Update to Biological Sequence & Alignment Viewer

Changed files

.codex-plugin/plugin.json →

.gitignore →

.mcp.json →

CAPABILITY_MATRIX.md →

LSC_109_QUALIFICATION.md →

PUBLIC_README.md →

README.md →

STARTER_EXAMPLES.md →

THIRD_PARTY_NOTICES.md →

buildkite/pipeline.yml →

dist/server.mjs →

dist/views/app.js.gz →

dist/views/styles.css →

e2e/build-harness.mjs →

e2e/codex-managed-starter.spec.ts →

e2e/installed-host-fault-injection.mjs →

e2e/installed-host-server.mjs →

e2e/installed-host.js →

e2e/installed.html →

e2e/model-host-app-mount.mjs →

e2e/model-host-root-proxy-lib.mjs →

e2e/model-host-root-proxy.mjs →

e2e/persistent-native-recovery.spec.ts →

e2e/plugin-runtime-root.mjs →

e2e/public-starter-evidence.spec.ts →

e2e/public-starter-failure-evidence.spec.ts →

e2e/sequence-viewer.spec.ts →

integrity.json →

launch_node →

launch_node.cmd →

lsc-109-qualification.json →

package.json →

playwright.config.ts →

pnpm-lock.yaml →

pnpm-workspace.yaml →

scripts/build.mjs →

scripts/bundle-digest.mjs →

scripts/bundle-digest.test.mjs →

scripts/bundle.mjs →

scripts/capture-marketplace-screenshots.mjs →

scripts/generate-third-party-notices.mjs →

scripts/manual-format-smoke.mjs →

scripts/manual-format-smoke.test.mjs →

scripts/model-host-root-proxy.test.mjs →

scripts/run-opt-in-vitest.mjs →

scripts/run-starter-qualification.mjs →

scripts/source-snapshot.mjs →

scripts/source-snapshot.test.mjs →

scripts/validate-example-prompts.mjs →

scripts/validate-example-prompts.test.mjs →

scripts/validate-public-bundle.mjs →

scripts/validate-starter-qualification.mjs →

scripts/validate-starter-qualification.test.mjs →

skills/biological-sequence-viewer/SKILL.md →

smoke-fixtures/aligned-fasta-likely-msa.fasta →

smoke-fixtures/alignment.msf →

smoke-fixtures/alignment.nex →

smoke-fixtures/alignment.pir →

smoke-fixtures/circular-plasmid.gb →

smoke-fixtures/clustal-consensus.aln →

smoke-fixtures/dna-demo.aln-fasta →

smoke-fixtures/dna-single.fasta →

smoke-fixtures/equal-width-ungapped-ambiguous.fasta →

smoke-fixtures/interleaved.phy →

smoke-fixtures/minimal-embl.embl →

smoke-fixtures/minimal-genbank.gb →

smoke-fixtures/multi-record-unaligned.fasta →

smoke-fixtures/not-an-alignment.txt →

smoke-fixtures/protein-profile.a2m →

smoke-fixtures/protein-profile.a3m →

smoke-fixtures/protein-single.faa →

smoke-fixtures/rna-single.fasta →

smoke-fixtures/rna-structure.sto →

smoke-fixtures/small.fastq →

src/amino-acid-alphabet.ts →

src/artifact-state-key.ts →

src/bam-decoder.test.ts →

src/bam-decoder.ts →

src/binary-sequence-envelope.test.ts →

src/binary-sequence-envelope.ts →

src/biological-sequence-artifact-classifier.test.ts →

src/biological-sequence-artifact-classifier.ts →

src/biological-sequence-viewer-model.test.ts →

src/biological-sequence-viewer-model.ts →

src/biological-sequence-viewer.test.tsx →

src/biological-sequence-viewer.tsx →

src/chat-file-resource.test.ts →

src/chat-file-resource.ts →

src/compressed-file-name.test.ts →

src/compressed-file-name.ts →

src/cram-decoder.test.ts →

src/cram-decoder.ts →

src/export-actions-workspace.test.tsx →

src/file-kind.test.ts →

src/file-kind.ts →

src/incremental-export-validator.test.ts →

src/incremental-export-validator.ts →

src/indexed-sequence-envelope.ts →

src/indexed-sequence-parser.test.ts →

src/indexed-sequence-parser.ts →

src/large-workspace-saveas.qualification.test.ts →

src/memory-filehandle.ts →

src/model-context-limits.test.ts →

src/model-context.test.ts →

src/model-context.ts →

src/msa/alignment-editing.test.ts →

src/msa/alignment-editing.ts →

src/msa/alignment-export-provenance.test.ts →

src/msa/alignment-export-provenance.ts →

src/msa/alignment-state.test.ts →

src/msa/alignment-state.ts →

src/msa/alignment-workbench-panel.test.tsx →

src/msa/alignment-workbench-panel.tsx →

src/msa/analysis.test.ts →

src/msa/analysis.ts →

src/msa/cell-hover-overlay.tsx →

src/msa/codon.ts →

src/msa/color-legend.tsx →

src/msa/colors.test.ts →

src/msa/colors.ts →

src/msa/consensus.ts →

src/msa/conservation.ts →

src/msa/coordinate-map.ts →

src/msa/export-actions.tsx →

src/msa/exports.test.ts →

src/msa/exports.ts →

src/msa/file-kind.test.ts →

src/msa/file-kind.ts →

src/msa/formats/a2m-a3m.ts →

src/msa/formats/aligned-fasta.ts →

src/msa/formats/clustal.ts →

src/msa/formats/fasta-records.ts →

src/msa/formats/msf.ts →

src/msa/formats/nexus.ts →

src/msa/formats/phylip.ts →

src/msa/formats/pir.ts →

src/msa/formats/stockholm.test.ts →

src/msa/formats/stockholm.ts →

src/msa/guide-tree-panel.tsx →

src/msa/guide-tree.test.ts →

src/msa/guide-tree.ts →

src/msa/hover-details.ts →

src/msa/matrix-renderer.tsx →

src/msa/metadata-panel.tsx →

src/msa/metric-tracks.tsx →

src/msa/model-context.ts →

src/msa/molecule-inference.ts →

src/msa/msa-analysis-worker-factory-vite.ts →

src/msa/msa-analysis-worker.ts →

src/msa/msa-rich-viewer.tsx →

src/msa/overview-strip.tsx →

src/msa/parser.test.ts →

src/msa/parser.ts →

src/msa/performance-banners.tsx →

src/msa/performance.test.ts →

src/msa/performance.ts →

src/msa/phylogenetic-tree-panel.test.ts →

src/msa/phylogenetic-tree-panel.tsx →

src/msa/phylogenetic-tree.test.ts →

src/msa/phylogenetic-tree.ts →

src/msa/pinned-inspector.tsx →

src/msa/preview.test.tsx →

src/msa/residue-alphabet.ts →

src/msa/rna-structure.ts →

src/msa/rows-panel.tsx →

src/msa/scientific-metrics.test.ts →

src/msa/search-results-panel.tsx →

src/msa/search.ts →

src/msa/types.ts →

src/msa/use-alignment-workbench-commands.test.ts →

src/msa/use-alignment-workbench-commands.ts →

src/msa/use-msa-document.ts →

src/msa/use-msa-viewport.ts →

src/msa/virtualization.test.ts →

src/msa/virtualization.ts →

src/msa/warnings-drawer.tsx →

src/msa/workbench-controller.test.ts →

src/msa/workbench-controller.ts →

src/msa/worker-client.test.ts →

src/msa/worker-client.ts →

src/msa/worker-protocol.ts →

src/nucleotide-alphabet.ts →

src/persistent/durable-viewer-state.test.ts →

src/persistent/durable-viewer-state.ts →

src/persistent/native-workspace-publisher.test.ts →

src/persistent/native-workspace-publisher.ts →

src/persistent/recovery-adapter.test.ts →

src/persistent/recovery-adapter.ts →

src/persistent/scientific-data-client.test.ts →

src/persistent/scientific-data-client.ts →

src/persistent/session-adapter.test.ts →

src/persistent/session-adapter.ts →

src/persistent/streaming-source-replacement.test.ts →

src/persistent/streaming-source-replacement.ts →

src/plugin-manifest.test.ts →

src/protocol.test.ts →

src/protocol.ts →

src/public-example-acquisition.live.test.ts →

src/public-example-acquisition.test.ts →

src/public-example-acquisition.ts →

src/resource-error.ts →

src/runtime-contract.ts →

src/scientific-platform-protocol.ts →

src/scientific-platform.test.ts →

src/scientific-platform.ts →

src/sequence/__fixtures__/chromatogram.ts →

src/sequence/__fixtures__/official-vcf-4.3-first-100-sample-variant.vcf →

src/sequence/analysis.test.ts →

src/sequence/analysis.ts →

src/sequence/binary-parser.ts →

src/sequence/chromatogram-panel.test.tsx →

src/sequence/chromatogram-panel.tsx →

src/sequence/chromatogram-query.test.ts →

src/sequence/chromatogram-query.ts →

src/sequence/colors.ts →

src/sequence/coordinate-map.ts →

src/sequence/editing.test.ts →

src/sequence/editing.ts →

src/sequence/evidence-track-panel.test.ts →

src/sequence/evidence-track-panel.test.tsx →

src/sequence/evidence-track-panel.tsx →

src/sequence/export-actions.tsx →

src/sequence/exports.test.ts →

src/sequence/exports.ts →

src/sequence/fastq-quality-analysis.test.ts →

src/sequence/fastq-quality-analysis.ts →

src/sequence/fastq-quality-charts.tsx →

src/sequence/fastq-quality-report.tsx →

src/sequence/fastq-summary-panel.test.tsx →

src/sequence/fastq-summary-panel.tsx →

src/sequence/feature-location.test.ts →

src/sequence/feature-location.ts →

src/sequence/feature-resolution.test.ts →

src/sequence/feature-resolution.ts →

src/sequence/feature-tracks.test.ts →

src/sequence/feature-tracks.tsx →

src/sequence/feature-translation.ts →

src/sequence/file-kind.test.ts →

src/sequence/file-kind.ts →

src/sequence/formats/chromatogram.test.ts →

src/sequence/formats/chromatogram.ts →

src/sequence/formats/embl.ts →

src/sequence/formats/fasta.ts →

src/sequence/formats/fastq.ts →

src/sequence/formats/genbank.ts →

src/sequence/formats/snapgene.test.ts →

src/sequence/formats/snapgene.ts →

src/sequence/genetic-code.test.ts →

src/sequence/genetic-code.ts →

src/sequence/interaction-state.test.ts →

src/sequence/interaction-state.ts →

src/sequence/interface-state.ts →

src/sequence/metadata-panel.tsx →

src/sequence/model-context.test.ts →

src/sequence/model-context.ts →

src/sequence/molecule-inference.test.ts →

src/sequence/molecule-inference.ts →

src/sequence/msa-sequence-adapter.test.ts →

src/sequence/msa-sequence-adapter.ts →

src/sequence/orientation.test.ts →

src/sequence/orientation.ts →

src/sequence/parser.test.ts →

src/sequence/parser.ts →

src/sequence/performance-banners.tsx →

src/sequence/pinned-inspector.tsx →

src/sequence/preview.test.tsx →

src/sequence/quality-track.tsx →

src/sequence/quality.ts →

src/sequence/read-pileup.test.ts →

src/sequence/read-pileup.ts →

src/sequence/record-list-panel.tsx →

src/sequence/search-panel.tsx →

src/sequence/search.test.ts →

src/sequence/search.ts →

src/sequence/selection.test.ts →

src/sequence/selection.ts →

src/sequence/sequence-legend.tsx →

src/sequence/sequence-line-layout.test.ts →

src/sequence/sequence-line-layout.ts →

src/sequence/sequence-overview-geometry.ts →

src/sequence/sequence-overview.test.ts →

src/sequence/sequence-overview.tsx →

src/sequence/sequence-palette.test.ts →

src/sequence/sequence-palette.ts →

src/sequence/sequence-renderer.tsx →

src/sequence/sequence-rich-viewer.tsx →

src/sequence/sequence-toolbar.tsx →

src/sequence/sequence-workbench-panel.test.tsx →

src/sequence/sequence-workbench-panel.tsx →

src/sequence/tracks.test.ts →

src/sequence/tracks.ts →

src/sequence/translation-track.test.ts →

src/sequence/translation-track.tsx →

src/sequence/translation.test.ts →

src/sequence/translation.ts →

src/sequence/types.ts →

src/sequence/use-sequence-interface-commands.ts →

src/sequence/use-sequence-search.ts →

src/sequence/use-sequence-workbench-commands.test.ts →

src/sequence/use-sequence-workbench-commands.ts →

src/sequence/virtualization.test.ts →

src/sequence/virtualization.ts →

src/sequence/warnings-drawer.tsx →

src/sequence/workbench-controller.test.ts →

src/sequence/workbench-controller.ts →

src/sequence/workspace-track-browser-dialog.test.tsx →

src/sequence/workspace-track-browser-dialog.tsx →

src/server-command-store.test.ts →

src/server-command-store.ts →

src/server-workbench-store.test.ts →

src/server-workbench-store.ts →

src/server-workbench-upload.test.ts →

src/server-workbench-upload.ts →

src/server.test.ts →

src/server.ts →

src/spreadsheet-safety.test.ts →

src/spreadsheet-safety.ts →

src/target-resolution.test.ts →

src/target-resolution.ts →

src/test-setup.ts →

src/text-lines.ts →

src/ui/button.tsx →

src/ui/status-panel.tsx →

src/ui/workbench-disclosure.tsx →

src/ui/workbench-feedback.ts →

src/ui/workbench-tool-controller.ts →

src/ui/workbench-tools.test.tsx →

src/ui/workbench-tools.tsx →

src/version.ts →

src/viewer-commands.test.ts →

src/viewer-commands.ts →

src/viewer-operations.test.ts →

src/viewer-operations.ts →

src/viewer-query.test.ts →

src/viewer-query.ts →

src/views/__fixtures__/app-host.ts →

src/views/app-native.test.tsx →

src/views/app-resource-loading.test.tsx →

src/views/app.test.tsx →

src/views/app.tsx →

src/views/scientific-platform-client.ts →

src/views/styles.css →

src/views/workbench-persistence.test.ts →

src/views/workbench-persistence.ts →

src/views/workspace-artifact-stream.test.ts →

src/views/workspace-artifact-stream.ts →

src/views/workspace-export-producers.test.ts →

src/views/workspace-export-producers.ts →

src/views/workspace-sessions.test.ts →

src/views/workspace-sessions.ts →

src/views/workspace-tracks.test.ts →

src/views/workspace-tracks.ts →

src/vite-env.d.ts →

src/workbench-exports.test.ts →

src/workbench-exports.ts →

src/workbench-persistence-protocol.test.ts →

src/workbench-persistence-protocol.ts →

src/workbench-persistence.integration.test.ts →

src/workbench-session-validation.test.ts →

src/workbench-session-validation.ts →

src/workbench-state.test.ts →

src/workbench-state.ts →

src/workspace-atomic-publisher.test.ts →

src/workspace-atomic-publisher.ts →

src/workspace-browser-protocol.test.ts →

src/workspace-browser-protocol.ts →

src/workspace-export-authorization.test.ts →

src/workspace-export-authorization.ts →

src/workspace-export-publisher.test.ts →

src/workspace-export-publisher.ts →

src/workspace-publish-button.test.tsx →

src/workspace-publish-button.tsx →

src/workspace-session-controls.test.tsx →

src/workspace-session-controls.tsx →

src/workspace-session-manager.test.ts →

src/workspace-session-manager.ts →

src/workspace-session-protocol.test.ts →

src/workspace-session-protocol.ts →

src/workspace-track-browser.test.ts →

src/workspace-track-browser.ts →

src/workspace-track-protocol.test.ts →

src/workspace-track-protocol.ts →

starter-examples.json →

tsconfig.json →

vite.config.ts →

dist/views/styles.css

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*){color:var(--color-amber-300)}}.dark\:text-emerald-400:where([data-theme=dark],[data-theme=dark] *){color:var(--color-emerald-400)}@media (prefers-color-scheme:dark){.dark\:text-emerald-400:where(:root:not([data-theme]),:root:not([data-theme]) *){color:var(--color-emerald-400)}}.dark\:text-red-400:where([data-theme=dark],[data-theme=dark] *){color:var(--color-red-400)}@media (prefers-color-scheme:dark){.dark\:text-red-400:where(:root:not([data-theme]),:root:not([data-theme]) *){color:var(--color-red-400)}}.\[\&\:focus-visible\>path\]\:stroke-token-text-primary:focus-visible>path{stroke:var(--color-token-text-primary)}.\[\&\:focus-visible\>path\]\:stroke-\[3\]:focus-visible>path{stroke-width:3px}.\[\&\:hover\>path\]\:brightness-110:hover>path{--tw-brightness:brightness(110%);filter:var(--tw-blur,) var(--tw-brightness,) var(--tw-contrast,) var(--tw-grayscale,) var(--tw-hue-rotate,) var(--tw-invert,) var(--tw-saturate,) var(--tw-sepia,) var(--tw-drop-shadow,)}}:root{--lightningcss-light:initial;--lightningcss-dark: ;color-scheme:light 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(prefers-color-scheme:dark){:root{--lightningcss-light: ;--lightningcss-dark:initial}:root:not([data-theme]){--bio-token-border:var(--color-border-primary,#3a3a3a);--bio-token-focus-border:var(--color-ring-primary,#9caea5);--bio-token-input-background:var(--color-background-primary,#1b1b1b);--bio-token-input-placeholder:var(--color-text-tertiary,#a0a0a0);--bio-token-surface-primary:var(--color-background-primary,#1b1b1b);--bio-token-surface-secondary:var(--color-background-secondary,#242424);--bio-token-text-primary:var(--color-text-primary,#ececec);--bio-token-text-secondary:var(--color-text-secondary,#bdbdbd);--bio-token-text-tertiary:var(--color-text-tertiary,#a0a0a0);--bio-token-accent:#a9c7b8;--bio-token-accent-surface:#29352e;--bio-sequence-a-surface:#342828;--bio-sequence-a-foreground:#e8b6b2;--bio-sequence-c-surface:#332f22;--bio-sequence-c-foreground:#d9c68a;--bio-sequence-g-surface:#222d3b;--bio-sequence-g-foreground:#acbed8;--bio-sequence-t-surface:#21332a;--bio-sequence-t-foreground:#a7cdb9;--bio-sequence-search-marker:#c9b079;--bio-protein-negative-surface:#30273a;--bio-protein-negative-foreground:#cfb8e5;--bio-protein-cysteine-surface:#382831;--bio-protein-cysteine-foreground:#d6b2c6;--bio-protein-glycine-surface:#342b23;--bio-protein-glycine-foreground:#d8bc99;--bio-protein-aromatic-surface:#223337;--bio-protein-aromatic-foreground:#afd0d6}}:root[data-theme=dark]{--bio-token-border:var(--color-border-primary,#3a3a3a);--bio-token-focus-border:var(--color-ring-primary,#9caea5);--bio-token-input-background:var(--color-background-primary,#1b1b1b);--bio-token-input-placeholder:var(--color-text-tertiary,#a0a0a0);--bio-token-surface-primary:var(--color-background-primary,#1b1b1b);--bio-token-surface-secondary:var(--color-background-secondary,#242424);--bio-token-text-primary:var(--color-text-primary,#ececec);--bio-token-text-secondary:var(--color-text-secondary,#bdbdbd);--bio-token-text-tertiary:var(--color-text-tertiary,#a0a0a0);--bio-token-accent:#a9c7b8;--bio-token-accent-surface:#29352e;--bio-sequence-a-surface:#342828;--bio-sequence-a-foreground:#e8b6b2;--bio-sequence-c-surface:#332f22;--bio-sequence-c-foreground:#d9c68a;--bio-sequence-g-surface:#222d3b;--bio-sequence-g-foreground:#acbed8;--bio-sequence-t-surface:#21332a;--bio-sequence-t-foreground:#a7cdb9;--bio-sequence-search-marker:#c9b079;--bio-protein-negative-surface:#30273a;--bio-protein-negative-foreground:#cfb8e5;--bio-protein-cysteine-surface:#382831;--bio-protein-cysteine-foreground:#d6b2c6;--bio-protein-glycine-surface:#342b23;--bio-protein-glycine-foreground:#d8bc99;--bio-protein-aromatic-surface:#223337;--bio-protein-aromatic-foreground:#afd0d6}*{box-sizing:border-box}html,body,#root{height:100%;margin:0}body{background:var(--bio-token-surface-primary);color:var(--bio-token-text-primary);font-family:var(--font-sans,Inter, ui-sans-serif, system-ui, -apple-system, BlinkMacSystemFont, "Segoe UI", sans-serif);font-size:14px;line-height:1.5}button,input,select,textarea{font:inherit}.sequence-viewer-shell :is(button,input,select,textarea,summary):focus-visible{outline:2px solid var(--bio-token-focus-border);outline-offset:2px}.bio-sequence-scroller,.bio-sequence-track-row{font-family:var(--font-mono,ui-monospace, SFMono-Regular, Menlo, Consolas, monospace);font-variant-ligatures:none;font-size:14px;font-weight:400;line-height:20px}.bio-sequence-scroller{overscroll-behavior-inline:contain;scrollbar-width:thin}.bio-sequence-line{flex-direction:column;justify-content:center;gap:4px;display:flex}.bio-sequence-track-row{flex-shrink:0;grid-template-columns:3.25rem minmax(0,1fr) 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--tw-space-y-reverse{syntax:"*";inherits:false;initial-value:0}@property --tw-divide-y-reverse{syntax:"*";inherits:false;initial-value:0}@property --tw-border-style{syntax:"*";inherits:false;initial-value:solid}@property --tw-leading{syntax:"*";inherits:false}@property --tw-font-weight{syntax:"*";inherits:false}@property --tw-tracking{syntax:"*";inherits:false}@property --tw-ordinal{syntax:"*";inherits:false}@property --tw-slashed-zero{syntax:"*";inherits:false}@property --tw-numeric-figure{syntax:"*";inherits:false}@property --tw-numeric-spacing{syntax:"*";inherits:false}@property --tw-numeric-fraction{syntax:"*";inherits:false}@property --tw-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-shadow-color{syntax:"*";inherits:false}@property --tw-shadow-alpha{syntax:"<percentage>";inherits:false;initial-value:100%}@property --tw-inset-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-inset-shadow-color{syntax:"*";inherits:false}@property --tw-inset-shadow-alpha{syntax:"<percentage>";inherits:false;initial-value:100%}@property --tw-ring-color{syntax:"*";inherits:false}@property --tw-ring-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-inset-ring-color{syntax:"*";inherits:false}@property --tw-inset-ring-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-ring-inset{syntax:"*";inherits:false}@property --tw-ring-offset-width{syntax:"<length>";inherits:false;initial-value:0}@property --tw-ring-offset-color{syntax:"*";inherits:false;initial-value:#fff}@property --tw-ring-offset-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-outline-style{syntax:"*";inherits:false;initial-value:solid}@property --tw-blur{syntax:"*";inherits:false}@property --tw-brightness{syntax:"*";inherits:false}@property --tw-contrast{syntax:"*";inherits:false}@property --tw-grayscale{syntax:"*";inherits:false}@property --tw-hue-rotate{syntax:"*";inherits:false}@property --tw-invert{syntax:"*";inherits:false}@property --tw-opacity{syntax:"*";inherits:false}@property --tw-saturate{syntax:"*";inherits:false}@property --tw-sepia{syntax:"*";inherits:false}@property --tw-drop-shadow{syntax:"*";inherits:false}@property --tw-drop-shadow-color{syntax:"*";inherits:false}@property --tw-drop-shadow-alpha{syntax:"<percentage>";inherits:false;initial-value:100%}@property --tw-drop-shadow-size{syntax:"*";inherits:false}