependencies +/build-wasm/ +/gui/wasm/ +/gui/node_modules/ + +/scripts/wasm/__pycache__/ diff --git a/ChangeLog b/ChangeLog index 09158edc..54b1340f 100644 --- a/ChangeLog +++ b/ChangeLog @@ -14,6 +14,58 @@ ## Interface and handling +- refine GUI seed and CSV control widths, filter examples by task, cap result + table height and use dark active tabs for additional output views (PR #303 review) + +- compact and left-align GUI parameter rows, split CSV controls into their own + tab, describe every additional output format and plot energy/probability files + with sequence names, source tabs and PNG export (PR #287 review) + +- reorganize GUI parameters, add conditional seed/accessibility controls and + grouped CSV defaults, expand FASTA limits and refine result headers (PR #299) + +- retain computed GUI runs as named, foldable sessions with JSON input restoration, + independent outputs, per-session ZIP export and deletion (PR #297 review) + +- permit clearing inherited CSV sorting when replaying JSON as text reports; + validate JSON/GUI behavior in native release/debug and real browsers (#287) + +- show prediction/evaluation tasks as always-visible choices with task-specific + descriptions and an expanded Seeds/Accessibility heading (PR #287 review) + +- upload or drop local FASTA files into each GUI strand with validation and + protection against stale asynchronous reads (PR #287 review) + +- clear all inputs on GUI reset and load named examples from maintainable JSON + files through an Example menu (PR #287 review) + +- load/store GUI settings as portable JSON; ZIPs contain parameter.json with + embedded inputs/provenance and all outputs (PR #287 review) + +- use one embedded-input JSON parameter document for each WASM invocation + (PR #287 review) + +- accept JSON parameter files with embedded text inputs and personality defaults + through --parameterFile while retaining legacy configuration (PR #287 review) + +- rename the browser interface directory and Pages URL to gui (PR #287 review) + +- add selected-interaction vaRRI embeds and reproducible all-output ZIP downloads + to the browser interface; compact parameters into accessible tabs and update + the Freiburg group header and full-width result/footer notes (PR #287 review) + +- extend the browser interface with vaRRI styling, prediction/evaluation tasks, + multi-FASTA, start indices, CLI parameter groups, selectable CSV columns and + additional output previews/downloads; label pair-relative differences mfe Δ + and display actual compiled versions (PR #287 review) + +- display sortable/filterable browser results and native CSV downloads; + publish the tested interface alongside existing Pages documentation (#286) + +- add responsive browser FASTA inputs, validation and abort dialog (#286, step 3) + +- run browser predictions in cancellable, isolated Web Workers (#286, step 2) + - orient probability SVGs from the upper-left corner and highlight every MFE pair, splitting seed/MFE cell borders into orange and green (PR #259 review) @@ -68,6 +120,28 @@ ## Technical changes and Optimizations +- reduce ordinary heuristic ensemble runtime by batching more source boundaries + and avoiding exhaustive span probes for sparse seed domains (issue #301) + +- record JSON/WASM/browser regression validation and preserve pinned JSON vendor + checksums while marking upstream files as vendored for review (PR #287) + +- build WASM with ViennaRNA 2.7.2 locally and the newest stable 2.x in CI; + verify published archive checksums, isolate versioned caches and retain + selected dependency provenance and notices (PR #292 review) + +- BUGFIX : restore WASM dependency downloads using the pinned official ViennaRNA + release asset; verify downloads before caching and recover invalid caches + (PR #291) + +- annotate inherited virtual methods/destructors with override, preserve compiled + WASM asset provenance through staging, and expand protocol/browser validation + for the PR #287 review + +- cross-compile IntaRNA and pinned dependencies to WebAssembly (#286, step 1) +- verify browser predictions against native accessibility/energy references and + exercise real WASM cancellation and nested Pages paths in Chromium/Firefox + - reuse MFE seed-extension scratch matrices and bound predecessor scans in exact and heuristic prediction; evaluate physical energies directly (PR #276 review) @@ -221,6 +295,276 @@ energies, restricted partition sums, and trackers. ################################################################################ ################################################################################ +261026 Alexander Mitrofanov + * gui/app.js, gui/{index.html,styles.css}, scripts/wasm/test-browser.py + * place Explicit seeds beside a half-width Seed constraint selector and halve + the CSV sort selector width; verify desktop/mobile control geometry + * show only examples for the selected task, retain complete CSV downloads while + scrolling result tables above 500 px, and match output tab selection styling + to the parameter tabs (PR #303 maintainer review) + * gui/docs/{json-workflow,step3-frontend-ui,step4-results-and-deployment}.md + * document task-specific examples, compact controls and the bounded result table + +261026 Alexander Mitrofanov + * gui/{app,options,sessions,output-visualization}.js, + gui/{index.html,styles.css} + * compact bounded parameter rows while preserving their grouping and align + wrapped labels above left-aligned controls + * move CSV sorting/column selection into a dedicated tab between Output and + Model & Energy; add content/use tooltips to all additional output formats + + show sequence-aware Plotly profiles, heatmaps and selected-spot bars beside + native file content; add header downloads and verified PNG export + * .gitattributes, gui/vendor/, scripts/wasm/stage.sh, + .github/workflows/build-wasm.yml + + vendor and checksum Plotly.js Cartesian 4.1.2, stage its MIT license and + verify both assets in the combined Pages artifact + * gui/tests/output-visualization.test.mjs, scripts/wasm/test-browser.py, + README.md, gui/docs/ + + cover signed categorical axes, file/sequence mapping, malformed data, + responsive compact layout, plot rendering and PNG downloads in real + Chromium/Firefox with the existing WASM engine + * address https://github.com/BackofenLab/IntaRNA/pull/287#issuecomment-6416573560 + * src/IntaRNA/SeededPartitionFunction.cpp + * Select sparse batch anchors by scanning admitted seeds instead of probing + every possible pair in every source span; retain the grid lookup for dense + domains and deterministic anchor order. + * Let partition-only heuristic ensembles batch up to 16 MiB of hybrid + coefficients, reducing repeated anchor-extension work without increasing + exact or pair-probability table budgets (issue #301). + * doc/analysis/{seed-extension-partition.md,heuristic-anchored-runtime.md} + * Document the adaptive anchor lookup and targeted runtime/memory tradeoff. + +261024 Alexander Mitrofanov + * gui/{app,options,columns}.js, gui/{index.html,styles.css} + * organize tabs/rows as Sequences, Seed, Output, Model & Energy, Query, + Target and CLI-only; align wrapped labels and place Compute first + + add a three-way seed selector, synchronized accessibility flags and + mode-dependent input availability; place SHAPE beside accessibility + * group compact CSV choices with descriptions and group selection actions; + default to 10 predictions and expanded task-specific energy columns, + explicitly preserving browser defaults in native-compatible JSON + * gui/{protocol,uploads,parameter-file}.js, gui/examples/ + * accept 50 FASTA records per strand of 2-5,000 nt each, with longest + selected query x longest selected target <= 1,000,000; allow 1 MB FASTA + + warn about ignored FASTA header descriptions while using first-token IDs + * gui/{sessions,results}.js + * select results from the header/name, order Show/Hide before the name and + ZIP/delete actions, compact table headings and distinguish selected rows + * gui/tests/, scripts/wasm/test-browser.py, README.md, gui/docs/ + + cover limits, native JSON replay/defaults, dependent controls, grouped CSV + choices, desktop/mobile alignment and result header selection + * address https://github.com/BackofenLab/IntaRNA/pull/299#issuecomment-6375752155 + +261023 Alexander Mitrofanov + * gui/{app,sessions,results,visualization}.js, gui/{index.html,styles.css} + + retain successful runs in browser memory with unique IDs, editable names, + independent results/diagnostics and JSON snapshots of their computed inputs + * restore inputs and fold other output areas on selection; preserve sessions + across edits, reset, imports, failures and aborts; unload folded viewers + + export each session's original JSON/outputs from its header and delete it + without overwriting editable inputs; keep controls keyboard accessible + * scripts/wasm/{stage.sh,test-browser.py}, README.md, gui/docs/ + * stage the sessions module, exercise session lifetime and archive isolation + in real browsers, and document temporary storage and updated reset behavior + * follow-up to https://github.com/BackofenLab/IntaRNA/pull/297#issuecomment-6367326708 + +261023 Alexander Mitrofanov + * .gitattributes, gui/docs/json-workflow.md + + Preserve exact upstream license whitespace and mark the JSON header and + license as vendored. Record native release/debug, WASM replay, browser, + distribution and provenance validation for the PR #287 revisions. + +261023 Alexander Mitrofanov + * src/bin/CommandLineParsing.cpp, ParameterFile.h, tests/testParameterFile.py + * Accept an explicitly empty CSV sort value to clear a parameter-file + setting when reproducing non-CSV reports from the same JSON document. + * gui/app.js, gui/styles.css, scripts/wasm/test-browser.py + * Keep pending auxiliary-file reads from restoring reset inputs, return + Reset to Sequence input and make the entire task label clickable. + * doc/{Makefile.am,json-parameters.md} + + Include JSON format documentation in source distributions and record the + observed WASM footprint and reproducible dependency comparison (#287). + +261023 Alexander Mitrofanov + * gui/{index.html,app.js,styles.css}, scripts/wasm/test-browser.py + * Replace the task dropdown with visible, highlighted native radio choices + and task descriptions; update the heading to include Seeds/Accessibility. + * Keep Example, Reset, Load and Store adjacent and test keyboard selection + and responsive layout (PR #287 review). + +261023 Alexander Mitrofanov + * gui/{uploads.js,app.js,index.html,styles.css}, gui/docs/json-workflow.md + + Add Upload controls and file-drop hints to both FASTA headers; validate + file size/contents before replacing a strand and invalidate stale reads. + * gui/tests/uploads.test.mjs, scripts/wasm/{test-browser.py,stage.sh} + + Test local upload/drop, invalid files and reset during a pending read; + stage the file-input module (PR #287 review). + +261023 Alexander Mitrofanov + * gui/{app.js,index.html,styles.css,examples/}, gui/docs/json-workflow.md + * Reset clears inputs/results and restores defaults; example FASTA is shown + only as placeholders. Add a described Example dropdown beside Reset. + + Ship two editable JSON examples and a manifest, using the common importer. + * gui/tests/parameter-file.test.mjs, scripts/wasm/{stage.sh,test-browser.py} + + Validate/stage example files and check empty startup/reset behavior (#287). + +261023 Alexander Mitrofanov + * gui/parameter-file.js, archive.js, app.js, index.html, protocol.js + + Load and Store non-default settings and embedded inputs using native JSON; + validate imports before replacing the form and retain CSV selection order. + * ZIP exports contain only parameter.json and outputs. Record version and + native replay commands, including overrides for additional report formats. + * gui/tests/, scripts/wasm/{smoke-protocol.mjs,test-browser.py,stage.sh}, + gui/docs/{json-workflow.md,step4-results-and-deployment.md} + + Test JSON round trips, invalid imports, real WASM replay and output equality; + stage the serializer and nlohmann/json license (PR #287 review). + +261023 Alexander Mitrofanov + * gui/protocol.js, gui/intarna-worker.js, gui/tests/protocol.test.mjs, + gui/docs/step2-worker-architecture.md + * Pass --parameterFile=/parameter.json to each WASM instance using the + native JSON format with embedded FASTA, SHAPE and accessibility text. + Preserve native output routing and independent report invocations (#287). + +261023 Alexander Mitrofanov + * src/bin/ParameterFile.{h,cpp}, CommandLineParsing.{h,cpp}, Makefile.am + + Detect JSON parameter files; reuse native CLI validation and precedence, + support embedded input text and retain files until computation finishes. + * Honor parameter-file personalities when selecting native defaults. + * src/bin/nlohmann/, doc/json-parameters.md, README.md, scripts/wasm/stage.sh + + Vendor nlohmann/json 3.12.0 with its license, document the schema, + dependency tradeoff and reproduction contract (PR #287 review). + * tests/runParameterFile.sh, tests/testParameterFile.py, tests/Makefile.am + + Check legacy/JSON equivalence, embedded inputs, precedence and errors. + +261023 Alexander Mitrofanov + * gui/, scripts/wasm/, .github/workflows/build-wasm.yml, README.md, + doc/api-documentation.md, .gitignore + * Rename webinterface to gui, including imports, staging, tests and the + combined Pages artifact at /IntaRNA/gui/ (PR #287 review). + +261022 Alexander Mitrofanov + * scripts/wasm/{vienna-release.py,vienna-release.json}, build.sh + + Resolve the newest stable ViennaRNA >=2.7.2 and <3 from all official GitHub + release pages in CI; require its release tarball and published SHA-256. + * Pin 2.7.2 for reproducible local builds and accept saved release manifests. + Isolate RNAlib sources/installations and IntaRNA objects by archive identity + and keep Boost/zlib in a separate prefix to prevent reuse or include-path + shadowing of libraries/headers from another release (PR #292). + * scripts/wasm/patch-vienna.py + - Remove the dlib 19.24 compatibility patch; ViennaRNA 2.7.2 bundles dlib 20.0. + * scripts/wasm/{write-build-info.mjs,stage.sh,smoke-protocol.mjs,test-browser.py} + * Record the selected archive URL/checksum, check the compiled ViennaRNA + version, stage matching dependency notices and test actual version exports. + * scripts/wasm/test-vienna-release.py, .github/workflows/build-wasm.yml + + Cover numeric version selection, pagination, major-3/prerelease exclusion, + missing/invalid asset metadata, API failures, manifest validation and + rejection of compiled engines with a stale ViennaRNA version. + * webinterface/docs/step1-wasm-compilation.md + * Document latest-2.x CI selection, pinned local reproduction, versioned + caches, current bundled dlib and archive provenance. + +261022 Alexander Mitrofanov + * scripts/wasm/{build,download}.sh + * Use the official GitHub ViennaRNA 2.7.0 release asset and pin its SHA-256; + the university endpoint returned a short HTTP 200 text response, failing + the WASM build before compilation (PR #291). + + Verify archives before caching, discard invalid cached responses and remove + failed partial downloads so rerunning a build can recover automatically. + * scripts/wasm/test-downloads.py, .github/workflows/build-wasm.yml + + Test verified-cache reuse, invalid-cache recovery, checksum failures, + HTTP errors and truncated transfers against a local HTTP server in CI. + * webinterface/docs/step1-wasm-compilation.md + * Document the release source, archive verification and download regression + command, including recovery behavior for failed or outdated caches. + +261022 Alexander Mitrofanov + * webinterface/{archive,visualization}.js + + Build local UTF-8 ZIPs with normalized FASTA, compiled version provenance, + portable parameter files, selected CSV, auxiliary inputs and all outputs; + include separate replay configurations for native text report modes. + + Construct selected-row vaRRI URLs from full target/query sequences, native + dot-bracket output, names and signed indices, preserving strand direction. + * webinterface/{app,results,protocol}.js, index.html, styles.css + + Add row selection, embedded vaRRI/full-viewer link and Download ZIP action; + preserve completed-run inputs and clear exports/viewer when inputs change. + * Replace folded groups with keyboard-accessible tabs and compact parameter + grids; link Bioinformatics - University of Freiburg to the group website + and remove artificial width limits from table/footer notes. + * scripts/wasm/{stage.sh,smoke-protocol.mjs,test-browser.py} + * Stage the new modules; verify byte-identical replay through fresh engines + and browser tab/selection/ZIP behavior in Chromium and Firefox. + * webinterface/tests/export.test.mjs, README.md, webinterface/docs/* + + Cover coordinate/identity mapping, effective settings and archive inputs; + document replay commands, external visualization and browser limitations + (https://github.com/BackofenLab/IntaRNA/pull/287#issuecomment-6321503136). + +261021 Alexander Mitrofanov + * src/IntaRNA/*.h + * Mark 194 inherited virtual methods and 45 derived destructors override; + keep algorithms, interfaces and third-party headers unchanged. + * webinterface/{options,columns,protocol,app,results,intarna-worker}.js + + Add CLI-based parameter groups and validation, multi-FASTA prediction, + signed per-strand start indices and IntaRNAeval structure evaluation. + + Provide all CSV columns, table visibility controls, pair-relative mfe Δ, + local SHAPE/accessibility data and previews/downloads of native extra files. + * webinterface/index.html, styles.css, assets/* + * Follow vaRRI main-v2 colors and institutional header; keep one parameter + group open at a time and adapt controls/defaults to the selected task. + * scripts/wasm/{build,stage}.sh, write-build-info.mjs + + Record actual compiled engine/library versions and asset hashes in text/JSON + at build time; preserve/check provenance during staging and show it in UI. + * Reject inconsistent missing overrides in the Emscripten build. + * webinterface/tests/*, scripts/wasm/{smoke-protocol.mjs,test-browser.py} + + Exercise task validation/defaults, real WASM evaluation/prediction, multiple + records/coordinates, imported data, columns/reports and worker lifecycle. + * .github/workflows/{build,build-wasm}.yml, README.md, webinterface/docs/* + * Run WASM/browser checks on dependent PRs and document revised behavior, + provenance, native option replacements and browser limits (PR #287 review). + +261020 Alexander Mitrofanov + * scripts/wasm/*, .github/workflows/build-wasm.yml, webinterface/app.js + + Execute dependency API probes and test structured accessibility costs, + native prediction references, C++ errors, nested paths and literal IDs. + * Download archives atomically and clear obsolete diagnostics on input edits. + * webinterface/docs/step4-results-and-deployment.md + + Record native API/CLI, real WASM and Chromium/Firefox validation (#286). + +261020 Alexander Mitrofanov + * webinterface/results.js, app.js, index.html, styles.css, tests/*, README.md + + Parse native CSV, preserve target/query orientation and inclusive indices, + and show energy/relative suboptimality with sorting, search and export. + * scripts/wasm/stage.sh, test-browser.py, .github/workflows/* + + Stage matching WASM assets, notices and provenance; verify the real engine + in Chromium and Firefox, including cancellation/restart and error recovery. + * Publish one combined Pages artifact with the existing guide/API and the + browser application at /webinterface/ (#286, step 4). + +261020 Alexander Mitrofanov + * webinterface/index.html, app.js, styles.css, mark.svg, docs/* + + Add paired query/target editors, a valid example, bounded RNA/FASTA + validation and result counts; normalize lowercase and DNA input. + + Keep the form responsive during predictions, display errors/diagnostics, + and abort by button or Escape (#286, step 3). + +261020 Alexander Mitrofanov + * webinterface/protocol.js, intarna-worker.js, runner.js, tests/* + + Validate FASTA at the worker boundary, run the existing CLI with MEMFS + input/output, and report CSV and bounded diagnostics asynchronously. + + Terminate each worker on completion, failure or abort; test clean restart + and stale-message handling (#286, step 2); document the worker protocol. + +261020 Alexander Mitrofanov + * scripts/wasm/*, .github/workflows/build-wasm.yml, configure.ac, + src/bin/Makefile.am, src/IntaRNA/Makefile.am + + Build pinned zlib, Boost and ViennaRNA for wasm32, then the existing + IntaRNA CLI as an isolated ES module with MEMFS and callMain exports. + * Omit pthread flags for single-thread Emscripten builds; retain native flags. + * Resolve generated CLI headers/pkg-config data in the build tree; adapt + bundled dlib Unicode and template code to the SDK libc++ and Clang. + + Document the toolchain and validate native-reference predictions in WASM + (https://github.com/BackofenLab/IntaRNA/issues/286, step 1). + 261020 Alexander Mitrofanov * PredictorMfe2dSeedExtension.*, PredictorMfe2dHeuristicSeedExtension.cpp - Remove extensionLoopE(), the local loop-energy table, known-value flags, diff --git a/README.md b/README.md index 5bbfd8d0..aeaab169 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,19 @@ + # IntaRNA [![releases](https://img.shields.io/github/tag/BackofenLab/IntaRNA.svg)](https://github.com/BackofenLab/IntaRNA/releases) [![Bioconda](https://anaconda.org/bioconda/intarna/badges/version.svg)](https://anaconda.org/bioconda/intarna) **Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites** +Predict short RNA pairs or evaluate supplied structures locally with the [browser interface](https://backofenlab.github.io/IntaRNA/gui/). +The browser accepts up to 50 records per strand, 2–5,000 nucleotides each, with longest selected query × longest selected target at most 1,000,000. Prediction defaults to 10 interactions per pair and includes opening and seed energies; evaluation selects all energy columns. +Computed runs stay in separate, foldable sessions under Results in the current tab. Name and select sessions to restore their inputs and compare results; editing or resetting parameters keeps earlier runs. +Select an interaction to view it in vaRRI, or download a session’s ZIP with inputs, compiled versions, reproducible parameters and all outputs. Sessions are temporary and are cleared when the page is reloaded. +Minimum-energy and interaction-probability output files include local Plotly visualizations with PNG export; every additional file retains its original text view and download. +See the [WebAssembly build instructions](gui/docs/step1-wasm-compilation.md) and +[interface/deployment notes](gui/docs/step4-results-and-deployment.md). + + During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repressionex @@ -23,7 +33,7 @@ as well as the existence of a user-definable seed interaction. We successfully a IntaRNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs. -For testing or ad hoc use of IntaRNA, you can use its webinterface at the +For testing or ad hoc use of IntaRNA, you can use its gui at the **==> [Freiburg RNA tools IntaRNA webserver](http://rna.informatik.uni-freiburg.de/IntaRNA/) <==** @@ -497,6 +507,11 @@ using `configure --disable-multithreading`.
+JSON parameter files, including embedded FASTA, accessibility, SHAPE and energy +parameter text, are also accepted by `--parameterFile` with automatic format +detection. See [JSON format, examples and precedence](doc/json-parameters.md). + + ## Load arguments from file If you are using IntaRNA with similar command line arguments (parameters), you diff --git a/configure.ac b/configure.ac index aeb4e0c9..11d72849 100644 --- a/configure.ac +++ b/configure.ac @@ -252,7 +252,10 @@ AS_IF([test x"$multithreadingEnabled" = x"yes"], [ ], [ AC_DEFINE([INTARNA_MULITHREADING], [0], [Disabling multi-threading support]) AC_SUBST([INTARNA_MULITHREADING],[0]) - AM_CXXFLAGS="$AM_CXXFLAGS -pthread" + # Emscripten's single-thread runtime supplies mutex stubs. -pthread would + # instead require SharedArrayBuffer and cross-origin isolation on Pages. + AS_CASE([$host_os], [emscripten*], [], + [AM_CXXFLAGS="$AM_CXXFLAGS -pthread"]) ]) ############################################################################### diff --git a/doc/Makefile.am b/doc/Makefile.am index 25910558..cf899e71 100644 --- a/doc/Makefile.am +++ b/doc/Makefile.am @@ -6,6 +6,7 @@ EXTRA_DIST = \ conda.txt \ api-documentation.md \ + json-parameters.md \ build-api.sh \ check-api.py \ doxygen.cfg \ diff --git a/doc/analysis/heuristic-anchored-runtime.md b/doc/analysis/heuristic-anchored-runtime.md index 816f04a2..8462ef59 100644 --- a/doc/analysis/heuristic-anchored-runtime.md +++ b/doc/analysis/heuristic-anchored-runtime.md @@ -43,6 +43,13 @@ passes join the same retained roots and use the same complete boundary factors. This reduces heuristic contraction work; one-sided paths can still require a full right table. See the [recurrence description](seed-extension-partition.md). +For ordinary prediction without pair-probability output, each batch may use up +to 16 MiB for its only complete-boundary table, still capped at 256 sources. +This reduces how often anchors crossing batches are recomputed. Candidate +discovery scans admitted anchors directly when they are sparser than a span +rectangle and retains the original grid lookup for dense seed domains. Exact +and pair-output computations keep their 2 MiB-per-table target. + ## Correctness checks Release and debug validation each passed all seven test drivers. Both ran 115 diff --git a/doc/analysis/seed-extension-partition.md b/doc/analysis/seed-extension-partition.md index beda1712..55233f82 100644 --- a/doc/analysis/seed-extension-partition.md +++ b/doc/analysis/seed-extension-partition.md @@ -125,20 +125,27 @@ mass exactly once. No pair is counted merely because it lies inside an outer boundary rectangle. Partition-only mode omits the outside storage and pass. Batching avoids storing all source/endpoint combinations across the sequences. -The batch is additionally limited to a 2 MiB target for its hybrid table, with -at least one left boundary even when a single span rectangle exceeds that -budget. Pair output saves one equally sized table of boundary coefficients. -The bound is independent of whether pair output is requested, preserving the -forward computation in both modes. Larger batches reuse anchor factors across -more sources but retain more boundary coefficients. +Exact prediction and pair output target 2 MiB for each hybrid or boundary +table, with at least one left boundary even when a single span rectangle +exceeds that budget. Partition-only heuristic prediction can target 16 MiB for +its sole hybrid table. This uses the existing cap of 256 boundaries to reuse +anchor factors across more sources without enlarging exact or outside-pass +workspaces. + +Candidate discovery also adapts to the admitted seed density. When the number +of canonical anchors is smaller than one span rectangle, the backend scans +those anchors against the current batch directly. Denser domains retain the +bounded span-grid lookup. Both paths emit anchors in the same deterministic +order and feed the unchanged recurrence. With `W1=min(span1,n)`, `W2=min(span2,m)`, maximum irredundant seed length `L`, and bounded batch size `B<=256`, workspace storage is `O(W1*W2*(max(2,L)+B) + n*m + S)` for `S` anchors. The `n*m` term includes a byte-valued validity cache and, for pair output, the returned mass matrix. Partition-only mode does not allocate adjoints or saved boundary factors. -Its cost is repeated anchor-table work between batches. This is an explicit -memory/runtime tradeoff, not a claim of a general speedup. The +Its cost is repeated anchor-table work between batches. The larger heuristic +batch is an explicit memory/runtime tradeoff; exact and pair-output bounds stay +unchanged. The [benchmark records](../benchmarks/seed-extension/README.md) compare all complete boundary coefficients, partitions and pair numerators against `985ba44`, and report allocation calls, requested bytes, runtime and process RSS separately. diff --git a/doc/api-documentation.md b/doc/api-documentation.md index e7382175..cd9ad808 100644 --- a/doc/api-documentation.md +++ b/doc/api-documentation.md @@ -38,28 +38,34 @@ fatal. New unresolved references should be fixed before merging. ## GitHub Pages -`.github/workflows/documentation.yml` builds documentation on pull requests to -`master`, on pushes to `master`, and on manual dispatch. Every successful build -uploads a `github-pages` artifact for review. Only a push or manual dispatch on -`BackofenLab/IntaRNA`'s `master` can deploy; pull requests and forks cannot publish. -The deployment job alone receives Pages and OIDC write permissions. +`.github/workflows/documentation.yml` is a reusable documentation build, called +by `build-wasm.yml` for pull requests and pushes to `master`; it can also be run +manually to inspect documentation artifacts. The documentation build uploads +`intarna-documentation`, with the README-based Jekyll guide and Doxygen output +under `api/`. -The workflow first builds the existing README-based Jekyll site with its Slate -theme, then adds Doxygen output under `api/`. It publishes both together: +`build-wasm.yml` combines that artifact with the tested browser interface under +`gui/` and publishes **one** Pages artifact. This preserves the existing +guide and API; two independent publishers would overwrite each other's site. +Only a push or manual dispatch on `BackofenLab/IntaRNA`'s `master` can deploy. +Pull requests and forks cannot publish. The deployment job alone receives Pages +and OIDC write permissions, and deployments share one concurrency group. - User guide: - Development API: +- Browser interface: -### One-time activation after merge +### Pages configuration -The repository currently publishes from the root of the `master` branch. After -merging the documentation workflow, a repository administrator must select -**Settings → Pages → Build and deployment → Source → GitHub Actions**, then run -the **Documentation** workflow on `master` (or push a subsequent commit). -Retain any required approval rules on the `github-pages` environment. The PR -does not change the live publishing settings. See GitHub's +The repository already uses **Settings → Pages → Build and deployment → Source +→ GitHub Actions**. For another repository, select that source before deploying, +and deliberately adjust the deployment repository guard. Run the **WebAssembly +and web interface** workflow on `master` or push a subsequent commit. Retain any +required approval rules on the `github-pages` environment. This PR does not +change live publishing settings. See GitHub's [custom Pages workflow documentation](https://docs.github.com/en/pages/getting-started-with-github-pages/using-custom-workflows-with-github-pages). -No generated HTML, access token, or separate documentation branch is needed. -Both the existing guide and the API are included in the deployment artifact; -deploying only the API would replace the guide at the site's root. +No generated HTML, access token, or separate documentation branch is committed. +The `intarna-pages-preview` artifact contains the combined site for PR review. +See [the browser deployment notes](../gui/docs/step4-results-and-deployment.md) +for the complete build and validation sequence. diff --git a/doc/json-parameters.md b/doc/json-parameters.md new file mode 100644 index 00000000..2a694d12 --- /dev/null +++ b/doc/json-parameters.md @@ -0,0 +1,79 @@ +# JSON parameter files + +`IntaRNA --parameterFile=parameter.json` accepts the same CLI option names and +values as a legacy `key = value` file. Detection uses the first non-whitespace +character, after an optional UTF-8 BOM, independent of the filename suffix. +Legacy files remain supported. Explicit scalar CLI options override file values; +composing options such as `out` accumulate as before. A file's `personality` +selects defaults before parsing; an explicit CLI personality takes precedence. + +```json +{ + "schema": "IntaRNA-parameters-v1", + "_comment": ["Reproduce: IntaRNA --parameterFile=parameter.json"], + "parameters": { + "query": {"text": ">query\nGGGAGGAGGG\n"}, + "target": {"text": ">target\nCCCUCCUCCC\n"}, + "temperature": 25, + "outMode": "C", + "out": ["interactions.csv", "qPu:query-pu.txt"] + } +} +``` + +`parameters` contains strings, JSON numbers and booleans. Repeated/composing +options accept nonempty arrays. Flags without values accept `true` or `false`. +Unknown options, duplicate keys, null values, unsupported nested values and +recursive `parameterFile` are errors. Existing native type, range and cross-option +validation still applies. JSON uses normal JSON escapes; `#`, whitespace and +newlines in string values are not interpreted as legacy configuration syntax. + +The optional `_comment` field holds provenance and reproduction instructions as +ordinary JSON data, so files work with standard JSON parsers. Optional `gui` +metadata describes browser-only output selections and is ignored by the CLI. +Other document fields and unsupported schema versions are rejected. + +## Embedded inputs + +For `query`, `target`, `qAccFile`, `tAccFile`, `qShape`, `tShape` and `energyVRNA`, +use `{"text": "file contents"}` to embed UTF-8 text. FASTA may contain multiple +records. Accessibility uses RNAplfold text; SHAPE and energy parameters retain +their native formats. Ordinary strings retain their original meaning (sequence, +preset or filesystem path). Relative paths remain relative to the working +directory, as with legacy configuration files. Binary `.agz` caches can still be +referenced by path; they are not a text encoding. + +For accessibility of multiple selected records, `{"texts": ["record 1 data", +"record 2 data"]}` materializes files with the existing `-sN` suffixes, indexed by +original FASTA record number. Use `text` when selecting a single record. No +user-specified paths are used for embedded files. A private temporary directory +keeps generated files alive for the entire prediction and removes them on normal +exit or exception unwinding. WASM uses its private in-memory filesystem. Like +other temporary resources, abrupt process termination can leave native files. + +## Dependency choice + +We evaluated [Boost.JSON](https://www.boost.org/doc/libs/1_87_0/libs/json/doc/html/json/overview.html) +and [nlohmann/json](https://json.nlohmann.me/integration/). Both provide typed JSON +and can avoid a separately linked JSON library. Boost.JSON would raise our +current Boost 1.50 minimum to a release containing JSON, or require another +vendored Boost component and its dependency integration. Boost.PropertyTree is +already available but loses JSON scalar/array type distinctions needed here. + +We chose the unmodified, MIT-licensed nlohmann/json 3.12.0 single header (953,436 +bytes), compiled in one CLI translation unit. It adds no system package, linker +flag, public library API or WASM build dependency. The tradeoff is a vendored +header to maintain and extra compile/binary size; the parser is outside prediction +loops. Checksums and update instructions live in `src/bin/nlohmann/README.md`. +The source distribution and staged GUI include the license. + +### Observed WASM footprint + +With Emscripten 4.0.23, ViennaRNA 2.7.2 and Boost 1.87.0 using +`scripts/wasm/build.sh`, the cached pre-JSON engine at `d44d7a6` is 3,217,224 bytes +(781,737 bytes with Python `gzip.compress(..., mtime=0)`). The JSON-enabled engine +is 3,362,458 bytes (823,241 gzip): an increase of 145,234 bytes raw and 41,504 +compressed. These are local artifact-size observations with matching dependency +versions, not runtime benchmarks or guarantees for other toolchains. Reproduce +by building both revisions, comparing `site/wasm/intarna.wasm`, and checking +`site/build-info.json` for compiler/library provenance. diff --git a/gui/app.js b/gui/app.js new file mode 100644 index 00000000..c95fcff2 --- /dev/null +++ b/gui/app.js @@ -0,0 +1,398 @@ +import { parseFasta, prepareRequest, CSV_COLUMNS } from './protocol.js'; +import { GROUPS, FIELDS, EXTRA_OUTPUTS, UI_DEFAULTS } from './options.js'; +import { CSV_CATALOG, CSV_GROUPS, defaultColumns } from './columns.js'; +import { PredictionRunner } from './runner.js'; +import { downloadText } from './results.js'; +import { SessionsView } from './sessions.js'; +import { importParameters, serializeParameters, MAX_PARAMETER_BYTES } from './parameter-file.js'; +import { readFastaFile } from './uploads.js'; + +const byId = (id) => document.getElementById(id); +const form = byId('prediction-form'), runner = new PredictionRunner(); +const getTask = () => form.querySelector('input[name=task]:checked').value; +const setTask = (task) => { for (const input of form.querySelectorAll('input[name=task]')) input.checked = input.value === task; }; +const dialog = byId('loading'), status = byId('result-status'), errorBox = byId('input-error'); +const sessions = new SessionsView(byId('sessions'), byId('session-template'), (request, name) => { + applyParameters(request, `${name} selected. Its computed inputs have been restored.`); +}, showInputError, (message) => { status.textContent = message; }); +const csvInputs = [], outputInputs = []; +let inputRevision = 0; +let csvOrder = CSV_COLUMNS.split(','); +function element(tag, text, className) { + const node = document.createElement(tag); + if (text) node.textContent = text; + if (className) node.className = className; + return node; +} +function activateGroup(key, focus = false) { + for (const tab of byId('parameter-tabs').children) { + const active = tab.getAttribute('aria-controls') === key; + tab.setAttribute('aria-selected', String(active)); tab.tabIndex = active ? 0 : -1; + byId(tab.getAttribute('aria-controls')).hidden = !active; + if (active && focus) tab.focus(); + } +} +function addTab(key, label) { + const tab = element('button', label); tab.type = 'button'; tab.id = `tab-${key}`; + tab.setAttribute('role', 'tab'); tab.setAttribute('aria-controls', key); + tab.addEventListener('click', () => activateGroup(key)); + byId('parameter-tabs').append(tab); +} +function group(key, label) { + const panel = element('section', '', 'parameter-group'); panel.id = key; + panel.setAttribute('role', 'tabpanel'); panel.setAttribute('aria-labelledby', `tab-${key}`); + const body = element('div', '', 'group-body'); panel.append(body); + byId('parameter-groups').append(panel); addTab(key, label); return body; +} +addTab('sequence-input', 'Sequences'); +byId('parameter-tabs').addEventListener('keydown', (event) => { + if (!['ArrowLeft', 'ArrowRight', 'Home', 'End'].includes(event.key)) return; + const tabs = [...byId('parameter-tabs').children].filter((tab) => !tab.hidden); + const current = tabs.indexOf(document.activeElement); + const next = event.key === 'Home' ? 0 : event.key === 'End' ? tabs.length - 1 : (current + (event.key === 'ArrowRight' ? 1 : -1) + tabs.length) % tabs.length; + event.preventDefault(); activateGroup(tabs[next].getAttribute('aria-controls'), true); +}); +// Render each requested row explicitly; labels share a grid row so wrapped +// labels do not push neighboring controls out of alignment. +function renderField(field, id = field.key) { + const wrapper = element('div', '', `field${field.type === 'checkbox' ? ' check' : ''}`); + const label = element('label', field.label); label.htmlFor = id; label.title = `--${field.key}`; + const input = element(field.type === 'select' ? 'select' : field.type === 'textarea' ? 'textarea' : 'input'); input.id = id; + if (input.tagName === 'INPUT') input.type = field.type; + if (field.type === 'select') for (const [value, name] of Object.entries(field.choices)) { const option = element('option', name); option.value = value; input.append(option); } + if (field.type === 'number') { input.min = field.min; input.max = field.max; input.step = field.step ?? 1; } + if (field.type === 'checkbox') { input.checked = field.value; wrapper.append(input, label); } + else { input.value = field.value; wrapper.append(label, input); } + if (field.hint) { const hint = element('p', field.hint, 'field-hint'); hint.id = `${id}-help`; input.setAttribute('aria-describedby', hint.id); wrapper.append(hint); } + if (field.type === 'textarea') { + input.spellcheck = false; + const upload = element('input'); upload.type = 'file'; upload.accept = '.txt,.csv,.shape,.dat'; upload.setAttribute('aria-label', `Load ${field.label} from a local text file`); + upload.dataset.for = field.key; + upload.addEventListener('change', async () => { + const file = upload.files[0]; upload.value = ''; if (!file) return; + const revision = ++inputRevision; + try { + if (file.size > 1000000) throw new Error('Choose a text file of at most 1 MB.'); + const content = await file.text(); + if (inputRevision !== revision || input.disabled) return; + input.value = content; input.dispatchEvent(new Event('input', { bubbles: true })); + } catch (error) { if (inputRevision === revision) showInputError(error); } + }); wrapper.append(upload); + } + if (field.key === 'noSeed') wrapper.hidden = true; + return wrapper; +} +function fieldRow(body, fields, suffix = '') { + const grid = element('div', '', `field-grid columns-${fields.length}`); + for (const field of fields) grid.append(renderField(field, field.key + suffix)); + body.append(grid); return grid; +} +for (const definition of GROUPS) { + const body = group(definition.key, definition.label); + if (definition.key === 'seed-options') { + const primary = element('div', '', 'seed-primary-row'); + const wrapper = element('div', '', 'field seed-mode'); + const label = element('label', 'Seed constraint'); label.htmlFor = 'seed-mode'; + const select = element('select'); select.id = 'seed-mode'; + for (const [value, name] of [['none', 'Disable seed constraint'], ['explicit', 'Explicit seed'], ['identify', 'Identify seeds']]) { + const option = element('option', name); option.value = value; select.append(option); + } + select.value = 'identify'; wrapper.append(label, select); + primary.append(wrapper, renderField(FIELDS.find((field) => field.key === 'seedTQ'))); + body.append(primary); + } + if (definition.rows) { + for (const row of definition.rows) { + if (definition.key === 'seed-options' && row[0].key === 'seedTQ') continue; + fieldRow(body, row); + } + } else fieldRow(body, definition.fields); + if (definition.strand) { + const p = definition.strand; + const shared = FIELDS.filter((field) => ['accNoLP', 'accNoGUend'].includes(field.key)); + fieldRow(body, shared, p === 't' ? '-target' : ''); + body.append(element('p', 'These two accessibility settings apply to both strands.', 'input-help')); + const columns = element('div', '', 'accessibility-columns'); body.append(columns); + const accessibility = element('div'), shape = element('div'); columns.append(accessibility, shape); + const field = (key) => FIELDS.find((entry) => entry.key === p + key); + fieldRow(accessibility, [field('AccConstr')]); + fieldRow(accessibility, [field('AccFile')]); + fieldRow(shape, [field('Shape')]); + fieldRow(shape, [field('ShapeMethod'), field('ShapeConversion')]); + } +} +function checkbox(container, key, labelText, description) { + const label = element('label'), input = element('input'); input.type = 'checkbox'; input.value = key; + if (description) label.title = description; + label.append(input, document.createTextNode(labelText)); container.append(label); return input; +} +const csvBody = byId('csv-options').querySelector('.group-body'); +csvBody.append(element('h3', 'CSV output columns', 'subheading')); +csvBody.append(element('p', 'seq1 is the target; seq2 is the query. Hover over a column name for details. Select columns for the table and CSV download; table visibility can be changed after computation.', 'input-help')); +const selectionTools = element('div', '', 'selection-tools'); csvBody.append(selectionTools); +const selectColumns = (selection) => { + csvOrder = [...selection]; for (const input of csvInputs) input.checked = selection.includes(input.value); inputsChanged(); +}; +for (const [name, selection] of [['Select all', () => CSV_CATALOG.map((c) => c.key)], ['Task defaults', () => defaultColumns(getTask())], ['Clear selection', () => []]]) { + const button = element('button', name); button.type = 'button'; + button.addEventListener('click', () => selectColumns(selection())); selectionTools.append(button); +} +for (const group of CSV_GROUPS) { + const section = element('fieldset', '', 'csv-group'), legend = element('legend', group.label); + section.dataset.csvGroup = group.label; + for (const [name, checked] of [['Select all', true], ['Deselect all', false]]) { + const button = element('button', name, 'text-button'); button.type = 'button'; + button.setAttribute('aria-label', `${name} ${group.label} columns`); + button.addEventListener('click', () => { + for (const input of csvInputs.filter((input) => group.keys.includes(input.value))) input.checked = checked; + inputsChanged(); + }); legend.append(button); + } + const picker = element('div', '', 'checkbox-grid csv-columns'); section.append(legend, picker); csvBody.append(section); + for (const key of group.keys) { + const column = CSV_CATALOG.find((column) => column.key === key); + csvInputs.push(checkbox(picker, key, key, column.description)); + } +} +const outputBody = byId('output-options').querySelector('.group-body'); +outputBody.append(element('h3', 'Additional output files', 'subheading')); +outputBody.append(element('p', 'Reports are computed with the same settings. ASCII, detailed and ensemble reports each run a fresh engine instance and can take extra time.', 'input-help')); +const outputPicker = element('div', '', 'checkbox-grid'); outputBody.append(outputPicker); +for (const output of EXTRA_OUTPUTS) outputInputs.push(checkbox(outputPicker, output.key, output.label, output.description)); +const generalBody = group('general-options', 'CLI-only'); +generalBody.append(element('p', 'Process-level settings (threads, log paths, parameter-file paths and terminal help) are available in the CLI.')); +const docs = element('a', 'Full CLI parameter documentation'); docs.href = 'https://github.com/BackofenLab/IntaRNA#readme'; generalBody.append(docs); + +function inputsChanged(message = 'Inputs changed. Compute to update the interactions.') { + inputRevision++; + sessions.deselect(); + byId('diagnostics').hidden = true; byId('diagnostic-text').textContent = ''; status.textContent = message; +} +function updateLength(name) { + const warning = byId(`${name}-warning`); warning.hidden = true; warning.textContent = ''; + if (!byId(name).value.trim()) { byId(`${name}-length`).textContent = 'No sequence entered'; return; } + try { + const parsed = parseFasta(byId(name).value, name === 'query' ? 'Query' : 'Target', getTask() === 'prediction'); + warning.textContent = parsed.warnings.join(' '); warning.hidden = !parsed.warnings.length; + byId(`${name}-length`).textContent = `${parsed.records.length} record${parsed.records.length === 1 ? '' : 's'}, ${parsed.records.reduce((sum, r) => sum + r.sequence.length, 0).toLocaleString()} nucleotides`; + } catch { byId(`${name}-length`).textContent = 'Check sequence format and length'; } +} +function updateAvailability() { + const evaluation = getTask() === 'evaluation'; + for (const button of byId('example-options').querySelectorAll('[data-example-task]')) { + button.hidden = button.dataset.exampleTask !== getTask(); + } + byId('evaluation-input').hidden = !evaluation; + byId('task-help').textContent = evaluation ? 'Evaluate supplied structures for one query and one target. Prediction constraints are ignored.' : 'Predict interactions for all query–target sequence pairs.'; + byId('compute').textContent = evaluation ? 'Evaluate interactions' : 'Compute interactions'; + for (const definition of GROUPS) { + const tab = byId(`tab-${definition.key}`); tab.hidden = evaluation && !!definition.prediction; + if (tab.hidden) { + byId(definition.key).hidden = true; + if (tab.getAttribute('aria-selected') === 'true') activateGroup('sequence-input'); + } + for (const field of definition.fields) { + const input = byId(field.key); + input.disabled = evaluation && !!field.prediction || field.key.startsWith('helix') && byId('model').value !== 'B' || field.key === 'kineticScore' && byId('mode').value !== 'K'; + } + } + byId('noSeed').checked = byId('seed-mode').value === 'none'; + for (const field of FIELDS.filter((field) => field.key.startsWith('seed'))) { + byId(field.key).disabled = evaluation || (field.key === 'seedTQ' ? byId('seed-mode').value !== 'explicit' : byId('seed-mode').value !== 'identify'); + } + for (const p of ['q', 't']) { + const mode = byId(`${p}Acc`).value; + for (const key of ['AccW', 'AccL', 'PfScale', 'AccConstr', 'AccFile', 'Shape', 'ShapeMethod', 'ShapeConversion']) { + byId(p + key).disabled = mode === 'N' || ['AccW', 'AccL'].includes(key) && mode !== 'C' || key === 'AccFile' && !['P', 'E'].includes(mode); + } + for (const key of ['accNoLP', 'accNoGUend']) byId(key + (p === 't' ? '-target' : '')).disabled = mode === 'N'; + } + // Upload controls follow the text area they populate, including async reads. + for (const upload of form.querySelectorAll('input[data-for]')) upload.disabled = byId(upload.dataset.for).disabled; + for (const input of outputInputs) { input.disabled = evaluation && EXTRA_OUTPUTS.find((entry) => entry.key === input.value).prediction; if (input.disabled) input.checked = false; } + updateLength('query'); updateLength('target'); +} +function resetParameters({ clearInputs = false } = {}) { + if (clearInputs) { + setTask('prediction'); + byId('query').value = ''; byId('target').value = ''; + for (const input of form.querySelectorAll('input[type=file]')) input.value = ''; + byId('examples-menu').open = false; activateGroup('sequence-input'); + } + csvOrder = defaultColumns(getTask()); + byId('seed-mode').value = 'identify'; + for (const field of FIELDS) { const input = byId(field.key); if (field.type === 'checkbox') input.checked = UI_DEFAULTS[field.key]; else input.value = UI_DEFAULTS[field.key]; } + syncAccessibilityFlags(); + for (const input of csvInputs) input.checked = csvOrder.includes(input.value); + for (const input of outputInputs) input.checked = false; + byId('qIdxPos0').value = 1; byId('tIdxPos0').value = 1; byId('rri').value = ''; + updateAvailability(); errorBox.hidden = true; inputsChanged(clearInputs ? 'Inputs cleared. Enter sequences or choose an example.' : 'Parameters reset to task defaults. Compute to update the interactions.'); +} +byId('task').addEventListener('change', resetParameters); +byId('reset').addEventListener('click', () => resetParameters({ clearInputs: true })); +function syncAccessibilityFlags(source) { + for (const key of ['accNoLP', 'accNoGUend']) { + if (source?.id === key + '-target') byId(key).checked = source.checked; + byId(key + '-target').checked = byId(key).checked; + } +} +form.addEventListener('input', (event) => { + if (event.target.type === 'file') return; + syncAccessibilityFlags(event.target); + updateAvailability(); errorBox.hidden = true; inputsChanged(); +}); +function showInputError(error) { + errorBox.textContent = error.message; errorBox.hidden = false; +} +function applyParameters(request, message = 'Parameters loaded. Compute to analyze the inputs.') { + // Import validates every setting before this atomic UI update. + setTask(request.task); + resetParameters(); + for (const key of ['query', 'target', 'qIdxPos0', 'tIdxPos0', 'rri']) byId(key).value = request[key]; + for (const field of FIELDS) { + const value = request.parameters[field.key] ?? field.value; + if (field.type === 'checkbox') byId(field.key).checked = value; + else byId(field.key).value = value; + } + byId('seed-mode').value = request.parameters.noSeed ? 'none' : request.parameters.seedTQ ? 'explicit' : 'identify'; + syncAccessibilityFlags(); + csvOrder = [...request.csvColumns]; + for (const input of csvInputs) input.checked = request.csvColumns.includes(input.value); + for (const input of outputInputs) input.checked = request.outputs.includes(input.value); + updateAvailability(); activateGroup('sequence-input'); inputsChanged(message); +} +for (const strand of ['query', 'target']) { + const input = byId(strand), picker = byId(`${strand}-upload`); + const loadFasta = async (files) => { + if (byId('inputs').disabled) return; + const revision = ++inputRevision; + try { + if (files.length !== 1) throw new Error('Choose or drop one FASTA file per field.'); + const content = await readFastaFile(files[0], strand === 'query' ? 'Query' : 'Target', getTask()); + if (inputRevision !== revision) return; + input.value = content; + updateAvailability(); errorBox.hidden = true; + inputsChanged(`${strand === 'query' ? 'Query' : 'Target'} FASTA loaded. Compute to analyze the inputs.`); + } catch (error) { if (inputRevision === revision) showInputError(error); } + }; + byId(`${strand}-upload-button`).addEventListener('click', () => picker.click()); + picker.addEventListener('change', () => { const files = [...picker.files]; picker.value = ''; if (files.length) loadFasta(files); }); + input.addEventListener('dragover', (event) => { + if (event.dataTransfer.types.includes('Files')) { event.preventDefault(); event.dataTransfer.dropEffect = 'copy'; input.classList.add('drag-over'); } + }); + input.addEventListener('dragleave', () => input.classList.remove('drag-over')); + input.addEventListener('drop', (event) => { + input.classList.remove('drag-over'); + if (!event.dataTransfer.types.includes('Files')) return; + event.preventDefault(); loadFasta([...event.dataTransfer.files]); + }); +} +byId('load-parameters').addEventListener('click', () => byId('parameter-upload').click()); +byId('parameter-upload').addEventListener('change', async (event) => { + const file = event.target.files[0]; event.target.value = ''; if (!file) return; + const revision = ++inputRevision; + try { + if (file.size > MAX_PARAMETER_BYTES) throw new Error('Choose a JSON file of at most 5 MB.'); + const imported = importParameters(await file.text()); + if (inputRevision !== revision) return; + applyParameters(imported); + } catch (error) { if (inputRevision === revision) showInputError(error); } +}); +byId('store-parameters').addEventListener('click', async () => { + // Snapshot before waiting for build metadata so edits cannot change the download. + const request = currentRequest(); + try { downloadText('parameter.json', serializeParameters(request, await buildInfo)); } + catch (error) { showInputError(error); } +}); +async function loadExamples() { + const container = byId('example-options'); + try { + const response = await fetch(new URL('./examples/index.json', import.meta.url)); + if (!response.ok) throw new Error('Example list is unavailable.'); + const files = await response.json(); + if (!Array.isArray(files) || !files.length || files.some((name) => typeof name !== 'string' || !/^[a-z0-9-]+\.json$/.test(name))) throw new Error('Invalid example list.'); + const examples = await Promise.all(files.map(async (filename) => { + const response = await fetch(new URL(`./examples/${filename}`, import.meta.url)); + if (!response.ok) throw new Error('An example is unavailable.'); + const example = await response.json(); + if (typeof example.name !== 'string' || typeof example.description !== 'string') throw new Error('Invalid example description.'); + const request = importParameters(example.configuration); + prepareRequest(request); + return { ...example, request }; + })); + container.replaceChildren(); + for (const example of examples) { + const button = element('button'); button.type = 'button'; + button.dataset.exampleTask = example.request.task; + button.append(element('strong', example.name), element('span', example.description)); + button.addEventListener('click', () => { + if (byId('inputs').disabled) return; + applyParameters(example.request, `${example.name} loaded. Compute to analyze the example.`); + byId('examples-menu').open = false; + }); + container.append(button); + } + updateAvailability(); + } catch (error) { container.replaceChildren(element('p', `${error.message} Reload to try again.`, 'input-help')); } +} +loadExamples(); +byId('examples-menu').addEventListener('keydown', (event) => { + if (event.key === 'Escape') { byId('examples-menu').open = false; byId('examples-menu').querySelector('summary').focus(); } +}); +byId('abort').addEventListener('click', () => runner.abort()); +dialog.addEventListener('cancel', (event) => { event.preventDefault(); runner.abort(); }); +window.addEventListener('pagehide', () => runner.abort()); +function currentParameters() { + // Keep inactive edits in the form for toggling back, but exclude them from + // validation, saved JSON and native computation. Shared flags stay active + // whenever either strand uses accessibility. + return Object.fromEntries(FIELDS.map((field) => { + const input = byId(field.key); + const inactive = ['accNoLP', 'accNoGUend'].includes(field.key) + ? input.disabled && byId(field.key + '-target').disabled : input.disabled; + return [field.key, inactive ? field.value : field.type === 'checkbox' ? input.checked : input.value]; + })); +} +function currentRequest() { + const selected = csvInputs.filter((input) => input.checked).map((input) => input.value); + const columns = [...csvOrder.filter((key) => selected.includes(key)), ...selected.filter((key) => !csvOrder.includes(key))]; + return { + task: getTask(), query: byId('query').value, target: byId('target').value, + qIdxPos0: byId('qIdxPos0').value, tIdxPos0: byId('tIdxPos0').value, rri: byId('rri').value, + parameters: currentParameters(), + csvColumns: columns, outputs: outputInputs.filter((input) => input.checked && !input.disabled).map((input) => input.value), + }; +} +form.addEventListener('submit', async (event) => { + event.preventDefault(); + const request = currentRequest(); + errorBox.hidden = true; + let prepared; + try { + if (getTask() === 'prediction' && byId('seed-mode').value === 'explicit' && !request.parameters.seedTQ.trim()) throw new Error('Explicit seed: enter target&query dot-bar encodings.'); + prepared = prepareRequest(request); } catch (error) { errorBox.textContent = error.message; errorBox.hidden = false; return; } + inputsChanged('Computing interactions…'); byId('loading-status').textContent = 'Loading the prediction engine…'; + byId('inputs').disabled = true; byId('results').setAttribute('aria-busy', 'true'); dialog.showModal(); + try { + const result = await runner.run(request, (message) => { byId('loading-status').textContent = message; }); + // Keep the executed inputs and outputs together, independent of later edits. + const provenance = await buildInfo.catch(() => 'Compiled version information is unavailable.'); + status.textContent = sessions.add(prepared, result, provenance); + } catch (error) { + if (error.name === 'AbortError') status.textContent = 'Computation aborted. You can edit the sequences and try again.'; + else { status.textContent = 'Computation failed.'; errorBox.textContent = error.message; errorBox.hidden = false; byId('diagnostic-text').textContent = error.diagnostics || ''; byId('diagnostics').hidden = !error.diagnostics; } + } finally { + byId('inputs').disabled = false; updateAvailability(); byId('results').setAttribute('aria-busy', 'false'); dialog.close(); byId('compute').focus(); + } +}); +activateGroup('sequence-input'); +resetParameters({ clearInputs: true }); +const buildInfo = fetch(new URL('./build-info.txt', import.meta.url)).then((response) => { + if (!response.ok) throw new Error('Missing build provenance'); return response.text(); +}); +// Keep the rejection handled even if no archive is requested. +buildInfo.catch(() => {}); +fetch(new URL('./build-info.json', import.meta.url)).then((response) => { + if (!response.ok) throw new Error('Missing build provenance'); return response.json(); +}).then((info) => { byId('version-info').textContent = `IntaRNA ${info.intarna} (${info.commit.slice(0, 12)}${info.dirty ? ', modified sources' : ''}) · ViennaRNA ${info.viennarna} · Emscripten ${info.emscripten}`; }).catch(() => { byId('version-info').textContent = 'Build versions unavailable. Serve the staged interface with its compiled engine and build-info files.'; }); +if (!globalThis.Worker || !globalThis.WebAssembly) { byId('compute').disabled = true; errorBox.textContent = 'This browser needs WebAssembly and Web Workers. Use a current browser or the command line version.'; errorBox.hidden = false; } diff --git a/gui/archive.js b/gui/archive.js new file mode 100644 index 00000000..8b1995ca --- /dev/null +++ b/gui/archive.js @@ -0,0 +1,60 @@ +import { serializeParameters } from './parameter-file.js'; +import { projectCsv } from './results.js'; + +const encoder = new TextEncoder(); +const crcTable = Uint32Array.from({ length: 256 }, (_, value) => { + for (let bit = 0; bit < 8; bit++) value = (value >>> 1) ^ (value & 1 ? 0xedb88320 : 0); + return value >>> 0; +}); +function crc32(bytes) { + let crc = 0xffffffff; + for (const byte of bytes) crc = crcTable[(crc ^ byte) & 255] ^ (crc >>> 8); + return (crc ^ 0xffffffff) >>> 0; +} + +// A standard, uncompressed ZIP: local generation needs no CDN or dependency. +// Fixed timestamps and UTF-8 names make the same completed run reproducible. +export function zipFiles(files) { + const local = [], central = [], names = new Set(); + let offset = 0, directorySize = 0; + if (files.length > 65535) throw new Error('Too many files for a ZIP archive.'); + for (const file of files) { + if (!file.name || /[/\\\x00]/.test(file.name) || ['.', '..'].includes(file.name) || names.has(file.name)) throw new Error('Invalid or duplicate archive filename.'); + names.add(file.name); + const name = encoder.encode(file.name), data = encoder.encode(file.text), crc = crc32(data); + if (name.length > 65535 || offset + name.length + data.length + 30 > 0xffffffff) throw new Error('ZIP archive is too large.'); + const header = new Uint8Array(30), view = new DataView(header.buffer); + view.setUint32(0, 0x04034b50, true); view.setUint16(4, 20, true); + view.setUint16(6, 0x800, true); view.setUint16(12, 33, true); // 1980-01-01 + view.setUint32(14, crc, true); view.setUint32(18, data.length, true); view.setUint32(22, data.length, true); + view.setUint16(26, name.length, true); + local.push(header, name, data); + const entry = new Uint8Array(46), record = new DataView(entry.buffer); + record.setUint32(0, 0x02014b50, true); record.setUint16(4, 20, true); record.setUint16(6, 20, true); + record.setUint16(8, 0x800, true); record.setUint16(14, 33, true); + record.setUint32(16, crc, true); record.setUint32(20, data.length, true); record.setUint32(24, data.length, true); + record.setUint16(28, name.length, true); record.setUint32(42, offset, true); + central.push(entry, name); directorySize += entry.length + name.length; + offset += header.length + name.length + data.length; + } + const end = new Uint8Array(22), view = new DataView(end.buffer); + view.setUint32(0, 0x06054b50, true); + view.setUint16(8, files.length, true); view.setUint16(10, files.length, true); + view.setUint32(12, directorySize, true); view.setUint32(16, offset, true); + const zip = new Uint8Array(offset + directorySize + end.length); + let position = 0; + for (const bytes of [...local, ...central, end]) { zip.set(bytes, position); position += bytes.length; } + return zip; +} + +export function archiveFiles(request, result, provenance) { + return [ + { name: 'parameter.json', text: serializeParameters({ ...request, qIdxPos0: request.parameters.qIdxPos0, tIdxPos0: request.parameters.tIdxPos0 }, provenance) }, + { name: 'intarna-interactions.csv', text: projectCsv(result.csv, request.csvColumns) }, + ...result.files, + ]; +} + +export function createArchive(request, result, provenance) { + return zipFiles(archiveFiles(request, result, provenance)); +} diff --git a/gui/assets/README.md b/gui/assets/README.md new file mode 100644 index 00000000..6ede01c4 --- /dev/null +++ b/gui/assets/README.md @@ -0,0 +1,12 @@ +# Institutional header assets + +The header follows [vaRRI main-v2](https://github.com/BackofenLab/vaRRI/blob/main-v2/src/ui/components/site-header.js). +The original institutional images were downloaded on 2026-10-21 from: + +- https://www.bioinf.uni-freiburg.de/assets/images/bioinf-fr-logo-blau.png +- https://www.bioinf.uni-freiburg.de/assets/images/logo-uni-freiburg.png + +These are institutional marks of the Bioinformatics Group Freiburg and the +University of Freiburg. They identify the affiliated research group/university; +they are not covered by the IntaRNA software license. Keep their proportions and +attribution links. Local copies avoid third-party requests from the interface. diff --git a/gui/assets/bioinf-fr-logo-blau.png b/gui/assets/bioinf-fr-logo-blau.png new file mode 100644 index 00000000..0d8409ba Binary files /dev/null and b/gui/assets/bioinf-fr-logo-blau.png differ diff --git a/gui/assets/logo-uni-freiburg.png b/gui/assets/logo-uni-freiburg.png new file mode 100644 index 00000000..1e2bb249 Binary files /dev/null and b/gui/assets/logo-uni-freiburg.png differ diff --git a/gui/columns.js b/gui/columns.js new file mode 100644 index 00000000..9c096021 --- /dev/null +++ b/gui/columns.js @@ -0,0 +1,335 @@ +// Column IDs and descriptions from OutputHandlerCsv.h; seq1 = target, seq2 = query. +export const CSV_CATALOG = [ + { + "key": "id1", + "label": "Target", + "description": "id of first sequence", + "numeric": false + }, + { + "key": "id2", + "label": "Query", + "description": "id of second sequence", + "numeric": false + }, + { + "key": "seq1", + "label": "seq1", + "description": "full first sequence", + "numeric": false + }, + { + "key": "seq2", + "label": "seq2", + "description": "full second sequence", + "numeric": false + }, + { + "key": "subseq1", + "label": "subseq1", + "description": "interacting subsequence of first sequence", + "numeric": false + }, + { + "key": "subseq2", + "label": "subseq2", + "description": "interacting subsequence of second sequence", + "numeric": false + }, + { + "key": "subseqDP", + "label": "subseqDP", + "description": "hybrid subsequences compatible with hybridDP", + "numeric": false + }, + { + "key": "subseqDB", + "label": "subseqDB", + "description": "hybrid subsequences compatible with hybridDB", + "numeric": false + }, + { + "key": "start1", + "label": "Target start", + "description": "start index of hybrid in seq1", + "numeric": true + }, + { + "key": "end1", + "label": "Target end", + "description": "end index of hybrid in seq1", + "numeric": true + }, + { + "key": "start2", + "label": "Query start", + "description": "start index of hybrid in seq2", + "numeric": true + }, + { + "key": "end2", + "label": "Query end", + "description": "end index of hybrid in seq2", + "numeric": true + }, + { + "key": "hybridDP", + "label": "hybridDP", + "description": "hybrid in VRNA dot-bracket notation", + "numeric": false + }, + { + "key": "hybridDB", + "label": "hybridDB", + "description": "hybrid in dot-bar notation", + "numeric": false + }, + { + "key": "hybridDPfull", + "label": "hybridDPfull", + "description": "hybrid in VRNA dot-bracket notation for full sequence lengths", + "numeric": false + }, + { + "key": "hybridDBfull", + "label": "hybridDBfull", + "description": "hybrid in dot-bar notation for full sequence lengths", + "numeric": false + }, + { + "key": "bpList", + "label": "bpList", + "description": "list of hybrid base pairs like (1,3),(4,2),...", + "numeric": false + }, + { + "key": "E", + "label": "Energy (kcal/mol)", + "description": "overall interaction energy", + "numeric": true + }, + { + "key": "Etotal", + "label": "Etotal", + "description": "overall energy of the interaction including the intra-molecular ensemble energies (E+Eall1+Eall2)", + "numeric": true + }, + { + "key": "ED1", + "label": "ED1", + "description": "ED value of seq1", + "numeric": true + }, + { + "key": "ED2", + "label": "ED2", + "description": "ED value of seq2", + "numeric": true + }, + { + "key": "Pu1", + "label": "Pu1", + "description": "probability to be accessible for seq1", + "numeric": true + }, + { + "key": "Pu2", + "label": "Pu2", + "description": "probability to be accessible for seq2", + "numeric": true + }, + { + "key": "E_init", + "label": "E_init", + "description": "initiation energy", + "numeric": true + }, + { + "key": "E_loops", + "label": "E_loops", + "description": "sum of loop energies (excluding E_init)", + "numeric": true + }, + { + "key": "E_dangleL", + "label": "E_dangleL", + "description": "dangling end contribution of base pair (start1,end2)", + "numeric": true + }, + { + "key": "E_dangleR", + "label": "E_dangleR", + "description": "dangling end contribution of base pair (end1,start2)", + "numeric": true + }, + { + "key": "E_endL", + "label": "E_endL", + "description": "penalty of closing base pair (start1,end2)", + "numeric": true + }, + { + "key": "E_endR", + "label": "E_endR", + "description": "penalty of closing base pair (end1,start2)", + "numeric": true + }, + { + "key": "E_hybrid", + "label": "E_hybrid", + "description": "energy of hybridization only = E - ED1 - ED2", + "numeric": true + }, + { + "key": "E_norm", + "label": "E_norm", + "description": "length normalized energy = E/ln(length(seq1)*length(seq2))", + "numeric": true + }, + { + "key": "E_hybridNorm", + "label": "E_hybridNorm", + "description": "length normalized energy of hybridization only = E_hybrid / ln(length(seq1)*length(seq2))", + "numeric": true + }, + { + "key": "E_add", + "label": "E_add", + "description": "user provided energy shift", + "numeric": true + }, + { + "key": "seedStart1", + "label": "seedStart1", + "description": "start index of the seed in seq1", + "numeric": true + }, + { + "key": "seedEnd1", + "label": "seedEnd1", + "description": "end index of the seed in seq1", + "numeric": true + }, + { + "key": "seedStart2", + "label": "seedStart2", + "description": "start index of the seed in seq2", + "numeric": true + }, + { + "key": "seedEnd2", + "label": "seedEnd2", + "description": "end index of the seed in seq2", + "numeric": true + }, + { + "key": "seedE", + "label": "seedE", + "description": "overall energy of the seed only (including accessibility etc)", + "numeric": true + }, + { + "key": "seedED1", + "label": "seedED1", + "description": "ED value of seq1 of the seed only (excluding rest)", + "numeric": true + }, + { + "key": "seedED2", + "label": "seedED2", + "description": "ED value of seq2 of the seed only (excluding rest)", + "numeric": true + }, + { + "key": "seedPu1", + "label": "seedPu1", + "description": "probability of seed region to be accessible for seq1", + "numeric": true + }, + { + "key": "seedPu2", + "label": "seedPu2", + "description": "probability of seed region to be accessible for seq2", + "numeric": true + }, + { + "key": "w", + "label": "w", + "description": "Boltzmann weight of the interaction energy", + "numeric": true + }, + { + "key": "Eall", + "label": "Eall", + "description": "ensemble energy of all interactions (outConstraint.needZall)", + "numeric": true + }, + { + "key": "Eall1", + "label": "Eall1", + "description": "ensemble energy of all intra-molecular structures of seq1", + "numeric": true + }, + { + "key": "Eall2", + "label": "Eall2", + "description": "ensemble energy of all intra-molecular structures of seq2", + "numeric": true + }, + { + "key": "Zall", + "label": "Zall", + "description": "partition function of all interactions (outConstraint.needZall)", + "numeric": true + }, + { + "key": "Zall1", + "label": "Zall1", + "description": "partition function of all intra-molecular structures of seq1", + "numeric": true + }, + { + "key": "Zall2", + "label": "Zall2", + "description": "partition function of all intra-molecular structures of seq2", + "numeric": true + }, + { + "key": "EallTotal", + "label": "EallTotal", + "description": "total ensemble energy (Eall+Eall1+Eall2) of all interactions including the intra-molecular ensemble energies (outConstraint.needZall)", + "numeric": true + }, + { + "key": "P_E", + "label": "P_E", + "description": "probability of mfe within interaction ensemble (outConstraint.needZall)", + "numeric": true + }, + { + "key": "RT", + "label": "RT", + "description": "the scaled temperature used for Boltzmann weight computation", + "numeric": true + } +]; + +// Every native column appears once. Ensemble energies and their components are +// grouped with probabilities so users can see the cost/meaning of those outputs. +export const CSV_GROUPS = [ + { label: 'Energy', keys: ['E', 'ED1', 'ED2', 'E_init', 'E_loops', 'E_dangleL', 'E_dangleR', 'E_endL', 'E_endR', 'E_hybrid', 'E_norm', 'E_hybridNorm', 'E_add', 'seedE', 'seedED1', 'seedED2'] }, + { label: 'Output', keys: ['subseqDP', 'subseqDB', 'hybridDP', 'hybridDB', 'hybridDPfull', 'hybridDBfull', 'bpList'] }, + { label: 'Sequence', keys: ['id1', 'id2', 'seq1', 'seq2', 'subseq1', 'subseq2'] }, + { label: 'Interaction', keys: ['start1', 'end1', 'start2', 'end2', 'seedStart1', 'seedEnd1', 'seedStart2', 'seedEnd2'] }, + { label: 'Partition Function', keys: ['Pu1', 'Pu2', 'seedPu1', 'seedPu2', 'w', 'Etotal', 'Eall', 'Eall1', 'Eall2', 'Zall', 'Zall1', 'Zall2', 'EallTotal', 'P_E', 'RT'] }, +]; + +export function defaultColumns(task) { + const context = ['id1', 'start1', 'end1', 'id2', 'start2', 'end2', 'subseqDP', 'hybridDP', 'E']; + // Seed energies remain available in evaluation, where native output is NAN. + // List them explicitly: seedEnd1/2 are coordinates, not energy columns. + const extra = task === 'evaluation' + ? [...CSV_CATALOG.filter(({ key }) => key.startsWith('E')).map(({ key }) => key), 'seedE', 'seedED1', 'seedED2'] + : ['ED1', 'ED2', 'seedE', 'seedStart1', 'seedStart2']; + return [...new Set([...context, ...extra])]; +} diff --git a/gui/docs/json-workflow.md b/gui/docs/json-workflow.md new file mode 100644 index 00000000..1c2d9dee --- /dev/null +++ b/gui/docs/json-workflow.md @@ -0,0 +1,150 @@ +# JSON settings and reproducible runs + +The action bar starts with Compute/Evaluate, followed by Input Parameters: +Examples, Store, Load and Reset. Store downloads +`parameter.json` containing non-default settings and embedded input text in the +[native JSON format](../../doc/json-parameters.md). `_comment` records compiled +tool/library versions and executable reproduction commands. It is JSON metadata, +not a nonstandard comment syntax. Settings can be saved before sequences are +complete; Compute still validates the complete job before loading WASM. + +Load validates the complete document before replacing the form, including the +task, signed start indices, input text, CSV selection/order and additional +outputs. Malformed documents and settings the browser cannot represent leave +the form unchanged with an error. Native-only settings and external file paths +must be used in the CLI; the browser requires embedded text. JSON uploads are +limited to 5 MB. The application never uploads these files to a server. + +ZIP uses the same serializer on the completed run, including normalized FASTA. +It contains **only** `parameter.json` and output files. Native replay uses: + +```sh +IntaRNA --parameterFile=parameter.json --out=intarna-interactions.csv +``` + +Additional report commands are listed in `_comment`. They override `outMode` +and CSV-only settings while retaining the same inputs and analysis settings. +Reports run independently, matching the worker. The WASM integration test +replays the JSON in fresh engines and compares every output byte. + +## Computed sessions + +Each successful computation, including a run with no interaction rows, creates a +new session with a unique ID within the page and a default name such as +`Prediction 1` or `Evaluation 2`. The session retains the computed inputs in JSON, +CSV output, additional files and diagnostics. Editing parameters, Load, examples, +Reset, invalid inputs, failed computations and cancellation preserve prior +sessions. Failed or aborted computations do not create a session. + +The newest session opens automatically under **Results**. Use **Show**, select +its header/name, or select its output area to restore that session’s +computed inputs and fold the other sessions. The task, sequence text, signed +indices, SHAPE/accessibility text, CSV selection/order and additional output +selection are restored together. **Hide** folds the output. Each session +keeps its own filter, sorting and visible columns; folded vaRRI frames are unloaded +and restored when their session is reopened. + +Edit **Session name** directly in the header. Names are plain text; an empty name +returns to the default. **Download ZIP** remains available while folded and always +archives that session’s original JSON and complete outputs, regardless of the +current form or table filters. The session name supplies a safe download filename; +ZIP members remain `parameter.json` and output files. The garbage-bin button +removes only its session and releases its output; it does not change form inputs. + +Sessions exist only in the current page’s browser memory. They are not written to +browser storage or uploaded. Reloading or closing the page discards them; use ZIP +exports to retain results. Memory use grows with the runs kept open, so delete +sessions that are no longer needed. Store continues to save the editable form. +If compiled metadata cannot be fetched, a completed run is still retained and its +JSON explicitly records that version information is unavailable. + +## Reset and examples + +Reset clears the editable sequences, interactions and uploaded files and restores +prediction defaults (10 interactions per pair, expanded energy/seed columns). +Evaluation defaults select all energy columns. These GUI defaults are written +explicitly in JSON when they differ from the CLI; importing existing JSON still +uses native defaults for omitted parameters. Inactive controls keep their edits +in the form for switching modes, but their values are omitted from executed and +stored settings. Previously computed sessions remain available. Empty FASTA +fields show the short demonstration sequences as placeholders only. The Examples +disclosure menu follows the Input Parameters label and lists only examples for +the selected Prediction or Evaluation task. + +Maintainers edit `gui/examples/index.json` (an array of local JSON filenames). +Each listed file contains `name`, `description`, and `configuration`, where the +configuration is the same native JSON document used by Load. Two replaceable +examples cover prediction and evaluation. Loading validates their settings and +sequences through the same importer and computation validator. Missing or invalid +examples show an error in the menu; they never overwrite the form. + +## Local FASTA files + +Each strand has an Upload button and accepts a text-file drop into its textarea. +Files are read locally (at most 1 MB), validated with the same FASTA checks as +manual entry, and replace only that strand after successful validation. Prediction +accepts up to 50 FASTA records per strand, each 2–5,000 nt; evaluation requires +one record. The longest selected query × longest selected target must be at most +1,000,000. Names end at the first whitespace; ignored header descriptions produce +a warning below the corresponding field. Both FASTA fields scroll horizontally +and vertically. Invalid files leave the +previous input intact. A later edit, reset, import or computation discards any +pending file read, so delayed reads cannot replace newer input. + +## Validation of the PR #287 revision (2026-10-23) + +- GCC 14 release and debug: `make tests -j2` passed all nine API/CLI groups, + including `runParameterFile.sh`. The existing out-of-tree CLI fixture harness + required source data files linked into each build's `tests/data` directory. +- `npm test --prefix gui`: all 18 tests passed. +- Emscripten 4.0.23 / ViennaRNA 2.7.2 / Boost 1.87.0: actual WASM build, + `node scripts/wasm/smoke.mjs` and `node scripts/wasm/smoke-protocol.mjs` passed. + Exported JSON reproduced selected CSV, signed/multiple sequences, additional + outputs and reports byte for byte in fresh engines. +- `scripts/wasm/test-browser.py` passed in Chromium and Firefox at a nested URL, + covering blank startup/reset, both JSON examples, Load/Store round trips, + FASTA file upload/drop, stale-read protection, task keyboard controls, JSON ZIP + contents, result exploration, cancellation/recovery and mobile overflow. + The desktop screenshot was inspected. +- Embedded ViennaRNA energy-parameter text matched native file input. Existing + dependency-download and ViennaRNA-release tests, shell syntax, workflow YAML, + source-distribution contents, vendor checksums and `git diff --check` passed. + +## Session follow-up validation (2026-10-23) + +- `npm test --prefix gui`: all 18 Node tests passed. +- `scripts/wasm/test-browser.py` passed in Chromium and Firefox with real WASM + at nested URLs. Session checks cover input/JSON restoration, task changes, + signed indices, SHAPE text, CSV order, reports, independent filters/columns, + edits/reset/imports, failed/aborted runs, keyboard selection, safe renaming, + folded-session archives, deletion, stale file reads and page reload. +- Desktop screenshots were inspected; session controls remain accessible at a + 390 px viewport without document overflow. +- `node scripts/wasm/smoke-protocol.mjs` passed native-reference checks and + byte-identical archive replay. Browser checks reused the parent branch’s + compiled Emscripten 4.0.23 / ViennaRNA 2.7.2 assets with their original metadata; + this follow-up changes no C++ code or worker protocol. +- A fresh GCC 14 release build passed `make tests -j2`: all nine native API/CLI + groups passed. Tracked fixtures were linked into the out-of-tree build’s + `tests/data` directory for the existing CLI harness. +- Static staging (including the new session module and engine digest checks), + shell syntax and `git diff --check` passed. + +## PR #299 review validation (2026-10-24) + +- `npm test --prefix gui`: all 20 tests passed, including FASTA limits, header + warnings, complete column grouping and explicit browser-default JSON replay. +- `scripts/wasm/test-browser.py` passed with real WASM in Chromium and Firefox. + It covers the reordered panels, aligned controls, shared accessibility flags, + seed/accessibility/helix modes, inactive values, explicit-seed Load/Store, + group selection, FASTA scrolling/warnings and result header/name selection, + plus the existing prediction/evaluation, ZIP, abort and session checks. +- Desktop and 390 px mobile screenshots were inspected. All seven panels have + no document overflow; table contents retain their own horizontal scrolling. +- `node scripts/wasm/smoke-protocol.mjs ` passed native-reference + checks and byte-identical JSON archive replay. The unchanged engine uses the + parent branch's Emscripten 4.0.23 / ViennaRNA 2.7.2 assets and original metadata. +- A fresh GCC 14 release build passed `make tests -j2`: all nine API/CLI groups. + Existing CLI fixtures were linked into the out-of-tree `tests/data` directory. +- Static staging with engine digest validation, JavaScript/Python syntax checks, + shell syntax and `git diff --check` passed. diff --git a/gui/docs/step1-wasm-compilation.md b/gui/docs/step1-wasm-compilation.md new file mode 100644 index 00000000..dc09f76c --- /dev/null +++ b/gui/docs/step1-wasm-compilation.md @@ -0,0 +1,121 @@ +# Step 1: WebAssembly compilation (#286) + +`scripts/wasm/build.sh` cross-compiles the unmodified CLI entry point and the +Autotools library source lists. `.github/workflows/build-wasm.yml` uses the official +[setup-emsdk action](https://github.com/emscripten-core/setup-emsdk) with Emscripten +4.0.23. It runs on pull requests, pushes to this repository's `master` branch, +and manual dispatches. Build tools (Autotools, pkg-config, a native C++ compiler, +curl, tar and bzip2) must be available. + +## Reproduce locally + +Activate Emscripten 4.0.23 with `source /path/to/emsdk/emsdk_env.sh`, then run: + +```sh +bash scripts/wasm/build.sh +node scripts/wasm/smoke.mjs +node scripts/wasm/smoke-protocol.mjs +``` + +`WASM_BUILD_DIR` changes the build directory; `JOBS` defaults to 2. Local builds +pin ViennaRNA 2.7.2 and its official GitHub release asset SHA-256 in +`scripts/wasm/vienna-release.json`. On every run, the GitHub workflow resolves +the newest stable **2.x** release (at least 2.7.2), excludes drafts/prereleases +and major 3, and uses the asset's published SHA-256. Selection compares numeric +versions across all API pages, rather than using GitHub's `/latest` endpoint. +Missing release assets, digests or failed API requests stop the build. + +To use that same selection locally (optionally set `GITHUB_TOKEN` for API limits): + +```sh +python3 scripts/wasm/vienna-release.py --latest > /tmp/vienna-release.json +WASM_VIENNA_RELEASE=/tmp/vienna-release.json bash scripts/wasm/build.sh +``` + +Keep the resolved manifest to reproduce that exact release later with +`WASM_VIENNA_RELEASE`. `build-info.json` and `build-info.txt` record the selected +archive URL and checksum as well as the actual compiled library version. + +Source archives are downloaded into `build-wasm/downloads` and verified by the +selected SHA-256 hashes on every invocation. Use the official GitHub release +asset, rather than an autogenerated source archive; the university endpoint +returned an HTTP 200 text response instead of the archive in PR #291's build. +`scripts/wasm/download.sh` removes invalid cached archives and checks new +downloads before moving them from `.part` into the cache. Failed transfers and +checksum mismatches leave no cached archive or partial file, so a subsequent +build can retry. Run `python3 scripts/wasm/test-downloads.py` to check download, +cache recovery and failure handling against a local HTTP server, and +`python3 scripts/wasm/test-vienna-release.py` for release selection and manifest +validation, without an SDK or external network access. The build directory is +ignored. ViennaRNA sources, its installation prefix and IntaRNA objects are +separated by the selected version and checksum, so upgrades cannot reuse an +older RNAlib or IntaRNA object cache (including the old 2.7.0 prefix). zlib and +Boost use a separate `build-wasm/deps/common` prefix, so legacy ViennaRNA headers +cannot override the selected release through Boost's include path. Their caches +remain reusable across ViennaRNA upgrades. Delete the build directory for a fresh build +after changing compiler flags or SDKs. Native libraries are never accepted +from system pkg-config paths. + +The script supplies absolute source and generated-header include paths for the +out-of-tree IntaRNA build, and uses generated files from the build directory. +ViennaRNA also needs an explicit source include path when its no-SVM build +omits the target's normal include flags. ViennaRNA 2.7.2 bundles dlib 20.0, +which already supports modern libc++; no downloaded sources are patched. +Staging takes the ViennaRNA, dlib and Naview notices from the source archive +identified by the compiled provenance, and displays their selected versions. + +The legacy Boost and zlib configure macros declare dummy test functions with +incorrect signatures (`exit()` and `inflateEnd()`), which wasm-ld correctly +rejects. Before caching just those probes, `dependency-probe.cpp` links and executes actual +filesystem, regex, options, archive, gzip and RNAlib APIs against the WASM +libraries. Configure still checks C++23, headers, serialization and RNAlib APIs; +the smoke test executes the real prediction. `VRNA_LIBS` supplies the static +RNAlib link flags because the upstream `.pc` includes native-only linker flags. + +## Dependencies and runtime + +- zlib 1.3.1: static library for compressed accessibility and Boost.Iostreams. +- Boost 1.87.0: headers plus static filesystem, program_options, regex, + iostreams, serialization and system libraries, built with Boost.Build's + Emscripten toolset. Optional bzip2, lzma and zstd backends are disabled. +- ViennaRNA 2.7.2 locally, newest stable 2.x in CI: static RNAlib, without OpenMP, pthreads, SIMD, external + solvers, bindings, documentation or companion applications. Compiling only + RNAlib avoids executing cross-compiled helper applications on the host. +- IntaRNA: C++23, bundled Kokkos mdspan, standard CLI, default energy models + and accessibility calculations. Single-thread Emscripten builds omit + `-pthread`; native builds retain their existing threading flags. + +All C++ compilation and linking enables exceptions (`-fexceptions`), including +Boost (`exception-handling-method=js`) and the CLI's input/error handling. The SDK's single-thread mutex support +retains ViennaRNA's normal setup/logger locking without requiring browser +`SharedArrayBuffer` or COOP/COEP headers (unavailable on ordinary GitHub Pages). + +The output is an ES module factory (`createIntaRNA`) in +`build-wasm/site/wasm/intarna.js`, paired with `intarna.wasm`. The factory does +not run main automatically; it exports `FS` and `callMain`. The runtime exits +and flushes C++ streams after one call. Each prediction must use a new instance. +Memory grows on demand to a maximum of 1 GiB; stack size is 8 MiB. Allocation +failure is reported as a failed prediction; devices may impose lower limits. + +See [Emscripten's Autotools guidance](https://emscripten.org/docs/compiling/Building-Projects.html) +for `emconfigure`/`emmake`. Generated configure files, dependency sources and WASM +binaries are build outputs, not tracked source. The artifact must keep JS and +WASM from the same build together. The Node smoke test runs real +Turner/default-accessibility predictions and checks energy, coordinates, +nonzero accessibility costs, suboptimal counts and C++ error handling against +the native CLI. + +## Compiled version information and virtual overrides (PR #287 review) + +After copying the paired JS/WASM assets, `write-build-info.mjs` invokes their +actual `--version` entry point. It records IntaRNA package version, ViennaRNA and +Boost versions, source repository/revision and dirty status, Emscripten version, +zlib version and asset hashes in `build-info.txt` and `build-info.json`. The +interface displays those versions and links both files. Staging checks the +hashes and preserves provenance even if the staging checkout has moved. + +IntaRNA's inherited virtual methods and destructors declare `override`, including +previously unannotated energy/accessibility, seed/helix, predictor and output +families. The Emscripten build treats inconsistent missing overrides as errors. +Vendored Easylogging++ remains unchanged. This annotation-only C++ change does +not alter algorithms, virtual extension points or scientific defaults. diff --git a/gui/docs/step2-worker-architecture.md b/gui/docs/step2-worker-architecture.md new file mode 100644 index 00000000..018d3470 --- /dev/null +++ b/gui/docs/step2-worker-architecture.md @@ -0,0 +1,35 @@ +# Step 2: worker and I/O architecture (#286, PR #287 review) + +`PredictionRunner` creates one module Web Worker per task and sends sequence +text, task, start indices, validated parameter values, CSV column IDs, optional +output IDs and evaluation structures. It receives status, result or error +messages. `prepareRequest` validates both the UI and worker boundary; argument +construction only accepts schema keys, enumerated output formats and fixed paths. + +The worker imports `wasm/intarna.js`, maps `locateFile` to the lowercase WASM +asset and creates an isolated `createIntaRNA` instance. It writes one `/parameter.json` document using the native +[JSON contract](../../doc/json-parameters.md), embedding normalized multi-FASTA +and SHAPE/accessibility text. Each invocation passes only +`--parameterFile=/parameter.json`. CSV is written to `/results.csv`; +additional native output prefixes write files under `/output/`. Multi-FASTA +filenames use the CLI's native record-number suffixes. + +Main is called once per WASM instance, keeping C++ globals, RNAlib state and files +isolated. Optional ASCII/detailed/ensemble reports each use another fresh +instance with the same inputs/settings. This costs an additional computation per +report and is explained next to those controls. Files are read only after main +returns and streams close. The worker sends CSV, selected columns, additional +file text and bounded diagnostics (25 lines, 2,000 characters each). Nonzero +exits and JS/runtime failures settle as errors, without partial successful files. + +Both success and failure terminate the worker. Abort uses `Worker.terminate()` +on the main thread and immediately rejects with `AbortError`, including during +synchronous C++ execution. Stale messages are ignored and the next task starts +fresh. Computation never uploads or persists inputs. Selecting a result to +visualize it loads the external vaRRI viewer with that pair and its structure +in the URL. The iframe is cleared on input edits; no third-party viewer is +loaded before selection. No backend, shared memory or cross-origin isolation +is needed for computation. A single WASM instance can grow up to 1 GiB. + +Run `npm test --prefix gui`, then the native-reference WASM smoke tests +and Chromium/Firefox suites described in step 4. diff --git a/gui/docs/step3-frontend-ui.md b/gui/docs/step3-frontend-ui.md new file mode 100644 index 00000000..3e41faf5 --- /dev/null +++ b/gui/docs/step3-frontend-ui.md @@ -0,0 +1,109 @@ +# Step 3: browser controls (#286, PR #287 review) + +## Design and layout + +The interface follows [vaRRI main-v2](https://github.com/BackofenLab/vaRRI/tree/main-v2): +header indigo `#344a9a`, action blue `#145a96`, dark blue `#0f4676`, pale blue +`#eaf2f8`, white `#ffffff` and focus gold `#f4bb44`. Segoe UI/Tahoma/Geneva serve +labels and body text; Consolas/Liberation Mono serve sequence and structure data. +The official group and university logos share the header with the IntaRNA mark. +Their local copies and source attribution are in `gui/assets/`. + +The layout puts the scientific task first, then mutually exclusive parameter +groups, followed by the compute button, results, additional files and versions. +All working content is left aligned; two equally sized strand editors collapse +into one column on mobile. The shared institutional header is the strongest +visual element. The wrapping tab bar identifies parameter groups. Numeric inputs +are at most 9 rem wide within bounded, left-aligned row grids; select/text inputs +use compact type-specific tracks and text/data fields retain useful width. Rows +keep their scientific grouping without stretching across the complete panel, +use 16 px horizontal gaps and bottom-align labels above their controls. +The Seed tab places the constraint selector (12 rem) beside Explicit seeds on +desktop; the CSV sort selector uses a 19 rem track. Both controls stack at mobile +widths. +The institutional link reads “Bioinformatics - University of Freiburg” and opens +the group website. Footer and table notes use the available width, wrapping only +when the viewport requires it. + +```text +Group logo IntaRNA package / RNA–RNA interaction analysis University logo +RNA–RNA interactions Computations stay on your device +Task: Prediction / Evaluation +[ Sequences | Seed | Output | CSV | Model & Energy | Query | Target | CLI-only ] +[ Active panel: e.g. query + target, start indices, evaluation structures ] +Compute Input Parameters: Examples / Store / Load / Reset +Results / Show-Hide / name / ZIP download / delete +Interactions / search / show-hide columns / CSV download +Selected interaction / embedded vaRRI +Additional output files / diagnostics / compiled versions +``` + +Every CLI group has a tab with one visible panel. Sequences is selected +initially. Tabs expose `aria-selected`, `aria-controls` and roving focus; Left/Right +move between available tabs, and Home/End select the first/last. Tab names wrap +on narrow screens. Prediction-only tabs and controls are disabled/hidden during +evaluation; if the selected tab becomes unavailable, Sequences is selected. +Changing task resets parameters to their task defaults while preserving sequence text; Load example also restores the +complementary pair. The browser defaults to 10 interactions per pair (the native default remains +one), and accepts 0–100. Zero enables accessibility-only output. + +## Inputs, defaults and validation + +`options.js` defines labels, types, defaults and ranges from +`src/bin/CommandLineParsing.cpp`. `protocol.js` validates them on both sides of +the worker boundary. Query/target retain their distinct interior-loop defaults +(16 and 10). Meta-options such as `acc`, `accW`, `accL`, `intLenMax` and +`intLoopMax` are represented by per-strand controls to avoid conflicting values. +FASTA headers supply sequence names instead of `qId`/`tId`. The dedicated CSV +tab contains `outCsvSort` and the interaction-table column choices; Output keeps +prediction filters and additional file formats. `outCsvSort` selects a native +download sort column; table sorting is independent. +CSV uses a fixed semicolon delimiter. +Process settings (threads, file/log paths, parameter files, help/version commands) +are replaced by the worker lifecycle, local data inputs, downloads and displayed +compiled versions. The base-pair maximization energy model is intentionally +excluded. The helix-block interaction model B is supported, with helix controls at the end +of Model & Energy, enabled only for model B. Seed constraint offers Disable, +Explicit seed and Identify seeds, enabling only the relevant controls. Query and +Target include their own accessibility/SHAPE columns and synchronized copies of +the two shared accessibility flags. Ignore disables accessibility controls; +import modes disable window/span and enable the data input. Disabled settings +remain editable when re-enabled but do not enter the request. Explicit row grids +align inputs even when their labels wrap. + +CSV columns are grouped as Energy, Output, Sequence, Interaction and Partition +Function, with per-group selection actions and name-only labels with description +tooltips. Prediction adds ED1, ED2, seedE, seedStart1 and seedStart2 to the native +CSV columns; evaluation selects all energy outputs. JSON records these browser +defaults explicitly so native replay retains the same output. +Every additional output checkbox has a descriptive tooltip covering its content, +format and intended use, including the model restrictions shown in its label. + +Prediction accepts plain sequence or up to 50 FASTA records per strand. +Evaluation requires one query and target and 1–100 predefined structures. +Wrapped/lowercase sequence text and DNA T normalize to uppercase RNA U. A/C/G/U/N +are accepted. Each record is 2–5,000 nt; seed predictions additionally require +at least `seedBP` nucleotides. FASTA IDs end at the first whitespace, matching the CLI. Duplicate IDs (including collisions after +native CSV semicolon replacement) are rejected. Ignored header descriptions are reported below the input. The longest selected +query length × longest selected target length is capped at 1,000,000, including +pairwise mode; the cap is not summed over records. +The per-strand start index applies to all records and defaults to one. Negative +indices skip zero, matching `RnaSequence`; output coordinates remain inclusive. + +Evaluation encodes target then query in 5′ to 3′ dot-bar notation, such as +`1|||&1|||`, separated by colons. Bars pair antiparallel. Validation checks bounds, +equal nonzero pair counts and AU/GC/GU complementarity. Evaluation retains energy, +accessibility and SHAPE controls while excluding prediction/seed/helix/region +and output-filter constraints, matching the native personality. + +Validation also covers numeric ranges, accessibility windows/spans, selected +FASTA subsets, regions, structural constraints, seed/helix compatibility, +probability-output requirements and window restrictions. SHAPE and RNAplfold +accessibility text can be pasted or loaded from a local file (up to 1 MB). Data +are written to fixed MEMFS paths, never used as user-provided CLI arguments. +Native diagnostics remain available for model-specific failures. + +Edits update the form while completed sessions retain their inputs and results; +the form disables during execution. Abort and Escape terminate the worker during startup or C++ execution. Status, errors, +empty output and diagnostic text have dedicated regions. Keyboard focus, +reduced motion and mobile overflow are covered by real browser tests. diff --git a/gui/docs/step4-results-and-deployment.md b/gui/docs/step4-results-and-deployment.md new file mode 100644 index 00000000..451181bf --- /dev/null +++ b/gui/docs/step4-results-and-deployment.md @@ -0,0 +1,249 @@ +# Step 4: results and Pages deployment (#286) + +## Results contract + +The CSV checklist covers all `OutputHandlerCsv` column IDs. The worker requests +those columns plus internal target/query IDs, coordinates, energy and `hybridDP` +needed for pair grouping, result validation and visualization. Downloads project the untouched native CSV +cells onto the user's selected columns, in selection order, retaining every row +regardless of table filtering/visibility. No computed mfe difference is inserted +into native CSV. The selected-column catalog is checked against the C++ mapping. + +Native output is unquoted and semicolon-delimited. Semicolons in IDs become +underscores; quotes remain literal. The parser checks column IDs, finite core +energy/coordinate values, integer inclusive coordinates and ascending bounds. +Signed coordinates are allowed. Optional `NAN` and colon-separated seed lists +remain strings; numeric sorting puts unavailable/list values after numbers. + +Sequence 1 is **target**, sequence 2 is **query**. Energy uses kcal/mol. The +computed **mfe Δ** is `E - min(reported E for the same query–target pair)`, rounded +to hundredths. Evaluation uses the best supplied structure as its reference. +This is relative suboptimality, not a free-energy change or probability. + +Every heading is a keyboard-operable sort button with `aria-sort`. Search covers +all returned values. A separate checklist shows/hides table columns after the +run; it does not change selected CSV output. All identifiers, output previews +and diagnostics render with `textContent`. The table has a 500 px maximum height +with vertical scrolling for longer results and a sticky heading; CSV downloads +still contain every selected row. Selected extra files appear below the +table with their original filename, covered sequence/sequence-pair names, a +header-level download, and bounded text previews, including SVG source. +Empty output is successful and still permits CSV/accessibility downloads. + +## Additional output visualizations + +Plot-capable additional CSV files open on a Visualization tab, with the original +File Content in an adjacent tab. Query/target minimum-energy and spot-probability +profiles use line plots; pair minimum-energy and all-spot probability matrices +use heatmaps; explicitly requested spot probabilities use a bar plot. Plot axes +use the literal coordinate strings from IntaRNA rather than numerical scales, so +signed indices cross from -1 to 1 without inventing coordinate zero. Plot titles +and additional-file headers identify the target/query records covered by native +`-t#q#` or `-s#` filename suffixes. + +Plotly renders locally from the pinned Cartesian bundle. A separate Export PNG +button produces a 1400 × 850 image for the active plot; the normal file download +and reproducible ZIP retain untouched native data. Plots render lazily when their +file is unfolded, resize with restored sessions, and are purged when a session is +deleted. Non-plot formats keep the direct content view. + +## Selected interaction in vaRRI + +Each row has a keyboard-accessible View button; clicking a row also selects it. +Selection survives table sorting, filtering and visibility changes within each +session. Input edits, new runs, errors and cancellation preserve prior sessions +and their archive snapshots. Folding a session unloads its viewer; reopening +restores its selected interaction. +`visualization.js` uses native seq1 = target, seq2 = query and maps the native +CSV identifiers to the completed run's normalized FASTA records (including +semicolon-to-underscore ID conversion). It pads the interaction dot-bracket +structure with unpaired positions to the full input lengths, using each start +index and the native negative-to-positive transition that skips zero. + +The URL follows [vaRRI's embedding API](https://github.com/BackofenLab/vaRRI/blob/main-v2/docs/sharing-and-input.md): +`sequence`, `structure`, `seqName1/2`, `startIndex1/2`, and +`showRenderingOnly=true`. Names use the main-v2 API; older deployed vaRRI versions +may retain generic strand names. A separate Open in vaRRI link opens the full +viewer. The local status always identifies the selected pair and coordinates. +Zero-based CLI start indices remain accepted for computation/export, but vaRRI +requires nonzero start indices; choosing View for such a run explains this limit. + +No external viewer loads until a row is selected. The interface explains that +selection shares that pair and structure through vaRRI's URL. Computation and +ZIP generation remain local. CSP permits frames only at the vaRRI deployment; +the iframe sends no referrer. Viewer availability depends on that external site; +the full-viewer link permits retry, and scientific outputs remain downloadable. + +## Reproducible ZIP download + +Download ZIP sits in each session header, including while its output is folded. +`archive.js` creates a standard UTF-8, uncompressed ZIP with CRC-32 checksums locally, without a library or CDN. It uses +the completed request and result, independent of table sorting/filtering and +column visibility. Editing inputs preserves every completed snapshot. + +The archive contains only `parameter.json`, `intarna-interactions.csv`, and every +generated additional output with its original filename and contents. JSON embeds +normalized FASTA and any SHAPE/accessibility text, non-default settings, selected +CSV columns, compiled provenance and native replay commands in `_comment`. +Additional report commands override CSV-only settings and use another native +invocation, matching the worker. All JSON is valid with standard parsers. + +Load/Store use this same JSON format. Store snapshots the current editable form; +ZIP snapshots the completed run and ignores table filtering/sorting/visibility. +Store requires the compiled version file. Completed sessions still retain their +results if that file is unavailable, recording the missing version information +explicitly in JSON. See [the JSON workflow](json-workflow.md). + +## Packaging and deployment + +```sh +bash scripts/wasm/build.sh +node scripts/wasm/smoke.mjs +node scripts/wasm/smoke-protocol.mjs +bash scripts/wasm/stage.sh +npm test --prefix gui +python3 -m pip install -r scripts/wasm/requirements-browser.txt +python3 -m playwright install chromium firefox +python3 -m http.server 8765 --directory build-wasm/site +# In another terminal: +python3 scripts/wasm/test-browser.py http://127.0.0.1:8765 +python3 scripts/wasm/test-browser.py http://127.0.0.1:8765 --browser firefox +``` + +The staging script includes matched WASM assets, only the application source +files needed at runtime, compiled version metadata and dependency notices. It +also verifies and stages the pinned Plotly.js 4.1.2 Cartesian bundle and MIT +license; no CDN is used. Build-time `build-info.json` +and `build-info.txt` record actual CLI IntaRNA/ViennaRNA/Boost versions, source +commit and tracked modifications, SDK version and asset SHA-256 digests. Staging +checks these digests and preserves the original metadata; it never replaces the +compiled revision with a later staging checkout. The footer displays versions. +It needs the same activated SDK and dependency build directory as the build. +No generated WASM artifacts are committed; the reviewed minified Plotly browser +distribution is the only new runtime artifact. HTTP(S), module workers and WebAssembly +are required; `file://` and legacy browsers are unsupported. No backend, +SharedArrayBuffer, credentials, CDN or cross-origin headers are needed. CSP +keeps scripts/styles same-origin and allows ephemeral blob images solely for +PNG export. + +The existing repository already publishes its user guide and API with Pages. +Publishing a second independent artifact would overwrite them. Therefore +`documentation.yml` is now a reusable build (also manually dispatchable), and +`build-wasm.yml` is the **single publisher**. Both builds run on PRs (including dependent feature-branch PRs) and on +the actual default branch, `master`. After JS tests, the real WASM smoke test and +Chromium/Firefox integration tests pass, the package job combines: + +- Existing Jekyll guide at `/IntaRNA/` and API at `/IntaRNA/api/`. +- Tested application at `/IntaRNA/gui/`. + +The artifact `intarna-pages-preview` permits PR review of the complete site. +Pull requests and manual runs on feature branches do not publish. Only a push +or manual run on `BackofenLab/IntaRNA`'s `master` may upload the Pages artifact +and use the `github-pages` deployment environment. Pages permissions are scoped +to that deploy job. Concurrent deployments are serialized without cancellation. + +The repository's current Pages source is already **GitHub Actions**. A fork +would need that source enabled, its repository guard adjusted deliberately, and +an environment allowing its default branch. Existing environment protection +rules still apply. After merging this PR, check the workflow's deploy job and +its returned environment URL. This implementation PR does not merge itself or +claim that deployment happened before merge. + +## Validation scope + +Node tests cover input boundaries, lifecycle races, parser failures, numeric +sorting and suboptimal differences. The WASM smoke test compares a real +Turner/default-accessibility prediction with the native reference. Browser +integration runs real WASM (no mocked scientific results), checking coordinates, +energy, sorting, filtering, CSV download, mobile overflow, abort during download +and active C++, clean restart, empty predictions and asset-load recovery. + +### Local verification, 2026-10-20 + +- Emscripten 4.0.23 with the exact SHA-256-pinned official archives: successful + dependency probe, cross-build and real WASM smoke test. The structured-strand + reference reports E = -28.04, ED1 = 4.60, ED2 = 4.86 kcal/mol; the short example + reports E = -21.40 with target/query coordinates 1–10 and ten suboptimals. + Invalid CLI input returns a nonzero status through C++ error handling. +- `npm test --prefix gui`: all five input/lifecycle/CSV test groups pass. +- Playwright 1.64.0, Chromium and Firefox: full integration suite passes with the + official-dependency engine, including a nested `/site/` URL as used by Pages, + active-C++ cancellation, literal HTML-like identifiers and retry after failure. + Desktop screenshot visually reviewed; 390 px viewport has no page overflow. +- Native release build with OpenMP, conda GCC 16.2.0 and ViennaRNA 2.7.2: + `make tests -j2` passes all eight API/CLI groups, including 462,689 assertions + across 119 API cases. For the separate build directory, tracked `tests/data` + fixtures were linked into the build's data directory because the existing + shell harness discovers fixtures relative to its working directory. +- Shell syntax, workflow YAML parsing and `git diff --check`: pass. + +GitHub's platform checks independently cover GCC 14 release/debug and Apple +Clang. Deployment itself occurs only after merge; local browser tests do not +claim a live Pages deployment. + +### PR #287 visualization review verification, 2026-10-26 + +- `npm test --prefix gui`: all 25 protocol, results, output-visualization, + archive, upload and worker tests pass. Profile and matrix cases cover signed + categorical coordinates, sequence names, missing values and malformed data. +- Playwright 1.64.0 with Chromium 156 and Firefox 157 passes the full real-WASM + suite, including the compact desktop/mobile parameter layout, separate CSV + tab, output tooltips, native-file headers, Plotly rendering and a PNG whose + signature is checked after download. The staged GUI uses the matching + revision `7378801` engine; scientific code and compiled assets are unchanged. +- Desktop screenshots for every parameter tab and the completed session were + visually reviewed; the 390 px viewport has no document overflow. +- Plotly 4.1.2 is pinned by npm integrity and bundle SHA-256, staged locally with + its MIT license. Shell/Python syntax and `git diff --check` pass. + +### PR #287 review verification, 2026-10-21 + +- Emscripten 4.0.23 rebuild using the pinned official dependency archives passes + with `-Werror=inconsistent-missing-override`. An all-public-header audit using + `-Wsuggest-override -Wsuggest-destructor-override` reports no project override + diagnostics (third-party Easylogging++ is intentionally unchanged). +- `node scripts/wasm/smoke.mjs` retains the original native-reference energy, + coordinates, structured accessibility and C++ error-handling checks. +- `node scripts/wasm/smoke-protocol.mjs` passes real CLI translations for default + prediction, shifted negative coordinates, all-vs-all/pairwise multi-FASTA, + evaluation with all CSV columns, extra reports/probability SVGs, imported + accessibility and non-default energy/seed/helix/SHAPE/overlap settings. + Native imported accessibility reserves one length column for dangling-end + treatment; its energy is compared with the corresponding restricted native + interaction length rather than the unrestricted prediction. +- `npm test --prefix gui`: ten protocol/results/lifecycle groups pass. +- Real Chromium/Firefox integration covers all parameter groups, CLI defaults, + compiled versions/logos, task changes, multiple records, signed coordinates, + selected/visible CSV columns, additional previews/downloads and the original + cancellation, empty/error, literal-ID and mobile checks. Desktop screenshot + reviewed; the 390 px viewport has no document overflow. +- Native OpenMP release build with GCC 16.2.0/ViennaRNA 2.7.2: + `make tests -j3` passes all eight groups, including 462,689 assertions across + 119 API cases. Tracked CLI fixtures are linked into the separate build data + directory as in the previous verification; expected results are unchanged. +- Staging preserves compiled metadata byte-for-byte; a deliberately changed + copied JS engine is rejected by its asset digest check. Shell syntax, + workflow YAML, Python syntax and `git diff --check` pass. + +### PR #287 follow-up verification, 2026-10-22 + +- All 12 Node test groups pass, including coordinate/strand mapping, non-default + export settings, auxiliary inputs and report configurations. +- `node scripts/wasm/smoke.mjs` and `node scripts/wasm/smoke-protocol.mjs` pass + using the previously compiled Emscripten 4.0.23 engine (revision `fc62a23`). + The latter executes exported parameter files in fresh engines with only + archived inputs and verifies byte-identical CSV, per-record outputs, + probability SVGs and ASCII/detailed/ensemble reports. Cases include signed + multi-FASTA, changed energy/seed settings, SHAPE and accessibility imports. +- Chromium 156 and Firefox 157 with Playwright 1.64.0 pass the real-WASM browser + suite at a nested URL. It covers tab keyboard behavior, selection/encoded + viewer URLs, Python `zipfile` validation of downloaded ZIP contents, hidden + CSV columns, evaluation reports, empty results and the existing lifecycle + checks. Only the third-party iframe response is stubbed in CI; computation + runs the real engine. Desktop/parameter/mobile screenshots were reviewed. +- A separate live Chromium check renders RNA base circles in the actual hosted + vaRRI iframe. An independent Python `zipfile` check verifies CRCs, Unicode + filenames/data and empty files in the ZIP writer's output. +- Native `make tests -j2` passes all eight API/CLI groups (462,689 assertions in + 119 API cases). No C++ or compiled engine changes were needed for this follow-up. +- Staging, shell/Python syntax and `git diff --check` pass. diff --git a/gui/examples/evaluation.json b/gui/examples/evaluation.json new file mode 100644 index 00000000..e019806f --- /dev/null +++ b/gui/examples/evaluation.json @@ -0,0 +1,18 @@ +{ + "name": "Evaluate a duplex", + "description": "Evaluate the energy of a supplied ten-base-pair RNA interaction.", + "configuration": { + "schema": "IntaRNA-parameters-v1", + "parameters": { + "personality": "IntaRNAeval", + "query": { + "text": ">ncRNA1\nAGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU\n" + }, + "target": { + "text": ">mRNA1\nUUUAAAUUAAAAAAUCAUAGAAAAAGUAUCGUUUGAUACUUGUGAUUAUACUCAGUUAUA\nCAGUAUCUUAAGGUGUUAUUAAUAGUGGUGAGGAGAAUUUAUGAAGCUUUUCAAAAGCUU\nGCUUGUGGCACCUGCAACUCUUGGUCUUUUAGCACCAAUGACCGCUACUGCUAAU\n" + }, + "rri": "85|||||||||||&21||||||||.|||", + "outCsvCols": "id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E,Etotal,ED1,ED2,E_init,E_loops,E_dangleL,E_dangleR,E_endL,E_endR,E_hybrid,E_norm,E_hybridNorm,E_add,Eall,Eall1,Eall2,EallTotal" + } + } +} diff --git a/gui/examples/index.json b/gui/examples/index.json new file mode 100644 index 00000000..947fd53d --- /dev/null +++ b/gui/examples/index.json @@ -0,0 +1 @@ +["prediction.json", "evaluation.json"] diff --git a/gui/examples/prediction.json b/gui/examples/prediction.json new file mode 100644 index 00000000..50d7600d --- /dev/null +++ b/gui/examples/prediction.json @@ -0,0 +1,17 @@ +{ + "name": "Short duplex", + "description": "Predict interactions between two complementary ten-nucleotide RNAs.", + "configuration": { + "schema": "IntaRNA-parameters-v1", + "parameters": { + "query": { + "text": ">ncRNA1\nAGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU\n>ncRNA2\nACUGAGGUACGAUCGUGGCAGGGCCUUUGACUGACUUUCGUACUUU" + }, + "target": { + "text": ">mRNA1\nUUUAAAUUAAAAAAUCAUAGAAAAAGUAUCGUUUGAUACUUGUGAUUAUACUCAGUUAUA\nCAGUAUCUUAAGGUGUUAUUAAUAGUGGUGAGGAGAAUUUAUGAAGCUUUUCAAAAGCUU\nGCUUGUGGCACCUGCAACUCUUGGUCUUUUAGCACCAAUGACCGCUACUGCUAAU\n>mRNA2\nUGCUUCUUAGUAAUGGCCAGCUCGGGGAUUUGGAACUGGUGGUUGUUAAUUCUAGGCAAA\nUAGAUUAAAAUUAAAUUACUCAAAUUGUGUGACGAGUUUUAUGAAGCUUUUUAAAAGCUU\nGUUGGUAGCUCCAGCAACGAUUGGGCUACUAGCUCCAUUUUCAACGUUUGCUGGC\n" + }, + "outNumber": 10, + "outCsvCols": "id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E,ED1,ED2,seedE,seedStart1,seedStart2" + } + } +} diff --git a/gui/index.html b/gui/index.html new file mode 100644 index 00000000..275f8b1f --- /dev/null +++ b/gui/index.html @@ -0,0 +1,98 @@ + + + + + + + + IntaRNA · RNA–RNA interactions + + + + + + + + +
+ + IntaRNA packageRNA–RNA interaction analysis + Bioinformatics -
University of Freiburg +
+
+
+

RNA–RNA interactions considering Seeds and Accessibility

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Computations stay on your device

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+ Task, sequences and parameters +
+ Analysis task + + +
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Predict interactions for all query–target sequence pairs.

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5′ to 3′
or drop in the field
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No sequence entered
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5′ to 3′
or drop in the field
+ +
No sequence entered
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+

Plain sequence or multi-FASTA (prediction only), A/C/G/U/T/N. Up to 50 records per field and 2–5,000 nt per record; longest selected query × longest selected target ≤ 1,000,000. FASTA names stop at the first whitespace. Seed predictions also require at least as many nucleotides as seed base pairs. Signed start indices apply to every record on that strand; negative indexing skips zero.

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Input Parameters:
Examples

Loading examples…

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Results

Enter your sequences or choose an example, then compute.

+

Completed runs stay in this tab until deleted or the page is reloaded. Select a session to restore its inputs; download its ZIP to keep a copy.

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+ + +
+ +
+

Computing interactions

Loading the prediction engine…

The first run downloads the engine. You can stop at any time.

 + + diff --git a/gui/intarna-worker.js b/gui/intarna-worker.js new file mode 100644 index 00000000..09568516 --- /dev/null +++ b/gui/intarna-worker.js @@ -0,0 +1,42 @@ +import { prepareRequest, makeParameterDocument } from './protocol.js'; + +// Each task owns a worker; each CLI invocation owns a fresh WASM instance. +let started = false; +self.onmessage = async ({ data }) => { + if (started) return; + started = true; + const diagnostics = []; + const log = (line) => { + diagnostics.push(String(line).slice(0, 2000)); + if (diagnostics.length > 25) diagnostics.shift(); + }; + try { + const request = prepareRequest(data); + self.postMessage({ type: 'status', message: 'Loading the prediction engine…' }); + const { default: createIntaRNA } = await import('./wasm/intarna.js'); + const run = async (format) => { + const module = await createIntaRNA({ + noInitialRun: true, + locateFile: () => new URL('./wasm/intarna.wasm', import.meta.url).href, + print: log, printErr: log, + }); + module.FS.writeFile('/parameter.json', JSON.stringify(makeParameterDocument(request, format))); + module.FS.mkdir('/output'); + self.postMessage({ type: 'status', message: request.task === 'evaluation' ? 'Evaluating supplied RNA interactions…' : 'Predicting RNA interactions…' }); + const code = module.callMain(['--parameterFile=/parameter.json']); + if (code !== 0) throw new Error(`IntaRNA exited with status ${code}. Check the diagnostics and input settings.`); + return module.FS; + }; + const fs = await run('C'); + const csv = fs.readFile('/results.csv', { encoding: 'utf8' }); + const files = fs.readdir('/output').filter((name) => name !== '.' && name !== '..').map((name) => ({ name, text: fs.readFile(`/output/${name}`, { encoding: 'utf8' }) })); + for (const [key, format] of [['normal', 'N'], ['detailed', 'D'], ['ensemble', 'E']]) { + if (!request.outputs.includes(key)) continue; + const reportFS = await run(format); + files.push({ name: `intarna-${key}.txt`, text: reportFS.readFile('/report.txt', { encoding: 'utf8' }) }); + } + self.postMessage({ type: 'result', csv, csvColumns: request.csvColumns, files, diagnostics: diagnostics.join('\n') }); + } catch (error) { + self.postMessage({ type: 'error', message: error instanceof Error ? error.message : String(error), diagnostics: diagnostics.join('\n') }); + } +}; diff --git a/gui/mark.svg b/gui/mark.svg new file mode 100644 index 00000000..cb535a7b --- /dev/null +++ b/gui/mark.svg @@ -0,0 +1 @@ + diff --git a/gui/options.js b/gui/options.js new file mode 100644 index 00000000..8bc600ff --- /dev/null +++ b/gui/options.js @@ -0,0 +1,118 @@ +import { CSV_CATALOG } from './columns.js'; + +// Browser controls mirror CommandLineParsing.cpp; process/file-management options +// are replaced by local text inputs, downloads and a single cancellable worker. +const number = (key, label, value, min, max, extra = {}) => ({ key, label, value, min, max, type: 'number', ...extra }); +const select = (key, label, value, choices, extra = {}) => ({ key, label, value, choices, type: 'select', ...extra }); +const flag = (key, label, extra = {}) => ({ key, label, value: false, type: 'checkbox', ...extra }); +const text = (key, label, extra = {}) => ({ key, label, value: '', type: 'text', ...extra }); +const prediction = { prediction: true }; +const strand = (prefix, label) => [ + text(`${prefix}Set`, 'FASTA record subset', { ...prediction, hint: 'Record numbers, e.g. 1-3,5-5. Empty selects all.' }), + select(`${prefix}Acc`, 'Accessibility', 'C', { C: 'Compute', N: 'Ignore', P: 'Import unpaired probabilities', E: 'Import opening energies' }), + number(`${prefix}AccW`, 'Accessibility window', 150, 0, 99999, { exclude: [1, 2], hint: '0 uses the full sequence; otherwise at least 3 nt.' }), + number(`${prefix}AccL`, 'Maximum base-pair span', 100, 0, 99999, { exclude: [1, 2], hint: '0 uses the accessibility window.' }), + text(`${prefix}AccConstr`, 'Accessibility constraints', { hint: 'One sequence only: ./x/p/b per base, or ranges such as b:3-4,p:6-7.' }), + text(`${prefix}AccFile`, 'Accessibility data', { type: 'textarea', hint: 'Paste RNAplfold text for one sequence when importing P or E.' }), + number(`${prefix}IntLenMax`, 'Maximum interaction length', 0, 0, 99999, { ...prediction, hint: '0 uses the full sequence, bounded by the accessibility window.' }), + number(`${prefix}IntLoopMax`, 'Maximum unpaired bases per interior loop', prefix === 'q' ? 16 : 10, 0, 30, prediction), + text(`${prefix}Region`, 'Interaction regions', { ...prediction, hint: 'Inclusive sequence coordinates, e.g. 1-20,30-50.' }), + number(`${prefix}RegionLenMax`, 'Automatic region length limit', 0, 0, 99999, { ...prediction, hint: '0 disables automatic region detection.' }), + number(`${prefix}PfScale`, `${label} partition-function scale`, 1.07, 1, 99999, { step: 'any' }), +]; +const fields = new Map([ + ...strand('q', 'Query'), ...strand('t', 'Target'), + flag('accNoLP', 'Exclude lonely pairs in accessibility'), + flag('accNoGUend', 'Exclude GU helix ends in accessibility'), + flag('noSeed', 'Do not require a seed', prediction), + text('seedTQ', 'Explicit seeds', { ...prediction, hint: 'Target&query dot-bar encodings, e.g. 1|||&1|||; separate seeds with commas.' }), + number('seedBP', 'Seed base pairs', 7, 2, 20, prediction), + number('seedMaxUP', 'Maximum unpaired seed bases (both strands)', 0, 0, 20, prediction), + number('seedQMaxUP', 'Maximum unpaired query seed bases', -1, -1, 20, { ...prediction, hint: '-1 uses the combined limit.' }), + number('seedTMaxUP', 'Maximum unpaired target seed bases', -1, -1, 20, prediction), + number('seedMaxE', 'Maximum seed energy (kcal/mol)', 0, -999, 999, { ...prediction, step: 'any' }), + number('seedMaxEhybrid', 'Maximum seed hybridization energy (kcal/mol)', 999, -999, 999, { ...prediction, step: 'any' }), + number('seedMinPu', 'Minimum seed unpaired probability', 0, 0, 1, { ...prediction, step: 'any' }), + text('seedQRange', 'Query seed regions', prediction), text('seedTRange', 'Target seed regions', prediction), + flag('seedNoGU', 'Exclude GU pairs in seeds', prediction), flag('seedNoGUend', 'Exclude GU pairs at seed ends', prediction), + number('helixMinBP', 'Minimum helix base pairs', 2, 2, 4, prediction), + number('helixMaxBP', 'Maximum helix base pairs', 10, 2, 20, prediction), + number('helixMaxIL', 'Maximum helix interior-loop size', 0, 0, 2, prediction), + number('helixMinPu', 'Minimum helix unpaired probability', 0, 0, 1, { ...prediction, step: 'any' }), + number('helixMaxE', 'Maximum helix energy (kcal/mol)', 0, -999, 999, { ...prediction, step: 'any' }), + flag('helixFullE', 'Use full helix energy for the energy limit', prediction), + select('model', 'Interaction model', 'X', { X: 'Seed extension (MFE)', S: 'Single site (MFE)', P: 'Ensemble energy', B: 'Helix blocks (MFE)' }, prediction), + select('mode', 'Prediction algorithm', 'H', { H: 'Heuristic', M: 'Exact', S: 'Seed only', K: 'Greedy seed extension' }, prediction), + select('kineticScore', 'Greedy extension score', 'A', { A: 'Energy change', B: 'Change / (1 + s1 + s2)', C: 'Change / (1 + 2 max(s1,s2))' }, prediction), + select('energyVRNA', 'ViennaRNA parameter set', 'Turner04', { Turner04: 'Turner 2004', Turner99: 'Turner 1999', Andronescu07: 'Andronescu 2007' }), + number('temperature', 'Temperature (°C)', 37, 0, 100, { step: 'any' }), + number('energyAdd', 'Additional energy (kcal/mol)', 0, -999, 999, { step: 'any' }), + flag('energyNoDangles', 'Exclude dangling-end energy'), + number('windowWidth', 'Prediction window width', 0, 0, 99999, { ...prediction, hint: '0 disables prediction windows; otherwise at least 10 nt.' }), + number('windowOverlap', 'Prediction window overlap', 150, 0, 99999, prediction), + number('outNumber', 'Maximum interactions per sequence pair', 1, 0, 100, { ...prediction, hint: 'Browser limit: 100; 0 computes accessibility only.' }), + select('outOverlap', 'Allow overlapping interactions', 'B', { B: 'Both strands', N: 'Neither strand', T: 'Target only', Q: 'Query only' }, prediction), + number('outMaxE', 'Maximum interaction energy (exclusive, kcal/mol)', 0, -999, 999, { ...prediction, step: 'any' }), + number('outDeltaE', 'Maximum difference from MFE (kcal/mol)', 100, 0, 100, { ...prediction, step: 'any' }), + number('outMinPu', 'Minimum unpaired probability', 0, 0, 1, { ...prediction, step: 'any' }), + flag('outBestSeedOnly', 'Report only the best seed', prediction), + flag('outNoLP', 'Exclude lonely interaction pairs', prediction), flag('outNoGUend', 'Exclude GU interaction helix ends', prediction), + flag('outPerRegion', 'Report each region combination separately', prediction), flag('outPairwise', 'Match FASTA records pairwise', prediction), + select('outCsvSort', 'CSV download sort column', '', { '': 'Native computation order', ...Object.fromEntries(CSV_CATALOG.map((column) => [column.key, column.label])) }), + text('outSpotProbSpots', 'Interaction probability spots', { ...prediction, hint: 'Optional target&query coordinate pairs, e.g. 3&7,5&9. Empty selects all spots.' }), + ...['q', 't'].flatMap((p) => [ + text(`${p}Shape`, `${p === 'q' ? 'Query' : 'Target'} SHAPE data`, { type: 'textarea', hint: 'One sequence only. Paste position and reactivity, one pair per line; positions start at 1.' }), + { ...text(`${p}ShapeMethod`, 'SHAPE method'), value: 'D', hint: 'D, Dm1.8b-0.6, Z, Zb0.89 or W.' }, + { ...text(`${p}ShapeConversion`, 'SHAPE conversion'), value: 'Os1.6i-2.29', hint: 'M, C0.25, S, Ls0.68i0.2 or Os1.6i-2.29.' }, + ]), +].map((field) => [field.key, field])); + +// Explicit rows separate visual order from native parameter defaults. +const rows = (keys) => keys.map((row) => row.map((key) => fields.get(key))); +const strandRows = (p) => rows([ + [`${p}Set`, `${p}Region`, `${p}IntLenMax`, `${p}IntLoopMax`, `${p}RegionLenMax`], + [`${p}Acc`, `${p}AccW`, `${p}AccL`, `${p}PfScale`], +]); +const strandGroup = (p, label) => ({ + key: `${label.toLowerCase()}-options`, label, strand: p, + rows: strandRows(p), + fields: [...strandRows(p).flat(), ...rows([ + ...(p === 'q' ? [['accNoLP', 'accNoGUend']] : []), + [`${p}AccConstr`, `${p}AccFile`, `${p}Shape`, `${p}ShapeMethod`, `${p}ShapeConversion`], + ]).flat()], +}); +export const GROUPS = [ + { key: 'seed-options', label: 'Seed', prediction: true, rows: rows([ + ['noSeed'], ['seedTQ'], ['seedBP', 'seedMaxUP', 'seedQMaxUP', 'seedTMaxUP'], + ['seedMaxE', 'seedMinPu', 'seedMaxEhybrid'], ['seedQRange', 'seedTRange'], ['seedNoGU', 'seedNoGUend'], + ]) }, + { key: 'output-options', label: 'Output', fields: [...fields.values()].filter((field) => field.key.startsWith('out') && field.key !== 'outCsvSort') }, + { key: 'csv-options', label: 'CSV', fields: [fields.get('outCsvSort')] }, + { key: 'interaction-options', label: 'Model & Energy', rows: rows([ + ['model', 'mode'], ['energyVRNA', 'temperature', 'energyAdd'], ['energyNoDangles'], + ['windowWidth', 'windowOverlap'], ['kineticScore'], + ['helixMinBP', 'helixMaxBP', 'helixMaxIL', 'helixMinPu', 'helixMaxE'], ['helixFullE'], + ]) }, + strandGroup('q', 'Query'), strandGroup('t', 'Target'), +].map((group) => ({ ...group, fields: group.fields ?? group.rows.flat() })); +export const FIELDS = GROUPS.flatMap((group) => group.fields); +export const PARAMETER_DEFAULTS = Object.freeze(Object.fromEntries(FIELDS.map((field) => [field.key, field.value]))); +export const UI_DEFAULTS = Object.freeze({ ...PARAMETER_DEFAULTS, outNumber: 10 }); +export const EXTRA_OUTPUTS = [ + ['qMinE', 'Query minimum energies', true, 'CSV position profile of the lowest interaction energy covering each query nucleotide. Useful for locating favorable query sites.'], + ['tMinE', 'Target minimum energies', true, 'CSV position profile of the lowest interaction energy covering each target nucleotide. Useful for locating favorable target sites.'], + ['qAcc', 'Query opening energies', false, 'RNAplfold-style opening-energy matrix for the query. Use it to inspect or reproduce query accessibility.'], + ['tAcc', 'Target opening energies', false, 'RNAplfold-style opening-energy matrix for the target. Use it to inspect or reproduce target accessibility.'], + ['qPu', 'Query unpaired probabilities', false, 'RNAplfold-style query unpaired-probability matrix, converted from rounded opening energies.'], + ['tPu', 'Target unpaired probabilities', false, 'RNAplfold-style target unpaired-probability matrix, converted from rounded opening energies.'], + ['qSpotProb', 'Query interaction probabilities', true, 'CSV position profile estimating the probability that each query nucleotide is covered by an interaction.'], + ['tSpotProb', 'Target interaction probabilities', true, 'CSV position profile estimating the probability that each target nucleotide is covered by an interaction.'], + ['pMinE', 'Pair minimum energies', true, 'CSV target-by-query matrix of the minimum interaction energy covering each nucleotide pair. Useful as an energy heatmap.'], + ['spotProb', 'Interaction spot probabilities', true, 'CSV target-by-query matrix, or selected spots, estimating interaction coverage probabilities. Useful as a probability heatmap.'], + ['bpProb', 'Actual base-pair probabilities (model P)', true, 'CSV target-by-query matrix of actual base-pair probabilities for the model P interaction ensemble.'], + ['bpsvg', 'Base-pair probability SVG (model P)', true, 'SVG dot plot of model P base-pair probabilities with accessibility frames and seed/MFE outlines.'], + ['normal', 'ASCII interaction structures', false, 'Compact text report with ASCII interaction structures and their overall energies.'], + ['detailed', 'Detailed interaction report', false, 'Expanded text report with interaction structures, coordinates and energy contributions.'], + ['ensemble', 'Ensemble report', false, 'Text report of interaction and intramolecular ensemble energies and partition functions.'], +].map(([key, label, predictionOnly, description]) => ({ key, label, prediction: predictionOnly, description })); +export const ENSEMBLE_COLUMNS = ['Eall', 'Zall', 'EallTotal', 'P_E']; diff --git a/gui/output-visualization.js b/gui/output-visualization.js new file mode 100644 index 00000000..9c901089 --- /dev/null +++ b/gui/output-visualization.js @@ -0,0 +1,230 @@ +const PROFILE_TYPES = new Map([ + ['qMinE', { strand: 'query', value: 'minE', title: 'Minimum-energy profile', yTitle: 'Minimum interaction energy (kcal/mol)' }], + ['tMinE', { strand: 'target', value: 'minE', title: 'Minimum-energy profile', yTitle: 'Minimum interaction energy (kcal/mol)' }], + ['qSpotProb', { strand: 'query', value: 'spotProb', title: 'Interaction-probability profile', yTitle: 'Interaction probability' }], + ['tSpotProb', { strand: 'target', value: 'spotProb', title: 'Interaction-probability profile', yTitle: 'Interaction probability' }], +]); +const MATRIX_TYPES = new Map([ + ['pMinE', { value: 'minE', title: 'Pair minimum energies', colorTitle: 'kcal/mol', colorscale: [[0, '#0f4676'], [0.5, '#8bbbd8'], [1, '#f8fbff']] }], + ['spotProb', { value: 'spotProb', title: 'Interaction spot probabilities', colorTitle: 'Probability', colorscale: [[0, '#f8fbff'], [0.5, '#80b6d8'], [1, '#145a96']] }], +]); + +function outputType(name) { + const match = /^(qMinE|tMinE|qSpotProb|tSpotProb|pMinE|spotProb)(?:-t\d+q\d+)?\.csv$/.exec(name); + return match?.[1] ?? null; +} + +function table(text) { + if (typeof text !== 'string' || !text.trim()) throw new Error('The output file is empty.'); + const lines = text.trimEnd().split(/\r?\n/), header = lines.shift().split(';'); + if (header.length < 2 || new Set(header).size !== header.length) throw new Error('The output file has an invalid header.'); + const rows = lines.filter((line) => line.trim()).map((line) => { + const cells = line.split(';'); + if (cells.length !== header.length) throw new Error('The output file contains a malformed row.'); + return cells; + }); + if (!rows.length) throw new Error('The output file contains no values to plot.'); + return { header, rows }; +} + +function number(value) { + if (/^(NA|NAN)$/i.test(value.trim())) return null; + const parsed = Number(value); + if (!Number.isFinite(parsed)) throw new Error(`The output contains a non-numeric value: ${value}`); + return parsed; +} + +function plotText(value) { + return String(value).replaceAll('&', '&').replaceAll('<', '<').replaceAll('>', '>'); +} + +function record(request, strand, index) { + return request?.[strand]?.records?.[index - 1]?.id ?? ''; +} + +export function outputFileContext(name, request) { + const type = outputType(name) ?? /^(qAcc|tAcc|qPu|tPu|bpProb|bpsvg)/.exec(name)?.[1] ?? ''; + const pair = /-t(\d+)q(\d+)(?=\.[^.]+$)/.exec(name); + if (pair) { + const target = record(request, 'target', Number(pair[1])), query = record(request, 'query', Number(pair[2])); + return { target, query, label: [target, query].filter(Boolean).join(' : ') }; + } + const single = /-s(\d+)(?=\.[^.]+$)/.exec(name); + if (single && /^[qt](Acc|Pu)/.test(type)) { + const strand = type.startsWith('q') ? 'query' : 'target', value = record(request, strand, Number(single[1])); + return { [strand]: value, label: value }; + } + const target = request?.target?.records?.length === 1 ? request.target.records[0].id : ''; + const query = request?.query?.records?.length === 1 ? request.query.records[0].id : ''; + if (/^[qt](Acc|Pu)$/.test(type)) { + const value = type.startsWith('q') ? query : target; + return { [type.startsWith('q') ? 'query' : 'target']: value, label: value }; + } + return { target, query, label: [target, query].filter(Boolean).join(' : ') }; +} + +function baseLayout(title) { + return { + title: { text: title, x: 0.04, xanchor: 'left', font: { size: 17 } }, + autosize: true, + height: 420, + margin: { l: 72, r: 28, t: 62, b: 78 }, + paper_bgcolor: 'rgba(0,0,0,0)', + plot_bgcolor: '#fff', + font: { family: 'Segoe UI, Tahoma, Geneva, sans-serif', color: '#1c2b39', size: 12 }, + }; +} + +function categoricalAxis(title, values) { + return { title: { text: title }, type: 'category', categoryorder: 'array', categoryarray: values, automargin: true, gridcolor: '#e0e8f0' }; +} + +export function outputVisualization(file, request) { + const type = outputType(file.name); + if (!type) return null; + const parsed = table(file.text), context = outputFileContext(file.name, request); + if (PROFILE_TYPES.has(type)) { + const profile = PROFILE_TYPES.get(type); + if (parsed.header.length !== 3 || parsed.header[0] !== 'idx' || parsed.header[2] !== profile.value) throw new Error(`Unexpected ${type} profile columns.`); + const x = parsed.rows.map((row) => String(row[0])), y = parsed.rows.map((row) => number(row[2])); + const sequence = parsed.header[1] || context[profile.strand] || (profile.strand === 'query' ? 'Query' : 'Target'); + return { + kind: 'profile', context, + traces: [{ + type: 'scatter', mode: 'lines+markers', x, y, text: parsed.rows.map((row) => row[1]), + name: plotText(sequence), line: { color: '#145a96', width: 2 }, marker: { color: '#145a96', size: 6 }, + connectgaps: false, hovertemplate: 'Index %{x}
Nucleotide %{text}
Value %{y}', + }], + layout: { + ...baseLayout(`${profile.title}: ${plotText(sequence)}`), + xaxis: categoricalAxis(`${profile.strand === 'query' ? 'Query' : 'Target'} index`, x), + yaxis: { title: { text: profile.yTitle }, automargin: true, gridcolor: '#e0e8f0', rangemode: profile.value === 'spotProb' ? 'tozero' : 'normal' }, + }, + }; + } + + const matrix = MATRIX_TYPES.get(type); + if (type === 'spotProb' && parsed.header[0] === 'spot') { + if (parsed.header.length !== 2 || parsed.header[1] !== 'probability') throw new Error('Unexpected selected-spot probability columns.'); + const x = parsed.rows.map((row) => String(row[0])), y = parsed.rows.map((row) => number(row[1])); + return { + kind: 'spots', context, + traces: [{ type: 'bar', x, y, marker: { color: '#145a96' }, hovertemplate: 'Spot %{x}
Probability %{y}' }], + layout: { + ...baseLayout(`${matrix.title}${context.label ? `: ${plotText(context.label)}` : ''}`), + xaxis: categoricalAxis('Target & query index', x), + yaxis: { title: { text: matrix.colorTitle }, automargin: true, gridcolor: '#e0e8f0', rangemode: 'tozero' }, + }, + }; + } + if (parsed.header[0] !== matrix.value || parsed.header.length < 2) throw new Error(`Unexpected ${type} matrix columns.`); + const x = parsed.header.slice(1).map(String), y = parsed.rows.map((row) => String(row[0])); + const z = parsed.rows.map((row) => row.slice(1).map(number)); + const target = context.target || 'Target', query = context.query || 'Query'; + return { + kind: 'matrix', context, + traces: [{ + type: 'heatmap', x, y, z, colorscale: matrix.colorscale, hoverongaps: false, + colorbar: { title: { text: matrix.colorTitle, side: 'right' } }, + hovertemplate: `${plotText(target)} %{y}
${plotText(query)} %{x}
Value %{z}`, + }], + layout: { + ...baseLayout(`${matrix.title}: ${plotText(target)} : ${plotText(query)}`), + xaxis: categoricalAxis(`${plotText(query)} index`, x), + yaxis: categoricalAxis(`${plotText(target)} index`, y), + }, + }; +} + +function button(text, className = '') { + const node = document.createElement('button'); node.type = 'button'; node.textContent = text; node.className = className; return node; +} + +export class AdditionalOutputView { + constructor(file, request, id, download) { + this.file = file; this.id = id; this.root = document.createElement('details'); this.root.className = 'output-file'; + const summary = document.createElement('summary'); summary.className = 'output-file-summary'; + const name = document.createElement('span'); name.className = 'output-file-name'; name.textContent = file.name; + const downloadButton = button('Download', 'text-button output-download'); + downloadButton.setAttribute('aria-label', `Download ${file.name}`); + downloadButton.addEventListener('click', (event) => { event.preventDefault(); event.stopPropagation(); download(); }); + const context = outputFileContext(file.name, request), description = document.createElement('span'); + description.className = 'output-file-context'; description.textContent = context.label ? `— ${context.label}` : ''; + summary.append(name, downloadButton, description); this.root.append(summary); + + const body = document.createElement('div'); body.className = 'output-file-body'; this.root.append(body); + const preview = document.createElement('pre'); preview.textContent = file.text.slice(0, 100000); + const contentPanel = document.createElement('section'); contentPanel.className = 'output-tab-panel'; contentPanel.append(preview); + if (file.text.length > 100000) { + const note = document.createElement('p'); note.textContent = 'Preview limited to 100,000 characters. Download contains the complete file.'; contentPanel.append(note); + } + + let spec = null, plotError = null; + try { spec = outputVisualization(file, request); } catch (error) { plotError = error; } + if (!spec && !plotError) { body.append(contentPanel); return; } + + const tabs = document.createElement('div'); tabs.className = 'output-tabs'; tabs.setAttribute('role', 'tablist'); tabs.setAttribute('aria-label', `${file.name} views`); + const visualizationTab = button('Visualization', 'output-tab'), contentTab = button('File Content', 'output-tab'); + const visualizationPanel = document.createElement('section'); visualizationPanel.className = 'output-tab-panel'; + visualizationTab.id = `${id}-visualization-tab`; visualizationPanel.id = `${id}-visualization-panel`; + contentTab.id = `${id}-content-tab`; contentPanel.id = `${id}-content-panel`; + for (const [tab, panel] of [[visualizationTab, visualizationPanel], [contentTab, contentPanel]]) { + tab.setAttribute('role', 'tab'); tab.setAttribute('aria-controls', panel.id); + panel.setAttribute('role', 'tabpanel'); panel.setAttribute('aria-labelledby', tab.id); + } + tabs.append(visualizationTab, contentTab); body.append(tabs, visualizationPanel, contentPanel); + this.tabs = [visualizationTab, contentTab]; this.panels = [visualizationPanel, contentPanel]; + this.selectTab = (index, focus = false) => { + this.tabs.forEach((tab, current) => { tab.setAttribute('aria-selected', String(current === index)); tab.tabIndex = current === index ? 0 : -1; this.panels[current].hidden = current !== index; }); + if (focus) this.tabs[index].focus(); + if (index === 0) this.render(); + }; + visualizationTab.addEventListener('click', () => this.selectTab(0)); contentTab.addEventListener('click', () => this.selectTab(1)); + tabs.addEventListener('keydown', (event) => { + if (!['ArrowLeft', 'ArrowRight', 'Home', 'End'].includes(event.key)) return; + const current = this.tabs.indexOf(document.activeElement); + const next = event.key === 'Home' ? 0 : event.key === 'End' ? 1 : (current + (event.key === 'ArrowRight' ? 1 : -1) + 2) % 2; + event.preventDefault(); this.selectTab(next, true); + }); + + const tools = document.createElement('div'); tools.className = 'plot-tools'; + const status = document.createElement('p'); status.className = 'output-plot-status'; status.setAttribute('role', 'status'); + visualizationPanel.append(tools, status); this.status = status; + if (plotError) { status.textContent = `Visualization unavailable: ${plotError.message}`; this.selectTab(0); return; } + const exportButton = button('Export PNG', 'secondary'); exportButton.disabled = true; + exportButton.addEventListener('click', async () => { + try { + await this.ready; + const image = await globalThis.Plotly.toImage(this.plot, { format: 'png', width: 1400, height: 850 }); + const encoded = image.slice(image.indexOf(',') + 1), bytes = Uint8Array.from(atob(encoded), (character) => character.charCodeAt(0)); + const url = URL.createObjectURL(new Blob([bytes], { type: 'image/png' })); + const link = document.createElement('a'); link.href = url; link.download = file.name.replace(/\.csv$/i, '.png'); + document.body.append(link); link.click(); link.remove(); setTimeout(() => URL.revokeObjectURL(url), 1000); + } catch (error) { status.textContent = `PNG export failed: ${error.message}`; } + }); + tools.append(exportButton); this.exportButton = exportButton; + this.plot = document.createElement('div'); this.plot.className = 'output-plot'; visualizationPanel.append(this.plot); this.spec = spec; + this.root.addEventListener('toggle', () => { if (this.root.open && !visualizationPanel.hidden) this.render(); }); + this.selectTab(0); + } + + render() { + if (!this.spec || this.rendered || !this.root.open) return; + if (!globalThis.Plotly?.newPlot) { this.status.textContent = 'Visualization unavailable: Plotly did not load.'; return; } + this.rendered = true; this.status.textContent = 'Rendering visualization…'; this.plot.setAttribute('aria-busy', 'true'); + this.ready = Promise.resolve(globalThis.Plotly.newPlot(this.plot, this.spec.traces, this.spec.layout, { + responsive: true, displaylogo: false, scrollZoom: false, + modeBarButtonsToRemove: ['sendDataToCloud', 'lasso2d', 'select2d'], + })).then(() => { + this.plot.removeAttribute('aria-busy'); this.status.textContent = ''; this.exportButton.disabled = false; + }).catch((error) => { this.plot.removeAttribute('aria-busy'); this.status.textContent = `Visualization unavailable: ${error.message}`; }); + } + + resize() { + if (this.rendered && this.root.open && !this.panels?.[0].hidden) requestAnimationFrame(() => globalThis.Plotly?.Plots?.resize(this.plot)); + } + + destroy() { + if (this.rendered) globalThis.Plotly?.purge?.(this.plot); + } +} diff --git a/gui/package.json b/gui/package.json new file mode 100644 index 00000000..307fd5df --- /dev/null +++ b/gui/package.json @@ -0,0 +1,6 @@ +{ + "name": "intarna-gui", + "private": true, + "type": "module", + "scripts": { "test": "node --test --test-isolation=none tests/*.test.mjs" } +} diff --git a/gui/parameter-file.js b/gui/parameter-file.js new file mode 100644 index 00000000..7e52f341 --- /dev/null +++ b/gui/parameter-file.js @@ -0,0 +1,116 @@ +import { JSON_SCHEMA, CSV_COLUMNS, LIMITS, normalizeParameters } from './protocol.js'; +import { FIELDS, PARAMETER_DEFAULTS, EXTRA_OUTPUTS } from './options.js'; +import { CSV_CATALOG } from './columns.js'; + +export const MAX_PARAMETER_BYTES = 5000000; +const reports = { normal: 'N', detailed: 'D', ensemble: 'E' }; +const embeddedKeys = ['qShape', 'tShape', 'qAccFile', 'tAccFile']; +const object = (value) => value !== null && typeof value === 'object' && !Array.isArray(value); +function text(value, label, limit = 1000000) { + if (typeof value !== 'string' || value.length > limit || value.includes('\0')) throw new Error(`${label}: invalid or oversized text.`); + return value; +} +function selections(request) { + const columns = request.csvColumns ?? CSV_COLUMNS.split(','), outputs = request.outputs ?? []; + for (const [values, catalog, label] of [[columns, CSV_CATALOG, 'CSV columns'], [outputs, EXTRA_OUTPUTS.filter((entry) => request.task !== 'evaluation' || !entry.prediction), 'output files']]) { + if (!Array.isArray(values) || new Set(values).size !== values.length || values.some((key) => !catalog.some((entry) => entry.key === key))) throw new Error(`Choose available ${label}, without duplicates.`); + } + return { columns, outputs }; +} + +// Save editable settings, even before sequences have been entered. Computation +// performs full sequence-dependent validation later through prepareRequest. +export function exportParameters(request, provenance) { + if (!provenance?.trim()) throw new Error('Compiled version information is unavailable'); + const normalized = normalizeParameters(request); + const { columns, outputs } = selections(request); + const parameters = { + query: { text: text(typeof request.query === 'string' ? request.query : request.query.fasta, 'Query', LIMITS.maxFastaBytes) }, + target: { text: text(typeof request.target === 'string' ? request.target : request.target.fasta, 'Target', LIMITS.maxFastaBytes) }, + }; + if (request.task === 'evaluation') parameters.personality = 'IntaRNAeval'; + for (const [key, value] of Object.entries(normalized)) { + if (key === 'outSpotProbSpots' || value === '' || value === (PARAMETER_DEFAULTS[key] ?? 1)) continue; + parameters[key] = embeddedKeys.includes(key) ? { text: value } : value; + } + if (request.task === 'evaluation' && request.rri) parameters.rri = text(request.rri, 'Interactions', 10000); + parameters.outMode = 'C'; + if (columns.join(',') !== CSV_COLUMNS) parameters.outCsvCols = columns.join(','); + const nativeOutputs = outputs.filter((key) => !Object.hasOwn(reports, key)).map((key) => { + const spots = key === 'spotProb' && normalized.outSpotProbSpots ? `${normalized.outSpotProbSpots}:` : ''; + return `${key}:${spots}${key}${key === 'bpsvg' ? '.svg' : '.csv'}`; + }); + if (nativeOutputs.length) parameters.out = nativeOutputs; + const selectedReports = outputs.filter((key) => Object.hasOwn(reports, key)); + const comments = [ + ...provenance.trimEnd().split(/\r?\n/), + 'Reproduce: IntaRNA --parameterFile=parameter.json --out=intarna-interactions.csv', + ...selectedReports.map((key) => `Additional report: IntaRNA --parameterFile=parameter.json --outMode=${reports[key]} --outCsvCols=${CSV_COLUMNS} --outCsvSort '' --out=intarna-${key}.txt`), + ]; + const gui = {}; + if (selectedReports.length) gui.reports = selectedReports; + if (normalized.outSpotProbSpots) gui.outSpotProbSpots = normalized.outSpotProbSpots; + return { schema: JSON_SCHEMA, _comment: comments, parameters, ...(Object.keys(gui).length ? { gui } : {}) }; +} + +export function serializeParameters(request, provenance) { + return JSON.stringify(exportParameters(request, provenance), null, 2) + '\n'; +} + +// Import only controls the browser can represent. Native-only settings produce +// an actionable error instead of being silently discarded or reaching WASM. +export function importParameters(source) { + if (typeof source === 'string' && source.length > MAX_PARAMETER_BYTES) throw new Error('Choose a JSON file of at most 5 MB.'); + const document = typeof source === 'string' ? JSON.parse(source.replace(/^\uFEFF/, '')) : source; + if (!object(document) || document.schema !== JSON_SCHEMA || !object(document.parameters)) throw new Error(`Expected a ${JSON_SCHEMA} parameter document.`); + for (const key of Object.keys(document)) if (!['schema', '_comment', 'parameters', 'gui'].includes(key)) throw new Error(`Unknown JSON document field: ${key}`); + const request = { task: 'prediction', query: '', target: '', qIdxPos0: 1, tIdxPos0: 1, rri: '', parameters: {}, outputs: [], csvColumns: CSV_COLUMNS.split(',') }; + const known = new Set(FIELDS.map((field) => field.key)); + for (const [key, value] of Object.entries(document.parameters)) { + if (value === null) throw new Error(`${key}: null is not a parameter value.`); + if (['query', 'target', ...embeddedKeys].includes(key)) { + const content = object(value) && Object.keys(value).length === 1 && typeof value.text === 'string' ? value.text : value; + // Plain nucleotide strings are native inline sequences; file paths need + // explicit embedding because the browser cannot open local paths. + if (typeof content !== 'string' || (content === value && (embeddedKeys.includes(key) || !/^[ACGUTNacgutn]*$/.test(value)))) throw new Error(`${key}: embed the input using {"text":"file contents"}.`); + if (key === 'query' || key === 'target') request[key] = text(content, key, LIMITS.maxFastaBytes); + else request.parameters[key] = text(content, key); + } else if (key === 'personality') { + if (!['IntaRNA', 'IntaRNAeval'].includes(value)) throw new Error('The browser supports IntaRNA prediction and IntaRNAeval evaluation.'); + request.task = value === 'IntaRNAeval' ? 'evaluation' : 'prediction'; + } else if (key === 'qIdxPos0' || key === 'tIdxPos0') request[key] = value; + else if (key === 'rri') request.rri = text(value, key, 10000); + else if (key === 'outMode') { if (value !== 'C') throw new Error('Use CSV outMode C and gui.reports for additional browser reports.'); } + else if (key === 'outCsvCols') request.csvColumns = text(value, key).split(',').filter(Boolean); + else if (key === 'out') { + const entries = Array.isArray(value) ? value : [value]; + for (const entry of entries) { + const match = /^([A-Za-z]+):(?:(-?[\d&,\-]+):)?([^:]+)$/.exec(text(entry, 'out')); + if (!match || !EXTRA_OUTPUTS.some((output) => output.key === match[1] && !Object.hasOwn(reports, output.key))) throw new Error('The browser supports named additional outputs; omit main output paths from the parameter file.'); + request.outputs.push(match[1]); + if (match[2]) { + if (match[1] !== 'spotProb') throw new Error('Only spotProb accepts explicit probability spots.'); + request.parameters.outSpotProbSpots = match[2]; + } + } + } else if (known.has(key)) request.parameters[key] = value; + else throw new Error(`The browser cannot represent parameter ${key}; use the native CLI.`); + } + if (document.gui !== undefined) { + if (!object(document.gui)) throw new Error('gui must be an object.'); + for (const [key, value] of Object.entries(document.gui)) { + if (key === 'reports' && Array.isArray(value) && value.every((entry) => Object.hasOwn(reports, entry))) request.outputs.push(...value); + else if (key === 'outSpotProbSpots') { + if (request.parameters.outSpotProbSpots && request.parameters.outSpotProbSpots !== value) throw new Error('Conflicting spotProb selections.'); + request.parameters.outSpotProbSpots = text(value, key, 10000); + } else throw new Error(`Unsupported GUI setting: ${key}`); + } + } + selections(request); + // Keep prediction-only controls from being silently ignored on import. + if (request.task === 'evaluation' && FIELDS.some((field) => field.prediction && Object.hasOwn(request.parameters, field.key))) throw new Error('Evaluation documents must omit prediction-only parameters.'); + const normalized = normalizeParameters(request); + request.qIdxPos0 = normalized.qIdxPos0; request.tIdxPos0 = normalized.tIdxPos0; + request.parameters = normalized; + return request; +} diff --git a/gui/protocol.js b/gui/protocol.js new file mode 100644 index 00000000..d452de28 --- /dev/null +++ b/gui/protocol.js @@ -0,0 +1,258 @@ +import { FIELDS, PARAMETER_DEFAULTS, EXTRA_OUTPUTS, ENSEMBLE_COLUMNS } from './options.js'; +import { CSV_CATALOG } from './columns.js'; + +// Bound the largest pair's matrix while allowing batches of shorter sequences. +export const LIMITS = Object.freeze({ minLength: 2, maxLength: 5000, maxRecords: 50, maxPairs: 1000000, maxFastaBytes: 1000000 }); +export const CSV_COLUMNS = 'id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E'; +export const CONTEXT_COLUMNS = ['id1', 'start1', 'end1', 'id2', 'start2', 'end2', 'E']; +export const DEFAULTS = Object.freeze({ query: '>query\nGGGAGGAGGG', target: '>target\nCCCUCCUCCC', task: 'prediction' }); +export const EVALUATION_EXAMPLE = '1||||||||||&1||||||||||'; + +export function parseFasta(text, label, multiple = true) { + if (typeof text !== 'string' || text.length > LIMITS.maxFastaBytes || !text.trim()) throw new Error(`${label}: enter a sequence or FASTA records (at most 1 MB).`); + const lines = text.trim().split(/\r?\n/).map((line) => line.trim()).filter(Boolean); + const records = [], warnings = []; + let current; + for (const line of lines) { + if (line.startsWith('>')) { + const header = line.slice(1).trim(); + current = { id: header.split(/\s+/)[0], sequence: '' }; + if (!current.id || current.id.length > 200 || /[\x00-\x1f\x7f]/.test(current.id)) throw new Error(`${label}: the FASTA header needs a name (at most 200 characters).`); + if (/\s+\S/.test(header)) warnings.push(`${label}: ignoring FASTA description after the name “${current.id}”.`); + records.push(current); + } else { + if (!current) { current = { id: label.toLowerCase(), sequence: '' }; records.push(current); } + current.sequence += line.replace(/\s/g, '').toUpperCase().replaceAll('T', 'U'); + } + } + if ((!multiple && records.length !== 1) || records.length > LIMITS.maxRecords) throw new Error(`${label}: ${multiple ? 'use at most 50 FASTA records' : 'evaluation requires exactly one FASTA record'}.`); + const ids = new Set(); + for (const record of records) { + if (!record.sequence || /[^ACGUN]/.test(record.sequence)) throw new Error(`${label}: use only A, C, G, U, T or N in every sequence.`); + if (record.sequence.length < LIMITS.minLength || record.sequence.length > LIMITS.maxLength) throw new Error(`${label}: use 2–5,000 nucleotides per record.`); + // Native CSV replaces semicolons with underscores. Keep pair grouping unique. + const id = record.id.replaceAll(';', '_'); + if (ids.has(id)) throw new Error(`${label}: FASTA identifiers must be unique (also after replacing semicolons with underscores).`); + ids.add(id); + } + return { records, warnings, fasta: records.map(({ id, sequence }) => `>${id}\n${sequence}\n`).join('') }; +} +export function parseSequence(text, label) { + const parsed = parseFasta(text, label, false); + return { ...parsed.records[0], fasta: parsed.fasta }; +} + +// IntaRNA omits coordinate zero when an index range crosses from negative to positive. +export function sequenceOffset(index, start) { + return index - start - (start < 0 && index > 0 ? 1 : 0); +} +function ranges(value, key, length, start = 1) { + if (!value) return []; + return value.split(',').map((part) => { + const match = /^(-?[1-9]\d*)-(-?[1-9]\d*)$/.exec(part); + if (!match) throw new Error(`${key}: use inclusive ranges such as 1-5,8-10 (coordinate zero is skipped).`); + const from = sequenceOffset(Number(match[1]), start), to = sequenceOffset(Number(match[2]), start); + if (from < 0 || to < from || to >= length) throw new Error(`${key}: ranges must be ascending and within the selected sequence.`); + return [from, to]; + }); +} +function selectedRecords(parsed, subset, key) { + const intervals = ranges(subset, key, parsed.records.length); + return intervals.length ? parsed.records.filter((_, index) => intervals.some(([a, b]) => a <= index && index <= b)) : parsed.records; +} +function oneRecord(records, key) { + if (records.length !== 1) throw new Error(`${key}: this setting requires exactly one selected sequence.`); + return records[0]; +} +function validateConstraints(value, records, start, key) { + const record = oneRecord(records, key); + if (/^[.xpb]+$/.test(value)) { + if (value.length !== record.sequence.length) throw new Error(`${key}: provide one constraint character per nucleotide.`); + return; + } + const sections = value.match(/[xpb]:[^xpb]+/g); + if (!sections || sections.join('') !== value) throw new Error(`${key}: use ./x/p/b per base or ranges such as b:3-4,p:6-7.`); + for (const section of sections) ranges(section.slice(2).replace(/,$/, ''), key, record.sequence.length, start); +} +function validateAccessibility(value, record, mode, key) { + const lines = value.split(/\r?\n/); + if (!/^#[\w\s]+$/.test(lines[0]) || !/^\s*#i.\s+l=1(\s+\d+)*\s*$/.test(lines[1] ?? '')) throw new Error(`${key}: paste RNAplfold text with its comment and length header lines.`); + const lengths = lines[1].match(/\d+/g).map(Number); + if (lengths.length < 2 || lengths.some((n, i) => n !== i + 1)) throw new Error(`${key}: accessibility lengths must be consecutive, starting at 1, with at least two columns.`); + const data = lines.slice(2).filter((line) => line.trim()); + if (data.length < record.sequence.length) throw new Error(`${key}: provide one data row per nucleotide.`); + for (let index = 0; index < record.sequence.length; index++) { + const cells = data[index].trim().split(/\s+/); + const values = cells.slice(1, 1 + Math.min(index + 1, lengths.length)); + if (Number(cells[0]) !== index + 1 || values.length !== Math.min(index + 1, lengths.length) || values.some((v) => !Number.isFinite(Number(v)) || Number(v) < 0 || mode === 'P' && Number(v) > 1)) throw new Error(`${key}: rows must be consecutive; required values must be finite ${mode === 'P' ? 'probabilities in [0,1]' : 'opening energies ≥ 0'}.`); + } +} +function complementary(a, b) { return ['AU', 'UA', 'GC', 'CG', 'GU', 'UG'].includes(a + b); } +export function validateInteractions(encoding, query, target, qStart, tStart, separator = ':') { + if (typeof encoding !== 'string' || !encoding || encoding.length > 10000 || encoding.split(separator).length > 100) throw new Error('Provide 1–100 target&query dot-bar interactions.'); + for (const entry of encoding.split(separator)) { + const strands = entry.split('&'); + if (strands.length !== 2) throw new Error('Each interaction needs target&query dot-bar encodings.'); + const positions = strands.map((strand, i) => { + const match = /^(-?[1-9]\d*)([.|]+)$/.exec(strand); + if (!match) throw new Error('Use a nonzero start index followed by dots and pairing bars, e.g. 1|||&1|||.'); + if (separator === ',' && (!match[2].startsWith('|') || !match[2].endsWith('|'))) throw new Error('Explicit seed strands must start and end with a pairing bar.'); + const record = i ? query : target, start = i ? qStart : tStart; + const offset = sequenceOffset(Number(match[1]), start); + if (offset < 0 || offset + match[2].length > record.sequence.length) throw new Error('A dot-bar interaction extends outside its sequence.'); + return [...match[2]].flatMap((c, p) => c === '|' ? [offset + p] : []); + }); + if (!positions[0].length || positions[0].length !== positions[1].length) throw new Error('Interaction strands must contain the same nonzero number of pairing bars.'); + for (let p = 0; p < positions[0].length; p++) { + if (!complementary(target.sequence[positions[0][p]], query.sequence[positions[1].at(-1 - p)])) throw new Error('The supplied interaction contains a non-complementary base pair.'); + } + } +} + +// Validate scalar controls independently so unfinished forms can be saved/loaded. +export function normalizeParameters(request) { + if (!['prediction', 'evaluation'].includes(request.task ?? 'prediction')) throw new Error('Choose prediction or evaluation.'); + const evaluating = request.task === 'evaluation'; + const parameters = {}; + const supplied = request.parameters ?? {}; + for (const field of FIELDS) { + if (evaluating && field.prediction) continue; + const value = supplied[field.key] ?? field.value; + if (field.type === 'checkbox') { + if (typeof value !== 'boolean') throw new Error(`${field.label}: choose on or off.`); + parameters[field.key] = value; + } else if (field.type === 'number') { + const n = typeof value === 'number' ? value : (typeof value === 'string' && value.trim() ? Number(value) : NaN); + if (!Number.isFinite(n) || n < field.min || n > field.max || (field.step !== 'any' && !Number.isInteger(n)) || field.exclude?.includes(n)) throw new Error(`${field.label}: use ${field.min}–${field.max}${field.exclude ? ', excluding 1 and 2' : ''}${field.step !== 'any' ? ' (whole numbers)' : ''}.`); + parameters[field.key] = n; + } else { + if (typeof value !== 'string' || value.length > (field.type === 'textarea' ? 1000000 : 10000) || /\x00/.test(value)) throw new Error(`${field.label}: invalid or oversized text input.`); + if (field.choices && !Object.hasOwn(field.choices, value)) throw new Error(`${field.label}: choose an available value.`); + parameters[field.key] = value.trim(); + } + } + for (const key of ['qIdxPos0', 'tIdxPos0']) { + const raw = request[key] ?? 1; + const n = typeof raw === 'number' || typeof raw === 'string' && raw.trim() ? Number(raw) : NaN; + if (!Number.isInteger(n) || n < -2000000000 || n > 2000000000) throw new Error(`${key}: use an integer between -2,000,000,000 and 2,000,000,000.`); + parameters[key] = n; + } + return parameters; +} + +export function prepareRequest(request) { + const task = request?.task ?? 'prediction'; + if (!['prediction', 'evaluation'].includes(task)) throw new Error('Choose prediction or evaluation.'); + const evaluating = task === 'evaluation'; + const query = parseFasta(request.query, 'Query', !evaluating), target = parseFasta(request.target, 'Target', !evaluating); + const parameters = normalizeParameters(request); + const qRecords = selectedRecords(query, parameters.qSet, 'qSet'), tRecords = selectedRecords(target, parameters.tSet, 'tSet'); + if (parameters.outPairwise && qRecords.length !== tRecords.length) throw new Error('Pairwise output requires the same number of selected query and target records.'); + const work = Math.max(...qRecords.map((q) => q.sequence.length)) * Math.max(...tRecords.map((t) => t.sequence.length)); + if (work > LIMITS.maxPairs) throw new Error('The longest selected query × longest selected target must be at most 1,000,000.'); + + // Validate sequence-dependent settings before loading the engine. + for (const [p, records] of [['q', qRecords], ['t', tRecords]]) { + const start = parameters[`${p}IdxPos0`]; + if (parameters[`${p}AccW`] && parameters[`${p}AccL`] > parameters[`${p}AccW`]) throw new Error(`${p}AccL must not exceed ${p}AccW.`); + if (parameters[`${p}RegionLenMax`] && (parameters[`${p}Acc`] === 'N' || parameters[`${p}Region`])) throw new Error(`${p}RegionLenMax: automatic regions require accessibility and cannot be combined with manual regions.`); + for (const record of records) ranges(parameters[`${p}Region`], `${p}Region`, record.sequence.length, start); + const seedRange = parameters[`seed${p.toUpperCase()}Range`]; + if (seedRange) ranges(seedRange, `seed${p.toUpperCase()}Range`, oneRecord(records, 'Seed regions').sequence.length, start); + if (parameters[`${p}AccConstr`]) validateConstraints(parameters[`${p}AccConstr`], records, start, `${p}AccConstr`); + if (['P', 'E'].includes(parameters[`${p}Acc`])) { + const record = oneRecord(records, 'Accessibility import'); + if (!parameters[`${p}AccFile`]) throw new Error(`${p}Acc: paste accessibility data for the selected import mode.`); + validateAccessibility(parameters[`${p}AccFile`], record, parameters[`${p}Acc`], `${p}AccFile`); + } + if (parameters[`${p}Shape`]) { + const record = oneRecord(records, 'SHAPE'); + for (const line of parameters[`${p}Shape`].split(/\r?\n/).filter((line) => line.trim() && !line.trim().startsWith('#'))) { + const cells = line.trim().split(/\s+/); + if (cells.length !== 2 || !/^\d+$/.test(cells[0]) || Number(cells[0]) < 1 || Number(cells[0]) > record.sequence.length || !Number.isFinite(Number(cells[1]))) throw new Error(`${p}Shape: use position (1-based) and finite reactivity on each line.`); + } + } + if (!/^(D(m-?\d+(\.\d+)?)?(b-?\d+(\.\d+)?)?|Z(b\d+(\.\d+)?)?|W)$/.test(parameters[`${p}ShapeMethod`])) throw new Error(`${p}ShapeMethod: invalid SHAPE method encoding.`); + if (!/^(M|C(\d+(\.\d+)?)?|S|[LO](s-?\d+(\.\d+)?i-?\d+(\.\d+)?)?)$/.test(parameters[`${p}ShapeConversion`])) throw new Error(`${p}ShapeConversion: invalid SHAPE conversion encoding.`); + } + const csvColumns = request.csvColumns ?? CSV_COLUMNS.split(','); + if (!Array.isArray(csvColumns) || !csvColumns.length || new Set(csvColumns).size !== csvColumns.length || csvColumns.some((key) => !CSV_CATALOG.some((c) => c.key === key))) throw new Error('Select at least one available CSV column, without duplicates.'); + if (parameters.outCsvSort && !csvColumns.includes(parameters.outCsvSort)) throw new Error('The CSV sort column must be selected for output.'); + const outputs = request.outputs ?? []; + if (!Array.isArray(outputs) || new Set(outputs).size !== outputs.length || outputs.some((key) => !EXTRA_OUTPUTS.some((entry) => entry.key === key && (!evaluating || !entry.prediction)))) throw new Error('Choose available additional output formats for this task.'); + if (outputs.includes('ensemble') && (qRecords.length !== 1 || tRecords.length !== 1)) throw new Error('Ensemble reports require one query and one target.'); + const needsEnsemble = csvColumns.some((c) => ENSEMBLE_COLUMNS.includes(c)) || outputs.some((c) => ['ensemble', 'spotProb', 'qSpotProb', 'tSpotProb'].includes(c)); + if (evaluating) { + validateInteractions(request.rri, query.records[0], target.records[0], parameters.qIdxPos0, parameters.tIdxPos0); + } else { + if (parameters.model === 'B' && parameters.mode !== 'H') throw new Error('Helix-block model B supports heuristic mode only.'); + if (parameters.noSeed && ['S', 'K'].includes(parameters.mode)) throw new Error('Seed-only and greedy prediction require a seed.'); + if (parameters.mode === 'K' && (parameters.model !== 'X' || needsEnsemble)) throw new Error('Greedy prediction requires model X and cannot produce ensemble/probability output.'); + if (parameters.seedTQ) validateInteractions(parameters.seedTQ, oneRecord(qRecords, 'Explicit seeds'), oneRecord(tRecords, 'Explicit seeds'), parameters.qIdxPos0, parameters.tIdxPos0, ','); + const minimumSeedLength = parameters.seedTQ ? Math.min(...parameters.seedTQ.split(',').map((seed) => seed.split('&')[0].split('|').length - 1)) : parameters.seedBP; + if (!parameters.noSeed && ['q', 't'].some((p) => parameters[`${p}IntLenMax`] && parameters[`${p}IntLenMax`] < minimumSeedLength)) throw new Error('Maximum interaction lengths must cover the required seed base pairs.'); + if (!parameters.noSeed && !parameters.seedTQ && [...qRecords, ...tRecords].some((r) => r.sequence.length < parameters.seedBP)) throw new Error('Every selected sequence must be at least as long as the seed; reduce Seed base pairs or disable the seed.'); + if (parameters.model === 'B' && (parameters.helixMinBP > parameters.helixMaxBP || !parameters.noSeed && minimumSeedLength > parameters.helixMaxBP)) throw new Error('Helix maximum must cover the helix minimum and required seed base pairs.'); + if (outputs.some((key) => ['bpProb', 'bpsvg'].includes(key)) && (parameters.model !== 'P' || !['H', 'M'].includes(parameters.mode) || parameters.windowWidth || parameters.mode === 'M' && !parameters.noSeed && (parameters.seedTQ || parameters.seedMaxUP || parameters.seedQMaxUP > 0 || parameters.seedTMaxUP > 0))) throw new Error('Base-pair probabilities require model P, heuristic/exact mode and no windows; exact mode supports no seed or stack-only seeds.'); + if (parameters.windowWidth) { + const maxLength = Math.max(...['q', 't'].map((p) => parameters[`${p}Acc`] === 'N' ? parameters[`${p}IntLenMax`] : Math.max(parameters[`${p}AccW`], parameters[`${p}IntLenMax`]))); + if (parameters.windowWidth < 10 || parameters.windowOverlap >= parameters.windowWidth || parameters.windowOverlap < maxLength || ['q', 't'].some((p) => !parameters[`${p}IntLenMax`] && (parameters[`${p}Acc`] === 'N' || !parameters[`${p}AccW`])) || parameters.outNumber > 1 && parameters.outOverlap !== 'B' || needsEnsemble || parameters.model === 'P') throw new Error('Prediction windows require width ≥ 10, overlap below width and at least the bounded interaction lengths, overlapping output, and no ensemble statistics/model P.'); + } + // Non-overlap constraints in native merged regions require a single region on + // the relevant strand; automatic region detection is only safe per region. + if (!parameters.outPerRegion && parameters.outOverlap !== 'B') { + for (const p of ['q', 't']) { + if ((parameters.outOverlap === 'N' || parameters.outOverlap === (p === 'q' ? 'T' : 'Q')) && (parameters[`${p}Region`].includes(',') || parameters[`${p}RegionLenMax`])) throw new Error('Non-overlapping output with multiple/automatic regions requires output per region.'); + } + } + if (parameters.outSpotProbSpots && !/^(-?[1-9]\d*&-?[1-9]\d*)(,-?[1-9]\d*&-?[1-9]\d*)*$/.test(parameters.outSpotProbSpots)) throw new Error('Probability spots must be target&query coordinate pairs, e.g. 3&7,5&9.'); + for (const spot of parameters.outSpotProbSpots ? parameters.outSpotProbSpots.split(',') : []) { + const [t, q] = spot.split('&').map(Number); + for (const [records, coordinate, start] of [[tRecords, t, parameters.tIdxPos0], [qRecords, q, parameters.qIdxPos0]]) { + const offset = sequenceOffset(coordinate, start); + if (records.some((record) => offset < 0 || offset >= record.sequence.length)) throw new Error('Probability spots must fall within every selected sequence.'); + } + } + } + return { task, query, target, parameters, csvColumns, outputs, rri: evaluating ? request.rri : '' }; +} + +export function makeArguments(request, format = 'C') { + const args = ['--query=/query.fa', '--target=/target.fa', `--outMode=${format}`, `--out=${format === 'C' ? '/results.csv' : '/report.txt'}`]; + if (request.task === 'evaluation') args.push('--personality=IntaRNAeval'); + for (const [key, value] of Object.entries(request.parameters)) { + if (key === 'outCsvSort' && format !== 'C' || key === 'outSpotProbSpots' || key === 'kineticScore' && request.parameters.mode !== 'K') continue; + // Omit defaults: the native parser distinguishes explicit values in several + // cross-option checks, especially accessibility/region constraints. + if (value === '' || value === PARAMETER_DEFAULTS[key]) continue; + const fileInput = /^(q|t)(Shape|AccFile)$/.test(key); + args.push(`--${key}=${fileInput ? `/${key}.txt` : value}`); + } + if (request.rri) args.push(`--rri=${request.rri}`); + if (format === 'C') { + args.push(`--outCsvCols=${[...new Set([...request.csvColumns, ...CONTEXT_COLUMNS, 'hybridDP'])].join(',')}`); + for (const key of request.outputs.filter((key) => !['normal', 'detailed', 'ensemble'].includes(key))) { + const spots = key === 'spotProb' && request.parameters.outSpotProbSpots ? `${request.parameters.outSpotProbSpots}:` : ''; + args.push(`--out=${key}:${spots}/output/${key}${key === 'bpsvg' ? '.svg' : '.csv'}`); + } + } + return args; +} + +export const JSON_SCHEMA = 'IntaRNA-parameters-v1'; + +// One parameter document crosses the JS/native boundary. File contents use the +// native JSON embedding contract, so no browser-specific input paths are needed. +export function makeParameterDocument(request, format = 'C') { + const parameters = {}; + for (const argument of makeArguments(request, format)) { + const separator = argument.indexOf('='), key = argument.slice(2, separator); + let value = argument.slice(separator + 1); + if (key === 'query' || key === 'target') value = { text: request[key].fasta }; + else if (/^[qt](Shape|AccFile)$/.test(key)) value = { text: request.parameters[key] + '\n' }; + else if (Object.hasOwn(request.parameters, key)) value = request.parameters[key]; + if (key === 'out') (parameters.out ??= []).push(value); + else if (!(['qIdxPos0', 'tIdxPos0'].includes(key) && value === 1)) parameters[key] = value; + } + return { schema: JSON_SCHEMA, parameters }; +} diff --git a/gui/results.js b/gui/results.js new file mode 100644 index 00000000..92a06f70 --- /dev/null +++ b/gui/results.js @@ -0,0 +1,147 @@ +import { CSV_CATALOG } from './columns.js'; +import { CONTEXT_COLUMNS } from './protocol.js'; +import { InteractionVisualization } from './visualization.js'; + +export const COLUMNS = Object.freeze([...CSV_CATALOG, { key: 'deltaE', label: 'mfe Δ (kcal/mol)', numeric: true }]); +const catalog = new Map(COLUMNS.map((column) => [column.key, column])); + +// Native CSV is unquoted, semicolon-separated; unavailable optional fields use +// NAN and seed fields may contain colon-separated lists. Preserve those strings. +export function parseResults(csv) { + if (typeof csv !== 'string') throw new Error('The engine did not return CSV text.'); + if (!csv.trim()) return []; + const lines = csv.trimEnd().split(/\r?\n/), keys = lines.shift().split(';'); + if (new Set(keys).size !== keys.length || keys.some((key) => !catalog.has(key)) || CONTEXT_COLUMNS.some((key) => !keys.includes(key))) throw new Error('Unexpected IntaRNA CSV columns. Serve the matching interface and engine.'); + const rows = lines.filter((line) => line.trim()).map((line) => { + const values = line.split(';'); + if (values.length !== keys.length) throw new Error('Malformed IntaRNA CSV row.'); + const row = Object.fromEntries(keys.map((key, index) => [key, values[index]])); + for (const key of CONTEXT_COLUMNS.filter((key) => key !== 'id1' && key !== 'id2')) { + if (!row[key].trim() || !Number.isFinite(Number(row[key]))) throw new Error(`Invalid ${key} in interaction output.`); + row[key] = Number(row[key]); + } + for (const key of ['start1', 'end1', 'start2', 'end2']) { + if (!Number.isInteger(row[key])) throw new Error('Invalid interaction coordinates.'); + } + if (row.start1 > row.end1 || row.start2 > row.end2) throw new Error('Reversed interaction coordinates.'); + return row; + }); + // Each sequence pair has its own optimum in a multi-FASTA screen. + const best = new Map(); + for (const row of rows) { + const pair = JSON.stringify([row.id1, row.id2]); + best.set(pair, Math.min(best.get(pair) ?? Infinity, row.E)); + } + return rows.map((row) => ({ ...row, deltaE: Number((row.E - best.get(JSON.stringify([row.id1, row.id2]))).toFixed(2)) })); +} +function numeric(value) { return String(value).trim() && Number.isFinite(Number(value)) ? Number(value) : null; } +export function selectRows(rows, search, key, direction) { + const query = search.toLowerCase().trim(), column = catalog.get(key); + return rows.filter((row) => Object.values(row).some((value) => String(value).toLowerCase().includes(query))).toSorted((a, b) => { + if (column?.numeric) { + const x = numeric(a[key]), y = numeric(b[key]); + if (x !== null && y !== null) return direction * (x - y); + if (x === null && y !== null) return 1; + if (x !== null && y === null) return -1; + } + return direction * String(a[key] ?? '').localeCompare(String(b[key] ?? '')); + }); +} +export function projectCsv(csv, columns) { + const lines = csv.trimEnd().split(/\r?\n/), keys = lines[0].split(';'); + const indices = columns.map((key) => keys.indexOf(key)); + if (indices.some((index) => index < 0)) throw new Error('Selected columns are absent from the engine output.'); + return lines.map((line) => { const cells = line.split(';'); return indices.map((index) => cells[index]).join(';'); }).join('\n') + '\n'; +} +export function downloadText(name, text) { + downloadBlob(name, new Blob([text], { type: 'text/plain;charset=utf-8' })); +} +export function downloadBlob(name, blob) { + const url = URL.createObjectURL(blob); + const link = document.createElement('a'); + link.href = url; link.download = name; link.click(); + setTimeout(() => URL.revokeObjectURL(url), 1000); +} +export class ResultsView { + constructor(root) { + this.root = root; this.rows = []; this.key = 'E'; this.direction = 1; + this.visualization = new InteractionVisualization(root); + this.search = root.querySelector('[data-role=search]'); + this.table = root.querySelector('table'); + this.body = this.table.querySelector('tbody'); + this.header = this.table.querySelector('thead tr'); + this.count = root.querySelector('[data-role=visible-count]'); + this.empty = root.querySelector('[data-role=no-matches]'); + this.picker = root.querySelector('[data-role=visible-columns]'); + this.search.addEventListener('input', () => this.render()); + root.querySelector('[data-role=download]').addEventListener('click', () => downloadText('intarna-interactions.csv', this.csv)); + } + clear() { + this.rows = []; this.csv = ''; this.body.replaceChildren(); this.root.hidden = true; + this.selected = null; this.visualization.clear(); + } + show(csv, columns = csv.trim().split('\n')[0].split(';'), request) { + this.rows = parseResults(csv); this.csv = projectCsv(csv, columns); + this.request = request; this.selected = null; this.visualization.clear(); + this.columns = columns.map((key) => catalog.get(key)); + if (columns.includes('E')) this.columns.push(catalog.get('deltaE')); + this.visible = new Set(this.columns.map((c) => c.key)); + this.picker.replaceChildren(); + for (const column of this.columns) { + const label = document.createElement('label'), input = document.createElement('input'); + input.type = 'checkbox'; input.checked = true; input.value = column.key; + input.addEventListener('change', () => { + if (input.checked) this.visible.add(column.key); else this.visible.delete(column.key); + this.render(); + }); + label.append(input, document.createTextNode(column.label)); this.picker.append(label); + } + this.search.value = ''; this.key = columns.includes('E') ? 'E' : columns[0]; this.direction = 1; + this.root.hidden = false; this.render(); return this.rows.length; + } + render() { + const rows = selectRows(this.rows, this.search.value, this.key, this.direction); + const columns = this.columns.filter((column) => this.visible.has(column.key)); + this.header.replaceChildren(); + const viewHeading = document.createElement('th'); viewHeading.scope = 'col'; viewHeading.setAttribute('aria-label', 'Interaction visualization'); + this.header.append(viewHeading); + for (const column of columns) { + const cell = document.createElement('th'), button = document.createElement('button'); + cell.scope = 'col'; button.type = 'button'; + const split = column.numeric ? column.label.indexOf(' ') : -1; + if (split > 0) button.append(document.createTextNode(column.label.slice(0, split)), document.createElement('br'), document.createTextNode(column.label.slice(split + 1))); + else button.textContent = column.label; + button.title = column.description ?? column.label; + const active = column.key === this.key, direction = this.direction === 1 ? 'ascending' : 'descending'; + cell.setAttribute('aria-sort', active ? direction : 'none'); + button.setAttribute('aria-label', `Sort by ${column.label}${active ? `, currently ${direction}` : ''}`); + button.addEventListener('click', () => { this.direction = active ? -this.direction : 1; this.key = column.key; this.render(); }); + cell.append(button); this.header.append(cell); + } + this.body.replaceChildren(); + for (const row of rows) { + const tr = document.createElement('tr'); + tr.classList.toggle('selected', row === this.selected); + const action = document.createElement('td'), view = document.createElement('button'); + view.type = 'button'; view.textContent = 'View'; view.className = 'view-interaction'; + view.setAttribute('aria-label', `Visualize ${row.id1} ${row.start1}–${row.end1} with ${row.id2} ${row.start2}–${row.end2}`); + view.setAttribute('aria-pressed', String(row === this.selected)); + tr.addEventListener('click', () => { + this.selected = row; this.visualization.show(row, this.request); + for (const other of this.body.children) { + other.classList.toggle('selected', other === tr); + other.querySelector('.view-interaction').setAttribute('aria-pressed', String(other === tr)); + } + }); + action.append(view); tr.append(action); + for (const column of columns) { + const cell = document.createElement('td'); + cell.textContent = ['E', 'deltaE'].includes(column.key) ? Number(row[column.key]).toFixed(2) : String(row[column.key]); + if (column.numeric) cell.className = 'number'; tr.append(cell); + } + this.body.append(tr); + } + this.count.textContent = `${rows.length} of ${this.rows.length} interactions`; + this.empty.hidden = rows.length > 0; + } +} diff --git a/gui/runner.js b/gui/runner.js new file mode 100644 index 00000000..91ccc6b2 --- /dev/null +++ b/gui/runner.js @@ -0,0 +1,49 @@ +// The main thread stays available even while synchronous C++ is calculating. +export class PredictionRunner { + constructor(workerFactory = () => new Worker(new URL('./intarna-worker.js', import.meta.url), { type: 'module' })) { + this.workerFactory = workerFactory; + this.worker = null; + this.cancel = null; + } + + run(request, onStatus = () => {}) { + if (this.worker) return Promise.reject(new Error('A prediction is already running.')); + return new Promise((resolve, reject) => { + const worker = this.workerFactory(); + this.worker = worker; + const finish = (error, result) => { + if (this.worker !== worker) return; // Ignore queued messages after abort. + worker.terminate(); + this.worker = null; + this.cancel = null; + if (error) reject(error); + else resolve(result); + }; + this.cancel = () => finish(new DOMException('Computation aborted.', 'AbortError')); + worker.onmessage = ({ data }) => { + if (this.worker !== worker) return; + if (data.type === 'status') onStatus(data.message); + else if (data.type === 'result') finish(null, data); + else if (data.type === 'error') { + const error = new Error(data.message); + error.diagnostics = data.diagnostics; + finish(error); + } + }; + worker.onerror = (event) => { + event.preventDefault(); + finish(new Error('Could not load or run the prediction engine. Reload the page and check that intarna.js and intarna.wasm are served together.')); + }; + worker.onmessageerror = () => finish(new Error('Could not read the prediction engine response.')); + try { + worker.postMessage(request); + } catch (error) { + finish(error); + } + }); + } + + abort() { + this.cancel?.(); + } +} diff --git a/gui/sessions.js b/gui/sessions.js new file mode 100644 index 00000000..ed3c873a --- /dev/null +++ b/gui/sessions.js @@ -0,0 +1,125 @@ +import { ResultsView, downloadBlob } from './results.js'; +import { serializeParameters, importParameters } from './parameter-file.js'; +import { zipFiles } from './archive.js'; +import { AdditionalOutputView } from './output-visualization.js'; + +// Sessions live only in this page. Each owns a JSON snapshot and its own view; +// editing the form or exploring another session cannot change an earlier run. +export class SessionsView { + constructor(root, template, restore, reportError, announce) { + this.root = root; this.template = template; this.restore = restore; this.reportError = reportError; this.announce = announce; + this.entries = new Map(); this.nextNumber = 1; this.selected = null; + } + + deselect() { + this.selected = null; + for (const session of this.entries.values()) { + session.root.dataset.selected = 'false'; + session.toggle.textContent = 'Show'; + } + } + + setExpanded(session, expanded) { + session.panel.hidden = !expanded; + session.toggle.setAttribute('aria-expanded', String(expanded)); + session.toggle.textContent = expanded ? 'Hide' : 'Show'; + // Unload third-party viewers while folded. The table selection is retained + // and can be visualized again without recomputing the prediction. + if (!expanded) session.view.visualization.clear(); + else { + if (session.view.selected) session.view.visualization.show(session.view.selected, session.view.request); + for (const fileView of session.fileViews) fileView.resize(); + } + } + + select(session, restore = true) { + if (restore) this.restore(importParameters(session.parameterJson), session.name); + this.selected = session.id; + for (const entry of this.entries.values()) { + entry.root.dataset.selected = String(entry === session); + this.setExpanded(entry, entry === session); + } + } + + add(request, result, provenance) { + // Prepared indices live in parameters, whereas the JSON serializer accepts + // editable requests with top-level indices. Preserve signed coordinates. + const parameterJson = serializeParameters({ ...request, qIdxPos0: request.parameters.qIdxPos0, tIdxPos0: request.parameters.tIdxPos0 }, provenance); + const root = this.template.content.firstElementChild.cloneNode(true); + const find = (role) => root.querySelector(`[data-role=${role}]`); + const id = `session-${this.nextNumber}`, task = request.task === 'evaluation' ? 'Evaluation' : 'Prediction'; + const session = { + id, name: `${task} ${this.nextNumber}`, parameterJson, root, + panel: find('panel'), toggle: find('toggle'), view: new ResultsView(find('results-view')), fileViews: [], + }; + const count = session.view.show(result.csv, result.csvColumns, request); + const summary = count ? `${task} complete: ${count} interaction${count === 1 ? '' : 's'}.` : request.task === 'prediction' && request.parameters.outNumber === 0 ? 'Accessibility computation complete. No interaction rows requested.' : 'No favorable interactions found with these sequences and settings.'; + find('summary').textContent = summary; + root.dataset.sessionId = id; + session.panel.id = `${id}-panel`; session.toggle.setAttribute('aria-controls', session.panel.id); + const name = find('name'); name.value = session.name; + const rename = () => { + session.name = name.value.trim() || `${task} ${id.slice('session-'.length)}`; + root.setAttribute('aria-label', session.name); + session.toggle.setAttribute('aria-label', `Show or hide results and restore inputs for ${session.name}`); + find('delete').setAttribute('aria-label', `Delete session ${session.name}`); + find('download-zip').setAttribute('aria-label', `Download ZIP for ${session.name}`); + }; + name.addEventListener('input', rename); + name.addEventListener('change', () => { rename(); name.value = session.name; }); + name.addEventListener('keydown', (event) => { if (event.key === 'Enter') name.blur(); }); + rename(); + // The name and header background also select a run. Action buttons retain + // their own behavior, so exporting/deleting cannot overwrite edited inputs. + const header = root.querySelector('.session-header'); + header.tabIndex = 0; header.setAttribute('role', 'group'); + header.setAttribute('aria-label', 'Select result and restore its inputs'); + for (const event of ['click', 'focusin']) header.addEventListener(event, (event) => { + if (!event.target.closest('button') && (this.selected !== id || session.panel.hidden)) this.select(session); + }); + header.addEventListener('keydown', (event) => { + if (event.target === header && ['Enter', ' '].includes(event.key)) { event.preventDefault(); this.select(session); } + }); + // Clicking or keyboard-focusing an output area selects its computed inputs. + for (const event of ['click', 'focusin']) session.panel.addEventListener(event, () => { + if (this.selected !== id) this.select(session); + }); + session.toggle.addEventListener('click', () => { + if (this.selected === id && !session.panel.hidden) this.setExpanded(session, false); + else this.select(session); + }); + + // Each archive uses the saved JSON and full outputs, never the current form, + // filtered table, or the session selected at download time. + find('download-zip').addEventListener('click', () => { + try { + const files = [{ name: 'parameter.json', text: parameterJson }, { name: 'intarna-interactions.csv', text: session.view.csv }, ...result.files]; + const filename = session.name.replace(/[^\p{L}\p{N}._-]+/gu, '-').replace(/^[.-]+|[.-]+$/g, '').slice(0, 80) || id; + downloadBlob(`${filename}.zip`, new Blob([zipFiles(files)], { type: 'application/zip' })); + } catch (error) { this.reportError(new Error(`ZIP download failed: ${error.message}`)); } + }); + for (const [index, file] of result.files.entries()) { + const fileView = new AdditionalOutputView(file, request, `${id}-file-${index}`, () => { + downloadBlob(file.name, new Blob([file.text], { type: 'text/plain;charset=utf-8' })); + }); + session.fileViews.push(fileView); find('file-list').append(fileView.root); + } + find('output-files').hidden = !result.files.length; + find('diagnostic-text').textContent = result.diagnostics; find('diagnostics').hidden = !result.diagnostics; + + find('delete').addEventListener('click', () => { + const entries = [...this.entries.values()], index = entries.indexOf(session); + const next = entries[index + 1] ?? entries[index - 1]; + session.view.clear(); + for (const fileView of session.fileViews) fileView.destroy(); + root.remove(); this.entries.delete(id); + // Deleting output does not silently overwrite an edited form. + if (this.selected === id) this.selected = null; + this.announce(`${session.name} deleted. ${this.entries.size} session${this.entries.size === 1 ? '' : 's'} remaining.`); + (next?.toggle ?? document.getElementById('compute')).focus(); + }); + this.entries.set(id, session); this.nextNumber++; + this.root.prepend(root); this.select(session, false); + return summary; + } +} diff --git a/gui/styles.css b/gui/styles.css new file mode 100644 index 00000000..ea60e124 --- /dev/null +++ b/gui/styles.css @@ -0,0 +1,885 @@ +/* Shared vaRRI main-v2 palette and institutional header. Keep all assets local. */ +:root { + color-scheme: light; + --brand-blue:#145a96; + --brand-blue-dark:#0f4676; + --brand-blue-soft:#eaf2f8; + --table-header:#d9e8f6; + --table-selection:#c6e5f4; + --brand-accent:#f4bb44; + --surface:#fff; + --surface-muted:#f3f7fb; + --text:#1c2b39; + --muted:#4f6478; + --border:#ccd9e5; + font-family:"Segoe UI",Tahoma,Geneva,sans-serif; + color:var(--text); + background:#f3f7fb; + font-size:16px; + line-height:1.5; +} + +* { + box-sizing:border-box; +} + +body { + margin:0; + background:linear-gradient(180deg,#f8fbff,#eef3fb 45%,#fff); + min-height:100vh; +} + +[hidden] { + display:none !important; +} + +a { + color:var(--brand-blue); + text-underline-offset:3px; +} + +button,input,select,textarea { + font:inherit; +} + +button,summary { + cursor:pointer; +} + +button { + border:1px solid var(--border); + border-radius:5px; + padding:.6rem 1rem; + font-weight:600; +} + +button:disabled { + opacity:.6; + cursor:wait; +} + +button.primary { + color:white; + background:var(--brand-blue); + border-color:var(--brand-blue); +} + +button.primary:hover { + background:var(--brand-blue-dark); +} + +button.secondary { + color:var(--brand-blue-dark); + background:var(--surface); +} + +button.secondary:hover { + background:var(--brand-blue-soft); +} + +:focus-visible { + outline:3px solid var(--brand-accent); + outline-offset:3px; +} + +input,select,textarea { + border:1px solid #9bafc2; + border-radius:4px; + color:var(--text); + background:var(--surface); + padding:.45rem .55rem; + min-width:0; + max-width:100%; +} + +input[type=checkbox] { + accent-color:var(--brand-blue); + width:1rem; + height:1rem; + margin:.2rem .4rem .2rem 0; + flex-shrink:0; +} + +textarea { + display:block; + width:100%; + resize:vertical; + min-height:7rem; + font-family:Consolas,"Liberation Mono",monospace; + line-height:1.65; +} + +label { + font-weight:600; +} + +small,.input-help,.table-note,.field-hint { + font-size:.85rem; + color:var(--muted); +} + +p { + max-width:80ch; +} + +h1,h2,h3,p { + margin:0 0 .75rem; +} + +h1 { + font-size:1.8rem; + line-height:1.2; +} + +h2 { + font-size:1.35rem; +} + +h3 { + font-size:1.1rem; +} + +.site-header { + min-height:100px; + padding:18px 28px; + display:flex; + align-items:center; + gap:24px; + background:#344a9a; + color:#f7fbff; +} + +.site-header a { + color:inherit; + text-decoration:none; +} + +.group-logo { + display:block; + width:auto; + height:60px; +} + +.uni-logo { + display:block; + width:auto; + height:52px; +} + +.brand { + display:flex; + align-items:center; + gap:12px; + font-weight:700; + font-size:1.6rem; + line-height:1.3; +} + +.brand small { + display:block; + font-size:.85rem; + font-weight:400; + color:#d9e8f6; +} + +.university-link { + margin-left:auto; + display:flex; + align-items:center; + gap:12px; + font-size:.85rem; + line-height:1.35; + text-align:right; +} + +main { + width:min(1300px,100%); + margin:auto; + padding:30px 20px; +} + +.introduction { + display:flex; + justify-content:space-between; + gap:24px; + align-items:start; + margin-bottom:20px; +} + +.introduction p { + color:var(--muted); +} + +.local-note { + flex-shrink:0; + font-size:.85rem; + padding-top:.3rem; +} + +fieldset { + border:0; + margin:0; + padding:0; + min-width:0; +} + +.compute-bar,.table-tools { + display:flex; + align-items:center; + flex-wrap:wrap; + justify-content:space-between; + gap:12px; +} + +#task-help { + font-size:.9rem; + color:var(--muted); +} + +#parameter-groups { + border:1px solid var(--border); + background:#fbfdff; + border-radius:8px; +} + +#parameter-tabs { + display:flex; + flex-wrap:wrap; + gap:4px; + padding:8px; + border-bottom:1px solid var(--border); + background:var(--brand-blue-soft); + border-radius:7px 7px 0 0; +} + +[role=tab] { + border-color:transparent; + background:transparent; + color:var(--brand-blue-dark); + padding:.55rem .75rem; + font-size:.85rem; +} + +[role=tab][aria-selected=true] { + background:var(--brand-blue); + color:white; +} + +[role=tab]:hover { + border-color:var(--brand-blue); +} + +.group-body { + padding:18px; +} + +.sequence-grid { + display:grid; + grid-template-columns:repeat(2,minmax(0,1fr)); + gap:18px 24px; +} + +.field-grid { + display:grid; + grid-template-columns:repeat(auto-fit,minmax(10rem,14rem)); + gap:12px 16px; + align-items:end; + justify-content:start; + margin-bottom:12px; +} + +/* Explicit rows preserve the requested grouping; subgrid aligns inputs below + labels of different heights without fixing a font-dependent label height. + Bounded tracks keep short rows left-aligned instead of stretching controls + across the complete panel. */ +.field-grid.columns-1 { grid-template-columns:minmax(10rem,38rem); } +.field-grid.columns-2 { grid-template-columns:repeat(2,minmax(10rem,18rem)); } +.field-grid.columns-3 { grid-template-columns:repeat(3,minmax(9rem,14rem)); } +.field-grid.columns-4 { grid-template-columns:repeat(4,minmax(8.5rem,12rem)); } +.field-grid.columns-5 { grid-template-columns:repeat(5,minmax(8rem,11rem)); } +.field-grid > .field:not(.check) { display:grid; grid-row:span 4; grid-template-rows:subgrid; row-gap:5px; } +.field-grid > .field:not(.check) > label { align-self:end; } +.field-grid > .field:not(.check) > :nth-child(2) { align-self:start; } +.accessibility-columns { display:grid; grid-template-columns:repeat(2,minmax(16rem,32rem)); gap:16px; justify-content:start; margin-top:12px; } +.accessibility-columns > div { min-width:0; } +.seed-primary-row { + display:grid; + grid-template-columns:minmax(10rem,12rem) minmax(12rem,24rem); + gap:12px 16px; + align-items:start; + margin-bottom:12px; +} +.seed-primary-row .field { min-width:0; } +#csv-options .field-grid.columns-1 { grid-template-columns:minmax(10rem,19rem); } +.field-grid:has(#noSeed) { display:none; } +#query,#target { + white-space:pre; + overflow:auto; + min-height:20rem; +} +#sequence-help,#general-options p { max-width:none; } +.input-warning { font-size:.85rem; color:#79510b; max-width:none; overflow-wrap:anywhere; } + +.strand-heading,.sequence-meta { + display:flex; + align-items:center; + justify-content:space-between; + gap:8px; + margin-bottom:8px; +} + +.strand-heading span { + color:var(--muted); + font-size:.85rem; +} + +.sequence-meta { + margin-top:8px; + font-size:.85rem; + flex-wrap:wrap; + color:var(--muted); +} + +.sequence-meta input { + width:8rem; +} + +.sequence-meta label { + font-weight:400; +} + +.input-help { + margin:12px 0 0; +} + +#evaluation-input { + margin-top:20px; +} + +.field { + display:flex; + flex-direction:column; + align-items:stretch; + gap:5px; + min-width:0; +} + +.field.check { + flex-direction:row; + align-items:center; + align-self:start; + gap:4px; +} + +.field label { + font-size:.9rem; +} + +.field input[type=number] { + width:9rem; +} + +.field-hint { + margin:0; +} + +.field input[type=file] { + font-size:.8rem; + padding:.2rem; + border:0; + background:transparent; +} + +.field:has(:disabled) { + opacity:.65; +} + +.compute-bar { + margin:20px 0; +} + +.checkbox-grid { + display:grid; + grid-template-columns:repeat(auto-fit,minmax(220px,1fr)); + gap:8px 16px; + padding:12px 0; +} + +.checkbox-grid label { + display:flex; + align-items:flex-start; + font-weight:400; + font-size:.85rem; + overflow-wrap:anywhere; +} + +.subheading { + margin-top:24px; +} + +.selection-tools { + display:flex; + gap:8px; + flex-wrap:wrap; +} + +.selection-tools button { + font-size:.8rem; + padding:.3rem .6rem; +} + +.csv-group { margin-top:16px; } +.csv-group legend { font-weight:600; } +.text-button { background:none; border:0; padding:.15rem .5rem; color:var(--brand-blue); font-size:.8rem; text-decoration:underline; font-weight:400; } +.csv-columns { grid-template-columns:repeat(auto-fill,minmax(125px,1fr)); gap:6px 16px; padding:6px 0; } + +.results { + background:var(--surface); + border:1px solid var(--border); + border-radius:8px; + margin-top:24px; + padding:22px; + min-width:0; +} + +#result-status { + color:var(--muted); +} + +.table-tools { + margin:18px 0 12px; +} + +.download-actions { + display:flex; + flex-wrap:wrap; + gap:8px; +} + +.table-tools label { + display:flex; + gap:8px; + align-items:center; + font-size:.9rem; +} + +[data-role=visible-count] { + font-size:.85rem; + color:var(--muted); +} + +.column-picker { + margin-bottom:12px; + font-size:.9rem; +} + +.table-scroll { + width:100%; + max-height:500px; + overflow:auto; + border:1px solid var(--border); +} + +table { + border-collapse:collapse; + width:100%; + white-space:nowrap; + font-size:.85rem; +} + +th { + background:var(--table-header); + text-align:left; + padding:0 5px; + position:sticky; + top:0; + z-index:1; +} + +th button { + background:transparent; + border:0; + padding:10px 0; + color:var(--brand-blue-dark); + width:100%; + text-align:left; +} + +th[aria-sort=ascending] button::after { + content:' ↑'; +} + +th[aria-sort=descending] button::after { + content:' ↓'; +} + +td { + border-top:1px solid #e0e8f0; + padding:10px 5px; +} + +tr:nth-child(even) { + background:#f8fbff; +} + +td.number { + text-align:right; + font-variant-numeric:tabular-nums; +} + +.table-note { + margin:12px 0; + max-width:none; +} + +.view-interaction { + padding:.25rem .35rem; + color:var(--brand-blue-dark); + background:var(--surface); +} + +tbody tr { + cursor:pointer; +} + +tbody tr:hover { + background:var(--brand-blue-soft); +} +tbody tr.selected { background:var(--table-selection); } + +.view-interaction[aria-pressed=true] { + background:var(--brand-blue); + color:white; +} + +[data-role=visualization] { + margin-top:20px; +} + +.visualization-heading { + display:flex; + align-items:baseline; + flex-wrap:wrap; + gap:16px; +} + +[data-role=varri-frame] { + display:block; + width:100%; + height:600px; + margin-top:12px; + border:1px solid var(--border); + border-radius:5px; + background:white; +} + +[data-role=visualization-status] { + max-width:none; + overflow-wrap:anywhere; + font-size:.9rem; +} + +[data-role=output-files] { + margin-top:24px; +} + +[data-role=file-list] details,:is(#diagnostics, [data-role=diagnostics]) { + border-top:1px solid var(--border); + margin-top:12px; + padding-top:12px; +} + +.output-file-summary { + display:flex; + align-items:center; + flex-wrap:wrap; + gap:6px 10px; + min-height:2.2rem; + color:var(--brand-blue-dark); + font-weight:600; + list-style:none; +} + +.output-file-summary::before { + content:'▸'; + width:.8rem; +} + +.output-file[open] > .output-file-summary::before { + content:'▾'; +} + +.output-file-name { + overflow-wrap:anywhere; +} + +.output-file-context { + color:var(--muted); + font-size:.85rem; + font-weight:400; +} + +.output-download { + padding:.1rem .35rem; +} + +.output-file-body { + padding:.8rem 0 .25rem 1.15rem; +} + +.output-tabs { + display:flex; + gap:4px; + padding:8px; + border-bottom:1px solid var(--border); + border-radius:5px 5px 0 0; + background:var(--brand-blue-soft); +} + +.output-tab { + border:1px solid transparent; + border-radius:5px; + padding:.55rem .75rem; + color:var(--brand-blue-dark); + background:transparent; +} + +.output-tab[aria-selected=true] { + border-color:var(--brand-blue); + background:var(--brand-blue); + color:white; +} + +.output-tab:hover { + border-color:var(--brand-blue); +} + +.output-tab-panel { + padding-top:12px; + min-width:0; +} + +.plot-tools { + display:flex; + justify-content:flex-end; + min-height:2.6rem; +} + +.plot-tools button { + font-size:.85rem; + padding:.35rem .7rem; +} + +.output-plot { + width:100%; + min-height:420px; +} + +.output-plot-status { + max-width:none; + color:var(--muted); + font-size:.85rem; +} + +.output-tab-panel pre { + margin:0; +} + +pre { + white-space:pre; + overflow:auto; + max-height:24rem; + font-size:.8rem; + background:var(--surface-muted); + padding:12px; +} + +:is(#diagnostics, [data-role=diagnostics]) pre { + white-space:pre-wrap; + overflow-wrap:anywhere; +} + +footer { + padding:24px 0; + font-size:.85rem; + color:var(--muted); +} + +footer p { + margin-bottom:8px; + max-width:none; +} + +.error { + color:#932d28; + border:1px solid #d8a8a5; + background:#fff1f0; + border-radius:5px; + padding:12px; + max-width:none; +} + +dialog { + border:1px solid var(--border); + border-radius:10px; + max-width:min(450px,calc(100% - 32px)); + padding:28px; + color:var(--text); +} + +dialog::backdrop { + background:rgba(20,45,75,.4); +} + +.spinner { + width:28px; + height:28px; + border:3px solid var(--border); + border-top-color:var(--brand-blue); + border-radius:50%; + animation:spin 1s linear infinite; + margin-bottom:14px; +} + +@keyframes spin { + to { + transform:rotate(360deg); + } +} + +.sr-only { + position:absolute; + width:1px; + height:1px; + padding:0; + margin:-1px; + overflow:hidden; + clip:rect(0,0,0,0); + white-space:nowrap; + border:0; +} + +.skip-link { + position:absolute; + left:12px; + top:-100px; + background:white; + padding:10px; + z-index:10; +} + +.skip-link:focus { + top:10px; +} + +@media(max-width:760px) { + .site-header { + padding:14px; + gap:14px; + flex-wrap:wrap; + } + .group-logo { + height:40px; + } + .uni-logo { + height:36px; + } + .university-link { + font-size:.75rem; + gap:8px; + } + .brand { + font-size:1.2rem; + } + .brand img { + width:32px; + height:32px; + } + .brand small { + display:none; + } + main { + padding:22px 12px; + } + .introduction { + display:block; + } + .local-note { + margin-top:12px; + } + .sequence-grid { + grid-template-columns:1fr; + } + .field-grid { + grid-template-columns:repeat(auto-fill,minmax(min(100%,220px),1fr)); + } + .field-grid[class*=columns-],.accessibility-columns { grid-template-columns:1fr; } + .seed-primary-row { grid-template-columns:1fr; } + #csv-options .field-grid.columns-1 { grid-template-columns:1fr; } + .results { + padding:14px; + } + .table-tools label { + flex-wrap:wrap; + } + .table-tools input { + width:100%; + } + h1 { + font-size:1.55rem; + } + .group-body { + padding:14px; + } + .output-file-body { + padding-left:0; + } +} + +@media(prefers-reduced-motion:reduce) { + .spinner { + animation:none; + } +} + +/* Examples are a compact disclosure list with descriptions, not another form. */ +.examples-menu { position:relative; } +.examples-menu > summary { list-style:none; padding:.6rem 1rem; border:1px solid var(--border); border-radius:5px; background:var(--surface); color:var(--brand-blue-dark); font-weight:600; } +.examples-menu > summary::after { content:' ▾'; } +.examples-menu > div { position:absolute; bottom:calc(100% + .5rem); left:0; width:min(26rem,80vw); padding:.4rem; background:var(--surface); border:1px solid var(--border); border-radius:5px; box-shadow:0 6px 20px #1c2b3920; z-index:2; } +.examples-menu button { width:100%; text-align:left; background:var(--surface); border:0; } +.examples-menu button:hover { background:var(--brand-blue-soft); } +.examples-menu button strong,.examples-menu button span { display:block; } +.examples-menu button span { font-size:.85rem; font-weight:400; color:var(--muted); } +textarea::placeholder { color:#687d8e; opacity:1; } + +.strand-heading { flex-wrap:wrap; gap:.4rem .7rem; } +.upload-controls { display:flex; align-items:center; flex-wrap:wrap; gap:.4rem; margin-left:auto; } +button.small-button { padding:.25rem .65rem; font-size:.85rem; } +textarea.drag-over { outline:3px solid var(--brand-accent); background:var(--brand-blue-soft); } + +/* Native radio semantics keep the task overview visible and keyboard operable. */ +.task-selector { display:flex; flex-wrap:wrap; gap:.5rem; margin-bottom:.6rem; } +.task-choice { position:relative; display:flex; align-items:baseline; gap:.6rem; padding:.55rem 1rem; border:1px solid var(--border); border-radius:5px; background:var(--surface); cursor:pointer; } +.task-choice input { position:absolute; inset:0; opacity:0; width:100%; height:100%; margin:0; cursor:pointer; z-index:1; } +.task-choice:has(:checked) { background:var(--brand-blue); color:white; border-color:var(--brand-blue); } +.task-choice:has(:checked) small { color:white; } +.task-choice:has(:focus-visible) { outline:3px solid var(--brand-accent); outline-offset:3px; } +.compute-bar { justify-content:flex-start; gap:8px; } +#compute { margin-right:24px; } +.parameter-actions-label { font-size:.9rem; } +@media(max-width:480px) { #compute { flex-basis:100%; margin-right:0; } .parameter-actions-label { flex-basis:100%; } } + +/* Every completed run owns its controls and output, even while folded. */ +.session { margin-top:18px; border:1px solid var(--border); border-radius:6px; min-width:0; } +.session[data-selected=true] { border-color:var(--brand-blue); } +.session-header { display:flex; align-items:center; flex-wrap:wrap; gap:10px; padding:14px; background:var(--surface-muted); border-radius:6px; } +.session-name { display:flex; align-items:center; flex:1 1 20rem; gap:10px; font-size:.85rem; } +.session-name input { flex:1; width:12rem; font-weight:600; } +.session-header button { font-size:.85rem; } +.session-header [data-role=toggle]::before { content:'▸ '; } +.session-header [aria-expanded=true]::before { content:'▾ '; } +.delete-session { display:inline-flex; align-items:center; } +.session-panel { padding:16px; } +.session-summary { color:var(--muted); } +@media(max-width:480px) { .session-header,.session-panel { padding:10px; } } diff --git a/gui/tests/export.test.mjs b/gui/tests/export.test.mjs new file mode 100644 index 00000000..6884cf2c --- /dev/null +++ b/gui/tests/export.test.mjs @@ -0,0 +1,40 @@ +import { test } from 'node:test'; +import assert from 'node:assert/strict'; +import { DEFAULTS, prepareRequest } from '../protocol.js'; +import { archiveFiles } from '../archive.js'; +import { visualizationUrl } from '../visualization.js'; + +test('visualization retains full strand orientation, bulges, names and indices crossing zero', () => { + const request = prepareRequest({ ...DEFAULTS, query: '>other\nGGGAGGAGGG\n>q;β\nGGGAGGAGGG', qIdxPos0: -3, tIdxPos0: -5 }); + const url = new URL(visualizationUrl({ id1: 'target', id2: 'q_β', start1: -3, end1: 3, start2: -2, end2: 4, E: -1, hybridDP: '((..((&)).)).' }, request)); + assert.equal(url.origin + url.pathname, 'https://backofenlab.github.io/vaRRI/'); + assert.equal(url.searchParams.get('sequence'), 'CCCUCCUCCC&GGGAGGAGGG'); + assert.equal(url.searchParams.get('structure'), '..((..((..&.)).))....'); + assert.equal(url.searchParams.get('seqName2'), 'q_β'); + assert.equal(url.searchParams.get('startIndex1'), '-5'); + assert.equal(url.searchParams.get('startIndex2'), '-3'); + assert.equal(url.searchParams.get('showRenderingOnly'), 'true'); + assert.throws(() => visualizationUrl({ id1: 'missing', hybridDP: '(&)' }, request), /not found/); + assert.throws(() => visualizationUrl({ id1: 'target', id2: 'q_β', start1: -5, end1: -4, hybridDP: '(((&)))' }, request), /coordinates/); + assert.throws(() => visualizationUrl({ id1: 'target', hybridDP: '(&)' }, { ...request, parameters: { ...request.parameters, tIdxPos0: 0 } }), /nonzero/); +}); + +test('archive preserves effective non-default settings, selected CSV, auxiliary inputs and reports', () => { + const request = prepareRequest({ ...DEFAULTS, task: 'evaluation', rri: '1||||||||||&3||||||||||', qIdxPos0: 3, parameters: { temperature: 21, qShape: '1 0.2\n2 0.3' }, csvColumns: ['E'] }); + request.outputs = ['detailed']; + const files = archiveFiles(request, { csv: 'id1;start1;end1;id2;start2;end2;E;hybridDP\ntarget;1;10;query;3;12;-21.4;((((((((((&))))))))))\n', files: [{ name: 'intarna-detailed.txt', text: 'report' }] }, 'IntaRNA 3.4.1\nViennaRNA 2.7.0\n'); + const entries = Object.fromEntries(files.map((file) => [file.name, file.text])); + assert.deepEqual(Object.keys(entries), ['parameter.json', 'intarna-interactions.csv', 'intarna-detailed.txt']); + const document = JSON.parse(entries['parameter.json']); + assert.equal(document.parameters.query.text, '>query\nGGGAGGAGGG\n'); + assert.equal(entries['intarna-interactions.csv'], 'E\n-21.4\n'); + assert.equal(document.parameters.qShape.text, '1 0.2\n2 0.3'); + assert.ok(document._comment.includes('ViennaRNA 2.7.0')); + for (const [key, value] of Object.entries({ personality: 'IntaRNAeval', temperature: 21, qIdxPos0: 3, outCsvCols: 'E' })) assert.equal(document.parameters[key], value); + assert.equal(document.parameters.tIdxPos0, undefined); + assert.equal(document.parameters.seedBP, undefined); + assert.deepEqual(document.gui.reports, ['detailed']); + assert.ok(document._comment.some((line) => line.includes('IntaRNA --parameterFile=parameter.json'))); + assert.equal(entries['intarna-detailed.txt'], 'report'); + assert.throws(() => archiveFiles(request, { csv: '', files: [] }, ''), /version/); +}); diff --git a/gui/tests/output-visualization.test.mjs b/gui/tests/output-visualization.test.mjs new file mode 100644 index 00000000..d8aa08f8 --- /dev/null +++ b/gui/tests/output-visualization.test.mjs @@ -0,0 +1,63 @@ +import { test } from 'node:test'; +import assert from 'node:assert/strict'; +import { outputFileContext, outputVisualization } from '../output-visualization.js'; + +const request = { + target: { records: [{ id: 'target-1' }, { id: 'target-2' }] }, + query: { records: [{ id: 'query-1' }, { id: 'query-2' }] }, +}; + +test('profile plots retain signed categorical indices and sequence names', () => { + const spec = outputVisualization({ + name: 'qMinE-t1q2.csv', + text: 'idx;query-2;minE\n-2;G;-3.2\n-1;C;NA\n1;A;-2.1\n', + }, request); + assert.equal(spec.kind, 'profile'); + assert.deepEqual(spec.traces[0].x, ['-2', '-1', '1']); + assert.deepEqual(spec.traces[0].y, [-3.2, null, -2.1]); + assert.equal(spec.layout.xaxis.type, 'category'); + assert.deepEqual(spec.layout.xaxis.categoryarray, ['-2', '-1', '1']); + assert.match(spec.layout.title.text, /query-2/); + assert.equal(spec.context.label, 'target-1 : query-2'); +}); + +test('pair energy and probability matrices use literal category axes', () => { + const energy = outputVisualization({ + name: 'pMinE-t2q1.csv', + text: 'minE;A_-1;C_1\nG_5;-4.2;NA\nU_6;-2.0;-1.5\n', + }, request); + assert.equal(energy.kind, 'matrix'); + assert.deepEqual(energy.traces[0].z, [[-4.2, null], [-2, -1.5]]); + assert.equal(energy.layout.xaxis.type, 'category'); + assert.equal(energy.layout.yaxis.type, 'category'); + assert.match(energy.layout.title.text, /target-2 : query-1/); + + const spots = outputVisualization({ + name: 'spotProb-t1q2.csv', + text: 'spotProb;A_-1;C_1\nG_5;0.1;0.2\n', + }, request); + assert.equal(spots.kind, 'matrix'); + assert.equal(spots.traces[0].type, 'heatmap'); + assert.deepEqual(spots.layout.xaxis.categoryarray, ['A_-1', 'C_1']); +}); + +test('selected spot probabilities use a categorical bar plot', () => { + const onePair = { target: { records: [{ id: 'target' }] }, query: { records: [{ id: 'query' }] } }; + const spec = outputVisualization({ name: 'spotProb.csv', text: 'spot;probability\n0&0;0.4\n5&-2;0.6\n' }, onePair); + assert.equal(spec.kind, 'spots'); + assert.equal(spec.traces[0].type, 'bar'); + assert.deepEqual(spec.traces[0].x, ['0&0', '5&-2']); + assert.equal(spec.context.label, 'target : query'); +}); + +test('output headers identify the sequence or sequence pair they cover', () => { + assert.equal(outputFileContext('tMinE-t2q1.csv', request).label, 'target-2 : query-1'); + assert.equal(outputFileContext('qAcc-s2.csv', request).label, 'query-2'); + assert.equal(outputFileContext('intarna-detailed.txt', request).label, ''); +}); + +test('non-plot files are ignored and malformed plot data fails clearly', () => { + assert.equal(outputVisualization({ name: 'qAcc.csv', text: '# accessibility' }, request), null); + assert.throws(() => outputVisualization({ name: 'qMinE-t1q1.csv', text: 'idx;query-1;wrong\n1;A;2\n' }, request), /Unexpected qMinE/); + assert.throws(() => outputVisualization({ name: 'pMinE-t1q1.csv', text: 'minE;A_1\nG_1;not-a-number\n' }, request), /non-numeric/); +}); diff --git a/gui/tests/parameter-file.test.mjs b/gui/tests/parameter-file.test.mjs new file mode 100644 index 00000000..25f9ba6d --- /dev/null +++ b/gui/tests/parameter-file.test.mjs @@ -0,0 +1,58 @@ +import { test } from 'node:test'; +import assert from 'node:assert/strict'; +import { DEFAULTS, EVALUATION_EXAMPLE, prepareRequest, CSV_COLUMNS } from '../protocol.js'; +import { FIELDS } from '../options.js'; +import { exportParameters, serializeParameters, importParameters } from '../parameter-file.js'; +const provenance = 'IntaRNA test\nViennaRNA test\n'; + +test('JSON round trip retains embedded inputs, typed options, selected columns and reports', () => { + for (const request of [ + { ...DEFAULTS, query: '>q1\nGGGAGGAGGG\n>q2\nGGGAGGAGGG', qIdxPos0: -3, tIdxPos0: -5, parameters: { temperature: 22, noSeed: true, mode: 'M', qRegion: '-3-7', outSpotProbSpots: '-5&-3' }, csvColumns: ['E', 'id2'], outputs: ['normal', 'qPu', 'spotProb'] }, + { ...DEFAULTS, task: 'evaluation', rri: EVALUATION_EXAMPLE, parameters: { qShape: '1 0.2\n2 0.3' }, outputs: ['detailed', 'ensemble'] }, + ]) { + const document = exportParameters(request, provenance); + const imported = importParameters(JSON.stringify(document)); + const actual = prepareRequest(imported), expected = prepareRequest(request); + actual.outputs.sort(); expected.outputs.sort(); + assert.deepEqual(actual, expected); + assert.deepEqual(exportParameters(imported, provenance), document); + assert.ok(!JSON.stringify(document).includes('/query.fa')); + } +}); + +test('empty inputs and unfinished forms remain editable after Load/Store', () => { + const request = { query: '', target: '', parameters: { seedBP: 12 }, csvColumns: [], outputs: [] }; + const document = serializeParameters(request, provenance); + const loaded = importParameters(document); + assert.equal(loaded.query, ''); assert.equal(loaded.target, ''); + assert.equal(loaded.parameters.seedBP, 12); assert.deepEqual(loaded.csvColumns, []); + assert.throws(() => prepareRequest(loaded), /enter a sequence/); + const defaults = exportParameters(DEFAULTS, provenance).parameters; + for (const field of FIELDS) assert.equal(defaults[field.key], undefined, field.key); + assert.equal(defaults.qIdxPos0, undefined); + assert.equal(defaults.outCsvCols, undefined); +}); + +test('invalid/native-only settings are rejected before replacing the form', () => { + const base = exportParameters(DEFAULTS, provenance); + for (const values of [{ threads: 8 }, { parameterFile: 'other.json' }, { query: '/input.fa' }, { qShape: '/data.txt' }, { noSeed: 'false' }, { temperature: null }, { out: ['../file'] }, { out: ['unknown:data'] }, { personality: 'IntaRNAens' }, { energyVRNA: { text: 'x' } }, { outMode: 'D' }, { query: { text: 'a', path: 'x' } }]) { + assert.throws(() => importParameters({ ...base, parameters: { ...base.parameters, ...values } }), JSON.stringify(values)); + } + for (const document of [[], null, { ...base, schema: 'new' }, { ...base, other: true }, { ...base, gui: [] }, { ...base, gui: { reports: ['unknown'] } }]) assert.throws(() => importParameters(document)); + assert.throws(() => importParameters('{invalid')); + assert.throws(() => importParameters(' '.repeat(5000001)), /5 MB/); + assert.deepEqual(importParameters('\ufeff'+JSON.stringify(base)).csvColumns, CSV_COLUMNS.split(',')); +}); + +test('maintainer examples use the same JSON import and prediction validation', async () => { + const { readFile } = await import('node:fs/promises'); + const examples = JSON.parse(await readFile(new URL('../examples/index.json', import.meta.url))); + assert.equal(examples.length, 2); + const tasks = new Set(); + for (const file of examples) { + const example = JSON.parse(await readFile(new URL(`../examples/${file}`, import.meta.url))); + assert.ok(example.name && example.description); + tasks.add(prepareRequest(importParameters(example.configuration)).task); + } + assert.deepEqual([...tasks].sort(), ['evaluation', 'prediction']); +}); diff --git a/gui/tests/protocol.test.mjs b/gui/tests/protocol.test.mjs new file mode 100644 index 00000000..07a60071 --- /dev/null +++ b/gui/tests/protocol.test.mjs @@ -0,0 +1,119 @@ +import { test } from 'node:test'; +import assert from 'node:assert/strict'; +import { readFileSync } from 'node:fs'; +import { DEFAULTS, EVALUATION_EXAMPLE, parseSequence, parseFasta, prepareRequest, makeArguments, CSV_COLUMNS, sequenceOffset } from '../protocol.js'; +import { FIELDS } from '../options.js'; +import { CSV_CATALOG, CSV_GROUPS, defaultColumns } from '../columns.js'; +const request = (parameters = {}, extra = {}) => ({ ...DEFAULTS, parameters, ...extra }); + +test('FASTA normalization, identifiers, bounded multi-record work and subsets', () => { + assert.equal(parseSequence('>test\r\nacgt n\r\nACG', 'Query').fasta, '>test\nACGUNACG\n'); + for (const input of ['', 'A', '>\nACGUACGU', '>one\n', 'ACGU-ACGU', '>a\nACGU\n>a\nACGU', '>a;b\nACGU\n>a_b\nACGU', '>a first\nACGU\n>a second\nACGU']) assert.throws(() => parseFasta(input, 'Query')); + const fasta = '>a\nGGGAGGAGGG\n>b\nGGGAGGAGGG'; + assert.equal(prepareRequest(request({}, { query: fasta })).query.records.length, 2); + assert.throws(() => prepareRequest(request({}, { task: 'evaluation', query: fasta, rri: EVALUATION_EXAMPLE })), /exactly one/); + assert.throws(() => prepareRequest(request({}, { query: '>a\n'+'A'.repeat(5000)+'\n>b\n'+'A'.repeat(2000), target: 'C'.repeat(300) })), /1,000,000/); + assert.doesNotThrow(() => prepareRequest(request({ qSet: '2-2' }, { query: '>a\n'+'A'.repeat(5000)+'\n>b\n'+'A'.repeat(2000), target: 'C'.repeat(300) }))); + assert.throws(() => prepareRequest(request({ outPairwise: true }, { query: fasta })), /same number/); + assert.throws(() => prepareRequest(request({ qSet: '3-3' })), /within/); + assert.throws(() => prepareRequest(request({}, { query: 'A'.repeat(5001) }))); +}); + +test('CLI defaults, ranges and strict typed controls reject invalid values', () => { + const prepared = prepareRequest(DEFAULTS); + assert.equal(prepared.parameters.outNumber, 1); + assert.equal(prepared.parameters.qIntLoopMax, 16); + assert.equal(prepared.parameters.tIntLoopMax, 10); + assert.equal(prepared.csvColumns.join(','), CSV_COLUMNS); + assert.ok(!makeArguments(prepared).some((arg) => arg.startsWith('--personality='))); + assert.ok(!makeArguments(prepared).some((arg) => arg.startsWith('--kineticScore='))); + for (const parameters of [{ outNumber: 101 }, { outNumber: 1.5 }, { temperature: '' }, { temperature: Infinity }, { qAccW: 2 }, { qAccW: 50 }, { model: '--help' }, { noSeed: 'false' }, { seedBP: 11 }]) assert.throws(() => prepareRequest(request(parameters))); + for (const qIdxPos0 of ['--help', NaN, 2e9+1, '', false]) assert.throws(() => prepareRequest(request({}, { qIdxPos0 }))); + assert.doesNotThrow(() => prepareRequest(request({}, { qIdxPos0: -2e9 }))); + assert.doesNotThrow(() => prepareRequest(request({}, { qIdxPos0: 0 }))); + assert.equal(sequenceOffset(1, -3), 3); + assert.equal(sequenceOffset(-1, -3), 2); + assert.throws(() => prepareRequest(request({}, { csvColumns: [] })), /at least one/); + assert.throws(() => prepareRequest(request({}, { outputs: ['../other'] })), /available/); +}); + +test('evaluation validates antiparallel supplied structures in signed coordinates', () => { + const evalRequest = request({ seedBP: 'ignored', model: 'ignored' }, { task: 'evaluation', rri: EVALUATION_EXAMPLE }); + const prepared = prepareRequest(evalRequest); + assert.equal(prepared.parameters.model, undefined); + assert.ok(makeArguments(prepared).includes('--personality=IntaRNAeval')); + assert.ok(makeArguments(prepared).includes(`--rri=${EVALUATION_EXAMPLE}`)); + for (const rri of ['', '1|||&1||', '1|||||||||||&1|||||||||||', '0|||&1|||', '1|||&1|||:', '1|||&1...']) assert.throws(() => prepareRequest({ ...evalRequest, rri })); + assert.doesNotThrow(() => prepareRequest({ ...evalRequest, qIdxPos0: -3, tIdxPos0: -5, rri: '-5||||||||||&-3||||||||||' })); + assert.throws(() => prepareRequest({ ...evalRequest, outputs: ['bpsvg'] }), /available/); +}); + +test('cross-option constraints, regions, probabilities, SHAPE and local file arguments', () => { + for (const parameters of [{ noSeed: true, mode: 'S' }, { mode: 'K', model: 'P' }, { model: 'B', mode: 'M' }, { model: 'B', helixMaxBP: 4 }, { qRegion: '8-2' }, { qAccConstr: 'b:1-20' }, { qAccConstr: 'bbb' }, { qShapeMethod: 'X' }, { tShapeConversion: 'bad' }, { qShape: '1 nope' }, { qAcc: 'P' }, { qAcc: 'P', qAccFile: 'bad' }, { outSpotProbSpots: '20&1' }, { windowWidth: 100 }, { qIntLenMax: 3 }, { qAcc: 'N', qRegionLenMax: 20 }, { qRegion: '1-10', qRegionLenMax: 20 }, { seedTQ: '1.|||||||||&1|||||||||.' }]) assert.throws(() => prepareRequest(request(parameters))); + assert.doesNotThrow(() => prepareRequest(request({ noSeed: true, qAccConstr: 'b:1-2,p:8-9', qRegion: '1-10' }))); + assert.throws(() => prepareRequest(request({ mode: 'K' }, { csvColumns: ['Eall'] })), /ensemble/); + assert.throws(() => prepareRequest(request({}, { outputs: ['bpsvg'] })), /model P/); + assert.throws(() => prepareRequest(request({ outCsvSort: 'ED1' })), /sort column/); + const prepared = prepareRequest(request({ model: 'P', mode: 'M', qShape: '1 0.2\n2 -999', outSpotProbSpots: '1&2' }, { outputs: ['bpProb', 'bpsvg', 'spotProb'] })); + const args = makeArguments(prepared); + assert.ok(args.includes('--qShape=/qShape.txt')); + assert.ok(args.includes('--out=spotProb:1&2:/output/spotProb.csv')); + assert.ok(args.includes('--out=bpsvg:/output/bpsvg.svg')); + assert.ok(!makeArguments(prepared, 'D').some((arg) => arg.startsWith('--outCsvCols'))); +}); + +test('browser catalog covers every native CSV column and every control names a CLI option', () => { + const header = readFileSync(new URL('../../src/IntaRNA/OutputHandlerCsv.h', import.meta.url), 'utf8'); + const ids = [...header.matchAll(/colType2string\[\w+\] = "(\w+)"/g)].map((match) => match[1]); + assert.deepEqual(CSV_CATALOG.map((c) => c.key).toSorted(), ids.toSorted()); + const source = readFileSync(new URL('../../src/bin/CommandLineParsing.cpp', import.meta.url), 'utf8'); + for (const field of FIELDS.filter((field) => field.key !== 'outSpotProbSpots')) assert.ok(source.includes(`"${field.key}"`), field.key); +}); + +test('JSON worker boundary embeds all inputs with typed non-default settings', async () => { + const { makeParameterDocument, JSON_SCHEMA } = await import('../protocol.js'); + const prepared = prepareRequest(request({ temperature: 20, noSeed: true, qShape: '1 0.2' }, { outputs: ['qPu'] })); + const document = JSON.parse(JSON.stringify(makeParameterDocument(prepared))); + assert.equal(document.schema, JSON_SCHEMA); + assert.equal(document.parameters.query.text, prepared.query.fasta); + assert.equal(document.parameters.target.text, prepared.target.fasta); + assert.equal(document.parameters.qShape.text, '1 0.2\n'); + assert.equal(document.parameters.temperature, 20); + assert.equal(document.parameters.noSeed, true); + assert.equal(document.parameters.qIdxPos0, undefined); + assert.deepEqual(document.parameters.out, ['/results.csv', 'qPu:/output/qPu.csv']); + const worker = readFileSync(new URL('../intarna-worker.js', import.meta.url), 'utf8'); + assert.ok(worker.includes("callMain(['--parameterFile=/parameter.json'])")); +}); + + +test('browser batches use longest selected strands and round-trip full FASTA inputs', async () => { + const batch = Array.from({ length: 50 }, (_, i) => `>q${i}\n${'A'.repeat(5000)}\n`).join(''); + assert.equal(parseFasta(batch, 'Query').records.length, 50); + assert.throws(() => parseFasta(batch + '>extra\nAA', 'Query'), /50 FASTA/); + assert.doesNotThrow(() => prepareRequest(request({}, { query: batch, target: 'C'.repeat(200) }))); + assert.throws(() => prepareRequest(request({}, { query: batch, target: 'C'.repeat(201) })), /1,000,000/); + const crossed = { query: '>q1\n' + 'A'.repeat(5000) + '\n>q2\nAA', target: '>t1\nCC\n>t2\n' + 'C'.repeat(5000) }; + assert.throws(() => prepareRequest(request({ outPairwise: true, noSeed: true }, crossed)), /1,000,000/); + const { serializeParameters, importParameters } = await import('../parameter-file.js'); + assert.equal(importParameters(serializeParameters(request({}, { query: batch }), 'test')).query, batch); + const parsed = parseFasta('>one\tdescription here\nACGU\n>two \nACGU', 'Query'); + assert.deepEqual(parsed.records.map((record) => record.id), ['one', 'two']); + assert.equal(parsed.warnings.length, 1); + assert.match(parsed.warnings[0], /one/); + assert.equal(parsed.fasta, '>one\nACGU\n>two\nACGU\n'); +}); + +test('CSV groups cover native columns once and task defaults serialize explicitly', async () => { + assert.deepEqual(CSV_GROUPS.flatMap((group) => group.keys).toSorted(), CSV_CATALOG.map((column) => column.key).toSorted()); + const energy = [...CSV_GROUPS.find((group) => group.label === 'Energy').keys, 'Etotal', 'Eall', 'Eall1', 'Eall2', 'EallTotal']; + for (const key of energy) assert.ok(defaultColumns('evaluation').includes(key), key); + for (const key of ['seedStart1', 'seedStart2', 'seedEnd1', 'seedEnd2']) assert.ok(!defaultColumns('evaluation').includes(key), key); + for (const key of ['ED1', 'ED2', 'seedE', 'seedStart1', 'seedStart2']) assert.ok(defaultColumns('prediction').includes(key), key); + const { exportParameters, importParameters } = await import('../parameter-file.js'); + const input = request({ outNumber: 10 }, { csvColumns: defaultColumns('prediction') }); + const saved = exportParameters(input, 'test'); + assert.equal(saved.parameters.outNumber, 10); + assert.equal(saved.parameters.outCsvCols, input.csvColumns.join(',')); + assert.deepEqual(prepareRequest(importParameters(saved)), prepareRequest(input)); +}); diff --git a/gui/tests/results.test.mjs b/gui/tests/results.test.mjs new file mode 100644 index 00000000..5ea65311 --- /dev/null +++ b/gui/tests/results.test.mjs @@ -0,0 +1,39 @@ +import { test } from 'node:test'; +import assert from 'node:assert/strict'; +import { parseResults, selectRows, projectCsv } from '../results.js'; +const header = 'id1;start1;end1;id2;start2;end2;E\n'; + +test('native CSV orientation, numeric coordinates, energy and relative suboptimality', () => { + const rows = parseResults(header + 'target;2;10;query;1;9;-19.6\ntarget;1;10;query;1;10;-21.4\n'); + assert.equal(rows[0].start1, 2); + assert.equal(rows[0].start2, 1); + assert.equal(rows[0].deltaE, 1.8); + assert.equal(rows[1].deltaE, 0); + assert.deepEqual(selectRows(rows, '', 'E', 1).map((row) => row.E), [-21.4, -19.6]); + assert.deepEqual(selectRows(rows, '', 'start1', -1).map((row) => row.start1), [2, 1]); + assert.equal(selectRows(rows, 'QUERY', 'id2', 1).length, 2); + assert.equal(selectRows(rows, 'missing', 'id2', 1).length, 0); +}); + +test('empty output and literal native ID quotes; malformed output fails clearly', () => { + assert.deepEqual(parseResults(''), []); + assert.deepEqual(parseResults(header), []); + assert.equal(parseResults(header + '"name";1;7;query;1;7;-3\n')[0].id1, '"name"'); + for (const csv of ['unexpected\n', header + 'too;few\n', header + 't;0.5;1;q;1;2;-3\n', header + 't;2;1;q;1;2;-3\n', header + 't;1;7;q;1;7;NAN\n', header + 't;1;7;q;1;7;\n']) { + assert.throws(() => parseResults(csv)); + } +}); + + +test('mfe difference is per sequence pair; signed coordinates and optional NAN/list fields survive', () => { + const csv = header.trim() + ';seedE;ED1\n' + + 't;-3;5;q;1;8;-20;NAN;0\n' + + 't;-3;4;q;1;7;-18;-3:-2;1.4\n' + + 't2;1;8;q;1;8;-5;NAN;0\n'; + const rows = parseResults(csv); + assert.deepEqual(rows.map((r) => r.deltaE), [0, 2, 0]); + assert.equal(rows[1].seedE, '-3:-2'); + assert.equal(rows[0].seedE, 'NAN'); + assert.equal(projectCsv(csv, ['id2','E']), 'id2;E\nq;-20\nq;-18\nq;-5\n'); + assert.throws(() => projectCsv(csv, ['absent'])); +}); diff --git a/gui/tests/uploads.test.mjs b/gui/tests/uploads.test.mjs new file mode 100644 index 00000000..76a13200 --- /dev/null +++ b/gui/tests/uploads.test.mjs @@ -0,0 +1,15 @@ +import { test } from 'node:test'; +import assert from 'node:assert/strict'; +import { readFastaFile } from '../uploads.js'; +const file = (text) => ({ size: new TextEncoder().encode(text).length, text: async () => text }); +test('FASTA uploads accept text/CRLF and validate size, format and task before replacement', async () => { + const input = '>q\r\ngggaggaggg\r\n'; + assert.equal(await readFastaFile(file(input), 'Query', 'prediction'), input); + const multi = '>q1\nGGGAGGAGGG\n>q2\nGGGAGGAGGG'; + assert.equal(await readFastaFile(file(multi), 'Query', 'prediction'), multi); + await assert.rejects(readFastaFile(file(multi), 'Query', 'evaluation'), /exactly one/); + for (const invalid of ['', '\u0000bin', '>q\n--!', '>q\n']) await assert.rejects(readFastaFile(file(invalid), 'Query', 'prediction')); + const batch = Array.from({ length: 50 }, (_, i) => `>q${i}\n${'A'.repeat(5000)}\n`).join(''); + assert.equal(await readFastaFile(file(batch), 'Query', 'prediction'), batch); + await assert.rejects(readFastaFile({ size: 1000001, text: () => { throw Error('must not read'); } }, 'Query', 'prediction'), /1 MB/); +}); diff --git a/gui/tests/worker.test.mjs b/gui/tests/worker.test.mjs new file mode 100644 index 00000000..e831c28c --- /dev/null +++ b/gui/tests/worker.test.mjs @@ -0,0 +1,38 @@ +import { test } from 'node:test'; +import assert from 'node:assert/strict'; +import { PredictionRunner } from '../runner.js'; +import { DEFAULTS } from '../protocol.js'; + +function fakeWorker() { + return { terminated: false, terminate() { this.terminated = true; }, postMessage() {}, send(data) { this.onmessage({ data }); } }; +} + +test('abort terminates computation, rejects and permits a clean restart', async () => { + const workers = []; + const runner = new PredictionRunner(() => { const worker = fakeWorker(); workers.push(worker); return worker; }); + const first = runner.run(DEFAULTS); + await assert.rejects(runner.run(DEFAULTS), /already running/); + runner.abort(); + await assert.rejects(first, { name: 'AbortError' }); + assert.equal(workers[0].terminated, true); + const second = runner.run(DEFAULTS); + workers[0].send({ type: 'result', csv: 'stale' }); + workers[1].send({ type: 'result', csv: 'fresh' }); + assert.equal((await second).csv, 'fresh'); + assert.equal(workers[1].terminated, true); +}); + +test('runtime, load and message errors release the worker', async () => { + for (const kind of ['error', 'load', 'message', 'post']) { + const worker = fakeWorker(); + if (kind === 'post') worker.postMessage = () => { throw new Error('post failed'); }; + const runner = new PredictionRunner(() => worker); + const result = runner.run(DEFAULTS); + if (kind === 'error') worker.send({ type: 'error', message: 'allocation failed', diagnostics: 'details' }); + if (kind === 'load') worker.onerror({ preventDefault() {} }); + if (kind === 'message') worker.onmessageerror(); + await assert.rejects(result); + assert.equal(worker.terminated, true); + assert.equal(runner.worker, null); + } +}); diff --git a/gui/uploads.js b/gui/uploads.js new file mode 100644 index 00000000..81748047 --- /dev/null +++ b/gui/uploads.js @@ -0,0 +1,9 @@ +import { parseFasta, LIMITS } from './protocol.js'; + +/** Read and validate a local text file before replacing a FASTA input. */ +export async function readFastaFile(file, label, task) { + if (!file || file.size > LIMITS.maxFastaBytes) throw new Error(`${label}: choose a FASTA text file of at most 1 MB.`); + const text = await file.text(); + parseFasta(text, label, task !== 'evaluation'); + return text; +} diff --git a/gui/vendor/README.md b/gui/vendor/README.md new file mode 100644 index 00000000..1789b6db --- /dev/null +++ b/gui/vendor/README.md @@ -0,0 +1,16 @@ +# Plotly browser bundle + +`plotly-cartesian.min.js` is the unmodified browser bundle from +`plotly.js-cartesian-dist-min` 4.1.2 (MIT). It provides the scatter, bar and +heatmap traces used for additional IntaRNA output visualizations. +`plotly.css` is a static copy of its runtime plot/modebar rules. Plotly normally +inserts those rules with CSSOM; the bundle's supported `no-inline-styles` sentinel +suppresses that insertion while the same-origin copy retains the GUI's strict +`style-src 'self'` content-security policy. + +- npm integrity: `sha512-3UkyAT7/U8f3sOLavLnUjA6mqFmnqEe246GZhxT0J3TT9oZ0mh6SgwsL1yo/3/4xfmRSDFdGOxe+EsvT2XiE0g==` +- bundle SHA-256: `aaf12ff1d4671f7e93f6df4291651ab4ca6b76c0ea5f1576ec1030e3c2819a20` +- static CSS SHA-256: `3bcf2679b557067d8a3492b74092e946544d1cb8b2a72f278bcba95df59afd33` +- source: + +Keep the adjacent `plotly-LICENSE.txt` when updating the bundle. diff --git a/gui/vendor/plotly-LICENSE.txt b/gui/vendor/plotly-LICENSE.txt new file mode 100644 index 00000000..13ffac3c --- /dev/null +++ b/gui/vendor/plotly-LICENSE.txt @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2016-2024 Plotly Technologies Inc. + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. diff --git a/gui/vendor/plotly-cartesian.min.js b/gui/vendor/plotly-cartesian.min.js new file mode 100644 index 00000000..11ced8ef --- /dev/null +++ b/gui/vendor/plotly-cartesian.min.js @@ -0,0 +1,149 @@ +/** +* plotly.js (cartesian - minified) v4.1.2 +* Copyright 2012-2026, Plotly, Inc. +* All rights reserved. +* Licensed under the MIT license +*/ +( + function(root, factory) { + if (typeof module === "object" && module.exports) { + module.exports = factory(); + } else { + root.moduleName = factory(); + } +} (typeof self !== "undefined" ? self : this, () => { +"use strict";var Plotly=(()=>{var jce=Object.create;var 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Math.abs(l)<1e-6?null:(l=1/l,n*=l,i*=l,o*=l,s=Math.sin(t),u=Math.cos(t),f=1-u,c=r[0],v=r[1],d=r[2],p=r[3],y=r[4],m=r[5],b=r[6],A=r[7],w=r[8],x=r[9],_=r[10],k=r[11],T=n*n*f+u,q=i*n*f+o*s,C=o*n*f-i*s,E=n*i*f-o*s,P=i*i*f+u,R=o*i*f+n*s,N=n*o*f+i*s,I=i*o*f-n*s,O=o*o*f+u,e[0]=c*T+y*q+w*C,e[1]=v*T+m*q+x*C,e[2]=d*T+b*q+_*C,e[3]=p*T+A*q+k*C,e[4]=c*E+y*P+w*R,e[5]=v*E+m*P+x*R,e[6]=d*E+b*P+_*R,e[7]=p*E+A*P+k*R,e[8]=c*N+y*I+w*O,e[9]=v*N+m*I+x*O,e[10]=d*N+b*I+_*O,e[11]=p*N+A*I+k*O,r!==e&&(e[12]=r[12],e[13]=r[13],e[14]=r[14],e[15]=r[15]),e)}});var lD=z((rWe,oD)=>{oD.exports=Spe;function Spe(e,r,t){var a=Math.sin(t),n=Math.cos(t),i=r[4],o=r[5],l=r[6],s=r[7],u=r[8],f=r[9],c=r[10],v=r[11];return r!==e&&(e[0]=r[0],e[1]=r[1],e[2]=r[2],e[3]=r[3],e[12]=r[12],e[13]=r[13],e[14]=r[14],e[15]=r[15]),e[4]=i*n+u*a,e[5]=o*n+f*a,e[6]=l*n+c*a,e[7]=s*n+v*a,e[8]=u*n-i*a,e[9]=f*n-o*a,e[10]=c*n-l*a,e[11]=v*n-s*a,e}});var uD=z((tWe,sD)=>{sD.exports=qpe;function qpe(e,r,t){var a=Math.sin(t),n=Math.cos(t),i=r[0],o=r[1],l=r[2],s=r[3],u=r[8],f=r[9],c=r[10],v=r[11];return r!==e&&(e[4]=r[4],e[5]=r[5],e[6]=r[6],e[7]=r[7],e[12]=r[12],e[13]=r[13],e[14]=r[14],e[15]=r[15]),e[0]=i*n-u*a,e[1]=o*n-f*a,e[2]=l*n-c*a,e[3]=s*n-v*a,e[8]=i*a+u*n,e[9]=o*a+f*n,e[10]=l*a+c*n,e[11]=s*a+v*n,e}});var cD=z((aWe,fD)=>{fD.exports=Lpe;function Lpe(e,r,t){var a=Math.sin(t),n=Math.cos(t),i=r[0],o=r[1],l=r[2],s=r[3],u=r[4],f=r[5],c=r[6],v=r[7];return r!==e&&(e[8]=r[8],e[9]=r[9],e[10]=r[10],e[11]=r[11],e[12]=r[12],e[13]=r[13],e[14]=r[14],e[15]=r[15]),e[0]=i*n+u*a,e[1]=o*n+f*a,e[2]=l*n+c*a,e[3]=s*n+v*a,e[4]=u*n-i*a,e[5]=f*n-o*a,e[6]=c*n-l*a,e[7]=v*n-s*a,e}});var hD=z((nWe,vD)=>{vD.exports=Cpe;function Cpe(e,r,t){var a,n,i,o=t[0],l=t[1],s=t[2],u=Math.sqrt(o*o+l*l+s*s);return Math.abs(u)<1e-6?null:(u=1/u,o*=u,l*=u,s*=u,a=Math.sin(r),n=Math.cos(r),i=1-n,e[0]=o*o*i+n,e[1]=l*o*i+s*a,e[2]=s*o*i-l*a,e[3]=0,e[4]=o*l*i-s*a,e[5]=l*l*i+n,e[6]=s*l*i+o*a,e[7]=0,e[8]=o*s*i+l*a,e[9]=l*s*i-o*a,e[10]=s*s*i+n,e[11]=0,e[12]=0,e[13]=0,e[14]=0,e[15]=1,e)}});var pD=z((iWe,dD)=>{dD.exports=Dpe;function Dpe(e,r,t){var a=r[0],n=r[1],i=r[2],o=r[3],l=a+a,s=n+n,u=i+i,f=a*l,c=a*s,v=a*u,d=n*s,p=n*u,y=i*u,m=o*l,b=o*s,A=o*u;return e[0]=1-(d+y),e[1]=c+A,e[2]=v-b,e[3]=0,e[4]=c-A,e[5]=1-(f+y),e[6]=p+m,e[7]=0,e[8]=v+b,e[9]=p-m,e[10]=1-(f+d),e[11]=0,e[12]=t[0],e[13]=t[1],e[14]=t[2],e[15]=1,e}});var yD=z((oWe,mD)=>{mD.exports=Epe;function Epe(e,r){return e[0]=r[0],e[1]=0,e[2]=0,e[3]=0,e[4]=0,e[5]=r[1],e[6]=0,e[7]=0,e[8]=0,e[9]=0,e[10]=r[2],e[11]=0,e[12]=0,e[13]=0,e[14]=0,e[15]=1,e}});var bD=z((lWe,gD)=>{gD.exports=Ppe;function Ppe(e,r){return e[0]=1,e[1]=0,e[2]=0,e[3]=0,e[4]=0,e[5]=1,e[6]=0,e[7]=0,e[8]=0,e[9]=0,e[10]=1,e[11]=0,e[12]=r[0],e[13]=r[1],e[14]=r[2],e[15]=1,e}});var 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T=s>m,q=$t.barLength+2*$t.barPad,C=$t.barWidth+2*$t.barPad,E=l,P=u+f;P+C>o&&(P=o-C);var R=this.container.selectAll("rect.scrollbar-horizontal").data(T?[0]:[]);R.exit().on(".drag",null).remove(),R.enter().append("rect").classed("scrollbar-horizontal",!0).call(cj.fill,$t.barColor),T?(this.hbar=R.attr({rx:$t.barRadius,ry:$t.barRadius,x:E,y:P,width:q,height:C}),this._hbarXMin=E+q/2,this._hbarTranslateMax=m-q):(delete this.hbar,delete this._hbarXMin,delete this._hbarTranslateMax);var N=f>b,I=$t.barWidth+2*$t.barPad,O=$t.barLength+2*$t.barPad,U=l+s,Y=u;U+I>i&&(U=i-I);var G=this.container.selectAll("rect.scrollbar-vertical").data(N?[0]:[]);G.exit().on(".drag",null).remove(),G.enter().append("rect").classed("scrollbar-vertical",!0).call(cj.fill,$t.barColor),N?(this.vbar=G.attr({rx:$t.barRadius,ry:$t.barRadius,x:U,y:Y,width:I,height:O}),this._vbarYMin=Y+O/2,this._vbarTranslateMax=b-O):(delete this.vbar,delete this._vbarYMin,delete this._vbarTranslateMax);var V=this.id,W=A-.5,j=N?w+I+.5:w+.5,J=x-.5,te=T?_+C+.5:_+.5,ae=n._topdefs.selectAll("#"+V).data(T||N?[0]:[]);if(ae.exit().remove(),ae.enter().append("clipPath").attr("id",V).append("rect"),T||N?(this._clipRect=ae.select("rect").attr({x:Math.floor(W),y:Math.floor(J),width:Math.ceil(j)-Math.floor(W),height:Math.ceil(te)-Math.floor(J)}),this.container.call(N0.setClipUrl,V,this.gd),this.bg.attr({x:l,y:u,width:s,height:f})):(this.bg.attr({width:0,height:0}),this.container.on("wheel",null).on(".drag",null).call(N0.setClipUrl,null),delete this._clipRect),T||N){var se=Uo.behavior.drag().on("dragstart",function(){Uo.event.sourceEvent.preventDefault()}).on("drag",this._onBoxDrag.bind(this));this.container.on("wheel",null).on("wheel",this._onBoxWheel.bind(this)).on(".drag",null).call(se);var 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r=this.translateX,t=this.translateY;this.hbar&&(r+=Uo.event.deltaY),this.vbar&&(t+=Uo.event.deltaY),this.setTranslate(r,t)};$t.prototype._onBarDrag=function(){var r=this.translateX,t=this.translateY;if(this.hbar){var a=r+this._hbarXMin,n=a+this._hbarTranslateMax,i=Dg.constrain(Uo.event.x,a,n),o=(i-a)/(n-a),l=this.position.w-this._box.w;r=o*l}if(this.vbar){var s=t+this._vbarYMin,u=s+this._vbarTranslateMax,f=Dg.constrain(Uo.event.y,s,u),c=(f-s)/(u-s),v=this.position.h-this._box.h;t=c*v}this.setTranslate(r,t)};$t.prototype.setTranslate=function(r,t){var a=this.position.w-this._box.w,n=this.position.h-this._box.h;if(r=Dg.constrain(r||0,0,a),t=Dg.constrain(t||0,0,n),this.translateX=r,this.translateY=t,this.container.call(N0.setTranslate,this._box.l-this.position.l-r,this._box.t-this.position.t-t),this._clipRect&&this._clipRect.attr({x:Math.floor(this.position.l+r-.5),y:Math.floor(this.position.t+t-.5)}),this.hbar){var 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kj=Ca(),dSe=qp(),pSe=Mt().extendDeepAll,mSe=qo().overrideAll,ySe=Ah(),Sj=Ct().templatedArray,Cf=(Jd(),ze($d)),gSe=Sj("step",{visible:{valType:"boolean",dflt:!0},method:{valType:"enumerated",values:["restyle","relayout","animate","update","skip"],dflt:"restyle"},args:{valType:"info_array",freeLength:!0,items:[{valType:"any"},{valType:"any"},{valType:"any"}]},label:{valType:"string"},value:{valType:"string"},execute:{valType:"boolean",dflt:!0}});qj.exports=mSe(Sj("slider",{visible:{valType:"boolean",dflt:!0},active:{valType:"number",min:0,dflt:0},steps:gSe,lenmode:{valType:"enumerated",values:["fraction","pixels"],dflt:"fraction"},len:{valType:"number",min:0,dflt:1},x:{valType:"number",min:-2,max:3,dflt:0},pad:pSe(dSe({editType:"arraydraw"}),{},{t:{dflt:20}}),xanchor:{valType:"enumerated",values:["auto","left","center","right"],dflt:"left"},y:{valType:"number",min:-2,max:3,dflt:0},yanchor:{valType:"enumerated",values:["auto","top","middle","bottom"],dflt:"top"},transition:{duration:{valType:"number",min:0,dflt:150},easing:{valType:"enumerated",values:ySe.transition.easing.values,dflt:"cubic-in-out"}},currentvalue:{visible:{valType:"boolean",dflt:!0},xanchor:{valType:"enumerated",values:["left","center","right"],dflt:"left"},offset:{valType:"number",dflt:10},prefix:{valType:"string"},suffix:{valType:"string"},font:kj({})},font:kj({}),activebgcolor:{valType:"color",dflt:Cf.gripBgActiveColor},bgcolor:{valType:"color",dflt:Cf.railBgColor},bordercolor:{valType:"color",dflt:Cf.railBorderColor},borderwidth:{valType:"number",min:0,dflt:Cf.railBorderWidth},ticklen:{valType:"number",min:0,dflt:Cf.tickLength},tickcolor:{valType:"color",dflt:Cf.tickColor},tickwidth:{valType:"number",min:0,dflt:1},minorticklen:{valType:"number",min:0,dflt:Cf.minorTickLength}}),"arraydraw","from-root")});var Ej=z((aKe,Dj)=>{"use strict";var O0=ke(),Lj=Po(),Cj=z8(),bSe=(Jd(),ze($d)),xSe=bSe.name,_Se=Cj.steps;Dj.exports=function(r,t){Lj(r,t,{name:xSe,handleItemDefaults:wSe})};function wSe(e,r,t){function a(c,v){return O0.coerce(e,r,Cj,c,v)}for(var n=Lj(e,r,{name:"steps",handleItemDefaults:ASe}),i=0,o=0;o{"use strict";var Go=Pr(),Pg=ma(),Ks=qr(),Yo=Jr(),qi=ke(),TSe=qi.strTranslate,Kd=Fa(),MSe=Ct().arrayEditor,Hr=(Jd(),ze($d)),B8=(on(),ze(nn)),Fj=B8.LINE_SPACING,N8=B8.FROM_TL,I8=B8.FROM_BR;Hj.exports=function(r){var t=r._context.staticPlot,a=r._fullLayout,n=kSe(a,r),i=a._infolayer.selectAll("g."+Hr.containerClassName).data(n.length>0?[0]:[]);i.enter().append("g").classed(Hr.containerClassName,!0).style("cursor",t?null:"ew-resize");function o(f){f._commandObserver&&(f._commandObserver.remove(),delete f._commandObserver),Pg.autoMargin(r,zj(f))}if(i.exit().each(function(){Go.select(this).selectAll("g."+Hr.groupClassName).each(o)}).remove(),n.length!==0){var l=i.selectAll("g."+Hr.groupClassName).data(n,SSe);l.enter().append("g").classed(Hr.groupClassName,!0),l.exit().each(o).remove();for(var s=0;s0&&(l=l.transition().duration(r.transition.duration).ease(r.transition.easing)),l.attr("transform",TSe(o-Hr.gripWidth*.5,r._dims.currentValueTotalHeight))}}function O8(e,r){var t=e._dims;return t.inputAreaStart+Hr.stepInset+(t.inputAreaLength-2*Hr.stepInset)*Math.min(1,Math.max(0,r))}function Rj(e,r){var t=e._dims;return Math.min(1,Math.max(0,(r-Hr.stepInset-t.inputAreaStart)/(t.inputAreaLength-2*Hr.stepInset-2*t.inputAreaStart)))}function RSe(e,r,t){var a=t._dims,n=qi.ensureSingle(e,"rect",Hr.railTouchRectClass,function(i){i.call(Bj,r,e,t).style("pointer-events","all")});n.attr({width:a.inputAreaLength,height:Math.max(a.inputAreaWidth,Hr.tickOffset+t.ticklen+a.labelHeight)}).call(Ks.fill,t.bgcolor).attr("opacity",0),Yo.setTranslate(n,0,a.currentValueTotalHeight)}function FSe(e,r){var t=r._dims,a=t.inputAreaLength-Hr.railInset*2,n=qi.ensureSingle(e,"rect",Hr.railRectClass);n.attr({width:a,height:Hr.railWidth,rx:Hr.railRadius,ry:Hr.railRadius,"shape-rendering":"crispEdges"}).call(Ks.stroke,r.bordercolor).call(Ks.fill,r.bgcolor).style("stroke-width",r.borderwidth+"px"),Yo.setTranslate(n,Hr.railInset,(t.inputAreaWidth-Hr.railWidth)*.5+t.currentValueTotalHeight)}});var Yj=z((iKe,Gj)=>{"use strict";var zSe=(Jd(),ze($d));Gj.exports={moduleType:"component",name:zSe.name,layoutAttributes:z8(),supplyLayoutDefaults:Ej(),draw:Uj()}});var Fg=z((oKe,jj)=>{"use strict";var Vj=Ii();jj.exports={bgcolor:{valType:"color",dflt:Vj.background,editType:"plot"},bordercolor:{valType:"color",dflt:Vj.defaultLine,editType:"plot"},borderwidth:{valType:"integer",dflt:0,min:0,editType:"plot"},autorange:{valType:"boolean",dflt:!0,editType:"calc",impliedEdits:{"range[0]":void 0,"range[1]":void 0}},range:{valType:"info_array",items:[{valType:"any",editType:"calc",impliedEdits:{"^autorange":!1}},{valType:"any",editType:"calc",impliedEdits:{"^autorange":!1}}],editType:"calc",impliedEdits:{autorange:!1}},thickness:{valType:"number",dflt:.15,min:0,max:1,editType:"plot"},visible:{valType:"boolean",dflt:!0,editType:"calc"},editType:"calc"}});var H8=z((lKe,Wj)=>{"use strict";Wj.exports={_isSubplotObj:!0,rangemode:{valType:"enumerated",values:["auto","fixed","match"],dflt:"match",editType:"calc"},range:{valType:"info_array",items:[{valType:"any",editType:"plot"},{valType:"any",editType:"plot"}],editType:"plot"},editType:"calc"}});var zg={};qt(zg,{bgClassName:()=>BSe,containerClassName:()=>ISe,extraPad:()=>sqe,grabAreaCursor:()=>aqe,grabAreaFill:()=>tqe,grabAreaMaxClassName:()=>XSe,grabAreaMinClassName:()=>VSe,grabAreaWidth:()=>nqe,grabberMaxClassName:()=>WSe,grabberMinClassName:()=>YSe,handleMaxClassName:()=>ZSe,handleMinClassName:()=>jSe,handleRadius:()=>oqe,handleStrokeWidth:()=>lqe,handleWidth:()=>iqe,maskColor:()=>KSe,maskMaxClassName:()=>USe,maskMaxOppAxisClassName:()=>JSe,maskMinClassName:()=>HSe,maskMinOppAxisClassName:()=>$Se,maskOppAxisColor:()=>QSe,name:()=>NSe,rangePlotClassName:()=>OSe,slideBoxClassName:()=>GSe,slideBoxCursor:()=>rqe,slideBoxFill:()=>eqe});var NSe,ISe,BSe,OSe,HSe,USe,GSe,YSe,VSe,jSe,WSe,XSe,ZSe,$Se,JSe,KSe,QSe,eqe,rqe,tqe,aqe,nqe,iqe,oqe,lqe,sqe,Ng=St(()=>{"use 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n=r[a],i=t[a];if(!(n.rangeslider||t._requestRangeslider[i._id]))return;Og.isPlainObject(n.rangeslider)||(n.rangeslider={});var o=n.rangeslider,l=Jj.newContainer(i,"rangeslider");function s(_,k){return Og.coerce(o,l,vqe,_,k)}var u,f;function c(_,k){return Og.coerce(u,f,hqe,_,k)}var v=s("visible");if(v){s("bgcolor",t.plot_bgcolor),s("bordercolor"),s("borderwidth"),s("thickness"),s("autorange",!i.isValidRange(o.range)),s("range");var d=t._subplots;if(d)for(var p=d.cartesian.filter(function(_){return _.slice(0,Math.max(0,_.indexOf("y")))===Kj.name2id(a)}).map(function(_){return _.slice(_.indexOf("y"),_.length)}),y=Og.simpleMap(p,Kj.id2name),m=0;m{"use strict";var dqe=Aa().list,pqe=Bh().getAutoRange,mqe=(Ng(),ze(zg));rW.exports=function(r){for(var t=dqe(r,"x",!0),a=0;a{"use strict";var Hg=Pr(),yqe=Tr(),gqe=ma(),ua=ke(),Ug=ua.strTranslate,nW=Jr(),Qs=qr(),bqe=n0(),xqe=io(),U8=Aa(),_qe=Vi(),wqe=Os(),Wr=(Ng(),ze(zg));iW.exports=function(e){for(var r=e._fullLayout,t=r._rangeSliderData,a=0;a=G.max)U=P[Y+1];else if(O=G.pmax)U=P[Y+1];else if(O0?e.touches[0].clientX:0}function Aqe(e,r,t,a){if(r._context.staticPlot)return;var n=e.select("rect."+Wr.slideBoxClassName).node(),i=e.select("rect."+Wr.grabAreaMinClassName).node(),o=e.select("rect."+Wr.grabAreaMaxClassName).node();function l(){var s=Hg.event,u=s.target,f=aW(s),c=f-e.node().getBoundingClientRect().left,v=a.d2p(t._rl[0]),d=a.d2p(t._rl[1]),p=_qe.coverSlip();this.addEventListener("touchmove",y),this.addEventListener("touchend",m),p.addEventListener("mousemove",y),p.addEventListener("mouseup",m);function y(b){var A=aW(b),w=+A-f,x,_,k;switch(u){case n:if(k="ew-resize",v+w>t._length||d+w<0)return;x=v+w,_=d+w;break;case i:if(k="col-resize",v+w>t._length)return;x=v+w,_=d;break;case o:if(k="col-resize",d+w<0)return;x=v,_=d+w;break;default:k="ew-resize",x=c,_=c+w;break}if(_{"use strict";var 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i=0;inv*u?(b=u,m=b*nv):(m=s,b=m/nv),A=o*m/s,w=l*b/u,p=r.l+r.w*n-m/2,y=r.t+r.h*(1-i)-b/2,t.x0=p,t.y0=y,t.w=m,t.h=b,t.sum=f,t.xaxis={type:"linear",range:[c+2*d-f,f-c-2*v],domain:[n-A/2,n+A/2],_id:"x"},x2(t.xaxis,t.graphDiv._fullLayout),t.xaxis.setScale(),t.xaxis.isPtWithinRange=function(I){return I.a>=t.aaxis.range[0]&&I.a<=t.aaxis.range[1]&&I.b>=t.baxis.range[1]&&I.b<=t.baxis.range[0]&&I.c>=t.caxis.range[1]&&I.c<=t.caxis.range[0]},t.yaxis={type:"linear",range:[c,f-v-d],domain:[i-w/2,i+w/2],_id:"y"},x2(t.yaxis,t.graphDiv._fullLayout),t.yaxis.setScale(),t.yaxis.isPtWithinRange=function(){return!0};var x=t.yaxis.domain[0],_=t.aaxis=TA({},e.aaxis,{range:[c,f-v-d],side:"left",tickangle:(+e.aaxis.tickangle||0)-30,domain:[x,x+w*nv],anchor:"free",position:0,_id:"y",_length:m});x2(_,t.graphDiv._fullLayout),_.setScale();var k=t.baxis=TA({},e.baxis,{range:[f-c-d,v],side:"bottom",domain:t.xaxis.domain,anchor:"free",position:0,_id:"x",_length:m});x2(k,t.graphDiv._fullLayout),k.setScale();var T=t.caxis=TA({},e.caxis,{range:[f-c-v,d],side:"right",tickangle:(+e.caxis.tickangle||0)+30,domain:[x,x+w*nv],anchor:"free",position:0,_id:"y",_length:m});x2(T,t.graphDiv._fullLayout),T.setScale();var q="M"+p+","+(y+b)+"h"+m+"l-"+m/2+",-"+b+"Z";t.clipDef.select("path").attr("d",q),t.layers.plotbg.select("path").attr("d",q);var C="M0,"+b+"h"+m+"l-"+m/2+",-"+b+"Z";t.clipDefRelative.select("path").attr("d",C);var E=Sl(p,y);t.plotContainer.selectAll(".scatterlayer,.maplayer").attr("transform",E),t.clipDefRelative.select("path").attr("transform",null);var P=Sl(p-k._offset,y+b);t.layers.baxis.attr("transform",P),t.layers.bgrid.attr("transform",P);var R=Sl(p+m/2,y)+"rotate(30)"+Sl(0,-_._offset);t.layers.aaxis.attr("transform",R),t.layers.agrid.attr("transform",R);var N=Sl(p+m/2,y)+"rotate(-30)"+Sl(0,-T._offset);t.layers.caxis.attr("transform",N),t.layers.cgrid.attr("transform",N),t.drawAxes(!0),t.layers.aline.select("path").attr("d",_.showline?"M"+p+","+(y+b)+"l"+m/2+",-"+b:"M0,0").call(Bf.stroke,_.linecolor||"#000").style("stroke-width",(_.linewidth||0)+"px"),t.layers.bline.select("path").attr("d",k.showline?"M"+p+","+(y+b)+"h"+m:"M0,0").call(Bf.stroke,k.linecolor||"#000").style("stroke-width",(k.linewidth||0)+"px"),t.layers.cline.select("path").attr("d",T.showline?"M"+(p+m/2)+","+y+"l"+m/2+","+b:"M0,0").call(Bf.stroke,T.linecolor||"#000").style("stroke-width",(T.linewidth||0)+"px"),t.graphDiv._context.staticPlot||t.initInteractions(),N3.setClipUrl(t.layers.frontplot,t._hasClipOnAxisFalse?null:t.clipId,t.graphDiv)};ql.drawAxes=function(e){var r=this,t=r.graphDiv,a=r.id.slice(7)+"title",n=r.layers,i=r.aaxis,o=r.baxis,l=r.caxis;if(r.drawAx(i),r.drawAx(o),r.drawAx(l),e){var s=Math.max(i.showticklabels?i.tickfont.size/2:0,(l.showticklabels?l.tickfont.size*.75:0)+(l.ticks==="outside"?l.ticklen*.87:0)),u=(o.showticklabels?o.tickfont.size:0)+(o.ticks==="outside"?o.ticklen:0)+3;n["a-title"]=MA.draw(t,"a"+a,{propContainer:i,propName:r.id+".aaxis.title.text",placeholder:z3(t,"Click to enter Component A title"),attributes:{x:r.x0+r.w/2,y:r.y0-i.title.font.size/3-s,"text-anchor":"middle"}}),n["b-title"]=MA.draw(t,"b"+a,{propContainer:o,propName:r.id+".baxis.title.text",placeholder:z3(t,"Click to enter Component B title"),attributes:{x:r.x0-u,y:r.y0+r.h+o.title.font.size*.83+u,"text-anchor":"middle"}}),n["c-title"]=MA.draw(t,"c"+a,{propContainer:l,propName:r.id+".caxis.title.text",placeholder:z3(t,"Click to enter Component C title"),attributes:{x:r.x0+r.w+u,y:r.y0+r.h+l.title.font.size*.83+u,"text-anchor":"middle"}})}};ql.drawAx=function(e){var r=this,t=r.graphDiv,a=e._name,n=a.charAt(0),i=e._id,o=r.layers[a],l=30,s=n+"tickLayout",u=JRe(e);r[s]!==u&&(o.selectAll("."+i+"tick").remove(),r[s]=u),e.setScale();var f=iu.calcTicks(e),c=iu.clipEnds(e,f),v=iu.makeTransTickFn(e),d=iu.getTickSigns(e)[2],p=ls.deg2rad(l),y=d*(e.linewidth||1)/2,m=d*e.ticklen,b=r.w,A=r.h,w=n==="b"?"M0,"+y+"l"+Math.sin(p)*m+","+Math.cos(p)*m:"M"+y+",0l"+Math.cos(p)*m+","+-Math.sin(p)*m,x={a:"M0,0l"+A+",-"+b/2,b:"M0,0l-"+b/2+",-"+A,c:"M0,0l-"+A+","+b/2}[n];iu.drawTicks(t,e,{vals:e.ticks==="inside"?c:f,layer:o,path:w,transFn:v,crisp:!1}),iu.drawGrid(t,e,{vals:c,layer:r.layers[n+"grid"],path:x,transFn:v,crisp:!1}),iu.drawLabels(t,e,{vals:f,layer:o,transFn:v,labelFns:iu.makeLabelFns(e,0,l)})};function JRe(e){return e.ticks+String(e.ticklen)+String(e.showticklabels)}var Ya=oee.MINZOOM/2+.87,KRe="m-0.87,.5h"+Ya+"v3h-"+(Ya+5.2)+"l"+(Ya/2+2.6)+",-"+(Ya*.87+4.5)+"l2.6,1.5l-"+Ya/2+","+Ya*.87+"Z",QRe="m0.87,.5h-"+Ya+"v3h"+(Ya+5.2)+"l-"+(Ya/2+2.6)+",-"+(Ya*.87+4.5)+"l-2.6,1.5l"+Ya/2+","+Ya*.87+"Z",eFe="m0,1l"+Ya/2+","+Ya*.87+"l2.6,-1.5l-"+(Ya/2+2.6)+",-"+(Ya*.87+4.5)+"l-"+(Ya/2+2.6)+","+(Ya*.87+4.5)+"l2.6,1.5l"+Ya/2+",-"+Ya*.87+"Z",rFe="m0.5,0.5h5v-2h-5v-5h-2v5h-5v2h5v5h2Z",tee=!0;ql.clearOutline=function(){$Re(this.dragOptions),ZRe(this.dragOptions.gd)};ql.initInteractions=function(){var e=this,r=e.layers.plotbg.select("path").node(),t=e.graphDiv,a=t._fullLayout._zoomlayer,n,i;this.dragOptions={element:r,gd:t,plotinfo:{id:e.id,domain:t._fullLayout[e.id].domain,xaxis:e.xaxis,yaxis:e.yaxis},subplot:e.id,prepFn:function(P,R,N){e.dragOptions.xaxes=[e.xaxis],e.dragOptions.yaxes=[e.yaxis],n=t._fullLayout._invScaleX,i=t._fullLayout._invScaleY;var I=e.dragOptions.dragmode=t._fullLayout.dragmode;ree(I)?e.dragOptions.minDrag=1:e.dragOptions.minDrag=void 0,I==="zoom"?(e.dragOptions.moveFn=k,e.dragOptions.clickFn=b,e.dragOptions.doneFn=T,A(P,R,N)):I==="pan"?(e.dragOptions.moveFn=C,e.dragOptions.clickFn=b,e.dragOptions.doneFn=E,q(),e.clearOutline(t)):(jRe(I)||ree(I))&&WRe(P,R,N,e.dragOptions,I)}};var o,l,s,u,f,c,v,d,p,y;function m(P){var R={};return R[e.id+".aaxis.min"]=P.a,R[e.id+".baxis.min"]=P.b,R[e.id+".caxis.min"]=P.c,R}function b(P,R){var N=t._fullLayout.clickmode;aee(t),P===2&&(t.emit("plotly_doubleclick",null),AA.call("_guiRelayout",t,m({a:0,b:0,c:0}))),N.indexOf("select")>-1&&P===1&&XRe(R,t,[e.xaxis],[e.yaxis],e.id,e.dragOptions),N.indexOf("event")>-1&&eee.click(t,R,e.id)}function A(P,R,N){var I=r.getBoundingClientRect();o=R-I.left,l=N-I.top,t._fullLayout._calcInverseTransform(t);var O=t._fullLayout._invTransform,U=ls.apply3DTransform(O)(o,l);o=U[0],l=U[1],s={a:e.aaxis.range[0],b:e.baxis.range[1],c:e.caxis.range[1]},f=s,u=e.aaxis.range[1]-s.a,c=Bf.luminosity(e.graphDiv._fullLayout[e.id].bgcolor),v="M0,"+e.h+"L"+e.w/2+", 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xx=On(),YYe=H0().attributes,VYe=Ca(),jYe=Ii(),{hovertemplateAttrs:WYe,texttemplateAttrs:XYe,templatefallbackAttrs:Ase}=di(),bu=Mt().extendFlat,ZYe=Bi().pattern,_x=VYe({editType:"plot",arrayOk:!0,colorEditType:"plot"});Tse.exports={labels:{valType:"data_array",editType:"calc"},label0:{valType:"number",dflt:0,editType:"calc"},dlabel:{valType:"number",dflt:1,editType:"calc"},values:{valType:"data_array",editType:"calc"},marker:{colors:{valType:"data_array",editType:"calc"},line:{color:{valType:"color",dflt:jYe.defaultLine,arrayOk:!0,editType:"style"},width:{valType:"number",min:0,dflt:0,arrayOk:!0,editType:"style"},editType:"calc"},pattern:ZYe,editType:"calc"},text:{valType:"data_array",editType:"plot"},hovertext:{valType:"string",dflt:"",arrayOk:!0,editType:"style"},scalegroup:{valType:"string",dflt:"",editType:"calc"},textinfo:{valType:"flaglist",flags:["label","text","value","percent"],extras:["none"],editType:"calc"},hoverinfo:bu({},xx.hoverinfo,{flags:["label","text","value","percent","name"]}),hovertemplate:WYe({},{keys:["label","color","value","percent","text"]}),hovertemplatefallback:Ase(),texttemplate:XYe({editType:"plot"},{keys:["label","color","value","percent","text"]}),texttemplatefallback:Ase({editType:"plot"}),textposition:{valType:"enumerated",values:["inside","outside","auto","none"],dflt:"auto",arrayOk:!0,editType:"plot"},textfont:bu({},_x,{}),insidetextorientation:{valType:"enumerated",values:["horizontal","radial","tangential","auto"],dflt:"auto",editType:"plot"},insidetextfont:bu({},_x,{}),outsidetextfont:bu({},_x,{}),automargin:{valType:"boolean",dflt:!1,editType:"plot"},showlegend:bu({},xx.showlegend,{arrayOk:!0}),legend:bu({},xx.legend,{arrayOk:!0}),legendrank:bu({},xx.legendrank,{arrayOk:!0}),title:{text:{valType:"string",dflt:"",editType:"plot"},font:bu({},_x,{}),position:{valType:"enumerated",values:["top left","top center","top right","middle center","bottom left","bottom center","bottom right"],editType:"plot"},editType:"plot"},domain:YYe({name:"pie",trace:!0,editType:"calc"}),hole:{valType:"number",min:0,max:1,dflt:0,editType:"calc"},sort:{valType:"boolean",dflt:!0,editType:"calc"},direction:{valType:"enumerated",values:["clockwise","counterclockwise"],dflt:"counterclockwise",editType:"calc"},rotation:{valType:"angle",dflt:0,editType:"calc"},pull:{valType:"number",min:0,max:1,dflt:0,arrayOk:!0,editType:"calc"}}});var qse=z((par,Sse)=>{"use strict";var $Ye=Br(),s1=ke(),JYe=WM(),KYe=H0().defaults,QYe=Rf().handleText,eVe=ke().coercePattern;function Mse(e,r){var t=s1.isArrayOrTypedArray(e),a=s1.isArrayOrTypedArray(r),n=Math.min(t?e.length:1/0,a?r.length:1/0);if(isFinite(n)||(n=0),n&&a){for(var i,o=0;o0){i=!0;break}}i||(n=0)}return{hasLabels:t,hasValues:a,len:n}}function kse(e,r,t,a,n){var i=a("marker.line.width");i&&a("marker.line.color",n?void 0:t.paper_bgcolor);var o=a("marker.colors");eVe(a,"marker.pattern",o),e.marker&&!r.marker.pattern.fgcolor&&(r.marker.pattern.fgcolor=e.marker.colors),r.marker.pattern.bgcolor||(r.marker.pattern.bgcolor=t.paper_bgcolor)}function rVe(e,r,t,a){function n(A,w){return s1.coerce(e,r,JYe,A,w)}var i=n("labels"),o=n("values"),l=Mse(i,o),s=l.len;if(r._hasLabels=l.hasLabels,r._hasValues=l.hasValues,!r._hasLabels&&r._hasValues&&(n("label0"),n("dlabel")),!s){r.visible=!1;return}r._length=s,kse(e,r,a,n,!0),n("scalegroup");var u=n("text"),f=n("texttemplate");n("texttemplatefallback");var c;if(f||(c=n("textinfo",s1.isArrayOrTypedArray(u)?"text+percent":"percent")),n("hovertext"),n("hovertemplate"),n("hovertemplatefallback"),f||c&&c!=="none"){var v=n("textposition");QYe(e,r,a,n,v,{moduleHasSelected:!1,moduleHasUnselected:!1,moduleHasConstrain:!1,moduleHasCliponaxis:!1,moduleHasTextangle:!1,moduleHasInsideanchor:!1});var d=Array.isArray(v)||v==="auto",p=d||v==="outside";p&&n("automargin"),(v==="inside"||v==="auto"||Array.isArray(v))&&n("insidetextorientation")}else c==="none"&&n("textposition","none");KYe(r,a,n);var y=n("hole"),m=n("title.text");if(m){var b=n("title.position",y?"middle center":"top center");!y&&b==="middle center"&&(r.title.position="top center"),s1.coerceFont(n,"title.font",a.font)}n("sort"),n("direction"),n("rotation"),n("pull")}Sse.exports={handleLabelsAndValues:Mse,handleMarkerDefaults:kse,supplyDefaults:rVe}});var XM=z((mar,Lse)=>{"use strict";Lse.exports={hiddenlabels:{valType:"data_array",editType:"calc"},piecolorway:{valType:"colorlist",editType:"calc"},extendpiecolors:{valType:"boolean",dflt:!0,editType:"calc"}}});var Dse=z((yar,Cse)=>{"use strict";var tVe=ke(),aVe=XM();Cse.exports=function(r,t){function a(n,i){return tVe.coerce(r,t,aVe,n,i)}a("hiddenlabels"),a("piecolorway",t.colorway),a("extendpiecolors")}});var ZM=z((gar,Rse)=>{"use strict";var nVe=Br(),Fv=qr(),iVe={};function oVe(e,r){var t=[],a=e._fullLayout,n=a.hiddenlabels||[],i=r.labels,o=r.marker.colors||[],l=r.values,s=r._length,u=r._hasValues&&s,f,c;if(r.dlabel)for(i=new Array(s),f=0;f=0});var x=r.type==="funnelarea"?y:r.sort;return x&&t.sort(function(_,k){return k.v-_.v}),t[0]&&(t[0].vTotal=p),t}function Ese(e){return function(t,a){if(!t||!Fv.isValid(t))return!1;let n=Fv.rgbaString(t);return e[a]||(e[a]=n),n}}function lVe(e,r){var t=(r||{}).type;t||(t="pie");var a=e._fullLayout,n=e.calcdata,i=a[t+"colorway"],o=a["_"+t+"colormap"];a["extend"+t+"colors"]&&(i=Pse(i,iVe));for(var l=0,s=0;s{"use strict";var sVe=Ro().appendArrayMultiPointValues;Fse.exports=function(r,t){var a={curveNumber:t.index,pointNumbers:r.pts,data:t._input,fullData:t,label:r.label,color:r.color,value:r.v,percent:r.percent,text:r.text,bbox:r.bbox,v:r.v};return r.pts.length===1&&(a.pointNumber=a.i=r.pts[0]),sVe(a,t,r.pts),t.type==="funnelarea"&&(delete a.v,delete a.i),a}});var nue=z((xar,aue)=>{"use strict";var fi=Pr(),uVe=ma(),wx=Un(),Use=qr(),vs=Jr(),vn=ke(),fVe=vn.strScale,Nse=vn.strTranslate,$M=Fa(),Gse=a2(),cVe=Gse.recordMinTextSize,vVe=Gse.clearMinTextSize,Yse=(Id(),ze(Nd)).TEXTPAD,Dr=Om(),Ax=zse(),Ise=ke().isValidTextValue;function hVe(e,r){var t=e._context.staticPlot,a=e._fullLayout,n=a._size;vVe("pie",a),Wse(r,e),eue(r,n);var i=vn.makeTraceGroups(a._pielayer,r,"trace").each(function(o){var l=fi.select(this),s=o[0],u=s.trace;wVe(o),l.attr("stroke-linejoin","round"),l.each(function(){var f=fi.select(this).selectAll("g.slice").data(o);f.enter().append("g").classed("slice",!0),f.exit().remove();var c=[[[],[]],[[],[]]],v=!1;f.each(function(x,_){if(x.hidden){fi.select(this).selectAll("path,g").remove();return}x.pointNumber=x.i,x.curveNumber=u.index,c[x.pxmid[1]<0?0:1][x.pxmid[0]<0?0:1].push(x);var k=s.cx,T=s.cy,q=fi.select(this),C=q.selectAll("path.surface").data([x]);if(C.enter().append("path").classed("surface",!0).style({"pointer-events":t?"none":"all"}),q.call(Vse,e,o),u.pull){var E=+Dr.castOption(u.pull,x.pts)||0;E>0&&(k+=E*x.pxmid[0],T+=E*x.pxmid[1])}x.cxFinal=k,x.cyFinal=T;function P(G,V,W,j){var J=j*(V[0]-G[0]),te=j*(V[1]-G[1]);return"a"+j*s.r+","+j*s.r+" 0 "+x.largeArc+(W?" 1 ":" 0 ")+J+","+te}var R=u.hole;if(x.v===s.vTotal){var N="M"+(k+x.px0[0])+","+(T+x.px0[1])+P(x.px0,x.pxmid,!0,1)+P(x.pxmid,x.px0,!0,1)+"Z";R?C.attr("d","M"+(k+R*x.px0[0])+","+(T+R*x.px0[1])+P(x.px0,x.pxmid,!1,R)+P(x.pxmid,x.px0,!1,R)+"Z"+N):C.attr("d",N)}else{var I=P(x.px0,x.px1,!0,1);if(R){var O=1-R;C.attr("d","M"+(k+R*x.px1[0])+","+(T+R*x.px1[1])+P(x.px1,x.px0,!1,R)+"l"+O*x.px0[0]+","+O*x.px0[1]+I+"Z")}else C.attr("d","M"+k+","+T+"l"+x.px0[0]+","+x.px0[1]+I+"Z")}rue(e,x,s);var U=Dr.castOption(u.textposition,x.pts),Y=q.selectAll("g.slicetext").data(x.text&&U!=="none"?[0]:[]);Y.enter().append("g").classed("slicetext",!0),Y.exit().remove(),Y.each(function(){var G=vn.ensureSingle(fi.select(this),"text","",function($){$.attr("data-notex",1)}),V=vn.ensureUniformFontSize(e,U==="outside"?pVe(u,x,a.font):jse(u,x,a.font));G.text(x.text).attr({class:"slicetext",transform:"","text-anchor":"middle"}).call(vs.font,V).call($M.convertToTspans,e);var W=vs.bBox(G.node()),j;if(U==="outside")j=Hse(W,x);else if(j=Xse(W,x,s),U==="auto"&&j.scale<1){var J=vn.ensureUniformFontSize(e,u.outsidetextfont);G.call(vs.font,J),W=vs.bBox(G.node()),j=Hse(W,x)}var te=j.textPosAngle,ae=te===void 0?x.pxmid:Tx(s.r,te);if(j.targetX=k+ae[0]*j.rCenter+(j.x||0),j.targetY=T+ae[1]*j.rCenter+(j.y||0),tue(j,W),j.outside){var se=j.targetY;x.yLabelMin=se-W.height/2,x.yLabelMid=se,x.yLabelMax=se+W.height/2,x.labelExtraX=0,x.labelExtraY=0,v=!0}j.fontSize=V.size,cVe(u.type,j,a),o[_].transform=j,vn.setTransormAndDisplay(G,j)})});var d=fi.select(this).selectAll("g.titletext").data(u.title.text?[0]:[]);if(d.enter().append("g").classed("titletext",!0),d.exit().remove(),d.each(function(){var x=vn.ensureSingle(fi.select(this),"text","",function(T){T.attr("data-notex",1)}),_=u.title.text;u._meta&&(_=vn.templateString(_,u._meta)),x.text(_).attr({class:"titletext",transform:"","text-anchor":"middle"}).call(vs.font,u.title.font).call($M.convertToTspans,e);var k;u.title.position==="middle center"?k=gVe(s):k=Kse(s,n),x.attr("transform",Nse(k.x,k.y)+fVe(Math.min(1,k.scale))+Nse(k.tx,k.ty))}),v&&xVe(c,u),dVe(f,u),v&&u.automargin){var p=vs.bBox(l.node()),y=u.domain,m=n.w*(y.x[1]-y.x[0]),b=n.h*(y.y[1]-y.y[0]),A=(.5*m-s.r)/n.w,w=(.5*b-s.r)/n.h;uVe.autoMargin(e,"pie."+u.uid+".automargin",{xl:y.x[0]-A,xr:y.x[1]+A,yb:y.y[0]-w,yt:y.y[1]+w,l:Math.max(s.cx-s.r-p.left,0),r:Math.max(p.right-(s.cx+s.r),0),b:Math.max(p.bottom-(s.cy+s.r),0),t:Math.max(s.cy-s.r-p.top,0),pad:5})}})});setTimeout(function(){i.selectAll("tspan").each(function(){var o=fi.select(this);o.attr("dy")&&o.attr("dy",o.attr("dy"))})},0)}function dVe(e,r){e.each(function(t){var a=fi.select(this);if(!t.labelExtraX&&!t.labelExtraY){a.select("path.textline").remove();return}var n=a.select("g.slicetext text");t.transform.targetX+=t.labelExtraX,t.transform.targetY+=t.labelExtraY,vn.setTransormAndDisplay(n,t.transform);var i=t.cxFinal+t.pxmid[0],o=t.cyFinal+t.pxmid[1],l="M"+i+","+o,s=(t.yLabelMax-t.yLabelMin)*(t.pxmid[0]<0?-1:1)/4;if(t.labelExtraX){var u=t.labelExtraX*t.pxmid[1]/t.pxmid[0],f=t.yLabelMid+t.labelExtraY-(t.cyFinal+t.pxmid[1]);Math.abs(u)>Math.abs(f)?l+="l"+f*t.pxmid[0]/t.pxmid[1]+","+f+"H"+(i+t.labelExtraX+s):l+="l"+t.labelExtraX+","+u+"v"+(f-u)+"h"+s}else l+="V"+(t.yLabelMid+t.labelExtraY)+"h"+s;vn.ensureSingle(a,"path","textline").call(Use.stroke,r.outsidetextfont.color).attr({"stroke-width":Math.min(2,r.outsidetextfont.size/8),d:l,fill:"none"})})}function Vse(e,r,t){var a=t[0],n=a.cx,i=a.cy,o=a.trace,l=o.type==="funnelarea";"_hasHoverLabel"in o||(o._hasHoverLabel=!1),"_hasHoverEvent"in o||(o._hasHoverEvent=!1),e.on("mouseover",function(s){var u=r._fullLayout,f=r._fullData[o.index];if(!(r._dragging||u.hovermode===!1)){var c=f.hoverinfo;if(Array.isArray(c)&&(c=wx.castHoverinfo({hoverinfo:[Dr.castOption(c,s.pts)],_module:o._module},u,0)),c==="all"&&(c="label+text+value+percent+name"),f.hovertemplate||c!=="none"&&c!=="skip"&&c){var v=s.rInscribed||0,d=n+s.pxmid[0]*(1-v),p=i+s.pxmid[1]*(1-v),y=u.separators,m=[];if(c&&c.indexOf("label")!==-1&&m.push(s.label),s.text=Dr.castOption(f.hovertext||f.text,s.pts),c&&c.indexOf("text")!==-1){var b=s.text;vn.isValidTextValue(b)&&m.push(b)}s.value=s.v,s.valueLabel=Dr.formatPieValue(s.v,y),c&&c.indexOf("value")!==-1&&m.push(s.valueLabel),s.percent=s.v/a.vTotal,s.percentLabel=Dr.formatPiePercent(s.percent,y),c&&c.indexOf("percent")!==-1&&m.push(s.percentLabel);var A=f.hoverlabel,w=A.font,x=[];wx.loneHover({trace:o,x0:d-v*a.r,x1:d+v*a.r,y:p,_x0:l?n+s.TL[0]:d-v*a.r,_x1:l?n+s.TR[0]:d+v*a.r,_y0:l?i+s.TL[1]:p-v*a.r,_y1:l?i+s.BL[1]:p+v*a.r,text:m.join("
"),name:f.hovertemplate||c.indexOf("name")!==-1?f.name:void 0,idealAlign:s.pxmid[0]<0?"left":"right",color:Dr.castOption(A.bgcolor,s.pts)||s.color,borderColor:Dr.castOption(A.bordercolor,s.pts),fontFamily:Dr.castOption(w.family,s.pts),fontSize:Dr.castOption(w.size,s.pts),fontColor:Dr.castOption(w.color,s.pts),nameLength:Dr.castOption(A.namelength,s.pts),textAlign:Dr.castOption(A.align,s.pts),hovertemplate:Dr.castOption(f.hovertemplate,s.pts),hovertemplateLabels:s,eventData:[Ax(s,f)]},{container:u._hoverlayer.node(),outerContainer:u._paper.node(),gd:r,inOut_bbox:x}),s.bbox=x[0],o._hasHoverLabel=!0}o._hasHoverEvent=!0,r.emit("plotly_hover",{points:[Ax(s,f)],event:fi.event})}}),e.on("mouseout",function(s){var u=r._fullLayout,f=r._fullData[o.index],c=fi.select(this).datum();o._hasHoverEvent&&(s.originalEvent=fi.event,r.emit("plotly_unhover",{points:[Ax(c,f)],event:fi.event}),o._hasHoverEvent=!1),o._hasHoverLabel&&(wx.loneUnhover(u._hoverlayer.node()),o._hasHoverLabel=!1)}),e.on("click",function(s){var u=r._fullLayout,f=r._fullData[o.index];r._dragging||u.hovermode===!1||(r._hoverdata=[Ax(s,f)],wx.click(r,fi.event))})}function pVe(e,r,t){var a=Dr.castOption(e.outsidetextfont.color,r.pts)||Dr.castOption(e.textfont.color,r.pts)||t.color,n=Dr.castOption(e.outsidetextfont.family,r.pts)||Dr.castOption(e.textfont.family,r.pts)||t.family,i=Dr.castOption(e.outsidetextfont.size,r.pts)||Dr.castOption(e.textfont.size,r.pts)||t.size,o=Dr.castOption(e.outsidetextfont.weight,r.pts)||Dr.castOption(e.textfont.weight,r.pts)||t.weight,l=Dr.castOption(e.outsidetextfont.style,r.pts)||Dr.castOption(e.textfont.style,r.pts)||t.style,s=Dr.castOption(e.outsidetextfont.variant,r.pts)||Dr.castOption(e.textfont.variant,r.pts)||t.variant,u=Dr.castOption(e.outsidetextfont.textcase,r.pts)||Dr.castOption(e.textfont.textcase,r.pts)||t.textcase,f=Dr.castOption(e.outsidetextfont.lineposition,r.pts)||Dr.castOption(e.textfont.lineposition,r.pts)||t.lineposition,c=Dr.castOption(e.outsidetextfont.shadow,r.pts)||Dr.castOption(e.textfont.shadow,r.pts)||t.shadow;return{color:a,family:n,size:i,weight:o,style:l,variant:s,textcase:u,lineposition:f,shadow:c}}function jse(e,r,t){var a=Dr.castOption(e.insidetextfont.color,r.pts);!a&&e._input.textfont&&(a=Dr.castOption(e._input.textfont.color,r.pts));var n=Dr.castOption(e.insidetextfont.family,r.pts)||Dr.castOption(e.textfont.family,r.pts)||t.family,i=Dr.castOption(e.insidetextfont.size,r.pts)||Dr.castOption(e.textfont.size,r.pts)||t.size,o=Dr.castOption(e.insidetextfont.weight,r.pts)||Dr.castOption(e.textfont.weight,r.pts)||t.weight,l=Dr.castOption(e.insidetextfont.style,r.pts)||Dr.castOption(e.textfont.style,r.pts)||t.style,s=Dr.castOption(e.insidetextfont.variant,r.pts)||Dr.castOption(e.textfont.variant,r.pts)||t.variant,u=Dr.castOption(e.insidetextfont.textcase,r.pts)||Dr.castOption(e.textfont.textcase,r.pts)||t.textcase,f=Dr.castOption(e.insidetextfont.lineposition,r.pts)||Dr.castOption(e.textfont.lineposition,r.pts)||t.lineposition,c=Dr.castOption(e.insidetextfont.shadow,r.pts)||Dr.castOption(e.textfont.shadow,r.pts)||t.shadow;return{color:a||Use.contrast(r.color),family:n,size:i,weight:o,style:l,variant:s,textcase:u,lineposition:f,shadow:c}}function Wse(e,r){for(var t,a,n=0;n=-4;A-=2)b(Math.PI*A,"tan");for(A=4;A>=-4;A-=2)b(Math.PI*(A+1),"tan")}if(c||d){for(A=4;A>=-4;A-=2)b(Math.PI*(A+1.5),"rad");for(A=4;A>=-4;A-=2)b(Math.PI*(A+.5),"rad")}}if(l||p||c){var w=Math.sqrt(e.width*e.width+e.height*e.height);if(m={scale:n*a*2/w,rCenter:1-n,rotate:0},m.textPosAngle=(r.startangle+r.stopangle)/2,m.scale>=1)return m;y.push(m)}(p||d)&&(m=Bse(e,a,o,s,u),m.textPosAngle=(r.startangle+r.stopangle)/2,y.push(m)),(p||v)&&(m=Ose(e,a,o,s,u),m.textPosAngle=(r.startangle+r.stopangle)/2,y.push(m));for(var x=0,_=0,k=0;k=1)break}return y[x]}function mVe(e,r){var t=e.startangle,a=e.stopangle;return t>r&&r>a||t0?1:-1)/2,y:i/(1+t*t/(a*a)),outside:!0}}function gVe(e){var r=Math.sqrt(e.titleBox.width*e.titleBox.width+e.titleBox.height*e.titleBox.height);return{x:e.cx,y:e.cy,scale:e.trace.hole*e.r*2/r,tx:0,ty:-e.titleBox.height/2+e.trace.title.font.size}}function Kse(e,r){var t=1,a=1,n,i=e.trace,o={x:e.cx,y:e.cy},l={tx:0,ty:0};l.ty+=i.title.font.size,n=Qse(i),i.title.position.indexOf("top")!==-1?(o.y-=(1+n)*e.r,l.ty-=e.titleBox.height):i.title.position.indexOf("bottom")!==-1&&(o.y+=(1+n)*e.r);var s=bVe(e.r,e.trace.aspectratio),u=r.w*(i.domain.x[1]-i.domain.x[0])/2;return i.title.position.indexOf("left")!==-1?(u=u+s,o.x-=(1+n)*s,l.tx+=e.titleBox.width/2):i.title.position.indexOf("center")!==-1?u*=2:i.title.position.indexOf("right")!==-1&&(u=u+s,o.x+=(1+n)*s,l.tx-=e.titleBox.width/2),t=u/e.titleBox.width,a=JM(e,r)/e.titleBox.height,{x:o.x,y:o.y,scale:Math.min(t,a),tx:l.tx,ty:l.ty}}function bVe(e,r){return e/(r===void 0?1:r)}function JM(e,r){var t=e.trace,a=r.h*(t.domain.y[1]-t.domain.y[0]);return Math.min(e.titleBox.height,a/2)}function Qse(e){var r=e.pull;if(!r)return 0;var t;if(vn.isArrayOrTypedArray(r))for(r=0,t=0;tr&&(r=e.pull[t]);return r}function xVe(e,r){var t,a,n,i,o,l,s,u,f,c,v,d,p;function y(w,x){return w.pxmid[1]-x.pxmid[1]}function m(w,x){return 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t=r._fullLayout._pielayer.selectAll(".trace");TVe(r,t,"pie"),t.each(function(a){var n=a[0],i=n.trace,o=iue.select(this);o.style({opacity:i.opacity}),o.selectAll("path.surface").each(function(l){iue.select(this).call(AVe,l,i,r)})})}});var uue=z(zv=>{"use strict";var sue=ma();zv.name="pie";zv.plot=function(e,r,t,a){sue.plotBasePlot(zv.name,e,r,t,a)};zv.clean=function(e,r,t,a){sue.cleanBasePlot(zv.name,e,r,t,a)}});var cue=z((Aar,fue)=>{"use strict";fue.exports={attributes:WM(),supplyDefaults:qse().supplyDefaults,supplyLayoutDefaults:Dse(),layoutAttributes:XM(),calc:ZM().calc,crossTraceCalc:ZM().crossTraceCalc,plot:nue().plot,style:lue(),styleOne:Hm(),moduleType:"trace",name:"pie",basePlotModule:uue(),categories:["pie-like","pie","showLegend"],meta:{}}});var hue=z((Tar,vue)=>{"use strict";vue.exports=cue()});var xn=z((Mar,pue)=>{"use strict";var due=Object.getOwnPropertySymbols,MVe=Object.prototype.hasOwnProperty,kVe=Object.prototype.propertyIsEnumerable;function SVe(e){if(e==null)throw 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KM(e,r,t,a){if(this._calendar=e,this._year=r,this._month=t,this._day=a,this._calendar._validateLevel===0&&!this._calendar.isValid(this._year,this._month,this._day))throw(Gr.local.invalidDate||Gr.regionalOptions[""].invalidDate).replace(/\{0\}/,this._calendar.local.name)}function Mx(e,r){return e=""+e,"000000".substring(0,r-e.length)+e}kx(KM.prototype,{newDate:function(e,r,t){return this._calendar.newDate(e==null?this:e,r,t)},year:function(e){return arguments.length===0?this._year:this.set(e,"y")},month:function(e){return arguments.length===0?this._month:this.set(e,"m")},day:function(e){return arguments.length===0?this._day:this.set(e,"d")},date:function(e,r,t){if(!this._calendar.isValid(e,r,t))throw(Gr.local.invalidDate||Gr.regionalOptions[""].invalidDate).replace(/\{0\}/,this._calendar.local.name);return this._year=e,this._month=r,this._day=t,this},leapYear:function(){return this._calendar.leapYear(this)},epoch:function(){return this._calendar.epoch(this)},formatYear:function(){return this._calendar.formatYear(this)},monthOfYear:function(){return this._calendar.monthOfYear(this)},weekOfYear:function(){return this._calendar.weekOfYear(this)},daysInYear:function(){return this._calendar.daysInYear(this)},dayOfYear:function(){return this._calendar.dayOfYear(this)},daysInMonth:function(){return this._calendar.daysInMonth(this)},dayOfWeek:function(){return this._calendar.dayOfWeek(this)},weekDay:function(){return this._calendar.weekDay(this)},extraInfo:function(){return this._calendar.extraInfo(this)},add:function(e,r){return this._calendar.add(this,e,r)},set:function(e,r){return this._calendar.set(this,e,r)},compareTo:function(e){if(this._calendar.name!==e._calendar.name)throw(Gr.local.differentCalendars||Gr.regionalOptions[""].differentCalendars).replace(/\{0\}/,this._calendar.local.name).replace(/\{1\}/,e._calendar.local.name);var r=this._year!==e._year?this._year-e._year:this._month!==e._month?this.monthOfYear()-e.monthOfYear():this._day-e._day;return r===0?0:r<0?-1:1},calendar:function(){return this._calendar},toJD:function(){return this._calendar.toJD(this)},fromJD:function(e){return this._calendar.fromJD(e)},toJSDate:function(){return this._calendar.toJSDate(this)},fromJSDate:function(e){return this._calendar.fromJSDate(e)},toString:function(){return(this.year()<0?"-":"")+Mx(Math.abs(this.year()),4)+"-"+Mx(this.month(),2)+"-"+Mx(this.day(),2)}});function QM(){this.shortYearCutoff="+10"}kx(QM.prototype,{_validateLevel:0,newDate:function(e,r,t){return e==null?this.today():(e.year&&(this._validate(e,r,t,Gr.local.invalidDate||Gr.regionalOptions[""].invalidDate),t=e.day(),r=e.month(),e=e.year()),new KM(this,e,r,t))},today:function(){return this.fromJSDate(new Date)},epoch:function(e){var r=this._validate(e,this.minMonth,this.minDay,Gr.local.invalidYear||Gr.regionalOptions[""].invalidYear);return r.year()<0?this.local.epochs[0]:this.local.epochs[1]},formatYear:function(e){var r=this._validate(e,this.minMonth,this.minDay,Gr.local.invalidYear||Gr.regionalOptions[""].invalidYear);return(r.year()<0?"-":"")+Mx(Math.abs(r.year()),4)},monthsInYear:function(e){return this._validate(e,this.minMonth,this.minDay,Gr.local.invalidYear||Gr.regionalOptions[""].invalidYear),12},monthOfYear:function(e,r){var t=this._validate(e,r,this.minDay,Gr.local.invalidMonth||Gr.regionalOptions[""].invalidMonth);return(t.month()+this.monthsInYear(t)-this.firstMonth)%this.monthsInYear(t)+this.minMonth},fromMonthOfYear:function(e,r){var t=(r+this.firstMonth-2*this.minMonth)%this.monthsInYear(e)+this.minMonth;return this._validate(e,t,this.minDay,Gr.local.invalidMonth||Gr.regionalOptions[""].invalidMonth),t},daysInYear:function(e){var r=this._validate(e,this.minMonth,this.minDay,Gr.local.invalidYear||Gr.regionalOptions[""].invalidYear);return this.leapYear(r)?366:365},dayOfYear:function(e,r,t){var a=this._validate(e,r,t,Gr.local.invalidDate||Gr.regionalOptions[""].invalidDate);return a.toJD()-this.newDate(a.year(),this.fromMonthOfYear(a.year(),this.minMonth),this.minDay).toJD()+1},daysInWeek:function(){return 7},dayOfWeek:function(e,r,t){var a=this._validate(e,r,t,Gr.local.invalidDate||Gr.regionalOptions[""].invalidDate);return(Math.floor(this.toJD(a))+2)%this.daysInWeek()},extraInfo:function(e,r,t){return this._validate(e,r,t,Gr.local.invalidDate||Gr.regionalOptions[""].invalidDate),{}},add:function(e,r,t){return this._validate(e,this.minMonth,this.minDay,Gr.local.invalidDate||Gr.regionalOptions[""].invalidDate),this._correctAdd(e,this._add(e,r,t),r,t)},_add:function(e,r,t){if(this._validateLevel++,t==="d"||t==="w"){var a=e.toJD()+r*(t==="w"?this.daysInWeek():1),n=e.calendar().fromJD(a);return this._validateLevel--,[n.year(),n.month(),n.day()]}try{var i=e.year()+(t==="y"?r:0),o=e.monthOfYear()+(t==="m"?r:0),n=e.day(),l=function(f){for(;oc-1+f.minMonth;)i++,o-=c,c=f.monthsInYear(i)};t==="y"?(e.month()!==this.fromMonthOfYear(i,o)&&(o=this.newDate(i,e.month(),this.minDay).monthOfYear()),o=Math.min(o,this.monthsInYear(i)),n=Math.min(n,this.daysInMonth(i,this.fromMonthOfYear(i,o)))):t==="m"&&(l(this),n=Math.min(n,this.daysInMonth(i,this.fromMonthOfYear(i,o))));var s=[i,this.fromMonthOfYear(i,o),n];return this._validateLevel--,s}catch(u){throw this._validateLevel--,u}},_correctAdd:function(e,r,t,a){if(!this.hasYearZero&&(a==="y"||a==="m")&&(r[0]===0||e.year()>0!=r[0]>0)){var n={y:[1,1,"y"],m:[1,this.monthsInYear(-1),"m"],w:[this.daysInWeek(),this.daysInYear(-1),"d"],d:[1,this.daysInYear(-1),"d"]}[a],i=t<0?-1:1;r=this._add(e,t*n[0]+i*n[1],n[2])}return e.date(r[0],r[1],r[2])},set:function(e,r,t){this._validate(e,this.minMonth,this.minDay,Gr.local.invalidDate||Gr.regionalOptions[""].invalidDate);var a=t==="y"?r:e.year(),n=t==="m"?r:e.month(),i=t==="d"?r:e.day();return(t==="y"||t==="m")&&(i=Math.min(i,this.daysInMonth(a,n))),e.date(a,n,i)},isValid:function(e,r,t){this._validateLevel++;var a=this.hasYearZero||e!==0;if(a){var n=this.newDate(e,r,this.minDay);a=r>=this.minMonth&&r-this.minMonth=this.minDay&&t-this.minDay13.5?13:1),u=n-(s>2.5?4716:4715);return u<=0&&u--,this.newDate(u,s,l)},toJSDate:function(e,r,t){var a=this._validate(e,r,t,Gr.local.invalidDate||Gr.regionalOptions[""].invalidDate),n=new Date(a.year(),a.month()-1,a.day());return n.setHours(0),n.setMinutes(0),n.setSeconds(0),n.setMilliseconds(0),n.setHours(n.getHours()>12?n.getHours()+2:0),n},fromJSDate:function(e){return this.newDate(e.getFullYear(),e.getMonth()+1,e.getDate())}});var Gr=yue.exports=new mue;Gr.cdate=KM;Gr.baseCalendar=QM;Gr.calendars.gregorian=ek});var gue=z(()=>{var rk=xn(),Za=_n();rk(Za.regionalOptions[""],{invalidArguments:"Invalid arguments",invalidFormat:"Cannot format a date from another calendar",missingNumberAt:"Missing number at position {0}",unknownNameAt:"Unknown name at position {0}",unexpectedLiteralAt:"Unexpected literal at position {0}",unexpectedText:"Additional text found at end"});Za.local=Za.regionalOptions[""];rk(Za.cdate.prototype,{formatDate:function(e,r){return typeof e!="string"&&(r=e,e=""),this._calendar.formatDate(e||"",this,r)}});rk(Za.baseCalendar.prototype,{UNIX_EPOCH:Za.instance().newDate(1970,1,1).toJD(),SECS_PER_DAY:1440*60,TICKS_EPOCH:Za.instance().jdEpoch,TICKS_PER_DAY:1440*60*1e7,ATOM:"yyyy-mm-dd",COOKIE:"D, dd M yyyy",FULL:"DD, MM d, yyyy",ISO_8601:"yyyy-mm-dd",JULIAN:"J",RFC_822:"D, d M yy",RFC_850:"DD, dd-M-yy",RFC_1036:"D, d M yy",RFC_1123:"D, d M yyyy",RFC_2822:"D, d M yyyy",RSS:"D, d M yy",TICKS:"!",TIMESTAMP:"@",W3C:"yyyy-mm-dd",formatDate:function(e,r,t){if(typeof e!="string"&&(t=r,r=e,e=""),!r)return"";if(r.calendar()!==this)throw Za.local.invalidFormat||Za.regionalOptions[""].invalidFormat;e=e||this.local.dateFormat,t=t||{};for(var a=t.dayNamesShort||this.local.dayNamesShort,n=t.dayNames||this.local.dayNames,i=t.monthNumbers||this.local.monthNumbers,o=t.monthNamesShort||this.local.monthNamesShort,l=t.monthNames||this.local.monthNames,s=t.calculateWeek||this.local.calculateWeek,u=function(x,_){for(var k=1;w+k1},f=function(x,_,k,T){var q=""+_;if(u(x,T))for(;q.length1},A=function(R,N){var I=b(R,N),O=[2,3,I?4:2,I?4:2,10,11,20]["oyYJ@!".indexOf(R)+1],U=new RegExp("^-?\\d{1,"+O+"}"),Y=r.substring(q).match(U);if(!Y)throw(Za.local.missingNumberAt||Za.regionalOptions[""].missingNumberAt).replace(/\{0\}/,q);return q+=Y[0].length,parseInt(Y[0],10)},w=this,x=function(){if(typeof l=="function"){b("m");var R=l.call(w,r.substring(q));return q+=R.length,R}return A("m")},_=function(R,N,I,O){for(var U=b(R,O)?I:N,Y=0;Y-1){v=1,d=p;for(var P=this.daysInMonth(c,v);d>P;P=this.daysInMonth(c,v))v++,d-=P}return f>-1?this.fromJD(f):this.newDate(c,v,d)},determineDate:function(e,r,t,a,n){t&&typeof t!="object"&&(n=a,a=t,t=null),typeof a!="string"&&(n=a,a="");var i=this,o=function(l){try{return i.parseDate(a,l,n)}catch(c){}l=l.toLowerCase();for(var s=(l.match(/^c/)&&t?t.newDate():null)||i.today(),u=/([+-]?[0-9]+)\s*(d|w|m|y)?/g,f=u.exec(l);f;)s.add(parseInt(f[1],10),f[2]||"d"),f=u.exec(l);return s};return r=r?r.newDate():null,e=e==null?r:typeof e=="string"?o(e):typeof e=="number"?isNaN(e)||e===1/0||e===-1/0?r:i.today().add(e,"d"):i.newDate(e),e}})});var bue=z(()=>{var xu=_n(),LVe=xn(),tk=xu.instance();function Sx(e){this.local=this.regionalOptions[e||""]||this.regionalOptions[""]}Sx.prototype=new xu.baseCalendar;LVe(Sx.prototype,{name:"Chinese",jdEpoch:17214255e-1,hasYearZero:!1,minMonth:0,firstMonth:0,minDay:1,regionalOptions:{"":{name:"Chinese",epochs:["BEC","EC"],monthNumbers:function(e,r){if(typeof e=="string"){var t=e.match(DVe);return t?t[0]:""}var a=this._validateYear(e),n=e.month(),i=""+this.toChineseMonth(a,n);return r&&i.length<2&&(i="0"+i),this.isIntercalaryMonth(a,n)&&(i+="i"),i},monthNames:function(e){if(typeof e=="string"){var r=e.match(EVe);return r?r[0]:""}var t=this._validateYear(e),a=e.month(),n=this.toChineseMonth(t,a),i=["\u4E00\u6708","\u4E8C\u6708","\u4E09\u6708","\u56DB\u6708","\u4E94\u6708","\u516D\u6708","\u4E03\u6708","\u516B\u6708","\u4E5D\u6708","\u5341\u6708","\u5341\u4E00\u6708","\u5341\u4E8C\u6708"][n-1];return this.isIntercalaryMonth(t,a)&&(i="\u95F0"+i),i},monthNamesShort:function(e){if(typeof e=="string"){var r=e.match(PVe);return r?r[0]:""}var t=this._validateYear(e),a=e.month(),n=this.toChineseMonth(t,a),i=["\u4E00","\u4E8C","\u4E09","\u56DB","\u4E94","\u516D","\u4E03","\u516B","\u4E5D","\u5341","\u5341\u4E00","\u5341\u4E8C"][n-1];return this.isIntercalaryMonth(t,a)&&(i="\u95F0"+i),i},parseMonth:function(e,r){e=this._validateYear(e);var t=parseInt(r),a;if(isNaN(t))r[0]==="\u95F0"&&(a=!0,r=r.substring(1)),r[r.length-1]==="\u6708"&&(r=r.substring(0,r.length-1)),t=1+["\u4E00","\u4E8C","\u4E09","\u56DB","\u4E94","\u516D","\u4E03","\u516B","\u4E5D","\u5341","\u5341\u4E00","\u5341\u4E8C"].indexOf(r);else{var n=r[r.length-1];a=n==="i"||n==="I"}var i=this.toMonthIndex(e,t,a);return i},dayNames:["Sunday","Monday","Tuesday","Wednesday","Thursday","Friday","Saturday"],dayNamesShort:["Sun","Mon","Tue","Wed","Thu","Fri","Sat"],dayNamesMin:["Su","Mo","Tu","We","Th","Fr","Sa"],digits:null,dateFormat:"yyyy/mm/dd",firstDay:1,isRTL:!1}},_validateYear:function(e,r){if(e.year&&(e=e.year()),typeof e!="number"||e<1888||e>2111)throw r.replace(/\{0\}/,this.local.name);return e},toMonthIndex:function(e,r,t){var a=this.intercalaryMonth(e),n=t&&r!==a;if(n||r<1||r>12)throw xu.local.invalidMonth.replace(/\{0\}/,this.local.name);var i;return a?!t&&r<=a?i=r-1:i=r:i=r-1,i},toChineseMonth:function(e,r){e.year&&(e=e.year(),r=e.month());var 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a=this._validate(e,i,t,xu.local.invalidDate);e=this._validateYear(a.year()),r=a.month(),t=a.day();var n=this.isIntercalaryMonth(e,r),i=this.toChineseMonth(e,r),o=FVe(e,i,t,n);return tk.toJD(o.year,o.month,o.day)},fromJD:function(e){var r=tk.fromJD(e),t=RVe(r.year(),r.month(),r.day()),a=this.toMonthIndex(t.year,t.month,t.isIntercalary);return this.newDate(t.year,a,t.day)},fromString:function(e){var r=e.match(CVe),t=this._validateYear(+r[1]),a=+r[2],n=!!r[3],i=this.toMonthIndex(t,a,n),o=+r[4];return this.newDate(t,i,o)},add:function(e,r,t){var a=e.year(),n=e.month(),i=this.isIntercalaryMonth(a,n),o=this.toChineseMonth(a,n),l=Object.getPrototypeOf(Sx.prototype).add.call(this,e,r,t);if(t==="y"){var s=l.year(),u=l.month(),f=this.isIntercalaryMonth(s,o),c=i&&f?this.toMonthIndex(s,o,!0):this.toMonthIndex(s,o,!1);c!==u&&l.month(c)}return l}});var 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r=this._validate(t,this.minMonth,this.minDay,ic.local.invalidYear),t=r.year()+(r.year()<0?1:0);return t%4===3||t%4===-1},monthsInYear:function(e){return this._validate(e,this.minMonth,this.minDay,ic.local.invalidYear||ic.regionalOptions[""].invalidYear),13},weekOfYear:function(e,r,t){var a=this.newDate(e,r,t);return a.add(-a.dayOfWeek(),"d"),Math.floor((a.dayOfYear()-1)/7)+1},daysInMonth:function(e,r){var t=this._validate(e,r,this.minDay,ic.local.invalidMonth);return this.daysPerMonth[t.month()-1]+(t.month()===13&&this.leapYear(t.year())?1:0)},weekDay:function(e,r,t){return(this.dayOfWeek(e,r,t)||7)<6},toJD:function(e,r,t){var a=this._validate(e,r,t,ic.local.invalidDate);return e=a.year(),e<0&&e++,a.day()+(a.month()-1)*30+(e-1)*365+Math.floor(e/4)+this.jdEpoch-1},fromJD:function(e){var r=Math.floor(e)+.5-this.jdEpoch,t=Math.floor((r-Math.floor((r+366)/1461))/365)+1;t<=0&&t--,r=Math.floor(e)+.5-this.newDate(t,1,1).toJD();var a=Math.floor(r/30)+1,n=r-(a-1)*30+1;return 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t=this._validate(e,r,this.minDay,f1.local.invalidMonth);return this.daysPerMonth[t.month()-1]+(t.month()===2&&this.leapYear(t.year())?1:0)},weekDay:function(e,r,t){return(this.dayOfWeek(e,r,t)||7)<6},toJD:function(e,r,t){var a=this._validate(e,r,t,f1.local.invalidDate);return e=a.year(),r=a.month(),t=a.day(),e<0&&e++,r<=2&&(e--,r+=12),Math.floor(365.25*(e+4716))+Math.floor(30.6001*(r+1))+t-1524.5},fromJD:function(e){var r=Math.floor(e+.5),t=r+1524,a=Math.floor((t-122.1)/365.25),n=Math.floor(365.25*a),i=Math.floor((t-n)/30.6001),o=i-Math.floor(i<14?1:13),l=a-Math.floor(o>2?4716:4715),s=t-n-Math.floor(30.6001*i);return l<=0&&l--,this.newDate(l,o,s)}});f1.calendars.julian=sk});var Sue=z(()=>{var _o=_n(),GVe=xn();function fk(e){this.local=this.regionalOptions[e||""]||this.regionalOptions[""]}fk.prototype=new 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this._validate(e,r,t,_o.local.invalidDate),!0},extraInfo:function(e,r,t){var a=this._validate(e,r,t,_o.local.invalidDate),n=a.toJD(),i=this._toHaab(n),o=this._toTzolkin(n);return{haabMonthName:this.local.haabMonths[i[0]-1],haabMonth:i[0],haabDay:i[1],tzolkinDayName:this.local.tzolkinMonths[o[0]-1],tzolkinDay:o[0],tzolkinTrecena:o[1]}},_toHaab:function(e){e-=this.jdEpoch;var r=uk(e+8+340,365);return[Math.floor(r/20)+1,uk(r,20)]},_toTzolkin:function(e){return e-=this.jdEpoch,[kue(e+20,20),kue(e+4,13)]},toJD:function(e,r,t){var a=this._validate(e,r,t,_o.local.invalidDate);return a.day()+a.month()*20+a.year()*360+this.jdEpoch},fromJD:function(e){e=Math.floor(e)+.5-this.jdEpoch;var r=Math.floor(e/360);e=e%360,e+=e<0?360:0;var t=Math.floor(e/20),a=e%20;return this.newDate(r,t,a)}});function uk(e,r){return e-r*Math.floor(e/r)}function kue(e,r){return uk(e-1,r)+1}_o.calendars.mayan=fk});var Lue=z(()=>{var oc=_n(),YVe=xn();function 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lc.baseCalendar;VVe(vk.prototype,{name:"Nepali",jdEpoch:17007095e-1,daysPerMonth:[31,31,32,32,31,30,30,29,30,29,30,30],hasYearZero:!1,minMonth:1,firstMonth:1,minDay:1,daysPerYear:365,regionalOptions:{"":{name:"Nepali",epochs:["BBS","ABS"],monthNames:["Baisakh","Jestha","Ashadh","Shrawan","Bhadra","Ashwin","Kartik","Mangsir","Paush","Mangh","Falgun","Chaitra"],monthNamesShort:["Bai","Je","As","Shra","Bha","Ash","Kar","Mang","Pau","Ma","Fal","Chai"],dayNames:["Aaitabaar","Sombaar","Manglbaar","Budhabaar","Bihibaar","Shukrabaar","Shanibaar"],dayNamesShort:["Aaita","Som","Mangl","Budha","Bihi","Shukra","Shani"],dayNamesMin:["Aai","So","Man","Bu","Bi","Shu","Sha"],digits:null,dateFormat:"dd/mm/yyyy",firstDay:1,isRTL:!1}},leapYear:function(e){return this.daysInYear(e)!==this.daysPerYear},weekOfYear:function(e,r,t){var a=this.newDate(e,r,t);return a.add(-a.dayOfWeek(),"d"),Math.floor((a.dayOfYear()-1)/7)+1},daysInYear:function(e){var r=this._validate(e,this.minMonth,this.minDay,lc.local.invalidYear);if(e=r.year(),typeof this.NEPALI_CALENDAR_DATA[e]=="undefined")return this.daysPerYear;for(var t=0,a=this.minMonth;a<=12;a++)t+=this.NEPALI_CALENDAR_DATA[e][a];return t},daysInMonth:function(e,r){return e.year&&(r=e.month(),e=e.year()),this._validate(e,r,this.minDay,lc.local.invalidMonth),typeof this.NEPALI_CALENDAR_DATA[e]=="undefined"?this.daysPerMonth[r-1]:this.NEPALI_CALENDAR_DATA[e][r]},weekDay:function(e,r,t){return this.dayOfWeek(e,r,t)!==6},toJD:function(e,r,t){var a=this._validate(e,r,t,lc.local.invalidDate);e=a.year(),r=a.month(),t=a.day();var n=lc.instance(),i=0,o=r,l=e;this._createMissingCalendarData(e);var s=e-(o>9||o===9&&t>=this.NEPALI_CALENDAR_DATA[l][0]?56:57);for(r!==9&&(i=t,o--);o!==9;)o<=0&&(o=12,l--),i+=this.NEPALI_CALENDAR_DATA[l][o],o--;return r===9?(i+=t-this.NEPALI_CALENDAR_DATA[l][0],i<0&&(i+=n.daysInYear(s))):i+=this.NEPALI_CALENDAR_DATA[l][9]-this.NEPALI_CALENDAR_DATA[l][0],n.newDate(s,1,1).add(i,"d").toJD()},fromJD:function(e){var r=lc.instance(),t=r.fromJD(e),a=t.year(),n=t.dayOfYear(),i=a+56;this._createMissingCalendarData(i);for(var o=9,l=this.NEPALI_CALENDAR_DATA[i][0],s=this.NEPALI_CALENDAR_DATA[i][o]-l+1;n>s;)o++,o>12&&(o=1,i++),s+=this.NEPALI_CALENDAR_DATA[i][o];var u=this.NEPALI_CALENDAR_DATA[i][o]-(s-n);return this.newDate(i,o,u)},_createMissingCalendarData:function(e){var r=this.daysPerMonth.slice(0);r.unshift(17);for(var t=e-1;t{var Nv=_n(),jVe=xn();function Cx(e){this.local=this.regionalOptions[e||""]||this.regionalOptions[""]}function Lx(e){var r=e-475;e<0&&r++;var t=.242197,a=t*r,n=t*(r+1),i=a-Math.floor(a),o=n-Math.floor(n);return i>o}Cx.prototype=new 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t=this._validate(e,r,this.minDay,Nv.local.invalidMonth);return this.daysPerMonth[t.month()-1]+(t.month()===12&&this.leapYear(t.year())?1:0)},weekDay:function(e,r,t){return this.dayOfWeek(e,r,t)!==5},toJD:function(e,r,t){var a=this._validate(e,r,t,Nv.local.invalidDate);e=a.year(),r=a.month(),t=a.day();var n=0;if(e>0)for(var i=1;i0?e-1:e)*365+n+this.jdEpoch-1},fromJD:function(e){e=Math.floor(e)+.5;var r=475+(e-this.toJD(475,1,1))/365.242197,t=Math.floor(r);t<=0&&t--,e>this.toJD(t,12,Lx(t)?30:29)&&(t++,t===0&&t++);var a=e-this.toJD(t,1,1)+1,n=a<=186?Math.ceil(a/31):Math.ceil((a-6)/30),i=e-this.toJD(t,n,1)+1;return this.newDate(t,n,i)}});Nv.calendars.persian=Cx;Nv.calendars.jalali=Cx});var Eue=z(()=>{var sc=_n(),WVe=xn(),Dx=sc.instance();function hk(e){this.local=this.regionalOptions[e||""]||this.regionalOptions[""]}hk.prototype=new 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#69738a;margin-top:8px;margin-right:-30px} diff --git a/gui/visualization.js b/gui/visualization.js new file mode 100644 index 00000000..7e9c46f0 --- /dev/null +++ b/gui/visualization.js @@ -0,0 +1,49 @@ +import { sequenceOffset } from './protocol.js'; + +export function visualizationUrl(row, request) { + // Native seq1 is target and seq2 is query; both structures run 5′ to 3′. + const structures = row.hybridDP?.split('&'); + if (structures?.length !== 2) throw new Error('The interaction has no dot-bracket structure.'); + const sequences = [], fullStructures = [], starts = []; + for (const [index, strand] of ['target', 'query'].entries()) { + const number = index + 1, start = request.parameters[index ? 'qIdxPos0' : 'tIdxPos0']; + const record = request[strand].records.find((record) => record.id.replaceAll(';', '_') === row[`id${number}`]); + if (!record) throw new Error('The interaction sequence was not found in this run.'); + if (start === 0) throw new Error('vaRRI requires nonzero sequence start indices. Choose a nonzero start index to visualize this pair.'); + const offset = sequenceOffset(row[`start${number}`], start), structure = structures[index]; + const end = sequenceOffset(row[`end${number}`], start); + if (offset < 0 || end >= record.sequence.length || structure.length !== end - offset + 1 || /[^.()]/.test(structure)) throw new Error('The interaction structure does not match its sequence coordinates.'); + sequences.push(record.sequence); starts.push(start); + fullStructures.push('.'.repeat(offset) + structure + '.'.repeat(record.sequence.length - end - 1)); + } + const url = new URL('https://backofenlab.github.io/vaRRI/'); + url.search = new URLSearchParams({ + sequence: sequences.join('&'), structure: fullStructures.join('&'), + seqName1: row.id1, seqName2: row.id2, startIndex1: starts[0], startIndex2: starts[1], + showRenderingOnly: 'true', forceLayout: 'false', forceLayoutLinearRRI: 'true', + cropping: 2 + }); + return url.href; +} + +export class InteractionVisualization { + constructor(root) { + this.frame = root.querySelector('[data-role=varri-frame]'); this.link = root.querySelector('[data-role=varri-link]'); + this.status = root.querySelector('[data-role=visualization-status]'); + } + clear() { + this.frame.removeAttribute('src'); this.frame.hidden = true; + this.link.removeAttribute('href'); this.link.hidden = true; + this.status.textContent = 'Select View on an interaction to visualize it.'; + } + show(row, request) { + this.clear(); + try { + const url = visualizationUrl(row, request); + this.frame.src = url; this.frame.hidden = false; + const fullUrl = new URL(url); fullUrl.searchParams.delete('showRenderingOnly'); + this.link.href = fullUrl.href; this.link.hidden = false; + this.status.textContent = `${row.id1} (${row.start1}–${row.end1}) & ${row.id2} (${row.start2}–${row.end2}), ${row.E.toFixed(2)} kcal/mol. If the viewer is unavailable, use Open in vaRRI to retry.`; + } catch (error) { this.status.textContent = error.message; } + } +} diff --git a/scripts/wasm/build.sh b/scripts/wasm/build.sh new file mode 100644 index 00000000..10499d68 --- /dev/null +++ b/scripts/wasm/build.sh @@ -0,0 +1,113 @@ +#!/usr/bin/env bash +# Build every linked dependency for wasm32; never reuse native libraries. +set -euo pipefail +repo=$(cd "$(dirname "$0")/../.." && pwd) +build=${WASM_BUILD_DIR:-"$repo/build-wasm"} +mkdir -p "$build" +build=$(cd "$build" && pwd) +# Keep legacy RNAlib headers out of Boost's -I path: ordinary -I searches take +# precedence over the -isystem ViennaRNA paths produced by IntaRNA's configure. +prefix="$build/deps/common" +jobs=${JOBS:-2} +for tool in emcc em++ emar emranlib emconfigure emmake curl pkg-config node python3; do + command -v "$tool" >/dev/null || { echo "Missing tool: $tool" >&2; exit 1; } +done +mkdir -p "$build/downloads" "$build/sources" "$prefix" "$build/site/wasm" +fetch() { + bash "$repo/scripts/wasm/download.sh" "$1" "$build/downloads/$2" "$3" +} +fetch https://zlib.net/fossils/zlib-1.3.1.tar.gz zlib-1.3.1.tar.gz \ + 9a93b2b7dfdac77ceba5a558a580e74667dd6fede4585b91eefb60f03b72df23 +fetch https://archives.boost.io/release/1.87.0/source/boost_1_87_0.tar.bz2 boost_1_87_0.tar.bz2 \ + af57be25cb4c4f4b413ed692fe378affb4352ea50fbe294a11ef548f4d527d89 +# CI supplies the newest stable 2.x manifest; local builds use the checked-in pin. +read -r vienna_version vienna_url vienna_sha256 < <( + python3 "$repo/scripts/wasm/vienna-release.py" --fields \ + --manifest "${WASM_VIENNA_RELEASE:-$repo/scripts/wasm/vienna-release.json}" +) +echo "Building ViennaRNA $vienna_version (SHA-256 $vienna_sha256)" +fetch "$vienna_url" "ViennaRNA-$vienna_version.tar.gz" "$vienna_sha256" +# Separate source, installed RNAlib and IntaRNA objects by archive identity so +# changing the release cannot reuse headers, libraries or objects from an old one. +vienna_id="vienna-$vienna_version-$vienna_sha256" +vienna_prefix="$build/deps/$vienna_id" +vienna_sources="$build/sources/$vienna_id" +intarna_build="$build/intarna-$vienna_id" + +# Keep pkg-config searches inside the WASM prefix, including configure probes. +export PKG_CONFIG_LIBDIR="$vienna_prefix/lib/pkgconfig:$prefix/lib/pkgconfig" +export PKG_CONFIG_PATH="$PKG_CONFIG_LIBDIR" +export CFLAGS='-O3 -fexceptions' +export CXXFLAGS='-O3 -fexceptions' +export CPPFLAGS="-I$vienna_prefix/include -I$prefix/include" +export LDFLAGS="-L$vienna_prefix/lib -L$prefix/lib -fexceptions" +if [[ ! -f "$prefix/lib/libz.a" ]]; then + tar -xzf "$build/downloads/zlib-1.3.1.tar.gz" -C "$build/sources" + (cd "$build/sources/zlib-1.3.1" + emconfigure ./configure --static --prefix="$prefix" + emmake make -j "$jobs" + emmake make install) +fi +if [[ ! -f "$prefix/.boost-1.87.0-js-exceptions-complete" ]]; then + tar -xjf "$build/downloads/boost_1_87_0.tar.bz2" -C "$build/sources" + (cd "$build/sources/boost_1_87_0" + ./bootstrap.sh --with-libraries=filesystem,program_options,regex,iostreams,serialization,system + ./b2 -j "$jobs" toolset=emscripten variant=release link=static threading=single \ + exception-handling=on exception-handling-method=js \ + --with-filesystem --with-program_options --with-regex --with-iostreams \ + --with-serialization --with-system cxxflags="-std=c++23 -fexceptions" \ + -sNO_BZIP2=1 -sNO_LZMA=1 -sNO_ZSTD=1 -sZLIB_INCLUDE="$prefix/include" \ + -sZLIB_LIBPATH="$prefix/lib" --prefix="$prefix" install) + touch "$prefix/.boost-1.87.0-js-exceptions-complete" +fi +if [[ ! -f "$vienna_prefix/.complete" ]]; then + mkdir -p "$vienna_sources" + tar -xzf "$build/downloads/ViennaRNA-$vienna_version.tar.gz" -C "$vienna_sources" + (cd "$vienna_sources/ViennaRNA-$vienna_version" + CPPFLAGS="$CPPFLAGS -I$PWD/src" emconfigure ./configure --host=wasm32-unknown-emscripten --prefix="$vienna_prefix" \ + --disable-shared --enable-static --disable-openmp --disable-pthreads \ + --disable-lto --disable-simd --disable-vectorize --disable-mpfr \ + --without-svm --without-gsl --without-swig --without-perl --without-python \ + --without-doc --without-cla --without-check --without-kinfold \ + --without-forester --without-rnalocmin --without-rnaxplorer + emmake make -C src/ViennaRNA -j "$jobs" + emmake make -C src/ViennaRNA install + emmake make install-pkgconfigDATA) + touch "$vienna_prefix/.complete" +fi + +# Legacy Autoconf probes declare exit()/inflateEnd() with the wrong signatures, +# which wasm-ld rejects. Verify real dependency APIs before caching those probes. +em++ -std=c++23 -O2 -fexceptions -I"$vienna_prefix/include" -I"$prefix/include" \ + "$repo/scripts/wasm/dependency-probe.cpp" -L"$vienna_prefix/lib" -L"$prefix/lib" \ + -lboost_filesystem -lboost_system -lboost_program_options -lboost_regex \ + -lboost_iostreams -lboost_serialization -lRNA -lz -o "$build/dependency-probe.js" +node "$build/dependency-probe.js" +export ac_cv_lib_boost_system_exit=yes +export ac_cv_lib_boost_filesystem_exit=yes +export ac_cv_lib_boost_program_options_exit=yes +export ac_cv_lib_boost_regex_exit=yes +export ac_cv_lib_boost_iostreams_exit=yes +export ac_cv_lib_z_inflateEnd=yes +# RNAlib's .pc embeds a native-only -Wl,-fno-lto; this is a static WASM build. +export VRNA_LIBS="-L$vienna_prefix/lib -lRNA -lm" + +# Use the native Autotools source lists and CLI entry point, with a JS output. +(cd "$repo" && bash autotools-init.sh) +mkdir -p "$intarna_build" +(cd "$intarna_build" + CXXFLAGS="$CXXFLAGS -Werror=inconsistent-missing-override" CPPFLAGS="-I$intarna_build/src -I$repo/src $CPPFLAGS" emconfigure "$repo/configure" --host=wasm32-unknown-emscripten \ + --disable-multithreading --disable-log-coloring --with-mdspan=kokkos \ + --with-vrna="$vienna_prefix" --with-boost="$prefix" \ + --with-boost-libdir="$prefix/lib" --with-zlib="$prefix" + emmake make -C src -j "$jobs" EXEEXT=.js \ + LDFLAGS="$LDFLAGS -sMODULARIZE=1 -sEXPORT_ES6=1 -sEXPORT_NAME=createIntaRNA -sENVIRONMENT=web,worker,node -sINVOKE_RUN=0 -sEXIT_RUNTIME=1 -sEXPORTED_RUNTIME_METHODS=FS,callMain -sALLOW_MEMORY_GROWTH=1 -sMAXIMUM_MEMORY=1073741824 -sSTACK_SIZE=8388608" + cp src/bin/IntaRNA.js "$build/site/wasm/intarna.js" + cp src/bin/IntaRNA.wasm "$build/site/wasm/intarna.wasm") +# ES modules also work in Node smoke tests without changing package scope. +printf '{"type":"module"}\n' > "$build/site/wasm/package.json" +node "$repo/scripts/wasm/write-build-info.mjs" "$repo" "$build/site" \ + "$(emcc -dumpversion)" "$(git -C "$repo" rev-parse HEAD)" \ + "$(git -C "$repo" status --porcelain --untracked-files=no)" \ + "$vienna_version" "$vienna_url" "$vienna_sha256" +echo "WASM assets: $build/site/wasm" diff --git a/scripts/wasm/dependency-probe.cpp b/scripts/wasm/dependency-probe.cpp new file mode 100644 index 00000000..bf428cb2 --- /dev/null +++ b/scripts/wasm/dependency-probe.cpp @@ -0,0 +1,26 @@ +// Link real APIs rather than the legacy configure macros' misdeclared exit(). +#include +#include +#include +#include +#include +#include +#include +extern "C" { +#include +} +int main() { + std::stringstream data; + boost::archive::binary_oarchive archive(data); + archive << 42; + boost::iostreams::filtering_ostream compressed; + compressed.push(boost::iostreams::gzip_compressor()); + compressed.push(data); + compressed << "RNA"; + compressed.reset(); + boost::program_options::options_description options("probe"); + options.add_options()("query", "RNA sequence"); + vrna_md_t model; + vrna_md_set_default(&model); + return boost::filesystem::exists("/") && boost::regex_match("RNA", boost::regex("RNA")) ? 0 : 1; +} diff --git a/scripts/wasm/download.sh b/scripts/wasm/download.sh new file mode 100644 index 00000000..359f7142 --- /dev/null +++ b/scripts/wasm/download.sh @@ -0,0 +1,23 @@ +#!/usr/bin/env bash +# Cache only verified dependency archives; recover from invalid cached responses. +set -euo pipefail +url=$1 +destination=$2 +checksum=$3 + +# Verify existing archives too, including caches from earlier build scripts. +if [[ -f "$destination" ]]; then + if printf '%s %s\n' "$checksum" "$destination" | sha256sum --check --status; then + echo "$destination: OK (cached)" + exit 0 + fi + echo "Discarding invalid cached archive: $destination" >&2 + rm -- "$destination" +fi + +# Never promote HTTP error pages or incomplete transfers to the download cache. +partial="$destination.part" +trap 'rm -f -- "$partial"' EXIT +curl --fail --location --retry 3 "$url" -o "$partial" +printf '%s %s\n' "$checksum" "$partial" | sha256sum --check - +mv -- "$partial" "$destination" diff --git a/scripts/wasm/requirements-browser.txt b/scripts/wasm/requirements-browser.txt new file mode 100644 index 00000000..718f8e96 --- /dev/null +++ b/scripts/wasm/requirements-browser.txt @@ -0,0 +1 @@ +playwright==1.64.0 diff --git a/scripts/wasm/smoke-protocol.mjs b/scripts/wasm/smoke-protocol.mjs new file mode 100644 index 00000000..9dd90369 --- /dev/null +++ b/scripts/wasm/smoke-protocol.mjs @@ -0,0 +1,72 @@ +// Integration coverage of browser argument translation against the real CLI. +import assert from 'node:assert/strict'; +import { readFileSync } from 'node:fs'; +import { resolve } from 'node:path'; +import { pathToFileURL } from 'node:url'; +import { DEFAULTS, CSV_COLUMNS, EVALUATION_EXAMPLE, prepareRequest, makeParameterDocument } from '../../gui/protocol.js'; +import { CSV_CATALOG } from '../../gui/columns.js'; +import { parseResults, projectCsv } from '../../gui/results.js'; +import { archiveFiles } from '../../gui/archive.js'; +const asset = resolve(process.argv[2] || 'build-wasm/site/wasm/intarna.js'); +const { default: createIntaRNA } = await import(pathToFileURL(asset)); +const compiledVersion = readFileSync(new URL('../build-info.txt', pathToFileURL(asset)), 'utf8'); +async function run(input, format = 'C') { + const request = prepareRequest({ ...DEFAULTS, ...input }); + const diagnostics = []; + const module = await createIntaRNA({ noInitialRun: true, locateFile: () => new URL('./intarna.wasm', pathToFileURL(asset)).href, print: (line) => diagnostics.push(line), printErr: (line) => diagnostics.push(line) }); + module.FS.writeFile('/parameter.json', JSON.stringify(makeParameterDocument(request, format))); + module.FS.mkdir('/output'); + const args = ['--parameterFile=/parameter.json']; + assert.equal(module.callMain(args), 0, `${args.join(' ')}\n${diagnostics.join('\n')}`); + const text = module.FS.readFile(format === 'C' ? '/results.csv' : '/report.txt', { encoding: 'utf8' }); + return { rows: format === 'C' ? parseResults(text) : [], text, fs: module.FS, request }; +} +const defaults = await run({ parameters: { outNumber: 10 } }); +assert.equal(defaults.rows.length, 10); +assert.equal(defaults.rows[0].E, -21.4); +const shifted = await run({ qIdxPos0: -3, tIdxPos0: -5 }); +assert.deepEqual(['start1', 'end1', 'start2', 'end2'].map((key) => shifted.rows[0][key]), [-5, 5, -3, 7]); +const multi = await run({ query: '>q1\nGGGAGGAGGG\n>q2\nGGGAGGAGGG', target: '>t1\nCCCUCCUCCC\n>t2\nCCCUCCUCCC', outputs: ['qMinE', 'tMinE'] }); +assert.equal(multi.rows.length, 4); +assert.ok(multi.rows.every((row) => row.deltaE === 0)); +assert.equal(multi.fs.readdir('/output').filter((name) => name.endsWith('.csv')).length, 8); +const pairwise = await run({ query: '>q1\nGGGAGGAGGG\n>q2\nGGGAGGAGGG', target: '>t1\nCCCUCCUCCC\n>t2\nCCCUCCUCCC', parameters: { outPairwise: true } }); +assert.equal(pairwise.rows.length, 2); +const evaluation = await run({ task: 'evaluation', rri: EVALUATION_EXAMPLE + ':1|||||||||&2|||||||||', outputs: ['qAcc', 'tPu'], csvColumns: CSV_CATALOG.map((c) => c.key) }); +assert.equal(evaluation.rows.length, 2); +assert.equal(evaluation.rows[0].E, -21.4); +assert.equal(evaluation.rows[0].seedE, 'NAN'); +assert.ok((await run({ task: 'evaluation', rri: EVALUATION_EXAMPLE }, 'D')).text.includes('-21.4')); +assert.ok((await run({ task: 'evaluation', rri: EVALUATION_EXAMPLE }, 'E')).text.length > 0); +const probabilities = await run({ parameters: { model: 'P' }, csvColumns: CSV_CATALOG.map((c) => c.key), outputs: ['bpProb', 'bpsvg', 'qSpotProb', 'tSpotProb', 'spotProb', 'pMinE'] }); +assert.equal(probabilities.rows.length, 1); +assert.ok(probabilities.fs.readFile('/output/bpsvg.svg', { encoding: 'utf8' }).includes('= 1); +console.log('Browser protocol: native-reference prediction/evaluation, signed coordinates, multi-FASTA, all columns, imported accessibility, energy/seed/helix/SHAPE options and output files passed'); + +// Execute exported parameter files in fresh engines with only archived inputs. +// Byte comparisons cover selected CSV, per-record extra files and report modes. +async function replayArchive(input) { + const original = await run(input), { request, fs } = original; + const outputs = fs.readdir('/output').filter((name) => name !== '.' && name !== '..').map((name) => ({ name, text: fs.readFile(`/output/${name}`, { encoding: 'utf8' }) })); + const reports = [['normal', 'N'], ['detailed', 'D'], ['ensemble', 'E']].filter(([key]) => request.outputs.includes(key)); + for (const [key, format] of reports) outputs.push({ name: `intarna-${key}.txt`, text: (await run(input, format)).text }); + const files = archiveFiles(request, { csv: original.text, files: outputs }, compiledVersion); + for (const config of ['parameters', ...reports.map(([key]) => key)]) { + const diagnostics = []; + const module = await createIntaRNA({ noInitialRun: true, locateFile: () => new URL('./intarna.wasm', pathToFileURL(asset)).href, print: (line) => diagnostics.push(line), printErr: (line) => diagnostics.push(line) }); + module.FS.writeFile('/parameter.json', files.find((file) => file.name === 'parameter.json').text); + const arguments_ = ['--parameterFile=/parameter.json', `--out=${config === 'parameters' ? 'intarna-interactions.csv' : `intarna-${config}.txt`}`]; + if (config !== 'parameters') arguments_.push(`--outMode=${reports.find(([key]) => key === config)[1]}`, `--outCsvCols=${CSV_COLUMNS}`, "--outCsvSort", ""); + assert.equal(module.callMain(arguments_), 0, diagnostics.join('\n')); + const expected = config === 'parameters' ? [{ name: 'intarna-interactions.csv', text: projectCsv(original.text, request.csvColumns) }, ...outputs.filter((file) => !file.name.startsWith('intarna-'))] : outputs.filter((file) => file.name === `intarna-${config}.txt`); + for (const file of expected) assert.equal(module.FS.readFile(`/${file.name}`, { encoding: 'utf8' }), file.text, file.name); + } +} +await replayArchive({ query: '>q1\nGGGAGGAGGG\n>q2\nGGGAGGAGGG', qIdxPos0: -3, tIdxPos0: -5, parameters: { temperature: 20, outNumber: 3, noSeed: true }, outputs: ['qMinE', 'tPu', 'normal', 'detailed'], csvColumns: ['id2', 'E'] }); +await replayArchive({ task: 'evaluation', rri: EVALUATION_EXAMPLE, parameters: { qShape: '1 0.2\n2 0.3' }, outputs: ['detailed', 'ensemble'] }); +await replayArchive({ parameters: { qAcc: 'P', qAccFile: accessibility.fs.readFile('/output/qPu.csv', { encoding: 'utf8' }), model: 'P' }, outputs: ['bpProb', 'bpsvg'], csvColumns: ['E'] }); +console.log('ZIP parameter replay: CSV, multi-FASTA/signed indices, non-default energy/seed options, SHAPE/accessibility imports, per-record outputs, probability SVG and ASCII/detailed/ensemble reports are byte-identical'); diff --git a/scripts/wasm/smoke.mjs b/scripts/wasm/smoke.mjs new file mode 100644 index 00000000..5bab9756 --- /dev/null +++ b/scripts/wasm/smoke.mjs @@ -0,0 +1,45 @@ +// Exercise the actual CLI and RNAlib in fresh WASM instances. +import assert from 'node:assert/strict'; +import { resolve } from 'node:path'; +import { pathToFileURL } from 'node:url'; +const asset = resolve(process.argv[2] || 'build-wasm/site/wasm/intarna.js'); +const { default: createIntaRNA } = await import(pathToFileURL(asset)); +async function predict(args) { + const diagnostics = []; + const module = await createIntaRNA({ + noInitialRun: true, + locateFile: () => new URL('./intarna.wasm', pathToFileURL(asset)).href, + print: (line) => diagnostics.push(line), + printErr: (line) => diagnostics.push(line), + }); + const code = module.callMain([...args, '--outMode=C', '--outOverlap=B', '--out=/results.csv']); + return { module, code, diagnostics: diagnostics.join('\n') }; +} +const columns = '--outCsvCols=id1,start1,end1,id2,start2,end2,E'; +const first = await predict([ + '--query=GGGAGGAGGG', '--target=CCCUCCUCCC', '--outNumber=10', columns, +]); +assert.equal(first.code, 0, first.diagnostics); +const csv = first.module.FS.readFile('/results.csv', { encoding: 'utf8' }); +assert.match(csv, /^id1;start1;end1;id2;start2;end2;E\n/); +// Reference from the native CLI with the same Turner/default-accessibility model. +assert.equal(csv.trim().split('\n')[1], 'target;1;10;query;1;10;-21.4'); +assert.equal(csv.trim().split('\n').length, 11); + +// Hairpin-forming strands check nonzero accessibility costs as well as pairing. +const structured = await predict([ + '--query=GGGAAACCCGGGAAACCC', '--target=GGGUUUCCCGGGUUUCCC', + '--outNumber=3', `${columns},ED1,ED2`, +]); +assert.equal(structured.code, 0, structured.diagnostics); +const structuredCsv = structured.module.FS.readFile('/results.csv', { encoding: 'utf8' }); +assert.equal(structuredCsv.trim().split('\n')[1], 'target;1;18;query;1;18;-28.04;4.6;4.86'); +assert.equal(structuredCsv.trim().split('\n').length, 4); + +// Input errors must travel through the C++ exception handler, not trap WASM. +const invalid = await predict(['--query=ACGU!ACGU', '--target=ACGUACGU', columns]); +assert.notEqual(invalid.code, 0); +assert.match(invalid.diagnostics, /error/i); +// The CLI's nonzero exit status is local to the deliberately invalid instance. +process.exitCode = 0; +console.log('WASM CLI: native-reference coordinates/energy, structured accessibility, suboptimals and C++ error handling passed'); diff --git a/scripts/wasm/stage.sh b/scripts/wasm/stage.sh new file mode 100644 index 00000000..62b6cb3c --- /dev/null +++ b/scripts/wasm/stage.sh @@ -0,0 +1,82 @@ +#!/usr/bin/env bash +# Package only the static application, matched WASM assets and distribution notices. +set -euo pipefail +repo=$(cd "$(dirname "$0")/../.." && pwd) +build=${WASM_BUILD_DIR:-"$repo/build-wasm"} +site="$build/site" +test -s "$site/wasm/intarna.js" +test -s "$site/wasm/intarna.wasm" +# Select notices from the archive used by these assets, including dlib upgrades. +read -r vienna_version vienna_sha256 dlib_directory < <(python3 - "$site" "$build" <<'PYSOURCE' +import json, re, sys +from pathlib import Path +site, build = map(Path, sys.argv[1:]) +metadata = json.loads((site / "build-info.json").read_text()) +archive = metadata["viennarnaArchive"] +version, digest = archive["version"], archive["sha256"] +if version != metadata["viennarna"] or not re.fullmatch(r"2\.\d+\.\d+", version) or not re.fullmatch(r"[0-9a-f]{64}", digest): + raise SystemExit("Invalid compiled ViennaRNA archive identity") +source = build / "sources" / f"vienna-{version}-{digest}" / f"ViennaRNA-{version}" +dlib = list((source / "src").glob("dlib-*/dlib/LICENSE.txt")) +if len(dlib) != 1 or not re.fullmatch(r"dlib-[0-9.]+", dlib[0].parent.parent.name): + raise SystemExit("Expected one bundled dlib license in the compiled ViennaRNA source") +print(version, digest, dlib[0].parent.parent.name) +PYSOURCE +) +vienna_source="$build/sources/vienna-$vienna_version-$vienna_sha256/ViennaRNA-$vienna_version" +mkdir -p "$site/licenses" +cp -R "$repo/gui/assets" "$repo/gui/examples" "$repo/gui/vendor" "$site/" +test "$(sha256sum "$repo/gui/vendor/plotly-cartesian.min.js" | cut -d' ' -f1)" = "aaf12ff1d4671f7e93f6df4291651ab4ca6b76c0ea5f1576ec1030e3c2819a20" +test "$(sha256sum "$repo/gui/vendor/plotly.css" | cut -d' ' -f1)" = "3bcf2679b557067d8a3492b74092e946544d1cb8b2a72f278bcba95df59afd33" +for file in index.html styles.css app.js mark.svg protocol.js runner.js results.js options.js columns.js archive.js sessions.js visualization.js output-visualization.js parameter-file.js uploads.js; do + cp "$repo/gui/$file" "$site/$file" +done +cp "$repo/gui/intarna-worker.js" "$site/intarna-worker.js" +touch "$site/.nojekyll" +cp "$repo/src/bin/nlohmann/LICENSE.MIT" "$site/licenses/nlohmann-json.txt" +cp "$repo/gui/vendor/plotly-LICENSE.txt" "$site/licenses/Plotly.txt" +cp "$repo/LICENSE" "$site/licenses/IntaRNA.txt" +cp "$repo/src/easylogging++.LICENCE.txt" "$site/licenses/easylogging.txt" +cp "$repo/src/mdspan/LICENSE" "$site/licenses/mdspan.txt" +cp "$build/sources/boost_1_87_0/LICENSE_1_0.txt" "$site/licenses/Boost.txt" +cp "$build/sources/zlib-1.3.1/zlib.h" "$site/licenses/zlib.h" +cp "$vienna_source/COPYING" "$site/licenses/ViennaRNA.txt" +cp "$vienna_source/src/$dlib_directory/dlib/LICENSE.txt" "$site/licenses/dlib.txt" +cp "$vienna_source/src/ViennaRNA/plotting/naview/naview.c" "$site/licenses/naview.c" +emscripten_dir=$(dirname "$(command -v emcc)") +cp "$emscripten_dir/LICENSE" "$site/licenses/Emscripten.txt" +cp "$emscripten_dir/system/lib/libc/musl/COPYRIGHT" "$site/licenses/musl.txt" +for library in libcxx libcxxabi libunwind compiler-rt; do + cp "$emscripten_dir/system/lib/$library/LICENSE.TXT" "$site/licenses/$library.txt" +done +cat > "$site/licenses/index.html" <IntaRNA licenses +

IntaRNA and third-party notices

+

IntaRNA: Bioinformatics Group of Prof. Backofen, University of Freiburg.
ViennaRNA: authors and Institute for Theoretical Chemistry, University of Vienna.

+

This distribution uses ViennaRNA $vienna_version, Boost 1.87.0, zlib 1.3.1, bundled dlib ${dlib_directory#dlib-}, Plotly.js 4.1.2, Kokkos mdspan, Easylogging++ and the Emscripten 4.0.23 runtime.

+

Build provenance · Back to IntaRNA

+ +HTML +# Provenance belongs to the compiled assets, never the later staging revision. +python3 - "$site" <<'PYINFO' +import hashlib, json, sys +from pathlib import Path +site = Path(sys.argv[1]) +metadata = json.loads((site / "build-info.json").read_text()) +if not (site / "build-info.txt").is_file(): + raise SystemExit("Missing compiled version text") +for name, digest in metadata["sha256"].items(): + if hashlib.sha256((site / "wasm" / name).read_bytes()).hexdigest() != digest: + raise SystemExit(f"Mismatched engine: {name}") +PYINFO +echo "Static site: $site" diff --git a/scripts/wasm/test-browser.py b/scripts/wasm/test-browser.py new file mode 100644 index 00000000..5152f68f --- /dev/null +++ b/scripts/wasm/test-browser.py @@ -0,0 +1,666 @@ +"""Exercise the staged browser interface with real WASM at a nested URL.""" +import argparse +from pathlib import Path +from io import BytesIO +import re +import json +from urllib.parse import parse_qs, urljoin, urlparse +from zipfile import ZipFile +from playwright.sync_api import sync_playwright, expect + +parser = argparse.ArgumentParser(description=__doc__) +parser.add_argument('url') +parser.add_argument('--browser', choices=['chromium', 'firefox'], default='chromium') +parser.add_argument('--screenshot') +args = parser.parse_args() + +with sync_playwright() as playwright: + browser = getattr(playwright, args.browser).launch(headless=True) + page = browser.new_page(viewport={'width': 1440, 'height': 1100}) + errors = [] + csp_errors = [] + page.on('pageerror', lambda error: errors.append(str(error))) + page.on('console', lambda message: csp_errors.append(message.text) if message.type == 'error' and ('Content Security Policy' in message.text or 'Refused to apply inline style' in message.text) else None) + # Keep browser tests offline and inspect the exact third-party URL separately. + visualization_urls = [] + def viewer(route): + visualization_urls.append(route.request.url) + route.fulfill(content_type='text/html', body='

vaRRI viewer

') + page.route('https://backofenlab.github.io/vaRRI/**', viewer) + page.goto(args.url) + page.wait_for_load_state('networkidle') + compute = page.locator('#compute') + status = page.locator('#result-status') + sessions = page.locator('.session') + active = page.locator('.session:has([data-role=panel]:not([hidden]))') + rows = active.locator('tbody tr') + + def open_group(key): + page.locator('#tab-' + key).click() + expect(page.locator('#' + key)).to_be_visible() + expect(page.locator('#tab-' + key)).to_have_attribute('aria-selected', 'true') + assert page.locator('.parameter-group:visible').count() == 1 + + def load_example(task='prediction'): + page.locator('#examples-menu summary').click() + page.get_by_role('button', name='Evaluate a duplex' if task == 'evaluation' else 'Short duplex', exact=False).click() + expect(page.locator('#query')).to_have_value('>query\nGGGAGGAGGG\n') + + def download_archive(session=None): + with page.expect_download() as downloaded: + (active if session is None else session).locator('[data-role=download-zip]').click() + with ZipFile(BytesIO(Path(downloaded.value.path()).read_bytes())) as archive: + assert archive.testzip() is None + return {name: archive.read(name).decode() for name in archive.namelist()} + + def fill(key, value): + parent = page.locator('#' + key).evaluate('node => node.closest(".parameter-group")?.id') + if parent: + open_group(parent) + page.locator('#' + key).fill(str(value)) + + def predict(): + count = sessions.count() + compute.click() + expect(status).to_contain_text('complete:', timeout=120000) + expect(page.locator('#input-error')).not_to_be_visible() + expect(sessions).to_have_count(count + 1) + + expect(page.locator('#query')).to_have_value('') + expect(page.locator('#target')).to_have_value('') + expect(page.locator('#query')).to_have_attribute('placeholder', '>query\nGGGAGGAGGG') + compute.click() + expect(page.locator('#input-error')).to_contain_text('enter a sequence') + metadata = page.request.get(urljoin(args.url, 'build-info.json')).json() + vienna_version = metadata['viennarna'] + assert re.fullmatch(r'2\.\d+\.\d+', vienna_version) + assert metadata['viennarnaArchive']['version'] == vienna_version + expect(page.locator('#version-info')).to_contain_text(f'ViennaRNA {vienna_version}') + for logo in page.locator('.site-header img').all(): + assert logo.evaluate('node => node.complete && node.naturalWidth > 0') + for key in ['seed-options', 'output-options', 'csv-options', 'interaction-options', 'query-options', 'target-options', 'general-options', 'sequence-input']: + open_group(key) + + expect(page.get_by_role('radio', name='Prediction')).to_be_checked() + expect(page.get_by_role('radio', name='Evaluation')).to_be_visible() + page.get_by_role('radio', name='Prediction').focus() + page.keyboard.press('ArrowRight') + expect(page.get_by_role('radio', name='Evaluation')).to_be_checked() + expect(page.locator('#task-help')).to_contain_text('Evaluate supplied structures') + page.keyboard.press('ArrowLeft') + expect(page.get_by_role('radio', name='Prediction')).to_be_checked() + page.locator('#examples-menu summary').click() + expect(page.get_by_role('button', name='Short duplex', exact=False)).to_be_visible() + expect(page.get_by_role('button', name='Evaluate a duplex', exact=False)).not_to_be_visible() + page.get_by_role('radio', name='Evaluation').check() + expect(page.get_by_role('button', name='Evaluate a duplex', exact=False)).to_be_visible() + expect(page.get_by_role('button', name='Short duplex', exact=False)).not_to_be_visible() + page.get_by_role('radio', name='Prediction').check() + page.locator('#examples-menu summary').click() + + # Tabs support keyboard navigation and wrap without page overflow. + page.locator('#tab-sequence-input').focus() + page.keyboard.press('ArrowRight') + expect(page.locator('#tab-seed-options')).to_be_focused() + expect(page.locator('#seed-options')).to_be_visible() + page.keyboard.press('End') + expect(page.locator('#tab-general-options')).to_be_focused() + page.keyboard.press('Home') + expect(page.locator('#tab-sequence-input')).to_be_focused() + + # Review layout, task defaults and modes work with native parameters. + assert page.locator('[role=tab]').all_text_contents() == ['Sequences', 'Seed', 'Output', 'CSV', 'Model & Energy', 'Query', 'Target', 'CLI-only'] + expect(page.locator('.brand')).to_contain_text('IntaRNA package') + expect(page.locator('#results-title')).to_have_text('Results') + expect(page.locator('#outNumber')).to_have_value('10') + assert page.locator('.compute-bar').evaluate('node => node.firstElementChild.id') == 'compute' + assert page.locator('.sequence-meta').first.evaluate('node => node.firstElementChild.tagName') == 'LABEL' + fill('query', '>named\tignored description\n' + 'G' * 1000 + '\n' * 20 + 'GG') + expect(page.locator('#query-warning')).to_contain_text('ignoring FASTA description') + expect(page.locator('#query-warning')).to_contain_text('named') + assert page.locator('#query').evaluate('node => node.scrollWidth > node.clientWidth && node.scrollHeight > node.clientHeight') + fill('query', '>named \nGGGAGGAGGG') + expect(page.locator('#query-warning')).not_to_be_visible() + + for prefix, group in [('q', 'query-options'), ('t', 'target-options')]: + open_group(group) + # Each explicit row shares label height, including wrapped labels, and + # compact controls stay left-aligned instead of filling the panel. + for keys in [[prefix + suffix for suffix in ['Set', 'Region', 'IntLenMax', 'IntLoopMax', 'RegionLenMax']], [prefix + suffix for suffix in ['Acc', 'AccW', 'AccL', 'PfScale']]]: + tops = [page.locator('#' + key).bounding_box()['y'] for key in keys] + assert max(tops) - min(tops) < 1, tops + label_bottoms = [page.locator('#' + key).locator('xpath=preceding-sibling::label').bounding_box()['y'] + page.locator('#' + key).locator('xpath=preceding-sibling::label').bounding_box()['height'] for key in keys] + assert max(label_bottoms) - min(label_bottoms) < 1, label_bottoms + first = page.locator('#' + prefix + 'Set').bounding_box() + second = page.locator('#' + prefix + 'Region').bounding_box() + assert 8 <= second['x'] - first['x'] - first['width'] <= 20 + assert page.locator('#' + prefix + 'AccW').bounding_box()['width'] <= 224 + expect(page.locator('#' + prefix + 'AccFile')).to_be_disabled() + page.locator('#' + prefix + 'Acc').select_option('P') + expect(page.locator('#' + prefix + 'AccFile')).to_be_enabled() + for suffix in ['AccW', 'AccL']: + expect(page.locator('#' + prefix + suffix)).to_be_disabled() + page.locator('#' + prefix + 'Acc').select_option('N') + for suffix in ['AccW', 'AccL', 'AccConstr', 'AccFile', 'PfScale', 'Shape', 'ShapeMethod', 'ShapeConversion']: + expect(page.locator('#' + prefix + suffix)).to_be_disabled() + expect(page.locator('input[data-for="' + prefix + 'Shape"]')).to_be_disabled() + page.locator('#' + prefix + 'Acc').select_option('C') + expect(page.locator('#' + prefix + 'Shape')).to_be_enabled() + page.locator('#accNoLP-target').check() + expect(page.locator('#accNoLP')).to_be_checked() + open_group('query-options') + page.locator('#accNoLP').uncheck() + expect(page.locator('#accNoLP-target')).not_to_be_checked() + open_group('interaction-options') + expect(page.locator('#helixMinBP')).to_be_disabled() + page.locator('#model').select_option('B') + expect(page.locator('#helixMinBP')).to_be_enabled() + page.locator('#model').select_option('X') + expect(page.locator('#helixMinBP')).to_be_disabled() + open_group('seed-options') + expect(page.locator('#seedTQ')).to_be_disabled() + seed_box = page.locator('#seed-mode').bounding_box() + explicit_box = page.locator('#seedTQ').bounding_box() + assert abs(seed_box['y'] - explicit_box['y']) < 5 + assert seed_box['x'] + seed_box['width'] < explicit_box['x'] + assert seed_box['width'] < explicit_box['width'] + page.locator('#seed-mode').select_option('none') + for key in ['seedBP', 'seedTQ', 'seedQRange', 'seedNoGU']: + expect(page.locator('#' + key)).to_be_disabled() + page.locator('#seed-mode').select_option('explicit') + expect(page.locator('#seedTQ')).to_be_enabled() + expect(page.locator('#seedBP')).to_be_disabled() + page.locator('#seed-mode').select_option('identify') + expect(page.locator('#seedBP')).to_be_enabled() + expect(page.locator('#seedTQ')).to_be_disabled() + open_group('output-options') + output_labels = page.locator('#output-options .checkbox-grid label') + assert output_labels.count() == 15 + assert all(label.get_attribute('title') for label in output_labels.all()) + expect(page.locator('#output-options input[value="pMinE"]').locator('xpath=..')).to_have_attribute('title', re.compile('energy heatmap')) + open_group('csv-options') + assert page.locator('#outCsvSort').bounding_box()['width'] < 310 + groups = page.locator('.csv-group') + assert groups.count() == 5 + for group in groups.all(): + group.get_by_role('button', name=re.compile('^Select all')).click() + assert group.locator('input:not(:checked)').count() == 0 + group.get_by_role('button', name='Deselect all').click() + assert group.locator('input:checked').count() == 0 + page.get_by_role('button', name='Task defaults', exact=True).click() + for key in ['ED1', 'ED2', 'seedE', 'seedStart1', 'seedStart2']: + expect(page.locator('.csv-group input[value="' + key + '"]')).to_be_checked() + assert all(label.get_attribute('title') and ' — ' not in label.inner_text() for label in groups.locator('label').all()) + # Inspect all changed panels at desktop and mobile widths. + for width in [1440, 390]: + page.set_viewport_size({'width': width, 'height': 1100 if width == 1440 else 844}) + for key in ['sequence-input', 'seed-options', 'output-options', 'csv-options', 'interaction-options', 'query-options', 'target-options', 'general-options']: + open_group(key) + assert page.evaluate('document.documentElement.scrollWidth <= innerWidth'), (width, key) + if args.screenshot: + path = Path(args.screenshot) + page.screenshot(path=str(path.with_name(f'{path.stem}-{key}-{width}.png')), full_page=True) + page.set_viewport_size({'width': 1440, 'height': 1100}) + page.locator('#reset').click() + + # Upload and file drop use local text, validate before replacing, and reset. + with page.expect_file_chooser() as chooser: + page.locator('#query-upload-button').click() + chooser.value.set_files({'name': 'query.fa', 'mimeType': 'text/plain', 'buffer': b'>uploaded\nGGGAGGAGGG\n'}) + expect(page.locator('#query')).to_have_value('>uploaded\nGGGAGGAGGG\n') + page.locator('#target').evaluate(r"""node => { + const transfer = new DataTransfer(); + transfer.items.add(new File(['>dropped\nCCCUCCUCCC\n'], 'target.fa', {type:'text/plain'})); + node.dispatchEvent(new DragEvent('drop', {dataTransfer:transfer, bubbles:true, cancelable:true})); + }""") + expect(page.locator('#target')).to_have_value('>dropped\nCCCUCCUCCC\n') + page.locator('#query-upload').set_input_files({'name': 'bad.fa', 'mimeType': 'text/plain', 'buffer': b'not a sequence!'}) + expect(page.locator('#input-error')).to_be_visible() + expect(page.locator('#query')).to_have_value('>uploaded\nGGGAGGAGGG\n') + # A file read completing after Reset cannot restore the previous input. + page.evaluate(r"""() => { window.originalFileText = File.prototype.text; File.prototype.text = function() { return new Promise(resolve => { window.finishRead = () => resolve('>late\nGGGAGGAGGG\n'); }); }; }""") + page.locator('#query-upload').set_input_files({'name': 'late.fa', 'mimeType': 'text/plain', 'buffer': b'>late\nGGGAGGAGGG\n'}) + page.locator('#reset').click() + page.evaluate('() => { File.prototype.text = window.originalFileText; window.finishRead(); }') + expect(page.locator('#query')).to_have_value('') + + # JavaScript validation works even when the offending control is in another tab. + fill('query', '>bad\nACGU-ACGU') + compute.click() + expect(page.locator('#input-error')).to_contain_text('use only') + expect(page.locator('#loading')).not_to_be_visible() + load_example() + fill('temperature', '101') + open_group('sequence-input') + compute.click() + expect(page.locator('#input-error')).to_contain_text('Temperature') + page.locator('#reset').click() + expect(page.locator('#query')).to_have_value('') + expect(page.locator('#target')).to_have_value('') + expect(page.locator('#rri')).to_have_value('') + load_example() + + # Disabled stale edits neither block a run nor leak into JSON. Re-enabling + # restores local edits; loading/storing uses effective native settings. + fill('seedBP', '') + page.locator('#seed-mode').select_option('explicit') + compute.click() + expect(page.locator('#input-error')).to_contain_text('Explicit seed: enter') + fill('seedTQ', '1|||&1|||') + predict() + explicit_settings = json.loads(download_archive()['parameter.json']) + assert explicit_settings['parameters']['seedTQ'] == '1|||&1|||' + assert 'seedBP' not in explicit_settings['parameters'] + with page.expect_download() as stored: + page.locator('#store-parameters').click() + explicit_file = Path(stored.value.path()).read_bytes() + page.locator('#reset').click() + page.locator('#parameter-upload').set_input_files({'name': 'explicit.json', 'mimeType': 'application/json', 'buffer': explicit_file}) + expect(page.locator('#seed-mode')).to_have_value('explicit') + open_group('seed-options') + page.locator('#seedTQ').fill('invalid inactive seed') + page.locator('#seed-mode').select_option('none') + fill('qShape', 'invalid inactive shape') + page.locator('#qAcc').select_option('N') + open_group('target-options') + page.locator('#accNoGUend-target').check() + predict() + inactive_settings = json.loads(download_archive()['parameter.json'])['parameters'] + assert inactive_settings['noSeed'] is True + assert inactive_settings['qAcc'] == 'N' + assert inactive_settings['accNoGUend'] is True + assert 'qShape' not in inactive_settings and 'seedTQ' not in inactive_settings + open_group('query-options') + page.locator('#qAcc').select_option('C') + expect(page.locator('#qShape')).to_have_value('invalid inactive shape') + page.locator('#reset').click() + load_example() + + # Reference prediction, selectable CSV output and independent table visibility. + fill('outNumber', 10) + open_group('csv-options') + page.locator('#outCsvSort').select_option('E') + predict() + expect(rows).to_have_count(10) + assert active.locator('.table-scroll').evaluate('''node => { + const body = node.querySelector('tbody'); + const copies = [...body.children].map(row => row.cloneNode(true)); + body.append(...copies); + const scrolls = node.clientHeight <= 500 && node.scrollHeight > node.clientHeight + && getComputedStyle(node).overflowY === 'auto'; + copies.forEach(copy => copy.remove()); + return scrolls; + }''') + assert rows.first.locator('td').all_text_contents()[1:7] == ['target', '1', '10', 'query', '1', '10'] + assert rows.first.locator('td').nth(9).inner_text() == '-21.40' + assert rows.first.locator('td').last.inner_text() == '0.00' + page.get_by_role('button', name='Sort by Energy (kcal/mol)', exact=False).click() + assert float(rows.first.locator('td').nth(9).inner_text()) == -14.3 + page.get_by_role('button', name='Sort by Energy (kcal/mol)', exact=False).click() + active.locator('[data-role=search]').fill('-21.4') + expect(rows).to_have_count(1) + active.locator('[data-role=search]').fill('no match') + expect(active.locator('[data-role=no-matches]')).to_be_visible() + active.locator('[data-role=search]').fill('') + active.locator('.column-picker summary').click() + active.locator('[data-role=visible-columns] input[value="start1"]').uncheck() + assert 'Target start' not in active.locator('thead').inner_text() + active.locator('[data-role=visible-columns] input[value="start1"]').check() + with page.expect_download() as downloaded: + active.locator('[data-role=download]').click() + csv = Path(downloaded.value.path()).read_text() + assert csv.splitlines()[0] == 'id1;start1;end1;id2;start2;end2;subseqDP;hybridDP;E;ED1;ED2;seedE;seedStart1;seedStart2' + assert 'target;1;10;query;1;10;' in csv + assert 'deltaE' not in csv + assert active.locator('thead th').first.inner_text() == '' + assert active.locator('thead th button br').count() >= 4 + assert rows.first.locator('td').first.evaluate('node => getComputedStyle(node).paddingLeft') == '5px' + assert not visualization_urls # Third-party content loads only on selection. + rows.first.get_by_role('button', name='Visualize').click() + expect(active.locator('[data-role=varri-frame]')).to_be_visible() + expect(active.frame_locator('[data-role=varri-frame]').get_by_role('heading', name='vaRRI viewer')).to_be_visible() + expect(rows.first.locator('button')).to_have_attribute('aria-pressed', 'true') + query = parse_qs(urlparse(active.locator('[data-role=varri-frame]').get_attribute('src')).query) + assert query['sequence'] == ['CCCUCCUCCC&GGGAGGAGGG'] + assert query['structure'] == ['((((((((((&))))))))))'] + assert query['seqName1'] == ['target'] and query['seqName2'] == ['query'] + assert query['startIndex1'] == ['1'] + assert query['showRenderingOnly'] == ['true'] + assert 'showRenderingOnly' not in active.locator('[data-role=varri-link]').get_attribute('href') + archive = download_archive() + assert archive['intarna-interactions.csv'] == csv + saved = json.loads(archive['parameter.json']) + assert set(archive) == {'parameter.json', 'intarna-interactions.csv'} + assert saved['parameters']['query']['text'] == '>query\nGGGAGGAGGG\n' + assert 'IntaRNA 3.4.1' in archive['parameter.json'] + assert f'Vienna RNA package {vienna_version}' in archive['parameter.json'] + assert saved['parameters']['outNumber'] == 10 + assert 'IntaRNA --parameterFile=parameter.json' in archive['parameter.json'] + assert 'temperature' not in saved['parameters'] + # Store snapshots the editable form; Load is atomic and preserves CSV order. + with page.expect_download() as stored: + page.locator('#store-parameters').click() + settings = Path(stored.value.path()).read_bytes() + imported = json.loads(settings) + imported['parameters']['outCsvCols'] = 'E,id2' + imported['parameters']['temperature'] = 24 + page.locator('#parameter-upload').set_input_files({'name': 'settings.json', 'mimeType': 'application/json', 'buffer': json.dumps(imported).encode()}) + expect(page.locator('#temperature')).to_have_value('24') + expect(active.locator('[data-role=results-view]')).to_be_visible() + with page.expect_download() as stored_again: + page.locator('#store-parameters').click() + assert json.loads(Path(stored_again.value.path()).read_text())['parameters']['outCsvCols'] == 'E,id2' + page.locator('#parameter-upload').set_input_files({'name': 'bad.json', 'mimeType': 'application/json', 'buffer': b'{invalid'}) + expect(page.locator('#input-error')).to_be_visible() + expect(page.locator('#temperature')).to_have_value('24') + page.locator('#parameter-upload').set_input_files({'name': 'settings.json', 'mimeType': 'application/json', 'buffer': settings}) + expect(page.locator('#temperature')).to_have_value('37') + predict() + if args.screenshot: + + open_group('sequence-input') + page.screenshot(path=args.screenshot, full_page=True) + page.set_viewport_size({'width': 390, 'height': 844}) + assert page.evaluate('document.documentElement.scrollWidth <= innerWidth') + page.set_viewport_size({'width': 1440, 'height': 1100}) + + # Multi-FASTA prediction, signed inclusive output and additional files. + load_example() + fill('outNumber', 1) + fill('query', '>q1\nGGGAGGAGGG\n>q2\nGGGAGGAGGG') + fill('qIdxPos0', -3) + fill('tIdxPos0', -5) + open_group('output-options') + page.locator('#output-options input[value="qMinE"]').check() + predict() + expect(rows).to_have_count(2) + assert rows.first.locator('td').all_text_contents()[1:7] == ['target', '-5', '5', 'q1', '-3', '7'] + output_files = active.locator('[data-role=file-list] details') + expect(output_files).to_have_count(2) + expect(output_files.nth(0).locator('summary')).to_contain_text('target : q1') + expect(output_files.nth(1).locator('summary')).to_contain_text('target : q2') + output_files.first.locator('summary').click() + expect(output_files.first.get_by_role('tab', name='Visualization')).to_have_attribute('aria-selected', 'true') + assert output_files.first.get_by_role('tab', name='Visualization').evaluate('node => getComputedStyle(node).backgroundColor') == page.locator('#tab-output-options').evaluate('node => getComputedStyle(node).backgroundColor') + expect(output_files.first.locator('.js-plotly-plot')).to_be_visible(timeout=30000) + expect(output_files.first.locator('.gtitle')).to_contain_text('q1') + if args.screenshot: + path = Path(args.screenshot) + page.screenshot(path=str(path.with_name(f'{path.stem}-additional-output.png')), full_page=True) + with page.expect_download(timeout=30000) as image: + output_files.first.get_by_role('button', name='Export PNG').click() + assert Path(image.value.path()).read_bytes().startswith(b'\x89PNG\r\n\x1a\n') + output_files.first.get_by_role('tab', name='File Content').click() + expect(output_files.first.locator('pre')).to_be_visible() + expect(output_files.first.locator('pre')).to_contain_text('minE') + with page.expect_download() as output_download: + output_files.first.get_by_role('button', name=re.compile('^Download qMinE')).click() + assert 'minE' in Path(output_download.value.path()).read_text() + archive = download_archive() + assert len([name for name in archive if name.startswith('qMinE')]) == 2 + saved = json.loads(archive['parameter.json']) + assert saved['parameters']['query']['text'].count('>') == 2 + assert saved['parameters']['qIdxPos0'] == -3 + rows.nth(1).get_by_role('button', name='Visualize').click() + query = parse_qs(urlparse(active.locator('[data-role=varri-frame]').get_attribute('src')).query) + assert query['seqName2'] == ['q2'] + assert query['startIndex1'] == ['-5'] and query['startIndex2'] == ['-3'] + + # FASTA identity follows native first-token naming, including collisions. + fill('query', '>q first\nGGGAGGAGGG\n>q second\nGGGAGGAGGG') + compute.click() + expect(page.locator('#input-error')).to_contain_text('unique') + expect(active.locator('[data-role=varri-frame]')).to_be_visible() + expect(active.locator('[data-role=download-zip]')).to_be_visible() + assert download_archive() == archive + + # Evaluation resets native defaults and removes prediction-only controls. + fill('query', '>q1\nGGGAGGAGGG\n>q2\nGGGAGGAGGG') + page.get_by_role('radio', name='Evaluation').check() + expect(page.locator('#seed-options')).not_to_be_visible() + expect(page.locator('#outNumber')).to_be_disabled() + fill('rri', '1||||||||||&1||||||||||') + compute.click() + expect(page.locator('#input-error')).to_contain_text('exactly one') + load_example('evaluation') + fill('rri', '1||||||||||&1||||||||||:1|||||||||&2|||||||||') + open_group('output-options') + page.locator('#output-options input[value="detailed"]').check() + open_group('csv-options') + page.locator('#csv-options input[value="ED1"]').check() + predict() + expect(status).to_contain_text('Evaluation complete') + expect(rows).to_have_count(2) + expect(active.locator('thead')).to_contain_text('ED1') + expect(active.locator('[data-role=file-list] summary')).to_contain_text('intarna-detailed.txt') + active.locator('[data-role=file-list] summary').click() + expect(active.locator('[data-role=file-list] pre')).to_contain_text('-21.4') + with page.expect_download() as report: + active.locator('[data-role=file-list] button').click() + assert '-21.4' in Path(report.value.path()).read_text() + archive = download_archive() + assert '-21.4' in archive['intarna-detailed.txt'] + saved = json.loads(archive['parameter.json']) + assert saved['parameters']['personality'] == 'IntaRNAeval' + assert saved['parameters']['rri'] == '1||||||||||&1||||||||||:1|||||||||&2|||||||||' + assert 'seedBP' not in saved['parameters'] + assert 'detailed' in saved['gui']['reports'] + + # Visualization stays available when structure/identity columns are deselected. + open_group('csv-options') + page.get_by_role('button', name='Clear selection', exact=True).click() + page.locator('#csv-options input[value="E"]').check() + predict() + rows.first.get_by_role('button', name='Visualize').click() + expect(active.locator('[data-role=varri-frame]')).to_be_visible() + archive = download_archive() + assert archive['intarna-interactions.csv'].splitlines()[0] == 'E' + assert json.loads(archive['parameter.json'])['parameters']['outCsvCols'] == 'E' + fill('rri', '1|||&1||') + compute.click() + expect(page.locator('#input-error')).to_contain_text('same nonzero') + + # Startup and synchronous C++ cancellation both allow a fresh prediction. + page.get_by_role('radio', name='Prediction').check() + load_example() + held_routes = [] + session_count = sessions.count() + page.route('**/wasm/intarna.wasm', lambda route: held_routes.append(route)) + compute.click() + expect(page.locator('#loading')).to_be_visible() + page.locator('#abort').click() + expect(status).to_contain_text('aborted') + expect(sessions).to_have_count(session_count) + for route in held_routes: + route.abort() + page.unroute('**/wasm/intarna.wasm') + fill('query', '>long_query\n' + 'G' * 1000) + fill('target', '>long_target\n' + 'C' * 1000) + compute.click() + expect(page.locator('#loading-status')).to_contain_text('Predicting RNA', timeout=120000) + page.keyboard.press('Escape') + expect(status).to_contain_text('aborted') + expect(sessions).to_have_count(session_count) + load_example() + predict() + + fill('query', '>no_pairs\nNNNNNNNNNN') + compute.click() + expect(status).to_contain_text('No favorable interactions', timeout=120000) + expect(rows).to_have_count(0) + expect(active.locator('[data-role=varri-frame]')).not_to_be_visible() + assert download_archive()['intarna-interactions.csv'].count('\n') == 1 + fill('query', '>\nGGGAGGAGGG') + predict() + assert active.locator('tbody img').count() == 0 + assert ' 1 + page.reload() + page.wait_for_load_state('networkidle') + expect(sessions).to_have_count(0) + load_example() + fill('temperature', 24) + fill('qIdxPos0', -3) + fill('tIdxPos0', -5) + fill('qShape', '1 0.2\n2 0.3') + fill('outNumber', 3) + open_group('output-options') + page.locator('#output-options input[value="qMinE"]').check() + predict() + first_id = active.get_attribute('data-session-id') + first = page.locator(f'[data-session-id="{first_id}"]') + first.get_by_label('Session name', exact=True).fill('Cool duplex') + first.get_by_label('Session name', exact=True).press('Enter') + first_archive = download_archive(first) + first_csv = first_archive['intarna-interactions.csv'] + first.locator('[data-role=search]').fill('no match') + expect(first.locator('[data-role=no-matches]')).to_be_visible() + first.locator('.column-picker summary').click() + first.locator('[data-role=visible-columns] input[value="start1"]').uncheck() + first_diagnostics = first.locator('[data-role=diagnostic-text]').text_content() + + # Edits and Reset preserve outputs. Restore also works for an unfolded run. + fill('temperature', 31) + expect(first.locator('[data-role=panel]')).to_be_visible() + assert download_archive(first) == first_archive + first.locator('[data-role=summary]').click() + expect(page.locator('#temperature')).to_have_value('24') + fill('temperature', 31) + first.locator('[data-role=toggle]').click() + expect(page.locator('#temperature')).to_have_value('24') + expect(first.locator('[data-role=panel]')).to_be_visible() + first.locator('[data-role=toggle]').click() + expect(first.locator('[data-role=panel]')).not_to_be_visible() + first.locator('[data-role=toggle]').press('Enter') + expect(first.locator('[data-role=panel]')).to_be_visible() + page.locator('#reset').click() + expect(sessions).to_have_count(1) + expect(page.locator('#query')).to_have_value('') + assert download_archive(first) == first_archive + + # A different task, CSV order and output report own a second result area. + page.get_by_role('radio', name='Evaluation').check() + load_example('evaluation') + with page.expect_download() as stored: + page.locator('#store-parameters').click() + second_settings = json.loads(Path(stored.value.path()).read_text()) + second_settings['parameters']['temperature'] = 42 + second_settings['parameters']['outCsvCols'] = 'E,id2' + second_settings['gui'] = {'reports': ['detailed']} + page.locator('#parameter-upload').set_input_files({'name': 'evaluation.json', 'mimeType': 'application/json', 'buffer': json.dumps(second_settings).encode()}) + predict() + expect(sessions).to_have_count(2) + second_id = active.get_attribute('data-session-id') + assert second_id != first_id + second = page.locator(f'[data-session-id="{second_id}"]') + expect(first.locator('[data-role=panel]')).not_to_be_visible() + expect(first.locator('[data-role=download-zip]')).to_be_visible() + assert download_archive(first) == first_archive + expect(page.get_by_role('radio', name='Evaluation')).to_be_checked() + expect(page.locator('#temperature')).to_have_value('42') + second_archive = download_archive(second) + assert second_archive['intarna-interactions.csv'].splitlines()[0] == 'E;id2' + assert 'intarna-detailed.txt' in second_archive + + # Selecting reloads all computed inputs while retaining each table's filter. + first.locator('.session-header').focus() + first.locator('.session-header').press('Space') + expect(second.locator('[data-role=panel]')).not_to_be_visible() + expect(first.locator('[data-role=panel]')).to_be_visible() + assert first.locator('.session-header').evaluate('node => node.firstElementChild.dataset.role') == 'toggle' + expect(first.locator('[data-role=toggle]')).to_have_text('Hide') + expect(page.get_by_role('radio', name='Prediction')).to_be_checked() + expect(page.locator('#qIdxPos0')).to_have_value('-3') + expect(page.locator('#tIdxPos0')).to_have_value('-5') + expect(page.locator('#qShape')).to_have_value('1 0.2\n2 0.3') + expect(page.locator('#temperature')).to_have_value('24') + expect(page.locator('#output-options input[value="qMinE"]')).to_be_checked() + expect(page.locator('#output-options input[value="detailed"]')).not_to_be_checked() + expect(first.locator('[data-role=search]')).to_have_value('no match') + expect(first.locator('[data-role=visible-columns] input[value="start1"]')).not_to_be_checked() + assert first.locator('[data-role=diagnostic-text]').text_content() == first_diagnostics + with page.expect_download() as restored: + page.locator('#store-parameters').click() + assert Path(restored.value.path()).read_text() == first_archive['parameter.json'] + first.locator('[data-role=search]').fill('') + expect(first.locator('tbody tr')).to_have_count(3) + first.locator('tbody tr').first.get_by_role('button', name='Visualize').click() + first_url = first.locator('[data-role=varri-frame]').get_attribute('src') + assert parse_qs(urlparse(first_url).query)['startIndex1'] == ['-5'] + + # A pending file read must not overwrite a selected session's snapshot. + page.evaluate(r"""() => { window.originalFileText = File.prototype.text; File.prototype.text = function() { return new Promise(resolve => { window.finishRead = () => resolve('>late\nGGGAGGAGGG\n'); }); }; }""") + page.locator('#query-upload').set_input_files({'name': 'late.fa', 'mimeType': 'text/plain', 'buffer': b'>late\nGGGAGGAGGG\n'}) + second.locator('[data-role=toggle]').click() + page.evaluate('() => { File.prototype.text = window.originalFileText; window.finishRead(); }') + expect(page.locator('#query')).to_have_value('>query\nGGGAGGAGGG\n') + expect(page.locator('#qShape')).to_have_value('') + expect(page.locator('#temperature')).to_have_value('42') + expect(page.get_by_role('radio', name='Evaluation')).to_be_checked() + expect(page.locator('#rri')).to_have_value(second_settings['parameters']['rri']) + expect(page.locator('#output-options input[value="detailed"]')).to_be_checked() + assert first.locator('[data-role=varri-frame]').get_attribute('src') is None + with page.expect_download() as restored: + page.locator('#store-parameters').click() + assert Path(restored.value.path()).read_text() == second_archive['parameter.json'] + assert download_archive(first)['intarna-interactions.csv'] == first_csv + + # Names are literal text and cannot introduce markup, duplicate IDs or paths. + first.get_by_label('Session name', exact=True).fill(' / β') + first.get_by_label('Session name', exact=True).press('Enter') + expect(page.locator('#temperature')).to_have_value('24') + expect(first.locator('[data-role=panel]')).to_be_visible() + assert first.locator('img').count() == 0 + with page.expect_download() as renamed: + first.locator('[data-role=download-zip]').click() + assert '/' not in renamed.value.suggested_filename + assert '\\' not in renamed.value.suggested_filename + ids = page.locator('[id]').evaluate_all('nodes => nodes.map(node => node.id)') + assert len(ids) == len(set(ids)) + first.get_by_label('Session name', exact=True).fill('') + first.get_by_label('Session name', exact=True).press('Enter') + expect(first.get_by_label('Session name', exact=True)).to_have_value('Prediction 1') + first.get_by_label('Session name', exact=True).fill('Cool duplex — 24 °C') + first.get_by_label('Session name', exact=True).press('Enter') + if args.screenshot: + page.screenshot(path=args.screenshot, full_page=True) + page.set_viewport_size({'width': 390, 'height': 844}) + assert page.evaluate('document.documentElement.scrollWidth <= innerWidth') + for session in [first, second]: + expect(session.locator('[data-role=download-zip]')).to_be_visible() + expect(session.locator('[data-role=delete]')).to_be_visible() + page.set_viewport_size({'width': 1440, 'height': 1100}) + + # Delete releases only that output; current inputs and other sessions survive. + second.locator('[data-role=toggle]').click() + first.locator('[data-role=delete]').click() + expect(sessions).to_have_count(1) + expect(page.locator('#temperature')).to_have_value('42') + assert download_archive(second) == second_archive + second.locator('[data-role=delete]').click() + expect(sessions).to_have_count(0) + expect(compute).to_be_focused() + expect(page.locator('#temperature')).to_have_value('42') + predict() + assert active.get_attribute('data-session-id') not in [first_id, second_id] + assert download_archive() == second_archive + page.reload() + page.wait_for_load_state('networkidle') + expect(sessions).to_have_count(0) + assert errors == [], errors + assert csp_errors == [], csp_errors + browser.close() +print(f'{args.browser}: real WASM, groups/defaults/versions, prediction/evaluation, FASTA/coordinates, tabs/keyboard, visualization URLs/selection, ZIP replay contents, columns/reports, mobile, abort/recovery and retained session lifecycle passed') diff --git a/scripts/wasm/test-downloads.py b/scripts/wasm/test-downloads.py new file mode 100644 index 00000000..6b0f7bc3 --- /dev/null +++ b/scripts/wasm/test-downloads.py @@ -0,0 +1,92 @@ +#!/usr/bin/env python3 +"""Exercise archive downloads against a local HTTP server, without Emscripten.""" +import hashlib +from http.server import BaseHTTPRequestHandler, ThreadingHTTPServer +from pathlib import Path +import subprocess +from tempfile import TemporaryDirectory +from threading import Thread +import unittest + + +ARCHIVE = b"pinned dependency archive\n" +CHECKSUM = hashlib.sha256(ARCHIVE).hexdigest() +DOWNLOADER = Path(__file__).with_name("download.sh") + + +class DownloadHandler(BaseHTTPRequestHandler): + def do_GET(self): + self.server.requests.append(self.path) + if self.path == "/missing": + self.send_error(404) + return + body = ARCHIVE if self.path == "/archive" else b"not an archive\n" + self.send_response(200) + self.send_header("Content-Length", str(len(body) + (10 if self.path == "/partial" else 0))) + self.end_headers() + self.wfile.write(body) + + def log_message(self, *_args): + pass + + +class DownloadTests(unittest.TestCase): + @classmethod + def setUpClass(cls): + cls.server = ThreadingHTTPServer(("127.0.0.1", 0), DownloadHandler) + cls.thread = Thread(target=cls.server.serve_forever, daemon=True) + cls.thread.start() + + @classmethod + def tearDownClass(cls): + cls.server.shutdown() + cls.server.server_close() + cls.thread.join() + + def setUp(self): + self.directory = TemporaryDirectory(prefix="intarna-download-") + self.addCleanup(self.directory.cleanup) + # Exercise quoted paths and the same .part/cache names used by builds. + self.destination = Path(self.directory.name) / "dependency archive.tar.gz" + self.server.requests = [] + + def download(self, path="/archive"): + url = f"http://127.0.0.1:{self.server.server_port}{path}" + return subprocess.run( + ["bash", str(DOWNLOADER), url, str(self.destination), CHECKSUM], + capture_output=True, text=True, timeout=30, + ) + + def test_download_and_reuse_verified_cache(self): + result = self.download() + self.assertEqual(result.returncode, 0, result.stderr) + self.assertEqual(self.destination.read_bytes(), ARCHIVE) + self.assertFalse(Path(str(self.destination) + ".part").exists()) + # A valid cache must work even when the remote archive is unavailable. + result = self.download("/missing") + self.assertEqual(result.returncode, 0, result.stderr) + self.assertEqual(self.server.requests, ["/archive"]) + + def test_replace_invalid_cache_and_stale_partial(self): + self.destination.write_bytes(b"old archive or cached HTTP error") + Path(str(self.destination) + ".part").write_bytes(b"interrupted download") + result = self.download() + self.assertEqual(result.returncode, 0, result.stderr) + self.assertEqual(self.destination.read_bytes(), ARCHIVE) + self.assertFalse(Path(str(self.destination) + ".part").exists()) + self.assertEqual(self.server.requests, ["/archive"]) + + def test_failed_responses_are_not_cached_and_next_run_recovers(self): + for path in ("/invalid", "/missing", "/partial"): + with self.subTest(path=path): + result = self.download(path) + self.assertNotEqual(result.returncode, 0) + self.assertFalse(self.destination.exists()) + self.assertFalse(Path(str(self.destination) + ".part").exists()) + result = self.download() + self.assertEqual(result.returncode, 0, result.stderr) + self.assertEqual(self.destination.read_bytes(), ARCHIVE) + + +if __name__ == "__main__": + unittest.main() diff --git a/scripts/wasm/test-vienna-release.py b/scripts/wasm/test-vienna-release.py new file mode 100644 index 00000000..2bf50995 --- /dev/null +++ b/scripts/wasm/test-vienna-release.py @@ -0,0 +1,120 @@ +#!/usr/bin/env python3 +"""Check stable-major selection, pagination and archive identity without GitHub.""" +from copy import deepcopy +import importlib.util +from io import BytesIO +import json +from pathlib import Path +import subprocess +from tempfile import TemporaryDirectory +import unittest +from unittest.mock import patch +from urllib.error import HTTPError + + +SCRIPT = Path(__file__).with_name("vienna-release.py") +SPEC = importlib.util.spec_from_file_location("vienna_release", SCRIPT) +resolver = importlib.util.module_from_spec(SPEC) +SPEC.loader.exec_module(resolver) +DIGEST = "a" * 64 + + +def release(version, **fields): + return { + "tag_name": f"v{version}", "draft": False, "prerelease": False, + "assets": [{ + "name": f"ViennaRNA-{version}.tar.gz", "digest": f"sha256:{DIGEST}", + "browser_download_url": f"{resolver.REPOSITORY}/releases/download/v{version}/ViennaRNA-{version}.tar.gz", + }], **fields, + } + + +class ReleaseTests(unittest.TestCase): + def resolve(self, pages): + with patch.object(resolver, "urlopen", side_effect=[BytesIO(json.dumps(page).encode()) for page in pages]) as fetch: + result = resolver.latest_release() + return result, fetch + + def test_numeric_selection_excludes_major3_drafts_and_prereleases(self): + result, _ = self.resolve([[ + release("3.0.0"), release("2.9.0"), release("2.10.0"), + release("2.11.0", prerelease=True), release("2.12.0", draft=True), + release("2.13.0-rc.1"), release("2.7.2"), release("2.7.1"), + ]]) + self.assertEqual(result["version"], "2.10.0") + self.assertEqual(result["sha256"], DIGEST) + + def test_pagination_finds_version2_after_one_hundred_newer_releases(self): + result, fetch = self.resolve([[release(f"3.0.{n}") for n in range(100)], [release("2.7.2")]]) + self.assertEqual(result["version"], "2.7.2") + self.assertEqual(fetch.call_count, 2) + self.assertTrue(fetch.call_args.args[0].full_url.endswith("per_page=100&page=2")) + + def test_newest_release_must_have_exact_asset_url_and_digest(self): + latest = release("2.8.0") + for field, value in [("name", "source.tar.gz"), ("digest", None), ("digest", "sha256:bad"), ("digest", "md5:" + DIGEST), ("browser_download_url", "https://example.com/archive.tar.gz")]: + with self.subTest(field=field, value=value): + invalid = deepcopy(latest) + invalid["assets"][0][field] = value + with self.assertRaises(ValueError): + self.resolve([[release("2.7.2"), invalid]]) + with self.assertRaises(ValueError): + self.resolve([[release("2.8.0", assets=latest["assets"] * 2)]]) + + def test_no_supported_release_or_api_failure_is_an_error(self): + with self.assertRaises(ValueError): + self.resolve([[release("3.0.0"), release("2.7.1"), release("2.8.0", prerelease=True)]]) + with patch.object(resolver, "urlopen", side_effect=HTTPError(resolver.API, 403, "rate limited", {}, None)): + with self.assertRaises(HTTPError): + resolver.latest_release() + + def test_checked_in_pin_and_shell_fields(self): + manifest = json.loads(subprocess.check_output(["python3", str(SCRIPT)], text=True)) + self.assertEqual(manifest["version"], "2.7.2") + fields = subprocess.check_output(["python3", str(SCRIPT), "--fields"], text=True).split() + self.assertEqual(fields, list(manifest.values())) + + def test_invalid_pin_fails_without_emitting_shell_fields(self): + manifest = json.loads(SCRIPT.with_suffix(".json").read_text()) + with TemporaryDirectory(prefix="vienna manifest ") as directory: + path = Path(directory) / "release.json" + for field, value in [("version", "3.0.0"), ("version", "2.7.0"), ("url", "https://example.com"), ("sha256", "bad")]: + with self.subTest(field=field): + path.write_text(json.dumps({**manifest, field: value})) + result = subprocess.run(["python3", str(SCRIPT), "--manifest", str(path), "--fields"], capture_output=True, text=True) + self.assertNotEqual(result.returncode, 0) + self.assertEqual(result.stdout, "") + + def test_provenance_rejects_stale_engine_and_records_selected_archive(self): + manifest = json.loads(SCRIPT.with_suffix(".json").read_text()) + with TemporaryDirectory(prefix="vienna engine ") as directory: + site = Path(directory) + assets = site / "wasm" + assets.mkdir() + (assets / "package.json").write_text('{"type":"module"}') + (assets / "intarna.wasm").write_bytes(b"test engine") + for version in ["2.7.0", manifest["version"]]: + (assets / "intarna.js").write_text( + "export default async ({print}) => ({callMain() {" + f"print('IntaRNA 3.4.1 using Vienna RNA package {version} and boost 1.87.0');" + "return 0;}});" + ) + result = subprocess.run([ + "node", str(SCRIPT.with_name("write-build-info.mjs")), + str(SCRIPT.parents[2]), str(site), "4.0.23", "test-commit", "", + manifest["version"], manifest["url"], manifest["sha256"], + ], capture_output=True, text=True) + if version == "2.7.0": + self.assertNotEqual(result.returncode, 0) + self.assertIn("differs from selected", result.stderr) + self.assertFalse((site / "build-info.json").exists()) + else: + self.assertEqual(result.returncode, 0, result.stderr) + metadata = json.loads((site / "build-info.json").read_text()) + self.assertEqual(metadata["viennarna"], version) + self.assertEqual(metadata["viennarnaArchive"], manifest) + self.assertIn(manifest["sha256"], (site / "build-info.txt").read_text()) + + +if __name__ == "__main__": + unittest.main() diff --git a/scripts/wasm/vienna-release.json b/scripts/wasm/vienna-release.json new file mode 100644 index 00000000..d54b5517 --- /dev/null +++ b/scripts/wasm/vienna-release.json @@ -0,0 +1,5 @@ +{ + "version": "2.7.2", + "url": "https://github.com/ViennaRNA/ViennaRNA/releases/download/v2.7.2/ViennaRNA-2.7.2.tar.gz", + "sha256": "4cb7aaca00dfac92cb36b030c9111487c170b90568759bd4ffedd8318cc9384f" +} diff --git a/scripts/wasm/vienna-release.py b/scripts/wasm/vienna-release.py new file mode 100644 index 00000000..f869e786 --- /dev/null +++ b/scripts/wasm/vienna-release.py @@ -0,0 +1,93 @@ +#!/usr/bin/env python3 +"""Resolve a stable ViennaRNA 2.x release asset, or validate a pinned manifest.""" +import argparse +import json +import os +from pathlib import Path +import re +from urllib.request import Request, urlopen + + +REPOSITORY = "https://github.com/ViennaRNA/ViennaRNA" +API = "https://api.github.com/repos/ViennaRNA/ViennaRNA/releases" +MINIMUM = (2, 7, 2) + + +def version_tuple(version): + if not isinstance(version, str) or not re.fullmatch(r"2\.\d+\.\d+", version): + raise ValueError("Expected a stable ViennaRNA 2.x version") + result = tuple(map(int, version.split("."))) + if result < MINIMUM: + raise ValueError("The WASM build requires ViennaRNA >= 2.7.2") + return result + + +def validate(manifest): + """Accept only official release tarballs with an explicit SHA-256.""" + version = manifest["version"] + version_tuple(version) + expected = f"{REPOSITORY}/releases/download/v{version}/ViennaRNA-{version}.tar.gz" + if manifest["url"] != expected: + raise ValueError("Expected the official ViennaRNA release asset URL") + if not isinstance(manifest["sha256"], str) or not re.fullmatch(r"[0-9a-f]{64}", manifest["sha256"]): + raise ValueError("Missing or invalid ViennaRNA archive SHA-256") + return {key: manifest[key] for key in ("version", "url", "sha256")} + + +def latest_release(): + # Enumerate all pages: /latest may select major 3, and release dates need not + # follow version order (for example, a maintenance release of an older minor). + headers = {"Accept": "application/vnd.github+json", "User-Agent": "IntaRNA-WASM"} + if os.environ.get("GITHUB_TOKEN"): + headers["Authorization"] = f"Bearer {os.environ['GITHUB_TOKEN']}" + candidates = [] + page = 1 + while True: + request = Request(f"{API}?per_page=100&page={page}", headers=headers) + with urlopen(request, timeout=30) as response: + releases = json.load(response) + if not isinstance(releases, list): + raise ValueError("Expected a GitHub release list") + for release in releases: + tag = release.get("tag_name", "") + if release.get("draft") or release.get("prerelease") or not re.fullmatch(r"v2\.\d+\.\d+", tag): + continue + version = tag[1:] + if tuple(map(int, version.split("."))) >= MINIMUM: + candidates.append(release) + if len(releases) < 100: + break + page += 1 + if not candidates: + raise ValueError("No stable ViennaRNA 2.x release >= 2.7.2 was found") + release = max(candidates, key=lambda item: version_tuple(item["tag_name"][1:])) + version = release["tag_name"][1:] + # Fail if the newest release lacks the asset/digest; do not silently select + # an older release or GitHub's differently packaged autogenerated source. + name = f"ViennaRNA-{version}.tar.gz" + assets = [asset for asset in release.get("assets", []) if asset["name"] == name] + if len(assets) != 1: + raise ValueError(f"Expected exactly one {name} release asset") + asset = assets[0] + digest = asset.get("digest") or "" + if not digest.startswith("sha256:"): + raise ValueError(f"Missing published SHA-256 for {name}") + return validate({"version": version, "url": asset["browser_download_url"], "sha256": digest[7:]}) + + +def main(): + parser = argparse.ArgumentParser(description=__doc__) + source = parser.add_mutually_exclusive_group() + source.add_argument("--latest", action="store_true", help="query the official GitHub releases API") + source.add_argument("--manifest", type=Path, default=Path(__file__).with_suffix(".json")) + parser.add_argument("--fields", action="store_true", help="emit version, URL and SHA-256 for build.sh") + args = parser.parse_args() + try: + manifest = latest_release() if args.latest else validate(json.loads(args.manifest.read_text())) + except (OSError, ValueError, KeyError, TypeError) as error: + parser.exit(1, f"Cannot resolve ViennaRNA release: {error}\n") + print(" ".join(manifest.values()) if args.fields else json.dumps(manifest, indent=2)) + + +if __name__ == "__main__": + main() diff --git a/scripts/wasm/write-build-info.mjs b/scripts/wasm/write-build-info.mjs new file mode 100644 index 00000000..4bf9fd47 --- /dev/null +++ b/scripts/wasm/write-build-info.mjs @@ -0,0 +1,25 @@ +// Record the versions of the compiled executable, alongside its exact assets. +import { createHash } from 'node:crypto'; +import { readFileSync, writeFileSync } from 'node:fs'; +import { resolve } from 'node:path'; +import { pathToFileURL } from 'node:url'; +const [repo, site, emscripten, commit, changes, viennaVersion, viennaUrl, viennaSha256] = process.argv.slice(2); +const { default: createIntaRNA } = await import(pathToFileURL(resolve(site, 'wasm/intarna.js'))); +const lines = []; +const module = await createIntaRNA({ noInitialRun: true, locateFile: () => pathToFileURL(resolve(site, 'wasm/intarna.wasm')).href, print: (line) => lines.push(line), printErr: (line) => lines.push(line) }); +if (module.callMain(['--version']) !== 0) throw new Error('Could not read compiled engine versions'); +const version = lines.join('\n'); +const match = /IntaRNA\s+(\S+)[\s\S]*Vienna RNA package\s+(\S+)\s+and boost\s+(\S+)/i.exec(version); +if (!match) throw new Error(`Unrecognized engine version output: ${version}`); +if (match[2] !== viennaVersion) throw new Error(`Compiled ViennaRNA ${match[2]} differs from selected ${viennaVersion}`); +const metadata = { + source: 'https://github.com/BackofenLab/IntaRNA', commit, + dirty: !!changes, + intarna: match[1], viennarna: match[2], boost: match[3], emscripten, zlib: '1.3.1', + viennarnaArchive: { version: viennaVersion, url: viennaUrl, sha256: viennaSha256 }, + threading: 'single worker per task', + sha256: Object.fromEntries(['intarna.js', 'intarna.wasm'].map((name) => [name, createHash('sha256').update(readFileSync(resolve(site, 'wasm', name))).digest('hex')])), +}; +writeFileSync(resolve(site, 'build-info.json'), JSON.stringify(metadata, null, 2) + '\n'); +writeFileSync(resolve(site, 'build-info.txt'), `${version}\nIntaRNA repository: ${metadata.source}\nIntaRNA revision: ${metadata.commit}${metadata.dirty ? ' (modified sources)' : ''}\nEmscripten: ${emscripten}\nzlib: ${metadata.zlib}\nViennaRNA archive: ${viennaUrl}\nViennaRNA archive SHA-256: ${viennaSha256}\n${Object.entries(metadata.sha256).map(([name, hash]) => `SHA-256 ${name}: ${hash}`).join('\n')}\n`); +console.log(`Recorded compiled versions: IntaRNA ${match[1]}, ViennaRNA ${match[2]}, Boost ${match[3]}`); diff --git a/src/IntaRNA/AccessibilityBasePair.h b/src/IntaRNA/AccessibilityBasePair.h index 54cf9471..f8866c0d 100644 --- a/src/IntaRNA/AccessibilityBasePair.h +++ b/src/IntaRNA/AccessibilityBasePair.h @@ -47,7 +47,7 @@ class AccessibilityBasePair: public Accessibility { /*** * Destructor of AccessibilityBasePair */ - virtual ~AccessibilityBasePair(); + virtual ~AccessibilityBasePair() override; /*** * Returns the accessibility energy value between the indices (from, to) @@ -59,7 +59,7 @@ class AccessibilityBasePair: public Accessibility { * * @throw std::runtime_error in case it does not hold 0 <= from <= to < seq.length */ - virtual E_type getED( const size_t from, const size_t to ) const; + virtual E_type getED( const size_t from, const size_t to ) const override; protected: diff --git a/src/IntaRNA/AccessibilityDisabled.h b/src/IntaRNA/AccessibilityDisabled.h index f50ba243..d72f9215 100644 --- a/src/IntaRNA/AccessibilityDisabled.h +++ b/src/IntaRNA/AccessibilityDisabled.h @@ -38,7 +38,7 @@ class AccessibilityDisabled: public Accessibility { /** * destruction */ - virtual ~AccessibilityDisabled(); + virtual ~AccessibilityDisabled() override; /** * Always returns a zero accessibility energy value. @@ -50,7 +50,7 @@ class AccessibilityDisabled: public Accessibility { */ virtual E_type - getED( const size_t from, const size_t to ) const; + getED( const size_t from, const size_t to ) const override; }; diff --git a/src/IntaRNA/AccessibilityFromStream.h b/src/IntaRNA/AccessibilityFromStream.h index 79493c0e..a3169214 100644 --- a/src/IntaRNA/AccessibilityFromStream.h +++ b/src/IntaRNA/AccessibilityFromStream.h @@ -52,7 +52,7 @@ class AccessibilityFromStream: public Accessibility /** * destruction */ - virtual ~AccessibilityFromStream(); + virtual ~AccessibilityFromStream() override; /** @@ -68,7 +68,7 @@ class AccessibilityFromStream: public Accessibility */ virtual E_type - getED( const size_t from, const size_t to ) const; + getED( const size_t from, const size_t to ) const override; /** * Access to the maximal length of accessible regions (>0) to be considered. @@ -80,7 +80,7 @@ class AccessibilityFromStream: public Accessibility */ virtual size_t - getMaxLength() const; + getMaxLength() const override; /** diff --git a/src/IntaRNA/AccessibilityVrna.h b/src/IntaRNA/AccessibilityVrna.h index 83a03c07..1f4ac3f4 100644 --- a/src/IntaRNA/AccessibilityVrna.h +++ b/src/IntaRNA/AccessibilityVrna.h @@ -57,7 +57,7 @@ class AccessibilityVrna : public Accessibility { /** * destruction */ - virtual ~AccessibilityVrna(); + virtual ~AccessibilityVrna() override; /** * Returns the accessibility energy value for the given range in the @@ -72,7 +72,7 @@ class AccessibilityVrna : public Accessibility { */ virtual E_type - getED( const size_t from, const size_t to ) const; + getED( const size_t from, const size_t to ) const override; /** diff --git a/src/IntaRNA/HelixHandlerIdxOffset.h b/src/IntaRNA/HelixHandlerIdxOffset.h index bd8dfe32..d06153bf 100644 --- a/src/IntaRNA/HelixHandlerIdxOffset.h +++ b/src/IntaRNA/HelixHandlerIdxOffset.h @@ -31,7 +31,7 @@ class HelixHandlerIdxOffset : public HelixHandler /** * destruction */ - virtual ~HelixHandlerIdxOffset(); + virtual ~HelixHandlerIdxOffset() override; /** * Access to the underlying interaction energy function @@ -39,7 +39,7 @@ class HelixHandlerIdxOffset : public HelixHandler */ virtual const InteractionEnergy& - getInteractionEnergy() const; + getInteractionEnergy() const override; /** * Access to the currently used index offset for sequence 1 @@ -73,7 +73,7 @@ class HelixHandlerIdxOffset : public HelixHandler */ virtual const HelixConstraint& - getConstraint() const; + getConstraint() const override; /** * Computes the helix matrix for the given interval boundaries @@ -89,7 +89,7 @@ class HelixHandlerIdxOffset : public HelixHandler */ virtual size_t - fillHelix(const size_t i1, const size_t j1, const size_t i2, const size_t j2); + fillHelix(const size_t i1, const size_t j1, const size_t i2, const size_t j2) override; /** * Computes the helix matrix for the given interval boundaries for helices containing a seed @@ -104,7 +104,7 @@ class HelixHandlerIdxOffset : public HelixHandler */ virtual size_t - fillHelixSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2); + fillHelixSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2) override; /** * Identifies the base pairs of the mfe helix interaction starting at i1,i2 @@ -120,7 +120,7 @@ class HelixHandlerIdxOffset : public HelixHandler */ virtual void - traceBackHelix( Interaction & interaction, const size_t i1, const size_t i2); + traceBackHelix( Interaction & interaction, const size_t i1, const size_t i2) override; /** * Identifies the base pairs of the mfe helix interaction, containing a seed, starting at i1,i2 @@ -134,7 +134,7 @@ class HelixHandlerIdxOffset : public HelixHandler */ virtual void - traceBackHelixSeed( Interaction & interaction, const size_t i1, const size_t i2); + traceBackHelixSeed( Interaction & interaction, const size_t i1, const size_t i2) override; /** * Access to the mfe of any helix with left-most base pair (i1,i2) @@ -147,7 +147,7 @@ class HelixHandlerIdxOffset : public HelixHandler */ virtual E_type - getHelixE( const size_t i1, const size_t i2 ) const; + getHelixE( const size_t i1, const size_t i2 ) const override; /** * Access to the mfe of any helix with left-most base pair (i1,i2) and containing a seed @@ -160,7 +160,7 @@ class HelixHandlerIdxOffset : public HelixHandler */ virtual E_type - getHelixSeedE( const size_t i1, const size_t i2 ) const; + getHelixSeedE( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq1 of the mfe helix with left-most base pair (i1,i2) @@ -173,7 +173,7 @@ class HelixHandlerIdxOffset : public HelixHandler */ virtual size_t - getHelixLength1( const size_t i1, const size_t i2 ) const; + getHelixLength1( const size_t i1, const size_t i2 ) const override; /** @@ -187,7 +187,7 @@ class HelixHandlerIdxOffset : public HelixHandler */ virtual size_t - getHelixLength2( const size_t i1, const size_t i2 ) const; + getHelixLength2( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq1 of the mfe helix with left-most base pair (i1,i2), containing a seed @@ -200,7 +200,7 @@ class HelixHandlerIdxOffset : public HelixHandler */ virtual size_t - getHelixSeedLength1( const size_t i1, const size_t i2 ) const; + getHelixSeedLength1( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq2 of the mfe helix with left-most base pair (i1,i2), containing a seed @@ -213,7 +213,7 @@ class HelixHandlerIdxOffset : public HelixHandler */ virtual size_t - getHelixSeedLength2( const size_t i1, const size_t i2 ) const; + getHelixSeedLength2( const size_t i1, const size_t i2 ) const override; /** * Check whether the given seedHandler is of type SeedHandlerIdxOffset @@ -223,7 +223,7 @@ class HelixHandlerIdxOffset : public HelixHandler */ virtual void - setSeedHandler( SeedHandler & seedHandler); + setSeedHandler( SeedHandler & seedHandler) override; protected: diff --git a/src/IntaRNA/HelixHandlerNoBulgeMax.h b/src/IntaRNA/HelixHandlerNoBulgeMax.h index 485ec935..cfbe5ca3 100644 --- a/src/IntaRNA/HelixHandlerNoBulgeMax.h +++ b/src/IntaRNA/HelixHandlerNoBulgeMax.h @@ -49,7 +49,7 @@ class HelixHandlerNoBulgeMax : public HelixHandler { /** * destructor */ - virtual ~HelixHandlerNoBulgeMax(); + virtual ~HelixHandlerNoBulgeMax() override; /** * Access to the underlying helix constraint @@ -57,7 +57,7 @@ class HelixHandlerNoBulgeMax : public HelixHandler { */ virtual const HelixConstraint& - getConstraint() const; + getConstraint() const override; /** * Access to the underlying interaction energy function @@ -65,7 +65,7 @@ class HelixHandlerNoBulgeMax : public HelixHandler { */ virtual const InteractionEnergy& - getInteractionEnergy() const; + getInteractionEnergy() const override; /** @@ -78,7 +78,7 @@ class HelixHandlerNoBulgeMax : public HelixHandler { */ virtual size_t - fillHelix( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ); + fillHelix( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) override; /** * Compute the helix matrix, containing a seed, for the given interval boundaries @@ -90,7 +90,7 @@ class HelixHandlerNoBulgeMax : public HelixHandler { */ virtual size_t - fillHelixSeed( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ); + fillHelixSeed( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) override; /** * Identifies the base pairs of the mfe helix interaction starting at i1,i2 @@ -104,7 +104,7 @@ class HelixHandlerNoBulgeMax : public HelixHandler { */ virtual void - traceBackHelix( Interaction & interaction, const size_t i1, const size_t i2); + traceBackHelix( Interaction & interaction, const size_t i1, const size_t i2) override; /** * Identifies the base pairs of the mfe helix interaction, containing a seed, starting at i1,i2 @@ -116,7 +116,7 @@ class HelixHandlerNoBulgeMax : public HelixHandler { */ virtual void - traceBackHelixSeed( Interaction & interaction, const size_t i1, size_t i2); + traceBackHelixSeed( Interaction & interaction, const size_t i1, size_t i2) override; /** * Access to the mfe of any helix with left-most base pair (i1, i2) @@ -126,7 +126,7 @@ class HelixHandlerNoBulgeMax : public HelixHandler { * or return 0 if bp is 0 or 1 (used in helixHandlerSeed computation to avoid too many conditions) */ virtual - E_type getHelixE( const size_t i1, const size_t i2 ) const; + E_type getHelixE( const size_t i1, const size_t i2 ) const override; /** * Access to the mfe of any helix, containing a seed, with left-most base pair (i1, i2) @@ -135,7 +135,7 @@ class HelixHandlerNoBulgeMax : public HelixHandler { * @return the mfe of any helix starting at (i1,i2) or E_INF if none possible */ virtual - E_type getHelixSeedE( const size_t i1, const size_t i2 ) const; + E_type getHelixSeedE( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq1 of the mfe helix with left-most base pair (i1,i2) @@ -145,7 +145,7 @@ class HelixHandlerNoBulgeMax : public HelixHandler { */ virtual size_t - getHelixLength1( const size_t i1, const size_t i2 ) const; + getHelixLength1( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq2 of the mfe helix with left-most base pair (i1,i2) @@ -155,7 +155,7 @@ class HelixHandlerNoBulgeMax : public HelixHandler { */ virtual size_t - getHelixLength2( const size_t i1, const size_t i2 ) const; + getHelixLength2( const size_t i1, const size_t i2 ) const override; /** @@ -166,7 +166,7 @@ class HelixHandlerNoBulgeMax : public HelixHandler { */ virtual size_t - getHelixSeedLength1( const size_t i1, const size_t i2 ) const; + getHelixSeedLength1( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq2 of the mfe helix, containing a seed, with left-most base pair (i1,i2) @@ -176,13 +176,13 @@ class HelixHandlerNoBulgeMax : public HelixHandler { */ virtual size_t - getHelixSeedLength2( const size_t i1, const size_t i2 ) const; + getHelixSeedLength2( const size_t i1, const size_t i2 ) const override; /** * Set the seedHandler in order to compute helixSeed * @param seedHandler seedHandler to be used in the helix computation */ - void setSeedHandler(SeedHandler & seedHandler); + void setSeedHandler(SeedHandler & seedHandler) override; protected: diff --git a/src/IntaRNA/HelixHandlerUnpaired.h b/src/IntaRNA/HelixHandlerUnpaired.h index 0be76450..dddafa95 100644 --- a/src/IntaRNA/HelixHandlerUnpaired.h +++ b/src/IntaRNA/HelixHandlerUnpaired.h @@ -58,7 +58,7 @@ class HelixHandlerUnpaired : public HelixHandler { /** * destructor */ - virtual ~HelixHandlerUnpaired(); + virtual ~HelixHandlerUnpaired() override; /** * Access to the underlying helix constraint @@ -66,7 +66,7 @@ class HelixHandlerUnpaired : public HelixHandler { */ virtual const HelixConstraint& - getConstraint() const; + getConstraint() const override; /** * Access to the underlying interaction energy function @@ -74,7 +74,7 @@ class HelixHandlerUnpaired : public HelixHandler { */ virtual const InteractionEnergy& - getInteractionEnergy() const; + getInteractionEnergy() const override; /** * Compute the helix matrix for the given interval boundaries @@ -86,7 +86,7 @@ class HelixHandlerUnpaired : public HelixHandler { */ virtual size_t - fillHelix( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ); + fillHelix( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) override; /** * Computes the helix information for the given interval boundaries for helices containing a seed @@ -98,7 +98,7 @@ class HelixHandlerUnpaired : public HelixHandler { */ virtual size_t - fillHelixSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2); + fillHelixSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2) override; /** * Identifies the base pairs of the mfe helix interaction starting at i1,i2 @@ -112,7 +112,7 @@ class HelixHandlerUnpaired : public HelixHandler { */ virtual void - traceBackHelix( Interaction & interaction, const size_t i1, const size_t i2); + traceBackHelix( Interaction & interaction, const size_t i1, const size_t i2) override; /** * Identifies the base pairs of the mfe helix interaction starting at i1,i2 @@ -126,7 +126,7 @@ class HelixHandlerUnpaired : public HelixHandler { */ virtual void - traceBackHelixSeed( Interaction & interaction, const size_t i1, const size_t i2); + traceBackHelixSeed( Interaction & interaction, const size_t i1, const size_t i2) override; /** * Access to the mfe of any helix with left-most base pair (i1, i2) @@ -136,7 +136,7 @@ class HelixHandlerUnpaired : public HelixHandler { */ virtual E_type - getHelixE( const size_t i1, const size_t i2 ) const; + getHelixE( const size_t i1, const size_t i2 ) const override; /** * Access to the mfe of any helix with left-most base pair (i1,i2) @@ -146,7 +146,7 @@ class HelixHandlerUnpaired : public HelixHandler { */ virtual E_type - getHelixSeedE( const size_t i1, const size_t i2 ) const; + getHelixSeedE( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq1 of the mfe helix with left-most base pair (i1,i2) @@ -156,7 +156,7 @@ class HelixHandlerUnpaired : public HelixHandler { */ virtual size_t - getHelixLength1( const size_t i1, const size_t i2 ) const; + getHelixLength1( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq2 of the mfe helix with left-most base pair (i1,i2) @@ -166,7 +166,7 @@ class HelixHandlerUnpaired : public HelixHandler { */ virtual size_t - getHelixLength2( const size_t i1, const size_t i2 ) const; + getHelixLength2( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq1 of the mfe helix with left-most base pair (i1,i2) @@ -198,7 +198,7 @@ class HelixHandlerUnpaired : public HelixHandler { */ virtual size_t - getHelixSeedLength1( const size_t i1, const size_t i2 ) const; + getHelixSeedLength1( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq2 of the mfe helix with left-most base pair (i1,i2) containing a seed @@ -208,13 +208,13 @@ class HelixHandlerUnpaired : public HelixHandler { */ virtual size_t - getHelixSeedLength2( const size_t i1, const size_t i2 ) const; + getHelixSeedLength2( const size_t i1, const size_t i2 ) const override; /** * Set the seedHandler in order to compute helixSeed * @param seedHandler seedHandler to be used in the helix computation */ - void setSeedHandler(SeedHandler & seedHandler); + void setSeedHandler(SeedHandler & seedHandler) override; protected: diff --git a/src/IntaRNA/InteractionEnergyBasePair.h b/src/IntaRNA/InteractionEnergyBasePair.h index 27804aeb..1d39ac36 100644 --- a/src/IntaRNA/InteractionEnergyBasePair.h +++ b/src/IntaRNA/InteractionEnergyBasePair.h @@ -61,7 +61,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { , const bool internalLoopGU = true ); - virtual ~InteractionEnergyBasePair(); + virtual ~InteractionEnergyBasePair() override; /** @@ -79,7 +79,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual E_type - getES1( const size_t i1, const size_t j1 ) const; + getES1( const size_t i1, const size_t j1 ) const override; /** * Provides the ensemble energy (ES) of all intramolecular substructures @@ -96,7 +96,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual E_type - getES2( const size_t i2, const size_t j2 ) const; + getES2( const size_t i2, const size_t j2 ) const override; /** * Provides the energy contribution for a given number of unpaired @@ -109,7 +109,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual E_type - getE_multiUnpaired( const size_t numUnpaired ) const; + getE_multiUnpaired( const size_t numUnpaired ) const override; /** @@ -125,7 +125,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual E_type - getE_multiHelix( const size_t j1, const size_t j2 ) const; + getE_multiHelix( const size_t j1, const size_t j2 ) const override; /** * Provides the energy contribution/penalty for closing an intermolecular @@ -135,7 +135,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual E_type - getE_multiClosing() const; + getE_multiClosing() const override; /** @@ -145,7 +145,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual E_type - getE_init() const; + getE_init() const override; /** @@ -165,7 +165,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual E_type - getE_interLeft( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) const; + getE_interLeft( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) const override; /** * Computes the dangling end energy penalty estimate for the left side of @@ -181,7 +181,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual E_type - getE_danglingLeft( const size_t i1, const size_t i2 ) const; + getE_danglingLeft( const size_t i1, const size_t i2 ) const override; /** @@ -196,7 +196,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual E_type - getE_danglingRight( const size_t j1, const size_t j2 ) const; + getE_danglingRight( const size_t j1, const size_t j2 ) const override; /** * Provides the penalty for closing an interaction with the given @@ -209,7 +209,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual E_type - getE_endLeft( const size_t i1, const size_t i2 ) const; + getE_endLeft( const size_t i1, const size_t i2 ) const override; /** * Provides the penalty for closing an interaction with the given @@ -222,7 +222,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual E_type - getE_endRight( const size_t j1, const size_t j2 ) const; + getE_endRight( const size_t j1, const size_t j2 ) const override; /** * Returns always RT=1 due to the lack of reasonable values for this energy @@ -231,7 +231,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual Z_type - getRT() const; + getRT() const override; /** * Provides the (constant) energy contribution of a base pair (sequence independent) @@ -249,7 +249,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual E_type - getEall1() const; + getEall1() const override; /** * Provides the overall ensemble energy for sequence 2 @@ -258,7 +258,7 @@ class InteractionEnergyBasePair: public InteractionEnergy { */ virtual E_type - getEall2() const; + getEall2() const override; private: diff --git a/src/IntaRNA/InteractionEnergyIdxOffset.h b/src/IntaRNA/InteractionEnergyIdxOffset.h index 1d0c7b69..f43e016e 100644 --- a/src/IntaRNA/InteractionEnergyIdxOffset.h +++ b/src/IntaRNA/InteractionEnergyIdxOffset.h @@ -30,7 +30,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy , const size_t offset2 = 0 ); - virtual ~InteractionEnergyIdxOffset(); + virtual ~InteractionEnergyIdxOffset() override; /** * Access to the currently used index offset for sequence 1 @@ -77,7 +77,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy E_type getE( const size_t i1, const size_t j1 , const size_t i2, const size_t j2 - , const E_type hybridE ) const; + , const E_type hybridE ) const override; /** * Provides the ensemble energy for a given partition function Z. @@ -88,7 +88,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getE( const Z_type Z ) const; + getE( const Z_type Z ) const override; /** * Checks whether or not two positions (shifted by offset) can form a base pair @@ -98,7 +98,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual bool - areComplementary( const size_t i1, const size_t i2 ) const; + areComplementary( const size_t i1, const size_t i2 ) const override; /** * Checks whether or not two positions can form a GU base pair @@ -108,7 +108,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual bool - isGU( const size_t i1, const size_t i2 ) const; + isGU( const size_t i1, const size_t i2 ) const override; /** * Length of sequence 1 excluding the index offset @@ -116,7 +116,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual size_t - size1() const; + size1() const override; /** * Length of sequence 2 excluding index offset @@ -124,7 +124,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual size_t - size2() const; + size2() const override; /** * Provides the ED penalty for making a region with sequence 1 accessible @@ -137,7 +137,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getED1( const size_t i1, const size_t j1 ) const; + getED1( const size_t i1, const size_t j1 ) const override; /** * Provides the ED penalty for making a region with (the reversed) @@ -151,7 +151,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getED2( const size_t i2, const size_t j2 ) const; + getED2( const size_t i2, const size_t j2 ) const override; /** * Whether or not position i is accessible for interaction in sequence 1 @@ -163,7 +163,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual bool - isAccessible1( const size_t i ) const; + isAccessible1( const size_t i ) const override; /** * Whether or not position i is accessible for interaction in sequence 2 @@ -175,7 +175,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual bool - isAccessible2( const size_t i ) const; + isAccessible2( const size_t i ) const override; /** * Provides the energy contribution of an interaction site gap, i.e. the @@ -197,7 +197,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy E_type getE_multi( const size_t i1, const size_t j1 , const size_t i2, const size_t j2 - , const ES_multi_mode ES_mode ) const; + , const ES_multi_mode ES_mode ) const override; /** * Provides the ensemble energy (ES) of all intramolecular substructures @@ -214,7 +214,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getES1( const size_t i1, const size_t j1 ) const; + getES1( const size_t i1, const size_t j1 ) const override; /** * Provides the ensemble energy (ES) of all intramolecular substructures @@ -231,7 +231,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getES2( const size_t i2, const size_t j2 ) const; + getES2( const size_t i2, const size_t j2 ) const override; /** * Provides the energy contribution for a given number of unpaired @@ -244,7 +244,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getE_multiUnpaired( const size_t numUnpaired ) const; + getE_multiUnpaired( const size_t numUnpaired ) const override; /** @@ -262,7 +262,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getE_multiHelix( const size_t j1, const size_t j2 ) const; + getE_multiHelix( const size_t j1, const size_t j2 ) const override; /** * Provides the energy contribution/penalty for closing an intermolecular @@ -273,7 +273,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getE_multiClosing() const; + getE_multiClosing() const override; /** * Provides the duplex initiation energy. @@ -282,7 +282,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getE_init( ) const; + getE_init( ) const override; /** @@ -306,7 +306,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getE_interLeft( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) const; + getE_interLeft( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) const override; /** @@ -323,7 +323,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getE_danglingLeft( const size_t i1, const size_t i2 ) const; + getE_danglingLeft( const size_t i1, const size_t i2 ) const override; /** @@ -340,7 +340,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getE_danglingRight( const size_t j1, const size_t j2 ) const; + getE_danglingRight( const size_t j1, const size_t j2 ) const override; /** * Provides the penalty for closing an interaction with the given @@ -355,7 +355,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getE_endLeft( const size_t i1, const size_t i2 ) const; + getE_endLeft( const size_t i1, const size_t i2 ) const override; /** * Provides the penalty for closing an interaction with the given @@ -370,7 +370,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getE_endRight( const size_t j1, const size_t j2 ) const; + getE_endRight( const size_t j1, const size_t j2 ) const override; /** * Computes the probability of the dangling ends for the left side @@ -388,7 +388,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual Z_type - getPr_danglingLeft( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) const; + getPr_danglingLeft( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) const override; /** * Computes the probability of the dangling ends for the right side @@ -406,7 +406,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual Z_type - getPr_danglingRight( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) const; + getPr_danglingRight( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) const override; @@ -415,7 +415,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual Z_type - getRT() const; + getRT() const override; /** * Provides the base pair encoding for the given indices after shifting by @@ -426,7 +426,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual Interaction::BasePair - getBasePair( const size_t i1, const size_t i2 ) const; + getBasePair( const size_t i1, const size_t i2 ) const override; /** @@ -436,7 +436,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual size_t - getIndex1( const Interaction::BasePair & bp ) const; + getIndex1( const Interaction::BasePair & bp ) const override; /** @@ -446,7 +446,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual size_t - getIndex2( const Interaction::BasePair & bp ) const; + getIndex2( const Interaction::BasePair & bp ) const override; /** @@ -467,7 +467,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual bool - isValidInternalLoop( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) const; + isValidInternalLoop( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) const override; /** * Provides the overall ensemble energy for sequence 1 @@ -476,7 +476,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getEall1() const; + getEall1() const override; /** * Provides the overall ensemble energy for sequence 2 @@ -485,7 +485,7 @@ class InteractionEnergyIdxOffset : public InteractionEnergy */ virtual E_type - getEall2() const; + getEall2() const override; protected: diff --git a/src/IntaRNA/InteractionEnergyVrna.h b/src/IntaRNA/InteractionEnergyVrna.h index 5374f1fb..4b17653b 100644 --- a/src/IntaRNA/InteractionEnergyVrna.h +++ b/src/IntaRNA/InteractionEnergyVrna.h @@ -75,7 +75,7 @@ class InteractionEnergyVrna: public InteractionEnergy { , const bool internalLoopGU = true ); - virtual ~InteractionEnergyVrna(); + virtual ~InteractionEnergyVrna() override; /** @@ -93,7 +93,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual E_type - getES1( const size_t i1, const size_t j1 ) const; + getES1( const size_t i1, const size_t j1 ) const override; /** * Provides the ensemble energy (ES) of all intramolecular substructures @@ -110,7 +110,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual E_type - getES2( const size_t i2, const size_t j2 ) const; + getES2( const size_t i2, const size_t j2 ) const override; /** * Provides the energy contribution for a given number of unpaired @@ -123,7 +123,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual E_type - getE_multiUnpaired( const size_t numUnpaired ) const; + getE_multiUnpaired( const size_t numUnpaired ) const override; /** * Provides the energy contribution/penalty of the helix repesented by the @@ -139,7 +139,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual E_type - getE_multiHelix( const size_t j1, const size_t j2 ) const; + getE_multiHelix( const size_t j1, const size_t j2 ) const override; /** * Provides the energy contribution/penalty for closing an intermolecular @@ -150,7 +150,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual E_type - getE_multiClosing() const; + getE_multiClosing() const override; /** * Provides the duplex initiation energy. @@ -159,7 +159,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual E_type - getE_init() const; + getE_init() const override; /** * Computes the energy estimate for the interaction loop region closed by @@ -180,7 +180,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual E_type - getE_interLeft( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) const; + getE_interLeft( const size_t i1, const size_t j1, const size_t i2, const size_t j2 ) const override; /** @@ -195,7 +195,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual E_type - getE_danglingLeft( const size_t i1, const size_t i2 ) const; + getE_danglingLeft( const size_t i1, const size_t i2 ) const override; /** @@ -210,7 +210,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual E_type - getE_danglingRight( const size_t j1, const size_t j2 ) const; + getE_danglingRight( const size_t j1, const size_t j2 ) const override; /** @@ -224,7 +224,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual E_type - getE_endLeft( const size_t i1, const size_t i2 ) const; + getE_endLeft( const size_t i1, const size_t i2 ) const override; /** * Provides the penalty for closing an interaction with the given @@ -237,7 +237,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual E_type - getE_endRight( const size_t j1, const size_t j2 ) const; + getE_endRight( const size_t j1, const size_t j2 ) const override; /** * Provides the overall ensemble energy for sequence 1 @@ -246,7 +246,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual E_type - getEall1() const; + getEall1() const override; /** * Provides the overall ensemble energy for sequence 2 @@ -255,7 +255,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual E_type - getEall2() const; + getEall2() const override; /** * Provides the overall partition function for sequence 2 @@ -264,7 +264,7 @@ class InteractionEnergyVrna: public InteractionEnergy { */ virtual Z_type - getRT() const; + getRT() const override; protected: diff --git a/src/IntaRNA/Makefile.am b/src/IntaRNA/Makefile.am index 178691d6..7ed89752 100644 --- a/src/IntaRNA/Makefile.am +++ b/src/IntaRNA/Makefile.am @@ -178,7 +178,7 @@ nodist_libIntaRNA_a_SOURCES = \ if enable_pkg_config pkgconfigdir = $(libdir)/pkgconfig -pkgconfig_DATA = $(top_srcdir)/IntaRNA.pc +pkgconfig_DATA = $(top_builddir)/IntaRNA.pc endif ############################################################################### diff --git a/src/IntaRNA/OutputHandlerCsv.h b/src/IntaRNA/OutputHandlerCsv.h index 7c707ec6..4a5e5480 100644 --- a/src/IntaRNA/OutputHandlerCsv.h +++ b/src/IntaRNA/OutputHandlerCsv.h @@ -202,7 +202,7 @@ class OutputHandlerCsv : public OutputHandler /** * destruction */ - virtual ~OutputHandlerCsv(); + virtual ~OutputHandlerCsv() override; /** * Write a given RNA-RNA interaction in simple text format to the output @@ -212,7 +212,7 @@ class OutputHandlerCsv : public OutputHandler */ virtual void - add( const Interaction & interaction ); + add( const Interaction & interaction ) override; /** * Converts a list of Coltypes to their string representation. diff --git a/src/IntaRNA/OutputHandlerEnsemble.h b/src/IntaRNA/OutputHandlerEnsemble.h index e19b408b..9e2391bf 100644 --- a/src/IntaRNA/OutputHandlerEnsemble.h +++ b/src/IntaRNA/OutputHandlerEnsemble.h @@ -37,7 +37,7 @@ class OutputHandlerEnsemble: public OutputHandler { * - prints ensemble information to stream and * - enforces a flush on the output stream. */ - virtual ~OutputHandlerEnsemble(); + virtual ~OutputHandlerEnsemble() override; /** * Does nothing but counts the call @@ -47,7 +47,7 @@ class OutputHandlerEnsemble: public OutputHandler { */ virtual void - add( const Interaction & interaction ); + add( const Interaction & interaction ) override; protected: diff --git a/src/IntaRNA/OutputHandlerHub.h b/src/IntaRNA/OutputHandlerHub.h index ac5e4cb2..9af6bb81 100644 --- a/src/IntaRNA/OutputHandlerHub.h +++ b/src/IntaRNA/OutputHandlerHub.h @@ -50,7 +50,7 @@ class OutputHandlerHub: public OutputHandler /** * destruction */ - virtual ~OutputHandlerHub(); + virtual ~OutputHandlerHub() override; /** @@ -61,7 +61,7 @@ class OutputHandlerHub: public OutputHandler */ virtual void - add( const Interaction & interaction ); + add( const Interaction & interaction ) override; /** * Returns the maximal number of reported interactions among all handlers @@ -70,7 +70,7 @@ class OutputHandlerHub: public OutputHandler */ virtual size_t - reported() const; + reported() const override; /** * Increments the overall partition function with the given value. @@ -83,7 +83,7 @@ class OutputHandlerHub: public OutputHandler */ virtual void - incrementZ( const Z_type subZ ); + incrementZ( const Z_type subZ ) override; /** * Access to the partition function (initialized with 0) aggregated via @@ -93,7 +93,7 @@ class OutputHandlerHub: public OutputHandler */ virtual Z_type - getZ() const; + getZ() const override; /** * Adds a new OutputHandler to the forwarding list. diff --git a/src/IntaRNA/OutputHandlerInteractionList.h b/src/IntaRNA/OutputHandlerInteractionList.h index abfbd905..c2735168 100644 --- a/src/IntaRNA/OutputHandlerInteractionList.h +++ b/src/IntaRNA/OutputHandlerInteractionList.h @@ -41,7 +41,7 @@ class OutputHandlerInteractionList: public OutputHandler , const size_t maxToStore); //! destruction - virtual ~OutputHandlerInteractionList(); + virtual ~OutputHandlerInteractionList() override; /** * Adds a given RNA-RNA interaction to the storage/output. @@ -50,7 +50,7 @@ class OutputHandlerInteractionList: public OutputHandler */ virtual void - add( const Interaction & interaction ); + add( const Interaction & interaction ) override; //! whether or not the container is empty //! @return true if no elements are stored diff --git a/src/IntaRNA/OutputHandlerText.h b/src/IntaRNA/OutputHandlerText.h index d95fb331..253cd33b 100644 --- a/src/IntaRNA/OutputHandlerText.h +++ b/src/IntaRNA/OutputHandlerText.h @@ -41,7 +41,7 @@ class OutputHandlerText: public OutputHandler { /** * destruction, enforces a flush on the output stream. */ - virtual ~OutputHandlerText(); + virtual ~OutputHandlerText() override; /** * Write a given RNA-RNA interaction in simple text format to the output @@ -51,7 +51,7 @@ class OutputHandlerText: public OutputHandler { */ virtual void - add( const Interaction & interaction ); + add( const Interaction & interaction ) override; protected: diff --git a/src/IntaRNA/OutputStreamHandlerSortedCsv.h b/src/IntaRNA/OutputStreamHandlerSortedCsv.h index d0108983..6d16683b 100644 --- a/src/IntaRNA/OutputStreamHandlerSortedCsv.h +++ b/src/IntaRNA/OutputStreamHandlerSortedCsv.h @@ -46,14 +46,14 @@ class OutputStreamHandlerSortedCsv : public OutputStreamHandler * - calls flush() on the final output * - destruction of the underlying OutputStreamHandler */ - virtual ~OutputStreamHandlerSortedCsv(); + virtual ~OutputStreamHandlerSortedCsv() override; /** * Access to the ostream to which unsorted CSV output is to be written. * @return the output stream to write unsorted CSV output to */ virtual - std::ostream& getOutStream(); + std::ostream& getOutStream() override; protected: diff --git a/src/IntaRNA/PredictionTrackerHub.h b/src/IntaRNA/PredictionTrackerHub.h index 2718f92b..6e7e4297 100644 --- a/src/IntaRNA/PredictionTrackerHub.h +++ b/src/IntaRNA/PredictionTrackerHub.h @@ -44,7 +44,7 @@ class PredictionTrackerHub: public PredictionTracker /** * destruction */ - virtual ~PredictionTrackerHub(); + virtual ~PredictionTrackerHub() override; /** * Informs all registered trackers that Predictor.updateOptima() was called @@ -61,7 +61,7 @@ class PredictionTrackerHub: public PredictionTracker updateOptimumCalled( const size_t i1, const size_t j1 , const size_t i2, const size_t j2 , const E_type energy - ); + ) override; /** * Adds a new PredictionTracker to the forwarding list. diff --git a/src/IntaRNA/PredictionTrackerPairMinE.h b/src/IntaRNA/PredictionTrackerPairMinE.h index 06bd9c2f..cf9fc55b 100644 --- a/src/IntaRNA/PredictionTrackerPairMinE.h +++ b/src/IntaRNA/PredictionTrackerPairMinE.h @@ -69,7 +69,7 @@ class PredictionTrackerPairMinE: public PredictionTracker /** * destruction: write the pair information to the according stream. */ - virtual ~PredictionTrackerPairMinE(); + virtual ~PredictionTrackerPairMinE() override; /** @@ -86,7 +86,7 @@ class PredictionTrackerPairMinE: public PredictionTracker updateOptimumCalled( const size_t i1, const size_t j1 , const size_t i2, const size_t j2 , const E_type energy - ); + ) override; protected: diff --git a/src/IntaRNA/PredictionTrackerProfileMinE.h b/src/IntaRNA/PredictionTrackerProfileMinE.h index f8747456..f36c1067 100644 --- a/src/IntaRNA/PredictionTrackerProfileMinE.h +++ b/src/IntaRNA/PredictionTrackerProfileMinE.h @@ -71,7 +71,7 @@ class PredictionTrackerProfileMinE: public PredictionTracker /** * destruction: write the profile(s) to the according streams. */ - virtual ~PredictionTrackerProfileMinE(); + virtual ~PredictionTrackerProfileMinE() override; /** @@ -88,7 +88,7 @@ class PredictionTrackerProfileMinE: public PredictionTracker updateOptimumCalled( const size_t i1, const size_t j1 , const size_t i2, const size_t j2 , const E_type energy - ); + ) override; protected: diff --git a/src/IntaRNA/PredictionTrackerProfileSpotProb.h b/src/IntaRNA/PredictionTrackerProfileSpotProb.h index 0a127fb6..632b2853 100644 --- a/src/IntaRNA/PredictionTrackerProfileSpotProb.h +++ b/src/IntaRNA/PredictionTrackerProfileSpotProb.h @@ -75,7 +75,7 @@ class PredictionTrackerProfileSpotProb: public PredictionTracker /** * destruction: write the profile(s) to the according streams. */ - virtual ~PredictionTrackerProfileSpotProb(); + virtual ~PredictionTrackerProfileSpotProb() override; /** @@ -92,7 +92,7 @@ class PredictionTrackerProfileSpotProb: public PredictionTracker updateOptimumCalled( const size_t i1, const size_t j1 , const size_t i2, const size_t j2 , const E_type energy - ); + ) override; protected: diff --git a/src/IntaRNA/PredictionTrackerSpotProb.h b/src/IntaRNA/PredictionTrackerSpotProb.h index a6e9afc4..01bdb05e 100644 --- a/src/IntaRNA/PredictionTrackerSpotProb.h +++ b/src/IntaRNA/PredictionTrackerSpotProb.h @@ -71,7 +71,7 @@ class PredictionTrackerSpotProb: public PredictionTracker /** * destruction: write the probabilities to stream. */ - virtual ~PredictionTrackerSpotProb(); + virtual ~PredictionTrackerSpotProb() override; /** @@ -88,7 +88,7 @@ class PredictionTrackerSpotProb: public PredictionTracker updateOptimumCalled( const size_t i1, const size_t j1 , const size_t i2, const size_t j2 , const E_type energy - ); + ) override; protected: diff --git a/src/IntaRNA/PredictionTrackerSpotProbAll.h b/src/IntaRNA/PredictionTrackerSpotProbAll.h index 906b49ba..0d6cffc0 100644 --- a/src/IntaRNA/PredictionTrackerSpotProbAll.h +++ b/src/IntaRNA/PredictionTrackerSpotProbAll.h @@ -69,7 +69,7 @@ class PredictionTrackerSpotProbAll: public PredictionTracker /** * destruction: write the profile(s) to the according streams. */ - virtual ~PredictionTrackerSpotProbAll(); + virtual ~PredictionTrackerSpotProbAll() override; /** @@ -87,7 +87,7 @@ class PredictionTrackerSpotProbAll: public PredictionTracker updateOptimumCalled( const size_t i1, const size_t j1 , const size_t i2, const size_t j2 , const E_type energy - ); + ) override; protected: diff --git a/src/IntaRNA/PredictorMfe.h b/src/IntaRNA/PredictorMfe.h index 35501d33..dd7fa7ea 100644 --- a/src/IntaRNA/PredictorMfe.h +++ b/src/IntaRNA/PredictorMfe.h @@ -75,7 +75,7 @@ class PredictorMfe : public Predictor { , OutputHandler & output , PredictionTracker * predTracker ); - virtual ~PredictorMfe(); + virtual ~PredictorMfe() override; protected: @@ -112,7 +112,7 @@ class PredictorMfe : public Predictor { */ virtual void - initOptima(); + initOptima() override; /** * Checks terminal GU and accessibility constraints for a complete site. @@ -145,7 +145,7 @@ class PredictorMfe : public Predictor { , const size_t i2, const size_t j2 , const E_type energy , const bool isHybridE - , const bool incrementZall ); + , const bool incrementZall ) override; /** @@ -199,7 +199,7 @@ class PredictorMfe : public Predictor { */ virtual void - reportOptima(); + reportOptima() override; }; diff --git a/src/IntaRNA/PredictorMfe2d.h b/src/IntaRNA/PredictorMfe2d.h index 2e060f49..de3d62d5 100644 --- a/src/IntaRNA/PredictorMfe2d.h +++ b/src/IntaRNA/PredictorMfe2d.h @@ -38,7 +38,7 @@ class PredictorMfe2d: public PredictorMfe { , OutputHandler & output , PredictionTracker * predTracker ); - virtual ~PredictorMfe2d(); + virtual ~PredictorMfe2d() override; /** * Computes the mfe for the given sequence ranges (i1-j1) in the first @@ -53,7 +53,7 @@ class PredictorMfe2d: public PredictorMfe { void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) - ); + ) override; protected: @@ -94,7 +94,7 @@ class PredictorMfe2d: public PredictorMfe { */ virtual void - traceBack( Interaction & interaction ); + traceBack( Interaction & interaction ) override; }; diff --git a/src/IntaRNA/PredictorMfe2dHelixBlockHeuristic.h b/src/IntaRNA/PredictorMfe2dHelixBlockHeuristic.h index 2370901c..7fb1e18e 100644 --- a/src/IntaRNA/PredictorMfe2dHelixBlockHeuristic.h +++ b/src/IntaRNA/PredictorMfe2dHelixBlockHeuristic.h @@ -47,7 +47,7 @@ class PredictorMfe2dHelixBlockHeuristic: public PredictorMfe2dHeuristic { , PredictionTracker * predTracker , const HelixConstraint & helixConstraint); - virtual ~PredictorMfe2dHelixBlockHeuristic(); + virtual ~PredictorMfe2dHelixBlockHeuristic() override; /** * Computes the mfe for the given sequence ranges (i1-j1) in the first @@ -61,7 +61,7 @@ class PredictorMfe2dHelixBlockHeuristic: public PredictorMfe2dHeuristic { virtual void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) - , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ); + , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override; protected: @@ -88,7 +88,7 @@ class PredictorMfe2dHelixBlockHeuristic: public PredictorMfe2dHeuristic { */ virtual void - fillHybridE(); + fillHybridE() override; /** * Fills a given interaction (boundaries given) with the according @@ -97,7 +97,7 @@ class PredictorMfe2dHelixBlockHeuristic: public PredictorMfe2dHeuristic { */ virtual void - traceBack( Interaction & interaction ); + traceBack( Interaction & interaction ) override; /** * Identifies the next best interaction with an energy equal to or higher @@ -111,7 +111,7 @@ class PredictorMfe2dHelixBlockHeuristic: public PredictorMfe2dHeuristic { */ virtual void - getNextBest( Interaction & curBest ); + getNextBest( Interaction & curBest ) override; /** * Overwrites function of super class to surpress the update. @@ -126,7 +126,7 @@ class PredictorMfe2dHelixBlockHeuristic: public PredictorMfe2dHeuristic { void updateMfe4leftEnd(const size_t i1, const size_t j1 , const size_t i2, const size_t j2 - , const Interaction & curInteraction ); + , const Interaction & curInteraction ) override; }; diff --git a/src/IntaRNA/PredictorMfe2dHelixBlockHeuristicSeed.h b/src/IntaRNA/PredictorMfe2dHelixBlockHeuristicSeed.h index 342a8c65..6238905b 100644 --- a/src/IntaRNA/PredictorMfe2dHelixBlockHeuristicSeed.h +++ b/src/IntaRNA/PredictorMfe2dHelixBlockHeuristicSeed.h @@ -49,7 +49,7 @@ class PredictorMfe2dHelixBlockHeuristicSeed: public PredictorMfe2dHelixBlockHeur , SeedHandler * seedHandlerInstance ); - virtual ~PredictorMfe2dHelixBlockHeuristicSeed(); + virtual ~PredictorMfe2dHelixBlockHeuristicSeed() override; /** * Computes the mfe for the given sequence ranges (i1-j1) in the first @@ -63,7 +63,7 @@ class PredictorMfe2dHelixBlockHeuristicSeed: public PredictorMfe2dHelixBlockHeur virtual void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) - , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos)); + , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos)) override; protected: @@ -98,7 +98,7 @@ class PredictorMfe2dHelixBlockHeuristicSeed: public PredictorMfe2dHelixBlockHeur */ virtual void - traceBack( Interaction & interaction ); + traceBack( Interaction & interaction ) override; /** @@ -114,7 +114,7 @@ class PredictorMfe2dHelixBlockHeuristicSeed: public PredictorMfe2dHelixBlockHeur */ virtual void - getNextBest( Interaction & curBest ); + getNextBest( Interaction & curBest ) override; /** * disables predictionTracker usage diff --git a/src/IntaRNA/PredictorMfe2dHeuristic.h b/src/IntaRNA/PredictorMfe2dHeuristic.h index 857c5f0f..059ece2a 100644 --- a/src/IntaRNA/PredictorMfe2dHeuristic.h +++ b/src/IntaRNA/PredictorMfe2dHeuristic.h @@ -44,7 +44,7 @@ class PredictorMfe2dHeuristic: public PredictorMfe { , OutputHandler & output , PredictionTracker * predTracker ); - virtual ~PredictorMfe2dHeuristic(); + virtual ~PredictorMfe2dHeuristic() override; /** * Computes the mfe for the given sequence ranges (i1-j1) in the first @@ -58,7 +58,7 @@ class PredictorMfe2dHeuristic: public PredictorMfe { virtual void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) - , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ); + , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override; protected: @@ -91,7 +91,7 @@ class PredictorMfe2dHeuristic: public PredictorMfe { */ virtual void - traceBack( Interaction & interaction ); + traceBack( Interaction & interaction ) override; /** * Identifies the next best interaction with an energy equal to or higher @@ -105,7 +105,7 @@ class PredictorMfe2dHeuristic: public PredictorMfe { */ virtual void - getNextBest( Interaction & curBest ); + getNextBest( Interaction & curBest ) override; /** * Overwrites function of super class to surpress the update. @@ -120,7 +120,7 @@ class PredictorMfe2dHeuristic: public PredictorMfe { void updateMfe4leftEnd(const size_t i1, const size_t j1 , const size_t i2, const size_t j2 - , const Interaction & curInteraction ); + , const Interaction & curInteraction ) override; }; diff --git a/src/IntaRNA/PredictorMfe2dHeuristicSeed.h b/src/IntaRNA/PredictorMfe2dHeuristicSeed.h index ef6fe824..5e4fcef3 100644 --- a/src/IntaRNA/PredictorMfe2dHeuristicSeed.h +++ b/src/IntaRNA/PredictorMfe2dHeuristicSeed.h @@ -45,7 +45,7 @@ class PredictorMfe2dHeuristicSeed: public PredictorMfe2dHeuristic { , PredictionTracker * predTracker , SeedHandler* seedHandler ); - virtual ~PredictorMfe2dHeuristicSeed(); + virtual ~PredictorMfe2dHeuristicSeed() override; /** * Computes the mfe for the given sequence ranges (i1-j1) in the first @@ -59,7 +59,7 @@ class PredictorMfe2dHeuristicSeed: public PredictorMfe2dHeuristic { virtual void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) - , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos)); + , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos)) override; protected: @@ -91,7 +91,7 @@ class PredictorMfe2dHeuristicSeed: public PredictorMfe2dHeuristic { */ virtual void - traceBack( Interaction & interaction ); + traceBack( Interaction & interaction ) override; /** @@ -100,7 +100,7 @@ class PredictorMfe2dHeuristicSeed: public PredictorMfe2dHeuristic { */ virtual void - fillHybridE(); + fillHybridE() override; /** @@ -116,7 +116,7 @@ class PredictorMfe2dHeuristicSeed: public PredictorMfe2dHeuristic { */ virtual void - getNextBest( Interaction & curBest ); + getNextBest( Interaction & curBest ) override; }; diff --git a/src/IntaRNA/PredictorMfe2dHeuristicSeedExtension.h b/src/IntaRNA/PredictorMfe2dHeuristicSeedExtension.h index 8d43a315..696ce5db 100644 --- a/src/IntaRNA/PredictorMfe2dHeuristicSeedExtension.h +++ b/src/IntaRNA/PredictorMfe2dHeuristicSeedExtension.h @@ -48,7 +48,7 @@ class PredictorMfe2dHeuristicSeedExtension: public PredictorMfe2dSeedExtension { /** * data cleanup */ - virtual ~PredictorMfe2dHeuristicSeedExtension(); + virtual ~PredictorMfe2dHeuristicSeedExtension() override; /** @@ -66,7 +66,7 @@ class PredictorMfe2dHeuristicSeedExtension: public PredictorMfe2dSeedExtension { virtual void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) - , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ); + , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override; protected: diff --git a/src/IntaRNA/PredictorMfe2dSeed.h b/src/IntaRNA/PredictorMfe2dSeed.h index d959f97d..e4d1330a 100644 --- a/src/IntaRNA/PredictorMfe2dSeed.h +++ b/src/IntaRNA/PredictorMfe2dSeed.h @@ -53,7 +53,7 @@ class PredictorMfe2dSeed: public PredictorMfe2d { /** * data cleanup */ - virtual ~PredictorMfe2dSeed(); + virtual ~PredictorMfe2dSeed() override; /** @@ -71,7 +71,7 @@ class PredictorMfe2dSeed: public PredictorMfe2d { virtual void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) - , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ); + , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override; protected: @@ -112,7 +112,7 @@ class PredictorMfe2dSeed: public PredictorMfe2d { fillHybridE( const size_t j1, const size_t j2 , const size_t i1init, const size_t i2init , const bool callUpdateOptima - ); + ) override; /** * Fills a given interaction (boundaries given) with the according @@ -121,7 +121,7 @@ class PredictorMfe2dSeed: public PredictorMfe2d { */ virtual void - traceBack( Interaction & interaction ); + traceBack( Interaction & interaction ) override; }; diff --git a/src/IntaRNA/PredictorMfe2dSeedExtension.h b/src/IntaRNA/PredictorMfe2dSeedExtension.h index 176e14a1..5fef17d9 100644 --- a/src/IntaRNA/PredictorMfe2dSeedExtension.h +++ b/src/IntaRNA/PredictorMfe2dSeedExtension.h @@ -52,7 +52,7 @@ class PredictorMfe2dSeedExtension: public PredictorMfe2d { /** * data cleanup */ - virtual ~PredictorMfe2dSeedExtension(); + virtual ~PredictorMfe2dSeedExtension() override; /** @@ -70,7 +70,7 @@ class PredictorMfe2dSeedExtension: public PredictorMfe2d { virtual void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) - , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ); + , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override; protected: @@ -122,7 +122,7 @@ class PredictorMfe2dSeedExtension: public PredictorMfe2d { */ virtual void - traceBack( Interaction & interaction ); + traceBack( Interaction & interaction ) override; void printMatrix( const E2dMatrix & matrix ); diff --git a/src/IntaRNA/PredictorMfe2dSeedExtensionRIblast.h b/src/IntaRNA/PredictorMfe2dSeedExtensionRIblast.h index c352cebf..788e70cf 100644 --- a/src/IntaRNA/PredictorMfe2dSeedExtensionRIblast.h +++ b/src/IntaRNA/PredictorMfe2dSeedExtensionRIblast.h @@ -60,7 +60,7 @@ class PredictorMfe2dSeedExtensionRIblast: public PredictorMfe2d { /** * data cleanup */ - virtual ~PredictorMfe2dSeedExtensionRIblast(); + virtual ~PredictorMfe2dSeedExtensionRIblast() override; /** @@ -78,7 +78,7 @@ class PredictorMfe2dSeedExtensionRIblast: public PredictorMfe2d { virtual void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) - , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ); + , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override; protected: @@ -141,7 +141,7 @@ class PredictorMfe2dSeedExtensionRIblast: public PredictorMfe2d { */ virtual void - traceBack( Interaction & interaction ); + traceBack( Interaction & interaction ) override; void printMatrix( const E2dMatrix & matrix ); diff --git a/src/IntaRNA/PredictorMfeEns.h b/src/IntaRNA/PredictorMfeEns.h index c51fd654..670b8b2d 100644 --- a/src/IntaRNA/PredictorMfeEns.h +++ b/src/IntaRNA/PredictorMfeEns.h @@ -36,7 +36,7 @@ class PredictorMfeEns : public PredictorMfe { , OutputHandler & output , PredictionTracker * predTracker ); - virtual ~PredictorMfeEns(); + virtual ~PredictorMfeEns() override; protected: @@ -127,7 +127,7 @@ class PredictorMfeEns : public PredictorMfe { */ virtual void - reportOptima(); + reportOptima() override; /** * Reports interaction boundaries only (no base pair tracking) @@ -135,7 +135,7 @@ class PredictorMfeEns : public PredictorMfe { */ virtual void - traceBack( Interaction & interaction ); + traceBack( Interaction & interaction ) override; private: diff --git a/src/IntaRNA/PredictorMfeEns2d.h b/src/IntaRNA/PredictorMfeEns2d.h index 2b77bb67..539d4576 100644 --- a/src/IntaRNA/PredictorMfeEns2d.h +++ b/src/IntaRNA/PredictorMfeEns2d.h @@ -45,7 +45,7 @@ class PredictorMfeEns2d: public PredictorMfeEns { , PredictionTracker * predTracker , BasePairProbabilities * pairProbabilities = nullptr ); - virtual ~PredictorMfeEns2d(); + virtual ~PredictorMfeEns2d() override; /** * Computes the mfe for the given sequence ranges (i1-j1) in the first @@ -60,7 +60,7 @@ class PredictorMfeEns2d: public PredictorMfeEns { void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) - ); + ) override; protected: diff --git a/src/IntaRNA/PredictorMfeEns2dHeuristic.h b/src/IntaRNA/PredictorMfeEns2dHeuristic.h index 75e5b935..5c789a25 100644 --- a/src/IntaRNA/PredictorMfeEns2dHeuristic.h +++ b/src/IntaRNA/PredictorMfeEns2dHeuristic.h @@ -52,7 +52,7 @@ class PredictorMfeEns2dHeuristic: public PredictorMfeEns2d { , PredictionTracker * predTracker , BasePairProbabilities * pairProbabilities = nullptr ); - virtual ~PredictorMfeEns2dHeuristic(); + virtual ~PredictorMfeEns2dHeuristic() override; /** * Computes the mfe for the given sequence ranges (i1-j1) in the first @@ -66,7 +66,7 @@ class PredictorMfeEns2dHeuristic: public PredictorMfeEns2d { virtual void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) - , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ); + , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override; protected: diff --git a/src/IntaRNA/PredictorMfeEns2dHeuristicSeedExtension.h b/src/IntaRNA/PredictorMfeEns2dHeuristicSeedExtension.h index 27b87452..7ab478eb 100644 --- a/src/IntaRNA/PredictorMfeEns2dHeuristicSeedExtension.h +++ b/src/IntaRNA/PredictorMfeEns2dHeuristicSeedExtension.h @@ -52,7 +52,7 @@ class PredictorMfeEns2dHeuristicSeedExtension: public PredictorMfeEns2dSeedExten /** * data cleanup */ - virtual ~PredictorMfeEns2dHeuristicSeedExtension(); + virtual ~PredictorMfeEns2dHeuristicSeedExtension() override; /** @@ -70,7 +70,7 @@ class PredictorMfeEns2dHeuristicSeedExtension: public PredictorMfeEns2dSeedExten virtual void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) - , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ); + , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override; protected: @@ -157,7 +157,7 @@ class PredictorMfeEns2dHeuristicSeedExtension: public PredictorMfeEns2dSeedExten */ virtual void - fillHybridZ_left( const size_t j1, const size_t j2 ); + fillHybridZ_left( const size_t j1, const size_t j2 ) override; }; diff --git a/src/IntaRNA/PredictorMfeEns2dSeedExtension.h b/src/IntaRNA/PredictorMfeEns2dSeedExtension.h index 5c509295..21255565 100644 --- a/src/IntaRNA/PredictorMfeEns2dSeedExtension.h +++ b/src/IntaRNA/PredictorMfeEns2dSeedExtension.h @@ -60,7 +60,7 @@ class PredictorMfeEns2dSeedExtension: public PredictorMfeEns { /** * data cleanup */ - virtual ~PredictorMfeEns2dSeedExtension(); + virtual ~PredictorMfeEns2dSeedExtension() override; /** @@ -78,7 +78,7 @@ class PredictorMfeEns2dSeedExtension: public PredictorMfeEns { virtual void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) - , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ); + , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override; protected: @@ -177,7 +177,7 @@ class PredictorMfeEns2dSeedExtension: public PredictorMfeEns { */ virtual void - traceBack( Interaction & interaction ); + traceBack( Interaction & interaction ) override; /** * Returns the hybridization energy of the non overlapping part of seeds diff --git a/src/IntaRNA/PredictorMfeEnsSeedOnly.h b/src/IntaRNA/PredictorMfeEnsSeedOnly.h index 3507917c..a93cd85f 100644 --- a/src/IntaRNA/PredictorMfeEnsSeedOnly.h +++ b/src/IntaRNA/PredictorMfeEnsSeedOnly.h @@ -37,7 +37,7 @@ class PredictorMfeEnsSeedOnly: public PredictorMfeEns { /** * data cleanup */ - virtual ~PredictorMfeEnsSeedOnly(); + virtual ~PredictorMfeEnsSeedOnly() override; /** * Computes the mfe seed for the given sequence ranges (i1-j1) in the first @@ -51,7 +51,7 @@ class PredictorMfeEnsSeedOnly: public PredictorMfeEns { virtual void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) - , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ); + , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override; protected: @@ -83,7 +83,7 @@ class PredictorMfeEnsSeedOnly: public PredictorMfeEns { */ virtual void - traceBack( Interaction & interaction ); + traceBack( Interaction & interaction ) override; }; diff --git a/src/IntaRNA/PredictorMfeSeedOnly.h b/src/IntaRNA/PredictorMfeSeedOnly.h index fee5fbee..00bcc940 100644 --- a/src/IntaRNA/PredictorMfeSeedOnly.h +++ b/src/IntaRNA/PredictorMfeSeedOnly.h @@ -37,7 +37,7 @@ class PredictorMfeSeedOnly: public PredictorMfe { /** * data cleanup */ - virtual ~PredictorMfeSeedOnly(); + virtual ~PredictorMfeSeedOnly() override; /** @@ -52,7 +52,7 @@ class PredictorMfeSeedOnly: public PredictorMfe { virtual void predict( const IndexRange & r1 = IndexRange(0,RnaSequence::lastPos) - , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ); + , const IndexRange & r2 = IndexRange(0,RnaSequence::lastPos) ) override; protected: @@ -84,7 +84,7 @@ class PredictorMfeSeedOnly: public PredictorMfe { */ virtual void - traceBack( Interaction & interaction ); + traceBack( Interaction & interaction ) override; }; diff --git a/src/IntaRNA/PredictorSeedExtensionKinetic.h b/src/IntaRNA/PredictorSeedExtensionKinetic.h index fd996428..390bffc1 100644 --- a/src/IntaRNA/PredictorSeedExtensionKinetic.h +++ b/src/IntaRNA/PredictorSeedExtensionKinetic.h @@ -51,7 +51,7 @@ class PredictorSeedExtensionKinetic : public PredictorMfe { SeedHandler * seedHandler, const char score = 'A'); /** Frees the owned seed handler and prediction tracker. */ - virtual ~PredictorSeedExtensionKinetic(); + virtual ~PredictorSeedExtensionKinetic() override; /** * Extends all feasible seeds within inclusive, zero-based sequence ranges. diff --git a/src/IntaRNA/ReverseAccessibility.h b/src/IntaRNA/ReverseAccessibility.h index 983e74d4..49ce5001 100644 --- a/src/IntaRNA/ReverseAccessibility.h +++ b/src/IntaRNA/ReverseAccessibility.h @@ -23,7 +23,7 @@ class ReverseAccessibility: public Accessibility { /** * destruction */ - virtual ~ReverseAccessibility(); + virtual ~ReverseAccessibility() override; /** * Access to the accessibility energy value (according to reversed indices). @@ -35,7 +35,7 @@ class ReverseAccessibility: public Accessibility { */ virtual E_type - getED( const size_t from, const size_t to ) const; + getED( const size_t from, const size_t to ) const override; /** @@ -44,7 +44,7 @@ class ReverseAccessibility: public Accessibility { */ virtual const RnaSequence & - getSequence() const; + getSequence() const override; /** @@ -56,7 +56,7 @@ class ReverseAccessibility: public Accessibility { */ virtual const AccessibilityConstraint& - getAccConstraint() const; + getAccConstraint() const override; /** * Access to the original not-reversed accessibility object. diff --git a/src/IntaRNA/SeedHandlerExplicit.h b/src/IntaRNA/SeedHandlerExplicit.h index a5af80c3..171fb7b4 100644 --- a/src/IntaRNA/SeedHandlerExplicit.h +++ b/src/IntaRNA/SeedHandlerExplicit.h @@ -37,7 +37,7 @@ class SeedHandlerExplicit : public SeedHandler /** * destruction */ - virtual ~SeedHandlerExplicit(); + virtual ~SeedHandlerExplicit() override; /** @@ -50,7 +50,7 @@ class SeedHandlerExplicit : public SeedHandler */ virtual size_t - fillSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2); + fillSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2) override; /** * Identifies the base pairs of the seed interaction starting at i1,i2 @@ -64,7 +64,7 @@ class SeedHandlerExplicit : public SeedHandler */ virtual void - traceBackSeed( Interaction & interaction, const size_t i1, const size_t i2) const; + traceBackSeed( Interaction & interaction, const size_t i1, const size_t i2) const override; /** @@ -75,7 +75,7 @@ class SeedHandlerExplicit : public SeedHandler */ virtual E_type - getSeedE( const size_t i1, const size_t i2 ) const; + getSeedE( const size_t i1, const size_t i2 ) const override; /** * Checks whether or not a given base pair is the left-most base pair of @@ -87,7 +87,7 @@ class SeedHandlerExplicit : public SeedHandler */ virtual bool - isSeedBound( const size_t i1, const size_t i2 ) const; + isSeedBound( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq1 of the seed with left-most base pair (i1,i2) @@ -97,7 +97,7 @@ class SeedHandlerExplicit : public SeedHandler */ virtual size_t - getSeedLength1( const size_t i1, const size_t i2 ) const; + getSeedLength1( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq2 of the seed with left-most base pair (i1,i2) @@ -107,7 +107,7 @@ class SeedHandlerExplicit : public SeedHandler */ virtual size_t - getSeedLength2( const size_t i1, const size_t i2 ) const; + getSeedLength2( const size_t i1, const size_t i2 ) const override; @@ -160,7 +160,7 @@ class SeedHandlerExplicit : public SeedHandler updateToNextSeed( size_t & i1, size_t & i2 , const size_t i1min = 0, const size_t i1max = RnaSequence::lastPos , const size_t i2min = 0, const size_t i2max = RnaSequence::lastPos - ) const; + ) const override; public: diff --git a/src/IntaRNA/SeedHandlerIdxOffset.h b/src/IntaRNA/SeedHandlerIdxOffset.h index 11b30f96..5b3b4445 100644 --- a/src/IntaRNA/SeedHandlerIdxOffset.h +++ b/src/IntaRNA/SeedHandlerIdxOffset.h @@ -43,7 +43,7 @@ class SeedHandlerIdxOffset : public SeedHandler /** * destruction of this object and the wrapped seed handler */ - virtual ~SeedHandlerIdxOffset(); + virtual ~SeedHandlerIdxOffset() override; /** * Access to the currently used index offset for sequence 1 @@ -79,7 +79,7 @@ class SeedHandlerIdxOffset : public SeedHandler */ virtual const SeedConstraint& - getConstraint() const; + getConstraint() const override; /** * Access to the underlying interaction energy function @@ -87,7 +87,7 @@ class SeedHandlerIdxOffset : public SeedHandler */ virtual const InteractionEnergy& - getInteractionEnergy() const; + getInteractionEnergy() const override; /** @@ -104,7 +104,7 @@ class SeedHandlerIdxOffset : public SeedHandler */ virtual size_t - fillSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2); + fillSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2) override; /** * Identifies the base pairs of the mfe seed interaction starting at i1,i2 @@ -120,7 +120,7 @@ class SeedHandlerIdxOffset : public SeedHandler */ virtual void - traceBackSeed( Interaction & interaction, const size_t i1, const size_t i2) const; + traceBackSeed( Interaction & interaction, const size_t i1, const size_t i2) const override; /** @@ -134,7 +134,7 @@ class SeedHandlerIdxOffset : public SeedHandler */ virtual E_type - getSeedE( const size_t i1, const size_t i2 ) const; + getSeedE( const size_t i1, const size_t i2 ) const override; /** * Checks whether or not a given base pair is the left-most base pair of @@ -146,7 +146,7 @@ class SeedHandlerIdxOffset : public SeedHandler */ virtual bool - isSeedBound( const size_t i1, const size_t i2 ) const; + isSeedBound( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq1 of the mfe seed with left-most base pair (i1,i2) @@ -159,7 +159,7 @@ class SeedHandlerIdxOffset : public SeedHandler */ virtual size_t - getSeedLength1( const size_t i1, const size_t i2 ) const; + getSeedLength1( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq2 of the mfe seed with left-most base pair (i1,i2) @@ -172,7 +172,7 @@ class SeedHandlerIdxOffset : public SeedHandler */ virtual size_t - getSeedLength2( const size_t i1, const size_t i2 ) const; + getSeedLength2( const size_t i1, const size_t i2 ) const override; /** @@ -212,7 +212,7 @@ class SeedHandlerIdxOffset : public SeedHandler updateToNextSeed( size_t & i1, size_t & i2 , const size_t i1min = 0, const size_t i1max = RnaSequence::lastPos , const size_t i2min = 0, const size_t i2max = RnaSequence::lastPos - ) const; + ) const override; /** * Adds all seeds to a given interaction that are completely covered by its @@ -223,7 +223,7 @@ class SeedHandlerIdxOffset : public SeedHandler */ virtual void - addSeeds( Interaction & i ) const; + addSeeds( Interaction & i ) const override; /** * Checks whether or not two seeds are loop overlapping, ie. given i1 < k1, the @@ -240,7 +240,7 @@ class SeedHandlerIdxOffset : public SeedHandler virtual bool areLoopOverlapping( const size_t i1, const size_t i2 - , const size_t k1, const size_t k2 ) const; + , const size_t k1, const size_t k2 ) const override; /** * Checks whether or not a given index pair is a valid seed base pair @@ -255,7 +255,7 @@ class SeedHandlerIdxOffset : public SeedHandler bool isFeasibleSeedBasePair( const size_t i1 , const size_t i2 - , const bool atEndOfSeed = false ) const; + , const bool atEndOfSeed = false ) const override; protected: diff --git a/src/IntaRNA/SeedHandlerMfe.h b/src/IntaRNA/SeedHandlerMfe.h index 94979fdf..00cee2c4 100644 --- a/src/IntaRNA/SeedHandlerMfe.h +++ b/src/IntaRNA/SeedHandlerMfe.h @@ -62,7 +62,7 @@ class SeedHandlerMfe : public SeedHandler /** * destruction */ - virtual ~SeedHandlerMfe(); + virtual ~SeedHandlerMfe() override; /** * Computes the seed matrix for the given interval boundaries @@ -74,7 +74,7 @@ class SeedHandlerMfe : public SeedHandler */ virtual size_t - fillSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2); + fillSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2) override; /** * Identifies the base pairs of the mfe seed interaction starting at i1,i2 @@ -88,7 +88,7 @@ class SeedHandlerMfe : public SeedHandler */ virtual void - traceBackSeed( Interaction & interaction, const size_t i1, const size_t i2) const; + traceBackSeed( Interaction & interaction, const size_t i1, const size_t i2) const override; /** @@ -99,7 +99,7 @@ class SeedHandlerMfe : public SeedHandler */ virtual E_type - getSeedE( const size_t i1, const size_t i2 ) const; + getSeedE( const size_t i1, const size_t i2 ) const override; /** * Checks whether or not a given base pair is the left-most base pair of @@ -111,7 +111,7 @@ class SeedHandlerMfe : public SeedHandler */ virtual bool - isSeedBound( const size_t i1, const size_t i2 ) const; + isSeedBound( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq1 of the mfe seed with left-most base pair (i1,i2) @@ -121,7 +121,7 @@ class SeedHandlerMfe : public SeedHandler */ virtual size_t - getSeedLength1( const size_t i1, const size_t i2 ) const; + getSeedLength1( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq2 of the mfe seed with left-most base pair (i1,i2) @@ -131,7 +131,7 @@ class SeedHandlerMfe : public SeedHandler */ virtual size_t - getSeedLength2( const size_t i1, const size_t i2 ) const; + getSeedLength2( const size_t i1, const size_t i2 ) const override; diff --git a/src/IntaRNA/SeedHandlerNoBulge.h b/src/IntaRNA/SeedHandlerNoBulge.h index 927643c9..8d504ffa 100644 --- a/src/IntaRNA/SeedHandlerNoBulge.h +++ b/src/IntaRNA/SeedHandlerNoBulge.h @@ -54,7 +54,7 @@ class SeedHandlerNoBulge : public SeedHandler /** * destruction */ - virtual ~SeedHandlerNoBulge(); + virtual ~SeedHandlerNoBulge() override; /** * Computes the seed information for the given interval boundaries @@ -66,7 +66,7 @@ class SeedHandlerNoBulge : public SeedHandler */ virtual size_t - fillSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2); + fillSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2) override; /** * Identifies the base pairs of the mfe seed interaction starting at i1,i2 @@ -80,7 +80,7 @@ class SeedHandlerNoBulge : public SeedHandler */ virtual void - traceBackSeed( Interaction & interaction, const size_t i1, const size_t i2) const; + traceBackSeed( Interaction & interaction, const size_t i1, const size_t i2) const override; /** @@ -91,7 +91,7 @@ class SeedHandlerNoBulge : public SeedHandler */ virtual E_type - getSeedE( const size_t i1, const size_t i2 ) const; + getSeedE( const size_t i1, const size_t i2 ) const override; /** * Checks whether or not a given base pair is the left-most base pair of @@ -103,7 +103,7 @@ class SeedHandlerNoBulge : public SeedHandler */ virtual bool - isSeedBound( const size_t i1, const size_t i2 ) const; + isSeedBound( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq1 of the mfe seed with left-most base pair (i1,i2) @@ -113,7 +113,7 @@ class SeedHandlerNoBulge : public SeedHandler */ virtual size_t - getSeedLength1( const size_t i1, const size_t i2 ) const; + getSeedLength1( const size_t i1, const size_t i2 ) const override; /** * Access to the length in seq2 of the mfe seed with left-most base pair (i1,i2) @@ -123,7 +123,7 @@ class SeedHandlerNoBulge : public SeedHandler */ virtual size_t - getSeedLength2( const size_t i1, const size_t i2 ) const; + getSeedLength2( const size_t i1, const size_t i2 ) const override; /** * Replace the input variables i1 and i2 to values to within the given range @@ -153,7 +153,7 @@ class SeedHandlerNoBulge : public SeedHandler updateToNextSeed( size_t & i1, size_t & i2 , const size_t i1min = 0, const size_t i1max = RnaSequence::lastPos , const size_t i2min = 0, const size_t i2max = RnaSequence::lastPos - ) const; + ) const override; protected: diff --git a/src/IntaRNA/SeededPartitionFunction.cpp b/src/IntaRNA/SeededPartitionFunction.cpp index dc4afff6..2c138d44 100644 --- a/src/IntaRNA/SeededPartitionFunction.cpp +++ b/src/IntaRNA/SeededPartitionFunction.cpp @@ -61,10 +61,12 @@ computeAnchored(const Kernel::Domain & d,const StackSeedDomain & seeds, for(size_t i=0;i hybrid(batchSize,cells),boundary; if(pairs) boundary.resize(batchSize,cells,false); @@ -343,10 +345,24 @@ computeAnchored(const Kernel::Domain & d,const StackSeedDomain & seeds, auto processBatch=[&]() { reset(hybrid,starts.size(),cells); if(pairs) reset(boundary,starts.size(),cells); candidates.clear(); initiation.clear(); - // Query only anchor starts inside the batch's span boxes, then restore - // deterministic seed order independently of hash-table iteration order. + // Query only anchor starts inside the batch's span boxes. Sparse seed + // domains are cheaper to scan directly than probing every possible pair + // in every source span; dense domains retain the bounded grid probe. for(const Pair p:starts) { initiation.push_back(A::check(w.initiation(p))); + } + if(anchors.size()anchor.i || p.second>anchor.j) continue; + const size_t i=anchor.i-p.first,j=anchor.j-p.second; + if(i>=maxN || j>=maxM || anchor.length>maxN-i || anchor.length>maxM-j) continue; + included[a]=1; candidates.push_back(a); break; + } + } + } else { + for(const Pair p:starts) for(size_t i=p.first;imaxN-(i-p.first) || anchor.length>maxM-(j-p.second)) continue; included[found->second]=1; candidates.push_back(found->second); } + std::sort(candidates.begin(),candidates.end()); } - std::sort(candidates.begin(),candidates.end()); for(const size_t a:candidates) { fill(a); contract(false); } for(size_t b=0;b(&(personalityParamValue)) , "IntaRNA personality to be used, which defines default values, available program arguments and tool behavior") ("parameterFile", value(&(configFileName)) - , "file from where to read additional command line arguments") + , "legacy key=value or JSON parameter file (auto-detected); JSON can embed text input files") ("help,h", "show the help page for basic parameters") ("fullhelp", "show the extended help page for all available parameters") ; @@ -1142,7 +1142,7 @@ parse(int argc, char** argv) LOG(ERROR) <<"Parsing of 'parameterFile' : could not open file '"<(paramfile, opts_cmdline_all), vm); + store( parameterFile.parse(paramfile, opts_cmdline_all), vm); } } catch (std::exception & ex) { LOG(ERROR) <<"error while parsing of 'parameterFile="< #include +#include "ParameterFile.h" + #include #include #include @@ -814,6 +816,9 @@ class CommandLineParsing { //! (optional) file name for input parameter configuration file std::string configFileName; + //! owns embedded parameter-file inputs until all predictions finish + ParameterFile parameterFile; + //! the vienna energy parameter handler initialized by #parse() mutable VrnaHandler vrnaHandler; diff --git a/src/bin/Makefile.am b/src/bin/Makefile.am index e85a84a6..1edf62a0 100644 --- a/src/bin/Makefile.am +++ b/src/bin/Makefile.am @@ -24,12 +24,17 @@ IntaRNA_CXXFLAGS = $(AM_CXXFLAGS) @INTARNA_SYSTEM_CPPFLAGS@ # generated intaRNA sources nodist_IntaRNA_SOURCES = \ ../config.h \ - IntaRNA/intarna_config.h + ../IntaRNA/intarna_config.h # intaRNA sources IntaRNA_SOURCES = IntaRNA.cpp \ CommandLineParsing.h \ - CommandLineParsing.cpp + CommandLineParsing.cpp \ + ParameterFile.h \ + ParameterFile.cpp \ + nlohmann/json.hpp + +EXTRA_DIST = nlohmann/LICENSE.MIT nlohmann/README.md IntaRNA_LDADD = $(top_builddir)/src/IntaRNA/libIntaRNA.a \ $(top_builddir)/src/libeasylogging.a diff --git a/src/bin/ParameterFile.cpp b/src/bin/ParameterFile.cpp new file mode 100644 index 00000000..f7f8443c --- /dev/null +++ b/src/bin/ParameterFile.cpp @@ -0,0 +1,162 @@ +#include "ParameterFile.h" +#include "nlohmann/json.hpp" + +#include +#include +#include +#include +#include +#include +#include + +namespace { +using Json = nlohmann::json; +using namespace boost::program_options; + +// Read once, remove a UTF-8 BOM, then detect JSON independently of the suffix. +std::string readText(std::istream& input) +{ + std::string text{std::istreambuf_iterator(input), {}}; + if (input.bad()) throw std::runtime_error("Could not read parameter file"); + if (text.starts_with("\xef\xbb\xbf")) text.erase(0, 3); + return text; +} + +bool isJson(const std::string& text) +{ + const auto first = text.find_first_not_of(" \t\r\n"); + return first != std::string::npos && (text[first] == '{' || text[first] == '['); +} + +Json readJson(const std::string& text) +{ + // Reject duplicate keys and excessive nesting rather than silently replacing + // settings or consuming an unbounded call stack on malformed input. + std::vector> keys; + auto callback = [&keys](int depth, Json::parse_event_t event, Json& value) { + if (depth > 32) throw std::runtime_error("JSON parameter nesting exceeds 32 levels"); + if (event == Json::parse_event_t::object_start) keys.emplace_back(); + if (event == Json::parse_event_t::key && !keys.back().insert(value.get()).second) + throw std::runtime_error("Duplicate JSON key: " + value.get()); + if (event == Json::parse_event_t::object_end) keys.pop_back(); + return true; + }; + Json document = Json::parse(text, callback); + if (!document.is_object()) throw std::runtime_error("JSON parameter file must be an object"); + for (const auto& [key, value] : document.items()) { + if (key != "parameters" && key != "schema" && key != "_comment" && key != "gui") + throw std::runtime_error("Unknown JSON document field: " + key); + } + if (document.value("schema", std::string()) != "IntaRNA-parameters-v1") + throw std::runtime_error("Expected schema IntaRNA-parameters-v1"); + if (!document.contains("parameters") || !document["parameters"].is_object()) + throw std::runtime_error("JSON parameters must be an object"); + return document["parameters"]; +} + +std::string scalar(const Json& value) +{ + if (value.is_string()) { + const auto text = value.get(); + if (text.find('\0') != std::string::npos) throw std::runtime_error("NUL in JSON parameter text"); + return text; + } + if (value.is_boolean() || value.is_number()) return value.dump(); + throw std::runtime_error("JSON parameter values must be strings, numbers, booleans or embedded text"); +} +} + +ParameterFile::~ParameterFile() +{ + // Cleanup must also succeed during exception unwinding and after failed input. + if (!directory.empty()) { + boost::system::error_code ignored; + boost::filesystem::remove_all(directory, ignored); + } +} + +std::string ParameterFile::writeText(const std::string& name, const std::string& text) +{ + // Never interpret embedded data or JSON keys as filesystem paths. + if (directory.empty()) { + const auto path = boost::filesystem::temp_directory_path() + / boost::filesystem::unique_path("intarna-json-%%%%-%%%%-%%%%-%%%%"); + if (!boost::filesystem::create_directory(path)) throw std::runtime_error("Could not create embedded-input directory"); + directory = path.string(); + boost::filesystem::permissions(path, boost::filesystem::owner_all); + } + const auto path = (boost::filesystem::path(directory) / name).string(); + std::ofstream file(path, std::ios::binary); + file.exceptions(std::ios::badbit | std::ios::failbit); + file.write(text.data(), text.size()); + file.close(); + return path; +} + +boost::program_options::parsed_options +ParameterFile::parse(std::istream& input, const boost::program_options::options_description& options) +{ + const auto text = readText(input); + if (!isJson(text)) { + std::istringstream legacy(text); + return boost::program_options::parse_config_file(legacy, options); + } + const auto parameters = readJson(text); + boost::program_options::parsed_options parsed(&options); + const std::set fileInputs = {"query", "target", "qAccFile", "tAccFile", "qShape", "tShape", "energyVRNA"}; + for (const auto& [key, value] : parameters.items()) { + // Reuse Program_options type conversion and validation without converting + // through config-file syntax (which would reinterpret # or newlines). + const auto* definition = options.find_nothrow(key, false); + if (!definition || definition->long_name() != key || key == "parameterFile") + throw std::runtime_error("Unknown or recursive JSON parameter: " + key); + auto append = [&](const Json& item) { + boost::program_options::option option; + option.string_key = key; + if (definition->semantic()->max_tokens() == 0) { + if (!item.is_boolean()) throw std::runtime_error(key + " requires a JSON boolean"); + if (!item.get()) return; + } else if (item.is_object()) { + if (!fileInputs.contains(key)) throw std::runtime_error(key + " does not accept embedded files"); + if (item.size() == 1 && item.contains("text") && item["text"].is_string()) { + option.value.push_back(writeText(key + ".txt", scalar(item["text"]))); + } else if ((key == "qAccFile" || key == "tAccFile") && item.size() == 1 && item.contains("texts") && item["texts"].is_array() && !item["texts"].empty()) { + // Multi-sequence accessibility follows the existing -sN naming + // convention; indices refer to original FASTA record numbers. + const auto& texts = item["texts"]; + for (size_t i = 0; i < texts.size(); ++i) { + if (!texts[i].is_string()) throw std::runtime_error(key + ": texts must contain strings"); + writeText(key + "-s" + std::to_string(i + 1) + ".txt", scalar(texts[i])); + } + option.value.push_back((boost::filesystem::path(directory) / (key + ".txt")).string()); + } else throw std::runtime_error(key + ": expected {\"text\":\"...\"} (or accessibility {\"texts\":[...]})"); + } else option.value.push_back(scalar(item)); + parsed.options.push_back(std::move(option)); + }; + if (value.is_array()) { + if (!definition->semantic()->is_composing() || value.empty()) throw std::runtime_error(key + " does not accept an empty or repeated-value array"); + for (const auto& item : value) append(item); + } else append(value); + } + return parsed; +} + +std::string ParameterFile::personality(const std::string& filename) +{ + std::ifstream input(filename, std::ios::binary); + if (!input) throw std::runtime_error("Could not open parameter file: " + filename); + const auto text = readText(input); + if (isJson(text)) { + const auto parameters = readJson(text); + if (!parameters.contains("personality")) return {}; + if (!parameters["personality"].is_string()) throw std::runtime_error("personality must be a string"); + return scalar(parameters["personality"]); + } + // Legacy parameter files receive the same personality/default precedence. + boost::program_options::options_description options; + options.add_options()("personality", boost::program_options::value()); + std::istringstream legacy(text); + boost::program_options::variables_map values; + store(boost::program_options::parse_config_file(legacy, options, true), values); + return values.count("personality") ? values["personality"].as() : ""; +} diff --git a/src/bin/ParameterFile.h b/src/bin/ParameterFile.h new file mode 100644 index 00000000..97bf13f5 --- /dev/null +++ b/src/bin/ParameterFile.h @@ -0,0 +1,45 @@ +#ifndef INTARNA_PARAMETERFILE_H_ +#define INTARNA_PARAMETERFILE_H_ + +#include +#include +#include + +/** Reads legacy or JSON CLI parameters and owns any embedded input files. */ +class ParameterFile { +public: + ParameterFile(); + ~ParameterFile(); + ParameterFile(const ParameterFile&) = delete; + ParameterFile& operator=(const ParameterFile&) = delete; + + /** + * Parse parameters through the existing option definitions. Embedded text + * lives in private temporary files until this object is destroyed. + * @param input parameter file stream (format detected from its contents) + * @param options supported CLI options, including their validators + * @return parsed options for boost::program_options::store + * @throws std::exception on malformed parameters or failed file operations + */ + boost::program_options::parsed_options + parse(std::istream& input, const boost::program_options::options_description& options); + + /** + * Read a file's personality before constructing personality-specific defaults. + * @param filename legacy or JSON parameter file + * @return personality name, or empty if not specified + */ + static std::string personality(const std::string& filename); + +private: + //! private directory containing generated filenames only; never user paths + std::string directory; + + /** Materialize text with a generated basename; return its absolute path. */ + std::string writeText(const std::string& name, const std::string& text); +}; + +inline +ParameterFile::ParameterFile() = default; + +#endif diff --git a/src/bin/nlohmann/LICENSE.MIT b/src/bin/nlohmann/LICENSE.MIT new file mode 100644 index 00000000..a1dacc8d --- /dev/null +++ b/src/bin/nlohmann/LICENSE.MIT @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2013-2025 Niels Lohmann + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/src/bin/nlohmann/README.md b/src/bin/nlohmann/README.md new file mode 100644 index 00000000..b4d4fac5 --- /dev/null +++ b/src/bin/nlohmann/README.md @@ -0,0 +1,12 @@ +# nlohmann/json 3.12.0 + +Unmodified single header and MIT license from +https://github.com/nlohmann/json/tree/v3.12.0. + +- `single_include/nlohmann/json.hpp`: SHA-256 `aaf127c04cb31c406e5b04a63f1ae89369fccde6d8fa7cdda1ed4f32dfc5de63` +- `LICENSE.MIT`: SHA-256 `46a65cffd1ea955132d95a8dd921640714a8d6b537d2e4e482d31145ae95b603` + +Only `ParameterFile.cpp` includes the header. No JSON types enter public library +headers. See [the format and dependency decision](../../../doc/json-parameters.md). +Update the header and license together from a tagged upstream release, record +checksums here, and run the native JSON, WASM and GUI round-trip tests. diff --git a/src/bin/nlohmann/json.hpp b/src/bin/nlohmann/json.hpp new file mode 100644 index 00000000..82d69f7c --- /dev/null +++ b/src/bin/nlohmann/json.hpp @@ -0,0 +1,25526 @@ +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + +/****************************************************************************\ + * Note on documentation: The source files contain links to the online * + * documentation of the public API at https://json.nlohmann.me. This URL * + * contains the most recent documentation and should also be applicable to * + * previous versions; documentation for deprecated functions is not * + * removed, but marked deprecated. See "Generate documentation" section in * + * file docs/README.md. * +\****************************************************************************/ + +#ifndef INCLUDE_NLOHMANN_JSON_HPP_ +#define INCLUDE_NLOHMANN_JSON_HPP_ + +#include // all_of, find, for_each +#include // nullptr_t, ptrdiff_t, size_t +#include // hash, less +#include // initializer_list +#ifndef JSON_NO_IO + #include // istream, ostream +#endif // JSON_NO_IO +#include // random_access_iterator_tag +#include // unique_ptr +#include // string, stoi, to_string +#include // declval, forward, move, pair, swap +#include // vector + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +#include + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +// This file contains all macro definitions affecting or depending on the ABI + +#ifndef JSON_SKIP_LIBRARY_VERSION_CHECK + #if defined(NLOHMANN_JSON_VERSION_MAJOR) && defined(NLOHMANN_JSON_VERSION_MINOR) && defined(NLOHMANN_JSON_VERSION_PATCH) + #if NLOHMANN_JSON_VERSION_MAJOR != 3 || NLOHMANN_JSON_VERSION_MINOR != 12 || NLOHMANN_JSON_VERSION_PATCH != 0 + #warning "Already included a different version of the library!" + #endif + #endif +#endif + +#define NLOHMANN_JSON_VERSION_MAJOR 3 // NOLINT(modernize-macro-to-enum) +#define NLOHMANN_JSON_VERSION_MINOR 12 // NOLINT(modernize-macro-to-enum) +#define NLOHMANN_JSON_VERSION_PATCH 0 // NOLINT(modernize-macro-to-enum) + +#ifndef JSON_DIAGNOSTICS + #define JSON_DIAGNOSTICS 0 +#endif + +#ifndef JSON_DIAGNOSTIC_POSITIONS + #define JSON_DIAGNOSTIC_POSITIONS 0 +#endif + +#ifndef JSON_USE_LEGACY_DISCARDED_VALUE_COMPARISON + #define JSON_USE_LEGACY_DISCARDED_VALUE_COMPARISON 0 +#endif + +#if JSON_DIAGNOSTICS + #define NLOHMANN_JSON_ABI_TAG_DIAGNOSTICS _diag +#else + #define NLOHMANN_JSON_ABI_TAG_DIAGNOSTICS +#endif + +#if JSON_DIAGNOSTIC_POSITIONS + #define NLOHMANN_JSON_ABI_TAG_DIAGNOSTIC_POSITIONS _dp +#else + #define NLOHMANN_JSON_ABI_TAG_DIAGNOSTIC_POSITIONS +#endif + +#if JSON_USE_LEGACY_DISCARDED_VALUE_COMPARISON + #define NLOHMANN_JSON_ABI_TAG_LEGACY_DISCARDED_VALUE_COMPARISON _ldvcmp +#else + #define NLOHMANN_JSON_ABI_TAG_LEGACY_DISCARDED_VALUE_COMPARISON +#endif + +#ifndef NLOHMANN_JSON_NAMESPACE_NO_VERSION + #define NLOHMANN_JSON_NAMESPACE_NO_VERSION 0 +#endif + +// Construct the namespace ABI tags component +#define NLOHMANN_JSON_ABI_TAGS_CONCAT_EX(a, b, c) json_abi ## a ## b ## c +#define NLOHMANN_JSON_ABI_TAGS_CONCAT(a, b, c) \ + NLOHMANN_JSON_ABI_TAGS_CONCAT_EX(a, b, c) + +#define NLOHMANN_JSON_ABI_TAGS \ + NLOHMANN_JSON_ABI_TAGS_CONCAT( \ + NLOHMANN_JSON_ABI_TAG_DIAGNOSTICS, \ + NLOHMANN_JSON_ABI_TAG_LEGACY_DISCARDED_VALUE_COMPARISON, \ + NLOHMANN_JSON_ABI_TAG_DIAGNOSTIC_POSITIONS) + +// Construct the namespace version component +#define NLOHMANN_JSON_NAMESPACE_VERSION_CONCAT_EX(major, minor, patch) \ + _v ## major ## _ ## minor ## _ ## patch +#define NLOHMANN_JSON_NAMESPACE_VERSION_CONCAT(major, minor, patch) \ + NLOHMANN_JSON_NAMESPACE_VERSION_CONCAT_EX(major, minor, patch) + +#if NLOHMANN_JSON_NAMESPACE_NO_VERSION +#define NLOHMANN_JSON_NAMESPACE_VERSION +#else +#define NLOHMANN_JSON_NAMESPACE_VERSION \ + NLOHMANN_JSON_NAMESPACE_VERSION_CONCAT(NLOHMANN_JSON_VERSION_MAJOR, \ + NLOHMANN_JSON_VERSION_MINOR, \ + NLOHMANN_JSON_VERSION_PATCH) +#endif + +// Combine namespace components +#define NLOHMANN_JSON_NAMESPACE_CONCAT_EX(a, b) a ## b +#define NLOHMANN_JSON_NAMESPACE_CONCAT(a, b) \ + NLOHMANN_JSON_NAMESPACE_CONCAT_EX(a, b) + +#ifndef NLOHMANN_JSON_NAMESPACE +#define NLOHMANN_JSON_NAMESPACE \ + nlohmann::NLOHMANN_JSON_NAMESPACE_CONCAT( \ + NLOHMANN_JSON_ABI_TAGS, \ + NLOHMANN_JSON_NAMESPACE_VERSION) +#endif + +#ifndef NLOHMANN_JSON_NAMESPACE_BEGIN +#define NLOHMANN_JSON_NAMESPACE_BEGIN \ + namespace nlohmann \ + { \ + inline namespace NLOHMANN_JSON_NAMESPACE_CONCAT( \ + NLOHMANN_JSON_ABI_TAGS, \ + NLOHMANN_JSON_NAMESPACE_VERSION) \ + { +#endif + +#ifndef NLOHMANN_JSON_NAMESPACE_END +#define NLOHMANN_JSON_NAMESPACE_END \ + } /* namespace (inline namespace) NOLINT(readability/namespace) */ \ + } // namespace nlohmann +#endif + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +#include // transform +#include // array +#include // forward_list +#include // inserter, front_inserter, end +#include // map +#ifdef JSON_HAS_CPP_17 + #include // optional +#endif +#include // string +#include // tuple, make_tuple +#include // is_arithmetic, is_same, is_enum, underlying_type, is_convertible +#include // unordered_map +#include // pair, declval +#include // valarray + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +#include // nullptr_t +#include // exception +#if JSON_DIAGNOSTICS + #include // accumulate +#endif +#include // runtime_error +#include // to_string +#include // vector + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +#include // array +#include // size_t +#include // uint8_t +#include // string + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +#include // declval, pair +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +#include + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +// #include + + +NLOHMANN_JSON_NAMESPACE_BEGIN +namespace detail +{ + +template struct make_void +{ + using type = void; +}; +template using void_t = typename make_void::type; + +} // namespace detail +NLOHMANN_JSON_NAMESPACE_END + + +NLOHMANN_JSON_NAMESPACE_BEGIN +namespace detail +{ + +// https://en.cppreference.com/w/cpp/experimental/is_detected +struct nonesuch +{ + nonesuch() = delete; + ~nonesuch() = delete; + nonesuch(nonesuch const&) = delete; + nonesuch(nonesuch const&&) = delete; + void operator=(nonesuch const&) = delete; + void operator=(nonesuch&&) = delete; +}; + +template class Op, + class... Args> +struct detector +{ + using value_t = std::false_type; + using type = Default; +}; + +template class Op, class... Args> +struct detector>, Op, Args...> +{ + using value_t = std::true_type; + using type = Op; +}; + +template class Op, class... Args> +using is_detected = typename detector::value_t; + +template class Op, class... Args> +struct is_detected_lazy : is_detected { }; + +template class Op, class... Args> +using detected_t = typename detector::type; + +template class Op, class... Args> +using detected_or = detector; + +template class Op, class... Args> +using detected_or_t = typename detected_or::type; + +template class Op, class... Args> +using is_detected_exact = std::is_same>; + +template class Op, class... Args> +using is_detected_convertible = + std::is_convertible, To>; + +} // namespace detail +NLOHMANN_JSON_NAMESPACE_END + +// #include + + +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-FileCopyrightText: 2016 - 2021 Evan Nemerson +// SPDX-License-Identifier: MIT + +/* Hedley - https://nemequ.github.io/hedley + * Created by Evan Nemerson + */ + +#if !defined(JSON_HEDLEY_VERSION) || (JSON_HEDLEY_VERSION < 15) +#if defined(JSON_HEDLEY_VERSION) + #undef JSON_HEDLEY_VERSION +#endif +#define JSON_HEDLEY_VERSION 15 + +#if defined(JSON_HEDLEY_STRINGIFY_EX) + #undef JSON_HEDLEY_STRINGIFY_EX +#endif +#define JSON_HEDLEY_STRINGIFY_EX(x) #x + +#if defined(JSON_HEDLEY_STRINGIFY) + #undef JSON_HEDLEY_STRINGIFY +#endif +#define JSON_HEDLEY_STRINGIFY(x) JSON_HEDLEY_STRINGIFY_EX(x) + +#if defined(JSON_HEDLEY_CONCAT_EX) + #undef JSON_HEDLEY_CONCAT_EX +#endif +#define JSON_HEDLEY_CONCAT_EX(a,b) a##b + +#if defined(JSON_HEDLEY_CONCAT) + #undef JSON_HEDLEY_CONCAT +#endif +#define JSON_HEDLEY_CONCAT(a,b) JSON_HEDLEY_CONCAT_EX(a,b) + +#if defined(JSON_HEDLEY_CONCAT3_EX) + #undef JSON_HEDLEY_CONCAT3_EX +#endif +#define JSON_HEDLEY_CONCAT3_EX(a,b,c) a##b##c + +#if defined(JSON_HEDLEY_CONCAT3) + #undef JSON_HEDLEY_CONCAT3 +#endif +#define JSON_HEDLEY_CONCAT3(a,b,c) JSON_HEDLEY_CONCAT3_EX(a,b,c) + +#if defined(JSON_HEDLEY_VERSION_ENCODE) + #undef JSON_HEDLEY_VERSION_ENCODE +#endif +#define JSON_HEDLEY_VERSION_ENCODE(major,minor,revision) (((major) * 1000000) + ((minor) * 1000) + (revision)) + +#if defined(JSON_HEDLEY_VERSION_DECODE_MAJOR) + #undef JSON_HEDLEY_VERSION_DECODE_MAJOR +#endif +#define JSON_HEDLEY_VERSION_DECODE_MAJOR(version) ((version) / 1000000) + +#if defined(JSON_HEDLEY_VERSION_DECODE_MINOR) + #undef JSON_HEDLEY_VERSION_DECODE_MINOR +#endif +#define JSON_HEDLEY_VERSION_DECODE_MINOR(version) (((version) % 1000000) / 1000) + +#if defined(JSON_HEDLEY_VERSION_DECODE_REVISION) + #undef JSON_HEDLEY_VERSION_DECODE_REVISION +#endif +#define JSON_HEDLEY_VERSION_DECODE_REVISION(version) ((version) % 1000) + +#if defined(JSON_HEDLEY_GNUC_VERSION) + #undef JSON_HEDLEY_GNUC_VERSION +#endif +#if defined(__GNUC__) && defined(__GNUC_PATCHLEVEL__) + #define JSON_HEDLEY_GNUC_VERSION JSON_HEDLEY_VERSION_ENCODE(__GNUC__, __GNUC_MINOR__, __GNUC_PATCHLEVEL__) +#elif defined(__GNUC__) + #define JSON_HEDLEY_GNUC_VERSION JSON_HEDLEY_VERSION_ENCODE(__GNUC__, __GNUC_MINOR__, 0) +#endif + +#if defined(JSON_HEDLEY_GNUC_VERSION_CHECK) + #undef JSON_HEDLEY_GNUC_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_GNUC_VERSION) + #define JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_GNUC_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_MSVC_VERSION) + #undef JSON_HEDLEY_MSVC_VERSION +#endif +#if defined(_MSC_FULL_VER) && (_MSC_FULL_VER >= 140000000) && !defined(__ICL) + #define JSON_HEDLEY_MSVC_VERSION JSON_HEDLEY_VERSION_ENCODE(_MSC_FULL_VER / 10000000, (_MSC_FULL_VER % 10000000) / 100000, (_MSC_FULL_VER % 100000) / 100) +#elif defined(_MSC_FULL_VER) && !defined(__ICL) + #define JSON_HEDLEY_MSVC_VERSION JSON_HEDLEY_VERSION_ENCODE(_MSC_FULL_VER / 1000000, (_MSC_FULL_VER % 1000000) / 10000, (_MSC_FULL_VER % 10000) / 10) +#elif defined(_MSC_VER) && !defined(__ICL) + #define JSON_HEDLEY_MSVC_VERSION JSON_HEDLEY_VERSION_ENCODE(_MSC_VER / 100, _MSC_VER % 100, 0) +#endif + +#if defined(JSON_HEDLEY_MSVC_VERSION_CHECK) + #undef JSON_HEDLEY_MSVC_VERSION_CHECK +#endif +#if !defined(JSON_HEDLEY_MSVC_VERSION) + #define JSON_HEDLEY_MSVC_VERSION_CHECK(major,minor,patch) (0) +#elif defined(_MSC_VER) && (_MSC_VER >= 1400) + #define JSON_HEDLEY_MSVC_VERSION_CHECK(major,minor,patch) (_MSC_FULL_VER >= ((major * 10000000) + (minor * 100000) + (patch))) +#elif defined(_MSC_VER) && (_MSC_VER >= 1200) + #define JSON_HEDLEY_MSVC_VERSION_CHECK(major,minor,patch) (_MSC_FULL_VER >= ((major * 1000000) + (minor * 10000) + (patch))) +#else + #define JSON_HEDLEY_MSVC_VERSION_CHECK(major,minor,patch) (_MSC_VER >= ((major * 100) + (minor))) +#endif + +#if defined(JSON_HEDLEY_INTEL_VERSION) + #undef JSON_HEDLEY_INTEL_VERSION +#endif +#if defined(__INTEL_COMPILER) && defined(__INTEL_COMPILER_UPDATE) && !defined(__ICL) + #define JSON_HEDLEY_INTEL_VERSION JSON_HEDLEY_VERSION_ENCODE(__INTEL_COMPILER / 100, __INTEL_COMPILER % 100, __INTEL_COMPILER_UPDATE) +#elif defined(__INTEL_COMPILER) && !defined(__ICL) + #define JSON_HEDLEY_INTEL_VERSION JSON_HEDLEY_VERSION_ENCODE(__INTEL_COMPILER / 100, __INTEL_COMPILER % 100, 0) +#endif + +#if defined(JSON_HEDLEY_INTEL_VERSION_CHECK) + #undef JSON_HEDLEY_INTEL_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_INTEL_VERSION) + #define JSON_HEDLEY_INTEL_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_INTEL_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_INTEL_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_INTEL_CL_VERSION) + #undef JSON_HEDLEY_INTEL_CL_VERSION +#endif +#if defined(__INTEL_COMPILER) && defined(__INTEL_COMPILER_UPDATE) && defined(__ICL) + #define JSON_HEDLEY_INTEL_CL_VERSION JSON_HEDLEY_VERSION_ENCODE(__INTEL_COMPILER, __INTEL_COMPILER_UPDATE, 0) +#endif + +#if defined(JSON_HEDLEY_INTEL_CL_VERSION_CHECK) + #undef JSON_HEDLEY_INTEL_CL_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_INTEL_CL_VERSION) + #define JSON_HEDLEY_INTEL_CL_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_INTEL_CL_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_INTEL_CL_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_PGI_VERSION) + #undef JSON_HEDLEY_PGI_VERSION +#endif +#if defined(__PGI) && defined(__PGIC__) && defined(__PGIC_MINOR__) && defined(__PGIC_PATCHLEVEL__) + #define JSON_HEDLEY_PGI_VERSION JSON_HEDLEY_VERSION_ENCODE(__PGIC__, __PGIC_MINOR__, __PGIC_PATCHLEVEL__) +#endif + +#if defined(JSON_HEDLEY_PGI_VERSION_CHECK) + #undef JSON_HEDLEY_PGI_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_PGI_VERSION) + #define JSON_HEDLEY_PGI_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_PGI_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_PGI_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_SUNPRO_VERSION) + #undef JSON_HEDLEY_SUNPRO_VERSION +#endif +#if defined(__SUNPRO_C) && (__SUNPRO_C > 0x1000) + #define JSON_HEDLEY_SUNPRO_VERSION JSON_HEDLEY_VERSION_ENCODE((((__SUNPRO_C >> 16) & 0xf) * 10) + ((__SUNPRO_C >> 12) & 0xf), (((__SUNPRO_C >> 8) & 0xf) * 10) + ((__SUNPRO_C >> 4) & 0xf), (__SUNPRO_C & 0xf) * 10) +#elif defined(__SUNPRO_C) + #define JSON_HEDLEY_SUNPRO_VERSION JSON_HEDLEY_VERSION_ENCODE((__SUNPRO_C >> 8) & 0xf, (__SUNPRO_C >> 4) & 0xf, (__SUNPRO_C) & 0xf) +#elif defined(__SUNPRO_CC) && (__SUNPRO_CC > 0x1000) + #define JSON_HEDLEY_SUNPRO_VERSION JSON_HEDLEY_VERSION_ENCODE((((__SUNPRO_CC >> 16) & 0xf) * 10) + ((__SUNPRO_CC >> 12) & 0xf), (((__SUNPRO_CC >> 8) & 0xf) * 10) + ((__SUNPRO_CC >> 4) & 0xf), (__SUNPRO_CC & 0xf) * 10) +#elif defined(__SUNPRO_CC) + #define JSON_HEDLEY_SUNPRO_VERSION JSON_HEDLEY_VERSION_ENCODE((__SUNPRO_CC >> 8) & 0xf, (__SUNPRO_CC >> 4) & 0xf, (__SUNPRO_CC) & 0xf) +#endif + +#if defined(JSON_HEDLEY_SUNPRO_VERSION_CHECK) + #undef JSON_HEDLEY_SUNPRO_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_SUNPRO_VERSION) + #define JSON_HEDLEY_SUNPRO_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_SUNPRO_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_SUNPRO_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_EMSCRIPTEN_VERSION) + #undef JSON_HEDLEY_EMSCRIPTEN_VERSION +#endif +#if defined(__EMSCRIPTEN__) + #define JSON_HEDLEY_EMSCRIPTEN_VERSION JSON_HEDLEY_VERSION_ENCODE(__EMSCRIPTEN_major__, __EMSCRIPTEN_minor__, __EMSCRIPTEN_tiny__) +#endif + +#if defined(JSON_HEDLEY_EMSCRIPTEN_VERSION_CHECK) + #undef JSON_HEDLEY_EMSCRIPTEN_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_EMSCRIPTEN_VERSION) + #define JSON_HEDLEY_EMSCRIPTEN_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_EMSCRIPTEN_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_EMSCRIPTEN_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_ARM_VERSION) + #undef JSON_HEDLEY_ARM_VERSION +#endif +#if defined(__CC_ARM) && defined(__ARMCOMPILER_VERSION) + #define JSON_HEDLEY_ARM_VERSION JSON_HEDLEY_VERSION_ENCODE(__ARMCOMPILER_VERSION / 1000000, (__ARMCOMPILER_VERSION % 1000000) / 10000, (__ARMCOMPILER_VERSION % 10000) / 100) +#elif defined(__CC_ARM) && defined(__ARMCC_VERSION) + #define JSON_HEDLEY_ARM_VERSION JSON_HEDLEY_VERSION_ENCODE(__ARMCC_VERSION / 1000000, (__ARMCC_VERSION % 1000000) / 10000, (__ARMCC_VERSION % 10000) / 100) +#endif + +#if defined(JSON_HEDLEY_ARM_VERSION_CHECK) + #undef JSON_HEDLEY_ARM_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_ARM_VERSION) + #define JSON_HEDLEY_ARM_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_ARM_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_ARM_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_IBM_VERSION) + #undef JSON_HEDLEY_IBM_VERSION +#endif +#if defined(__ibmxl__) + #define JSON_HEDLEY_IBM_VERSION JSON_HEDLEY_VERSION_ENCODE(__ibmxl_version__, __ibmxl_release__, __ibmxl_modification__) +#elif defined(__xlC__) && defined(__xlC_ver__) + #define JSON_HEDLEY_IBM_VERSION JSON_HEDLEY_VERSION_ENCODE(__xlC__ >> 8, __xlC__ & 0xff, (__xlC_ver__ >> 8) & 0xff) +#elif defined(__xlC__) + #define JSON_HEDLEY_IBM_VERSION JSON_HEDLEY_VERSION_ENCODE(__xlC__ >> 8, __xlC__ & 0xff, 0) +#endif + +#if defined(JSON_HEDLEY_IBM_VERSION_CHECK) + #undef JSON_HEDLEY_IBM_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_IBM_VERSION) + #define JSON_HEDLEY_IBM_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_IBM_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_IBM_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_TI_VERSION) + #undef JSON_HEDLEY_TI_VERSION +#endif +#if \ + defined(__TI_COMPILER_VERSION__) && \ + ( \ + defined(__TMS470__) || defined(__TI_ARM__) || \ + defined(__MSP430__) || \ + defined(__TMS320C2000__) \ + ) +#if (__TI_COMPILER_VERSION__ >= 16000000) + #define JSON_HEDLEY_TI_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) +#endif +#endif + +#if defined(JSON_HEDLEY_TI_VERSION_CHECK) + #undef JSON_HEDLEY_TI_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_TI_VERSION) + #define JSON_HEDLEY_TI_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_TI_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_TI_CL2000_VERSION) + #undef JSON_HEDLEY_TI_CL2000_VERSION +#endif +#if defined(__TI_COMPILER_VERSION__) && defined(__TMS320C2000__) + #define JSON_HEDLEY_TI_CL2000_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) +#endif + +#if defined(JSON_HEDLEY_TI_CL2000_VERSION_CHECK) + #undef JSON_HEDLEY_TI_CL2000_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_TI_CL2000_VERSION) + #define JSON_HEDLEY_TI_CL2000_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_CL2000_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_TI_CL2000_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_TI_CL430_VERSION) + #undef JSON_HEDLEY_TI_CL430_VERSION +#endif +#if defined(__TI_COMPILER_VERSION__) && defined(__MSP430__) + #define JSON_HEDLEY_TI_CL430_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) +#endif + +#if defined(JSON_HEDLEY_TI_CL430_VERSION_CHECK) + #undef JSON_HEDLEY_TI_CL430_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_TI_CL430_VERSION) + #define JSON_HEDLEY_TI_CL430_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_CL430_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_TI_CL430_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_TI_ARMCL_VERSION) + #undef JSON_HEDLEY_TI_ARMCL_VERSION +#endif +#if defined(__TI_COMPILER_VERSION__) && (defined(__TMS470__) || defined(__TI_ARM__)) + #define JSON_HEDLEY_TI_ARMCL_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) +#endif + +#if defined(JSON_HEDLEY_TI_ARMCL_VERSION_CHECK) + #undef JSON_HEDLEY_TI_ARMCL_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_TI_ARMCL_VERSION) + #define JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_ARMCL_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_TI_CL6X_VERSION) + #undef JSON_HEDLEY_TI_CL6X_VERSION +#endif +#if defined(__TI_COMPILER_VERSION__) && defined(__TMS320C6X__) + #define JSON_HEDLEY_TI_CL6X_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) +#endif + +#if defined(JSON_HEDLEY_TI_CL6X_VERSION_CHECK) + #undef JSON_HEDLEY_TI_CL6X_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_TI_CL6X_VERSION) + #define JSON_HEDLEY_TI_CL6X_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_CL6X_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_TI_CL6X_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_TI_CL7X_VERSION) + #undef JSON_HEDLEY_TI_CL7X_VERSION +#endif +#if defined(__TI_COMPILER_VERSION__) && defined(__C7000__) + #define JSON_HEDLEY_TI_CL7X_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) +#endif + +#if defined(JSON_HEDLEY_TI_CL7X_VERSION_CHECK) + #undef JSON_HEDLEY_TI_CL7X_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_TI_CL7X_VERSION) + #define JSON_HEDLEY_TI_CL7X_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_CL7X_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_TI_CL7X_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_TI_CLPRU_VERSION) + #undef JSON_HEDLEY_TI_CLPRU_VERSION +#endif +#if defined(__TI_COMPILER_VERSION__) && defined(__PRU__) + #define JSON_HEDLEY_TI_CLPRU_VERSION JSON_HEDLEY_VERSION_ENCODE(__TI_COMPILER_VERSION__ / 1000000, (__TI_COMPILER_VERSION__ % 1000000) / 1000, (__TI_COMPILER_VERSION__ % 1000)) +#endif + +#if defined(JSON_HEDLEY_TI_CLPRU_VERSION_CHECK) + #undef JSON_HEDLEY_TI_CLPRU_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_TI_CLPRU_VERSION) + #define JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TI_CLPRU_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_CRAY_VERSION) + #undef JSON_HEDLEY_CRAY_VERSION +#endif +#if defined(_CRAYC) + #if defined(_RELEASE_PATCHLEVEL) + #define JSON_HEDLEY_CRAY_VERSION JSON_HEDLEY_VERSION_ENCODE(_RELEASE_MAJOR, _RELEASE_MINOR, _RELEASE_PATCHLEVEL) + #else + #define JSON_HEDLEY_CRAY_VERSION JSON_HEDLEY_VERSION_ENCODE(_RELEASE_MAJOR, _RELEASE_MINOR, 0) + #endif +#endif + +#if defined(JSON_HEDLEY_CRAY_VERSION_CHECK) + #undef JSON_HEDLEY_CRAY_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_CRAY_VERSION) + #define JSON_HEDLEY_CRAY_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_CRAY_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_CRAY_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_IAR_VERSION) + #undef JSON_HEDLEY_IAR_VERSION +#endif +#if defined(__IAR_SYSTEMS_ICC__) + #if __VER__ > 1000 + #define JSON_HEDLEY_IAR_VERSION JSON_HEDLEY_VERSION_ENCODE((__VER__ / 1000000), ((__VER__ / 1000) % 1000), (__VER__ % 1000)) + #else + #define JSON_HEDLEY_IAR_VERSION JSON_HEDLEY_VERSION_ENCODE(__VER__ / 100, __VER__ % 100, 0) + #endif +#endif + +#if defined(JSON_HEDLEY_IAR_VERSION_CHECK) + #undef JSON_HEDLEY_IAR_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_IAR_VERSION) + #define JSON_HEDLEY_IAR_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_IAR_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_IAR_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_TINYC_VERSION) + #undef JSON_HEDLEY_TINYC_VERSION +#endif +#if defined(__TINYC__) + #define JSON_HEDLEY_TINYC_VERSION JSON_HEDLEY_VERSION_ENCODE(__TINYC__ / 1000, (__TINYC__ / 100) % 10, __TINYC__ % 100) +#endif + +#if defined(JSON_HEDLEY_TINYC_VERSION_CHECK) + #undef JSON_HEDLEY_TINYC_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_TINYC_VERSION) + #define JSON_HEDLEY_TINYC_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_TINYC_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_TINYC_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_DMC_VERSION) + #undef JSON_HEDLEY_DMC_VERSION +#endif +#if defined(__DMC__) + #define JSON_HEDLEY_DMC_VERSION JSON_HEDLEY_VERSION_ENCODE(__DMC__ >> 8, (__DMC__ >> 4) & 0xf, __DMC__ & 0xf) +#endif + +#if defined(JSON_HEDLEY_DMC_VERSION_CHECK) + #undef JSON_HEDLEY_DMC_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_DMC_VERSION) + #define JSON_HEDLEY_DMC_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_DMC_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_DMC_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_COMPCERT_VERSION) + #undef JSON_HEDLEY_COMPCERT_VERSION +#endif +#if defined(__COMPCERT_VERSION__) + #define JSON_HEDLEY_COMPCERT_VERSION JSON_HEDLEY_VERSION_ENCODE(__COMPCERT_VERSION__ / 10000, (__COMPCERT_VERSION__ / 100) % 100, __COMPCERT_VERSION__ % 100) +#endif + +#if defined(JSON_HEDLEY_COMPCERT_VERSION_CHECK) + #undef JSON_HEDLEY_COMPCERT_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_COMPCERT_VERSION) + #define JSON_HEDLEY_COMPCERT_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_COMPCERT_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_COMPCERT_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_PELLES_VERSION) + #undef JSON_HEDLEY_PELLES_VERSION +#endif +#if defined(__POCC__) + #define JSON_HEDLEY_PELLES_VERSION JSON_HEDLEY_VERSION_ENCODE(__POCC__ / 100, __POCC__ % 100, 0) +#endif + +#if defined(JSON_HEDLEY_PELLES_VERSION_CHECK) + #undef JSON_HEDLEY_PELLES_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_PELLES_VERSION) + #define JSON_HEDLEY_PELLES_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_PELLES_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_PELLES_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_MCST_LCC_VERSION) + #undef JSON_HEDLEY_MCST_LCC_VERSION +#endif +#if defined(__LCC__) && defined(__LCC_MINOR__) + #define JSON_HEDLEY_MCST_LCC_VERSION JSON_HEDLEY_VERSION_ENCODE(__LCC__ / 100, __LCC__ % 100, __LCC_MINOR__) +#endif + +#if defined(JSON_HEDLEY_MCST_LCC_VERSION_CHECK) + #undef JSON_HEDLEY_MCST_LCC_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_MCST_LCC_VERSION) + #define JSON_HEDLEY_MCST_LCC_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_MCST_LCC_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_MCST_LCC_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_GCC_VERSION) + #undef JSON_HEDLEY_GCC_VERSION +#endif +#if \ + defined(JSON_HEDLEY_GNUC_VERSION) && \ + !defined(__clang__) && \ + !defined(JSON_HEDLEY_INTEL_VERSION) && \ + !defined(JSON_HEDLEY_PGI_VERSION) && \ + !defined(JSON_HEDLEY_ARM_VERSION) && \ + !defined(JSON_HEDLEY_CRAY_VERSION) && \ + !defined(JSON_HEDLEY_TI_VERSION) && \ + !defined(JSON_HEDLEY_TI_ARMCL_VERSION) && \ + !defined(JSON_HEDLEY_TI_CL430_VERSION) && \ + !defined(JSON_HEDLEY_TI_CL2000_VERSION) && \ + !defined(JSON_HEDLEY_TI_CL6X_VERSION) && \ + !defined(JSON_HEDLEY_TI_CL7X_VERSION) && \ + !defined(JSON_HEDLEY_TI_CLPRU_VERSION) && \ + !defined(__COMPCERT__) && \ + !defined(JSON_HEDLEY_MCST_LCC_VERSION) + #define JSON_HEDLEY_GCC_VERSION JSON_HEDLEY_GNUC_VERSION +#endif + +#if defined(JSON_HEDLEY_GCC_VERSION_CHECK) + #undef JSON_HEDLEY_GCC_VERSION_CHECK +#endif +#if defined(JSON_HEDLEY_GCC_VERSION) + #define JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) (JSON_HEDLEY_GCC_VERSION >= JSON_HEDLEY_VERSION_ENCODE(major, minor, patch)) +#else + #define JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) (0) +#endif + +#if defined(JSON_HEDLEY_HAS_ATTRIBUTE) + #undef JSON_HEDLEY_HAS_ATTRIBUTE +#endif +#if \ + defined(__has_attribute) && \ + ( \ + (!defined(JSON_HEDLEY_IAR_VERSION) || JSON_HEDLEY_IAR_VERSION_CHECK(8,5,9)) \ + ) +# define JSON_HEDLEY_HAS_ATTRIBUTE(attribute) __has_attribute(attribute) +#else +# define JSON_HEDLEY_HAS_ATTRIBUTE(attribute) (0) +#endif + +#if defined(JSON_HEDLEY_GNUC_HAS_ATTRIBUTE) + #undef JSON_HEDLEY_GNUC_HAS_ATTRIBUTE +#endif +#if defined(__has_attribute) + #define JSON_HEDLEY_GNUC_HAS_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_HAS_ATTRIBUTE(attribute) +#else + #define JSON_HEDLEY_GNUC_HAS_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_GCC_HAS_ATTRIBUTE) + #undef JSON_HEDLEY_GCC_HAS_ATTRIBUTE +#endif +#if defined(__has_attribute) + #define JSON_HEDLEY_GCC_HAS_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_HAS_ATTRIBUTE(attribute) +#else + #define JSON_HEDLEY_GCC_HAS_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_HAS_CPP_ATTRIBUTE) + #undef JSON_HEDLEY_HAS_CPP_ATTRIBUTE +#endif +#if \ + defined(__has_cpp_attribute) && \ + defined(__cplusplus) && \ + (!defined(JSON_HEDLEY_SUNPRO_VERSION) || JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,15,0)) + #define JSON_HEDLEY_HAS_CPP_ATTRIBUTE(attribute) __has_cpp_attribute(attribute) +#else + #define JSON_HEDLEY_HAS_CPP_ATTRIBUTE(attribute) (0) +#endif + +#if defined(JSON_HEDLEY_HAS_CPP_ATTRIBUTE_NS) + #undef JSON_HEDLEY_HAS_CPP_ATTRIBUTE_NS +#endif +#if !defined(__cplusplus) || !defined(__has_cpp_attribute) + #define JSON_HEDLEY_HAS_CPP_ATTRIBUTE_NS(ns,attribute) (0) +#elif \ + !defined(JSON_HEDLEY_PGI_VERSION) && \ + !defined(JSON_HEDLEY_IAR_VERSION) && \ + (!defined(JSON_HEDLEY_SUNPRO_VERSION) || JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,15,0)) && \ + (!defined(JSON_HEDLEY_MSVC_VERSION) || JSON_HEDLEY_MSVC_VERSION_CHECK(19,20,0)) + #define JSON_HEDLEY_HAS_CPP_ATTRIBUTE_NS(ns,attribute) JSON_HEDLEY_HAS_CPP_ATTRIBUTE(ns::attribute) +#else + #define JSON_HEDLEY_HAS_CPP_ATTRIBUTE_NS(ns,attribute) (0) +#endif + +#if defined(JSON_HEDLEY_GNUC_HAS_CPP_ATTRIBUTE) + #undef JSON_HEDLEY_GNUC_HAS_CPP_ATTRIBUTE +#endif +#if defined(__has_cpp_attribute) && defined(__cplusplus) + #define JSON_HEDLEY_GNUC_HAS_CPP_ATTRIBUTE(attribute,major,minor,patch) __has_cpp_attribute(attribute) +#else + #define JSON_HEDLEY_GNUC_HAS_CPP_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_GCC_HAS_CPP_ATTRIBUTE) + #undef JSON_HEDLEY_GCC_HAS_CPP_ATTRIBUTE +#endif +#if defined(__has_cpp_attribute) && defined(__cplusplus) + #define JSON_HEDLEY_GCC_HAS_CPP_ATTRIBUTE(attribute,major,minor,patch) __has_cpp_attribute(attribute) +#else + #define JSON_HEDLEY_GCC_HAS_CPP_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_HAS_BUILTIN) + #undef JSON_HEDLEY_HAS_BUILTIN +#endif +#if defined(__has_builtin) + #define JSON_HEDLEY_HAS_BUILTIN(builtin) __has_builtin(builtin) +#else + #define JSON_HEDLEY_HAS_BUILTIN(builtin) (0) +#endif + +#if defined(JSON_HEDLEY_GNUC_HAS_BUILTIN) + #undef JSON_HEDLEY_GNUC_HAS_BUILTIN +#endif +#if defined(__has_builtin) + #define JSON_HEDLEY_GNUC_HAS_BUILTIN(builtin,major,minor,patch) __has_builtin(builtin) +#else + #define JSON_HEDLEY_GNUC_HAS_BUILTIN(builtin,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_GCC_HAS_BUILTIN) + #undef JSON_HEDLEY_GCC_HAS_BUILTIN +#endif +#if defined(__has_builtin) + #define JSON_HEDLEY_GCC_HAS_BUILTIN(builtin,major,minor,patch) __has_builtin(builtin) +#else + #define JSON_HEDLEY_GCC_HAS_BUILTIN(builtin,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_HAS_FEATURE) + #undef JSON_HEDLEY_HAS_FEATURE +#endif +#if defined(__has_feature) + #define JSON_HEDLEY_HAS_FEATURE(feature) __has_feature(feature) +#else + #define JSON_HEDLEY_HAS_FEATURE(feature) (0) +#endif + +#if defined(JSON_HEDLEY_GNUC_HAS_FEATURE) + #undef JSON_HEDLEY_GNUC_HAS_FEATURE +#endif +#if defined(__has_feature) + #define JSON_HEDLEY_GNUC_HAS_FEATURE(feature,major,minor,patch) __has_feature(feature) +#else + #define JSON_HEDLEY_GNUC_HAS_FEATURE(feature,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_GCC_HAS_FEATURE) + #undef JSON_HEDLEY_GCC_HAS_FEATURE +#endif +#if defined(__has_feature) + #define JSON_HEDLEY_GCC_HAS_FEATURE(feature,major,minor,patch) __has_feature(feature) +#else + #define JSON_HEDLEY_GCC_HAS_FEATURE(feature,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_HAS_EXTENSION) + #undef JSON_HEDLEY_HAS_EXTENSION +#endif +#if defined(__has_extension) + #define JSON_HEDLEY_HAS_EXTENSION(extension) __has_extension(extension) +#else + #define JSON_HEDLEY_HAS_EXTENSION(extension) (0) +#endif + +#if defined(JSON_HEDLEY_GNUC_HAS_EXTENSION) + #undef JSON_HEDLEY_GNUC_HAS_EXTENSION +#endif +#if defined(__has_extension) + #define JSON_HEDLEY_GNUC_HAS_EXTENSION(extension,major,minor,patch) __has_extension(extension) +#else + #define JSON_HEDLEY_GNUC_HAS_EXTENSION(extension,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_GCC_HAS_EXTENSION) + #undef JSON_HEDLEY_GCC_HAS_EXTENSION +#endif +#if defined(__has_extension) + #define JSON_HEDLEY_GCC_HAS_EXTENSION(extension,major,minor,patch) __has_extension(extension) +#else + #define JSON_HEDLEY_GCC_HAS_EXTENSION(extension,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_HAS_DECLSPEC_ATTRIBUTE) + #undef JSON_HEDLEY_HAS_DECLSPEC_ATTRIBUTE +#endif +#if defined(__has_declspec_attribute) + #define JSON_HEDLEY_HAS_DECLSPEC_ATTRIBUTE(attribute) __has_declspec_attribute(attribute) +#else + #define JSON_HEDLEY_HAS_DECLSPEC_ATTRIBUTE(attribute) (0) +#endif + +#if defined(JSON_HEDLEY_GNUC_HAS_DECLSPEC_ATTRIBUTE) + #undef JSON_HEDLEY_GNUC_HAS_DECLSPEC_ATTRIBUTE +#endif +#if defined(__has_declspec_attribute) + #define JSON_HEDLEY_GNUC_HAS_DECLSPEC_ATTRIBUTE(attribute,major,minor,patch) __has_declspec_attribute(attribute) +#else + #define JSON_HEDLEY_GNUC_HAS_DECLSPEC_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_GCC_HAS_DECLSPEC_ATTRIBUTE) + #undef JSON_HEDLEY_GCC_HAS_DECLSPEC_ATTRIBUTE +#endif +#if defined(__has_declspec_attribute) + #define JSON_HEDLEY_GCC_HAS_DECLSPEC_ATTRIBUTE(attribute,major,minor,patch) __has_declspec_attribute(attribute) +#else + #define JSON_HEDLEY_GCC_HAS_DECLSPEC_ATTRIBUTE(attribute,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_HAS_WARNING) + #undef JSON_HEDLEY_HAS_WARNING +#endif +#if defined(__has_warning) + #define JSON_HEDLEY_HAS_WARNING(warning) __has_warning(warning) +#else + #define JSON_HEDLEY_HAS_WARNING(warning) (0) +#endif + +#if defined(JSON_HEDLEY_GNUC_HAS_WARNING) + #undef JSON_HEDLEY_GNUC_HAS_WARNING +#endif +#if defined(__has_warning) + #define JSON_HEDLEY_GNUC_HAS_WARNING(warning,major,minor,patch) __has_warning(warning) +#else + #define JSON_HEDLEY_GNUC_HAS_WARNING(warning,major,minor,patch) JSON_HEDLEY_GNUC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_GCC_HAS_WARNING) + #undef JSON_HEDLEY_GCC_HAS_WARNING +#endif +#if defined(__has_warning) + #define JSON_HEDLEY_GCC_HAS_WARNING(warning,major,minor,patch) __has_warning(warning) +#else + #define JSON_HEDLEY_GCC_HAS_WARNING(warning,major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) +#endif + +#if \ + (defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L)) || \ + defined(__clang__) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(3,0,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) || \ + JSON_HEDLEY_PGI_VERSION_CHECK(18,4,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ + JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,7,0) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(2,0,1) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,1,0) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,0,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ + JSON_HEDLEY_CRAY_VERSION_CHECK(5,0,0) || \ + JSON_HEDLEY_TINYC_VERSION_CHECK(0,9,17) || \ + JSON_HEDLEY_SUNPRO_VERSION_CHECK(8,0,0) || \ + (JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) && defined(__C99_PRAGMA_OPERATOR)) + #define JSON_HEDLEY_PRAGMA(value) _Pragma(#value) +#elif JSON_HEDLEY_MSVC_VERSION_CHECK(15,0,0) + #define JSON_HEDLEY_PRAGMA(value) __pragma(value) +#else + #define JSON_HEDLEY_PRAGMA(value) +#endif + +#if defined(JSON_HEDLEY_DIAGNOSTIC_PUSH) + #undef JSON_HEDLEY_DIAGNOSTIC_PUSH +#endif +#if defined(JSON_HEDLEY_DIAGNOSTIC_POP) + #undef JSON_HEDLEY_DIAGNOSTIC_POP +#endif +#if defined(__clang__) + #define JSON_HEDLEY_DIAGNOSTIC_PUSH _Pragma("clang diagnostic push") + #define JSON_HEDLEY_DIAGNOSTIC_POP _Pragma("clang diagnostic pop") +#elif JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_PUSH _Pragma("warning(push)") + #define JSON_HEDLEY_DIAGNOSTIC_POP _Pragma("warning(pop)") +#elif JSON_HEDLEY_GCC_VERSION_CHECK(4,6,0) + #define JSON_HEDLEY_DIAGNOSTIC_PUSH _Pragma("GCC diagnostic push") + #define JSON_HEDLEY_DIAGNOSTIC_POP _Pragma("GCC diagnostic pop") +#elif \ + JSON_HEDLEY_MSVC_VERSION_CHECK(15,0,0) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) + #define JSON_HEDLEY_DIAGNOSTIC_PUSH __pragma(warning(push)) + #define JSON_HEDLEY_DIAGNOSTIC_POP __pragma(warning(pop)) +#elif JSON_HEDLEY_ARM_VERSION_CHECK(5,6,0) + #define JSON_HEDLEY_DIAGNOSTIC_PUSH _Pragma("push") + #define JSON_HEDLEY_DIAGNOSTIC_POP _Pragma("pop") +#elif \ + JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,4,0) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,1,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) + #define JSON_HEDLEY_DIAGNOSTIC_PUSH _Pragma("diag_push") + #define JSON_HEDLEY_DIAGNOSTIC_POP _Pragma("diag_pop") +#elif JSON_HEDLEY_PELLES_VERSION_CHECK(2,90,0) + #define JSON_HEDLEY_DIAGNOSTIC_PUSH _Pragma("warning(push)") + #define JSON_HEDLEY_DIAGNOSTIC_POP _Pragma("warning(pop)") +#else + #define JSON_HEDLEY_DIAGNOSTIC_PUSH + #define JSON_HEDLEY_DIAGNOSTIC_POP +#endif + +/* JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_ is for + HEDLEY INTERNAL USE ONLY. API subject to change without notice. */ +#if defined(JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_) + #undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_ +#endif +#if defined(__cplusplus) +# if JSON_HEDLEY_HAS_WARNING("-Wc++98-compat") +# if JSON_HEDLEY_HAS_WARNING("-Wc++17-extensions") +# if JSON_HEDLEY_HAS_WARNING("-Wc++1z-extensions") +# define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_(xpr) \ + JSON_HEDLEY_DIAGNOSTIC_PUSH \ + _Pragma("clang diagnostic ignored \"-Wc++98-compat\"") \ + _Pragma("clang diagnostic ignored \"-Wc++17-extensions\"") \ + _Pragma("clang diagnostic ignored \"-Wc++1z-extensions\"") \ + xpr \ + JSON_HEDLEY_DIAGNOSTIC_POP +# else +# define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_(xpr) \ + JSON_HEDLEY_DIAGNOSTIC_PUSH \ + _Pragma("clang diagnostic ignored \"-Wc++98-compat\"") \ + _Pragma("clang diagnostic ignored \"-Wc++17-extensions\"") \ + xpr \ + JSON_HEDLEY_DIAGNOSTIC_POP +# endif +# else +# define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_(xpr) \ + JSON_HEDLEY_DIAGNOSTIC_PUSH \ + _Pragma("clang diagnostic ignored \"-Wc++98-compat\"") \ + xpr \ + JSON_HEDLEY_DIAGNOSTIC_POP +# endif +# endif +#endif +#if !defined(JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_(x) x +#endif + +#if defined(JSON_HEDLEY_CONST_CAST) + #undef JSON_HEDLEY_CONST_CAST +#endif +#if defined(__cplusplus) +# define JSON_HEDLEY_CONST_CAST(T, expr) (const_cast(expr)) +#elif \ + JSON_HEDLEY_HAS_WARNING("-Wcast-qual") || \ + JSON_HEDLEY_GCC_VERSION_CHECK(4,6,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) +# define JSON_HEDLEY_CONST_CAST(T, expr) (__extension__ ({ \ + JSON_HEDLEY_DIAGNOSTIC_PUSH \ + JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL \ + ((T) (expr)); \ + JSON_HEDLEY_DIAGNOSTIC_POP \ + })) +#else +# define JSON_HEDLEY_CONST_CAST(T, expr) ((T) (expr)) +#endif + +#if defined(JSON_HEDLEY_REINTERPRET_CAST) + #undef JSON_HEDLEY_REINTERPRET_CAST +#endif +#if defined(__cplusplus) + #define JSON_HEDLEY_REINTERPRET_CAST(T, expr) (reinterpret_cast(expr)) +#else + #define JSON_HEDLEY_REINTERPRET_CAST(T, expr) ((T) (expr)) +#endif + +#if defined(JSON_HEDLEY_STATIC_CAST) + #undef JSON_HEDLEY_STATIC_CAST +#endif +#if defined(__cplusplus) + #define JSON_HEDLEY_STATIC_CAST(T, expr) (static_cast(expr)) +#else + #define JSON_HEDLEY_STATIC_CAST(T, expr) ((T) (expr)) +#endif + +#if defined(JSON_HEDLEY_CPP_CAST) + #undef JSON_HEDLEY_CPP_CAST +#endif +#if defined(__cplusplus) +# if JSON_HEDLEY_HAS_WARNING("-Wold-style-cast") +# define JSON_HEDLEY_CPP_CAST(T, expr) \ + JSON_HEDLEY_DIAGNOSTIC_PUSH \ + _Pragma("clang diagnostic ignored \"-Wold-style-cast\"") \ + ((T) (expr)) \ + JSON_HEDLEY_DIAGNOSTIC_POP +# elif JSON_HEDLEY_IAR_VERSION_CHECK(8,3,0) +# define JSON_HEDLEY_CPP_CAST(T, expr) \ + JSON_HEDLEY_DIAGNOSTIC_PUSH \ + _Pragma("diag_suppress=Pe137") \ + JSON_HEDLEY_DIAGNOSTIC_POP +# else +# define JSON_HEDLEY_CPP_CAST(T, expr) ((T) (expr)) +# endif +#else +# define JSON_HEDLEY_CPP_CAST(T, expr) (expr) +#endif + +#if defined(JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED) + #undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED +#endif +#if JSON_HEDLEY_HAS_WARNING("-Wdeprecated-declarations") + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("clang diagnostic ignored \"-Wdeprecated-declarations\"") +#elif JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("warning(disable:1478 1786)") +#elif JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED __pragma(warning(disable:1478 1786)) +#elif JSON_HEDLEY_PGI_VERSION_CHECK(20,7,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("diag_suppress 1215,1216,1444,1445") +#elif JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("diag_suppress 1215,1444") +#elif JSON_HEDLEY_GCC_VERSION_CHECK(4,3,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("GCC diagnostic ignored \"-Wdeprecated-declarations\"") +#elif JSON_HEDLEY_MSVC_VERSION_CHECK(15,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED __pragma(warning(disable:4996)) +#elif JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("diag_suppress 1215,1444") +#elif \ + JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ + (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ + (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ + (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ + (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("diag_suppress 1291,1718") +#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,13,0) && !defined(__cplusplus) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("error_messages(off,E_DEPRECATED_ATT,E_DEPRECATED_ATT_MESS)") +#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,13,0) && defined(__cplusplus) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("error_messages(off,symdeprecated,symdeprecated2)") +#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("diag_suppress=Pe1444,Pe1215") +#elif JSON_HEDLEY_PELLES_VERSION_CHECK(2,90,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED _Pragma("warn(disable:2241)") +#else + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_DEPRECATED +#endif + +#if defined(JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS) + #undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS +#endif +#if JSON_HEDLEY_HAS_WARNING("-Wunknown-pragmas") + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("clang diagnostic ignored \"-Wunknown-pragmas\"") +#elif JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("warning(disable:161)") +#elif JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS __pragma(warning(disable:161)) +#elif JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("diag_suppress 1675") +#elif JSON_HEDLEY_GCC_VERSION_CHECK(4,3,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("GCC diagnostic ignored \"-Wunknown-pragmas\"") +#elif JSON_HEDLEY_MSVC_VERSION_CHECK(15,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS __pragma(warning(disable:4068)) +#elif \ + JSON_HEDLEY_TI_VERSION_CHECK(16,9,0) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,0,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,3,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("diag_suppress 163") +#elif JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("diag_suppress 163") +#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("diag_suppress=Pe161") +#elif JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS _Pragma("diag_suppress 161") +#else + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS +#endif + +#if defined(JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES) + #undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES +#endif +#if JSON_HEDLEY_HAS_WARNING("-Wunknown-attributes") + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("clang diagnostic ignored \"-Wunknown-attributes\"") +#elif JSON_HEDLEY_GCC_VERSION_CHECK(4,6,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("GCC diagnostic ignored \"-Wdeprecated-declarations\"") +#elif JSON_HEDLEY_INTEL_VERSION_CHECK(17,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("warning(disable:1292)") +#elif JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES __pragma(warning(disable:1292)) +#elif JSON_HEDLEY_MSVC_VERSION_CHECK(19,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES __pragma(warning(disable:5030)) +#elif JSON_HEDLEY_PGI_VERSION_CHECK(20,7,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("diag_suppress 1097,1098") +#elif JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("diag_suppress 1097") +#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,14,0) && defined(__cplusplus) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("error_messages(off,attrskipunsup)") +#elif \ + JSON_HEDLEY_TI_VERSION_CHECK(18,1,0) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,3,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("diag_suppress 1173") +#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("diag_suppress=Pe1097") +#elif JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES _Pragma("diag_suppress 1097") +#else + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_CPP_ATTRIBUTES +#endif + +#if defined(JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL) + #undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL +#endif +#if JSON_HEDLEY_HAS_WARNING("-Wcast-qual") + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL _Pragma("clang diagnostic ignored \"-Wcast-qual\"") +#elif JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL _Pragma("warning(disable:2203 2331)") +#elif JSON_HEDLEY_GCC_VERSION_CHECK(3,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL _Pragma("GCC diagnostic ignored \"-Wcast-qual\"") +#else + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL +#endif + +#if defined(JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNUSED_FUNCTION) + #undef JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNUSED_FUNCTION +#endif +#if JSON_HEDLEY_HAS_WARNING("-Wunused-function") + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNUSED_FUNCTION _Pragma("clang diagnostic ignored \"-Wunused-function\"") +#elif JSON_HEDLEY_GCC_VERSION_CHECK(3,4,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNUSED_FUNCTION _Pragma("GCC diagnostic ignored \"-Wunused-function\"") +#elif JSON_HEDLEY_MSVC_VERSION_CHECK(1,0,0) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNUSED_FUNCTION __pragma(warning(disable:4505)) +#elif JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNUSED_FUNCTION _Pragma("diag_suppress 3142") +#else + #define JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNUSED_FUNCTION +#endif + +#if defined(JSON_HEDLEY_DEPRECATED) + #undef JSON_HEDLEY_DEPRECATED +#endif +#if defined(JSON_HEDLEY_DEPRECATED_FOR) + #undef JSON_HEDLEY_DEPRECATED_FOR +#endif +#if \ + JSON_HEDLEY_MSVC_VERSION_CHECK(14,0,0) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) + #define JSON_HEDLEY_DEPRECATED(since) __declspec(deprecated("Since " # since)) + #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) __declspec(deprecated("Since " #since "; use " #replacement)) +#elif \ + (JSON_HEDLEY_HAS_EXTENSION(attribute_deprecated_with_message) && !defined(JSON_HEDLEY_IAR_VERSION)) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(4,5,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(5,6,0) || \ + JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,13,0) || \ + JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) || \ + JSON_HEDLEY_TI_VERSION_CHECK(18,1,0) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(18,1,0) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,3,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,3,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_DEPRECATED(since) __attribute__((__deprecated__("Since " #since))) + #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) __attribute__((__deprecated__("Since " #since "; use " #replacement))) +#elif defined(__cplusplus) && (__cplusplus >= 201402L) + #define JSON_HEDLEY_DEPRECATED(since) JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[deprecated("Since " #since)]]) + #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[deprecated("Since " #since "; use " #replacement)]]) +#elif \ + JSON_HEDLEY_HAS_ATTRIBUTE(deprecated) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(3,1,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ + JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ + (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ + (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ + (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ + (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) || \ + JSON_HEDLEY_IAR_VERSION_CHECK(8,10,0) + #define JSON_HEDLEY_DEPRECATED(since) __attribute__((__deprecated__)) + #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) __attribute__((__deprecated__)) +#elif \ + JSON_HEDLEY_MSVC_VERSION_CHECK(13,10,0) || \ + JSON_HEDLEY_PELLES_VERSION_CHECK(6,50,0) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) + #define JSON_HEDLEY_DEPRECATED(since) __declspec(deprecated) + #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) __declspec(deprecated) +#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) + #define JSON_HEDLEY_DEPRECATED(since) _Pragma("deprecated") + #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) _Pragma("deprecated") +#else + #define JSON_HEDLEY_DEPRECATED(since) + #define JSON_HEDLEY_DEPRECATED_FOR(since, replacement) +#endif + +#if defined(JSON_HEDLEY_UNAVAILABLE) + #undef JSON_HEDLEY_UNAVAILABLE +#endif +#if \ + JSON_HEDLEY_HAS_ATTRIBUTE(warning) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(4,3,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_UNAVAILABLE(available_since) __attribute__((__warning__("Not available until " #available_since))) +#else + #define JSON_HEDLEY_UNAVAILABLE(available_since) +#endif + +#if defined(JSON_HEDLEY_WARN_UNUSED_RESULT) + #undef JSON_HEDLEY_WARN_UNUSED_RESULT +#endif +#if defined(JSON_HEDLEY_WARN_UNUSED_RESULT_MSG) + #undef JSON_HEDLEY_WARN_UNUSED_RESULT_MSG +#endif +#if \ + JSON_HEDLEY_HAS_ATTRIBUTE(warn_unused_result) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(3,4,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ + (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ + (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ + (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ + (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ + (JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,15,0) && defined(__cplusplus)) || \ + JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_WARN_UNUSED_RESULT __attribute__((__warn_unused_result__)) + #define JSON_HEDLEY_WARN_UNUSED_RESULT_MSG(msg) __attribute__((__warn_unused_result__)) +#elif (JSON_HEDLEY_HAS_CPP_ATTRIBUTE(nodiscard) >= 201907L) + #define JSON_HEDLEY_WARN_UNUSED_RESULT JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[nodiscard]]) + #define JSON_HEDLEY_WARN_UNUSED_RESULT_MSG(msg) JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[nodiscard(msg)]]) +#elif JSON_HEDLEY_HAS_CPP_ATTRIBUTE(nodiscard) + #define JSON_HEDLEY_WARN_UNUSED_RESULT JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[nodiscard]]) + #define JSON_HEDLEY_WARN_UNUSED_RESULT_MSG(msg) JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[nodiscard]]) +#elif defined(_Check_return_) /* SAL */ + #define JSON_HEDLEY_WARN_UNUSED_RESULT _Check_return_ + #define JSON_HEDLEY_WARN_UNUSED_RESULT_MSG(msg) _Check_return_ +#else + #define JSON_HEDLEY_WARN_UNUSED_RESULT + #define JSON_HEDLEY_WARN_UNUSED_RESULT_MSG(msg) +#endif + +#if defined(JSON_HEDLEY_SENTINEL) + #undef JSON_HEDLEY_SENTINEL +#endif +#if \ + JSON_HEDLEY_HAS_ATTRIBUTE(sentinel) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(4,0,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(5,4,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_SENTINEL(position) __attribute__((__sentinel__(position))) +#else + #define JSON_HEDLEY_SENTINEL(position) +#endif + +#if defined(JSON_HEDLEY_NO_RETURN) + #undef JSON_HEDLEY_NO_RETURN +#endif +#if JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) + #define JSON_HEDLEY_NO_RETURN __noreturn +#elif \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_NO_RETURN __attribute__((__noreturn__)) +#elif defined(__STDC_VERSION__) && __STDC_VERSION__ >= 201112L + #define JSON_HEDLEY_NO_RETURN _Noreturn +#elif defined(__cplusplus) && (__cplusplus >= 201103L) + #define JSON_HEDLEY_NO_RETURN JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[noreturn]]) +#elif \ + JSON_HEDLEY_HAS_ATTRIBUTE(noreturn) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(3,2,0) || \ + JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ + JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ + (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ + (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ + (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ + (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ + JSON_HEDLEY_IAR_VERSION_CHECK(8,10,0) + #define JSON_HEDLEY_NO_RETURN __attribute__((__noreturn__)) +#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,10,0) + #define JSON_HEDLEY_NO_RETURN _Pragma("does_not_return") +#elif \ + JSON_HEDLEY_MSVC_VERSION_CHECK(13,10,0) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) + #define JSON_HEDLEY_NO_RETURN __declspec(noreturn) +#elif JSON_HEDLEY_TI_CL6X_VERSION_CHECK(6,0,0) && defined(__cplusplus) + #define JSON_HEDLEY_NO_RETURN _Pragma("FUNC_NEVER_RETURNS;") +#elif JSON_HEDLEY_COMPCERT_VERSION_CHECK(3,2,0) + #define JSON_HEDLEY_NO_RETURN __attribute((noreturn)) +#elif JSON_HEDLEY_PELLES_VERSION_CHECK(9,0,0) + #define JSON_HEDLEY_NO_RETURN __declspec(noreturn) +#else + #define JSON_HEDLEY_NO_RETURN +#endif + +#if defined(JSON_HEDLEY_NO_ESCAPE) + #undef JSON_HEDLEY_NO_ESCAPE +#endif +#if JSON_HEDLEY_HAS_ATTRIBUTE(noescape) + #define JSON_HEDLEY_NO_ESCAPE __attribute__((__noescape__)) +#else + #define JSON_HEDLEY_NO_ESCAPE +#endif + +#if defined(JSON_HEDLEY_UNREACHABLE) + #undef JSON_HEDLEY_UNREACHABLE +#endif +#if defined(JSON_HEDLEY_UNREACHABLE_RETURN) + #undef JSON_HEDLEY_UNREACHABLE_RETURN +#endif +#if defined(JSON_HEDLEY_ASSUME) + #undef JSON_HEDLEY_ASSUME +#endif +#if \ + JSON_HEDLEY_MSVC_VERSION_CHECK(13,10,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) + #define JSON_HEDLEY_ASSUME(expr) __assume(expr) +#elif JSON_HEDLEY_HAS_BUILTIN(__builtin_assume) + #define JSON_HEDLEY_ASSUME(expr) __builtin_assume(expr) +#elif \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,2,0) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(4,0,0) + #if defined(__cplusplus) + #define JSON_HEDLEY_ASSUME(expr) std::_nassert(expr) + #else + #define JSON_HEDLEY_ASSUME(expr) _nassert(expr) + #endif +#endif +#if \ + (JSON_HEDLEY_HAS_BUILTIN(__builtin_unreachable) && (!defined(JSON_HEDLEY_ARM_VERSION))) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(4,5,0) || \ + JSON_HEDLEY_PGI_VERSION_CHECK(18,10,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(13,1,5) || \ + JSON_HEDLEY_CRAY_VERSION_CHECK(10,0,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_UNREACHABLE() __builtin_unreachable() +#elif defined(JSON_HEDLEY_ASSUME) + #define JSON_HEDLEY_UNREACHABLE() JSON_HEDLEY_ASSUME(0) +#endif +#if !defined(JSON_HEDLEY_ASSUME) + #if defined(JSON_HEDLEY_UNREACHABLE) + #define JSON_HEDLEY_ASSUME(expr) JSON_HEDLEY_STATIC_CAST(void, ((expr) ? 1 : (JSON_HEDLEY_UNREACHABLE(), 1))) + #else + #define JSON_HEDLEY_ASSUME(expr) JSON_HEDLEY_STATIC_CAST(void, expr) + #endif +#endif +#if defined(JSON_HEDLEY_UNREACHABLE) + #if \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,2,0) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(4,0,0) + #define JSON_HEDLEY_UNREACHABLE_RETURN(value) return (JSON_HEDLEY_STATIC_CAST(void, JSON_HEDLEY_ASSUME(0)), (value)) + #else + #define JSON_HEDLEY_UNREACHABLE_RETURN(value) JSON_HEDLEY_UNREACHABLE() + #endif +#else + #define JSON_HEDLEY_UNREACHABLE_RETURN(value) return (value) +#endif +#if !defined(JSON_HEDLEY_UNREACHABLE) + #define JSON_HEDLEY_UNREACHABLE() JSON_HEDLEY_ASSUME(0) +#endif + +JSON_HEDLEY_DIAGNOSTIC_PUSH +#if JSON_HEDLEY_HAS_WARNING("-Wpedantic") + #pragma clang diagnostic ignored "-Wpedantic" +#endif +#if JSON_HEDLEY_HAS_WARNING("-Wc++98-compat-pedantic") && defined(__cplusplus) + #pragma clang diagnostic ignored "-Wc++98-compat-pedantic" +#endif +#if JSON_HEDLEY_GCC_HAS_WARNING("-Wvariadic-macros",4,0,0) + #if defined(__clang__) + #pragma clang diagnostic ignored "-Wvariadic-macros" + #elif defined(JSON_HEDLEY_GCC_VERSION) + #pragma GCC diagnostic ignored "-Wvariadic-macros" + #endif +#endif +#if defined(JSON_HEDLEY_NON_NULL) + #undef JSON_HEDLEY_NON_NULL +#endif +#if \ + JSON_HEDLEY_HAS_ATTRIBUTE(nonnull) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(3,3,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) + #define JSON_HEDLEY_NON_NULL(...) __attribute__((__nonnull__(__VA_ARGS__))) +#else + #define JSON_HEDLEY_NON_NULL(...) +#endif +JSON_HEDLEY_DIAGNOSTIC_POP + +#if defined(JSON_HEDLEY_PRINTF_FORMAT) + #undef JSON_HEDLEY_PRINTF_FORMAT +#endif +#if defined(__MINGW32__) && JSON_HEDLEY_GCC_HAS_ATTRIBUTE(format,4,4,0) && !defined(__USE_MINGW_ANSI_STDIO) + #define JSON_HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) __attribute__((__format__(ms_printf, string_idx, first_to_check))) +#elif defined(__MINGW32__) && JSON_HEDLEY_GCC_HAS_ATTRIBUTE(format,4,4,0) && defined(__USE_MINGW_ANSI_STDIO) + #define JSON_HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) __attribute__((__format__(gnu_printf, string_idx, first_to_check))) +#elif \ + JSON_HEDLEY_HAS_ATTRIBUTE(format) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(3,1,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(5,6,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ + JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ + (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ + (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ + (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ + (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) __attribute__((__format__(__printf__, string_idx, first_to_check))) +#elif JSON_HEDLEY_PELLES_VERSION_CHECK(6,0,0) + #define JSON_HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) __declspec(vaformat(printf,string_idx,first_to_check)) +#else + #define JSON_HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) +#endif + +#if defined(JSON_HEDLEY_CONSTEXPR) + #undef JSON_HEDLEY_CONSTEXPR +#endif +#if defined(__cplusplus) + #if __cplusplus >= 201103L + #define JSON_HEDLEY_CONSTEXPR JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_(constexpr) + #endif +#endif +#if !defined(JSON_HEDLEY_CONSTEXPR) + #define JSON_HEDLEY_CONSTEXPR +#endif + +#if defined(JSON_HEDLEY_PREDICT) + #undef JSON_HEDLEY_PREDICT +#endif +#if defined(JSON_HEDLEY_LIKELY) + #undef JSON_HEDLEY_LIKELY +#endif +#if defined(JSON_HEDLEY_UNLIKELY) + #undef JSON_HEDLEY_UNLIKELY +#endif +#if defined(JSON_HEDLEY_UNPREDICTABLE) + #undef JSON_HEDLEY_UNPREDICTABLE +#endif +#if JSON_HEDLEY_HAS_BUILTIN(__builtin_unpredictable) + #define JSON_HEDLEY_UNPREDICTABLE(expr) __builtin_unpredictable((expr)) +#endif +#if \ + (JSON_HEDLEY_HAS_BUILTIN(__builtin_expect_with_probability) && !defined(JSON_HEDLEY_PGI_VERSION)) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(9,0,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) +# define JSON_HEDLEY_PREDICT(expr, value, probability) __builtin_expect_with_probability( (expr), (value), (probability)) +# define JSON_HEDLEY_PREDICT_TRUE(expr, probability) __builtin_expect_with_probability(!!(expr), 1 , (probability)) +# define JSON_HEDLEY_PREDICT_FALSE(expr, probability) __builtin_expect_with_probability(!!(expr), 0 , (probability)) +# define JSON_HEDLEY_LIKELY(expr) __builtin_expect (!!(expr), 1 ) +# define JSON_HEDLEY_UNLIKELY(expr) __builtin_expect (!!(expr), 0 ) +#elif \ + (JSON_HEDLEY_HAS_BUILTIN(__builtin_expect) && !defined(JSON_HEDLEY_INTEL_CL_VERSION)) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(3,0,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + (JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,15,0) && defined(__cplusplus)) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ + JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,7,0) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(3,1,0) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,1,0) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(6,1,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ + JSON_HEDLEY_TINYC_VERSION_CHECK(0,9,27) || \ + JSON_HEDLEY_CRAY_VERSION_CHECK(8,1,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) +# define JSON_HEDLEY_PREDICT(expr, expected, probability) \ + (((probability) >= 0.9) ? __builtin_expect((expr), (expected)) : (JSON_HEDLEY_STATIC_CAST(void, expected), (expr))) +# define JSON_HEDLEY_PREDICT_TRUE(expr, probability) \ + (__extension__ ({ \ + double hedley_probability_ = (probability); \ + ((hedley_probability_ >= 0.9) ? __builtin_expect(!!(expr), 1) : ((hedley_probability_ <= 0.1) ? __builtin_expect(!!(expr), 0) : !!(expr))); \ + })) +# define JSON_HEDLEY_PREDICT_FALSE(expr, probability) \ + (__extension__ ({ \ + double hedley_probability_ = (probability); \ + ((hedley_probability_ >= 0.9) ? __builtin_expect(!!(expr), 0) : ((hedley_probability_ <= 0.1) ? __builtin_expect(!!(expr), 1) : !!(expr))); \ + })) +# define JSON_HEDLEY_LIKELY(expr) __builtin_expect(!!(expr), 1) +# define JSON_HEDLEY_UNLIKELY(expr) __builtin_expect(!!(expr), 0) +#else +# define JSON_HEDLEY_PREDICT(expr, expected, probability) (JSON_HEDLEY_STATIC_CAST(void, expected), (expr)) +# define JSON_HEDLEY_PREDICT_TRUE(expr, probability) (!!(expr)) +# define JSON_HEDLEY_PREDICT_FALSE(expr, probability) (!!(expr)) +# define JSON_HEDLEY_LIKELY(expr) (!!(expr)) +# define JSON_HEDLEY_UNLIKELY(expr) (!!(expr)) +#endif +#if !defined(JSON_HEDLEY_UNPREDICTABLE) + #define JSON_HEDLEY_UNPREDICTABLE(expr) JSON_HEDLEY_PREDICT(expr, 1, 0.5) +#endif + +#if defined(JSON_HEDLEY_MALLOC) + #undef JSON_HEDLEY_MALLOC +#endif +#if \ + JSON_HEDLEY_HAS_ATTRIBUTE(malloc) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(3,1,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(12,1,0) || \ + JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ + (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ + (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ + (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ + (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_MALLOC __attribute__((__malloc__)) +#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,10,0) + #define JSON_HEDLEY_MALLOC _Pragma("returns_new_memory") +#elif \ + JSON_HEDLEY_MSVC_VERSION_CHECK(14,0,0) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) + #define JSON_HEDLEY_MALLOC __declspec(restrict) +#else + #define JSON_HEDLEY_MALLOC +#endif + +#if defined(JSON_HEDLEY_PURE) + #undef JSON_HEDLEY_PURE +#endif +#if \ + JSON_HEDLEY_HAS_ATTRIBUTE(pure) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(2,96,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ + JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ + (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ + (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ + (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ + (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ + JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) +# define JSON_HEDLEY_PURE __attribute__((__pure__)) +#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,10,0) +# define JSON_HEDLEY_PURE _Pragma("does_not_write_global_data") +#elif defined(__cplusplus) && \ + ( \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(2,0,1) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(4,0,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) \ + ) +# define JSON_HEDLEY_PURE _Pragma("FUNC_IS_PURE;") +#else +# define JSON_HEDLEY_PURE +#endif + +#if defined(JSON_HEDLEY_CONST) + #undef JSON_HEDLEY_CONST +#endif +#if \ + JSON_HEDLEY_HAS_ATTRIBUTE(const) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(2,5,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ + JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ + (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ + (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ + (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ + (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ + JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_CONST __attribute__((__const__)) +#elif \ + JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,10,0) + #define JSON_HEDLEY_CONST _Pragma("no_side_effect") +#else + #define JSON_HEDLEY_CONST JSON_HEDLEY_PURE +#endif + +#if defined(JSON_HEDLEY_RESTRICT) + #undef JSON_HEDLEY_RESTRICT +#endif +#if defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) && !defined(__cplusplus) + #define JSON_HEDLEY_RESTRICT restrict +#elif \ + JSON_HEDLEY_GCC_VERSION_CHECK(3,1,0) || \ + JSON_HEDLEY_MSVC_VERSION_CHECK(14,0,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ + JSON_HEDLEY_PGI_VERSION_CHECK(17,10,0) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,2,4) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,1,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + (JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,14,0) && defined(__cplusplus)) || \ + JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) || \ + defined(__clang__) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_RESTRICT __restrict +#elif JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,3,0) && !defined(__cplusplus) + #define JSON_HEDLEY_RESTRICT _Restrict +#else + #define JSON_HEDLEY_RESTRICT +#endif + +#if defined(JSON_HEDLEY_INLINE) + #undef JSON_HEDLEY_INLINE +#endif +#if \ + (defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L)) || \ + (defined(__cplusplus) && (__cplusplus >= 199711L)) + #define JSON_HEDLEY_INLINE inline +#elif \ + defined(JSON_HEDLEY_GCC_VERSION) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(6,2,0) + #define JSON_HEDLEY_INLINE __inline__ +#elif \ + JSON_HEDLEY_MSVC_VERSION_CHECK(12,0,0) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,1,0) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(3,1,0) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,2,0) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(8,0,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_INLINE __inline +#else + #define JSON_HEDLEY_INLINE +#endif + +#if defined(JSON_HEDLEY_ALWAYS_INLINE) + #undef JSON_HEDLEY_ALWAYS_INLINE +#endif +#if \ + JSON_HEDLEY_HAS_ATTRIBUTE(always_inline) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(4,0,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ + JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ + (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ + (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ + (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ + (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) || \ + JSON_HEDLEY_IAR_VERSION_CHECK(8,10,0) +# define JSON_HEDLEY_ALWAYS_INLINE __attribute__((__always_inline__)) JSON_HEDLEY_INLINE +#elif \ + JSON_HEDLEY_MSVC_VERSION_CHECK(12,0,0) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) +# define JSON_HEDLEY_ALWAYS_INLINE __forceinline +#elif defined(__cplusplus) && \ + ( \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(6,1,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) \ + ) +# define JSON_HEDLEY_ALWAYS_INLINE _Pragma("FUNC_ALWAYS_INLINE;") +#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) +# define JSON_HEDLEY_ALWAYS_INLINE _Pragma("inline=forced") +#else +# define JSON_HEDLEY_ALWAYS_INLINE JSON_HEDLEY_INLINE +#endif + +#if defined(JSON_HEDLEY_NEVER_INLINE) + #undef JSON_HEDLEY_NEVER_INLINE +#endif +#if \ + JSON_HEDLEY_HAS_ATTRIBUTE(noinline) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(4,0,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(10,1,0) || \ + JSON_HEDLEY_TI_VERSION_CHECK(15,12,0) || \ + (JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(4,8,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_ARMCL_VERSION_CHECK(5,2,0) || \ + (JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL2000_VERSION_CHECK(6,4,0) || \ + (JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,0,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(4,3,0) || \ + (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) || \ + JSON_HEDLEY_TI_CL7X_VERSION_CHECK(1,2,0) || \ + JSON_HEDLEY_TI_CLPRU_VERSION_CHECK(2,1,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) || \ + JSON_HEDLEY_IAR_VERSION_CHECK(8,10,0) + #define JSON_HEDLEY_NEVER_INLINE __attribute__((__noinline__)) +#elif \ + JSON_HEDLEY_MSVC_VERSION_CHECK(13,10,0) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) + #define JSON_HEDLEY_NEVER_INLINE __declspec(noinline) +#elif JSON_HEDLEY_PGI_VERSION_CHECK(10,2,0) + #define JSON_HEDLEY_NEVER_INLINE _Pragma("noinline") +#elif JSON_HEDLEY_TI_CL6X_VERSION_CHECK(6,0,0) && defined(__cplusplus) + #define JSON_HEDLEY_NEVER_INLINE _Pragma("FUNC_CANNOT_INLINE;") +#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) + #define JSON_HEDLEY_NEVER_INLINE _Pragma("inline=never") +#elif JSON_HEDLEY_COMPCERT_VERSION_CHECK(3,2,0) + #define JSON_HEDLEY_NEVER_INLINE __attribute((noinline)) +#elif JSON_HEDLEY_PELLES_VERSION_CHECK(9,0,0) + #define JSON_HEDLEY_NEVER_INLINE __declspec(noinline) +#else + #define JSON_HEDLEY_NEVER_INLINE +#endif + +#if defined(JSON_HEDLEY_PRIVATE) + #undef JSON_HEDLEY_PRIVATE +#endif +#if defined(JSON_HEDLEY_PUBLIC) + #undef JSON_HEDLEY_PUBLIC +#endif +#if defined(JSON_HEDLEY_IMPORT) + #undef JSON_HEDLEY_IMPORT +#endif +#if defined(_WIN32) || defined(__CYGWIN__) +# define JSON_HEDLEY_PRIVATE +# define JSON_HEDLEY_PUBLIC __declspec(dllexport) +# define JSON_HEDLEY_IMPORT __declspec(dllimport) +#else +# if \ + JSON_HEDLEY_HAS_ATTRIBUTE(visibility) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(3,3,0) || \ + JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,11,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(13,1,0) || \ + ( \ + defined(__TI_EABI__) && \ + ( \ + (JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,2,0) && defined(__TI_GNU_ATTRIBUTE_SUPPORT__)) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(7,5,0) \ + ) \ + ) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) +# define JSON_HEDLEY_PRIVATE __attribute__((__visibility__("hidden"))) +# define JSON_HEDLEY_PUBLIC __attribute__((__visibility__("default"))) +# else +# define JSON_HEDLEY_PRIVATE +# define JSON_HEDLEY_PUBLIC +# endif +# define JSON_HEDLEY_IMPORT extern +#endif + +#if defined(JSON_HEDLEY_NO_THROW) + #undef JSON_HEDLEY_NO_THROW +#endif +#if \ + JSON_HEDLEY_HAS_ATTRIBUTE(nothrow) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(3,3,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_NO_THROW __attribute__((__nothrow__)) +#elif \ + JSON_HEDLEY_MSVC_VERSION_CHECK(13,1,0) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) + #define JSON_HEDLEY_NO_THROW __declspec(nothrow) +#else + #define JSON_HEDLEY_NO_THROW +#endif + +#if defined(JSON_HEDLEY_FALL_THROUGH) + #undef JSON_HEDLEY_FALL_THROUGH +#endif +#if \ + JSON_HEDLEY_HAS_ATTRIBUTE(fallthrough) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(7,0,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_FALL_THROUGH __attribute__((__fallthrough__)) +#elif JSON_HEDLEY_HAS_CPP_ATTRIBUTE_NS(clang,fallthrough) + #define JSON_HEDLEY_FALL_THROUGH JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[clang::fallthrough]]) +#elif JSON_HEDLEY_HAS_CPP_ATTRIBUTE(fallthrough) + #define JSON_HEDLEY_FALL_THROUGH JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_([[fallthrough]]) +#elif defined(__fallthrough) /* SAL */ + #define JSON_HEDLEY_FALL_THROUGH __fallthrough +#else + #define JSON_HEDLEY_FALL_THROUGH +#endif + +#if defined(JSON_HEDLEY_RETURNS_NON_NULL) + #undef JSON_HEDLEY_RETURNS_NON_NULL +#endif +#if \ + JSON_HEDLEY_HAS_ATTRIBUTE(returns_nonnull) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(4,9,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_RETURNS_NON_NULL __attribute__((__returns_nonnull__)) +#elif defined(_Ret_notnull_) /* SAL */ + #define JSON_HEDLEY_RETURNS_NON_NULL _Ret_notnull_ +#else + #define JSON_HEDLEY_RETURNS_NON_NULL +#endif + +#if defined(JSON_HEDLEY_ARRAY_PARAM) + #undef JSON_HEDLEY_ARRAY_PARAM +#endif +#if \ + defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) && \ + !defined(__STDC_NO_VLA__) && \ + !defined(__cplusplus) && \ + !defined(JSON_HEDLEY_PGI_VERSION) && \ + !defined(JSON_HEDLEY_TINYC_VERSION) + #define JSON_HEDLEY_ARRAY_PARAM(name) (name) +#else + #define JSON_HEDLEY_ARRAY_PARAM(name) +#endif + +#if defined(JSON_HEDLEY_IS_CONSTANT) + #undef JSON_HEDLEY_IS_CONSTANT +#endif +#if defined(JSON_HEDLEY_REQUIRE_CONSTEXPR) + #undef JSON_HEDLEY_REQUIRE_CONSTEXPR +#endif +/* JSON_HEDLEY_IS_CONSTEXPR_ is for + HEDLEY INTERNAL USE ONLY. API subject to change without notice. */ +#if defined(JSON_HEDLEY_IS_CONSTEXPR_) + #undef JSON_HEDLEY_IS_CONSTEXPR_ +#endif +#if \ + JSON_HEDLEY_HAS_BUILTIN(__builtin_constant_p) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(3,4,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_TINYC_VERSION_CHECK(0,9,19) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(4,1,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(13,1,0) || \ + JSON_HEDLEY_TI_CL6X_VERSION_CHECK(6,1,0) || \ + (JSON_HEDLEY_SUNPRO_VERSION_CHECK(5,10,0) && !defined(__cplusplus)) || \ + JSON_HEDLEY_CRAY_VERSION_CHECK(8,1,0) || \ + JSON_HEDLEY_MCST_LCC_VERSION_CHECK(1,25,10) + #define JSON_HEDLEY_IS_CONSTANT(expr) __builtin_constant_p(expr) +#endif +#if !defined(__cplusplus) +# if \ + JSON_HEDLEY_HAS_BUILTIN(__builtin_types_compatible_p) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(3,4,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(13,1,0) || \ + JSON_HEDLEY_CRAY_VERSION_CHECK(8,1,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(5,4,0) || \ + JSON_HEDLEY_TINYC_VERSION_CHECK(0,9,24) +#if defined(__INTPTR_TYPE__) + #define JSON_HEDLEY_IS_CONSTEXPR_(expr) __builtin_types_compatible_p(__typeof__((1 ? (void*) ((__INTPTR_TYPE__) ((expr) * 0)) : (int*) 0)), int*) +#else + #include + #define JSON_HEDLEY_IS_CONSTEXPR_(expr) __builtin_types_compatible_p(__typeof__((1 ? (void*) ((intptr_t) ((expr) * 0)) : (int*) 0)), int*) +#endif +# elif \ + ( \ + defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 201112L) && \ + !defined(JSON_HEDLEY_SUNPRO_VERSION) && \ + !defined(JSON_HEDLEY_PGI_VERSION) && \ + !defined(JSON_HEDLEY_IAR_VERSION)) || \ + (JSON_HEDLEY_HAS_EXTENSION(c_generic_selections) && !defined(JSON_HEDLEY_IAR_VERSION)) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(4,9,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(17,0,0) || \ + JSON_HEDLEY_IBM_VERSION_CHECK(12,1,0) || \ + JSON_HEDLEY_ARM_VERSION_CHECK(5,3,0) +#if defined(__INTPTR_TYPE__) + #define JSON_HEDLEY_IS_CONSTEXPR_(expr) _Generic((1 ? (void*) ((__INTPTR_TYPE__) ((expr) * 0)) : (int*) 0), int*: 1, void*: 0) +#else + #include + #define JSON_HEDLEY_IS_CONSTEXPR_(expr) _Generic((1 ? (void*) ((intptr_t) * 0) : (int*) 0), int*: 1, void*: 0) +#endif +# elif \ + defined(JSON_HEDLEY_GCC_VERSION) || \ + defined(JSON_HEDLEY_INTEL_VERSION) || \ + defined(JSON_HEDLEY_TINYC_VERSION) || \ + defined(JSON_HEDLEY_TI_ARMCL_VERSION) || \ + JSON_HEDLEY_TI_CL430_VERSION_CHECK(18,12,0) || \ + defined(JSON_HEDLEY_TI_CL2000_VERSION) || \ + defined(JSON_HEDLEY_TI_CL6X_VERSION) || \ + defined(JSON_HEDLEY_TI_CL7X_VERSION) || \ + defined(JSON_HEDLEY_TI_CLPRU_VERSION) || \ + defined(__clang__) +# define JSON_HEDLEY_IS_CONSTEXPR_(expr) ( \ + sizeof(void) != \ + sizeof(*( \ + 1 ? \ + ((void*) ((expr) * 0L) ) : \ +((struct { char v[sizeof(void) * 2]; } *) 1) \ + ) \ + ) \ + ) +# endif +#endif +#if defined(JSON_HEDLEY_IS_CONSTEXPR_) + #if !defined(JSON_HEDLEY_IS_CONSTANT) + #define JSON_HEDLEY_IS_CONSTANT(expr) JSON_HEDLEY_IS_CONSTEXPR_(expr) + #endif + #define JSON_HEDLEY_REQUIRE_CONSTEXPR(expr) (JSON_HEDLEY_IS_CONSTEXPR_(expr) ? (expr) : (-1)) +#else + #if !defined(JSON_HEDLEY_IS_CONSTANT) + #define JSON_HEDLEY_IS_CONSTANT(expr) (0) + #endif + #define JSON_HEDLEY_REQUIRE_CONSTEXPR(expr) (expr) +#endif + +#if defined(JSON_HEDLEY_BEGIN_C_DECLS) + #undef JSON_HEDLEY_BEGIN_C_DECLS +#endif +#if defined(JSON_HEDLEY_END_C_DECLS) + #undef JSON_HEDLEY_END_C_DECLS +#endif +#if defined(JSON_HEDLEY_C_DECL) + #undef JSON_HEDLEY_C_DECL +#endif +#if defined(__cplusplus) + #define JSON_HEDLEY_BEGIN_C_DECLS extern "C" { + #define JSON_HEDLEY_END_C_DECLS } + #define JSON_HEDLEY_C_DECL extern "C" +#else + #define JSON_HEDLEY_BEGIN_C_DECLS + #define JSON_HEDLEY_END_C_DECLS + #define JSON_HEDLEY_C_DECL +#endif + +#if defined(JSON_HEDLEY_STATIC_ASSERT) + #undef JSON_HEDLEY_STATIC_ASSERT +#endif +#if \ + !defined(__cplusplus) && ( \ + (defined(__STDC_VERSION__) && (__STDC_VERSION__ >= 201112L)) || \ + (JSON_HEDLEY_HAS_FEATURE(c_static_assert) && !defined(JSON_HEDLEY_INTEL_CL_VERSION)) || \ + JSON_HEDLEY_GCC_VERSION_CHECK(6,0,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) || \ + defined(_Static_assert) \ + ) +# define JSON_HEDLEY_STATIC_ASSERT(expr, message) _Static_assert(expr, message) +#elif \ + (defined(__cplusplus) && (__cplusplus >= 201103L)) || \ + JSON_HEDLEY_MSVC_VERSION_CHECK(16,0,0) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) +# define JSON_HEDLEY_STATIC_ASSERT(expr, message) JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_(static_assert(expr, message)) +#else +# define JSON_HEDLEY_STATIC_ASSERT(expr, message) +#endif + +#if defined(JSON_HEDLEY_NULL) + #undef JSON_HEDLEY_NULL +#endif +#if defined(__cplusplus) + #if __cplusplus >= 201103L + #define JSON_HEDLEY_NULL JSON_HEDLEY_DIAGNOSTIC_DISABLE_CPP98_COMPAT_WRAP_(nullptr) + #elif defined(NULL) + #define JSON_HEDLEY_NULL NULL + #else + #define JSON_HEDLEY_NULL JSON_HEDLEY_STATIC_CAST(void*, 0) + #endif +#elif defined(NULL) + #define JSON_HEDLEY_NULL NULL +#else + #define JSON_HEDLEY_NULL ((void*) 0) +#endif + +#if defined(JSON_HEDLEY_MESSAGE) + #undef JSON_HEDLEY_MESSAGE +#endif +#if JSON_HEDLEY_HAS_WARNING("-Wunknown-pragmas") +# define JSON_HEDLEY_MESSAGE(msg) \ + JSON_HEDLEY_DIAGNOSTIC_PUSH \ + JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS \ + JSON_HEDLEY_PRAGMA(message msg) \ + JSON_HEDLEY_DIAGNOSTIC_POP +#elif \ + JSON_HEDLEY_GCC_VERSION_CHECK(4,4,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) +# define JSON_HEDLEY_MESSAGE(msg) JSON_HEDLEY_PRAGMA(message msg) +#elif JSON_HEDLEY_CRAY_VERSION_CHECK(5,0,0) +# define JSON_HEDLEY_MESSAGE(msg) JSON_HEDLEY_PRAGMA(_CRI message msg) +#elif JSON_HEDLEY_IAR_VERSION_CHECK(8,0,0) +# define JSON_HEDLEY_MESSAGE(msg) JSON_HEDLEY_PRAGMA(message(msg)) +#elif JSON_HEDLEY_PELLES_VERSION_CHECK(2,0,0) +# define JSON_HEDLEY_MESSAGE(msg) JSON_HEDLEY_PRAGMA(message(msg)) +#else +# define JSON_HEDLEY_MESSAGE(msg) +#endif + +#if defined(JSON_HEDLEY_WARNING) + #undef JSON_HEDLEY_WARNING +#endif +#if JSON_HEDLEY_HAS_WARNING("-Wunknown-pragmas") +# define JSON_HEDLEY_WARNING(msg) \ + JSON_HEDLEY_DIAGNOSTIC_PUSH \ + JSON_HEDLEY_DIAGNOSTIC_DISABLE_UNKNOWN_PRAGMAS \ + JSON_HEDLEY_PRAGMA(clang warning msg) \ + JSON_HEDLEY_DIAGNOSTIC_POP +#elif \ + JSON_HEDLEY_GCC_VERSION_CHECK(4,8,0) || \ + JSON_HEDLEY_PGI_VERSION_CHECK(18,4,0) || \ + JSON_HEDLEY_INTEL_VERSION_CHECK(13,0,0) +# define JSON_HEDLEY_WARNING(msg) JSON_HEDLEY_PRAGMA(GCC warning msg) +#elif \ + JSON_HEDLEY_MSVC_VERSION_CHECK(15,0,0) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) +# define JSON_HEDLEY_WARNING(msg) JSON_HEDLEY_PRAGMA(message(msg)) +#else +# define JSON_HEDLEY_WARNING(msg) JSON_HEDLEY_MESSAGE(msg) +#endif + +#if defined(JSON_HEDLEY_REQUIRE) + #undef JSON_HEDLEY_REQUIRE +#endif +#if defined(JSON_HEDLEY_REQUIRE_MSG) + #undef JSON_HEDLEY_REQUIRE_MSG +#endif +#if JSON_HEDLEY_HAS_ATTRIBUTE(diagnose_if) +# if JSON_HEDLEY_HAS_WARNING("-Wgcc-compat") +# define JSON_HEDLEY_REQUIRE(expr) \ + JSON_HEDLEY_DIAGNOSTIC_PUSH \ + _Pragma("clang diagnostic ignored \"-Wgcc-compat\"") \ + __attribute__((diagnose_if(!(expr), #expr, "error"))) \ + JSON_HEDLEY_DIAGNOSTIC_POP +# define JSON_HEDLEY_REQUIRE_MSG(expr,msg) \ + JSON_HEDLEY_DIAGNOSTIC_PUSH \ + _Pragma("clang diagnostic ignored \"-Wgcc-compat\"") \ + __attribute__((diagnose_if(!(expr), msg, "error"))) \ + JSON_HEDLEY_DIAGNOSTIC_POP +# else +# define JSON_HEDLEY_REQUIRE(expr) __attribute__((diagnose_if(!(expr), #expr, "error"))) +# define JSON_HEDLEY_REQUIRE_MSG(expr,msg) __attribute__((diagnose_if(!(expr), msg, "error"))) +# endif +#else +# define JSON_HEDLEY_REQUIRE(expr) +# define JSON_HEDLEY_REQUIRE_MSG(expr,msg) +#endif + +#if defined(JSON_HEDLEY_FLAGS) + #undef JSON_HEDLEY_FLAGS +#endif +#if JSON_HEDLEY_HAS_ATTRIBUTE(flag_enum) && (!defined(__cplusplus) || JSON_HEDLEY_HAS_WARNING("-Wbitfield-enum-conversion")) + #define JSON_HEDLEY_FLAGS __attribute__((__flag_enum__)) +#else + #define JSON_HEDLEY_FLAGS +#endif + +#if defined(JSON_HEDLEY_FLAGS_CAST) + #undef JSON_HEDLEY_FLAGS_CAST +#endif +#if JSON_HEDLEY_INTEL_VERSION_CHECK(19,0,0) +# define JSON_HEDLEY_FLAGS_CAST(T, expr) (__extension__ ({ \ + JSON_HEDLEY_DIAGNOSTIC_PUSH \ + _Pragma("warning(disable:188)") \ + ((T) (expr)); \ + JSON_HEDLEY_DIAGNOSTIC_POP \ + })) +#else +# define JSON_HEDLEY_FLAGS_CAST(T, expr) JSON_HEDLEY_STATIC_CAST(T, expr) +#endif + +#if defined(JSON_HEDLEY_EMPTY_BASES) + #undef JSON_HEDLEY_EMPTY_BASES +#endif +#if \ + (JSON_HEDLEY_MSVC_VERSION_CHECK(19,0,23918) && !JSON_HEDLEY_MSVC_VERSION_CHECK(20,0,0)) || \ + JSON_HEDLEY_INTEL_CL_VERSION_CHECK(2021,1,0) + #define JSON_HEDLEY_EMPTY_BASES __declspec(empty_bases) +#else + #define JSON_HEDLEY_EMPTY_BASES +#endif + +/* Remaining macros are deprecated. */ + +#if defined(JSON_HEDLEY_GCC_NOT_CLANG_VERSION_CHECK) + #undef JSON_HEDLEY_GCC_NOT_CLANG_VERSION_CHECK +#endif +#if defined(__clang__) + #define JSON_HEDLEY_GCC_NOT_CLANG_VERSION_CHECK(major,minor,patch) (0) +#else + #define JSON_HEDLEY_GCC_NOT_CLANG_VERSION_CHECK(major,minor,patch) JSON_HEDLEY_GCC_VERSION_CHECK(major,minor,patch) +#endif + +#if defined(JSON_HEDLEY_CLANG_HAS_ATTRIBUTE) + #undef JSON_HEDLEY_CLANG_HAS_ATTRIBUTE +#endif +#define JSON_HEDLEY_CLANG_HAS_ATTRIBUTE(attribute) JSON_HEDLEY_HAS_ATTRIBUTE(attribute) + +#if defined(JSON_HEDLEY_CLANG_HAS_CPP_ATTRIBUTE) + #undef JSON_HEDLEY_CLANG_HAS_CPP_ATTRIBUTE +#endif +#define JSON_HEDLEY_CLANG_HAS_CPP_ATTRIBUTE(attribute) JSON_HEDLEY_HAS_CPP_ATTRIBUTE(attribute) + +#if defined(JSON_HEDLEY_CLANG_HAS_BUILTIN) + #undef JSON_HEDLEY_CLANG_HAS_BUILTIN +#endif +#define JSON_HEDLEY_CLANG_HAS_BUILTIN(builtin) JSON_HEDLEY_HAS_BUILTIN(builtin) + +#if defined(JSON_HEDLEY_CLANG_HAS_FEATURE) + #undef JSON_HEDLEY_CLANG_HAS_FEATURE +#endif +#define JSON_HEDLEY_CLANG_HAS_FEATURE(feature) JSON_HEDLEY_HAS_FEATURE(feature) + +#if defined(JSON_HEDLEY_CLANG_HAS_EXTENSION) + #undef JSON_HEDLEY_CLANG_HAS_EXTENSION +#endif +#define JSON_HEDLEY_CLANG_HAS_EXTENSION(extension) JSON_HEDLEY_HAS_EXTENSION(extension) + +#if defined(JSON_HEDLEY_CLANG_HAS_DECLSPEC_DECLSPEC_ATTRIBUTE) + #undef JSON_HEDLEY_CLANG_HAS_DECLSPEC_DECLSPEC_ATTRIBUTE +#endif +#define JSON_HEDLEY_CLANG_HAS_DECLSPEC_ATTRIBUTE(attribute) JSON_HEDLEY_HAS_DECLSPEC_ATTRIBUTE(attribute) + +#if defined(JSON_HEDLEY_CLANG_HAS_WARNING) + #undef JSON_HEDLEY_CLANG_HAS_WARNING +#endif +#define JSON_HEDLEY_CLANG_HAS_WARNING(warning) JSON_HEDLEY_HAS_WARNING(warning) + +#endif /* !defined(JSON_HEDLEY_VERSION) || (JSON_HEDLEY_VERSION < X) */ + + +// This file contains all internal macro definitions (except those affecting ABI) +// You MUST include macro_unscope.hpp at the end of json.hpp to undef all of them + +// #include + + +// exclude unsupported compilers +#if !defined(JSON_SKIP_UNSUPPORTED_COMPILER_CHECK) + #if defined(__clang__) + #if (__clang_major__ * 10000 + __clang_minor__ * 100 + __clang_patchlevel__) < 30400 + #error "unsupported Clang version - see https://github.com/nlohmann/json#supported-compilers" + #endif + #elif defined(__GNUC__) && !(defined(__ICC) || defined(__INTEL_COMPILER)) + #if (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__) < 40800 + #error "unsupported GCC version - see https://github.com/nlohmann/json#supported-compilers" + #endif + #endif +#endif + +// C++ language standard detection +// if the user manually specified the used c++ version this is skipped +#if !defined(JSON_HAS_CPP_23) && !defined(JSON_HAS_CPP_20) && !defined(JSON_HAS_CPP_17) && !defined(JSON_HAS_CPP_14) && !defined(JSON_HAS_CPP_11) + #if (defined(__cplusplus) && __cplusplus > 202002L) || (defined(_MSVC_LANG) && _MSVC_LANG > 202002L) + #define JSON_HAS_CPP_23 + #define JSON_HAS_CPP_20 + #define JSON_HAS_CPP_17 + #define JSON_HAS_CPP_14 + #elif (defined(__cplusplus) && __cplusplus > 201703L) || (defined(_MSVC_LANG) && _MSVC_LANG > 201703L) + #define JSON_HAS_CPP_20 + #define JSON_HAS_CPP_17 + #define JSON_HAS_CPP_14 + #elif (defined(__cplusplus) && __cplusplus > 201402L) || (defined(_HAS_CXX17) && _HAS_CXX17 == 1) // fix for issue #464 + #define JSON_HAS_CPP_17 + #define JSON_HAS_CPP_14 + #elif (defined(__cplusplus) && __cplusplus > 201103L) || (defined(_HAS_CXX14) && _HAS_CXX14 == 1) + #define JSON_HAS_CPP_14 + #endif + // the cpp 11 flag is always specified because it is the minimal required version + #define JSON_HAS_CPP_11 +#endif + +#ifdef __has_include + #if __has_include() + #include + #endif +#endif + +#if !defined(JSON_HAS_FILESYSTEM) && !defined(JSON_HAS_EXPERIMENTAL_FILESYSTEM) + #ifdef JSON_HAS_CPP_17 + #if defined(__cpp_lib_filesystem) + #define JSON_HAS_FILESYSTEM 1 + #elif defined(__cpp_lib_experimental_filesystem) + #define JSON_HAS_EXPERIMENTAL_FILESYSTEM 1 + #elif !defined(__has_include) + #define JSON_HAS_EXPERIMENTAL_FILESYSTEM 1 + #elif __has_include() + #define JSON_HAS_FILESYSTEM 1 + #elif __has_include() + #define JSON_HAS_EXPERIMENTAL_FILESYSTEM 1 + #endif + + // std::filesystem does not work on MinGW GCC 8: https://sourceforge.net/p/mingw-w64/bugs/737/ + #if defined(__MINGW32__) && defined(__GNUC__) && __GNUC__ == 8 + #undef JSON_HAS_FILESYSTEM + #undef JSON_HAS_EXPERIMENTAL_FILESYSTEM + #endif + + // no filesystem support before GCC 8: https://en.cppreference.com/w/cpp/compiler_support + #if defined(__GNUC__) && !defined(__clang__) && __GNUC__ < 8 + #undef JSON_HAS_FILESYSTEM + #undef JSON_HAS_EXPERIMENTAL_FILESYSTEM + #endif + + // no filesystem support before Clang 7: https://en.cppreference.com/w/cpp/compiler_support + #if defined(__clang_major__) && __clang_major__ < 7 + #undef JSON_HAS_FILESYSTEM + #undef JSON_HAS_EXPERIMENTAL_FILESYSTEM + #endif + + // no filesystem support before MSVC 19.14: https://en.cppreference.com/w/cpp/compiler_support + #if defined(_MSC_VER) && _MSC_VER < 1914 + #undef JSON_HAS_FILESYSTEM + #undef JSON_HAS_EXPERIMENTAL_FILESYSTEM + #endif + + // no filesystem support before iOS 13 + #if defined(__IPHONE_OS_VERSION_MIN_REQUIRED) && __IPHONE_OS_VERSION_MIN_REQUIRED < 130000 + #undef JSON_HAS_FILESYSTEM + #undef JSON_HAS_EXPERIMENTAL_FILESYSTEM + #endif + + // no filesystem support before macOS Catalina + #if defined(__MAC_OS_X_VERSION_MIN_REQUIRED) && __MAC_OS_X_VERSION_MIN_REQUIRED < 101500 + #undef JSON_HAS_FILESYSTEM + #undef JSON_HAS_EXPERIMENTAL_FILESYSTEM + #endif + #endif +#endif + +#ifndef JSON_HAS_EXPERIMENTAL_FILESYSTEM + #define JSON_HAS_EXPERIMENTAL_FILESYSTEM 0 +#endif + +#ifndef JSON_HAS_FILESYSTEM + #define JSON_HAS_FILESYSTEM 0 +#endif + +#ifndef JSON_HAS_THREE_WAY_COMPARISON + #if defined(__cpp_impl_three_way_comparison) && __cpp_impl_three_way_comparison >= 201907L \ + && defined(__cpp_lib_three_way_comparison) && __cpp_lib_three_way_comparison >= 201907L + #define JSON_HAS_THREE_WAY_COMPARISON 1 + #else + #define JSON_HAS_THREE_WAY_COMPARISON 0 + #endif +#endif + +#ifndef JSON_HAS_RANGES + // ranges header shipping in GCC 11.1.0 (released 2021-04-27) has syntax error + #if defined(__GLIBCXX__) && __GLIBCXX__ == 20210427 + #define JSON_HAS_RANGES 0 + #elif defined(__cpp_lib_ranges) + #define JSON_HAS_RANGES 1 + #else + #define JSON_HAS_RANGES 0 + #endif +#endif + +#ifndef JSON_HAS_STATIC_RTTI + #if !defined(_HAS_STATIC_RTTI) || _HAS_STATIC_RTTI != 0 + #define JSON_HAS_STATIC_RTTI 1 + #else + #define JSON_HAS_STATIC_RTTI 0 + #endif +#endif + +#ifdef JSON_HAS_CPP_17 + #define JSON_INLINE_VARIABLE inline +#else + #define JSON_INLINE_VARIABLE +#endif + +#if JSON_HEDLEY_HAS_ATTRIBUTE(no_unique_address) + #define JSON_NO_UNIQUE_ADDRESS [[no_unique_address]] +#else + #define JSON_NO_UNIQUE_ADDRESS +#endif + +// disable documentation warnings on clang +#if defined(__clang__) + #pragma clang diagnostic push + #pragma clang diagnostic ignored "-Wdocumentation" + #pragma clang diagnostic ignored "-Wdocumentation-unknown-command" +#endif + +// allow disabling exceptions +#if (defined(__cpp_exceptions) || defined(__EXCEPTIONS) || defined(_CPPUNWIND)) && !defined(JSON_NOEXCEPTION) + #define JSON_THROW(exception) throw exception + #define JSON_TRY try + #define JSON_CATCH(exception) catch(exception) + #define JSON_INTERNAL_CATCH(exception) catch(exception) +#else + #include + #define JSON_THROW(exception) std::abort() + #define JSON_TRY if(true) + #define JSON_CATCH(exception) if(false) + #define JSON_INTERNAL_CATCH(exception) if(false) +#endif + +// override exception macros +#if defined(JSON_THROW_USER) + #undef JSON_THROW + #define JSON_THROW JSON_THROW_USER +#endif +#if defined(JSON_TRY_USER) + #undef JSON_TRY + #define JSON_TRY JSON_TRY_USER +#endif +#if defined(JSON_CATCH_USER) + #undef JSON_CATCH + #define JSON_CATCH JSON_CATCH_USER + #undef JSON_INTERNAL_CATCH + #define JSON_INTERNAL_CATCH JSON_CATCH_USER +#endif +#if defined(JSON_INTERNAL_CATCH_USER) + #undef JSON_INTERNAL_CATCH + #define JSON_INTERNAL_CATCH JSON_INTERNAL_CATCH_USER +#endif + +// allow overriding assert +#if !defined(JSON_ASSERT) + #include // assert + #define JSON_ASSERT(x) assert(x) +#endif + +// allow to access some private functions (needed by the test suite) +#if defined(JSON_TESTS_PRIVATE) + #define JSON_PRIVATE_UNLESS_TESTED public +#else + #define JSON_PRIVATE_UNLESS_TESTED private +#endif + +/*! +@brief macro to briefly define a mapping between an enum and JSON +@def NLOHMANN_JSON_SERIALIZE_ENUM +@since version 3.4.0 +*/ +#define NLOHMANN_JSON_SERIALIZE_ENUM(ENUM_TYPE, ...) \ + template \ + inline void to_json(BasicJsonType& j, const ENUM_TYPE& e) \ + { \ + /* NOLINTNEXTLINE(modernize-type-traits) we use C++11 */ \ + static_assert(std::is_enum::value, #ENUM_TYPE " must be an enum!"); \ + /* NOLINTNEXTLINE(modernize-avoid-c-arrays) we don't want to depend on */ \ + static const std::pair m[] = __VA_ARGS__; \ + auto it = std::find_if(std::begin(m), std::end(m), \ + [e](const std::pair& ej_pair) -> bool \ + { \ + return ej_pair.first == e; \ + }); \ + j = ((it != std::end(m)) ? it : std::begin(m))->second; \ + } \ + template \ + inline void from_json(const BasicJsonType& j, ENUM_TYPE& e) \ + { \ + /* NOLINTNEXTLINE(modernize-type-traits) we use C++11 */ \ + static_assert(std::is_enum::value, #ENUM_TYPE " must be an enum!"); \ + /* NOLINTNEXTLINE(modernize-avoid-c-arrays) we don't want to depend on */ \ + static const std::pair m[] = __VA_ARGS__; \ + auto it = std::find_if(std::begin(m), std::end(m), \ + [&j](const std::pair& ej_pair) -> bool \ + { \ + return ej_pair.second == j; \ + }); \ + e = ((it != std::end(m)) ? it : std::begin(m))->first; \ + } + +// Ugly macros to avoid uglier copy-paste when specializing basic_json. They +// may be removed in the future once the class is split. + +#define NLOHMANN_BASIC_JSON_TPL_DECLARATION \ + template class ObjectType, \ + template class ArrayType, \ + class StringType, class BooleanType, class NumberIntegerType, \ + class NumberUnsignedType, class NumberFloatType, \ + template class AllocatorType, \ + template class JSONSerializer, \ + class BinaryType, \ + class CustomBaseClass> + +#define NLOHMANN_BASIC_JSON_TPL \ + basic_json + +// Macros to simplify conversion from/to types + +#define NLOHMANN_JSON_EXPAND( x ) x +#define NLOHMANN_JSON_GET_MACRO(_1, _2, _3, _4, _5, _6, _7, _8, _9, _10, _11, _12, _13, _14, _15, _16, _17, _18, _19, _20, _21, _22, _23, _24, _25, _26, _27, _28, _29, _30, _31, _32, _33, _34, _35, _36, _37, _38, _39, _40, _41, _42, _43, _44, _45, _46, _47, _48, _49, _50, _51, _52, _53, _54, _55, _56, _57, _58, _59, _60, _61, _62, _63, _64, NAME,...) NAME +#define NLOHMANN_JSON_PASTE(...) NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_GET_MACRO(__VA_ARGS__, \ + NLOHMANN_JSON_PASTE64, \ + NLOHMANN_JSON_PASTE63, \ + NLOHMANN_JSON_PASTE62, \ + NLOHMANN_JSON_PASTE61, \ + NLOHMANN_JSON_PASTE60, \ + NLOHMANN_JSON_PASTE59, \ + NLOHMANN_JSON_PASTE58, \ + NLOHMANN_JSON_PASTE57, \ + NLOHMANN_JSON_PASTE56, \ + NLOHMANN_JSON_PASTE55, \ + NLOHMANN_JSON_PASTE54, \ + NLOHMANN_JSON_PASTE53, \ + NLOHMANN_JSON_PASTE52, \ + NLOHMANN_JSON_PASTE51, \ + NLOHMANN_JSON_PASTE50, \ + NLOHMANN_JSON_PASTE49, \ + NLOHMANN_JSON_PASTE48, \ + NLOHMANN_JSON_PASTE47, \ + NLOHMANN_JSON_PASTE46, \ + NLOHMANN_JSON_PASTE45, \ + NLOHMANN_JSON_PASTE44, \ + NLOHMANN_JSON_PASTE43, \ + NLOHMANN_JSON_PASTE42, \ + NLOHMANN_JSON_PASTE41, \ + NLOHMANN_JSON_PASTE40, \ + NLOHMANN_JSON_PASTE39, \ + NLOHMANN_JSON_PASTE38, \ + NLOHMANN_JSON_PASTE37, \ + NLOHMANN_JSON_PASTE36, \ + NLOHMANN_JSON_PASTE35, \ + NLOHMANN_JSON_PASTE34, \ + NLOHMANN_JSON_PASTE33, \ + NLOHMANN_JSON_PASTE32, \ + NLOHMANN_JSON_PASTE31, \ + NLOHMANN_JSON_PASTE30, \ + NLOHMANN_JSON_PASTE29, \ + NLOHMANN_JSON_PASTE28, \ + NLOHMANN_JSON_PASTE27, \ + NLOHMANN_JSON_PASTE26, \ + NLOHMANN_JSON_PASTE25, \ + NLOHMANN_JSON_PASTE24, \ + NLOHMANN_JSON_PASTE23, \ + NLOHMANN_JSON_PASTE22, \ + NLOHMANN_JSON_PASTE21, \ + NLOHMANN_JSON_PASTE20, \ + NLOHMANN_JSON_PASTE19, \ + NLOHMANN_JSON_PASTE18, \ + NLOHMANN_JSON_PASTE17, \ + NLOHMANN_JSON_PASTE16, \ + NLOHMANN_JSON_PASTE15, \ + NLOHMANN_JSON_PASTE14, \ + NLOHMANN_JSON_PASTE13, \ + NLOHMANN_JSON_PASTE12, \ + NLOHMANN_JSON_PASTE11, \ + NLOHMANN_JSON_PASTE10, \ + NLOHMANN_JSON_PASTE9, \ + NLOHMANN_JSON_PASTE8, \ + NLOHMANN_JSON_PASTE7, \ + NLOHMANN_JSON_PASTE6, \ + NLOHMANN_JSON_PASTE5, \ + NLOHMANN_JSON_PASTE4, \ + NLOHMANN_JSON_PASTE3, \ + NLOHMANN_JSON_PASTE2, \ + NLOHMANN_JSON_PASTE1)(__VA_ARGS__)) +#define NLOHMANN_JSON_PASTE2(func, v1) func(v1) +#define NLOHMANN_JSON_PASTE3(func, v1, v2) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE2(func, v2) +#define NLOHMANN_JSON_PASTE4(func, v1, v2, v3) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE3(func, v2, v3) +#define NLOHMANN_JSON_PASTE5(func, v1, v2, v3, v4) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE4(func, v2, v3, v4) +#define NLOHMANN_JSON_PASTE6(func, v1, v2, v3, v4, v5) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE5(func, v2, v3, v4, v5) +#define NLOHMANN_JSON_PASTE7(func, v1, v2, v3, v4, v5, v6) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE6(func, v2, v3, v4, v5, v6) +#define NLOHMANN_JSON_PASTE8(func, v1, v2, v3, v4, v5, v6, v7) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE7(func, v2, v3, v4, v5, v6, v7) +#define NLOHMANN_JSON_PASTE9(func, v1, v2, v3, v4, v5, v6, v7, v8) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE8(func, v2, v3, v4, v5, v6, v7, v8) +#define NLOHMANN_JSON_PASTE10(func, v1, v2, v3, v4, v5, v6, v7, v8, v9) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE9(func, v2, v3, v4, v5, v6, v7, v8, v9) +#define NLOHMANN_JSON_PASTE11(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE10(func, v2, v3, v4, v5, v6, v7, v8, v9, v10) +#define NLOHMANN_JSON_PASTE12(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE11(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11) +#define NLOHMANN_JSON_PASTE13(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE12(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12) +#define NLOHMANN_JSON_PASTE14(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE13(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13) +#define NLOHMANN_JSON_PASTE15(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE14(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14) +#define NLOHMANN_JSON_PASTE16(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE15(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15) +#define NLOHMANN_JSON_PASTE17(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE16(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16) +#define NLOHMANN_JSON_PASTE18(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE17(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17) +#define NLOHMANN_JSON_PASTE19(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE18(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18) +#define NLOHMANN_JSON_PASTE20(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE19(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19) +#define NLOHMANN_JSON_PASTE21(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE20(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20) +#define NLOHMANN_JSON_PASTE22(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE21(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21) +#define NLOHMANN_JSON_PASTE23(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE22(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22) +#define NLOHMANN_JSON_PASTE24(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE23(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23) +#define NLOHMANN_JSON_PASTE25(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE24(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24) +#define NLOHMANN_JSON_PASTE26(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE25(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25) +#define NLOHMANN_JSON_PASTE27(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE26(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26) +#define NLOHMANN_JSON_PASTE28(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE27(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27) +#define NLOHMANN_JSON_PASTE29(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE28(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28) +#define NLOHMANN_JSON_PASTE30(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE29(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29) +#define NLOHMANN_JSON_PASTE31(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE30(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30) +#define NLOHMANN_JSON_PASTE32(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE31(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31) +#define NLOHMANN_JSON_PASTE33(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE32(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32) +#define NLOHMANN_JSON_PASTE34(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE33(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33) +#define NLOHMANN_JSON_PASTE35(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE34(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34) +#define NLOHMANN_JSON_PASTE36(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE35(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35) +#define NLOHMANN_JSON_PASTE37(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE36(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36) +#define NLOHMANN_JSON_PASTE38(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE37(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37) +#define NLOHMANN_JSON_PASTE39(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE38(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38) +#define NLOHMANN_JSON_PASTE40(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE39(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39) +#define NLOHMANN_JSON_PASTE41(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE40(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40) +#define NLOHMANN_JSON_PASTE42(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE41(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41) +#define NLOHMANN_JSON_PASTE43(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE42(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42) +#define NLOHMANN_JSON_PASTE44(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE43(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43) +#define NLOHMANN_JSON_PASTE45(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE44(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44) +#define NLOHMANN_JSON_PASTE46(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE45(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45) +#define NLOHMANN_JSON_PASTE47(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE46(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46) +#define NLOHMANN_JSON_PASTE48(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE47(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47) +#define NLOHMANN_JSON_PASTE49(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE48(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48) +#define NLOHMANN_JSON_PASTE50(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE49(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49) +#define NLOHMANN_JSON_PASTE51(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE50(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50) +#define NLOHMANN_JSON_PASTE52(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE51(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51) +#define NLOHMANN_JSON_PASTE53(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE52(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52) +#define NLOHMANN_JSON_PASTE54(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE53(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53) +#define NLOHMANN_JSON_PASTE55(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE54(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54) +#define NLOHMANN_JSON_PASTE56(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE55(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55) +#define NLOHMANN_JSON_PASTE57(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE56(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56) +#define NLOHMANN_JSON_PASTE58(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE57(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57) +#define NLOHMANN_JSON_PASTE59(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE58(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58) +#define NLOHMANN_JSON_PASTE60(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE59(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59) +#define NLOHMANN_JSON_PASTE61(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE60(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60) +#define NLOHMANN_JSON_PASTE62(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60, v61) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE61(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60, v61) +#define NLOHMANN_JSON_PASTE63(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60, v61, v62) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE62(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60, v61, v62) +#define NLOHMANN_JSON_PASTE64(func, v1, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60, v61, v62, v63) NLOHMANN_JSON_PASTE2(func, v1) NLOHMANN_JSON_PASTE63(func, v2, v3, v4, v5, v6, v7, v8, v9, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v40, v41, v42, v43, v44, v45, v46, v47, v48, v49, v50, v51, v52, v53, v54, v55, v56, v57, v58, v59, v60, v61, v62, v63) + +#define NLOHMANN_JSON_TO(v1) nlohmann_json_j[#v1] = nlohmann_json_t.v1; +#define NLOHMANN_JSON_FROM(v1) nlohmann_json_j.at(#v1).get_to(nlohmann_json_t.v1); +#define NLOHMANN_JSON_FROM_WITH_DEFAULT(v1) nlohmann_json_t.v1 = !nlohmann_json_j.is_null() ? nlohmann_json_j.value(#v1, nlohmann_json_default_obj.v1) : nlohmann_json_default_obj.v1; + +/*! +@brief macro +@def NLOHMANN_DEFINE_TYPE_INTRUSIVE +@since version 3.9.0 +@sa https://json.nlohmann.me/api/macros/nlohmann_define_type_intrusive/ +*/ +#define NLOHMANN_DEFINE_TYPE_INTRUSIVE(Type, ...) \ + template::value, int> = 0> \ + friend void to_json(BasicJsonType& nlohmann_json_j, const Type& nlohmann_json_t) { NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } \ + template::value, int> = 0> \ + friend void from_json(const BasicJsonType& nlohmann_json_j, Type& nlohmann_json_t) { NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_FROM, __VA_ARGS__)) } + +/*! +@brief macro +@def NLOHMANN_DEFINE_TYPE_INTRUSIVE_WITH_DEFAULT +@since version 3.11.0 +@sa https://json.nlohmann.me/api/macros/nlohmann_define_type_intrusive/ +*/ +#define NLOHMANN_DEFINE_TYPE_INTRUSIVE_WITH_DEFAULT(Type, ...) \ + template::value, int> = 0> \ + friend void to_json(BasicJsonType& nlohmann_json_j, const Type& nlohmann_json_t) { NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } \ + template::value, int> = 0> \ + friend void from_json(const BasicJsonType& nlohmann_json_j, Type& nlohmann_json_t) { const Type nlohmann_json_default_obj{}; NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_FROM_WITH_DEFAULT, __VA_ARGS__)) } + +/*! +@brief macro +@def NLOHMANN_DEFINE_TYPE_INTRUSIVE_ONLY_SERIALIZE +@since version 3.11.3 +@sa https://json.nlohmann.me/api/macros/nlohmann_define_type_intrusive/ +*/ +#define NLOHMANN_DEFINE_TYPE_INTRUSIVE_ONLY_SERIALIZE(Type, ...) \ + template::value, int> = 0> \ + friend void to_json(BasicJsonType& nlohmann_json_j, const Type& nlohmann_json_t) { NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } + +/*! +@brief macro +@def NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE +@since version 3.9.0 +@sa https://json.nlohmann.me/api/macros/nlohmann_define_type_non_intrusive/ +*/ +#define NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE(Type, ...) \ + template::value, int> = 0> \ + void to_json(BasicJsonType& nlohmann_json_j, const Type& nlohmann_json_t) { NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } \ + template::value, int> = 0> \ + void from_json(const BasicJsonType& nlohmann_json_j, Type& nlohmann_json_t) { NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_FROM, __VA_ARGS__)) } + +/*! +@brief macro +@def NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE_WITH_DEFAULT +@since version 3.11.0 +@sa https://json.nlohmann.me/api/macros/nlohmann_define_type_non_intrusive/ +*/ +#define NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE_WITH_DEFAULT(Type, ...) \ + template::value, int> = 0> \ + void to_json(BasicJsonType& nlohmann_json_j, const Type& nlohmann_json_t) { NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } \ + template::value, int> = 0> \ + void from_json(const BasicJsonType& nlohmann_json_j, Type& nlohmann_json_t) { const Type nlohmann_json_default_obj{}; NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_FROM_WITH_DEFAULT, __VA_ARGS__)) } + +/*! +@brief macro +@def NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE_ONLY_SERIALIZE +@since version 3.11.3 +@sa https://json.nlohmann.me/api/macros/nlohmann_define_type_non_intrusive/ +*/ +#define NLOHMANN_DEFINE_TYPE_NON_INTRUSIVE_ONLY_SERIALIZE(Type, ...) \ + template::value, int> = 0> \ + void to_json(BasicJsonType& nlohmann_json_j, const Type& nlohmann_json_t) { NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } + +/*! +@brief macro +@def NLOHMANN_DEFINE_DERIVED_TYPE_INTRUSIVE +@since version 3.12.0 +@sa https://json.nlohmann.me/api/macros/nlohmann_define_derived_type/ +*/ +#define NLOHMANN_DEFINE_DERIVED_TYPE_INTRUSIVE(Type, BaseType, ...) \ + template::value, int> = 0> \ + friend void to_json(BasicJsonType& nlohmann_json_j, const Type& nlohmann_json_t) { nlohmann::to_json(nlohmann_json_j, static_cast(nlohmann_json_t)); NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } \ + template::value, int> = 0> \ + friend void from_json(const BasicJsonType& nlohmann_json_j, Type& nlohmann_json_t) { nlohmann::from_json(nlohmann_json_j, static_cast(nlohmann_json_t)); NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_FROM, __VA_ARGS__)) } + +/*! +@brief macro +@def NLOHMANN_DEFINE_DERIVED_TYPE_INTRUSIVE_WITH_DEFAULT +@since version 3.12.0 +@sa https://json.nlohmann.me/api/macros/nlohmann_define_derived_type/ +*/ +#define NLOHMANN_DEFINE_DERIVED_TYPE_INTRUSIVE_WITH_DEFAULT(Type, BaseType, ...) \ + template::value, int> = 0> \ + friend void to_json(BasicJsonType& nlohmann_json_j, const Type& nlohmann_json_t) { nlohmann::to_json(nlohmann_json_j, static_cast(nlohmann_json_t)); NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } \ + template::value, int> = 0> \ + friend void from_json(const BasicJsonType& nlohmann_json_j, Type& nlohmann_json_t) { nlohmann::from_json(nlohmann_json_j, static_cast(nlohmann_json_t)); const Type nlohmann_json_default_obj{}; NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_FROM_WITH_DEFAULT, __VA_ARGS__)) } + +/*! +@brief macro +@def NLOHMANN_DEFINE_DERIVED_TYPE_INTRUSIVE_ONLY_SERIALIZE +@since version 3.12.0 +@sa https://json.nlohmann.me/api/macros/nlohmann_define_derived_type/ +*/ +#define NLOHMANN_DEFINE_DERIVED_TYPE_INTRUSIVE_ONLY_SERIALIZE(Type, BaseType, ...) \ + template::value, int> = 0> \ + friend void to_json(BasicJsonType& nlohmann_json_j, const Type& nlohmann_json_t) { nlohmann::to_json(nlohmann_json_j, static_cast(nlohmann_json_t)); NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } + +/*! +@brief macro +@def NLOHMANN_DEFINE_DERIVED_TYPE_NON_INTRUSIVE +@since version 3.12.0 +@sa https://json.nlohmann.me/api/macros/nlohmann_define_derived_type/ +*/ +#define NLOHMANN_DEFINE_DERIVED_TYPE_NON_INTRUSIVE(Type, BaseType, ...) \ + template::value, int> = 0> \ + void to_json(BasicJsonType& nlohmann_json_j, const Type& nlohmann_json_t) { nlohmann::to_json(nlohmann_json_j, static_cast(nlohmann_json_t)); NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } \ + template::value, int> = 0> \ + void from_json(const BasicJsonType& nlohmann_json_j, Type& nlohmann_json_t) { nlohmann::from_json(nlohmann_json_j, static_cast(nlohmann_json_t)); NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_FROM, __VA_ARGS__)) } + +/*! +@brief macro +@def NLOHMANN_DEFINE_DERIVED_TYPE_NON_INTRUSIVE_WITH_DEFAULT +@since version 3.12.0 +@sa https://json.nlohmann.me/api/macros/nlohmann_define_derived_type/ +*/ +#define NLOHMANN_DEFINE_DERIVED_TYPE_NON_INTRUSIVE_WITH_DEFAULT(Type, BaseType, ...) \ + template::value, int> = 0> \ + void to_json(BasicJsonType& nlohmann_json_j, const Type& nlohmann_json_t) { nlohmann::to_json(nlohmann_json_j, static_cast(nlohmann_json_t)); NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } \ + template::value, int> = 0> \ + void from_json(const BasicJsonType& nlohmann_json_j, Type& nlohmann_json_t) { nlohmann::from_json(nlohmann_json_j, static_cast(nlohmann_json_t)); const Type nlohmann_json_default_obj{}; NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_FROM_WITH_DEFAULT, __VA_ARGS__)) } + +/*! +@brief macro +@def NLOHMANN_DEFINE_DERIVED_TYPE_NON_INTRUSIVE_ONLY_SERIALIZE +@since version 3.12.0 +@sa https://json.nlohmann.me/api/macros/nlohmann_define_derived_type/ +*/ +#define NLOHMANN_DEFINE_DERIVED_TYPE_NON_INTRUSIVE_ONLY_SERIALIZE(Type, BaseType, ...) \ + template::value, int> = 0> \ + void to_json(BasicJsonType& nlohmann_json_j, const Type& nlohmann_json_t) { nlohmann::to_json(nlohmann_json_j, static_cast(nlohmann_json_t)); NLOHMANN_JSON_EXPAND(NLOHMANN_JSON_PASTE(NLOHMANN_JSON_TO, __VA_ARGS__)) } + +// inspired from https://stackoverflow.com/a/26745591 +// allows calling any std function as if (e.g., with begin): +// using std::begin; begin(x); +// +// it allows using the detected idiom to retrieve the return type +// of such an expression +#define NLOHMANN_CAN_CALL_STD_FUNC_IMPL(std_name) \ + namespace detail { \ + using std::std_name; \ + \ + template \ + using result_of_##std_name = decltype(std_name(std::declval()...)); \ + } \ + \ + namespace detail2 { \ + struct std_name##_tag \ + { \ + }; \ + \ + template \ + std_name##_tag std_name(T&&...); \ + \ + template \ + using result_of_##std_name = decltype(std_name(std::declval()...)); \ + \ + template \ + struct would_call_std_##std_name \ + { \ + static constexpr auto const value = ::nlohmann::detail:: \ + is_detected_exact::value; \ + }; \ + } /* namespace detail2 */ \ + \ + template \ + struct would_call_std_##std_name : detail2::would_call_std_##std_name \ + { \ + } + +#ifndef JSON_USE_IMPLICIT_CONVERSIONS + #define JSON_USE_IMPLICIT_CONVERSIONS 1 +#endif + +#if JSON_USE_IMPLICIT_CONVERSIONS + #define JSON_EXPLICIT +#else + #define JSON_EXPLICIT explicit +#endif + +#ifndef JSON_DISABLE_ENUM_SERIALIZATION + #define JSON_DISABLE_ENUM_SERIALIZATION 0 +#endif + +#ifndef JSON_USE_GLOBAL_UDLS + #define JSON_USE_GLOBAL_UDLS 1 +#endif + +#if JSON_HAS_THREE_WAY_COMPARISON + #include // partial_ordering +#endif + +NLOHMANN_JSON_NAMESPACE_BEGIN +namespace detail +{ + +/////////////////////////// +// JSON type enumeration // +/////////////////////////// + +/*! +@brief the JSON type enumeration + +This enumeration collects the different JSON types. It is internally used to +distinguish the stored values, and the functions @ref basic_json::is_null(), +@ref basic_json::is_object(), @ref basic_json::is_array(), +@ref basic_json::is_string(), @ref basic_json::is_boolean(), +@ref basic_json::is_number() (with @ref basic_json::is_number_integer(), +@ref basic_json::is_number_unsigned(), and @ref basic_json::is_number_float()), +@ref basic_json::is_discarded(), @ref basic_json::is_primitive(), and +@ref basic_json::is_structured() rely on it. + +@note There are three enumeration entries (number_integer, number_unsigned, and +number_float), because the library distinguishes these three types for numbers: +@ref basic_json::number_unsigned_t is used for unsigned integers, +@ref basic_json::number_integer_t is used for signed integers, and +@ref basic_json::number_float_t is used for floating-point numbers or to +approximate integers which do not fit in the limits of their respective type. + +@sa see @ref basic_json::basic_json(const value_t value_type) -- create a JSON +value with the default value for a given type + +@since version 1.0.0 +*/ +enum class value_t : std::uint8_t +{ + null, ///< null value + object, ///< object (unordered set of name/value pairs) + array, ///< array (ordered collection of values) + string, ///< string value + boolean, ///< boolean value + number_integer, ///< number value (signed integer) + number_unsigned, ///< number value (unsigned integer) + number_float, ///< number value (floating-point) + binary, ///< binary array (ordered collection of bytes) + discarded ///< discarded by the parser callback function +}; + +/*! +@brief comparison operator for JSON types + +Returns an ordering that is similar to Python: +- order: null < boolean < number < object < array < string < binary +- furthermore, each type is not smaller than itself +- discarded values are not comparable +- binary is represented as a b"" string in python and directly comparable to a + string; however, making a binary array directly comparable with a string would + be surprising behavior in a JSON file. + +@since version 1.0.0 +*/ +#if JSON_HAS_THREE_WAY_COMPARISON + inline std::partial_ordering operator<=>(const value_t lhs, const value_t rhs) noexcept // *NOPAD* +#else + inline bool operator<(const value_t lhs, const value_t rhs) noexcept +#endif +{ + static constexpr std::array order = {{ + 0 /* null */, 3 /* object */, 4 /* array */, 5 /* string */, + 1 /* boolean */, 2 /* integer */, 2 /* unsigned */, 2 /* float */, + 6 /* binary */ + } + }; + + const auto l_index = static_cast(lhs); + const auto r_index = static_cast(rhs); +#if JSON_HAS_THREE_WAY_COMPARISON + if (l_index < order.size() && r_index < order.size()) + { + return order[l_index] <=> order[r_index]; // *NOPAD* + } + return std::partial_ordering::unordered; +#else + return l_index < order.size() && r_index < order.size() && order[l_index] < order[r_index]; +#endif +} + +// GCC selects the built-in operator< over an operator rewritten from +// a user-defined spaceship operator +// Clang, MSVC, and ICC select the rewritten candidate +// (see GCC bug https://gcc.gnu.org/bugzilla/show_bug.cgi?id=105200) +#if JSON_HAS_THREE_WAY_COMPARISON && defined(__GNUC__) +inline bool operator<(const value_t lhs, const value_t rhs) noexcept +{ + return std::is_lt(lhs <=> rhs); // *NOPAD* +} +#endif + +} // namespace detail +NLOHMANN_JSON_NAMESPACE_END + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +// #include + + +NLOHMANN_JSON_NAMESPACE_BEGIN +namespace detail +{ + +/*! +@brief replace all occurrences of a substring by another string + +@param[in,out] s the string to manipulate; changed so that all + occurrences of @a f are replaced with @a t +@param[in] f the substring to replace with @a t +@param[in] t the string to replace @a f + +@pre The search string @a f must not be empty. **This precondition is +enforced with an assertion.** + +@since version 2.0.0 +*/ +template +inline void replace_substring(StringType& s, const StringType& f, + const StringType& t) +{ + JSON_ASSERT(!f.empty()); + for (auto pos = s.find(f); // find first occurrence of f + pos != StringType::npos; // make sure f was found + s.replace(pos, f.size(), t), // replace with t, and + pos = s.find(f, pos + t.size())) // find next occurrence of f + {} +} + +/*! + * @brief string escaping as described in RFC 6901 (Sect. 4) + * @param[in] s string to escape + * @return escaped string + * + * Note the order of escaping "~" to "~0" and "/" to "~1" is important. + */ +template +inline StringType escape(StringType s) +{ + replace_substring(s, StringType{"~"}, StringType{"~0"}); + replace_substring(s, StringType{"/"}, StringType{"~1"}); + return s; +} + +/*! + * @brief string unescaping as described in RFC 6901 (Sect. 4) + * @param[in] s string to unescape + * @return unescaped string + * + * Note the order of escaping "~1" to "/" and "~0" to "~" is important. + */ +template +static void unescape(StringType& s) +{ + replace_substring(s, StringType{"~1"}, StringType{"/"}); + replace_substring(s, StringType{"~0"}, StringType{"~"}); +} + +} // namespace detail +NLOHMANN_JSON_NAMESPACE_END + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +#include // size_t + +// #include + + +NLOHMANN_JSON_NAMESPACE_BEGIN +namespace detail +{ + +/// struct to capture the start position of the current token +struct position_t +{ + /// the total number of characters read + std::size_t chars_read_total = 0; + /// the number of characters read in the current line + std::size_t chars_read_current_line = 0; + /// the number of lines read + std::size_t lines_read = 0; + + /// conversion to size_t to preserve SAX interface + constexpr operator size_t() const + { + return chars_read_total; + } +}; + +} // namespace detail +NLOHMANN_JSON_NAMESPACE_END + +// #include + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-FileCopyrightText: 2018 The Abseil Authors +// SPDX-License-Identifier: MIT + + + +#include // array +#include // size_t +#include // conditional, enable_if, false_type, integral_constant, is_constructible, is_integral, is_same, remove_cv, remove_reference, true_type +#include // index_sequence, make_index_sequence, index_sequence_for + +// #include + + +NLOHMANN_JSON_NAMESPACE_BEGIN +namespace detail +{ + +template +using uncvref_t = typename std::remove_cv::type>::type; + +#ifdef JSON_HAS_CPP_14 + +// the following utilities are natively available in C++14 +using std::enable_if_t; +using std::index_sequence; +using std::make_index_sequence; +using std::index_sequence_for; + +#else + +// alias templates to reduce boilerplate +template +using enable_if_t = typename std::enable_if::type; + +// The following code is taken from https://github.com/abseil/abseil-cpp/blob/10cb35e459f5ecca5b2ff107635da0bfa41011b4/absl/utility/utility.h +// which is part of Google Abseil (https://github.com/abseil/abseil-cpp), licensed under the Apache License 2.0. + +//// START OF CODE FROM GOOGLE ABSEIL + +// integer_sequence +// +// Class template representing a compile-time integer sequence. An instantiation +// of `integer_sequence` has a sequence of integers encoded in its +// type through its template arguments (which is a common need when +// working with C++11 variadic templates). `absl::integer_sequence` is designed +// to be a drop-in replacement for C++14's `std::integer_sequence`. +// +// Example: +// +// template< class T, T... Ints > +// void user_function(integer_sequence); +// +// int main() +// { +// // user_function's `T` will be deduced to `int` and `Ints...` +// // will be deduced to `0, 1, 2, 3, 4`. +// user_function(make_integer_sequence()); +// } +template +struct integer_sequence +{ + using value_type = T; + static constexpr std::size_t size() noexcept + { + return sizeof...(Ints); + } +}; + +// index_sequence +// +// A helper template for an `integer_sequence` of `size_t`, +// `absl::index_sequence` is designed to be a drop-in replacement for C++14's +// `std::index_sequence`. +template +using index_sequence = integer_sequence; + +namespace utility_internal +{ + +template +struct Extend; + +// Note that SeqSize == sizeof...(Ints). It's passed explicitly for efficiency. +template +struct Extend, SeqSize, 0> +{ + using type = integer_sequence < T, Ints..., (Ints + SeqSize)... >; +}; + +template +struct Extend, SeqSize, 1> +{ + using type = integer_sequence < T, Ints..., (Ints + SeqSize)..., 2 * SeqSize >; +}; + +// Recursion helper for 'make_integer_sequence'. +// 'Gen::type' is an alias for 'integer_sequence'. +template +struct Gen +{ + using type = + typename Extend < typename Gen < T, N / 2 >::type, N / 2, N % 2 >::type; +}; + +template +struct Gen +{ + using type = integer_sequence; +}; + +} // namespace utility_internal + +// Compile-time sequences of integers + +// make_integer_sequence +// +// This template alias is equivalent to +// `integer_sequence`, and is designed to be a drop-in +// replacement for C++14's `std::make_integer_sequence`. +template +using make_integer_sequence = typename utility_internal::Gen::type; + +// make_index_sequence +// +// This template alias is equivalent to `index_sequence<0, 1, ..., N-1>`, +// and is designed to be a drop-in replacement for C++14's +// `std::make_index_sequence`. +template +using make_index_sequence = make_integer_sequence; + +// index_sequence_for +// +// Converts a typename pack into an index sequence of the same length, and +// is designed to be a drop-in replacement for C++14's +// `std::index_sequence_for()` +template +using index_sequence_for = make_index_sequence; + +//// END OF CODE FROM GOOGLE ABSEIL + +#endif + +// dispatch utility (taken from ranges-v3) +template struct priority_tag : priority_tag < N - 1 > {}; +template<> struct priority_tag<0> {}; + +// taken from ranges-v3 +template +struct static_const +{ + static JSON_INLINE_VARIABLE constexpr T value{}; +}; + +#ifndef JSON_HAS_CPP_17 + template + constexpr T static_const::value; +#endif + +template +constexpr std::array make_array(Args&& ... args) +{ + return std::array {{static_cast(std::forward(args))...}}; +} + +} // namespace detail +NLOHMANN_JSON_NAMESPACE_END + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +#include // numeric_limits +#include // char_traits +#include // tuple +#include // false_type, is_constructible, is_integral, is_same, true_type +#include // declval + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +#include // random_access_iterator_tag + +// #include + +// #include + +// #include + + +NLOHMANN_JSON_NAMESPACE_BEGIN +namespace detail +{ + +template +struct iterator_types {}; + +template +struct iterator_types < + It, + void_t> +{ + using difference_type = typename It::difference_type; + using value_type = typename It::value_type; + using pointer = typename It::pointer; + using reference = typename It::reference; + using iterator_category = typename It::iterator_category; +}; + +// This is required as some compilers implement std::iterator_traits in a way that +// doesn't work with SFINAE. See https://github.com/nlohmann/json/issues/1341. +template +struct iterator_traits +{ +}; + +template +struct iterator_traits < T, enable_if_t < !std::is_pointer::value >> + : iterator_types +{ +}; + +template +struct iterator_traits::value>> +{ + using iterator_category = std::random_access_iterator_tag; + using value_type = T; + using difference_type = ptrdiff_t; + using pointer = T*; + using reference = T&; +}; + +} // namespace detail +NLOHMANN_JSON_NAMESPACE_END + +// #include + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +// #include + + +NLOHMANN_JSON_NAMESPACE_BEGIN + +NLOHMANN_CAN_CALL_STD_FUNC_IMPL(begin); + +NLOHMANN_JSON_NAMESPACE_END + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + + + +// #include + + +NLOHMANN_JSON_NAMESPACE_BEGIN + +NLOHMANN_CAN_CALL_STD_FUNC_IMPL(end); + +NLOHMANN_JSON_NAMESPACE_END + +// #include + +// #include + +// #include +// __ _____ _____ _____ +// __| | __| | | | JSON for Modern C++ +// | | |__ | | | | | | version 3.12.0 +// |_____|_____|_____|_|___| https://github.com/nlohmann/json +// +// SPDX-FileCopyrightText: 2013 - 2025 Niels Lohmann +// SPDX-License-Identifier: MIT + +#ifndef INCLUDE_NLOHMANN_JSON_FWD_HPP_ + #define INCLUDE_NLOHMANN_JSON_FWD_HPP_ + + #include // int64_t, uint64_t + #include // map + #include // allocator + #include // string + #include // vector + + // #include + + + /*! + @brief namespace for Niels Lohmann + @see https://github.com/nlohmann + @since version 1.0.0 + */ + NLOHMANN_JSON_NAMESPACE_BEGIN + + /*! + @brief default JSONSerializer template argument + + This serializer ignores the template arguments and uses ADL + ([argument-dependent lookup](https://en.cppreference.com/w/cpp/language/adl)) + for serialization. + */ + template + struct adl_serializer; + + /// a class to store JSON values + /// @sa https://json.nlohmann.me/api/basic_json/ + template class ObjectType = + std::map, + template class ArrayType = std::vector, + class StringType = std::string, class BooleanType = bool, + class NumberIntegerType = std::int64_t, + class NumberUnsignedType = std::uint64_t, + class NumberFloatType = double, + template class AllocatorType = std::allocator, + template class JSONSerializer = + adl_serializer, + class BinaryType = std::vector, // cppcheck-suppress syntaxError + class CustomBaseClass = void> + class basic_json; + + /// @brief JSON Pointer defines a string syntax for identifying a specific value within a JSON document + /// @sa https://json.nlohmann.me/api/json_pointer/ + template + class json_pointer; + + /*! + @brief default specialization + @sa https://json.nlohmann.me/api/json/ + */ + using json = basic_json<>; + + /// @brief a minimal map-like container that preserves insertion order + /// @sa https://json.nlohmann.me/api/ordered_map/ + template + struct ordered_map; + + /// @brief specialization that maintains the insertion order of object keys + /// @sa https://json.nlohmann.me/api/ordered_json/ + using ordered_json = basic_json; + + NLOHMANN_JSON_NAMESPACE_END + +#endif // INCLUDE_NLOHMANN_JSON_FWD_HPP_ + + +NLOHMANN_JSON_NAMESPACE_BEGIN +/*! +@brief detail namespace with internal helper functions + +This namespace collects functions that should not be exposed, +implementations of some @ref basic_json methods, and meta-programming helpers. + +@since version 2.1.0 +*/ +namespace detail +{ + +///////////// +// helpers // +///////////// + +// Note to maintainers: +// +// Every trait in this file expects a non CV-qualified type. +// The only exceptions are in the 'aliases for detected' section +// (i.e. those of the form: decltype(T::member_function(std::declval()))) +// +// In this case, T has to be properly CV-qualified to constraint the function arguments +// (e.g. to_json(BasicJsonType&, const T&)) + +template struct is_basic_json : std::false_type {}; + +NLOHMANN_BASIC_JSON_TPL_DECLARATION +struct is_basic_json : std::true_type {}; + +// used by exceptions create() member functions +// true_type for pointer to possibly cv-qualified basic_json or std::nullptr_t +// false_type otherwise +template +struct is_basic_json_context : + std::integral_constant < bool, + is_basic_json::type>::type>::value + || std::is_same::value > +{}; + +////////////////////// +// json_ref helpers // +////////////////////// + +template +class json_ref; + +template +struct is_json_ref : std::false_type {}; + +template +struct is_json_ref> : std::true_type {}; + +////////////////////////// +// aliases for detected // +////////////////////////// + +template +using mapped_type_t = typename T::mapped_type; + +template +using key_type_t = typename T::key_type; + +template +using value_type_t = typename T::value_type; + +template +using difference_type_t = typename T::difference_type; + +template +using pointer_t = typename T::pointer; + +template +using reference_t = typename T::reference; + +template +using iterator_category_t = typename T::iterator_category; + +template +using to_json_function = decltype(T::to_json(std::declval()...)); + +template +using from_json_function = decltype(T::from_json(std::declval()...)); + +template +using get_template_function = decltype(std::declval().template get()); + +// trait checking if JSONSerializer::from_json(json const&, udt&) exists +template +struct has_from_json : std::false_type {}; + +// trait checking if j.get is valid +// use this trait instead of std::is_constructible or std::is_convertible, +// both rely on, or make use of implicit conversions, and thus fail when T +// has several constructors/operator= (see https://github.com/nlohmann/json/issues/958) +template +struct is_getable +{ + static constexpr bool value = is_detected::value; +}; + +template +struct has_from_json < BasicJsonType, T, enable_if_t < !is_basic_json::value >> +{ + using serializer = typename BasicJsonType::template json_serializer; + + static constexpr bool value = + is_detected_exact::value; +}; + +// This trait checks if JSONSerializer::from_json(json const&) exists +// this overload is used for non-default-constructible user-defined-types +template +struct has_non_default_from_json : std::false_type {}; + +template +struct has_non_default_from_json < BasicJsonType, T, enable_if_t < !is_basic_json::value >> +{ + using serializer = typename BasicJsonType::template json_serializer; + + static constexpr bool value = + is_detected_exact::value; +}; + +// This trait checks if BasicJsonType::json_serializer::to_json exists +// Do not evaluate the trait when T is a basic_json type, to avoid template instantiation infinite recursion. +template +struct has_to_json : std::false_type {}; + +template +struct has_to_json < BasicJsonType, T, enable_if_t < !is_basic_json::value >> +{ + using serializer = typename BasicJsonType::template json_serializer; + + static constexpr bool value = + is_detected_exact::value; +}; + +template +using detect_key_compare = typename T::key_compare; + +template +struct has_key_compare : std::integral_constant::value> {}; + +// obtains the actual object key comparator +template +struct actual_object_comparator +{ + using object_t = typename BasicJsonType::object_t; + using object_comparator_t = typename BasicJsonType::default_object_comparator_t; + using type = typename std::conditional < has_key_compare::value, + typename object_t::key_compare, object_comparator_t>::type; +}; + +template +using actual_object_comparator_t = typename actual_object_comparator::type; + +///////////////// +// char_traits // +///////////////// + +// Primary template of char_traits calls std char_traits +template +struct char_traits : std::char_traits +{}; + +// Explicitly define char traits for unsigned char since it is not standard +template<> +struct char_traits : std::char_traits +{ + using char_type = unsigned char; + using int_type = uint64_t; + + // Redefine to_int_type function + static int_type to_int_type(char_type c) noexcept + { + return static_cast(c); + } + + static char_type to_char_type(int_type i) noexcept + { + return static_cast(i); + } + + static constexpr int_type eof() noexcept + { + return static_cast(std::char_traits::eof()); + } +}; + +// Explicitly define char traits for signed char since it is not standard +template<> +struct char_traits : std::char_traits +{ + using char_type = signed char; + using int_type = uint64_t; + + // Redefine to_int_type function + static int_type to_int_type(char_type c) noexcept + { + return static_cast(c); + } + + static char_type to_char_type(int_type i) noexcept + { + return static_cast(i); + } + + static constexpr int_type eof() noexcept + { + return static_cast(std::char_traits::eof()); + } +}; + +/////////////////// +// is_ functions // +/////////////////// + +// https://en.cppreference.com/w/cpp/types/conjunction +template struct conjunction : std::true_type { }; +template struct conjunction : B { }; +template +struct conjunction +: std::conditional(B::value), conjunction, B>::type {}; + +// https://en.cppreference.com/w/cpp/types/negation +template struct negation : std::integral_constant < bool, !B::value > { }; + +// Reimplementation of is_constructible and is_default_constructible, due to them being broken for +// std::pair and std::tuple until LWG 2367 fix (see https://cplusplus.github.io/LWG/lwg-defects.html#2367). +// This causes compile errors in e.g. clang 3.5 or gcc 4.9. +template +struct is_default_constructible : std::is_default_constructible {}; + +template +struct is_default_constructible> + : conjunction, is_default_constructible> {}; + +template +struct is_default_constructible> + : conjunction, is_default_constructible> {}; + +template +struct is_default_constructible> + : conjunction...> {}; + +template +struct is_default_constructible> + : conjunction...> {}; + +template +struct is_constructible : std::is_constructible {}; + +template +struct is_constructible> : is_default_constructible> {}; + +template +struct is_constructible> : is_default_constructible> {}; + +template +struct is_constructible> : is_default_constructible> {}; + +template +struct is_constructible> : is_default_constructible> {}; + +template +struct is_iterator_traits : std::false_type {}; + +template +struct is_iterator_traits> +{ + private: + using traits = iterator_traits; + + public: + static constexpr auto value = + is_detected::value && + is_detected::value && + is_detected::value && + is_detected::value && + is_detected::value; +}; + +template +struct is_range +{ + private: + using t_ref = typename std::add_lvalue_reference::type; + + using iterator = detected_t; + using sentinel = detected_t; + + // to be 100% correct, it should use https://en.cppreference.com/w/cpp/iterator/input_or_output_iterator + // and https://en.cppreference.com/w/cpp/iterator/sentinel_for + // but reimplementing these would be too much work, as a lot of other concepts are used underneath + static constexpr auto is_iterator_begin = + is_iterator_traits>::value; + + public: + static constexpr bool value = !std::is_same::value && !std::is_same::value && is_iterator_begin; +}; + +template +using iterator_t = enable_if_t::value, result_of_begin())>>; + +template +using range_value_t = value_type_t>>; + +// The following implementation of is_complete_type is taken from +// https://blogs.msdn.microsoft.com/vcblog/2015/12/02/partial-support-for-expression-sfinae-in-vs-2015-update-1/ +// and is written by Xiang Fan who agreed to using it in this library. + +template +struct is_complete_type : std::false_type {}; + +template +struct is_complete_type : std::true_type {}; + +template +struct is_compatible_object_type_impl : std::false_type {}; + +template +struct is_compatible_object_type_impl < + BasicJsonType, CompatibleObjectType, + enable_if_t < is_detected::value&& + is_detected::value >> +{ + using object_t = typename BasicJsonType::object_t; + + // macOS's is_constructible does not play well with nonesuch... + static constexpr bool value = + is_constructible::value && + is_constructible::value; +}; + +template +struct is_compatible_object_type + : is_compatible_object_type_impl {}; + +template +struct is_constructible_object_type_impl : std::false_type {}; + +template +struct is_constructible_object_type_impl < + BasicJsonType, ConstructibleObjectType, + enable_if_t < is_detected::value&& + is_detected::value >> +{ + using object_t = typename BasicJsonType::object_t; + + static constexpr bool value = + (is_default_constructible::value && + (std::is_move_assignable::value || + std::is_copy_assignable::value) && + (is_constructible::value && + std::is_same < + typename object_t::mapped_type, + typename ConstructibleObjectType::mapped_type >::value)) || + (has_from_json::value || + has_non_default_from_json < + BasicJsonType, + typename ConstructibleObjectType::mapped_type >::value); +}; + +template +struct is_constructible_object_type + : is_constructible_object_type_impl {}; + +template +struct is_compatible_string_type +{ + static constexpr auto value = + is_constructible::value; +}; + +template +struct is_constructible_string_type +{ + // launder type through decltype() to fix compilation failure on ICPC +#ifdef __INTEL_COMPILER + using laundered_type = decltype(std::declval()); +#else + using laundered_type = ConstructibleStringType; +#endif + + static constexpr auto value = + conjunction < + is_constructible, + is_detected_exact>::value; +}; + +template +struct is_compatible_array_type_impl : std::false_type {}; + +template +struct is_compatible_array_type_impl < + BasicJsonType, CompatibleArrayType, + enable_if_t < + is_detected::value&& + is_iterator_traits>>::value&& +// special case for types like std::filesystem::path whose iterator's value_type are themselves +// c.f. https://github.com/nlohmann/json/pull/3073 + !std::is_same>::value >> +{ + static constexpr bool value = + is_constructible>::value; +}; + +template +struct is_compatible_array_type + : is_compatible_array_type_impl {}; + +template +struct is_constructible_array_type_impl : std::false_type {}; + +template +struct is_constructible_array_type_impl < + BasicJsonType, ConstructibleArrayType, + enable_if_t::value >> + : std::true_type {}; + +template +struct is_constructible_array_type_impl < + BasicJsonType, ConstructibleArrayType, + enable_if_t < !std::is_same::value&& + !is_compatible_string_type::value&& + is_default_constructible::value&& +(std::is_move_assignable::value || + std::is_copy_assignable::value)&& +is_detected::value&& +is_iterator_traits>>::value&& +is_detected::value&& +// special case for types like std::filesystem::path whose iterator's value_type are themselves +// c.f. https://github.com/nlohmann/json/pull/3073 +!std::is_same>::value&& +is_complete_type < +detected_t>::value >> +{ + using value_type = range_value_t; + + static constexpr bool value = + std::is_same::value || + has_from_json::value || + has_non_default_from_json < + BasicJsonType, + value_type >::value; +}; + +template +struct is_constructible_array_type + : is_constructible_array_type_impl {}; + +template +struct is_compatible_integer_type_impl : std::false_type {}; + +template +struct is_compatible_integer_type_impl < + RealIntegerType, CompatibleNumberIntegerType, + enable_if_t < std::is_integral::value&& + std::is_integral::value&& + !std::is_same::value >> +{ + // is there an assert somewhere on overflows? + using RealLimits = std::numeric_limits; + using CompatibleLimits = std::numeric_limits; + + static constexpr auto value = + is_constructible::value && + CompatibleLimits::is_integer && + RealLimits::is_signed == CompatibleLimits::is_signed; +}; + +template +struct is_compatible_integer_type + : is_compatible_integer_type_impl {}; + +template +struct is_compatible_type_impl: std::false_type {}; + +template +struct is_compatible_type_impl < + BasicJsonType, CompatibleType, + enable_if_t::value >> +{ + static constexpr bool value = + has_to_json::value; +}; + +template +struct is_compatible_type + : is_compatible_type_impl {}; + +template +struct is_constructible_tuple : std::false_type {}; + +template +struct is_constructible_tuple> : conjunction...> {}; + +template +struct is_json_iterator_of : std::false_type {}; + +template +struct is_json_iterator_of : std::true_type {}; + +template +struct is_json_iterator_of : std::true_type +{}; + +// checks if a given type T is a template specialization of Primary +template