react-msaview 8.3.0 → 8.4.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/bundle/index.js +77 -287
- package/bundle/index.js.map +4 -4
- package/dist/blockFasta.d.ts +6 -0
- package/dist/blockFasta.js +12 -0
- package/dist/blockFasta.js.map +1 -0
- package/dist/colorSchemes.d.ts +7 -0
- package/dist/colorSchemes.js +15 -0
- package/dist/colorSchemes.js.map +1 -1
- package/dist/components/MSAView.js +15 -9
- package/dist/components/MSAView.js.map +1 -1
- package/dist/components/MSAViewer.d.ts +28 -7
- package/dist/components/MSAViewer.js +61 -22
- package/dist/components/MSAViewer.js.map +1 -1
- package/dist/components/MetadataTable.d.ts +5 -0
- package/dist/components/MetadataTable.js +29 -0
- package/dist/components/MetadataTable.js.map +1 -0
- package/dist/components/Track.js +11 -2
- package/dist/components/Track.js.map +1 -1
- package/dist/components/dialogs/MetadataDialog.js +5 -6
- package/dist/components/dialogs/MetadataDialog.js.map +1 -1
- package/dist/components/header/ColorSchemeMenu.d.ts +6 -0
- package/dist/components/header/ColorSchemeMenu.js +23 -5
- package/dist/components/header/ColorSchemeMenu.js.map +1 -1
- package/dist/components/header/{RowSearch.d.ts → GoToBox.d.ts} +2 -2
- package/dist/components/header/GoToBox.js +21 -0
- package/dist/components/header/GoToBox.js.map +1 -0
- package/dist/components/header/Header.js +4 -2
- package/dist/components/header/Header.js.map +1 -1
- package/dist/components/header/SelectionMenu.d.ts +12 -0
- package/dist/components/header/SelectionMenu.js +72 -0
- package/dist/components/header/SelectionMenu.js.map +1 -0
- package/dist/components/header/goTo.d.ts +20 -0
- package/dist/components/header/goTo.js +69 -0
- package/dist/components/header/goTo.js.map +1 -0
- package/dist/components/msa/MSACanvas.js +13 -2
- package/dist/components/msa/MSACanvas.js.map +1 -1
- package/dist/components/msa/MSACanvasBlock.js +5 -1
- package/dist/components/msa/MSACanvasBlock.js.map +1 -1
- package/dist/components/msa/msaKeys.js +6 -0
- package/dist/components/msa/msaKeys.js.map +1 -1
- package/dist/components/msa/msaRaster.js +1 -0
- package/dist/components/msa/msaRaster.js.map +1 -1
- package/dist/components/msa/renderHighlights.d.ts +14 -3
- package/dist/components/msa/renderHighlights.js +29 -4
- package/dist/components/msa/renderHighlights.js.map +1 -1
- package/dist/components/msa/tileColor.js +9 -8
- package/dist/components/msa/tileColor.js.map +1 -1
- package/dist/components/msa/useMsaBlockMouse.d.ts +1 -1
- package/dist/components/msa/useMsaBlockMouse.js +18 -11
- package/dist/components/msa/useMsaBlockMouse.js.map +1 -1
- package/dist/components/overlayColors.d.ts +2 -0
- package/dist/components/overlayColors.js +3 -0
- package/dist/components/overlayColors.js.map +1 -1
- package/dist/components/selectionDrag.d.ts +17 -0
- package/dist/components/selectionDrag.js +30 -0
- package/dist/components/selectionDrag.js.map +1 -0
- package/dist/components/tracks/useTrackHover.d.ts +3 -1
- package/dist/components/tracks/useTrackHover.js +26 -6
- package/dist/components/tracks/useTrackHover.js.map +1 -1
- package/dist/components/tree/dialogs/TreeNodeInfoDialog.js +9 -8
- package/dist/components/tree/dialogs/TreeNodeInfoDialog.js.map +1 -1
- package/dist/constants.d.ts +1 -1
- package/dist/constants.js +6 -6
- package/dist/constants.js.map +1 -1
- package/dist/element.d.ts +7 -3
- package/dist/element.js +32 -4
- package/dist/element.js.map +1 -1
- package/dist/featuresLayer.d.ts +8 -0
- package/dist/featuresLayer.js +42 -0
- package/dist/featuresLayer.js.map +1 -0
- package/dist/index.d.ts +1 -1
- package/dist/model/DataModel.d.ts +1 -1
- package/dist/model/DataModel.js +3 -3
- package/dist/model/DataModel.js.map +1 -1
- package/dist/model/msaModel.d.ts +14 -1
- package/dist/model/msaModel.js +17 -1
- package/dist/model/msaModel.js.map +1 -1
- package/dist/model.d.ts +122 -11
- package/dist/model.js +260 -41
- package/dist/model.js.map +1 -1
- package/dist/svgTestUtil.d.ts +68 -8
- package/dist/types.d.ts +50 -0
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/package.json +3 -3
- package/src/blockFasta.ts +18 -0
- package/src/colorSchemes.ts +20 -0
- package/src/components/MSAView.tsx +16 -9
- package/src/components/MSAViewer.tsx +95 -26
- package/src/components/MetadataTable.tsx +55 -0
- package/src/components/Track.tsx +14 -1
- package/src/components/dialogs/MetadataDialog.tsx +9 -8
- package/src/components/header/ColorSchemeMenu.tsx +31 -12
- package/src/components/header/GoToBox.tsx +50 -0
- package/src/components/header/Header.tsx +6 -2
- package/src/components/header/SelectionMenu.tsx +117 -0
- package/src/components/header/goTo.ts +75 -0
- package/src/components/msa/MSACanvas.tsx +12 -2
- package/src/components/msa/MSACanvasBlock.tsx +5 -1
- package/src/components/msa/msaKeys.ts +6 -0
- package/src/components/msa/msaRaster.ts +1 -0
- package/src/components/msa/renderHighlights.ts +46 -4
- package/src/components/msa/tileColor.ts +9 -8
- package/src/components/msa/useMsaBlockMouse.ts +24 -27
- package/src/components/overlayColors.ts +4 -0
- package/src/components/selectionDrag.ts +42 -0
- package/src/components/tracks/useTrackHover.ts +28 -6
- package/src/components/tree/dialogs/TreeNodeInfoDialog.tsx +14 -16
- package/src/constants.ts +6 -6
- package/src/element.ts +45 -5
- package/src/featuresLayer.ts +48 -0
- package/src/index.ts +5 -0
- package/src/model/DataModel.ts +3 -3
- package/src/model/msaModel.ts +19 -1
- package/src/model.ts +309 -51
- package/src/types.ts +58 -0
- package/src/version.ts +1 -1
- package/dist/components/header/RowSearch.js +0 -15
- package/dist/components/header/RowSearch.js.map +0 -1
- package/dist/components/header/revealRow.d.ts +0 -3
- package/dist/components/header/revealRow.js +0 -15
- package/dist/components/header/revealRow.js.map +0 -1
- package/src/components/header/RowSearch.tsx +0 -34
- package/src/components/header/revealRow.ts +0 -17
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@@ -0,0 +1,6 @@
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/**
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* FASTA for a block of the alignment: each row's letters from column `start`
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* to `end`, 1-based and inclusive, under its name. Gaps stay in, and a row that
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* ends before `end` is padded with gaps, so every record is the block's width.
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*/
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export declare function blockFasta(rows: readonly (readonly [string, string])[], start: number, end: number): string;
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@@ -0,0 +1,12 @@
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/**
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* FASTA for a block of the alignment: each row's letters from column `start`
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* to `end`, 1-based and inclusive, under its name. Gaps stay in, and a row that
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* ends before `end` is padded with gaps, so every record is the block's width.
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*/
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export function blockFasta(rows, start, end) {
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const width = Math.max(0, end - start + 1);
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return rows
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.map(([name, seq]) => `>${name}\n${seq.slice(start - 1, end).padEnd(width, '-')}\n`)
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.join('');
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}
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//# sourceMappingURL=blockFasta.js.map
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{"version":3,"file":"blockFasta.js","sourceRoot":"","sources":["../src/blockFasta.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,MAAM,UAAU,UAAU,CACxB,IAA4C,EAC5C,KAAa,EACb,GAAW;IAEX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;IAC1C,OAAO,IAAI;SACR,GAAG,CACF,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,EAAE,EAAE,CACd,IAAI,IAAI,KAAK,GAAG,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,EAAE,GAAG,CAAC,CAAC,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,CAChE;SACA,IAAI,CAAC,EAAE,CAAC,CAAA;AACb,CAAC"}
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package/dist/colorSchemes.d.ts
CHANGED
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@@ -2,3 +2,10 @@ declare const _default: {
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[k: string]: Record<string, string>;
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};
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export default _default;
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/**
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* A letter map as the renderer looks letters up. The model upper-cases every
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* row before coloring it, so a table keys its letters in upper case and a map
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* may key them in either. The table is cached per map, so its identity is
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* stable enough for the raster cache to key on.
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*/
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export declare function letterColorTable(map: Record<string, string>): Record<string, string>;
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package/dist/colorSchemes.js
CHANGED
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@@ -343,4 +343,19 @@ export default transform(colorSchemes, ([key, val]) => [
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key,
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transform(val, ([letter, color]) => [letter, colord(color).toHex()]),
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]);
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const letterTables = new WeakMap();
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/**
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* A letter map as the renderer looks letters up. The model upper-cases every
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* row before coloring it, so a table keys its letters in upper case and a map
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* may key them in either. The table is cached per map, so its identity is
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* stable enough for the raster cache to key on.
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*/
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export function letterColorTable(map) {
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let table = letterTables.get(map);
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if (!table) {
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table = transform(map, ([letter, color]) => [letter.toUpperCase(), color]);
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letterTables.set(map, table);
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}
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return table;
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}
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//# sourceMappingURL=colorSchemes.js.map
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package/dist/colorSchemes.js.map
CHANGED
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+
{"version":3,"file":"colorSchemes.js","sourceRoot":"","sources":["../src/colorSchemes.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,sBAAsB,CAAA;AAC/D,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,WAAW,MAAM,sBAAsB,CAAA;AAE9C,OAAO,EAAE,SAAS,EAAE,MAAM,WAAW,CAAA;AAErC,MAAM,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;AAErB,8EAA8E;AAC9E,eAAe;AACf,MAAM,GAAG,GAAG;IACV,CAAC,EAAE,KAAK,CAAC,GAAG,CAAC;IACb,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC;IACZ,CAAC,EAAE,MAAM,CAAC,GAAG,CAAC;IACd,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC;IACX,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC;CACZ,CAAA;AAED,gEAAgE;AAChE,MAAM,YAAY,GAA2C;IAC3D,IAAI,EAAE,EAAE;IACR,UAAU,EAAE,GAAG;IACf,OAAO,EAAE;QACP,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;KACX;IACD,IAAI,EAAE;QACJ,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;KACV;IACD,QAAQ,EAAE;QACR,CAAC,EAAE,YAAY;QACf,CAAC,EAAE,YAAY;QACf,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,UAAU;QACb,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;KACT;IAED,wBAAwB,EAAE,EAAE;IAC5B,+IAA+I;IAC/I,MAAM,EAAE;QACN,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IACD,WAAW,EAAE;QACX,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,yJAAyJ;IACzJ,gBAAgB,EAAE;QAChB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,4BAA4B;IAC5B,wBAAwB,EAAE,EAAE;IAE5B,YAAY,EAAE;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IACD,WAAW,EAAE,GAAG;IAChB,cAAc,EAAE;QACd,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,sBAAsB,EAAE;QACtB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,iBAAiB,EAAE;QACjB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,kBAAkB,EAAE;QAClB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,gBAAgB,EAAE;QAChB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAA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@@ -6,7 +6,7 @@ import VerticalScrollbar from './VerticalScrollbar.js';
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6
6
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import Header from './header/Header.js';
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7
7
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import Minimap from './minimap/Minimap.js';
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8
8
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import MSAPanel from './msa/MSAPanel.js';
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9
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-
import { clickColor, hoverColor } from './overlayColors.js';
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9
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+
import { clickColor, hoverColor, selectionFill } from './overlayColors.js';
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10
10
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import RowPanelHeaders from './rowpanels/RowPanelHeaders.js';
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11
11
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import RowPanels from './rowpanels/RowPanels.js';
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12
12
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import TreeOverview from './tree/TreeOverview.js';
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@@ -26,11 +26,17 @@ const TopArea = observer(function ({ model }) {
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26
26
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showHorizontalScrollbar ? React.createElement(Minimap, { model: model }) : null));
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27
27
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});
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28
28
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const TrackColumnIndicator = observer(function ({ model, }) {
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29
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-
const { mouseCol, mouseClickCol, colWidth, scrollX, treeAreaWidth, rowPanelsWidth, resizeHandleWidth, totalTrackAreaHeight, msaCanvasWidth, } = model;
|
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30
|
-
// hovered column, then the pinned one, matching
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29
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+
const { mouseCol, mouseClickCol, colWidth, scrollX, treeAreaWidth, rowPanelsWidth, resizeHandleWidth, totalTrackAreaHeight, msaCanvasWidth, resolvedSelection, } = model;
|
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30
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+
// the selected columns, the hovered column, then the pinned one, matching
|
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31
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+
// the alignment's own overlay
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31
32
|
const bands = [
|
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32
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-
{
|
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33
|
-
|
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33
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+
{
|
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34
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+
start: resolvedSelection?.startCol,
|
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35
|
+
end: resolvedSelection?.endCol,
|
|
36
|
+
color: selectionFill,
|
|
37
|
+
},
|
|
38
|
+
{ start: mouseCol, end: mouseCol, color: hoverColor },
|
|
39
|
+
{ start: mouseClickCol, end: mouseClickCol, color: clickColor },
|
|
34
40
|
];
|
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35
41
|
return (React.createElement("div", { style: {
|
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36
42
|
position: 'absolute',
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@@ -40,11 +46,11 @@ const TrackColumnIndicator = observer(function ({ model, }) {
|
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|
40
46
|
height: totalTrackAreaHeight,
|
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41
47
|
overflow: 'hidden',
|
|
42
48
|
pointerEvents: 'none',
|
|
43
|
-
} }, bands.map(({
|
|
49
|
+
} }, bands.map(({ start, end, color }) => start === undefined || end === undefined ? null : (React.createElement("div", { key: color, style: {
|
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44
50
|
position: 'absolute',
|
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45
|
-
left:
|
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51
|
+
left: start * colWidth + scrollX,
|
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46
52
|
top: 0,
|
|
47
|
-
width: colWidth,
|
|
53
|
+
width: (end - start + 1) * colWidth,
|
|
48
54
|
height: totalTrackAreaHeight,
|
|
49
55
|
backgroundColor: color,
|
|
50
56
|
zIndex: 100,
|
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@@ -77,7 +83,7 @@ const View = observer(function ({ model }) {
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77
83
|
const MSAView = observer(function ({ model }) {
|
|
78
84
|
const { height, hideHeader, viewInitialized, DialogComponent, DialogProps } = model;
|
|
79
85
|
return (React.createElement("div", null, viewInitialized ? (React.createElement(React.Fragment, null,
|
|
80
|
-
React.createElement("div", { style: { height, overflow: '
|
|
86
|
+
React.createElement("div", { style: { height, overflow: 'clip' } },
|
|
81
87
|
hideHeader ? null : React.createElement(Header, { model: model }),
|
|
82
88
|
React.createElement(View, { model: model })),
|
|
83
89
|
React.createElement(HorizontalResizeHandle, { model: model }),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"MSAView.js","sourceRoot":"","sources":["../../src/components/MSAView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EACL,sBAAsB,EACtB,oBAAoB,GACrB,MAAM,oBAAqB,CAAA;AAC5B,OAAO,KAAK,MAAM,YAAa,CAAA;AAC/B,OAAO,iBAAiB,MAAM,wBAAyB,CAAA;AACvD,OAAO,MAAM,MAAM,oBAAqB,CAAA;AACxC,OAAO,OAAO,MAAM,sBAAuB,CAAA;AAC3C,OAAO,QAAQ,MAAM,mBAAoB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;
|
|
1
|
+
{"version":3,"file":"MSAView.js","sourceRoot":"","sources":["../../src/components/MSAView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EACL,sBAAsB,EACtB,oBAAoB,GACrB,MAAM,oBAAqB,CAAA;AAC5B,OAAO,KAAK,MAAM,YAAa,CAAA;AAC/B,OAAO,iBAAiB,MAAM,wBAAyB,CAAA;AACvD,OAAO,MAAM,MAAM,oBAAqB,CAAA;AACxC,OAAO,OAAO,MAAM,sBAAuB,CAAA;AAC3C,OAAO,QAAQ,MAAM,mBAAoB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAC1E,OAAO,eAAe,MAAM,gCAAiC,CAAA;AAC7D,OAAO,SAAS,MAAM,0BAA2B,CAAA;AACjD,OAAO,YAAY,MAAM,wBAAyB,CAAA;AAClD,OAAO,SAAS,MAAM,qBAAsB,CAAA;AAC5C,OAAO,SAAS,MAAM,qBAAsB,CAAA;AAI5C,wEAAwE;AACxE,4EAA4E;AAC5E,gFAAgF;AAChF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,uBAAuB,EAAE,gBAAgB,EAAE,iBAAiB,EAAE,GAAG,KAAK,CAAA;IAC9E,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,CAAC,EAAE;YAC1B,gBAAgB,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YACzD,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,CACvB;QACN,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,iBAAiB,EAAE,UAAU,EAAE,CAAC,EAAE,GAAI;QAC1D,uBAAuB,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI,CACvD,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EAC9C,KAAK,GAGN;IACC,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,QAAQ,EACR,OAAO,EACP,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,oBAAoB,EACpB,cAAc,EACd,iBAAiB,GAClB,GAAG,KAAK,CAAA;IAET,0EAA0E;IAC1E,8BAA8B;IAC9B,MAAM,KAAK,GAAG;QACZ;YACE,KAAK,EAAE,iBAAiB,EAAE,QAAQ;YAClC,GAAG,EAAE,iBAAiB,EAAE,MAAM;YAC9B,KAAK,EAAE,aAAa;SACrB;QACD,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,UAAU,EAAE;QACrD,EAAE,KAAK,EAAE,aAAa,EAAE,GAAG,EAAE,aAAa,EAAE,KAAK,EAAE,UAAU,EAAE;KAChE,CAAA;IAED,OAAO,CACL,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,IAAI,EAAE,aAAa,GAAG,cAAc,GAAG,iBAAiB;YACxD,GAAG,EAAE,CAAC;YACN,KAAK,EAAE,cAAc;YACrB,MAAM,EAAE,oBAAoB;YAC5B,QAAQ,EAAE,QAAQ;YAClB,aAAa,EAAE,MAAM;SACtB,IAEA,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,EAAE,CACnC,KAAK,KAAK,SAAS,IAAI,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAChD,6BACE,GAAG,EAAE,KAAK,EACV,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,IAAI,EAAE,KAAK,GAAG,QAAQ,GAAG,OAAO;YAChC,GAAG,EAAE,CAAC;YACN,KAAK,EAAE,CAAC,GAAG,GAAG,KAAK,GAAG,CAAC,CAAC,GAAG,QAAQ;YACnC,MAAM,EAAE,oBAAoB;YAC5B,eAAe,EAAE,KAAK;YACtB,MAAM,EAAE,GAAG;SACZ,GACD,CACH,CACF,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,IAAI,cAAc,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAChC,OAAO,IAAI,CAAA;IACb,CAAC;IACD,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAClC,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,GAAI;QACrC,cAAc,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAC3B,oBAAC,KAAK,IAAC,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CAC3D,CAAC,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACpE,MAAM,EAAE,qBAAqB,EAAE,GAAG,KAAK,CAAA;IAEvC,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,GAAI;QACtC,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QACzB,qBAAqB,CAAC,CAAC,CAAC,oBAAC,iBAAiB,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI,CAC/D,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,IAAI,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAChE,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAClC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI;QACzB,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI,CACtB,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,eAAe,EAAE,eAAe,EAAE,WAAW,EAAE,GACzE,KAAK,CAAA;IAEP,OAAO,CACL,iCACG,eAAe,CAAC,CAAC,CAAC,CACjB;QACE,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE;YACrC,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,oBAAC,MAAM,IAAC,KAAK,EAAE,KAAK,GAAI;YAC7C,oBAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI,CAClB;QACN,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI;QAEvC,eAAe,CAAC,CAAC,CAAC,CACjB,oBAAC,QAAQ,IAAC,QAAQ,EAAE,IAAI;YACtB,oBAAC,eAAe,OAAK,WAAW,GAAI,CAC3B,CACZ,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}
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@@ -1,6 +1,6 @@
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1
1
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import React from 'react';
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2
2
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import type { MsaViewModel } from '../model.ts';
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3
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-
import type { Cell, Clade, ColumnTrackSpec, Encoding, Highlight, Region, ResidueEncoding, ResidueMapping, RowPanelSpec, TreeOrder, TreeRoot, Viewport } from '../types.ts';
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3
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+
import type { Cell, Clade, ColorScheme, ColumnTrackSpec, Encoding, Feature, Highlight, MsaSelection, Region, ResidueEncoding, ResidueMapping, RowDataInput, RowPanelSpec, TreeOrder, TreeRoot, Viewport } from '../types.ts';
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4
4
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import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
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import type { ThemeOptions } from '@mui/material/styles';
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export interface MSAViewerProps {
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@@ -10,7 +10,11 @@ export interface MSAViewerProps {
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msaFilehandle?: FileLocationType;
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treeFilehandle?: FileLocationType;
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gffFilehandle?: FileLocationType;
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-
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/**
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* a scheme name from the built-in table, or `{map}`, a color per residue
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+
* letter that leaves every other letter uncolored
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*/
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colorScheme?: ColorScheme;
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height?: number;
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19
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/** initial per-column pixel width (zoom level) */
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colWidth?: number;
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@@ -28,6 +32,13 @@ export interface MSAViewerProps {
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* for whole rows, each with an optional `label` and `color`
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*/
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highlights?: Highlight[];
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/**
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+
* features on the rows as data, drawn with the GFF's: `{row, start, end}` in
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37
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+
* residues of that row, 1-based and inclusive, with an optional `name`,
|
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38
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+
* `description`, `type`, `strand` and `color`, and any other field an
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39
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+
* encoding reads (see docs/layers.md)
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+
*/
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+
features?: Feature[];
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42
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/**
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32
43
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* clades of the tree with a mark drawn over them: `{mrca, tips, mark}` or
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33
44
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* `{range, tips, mark}`, where `mark` is `highlight`, `bracket`, `collapse`
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@@ -41,7 +52,7 @@ export interface MSAViewerProps {
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/** which residue of which structure each row's residues are (see docs/layers.md) */
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42
53
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residueMappings?: ResidueMapping[];
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43
54
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/** extra fields per row name, such as a lineage or a host (see docs/layers.md) */
|
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44
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-
rowData?:
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55
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+
rowData?: RowDataInput;
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45
56
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/**
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46
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* what the viewer's marks read from a table: `{channel, field, scale?}`,
|
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47
58
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* where `channel` is `tipLabel`, `rowTint` or `branch` over `rowData`, or
|
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@@ -86,6 +97,11 @@ export interface MSAViewerProps {
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86
97
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* in columns, 1-based and inclusive
|
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87
98
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*/
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88
99
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region?: Region;
|
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100
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+
/**
|
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101
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+
* the selected block: `{start, end}` columns of the file, 1-based and
|
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102
|
+
* inclusive, and `rows` by name, every row where absent
|
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103
|
+
*/
|
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104
|
+
selection?: MsaSelection;
|
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89
105
|
/** leave out the toolbar, for a page drawing its own controls */
|
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90
106
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hideHeader?: boolean;
|
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91
107
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/**
|
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@@ -99,15 +115,20 @@ export interface MSAViewerProps {
|
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99
115
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onCellClick?: (cell: Cell | undefined) => void;
|
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100
116
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/** the alignment columns on screen, after every scroll, zoom and resize */
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101
117
|
onViewportChange?: (viewport: Viewport | undefined) => void;
|
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118
|
+
/**
|
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119
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+
* the selected block, after each change a drag, the header menu, Escape or
|
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120
|
+
* the `selection` prop makes, or undefined when it clears
|
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121
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+
*/
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122
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+
onSelectionChange?: (selection: MsaSelection | undefined) => void;
|
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102
123
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/**
|
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103
124
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* the model the viewer built, for the model API; called again with the new
|
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104
|
-
* model when msa, tree,
|
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125
|
+
* model when msa, tree, msaFilehandle or treeFilehandle changes
|
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105
126
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*/
|
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106
127
|
onModel?: (model: MsaViewModel) => void;
|
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107
128
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}
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129
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/**
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109
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-
* A new alignment
|
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110
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-
*
|
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111
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-
*
|
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130
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+
* A new alignment or tree needs a new model, so the viewer remounts when one
|
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131
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+
* of those props changes and keeps its model across every other change,
|
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132
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+
* including a new annotation file.
|
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112
133
|
*/
|
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134
|
export default function MSAViewer(props: MSAViewerProps): React.JSX.Element;
|
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@@ -13,28 +13,27 @@ function resolveTheme(theme) {
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13
13
|
? theme
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14
14
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: undefined);
|
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15
15
|
}
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16
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+
function colorSchemeSnapshot(scheme) {
|
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17
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+
return typeof scheme === 'string'
|
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18
|
+
? { colorSchemeName: scheme }
|
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+
: scheme
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20
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+
? { customColorScheme: scheme.map }
|
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21
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+
: {};
|
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22
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+
}
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16
23
|
function sameSource(a, b) {
|
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17
24
|
return (a.msa === b.msa &&
|
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18
25
|
a.tree === b.tree &&
|
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19
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-
a.
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20
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-
|
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21
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-
JSON.stringify([b.msaFilehandle, b.treeFilehandle, b.gffFilehandle]));
|
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26
|
+
JSON.stringify([a.msaFilehandle, a.treeFilehandle]) ===
|
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27
|
+
JSON.stringify([b.msaFilehandle, b.treeFilehandle]));
|
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22
28
|
}
|
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23
29
|
/**
|
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24
|
-
* A new alignment
|
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25
|
-
*
|
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26
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-
*
|
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30
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+
* A new alignment or tree needs a new model, so the viewer remounts when one
|
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31
|
+
* of those props changes and keeps its model across every other change,
|
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32
|
+
* including a new annotation file.
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27
33
|
*/
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28
34
|
export default function MSAViewer(props) {
|
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29
|
-
const { msa, tree,
|
|
30
|
-
const source = {
|
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31
|
-
msa,
|
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32
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-
tree,
|
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33
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-
gff,
|
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34
|
-
msaFilehandle,
|
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35
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-
treeFilehandle,
|
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36
|
-
gffFilehandle,
|
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37
|
-
};
|
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35
|
+
const { msa, tree, msaFilehandle, treeFilehandle } = props;
|
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36
|
+
const source = { msa, tree, msaFilehandle, treeFilehandle };
|
|
38
37
|
const [shown, setShown] = useState({ source, generation: 0 });
|
|
39
38
|
if (!sameSource(shown.source, source)) {
|
|
40
39
|
setShown({ source, generation: shown.generation + 1 });
|
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@@ -53,7 +52,7 @@ function useModelReaction(model, key, handler) {
|
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53
52
|
}, { equals: compareStructural })
|
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54
53
|
: undefined, [model, key, listening]);
|
|
55
54
|
}
|
|
56
|
-
function Viewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, allowedGappyness, highlightColumns, highlights, clades, relativeTo, columnTracks, residueMappings, rowData, encodings, rowPanels, drawTree, residueEncoding, treeAreaWidth, autoTreeAreaWidth, showBranchLen, treeOrder, treeRoot, region, hideHeader, theme, onCellHover, onCellClick, onViewportChange, onModel, }) {
|
|
55
|
+
function Viewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, allowedGappyness, highlightColumns, highlights, features, clades, relativeTo, columnTracks, residueMappings, rowData, encodings, rowPanels, drawTree, residueEncoding, treeAreaWidth, autoTreeAreaWidth, showBranchLen, treeOrder, treeRoot, region, selection, hideHeader, theme, onCellHover, onCellClick, onViewportChange, onSelectionChange, onModel, }) {
|
|
57
56
|
const [model] = useState(() => MSAModelF().create({
|
|
58
57
|
type: 'MsaView',
|
|
59
58
|
...(msa || tree || gff || rowData
|
|
@@ -71,13 +70,15 @@ function Viewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle,
|
|
|
71
70
|
...(msaFilehandle ? { msaFilehandle } : {}),
|
|
72
71
|
...(treeFilehandle ? { treeFilehandle } : {}),
|
|
73
72
|
...(gffFilehandle ? { gffFilehandle } : {}),
|
|
74
|
-
...(colorScheme
|
|
73
|
+
...colorSchemeSnapshot(colorScheme),
|
|
75
74
|
...(height ? { height } : {}),
|
|
76
75
|
...(colWidth ? { colWidth } : {}),
|
|
77
76
|
...(rowHeight ? { rowHeight } : {}),
|
|
78
77
|
...(allowedGappyness !== undefined ? { allowedGappyness } : {}),
|
|
79
78
|
...(highlightColumns ? { highlightColumns } : {}),
|
|
80
79
|
...(highlights ? { highlights } : {}),
|
|
80
|
+
...(features ? { features } : {}),
|
|
81
|
+
...(selection ? { selection } : {}),
|
|
81
82
|
...(clades ? { clades } : {}),
|
|
82
83
|
...(relativeTo ? { relativeTo } : {}),
|
|
83
84
|
...(columnTracks ? { columnTracks } : {}),
|
|
@@ -108,11 +109,6 @@ function Viewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle,
|
|
|
108
109
|
model.setHeight(height);
|
|
109
110
|
}
|
|
110
111
|
}, [model, height]);
|
|
111
|
-
useEffect(() => {
|
|
112
|
-
if (colorScheme !== undefined) {
|
|
113
|
-
model.setColorSchemeName(colorScheme);
|
|
114
|
-
}
|
|
115
|
-
}, [model, colorScheme]);
|
|
116
112
|
useEffect(() => {
|
|
117
113
|
if (colWidth !== undefined) {
|
|
118
114
|
model.setColWidth(colWidth);
|
|
@@ -160,12 +156,54 @@ function Viewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle,
|
|
|
160
156
|
useEffect(() => {
|
|
161
157
|
model.drawRelativeTo(relativeTo);
|
|
162
158
|
}, [model, relativeTo]);
|
|
159
|
+
// The snapshot already holds the first gff and gffFilehandle, so these
|
|
160
|
+
// effects apply only a later change. Removing either one sets the text back
|
|
161
|
+
// to the gff prop, which clears the annotations when that is absent too.
|
|
162
|
+
const appliedGff = useRef(gff);
|
|
163
|
+
const gffFilehandleKey = JSON.stringify(gffFilehandle ?? null);
|
|
164
|
+
const appliedGffFilehandle = useRef(gffFilehandleKey);
|
|
165
|
+
useEffect(() => {
|
|
166
|
+
if (appliedGffFilehandle.current !== gffFilehandleKey) {
|
|
167
|
+
appliedGffFilehandle.current = gffFilehandleKey;
|
|
168
|
+
const location = JSON.parse(gffFilehandleKey);
|
|
169
|
+
if (location) {
|
|
170
|
+
model.setGFFFilehandle(location);
|
|
171
|
+
}
|
|
172
|
+
else {
|
|
173
|
+
model.setGFF(appliedGff.current);
|
|
174
|
+
}
|
|
175
|
+
}
|
|
176
|
+
}, [model, gffFilehandleKey]);
|
|
177
|
+
useEffect(() => {
|
|
178
|
+
if (appliedGff.current !== gff) {
|
|
179
|
+
appliedGff.current = gff;
|
|
180
|
+
model.setGFF(gff);
|
|
181
|
+
}
|
|
182
|
+
}, [model, gff]);
|
|
163
183
|
// keyed by content, since a host computing a layer inline passes a new array
|
|
164
184
|
// on every render
|
|
185
|
+
const colorSchemeKey = JSON.stringify(colorScheme ?? null);
|
|
186
|
+
useEffect(() => {
|
|
187
|
+
const scheme = JSON.parse(colorSchemeKey);
|
|
188
|
+
if (typeof scheme === 'string') {
|
|
189
|
+
model.setColorSchemeName(scheme);
|
|
190
|
+
}
|
|
191
|
+
else if (scheme) {
|
|
192
|
+
model.setCustomColorScheme(scheme.map);
|
|
193
|
+
}
|
|
194
|
+
}, [model, colorSchemeKey]);
|
|
165
195
|
const highlightsKey = JSON.stringify(highlights ?? []);
|
|
166
196
|
useEffect(() => {
|
|
167
197
|
model.setHighlights(JSON.parse(highlightsKey));
|
|
168
198
|
}, [model, highlightsKey]);
|
|
199
|
+
const featuresKey = JSON.stringify(features ?? []);
|
|
200
|
+
useEffect(() => {
|
|
201
|
+
model.setFeatures(JSON.parse(featuresKey));
|
|
202
|
+
}, [model, featuresKey]);
|
|
203
|
+
const selectionKey = JSON.stringify(selection ?? null);
|
|
204
|
+
useEffect(() => {
|
|
205
|
+
model.setSelection(JSON.parse(selectionKey) ?? undefined);
|
|
206
|
+
}, [model, selectionKey]);
|
|
169
207
|
const treeRootKey = JSON.stringify(treeRoot ?? null);
|
|
170
208
|
useEffect(() => {
|
|
171
209
|
model.setTreeRoot(JSON.parse(treeRootKey) ?? undefined);
|
|
@@ -214,6 +252,7 @@ function Viewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle,
|
|
|
214
252
|
useModelReaction(model, 'hoveredCell', onCellHover);
|
|
215
253
|
useModelReaction(model, 'clickedCell', onCellClick);
|
|
216
254
|
useModelReaction(model, 'viewport', onViewportChange);
|
|
255
|
+
useModelReaction(model, 'selection', onSelectionChange);
|
|
217
256
|
const latestOnModel = useRef(onModel);
|
|
218
257
|
useEffect(() => {
|
|
219
258
|
latestOnModel.current = onModel;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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M,EAAE,CAAC;YAC9B,KAAK,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;QACzB,CAAC;IACH,CAAC,EAAE,CAAC,KAAK,EAAE,UAAU,CAAC,CAAC,CAAA;IACvB,MAAM,YAAY,GAAG,IAAI,CAAC,SAAS,CAAC,SAAS,IAAI,EAAE,CAAC,CAAA;IACpD,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,CAAA;IAC9C,CAAC,EAAE,CAAC,KAAK,EAAE,YAAY,CAAC,CAAC,CAAA;IACzB,MAAM,YAAY,GAAG,IAAI,CAAC,SAAS,CAAC,SAAS,IAAI,EAAE,CAAC,CAAA;IACpD,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,CAAA;IAC9C,CAAC,EAAE,CAAC,KAAK,EAAE,YAAY,CAAC,CAAC,CAAA;IACzB,MAAM,mBAAmB,GAAG,IAAI,CAAC,SAAS,CAAC,gBAAgB,IAAI,IAAI,CAAC,CAAA;IACpE,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,qBAAqB,CAAC,IAAI,CAAC,KAAK,CAAC,mBAAmB,CAAC,IAAI,SAAS,CAAC,CAAA;IAC3E,CAAC,EAAE,CAAC,KAAK,EAAE,mBAAmB,CAAC,CAAC,CAAA;IAEhC,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,IAAI,IAAI,CAAC,CAAA;IAChD,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,SAAS,CAAkB,CAAA;QACrD,OAAO,MAAM;YACX,CAAC,CAAC,IAAI,CACF,GAAG,EAAE,CAAC,KAAK,CAAC,eAAe,IAAI,KAAK,CAAC,UAAU,GAAG,CAAC,EACnD,GAAG,EAAE;gBACH,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC,CAAA;YAC5B,CAAC,CACF;YACH,CAAC,CAAC,SAAS,CAAA;IACf,CAAC,EAAE,CAAC,KAAK,EAAE,SAAS,CAAC,CAAC,CAAA;IAEtB,gBAAgB,CAAC,KAAK,EAAE,aAAa,EAAE,WAAW,CAAC,CAAA;IACnD,gBAAgB,CAAC,KAAK,EAAE,aAAa,EAAE,WAAW,CAAC,CAAA;IACnD,gBAAgB,CAAC,KAAK,EAAE,UAAU,EAAE,gBAAgB,CAAC,CAAA;IACrD,gBAAgB,CAAC,KAAK,EAAE,WAAW,EAAE,iBAAiB,CAAC,CAAA;IAEvD,MAAM,aAAa,GAAG,MAAM,CAAC,OAAO,CAAC,CAAA;IACrC,SAAS,CAAC,GAAG,EAAE;QACb,aAAa,CAAC,OAAO,GAAG,OAAO,CAAA;IACjC,CAAC,CAAC,CAAA;IACF,SAAS,CAAC,GAAG,EAAE;QACb,aAAa,CAAC,OAAO,EAAE,CAAC,KAAK,CAAC,CAAA;IAChC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAA;IAEX,2EAA2E;IAC3E,0EAA0E;IAC1E,qBAAqB;IACrB,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,YAAY,CAAC,OAAO,KAAK,SAAS,EAAE,CAAC;YACvC,YAAY,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;YAClC,YAAY,CAAC,OAAO,GAAG,SAAS,CAAA;QAClC,CAAC;QACD,OAAO,GAAG,EAAE;YACV,YAAY,CAAC,OAAO,GAAG,UAAU,CAAC,GAAG,EAAE;gBACrC,YAAY,CAAC,OAAO,GAAG,SAAS,CAAA;gBAChC,IAAI,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;oBACnB,OAAO,CAAC,KAAK,CAAC,CAAA;gBAChB,CAAC;YACH,CAAC,CAAC,CAAA;QACJ,CAAC,CAAA;IACH,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAA;IAEX,OAAO,CACL,oBAAC,aAAa,IAAC,KAAK,EAAE,YAAY,CAAC,KAAK,CAAC;QACvC,6BAAK,GAAG,EAAE,GAAG;YACX,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CACrB,CACQ,CACjB,CAAA;AACH,CAAC"}
|
|
@@ -0,0 +1,29 @@
|
|
|
1
|
+
import React from 'react';
|
|
2
|
+
import { makeStyles } from '@jbrowse/core/util/tss-react';
|
|
3
|
+
import { Table, TableBody, TableCell, TableRow } from '@mui/material';
|
|
4
|
+
const useStyles = makeStyles()({
|
|
5
|
+
key: {
|
|
6
|
+
fontWeight: 'bold',
|
|
7
|
+
verticalAlign: 'top',
|
|
8
|
+
},
|
|
9
|
+
value: {
|
|
10
|
+
whiteSpace: 'pre-wrap',
|
|
11
|
+
wordBreak: 'break-word',
|
|
12
|
+
},
|
|
13
|
+
});
|
|
14
|
+
function isRecord(value) {
|
|
15
|
+
return typeof value === 'object' && value !== null && !Array.isArray(value);
|
|
16
|
+
}
|
|
17
|
+
export function isEmpty(value) {
|
|
18
|
+
return isRecord(value) && Object.keys(value).length === 0;
|
|
19
|
+
}
|
|
20
|
+
export default function MetadataTable({ record, }) {
|
|
21
|
+
const { classes } = useStyles();
|
|
22
|
+
return (React.createElement(Table, { size: "small" },
|
|
23
|
+
React.createElement(TableBody, null, Object.entries(record)
|
|
24
|
+
.filter(([, value]) => value != null && !isEmpty(value))
|
|
25
|
+
.map(([key, value]) => (React.createElement(TableRow, { key: key },
|
|
26
|
+
React.createElement(TableCell, { component: "th", className: classes.key }, key),
|
|
27
|
+
React.createElement(TableCell, { className: classes.value }, isRecord(value) ? (React.createElement(MetadataTable, { record: value })) : Array.isArray(value) ? (value.join('\n')) : (String(value)))))))));
|
|
28
|
+
}
|
|
29
|
+
//# sourceMappingURL=MetadataTable.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"MetadataTable.js","sourceRoot":"","sources":["../../src/components/MetadataTable.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAErE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,GAAG,EAAE;QACH,UAAU,EAAE,MAAM;QAClB,aAAa,EAAE,KAAK;KACrB;IACD,KAAK,EAAE;QACL,UAAU,EAAE,UAAU;QACtB,SAAS,EAAE,YAAY;KACxB;CACF,CAAC,CAAA;AAEF,SAAS,QAAQ,CAAC,KAAc;IAC9B,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;AAC7E,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,KAAc;IACpC,OAAO,QAAQ,CAAC,KAAK,CAAC,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,MAAM,KAAK,CAAC,CAAA;AAC3D,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,EACpC,MAAM,GAGP;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,oBAAC,KAAK,IAAC,IAAI,EAAC,OAAO;QACjB,oBAAC,SAAS,QACP,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC;aACpB,MAAM,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,KAAK,IAAI,IAAI,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;aACvD,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CACrB,oBAAC,QAAQ,IAAC,GAAG,EAAE,GAAG;YAChB,oBAAC,SAAS,IAAC,SAAS,EAAC,IAAI,EAAC,SAAS,EAAE,OAAO,CAAC,GAAG,IAC7C,GAAG,CACM;YACZ,oBAAC,SAAS,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,IAChC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CACjB,oBAAC,aAAa,IAAC,MAAM,EAAE,KAAK,GAAI,CACjC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CACzB,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CACjB,CAAC,CAAC,CAAC,CACF,MAAM,CAAC,KAAK,CAAC,CACd,CACS,CACH,CACZ,CAAC,CACM,CACN,CACT,CAAA;AACH,CAAC"}
|
package/dist/components/Track.js
CHANGED
|
@@ -5,6 +5,7 @@ import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown';
|
|
|
5
5
|
import { IconButton, Menu, MenuItem } from '@mui/material';
|
|
6
6
|
import { observer } from 'mobx-react';
|
|
7
7
|
import { useWheelScroll } from '../useWheelScroll.js';
|
|
8
|
+
import { onMsaKey } from './msa/msaKeys.js';
|
|
8
9
|
import TrackTooltipContent from './tracks/TrackTooltipContent.js';
|
|
9
10
|
import { useTrackHover } from './tracks/useTrackHover.js';
|
|
10
11
|
const TrackInfoDialog = lazy(() => import('./dialogs/TrackInfoDialog.js'));
|
|
@@ -80,17 +81,25 @@ const Track = observer(function ({ model, track, }) {
|
|
|
80
81
|
}, [model]);
|
|
81
82
|
useWheelScroll({ ref, onScrollX });
|
|
82
83
|
const { classes } = useStyles();
|
|
83
|
-
const { anchor, onMouseMove, onMouseLeave } = useTrackHover({
|
|
84
|
+
const { anchor, onMouseMove, onMouseDown, onMouseLeave } = useTrackHover({
|
|
84
85
|
model,
|
|
85
86
|
tooltip: showColumnStats,
|
|
86
87
|
});
|
|
87
88
|
return (React.createElement("div", { className: classes.row, style: { height } },
|
|
88
89
|
React.createElement(TrackLabel, { model: model, track: track }),
|
|
89
90
|
React.createElement("div", { style: { width: rowPanelsWidth + resizeHandleWidth, flexShrink: 0 } }),
|
|
90
|
-
React.createElement("div", { ref: ref, "data-testid": `track_${track.model.id}`,
|
|
91
|
+
React.createElement("div", { ref: ref, "data-testid": `track_${track.model.id}`, tabIndex: -1, style: { outline: 'none' }, onKeyDown: event => {
|
|
92
|
+
if (onMsaKey(model, event)) {
|
|
93
|
+
event.preventDefault();
|
|
94
|
+
}
|
|
95
|
+
}, onMouseMove: event => {
|
|
91
96
|
if (ref.current) {
|
|
92
97
|
onMouseMove(event, ref.current);
|
|
93
98
|
}
|
|
99
|
+
}, onMouseDown: event => {
|
|
100
|
+
if (ref.current) {
|
|
101
|
+
onMouseDown(event, ref.current);
|
|
102
|
+
}
|
|
94
103
|
}, onMouseLeave: () => {
|
|
95
104
|
onMouseLeave();
|
|
96
105
|
} },
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"Track.js","sourceRoot":"","sources":["../../src/components/Track.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAElE,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,iBAAiB,MAAM,mCAAmC,CAAA;AACjE,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC1D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAA;AACrD,OAAO,mBAAmB,MAAM,iCAAkC,CAAA;AAClE,OAAO,EAAE,aAAa,EAAE,MAAM,2BAA2B,CAAA;AAKzD,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,8BAA+B,CAAC,CAAC,CAAA;AAE3E,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,MAAM,EAAE;QACN,OAAO,EAAE,CAAC;KACX;IACD,0EAA0E;IAC1E,2EAA2E;IAC3E,6EAA6E;IAC7E,4EAA4E;IAC5E,8DAA8D;IAC9D,GAAG,EAAE;QACH,OAAO,EAAE,MAAM;QACf,oBAAoB,EAAE;YACpB,SAAS,EAAE,kBAAkB,KAAK,CAAC,OAAO,CAAC,OAAO,EAAE;SACrD;KACF;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,UAAU,GAAG,QAAQ,CAAC,SAAS,UAAU,CAAC,EAC9C,KAAK,EACL,KAAK,GAIN;IACC,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAqB,CAAA;IAC7D,MAAM,SAAS,GAAG,GAAG,EAAE;QACrB,WAAW,CAAC,SAAS,CAAC,CAAA;IACxB,CAAC,CAAA;IACD,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,aAAa,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAC5D,MAAM,EACJ,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,GACxB,GAAG,KAAK,CAAA;IACT,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,gBAAgB,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IAEnD,OAAO,CAIL,6BACE,KAAK,EAAE;YACL,KAAK;YACL,MAAM;YACN,UAAU,EAAE,CAAC;YACb,OAAO,EAAE,MAAM;YACf,UAAU,EAAE,YAAY;YACxB,cAAc,EAAE,UAAU;YAC1B,GAAG,EAAE,CAAC;YACN,QAAQ,EAAE,gBAAgB;SAC3B;QAED,8BACE,KAAK,EAAE,IAAI,EACX,KAAK,EAAE;gBACL,QAAQ,EAAE,QAAQ;gBAClB,YAAY,EAAE,UAAU;gBACxB,UAAU,EAAE,QAAQ;aACrB,IAEA,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAClB;QACP,oBAAC,UAAU,IACT,SAAS,EAAE,OAAO,CAAC,MAAM,gBACb,GAAG,IAAI,aAAa,EAChC,KAAK,EAAE;gBACL,KAAK,EAAE,gBAAgB;gBACvB,MAAM,EAAE,gBAAgB;gBACxB,UAAU,EAAE,CAAC;aACd,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,WAAW,CAAC,KAAK,CAAC,aAAa,CAAC,CAAA;YAClC,CAAC;YAED,oBAAC,iBAAiB,OAAG,CACV;QACZ,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,IAAI,IACH,QAAQ,EAAE,QAAQ,EAClB,kBAAkB,EAAE,CAAC,EACrB,IAAI,QACJ,OAAO,EAAE,GAAG,EAAE;gBACZ,SAAS,EAAE,CAAA;YACb,CAAC;YAED,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;oBACjC,SAAS,EAAE,CAAA;gBACb,CAAC,iBAGQ;YACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,eAAe;wBACf,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE;qBAChC,CAAC,CAAA;oBACF,SAAS,EAAE,CAAA;gBACb,CAAC,eAGQ,CACN,CACR,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,EAC/B,KAAK,EACL,KAAK,GAIN;IACC,MAAM,EAAE,iBAAiB,EAAE,cAAc,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACpE,MAAM,EACJ,KAAK,EAAE,EAAE,MAAM,EAAE,GAClB,GAAG,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,SAAS,GAAG,WAAW,CAC3B,CAAC,CAAS,EAAE,EAAE;QACZ,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,cAAc,CAAC,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,CAAA;IAClC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,YAAY,EAAE,GAAG,aAAa,CAAC;
|
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1
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+
{"version":3,"file":"Track.js","sourceRoot":"","sources":["../../src/components/Track.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAElE,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,iBAAiB,MAAM,mCAAmC,CAAA;AACjE,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC1D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAA;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAA;AAC3C,OAAO,mBAAmB,MAAM,iCAAkC,CAAA;AAClE,OAAO,EAAE,aAAa,EAAE,MAAM,2BAA2B,CAAA;AAKzD,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,8BAA+B,CAAC,CAAC,CAAA;AAE3E,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,MAAM,EAAE;QACN,OAAO,EAAE,CAAC;KACX;IACD,0EAA0E;IAC1E,2EAA2E;IAC3E,6EAA6E;IAC7E,4EAA4E;IAC5E,8DAA8D;IAC9D,GAAG,EAAE;QACH,OAAO,EAAE,MAAM;QACf,oBAAoB,EAAE;YACpB,SAAS,EAAE,kBAAkB,KAAK,CAAC,OAAO,CAAC,OAAO,EAAE;SACrD;KACF;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,UAAU,GAAG,QAAQ,CAAC,SAAS,UAAU,CAAC,EAC9C,KAAK,EACL,KAAK,GAIN;IACC,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAqB,CAAA;IAC7D,MAAM,SAAS,GAAG,GAAG,EAAE;QACrB,WAAW,CAAC,SAAS,CAAC,CAAA;IACxB,CAAC,CAAA;IACD,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,aAAa,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAC5D,MAAM,EACJ,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,GACxB,GAAG,KAAK,CAAA;IACT,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,gBAAgB,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IAEnD,OAAO,CAIL,6BACE,KAAK,EAAE;YACL,KAAK;YACL,MAAM;YACN,UAAU,EAAE,CAAC;YACb,OAAO,EAAE,MAAM;YACf,UAAU,EAAE,YAAY;YACxB,cAAc,EAAE,UAAU;YAC1B,GAAG,EAAE,CAAC;YACN,QAAQ,EAAE,gBAAgB;SAC3B;QAED,8BACE,KAAK,EAAE,IAAI,EACX,KAAK,EAAE;gBACL,QAAQ,EAAE,QAAQ;gBAClB,YAAY,EAAE,UAAU;gBACxB,UAAU,EAAE,QAAQ;aACrB,IAEA,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAClB;QACP,oBAAC,UAAU,IACT,SAAS,EAAE,OAAO,CAAC,MAAM,gBACb,GAAG,IAAI,aAAa,EAChC,KAAK,EAAE;gBACL,KAAK,EAAE,gBAAgB;gBACvB,MAAM,EAAE,gBAAgB;gBACxB,UAAU,EAAE,CAAC;aACd,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,WAAW,CAAC,KAAK,CAAC,aAAa,CAAC,CAAA;YAClC,CAAC;YAED,oBAAC,iBAAiB,OAAG,CACV;QACZ,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,IAAI,IACH,QAAQ,EAAE,QAAQ,EAClB,kBAAkB,EAAE,CAAC,EACrB,IAAI,QACJ,OAAO,EAAE,GAAG,EAAE;gBACZ,SAAS,EAAE,CAAA;YACb,CAAC;YAED,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;oBACjC,SAAS,EAAE,CAAA;gBACb,CAAC,iBAGQ;YACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,eAAe;wBACf,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE;qBAChC,CAAC,CAAA;oBACF,SAAS,EAAE,CAAA;gBACb,CAAC,eAGQ,CACN,CACR,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,EAC/B,KAAK,EACL,KAAK,GAIN;IACC,MAAM,EAAE,iBAAiB,EAAE,cAAc,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACpE,MAAM,EACJ,KAAK,EAAE,EAAE,MAAM,EAAE,GAClB,GAAG,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,SAAS,GAAG,WAAW,CAC3B,CAAC,CAAS,EAAE,EAAE;QACZ,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,cAAc,CAAC,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,CAAA;IAClC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,YAAY,EAAE,GAAG,aAAa,CAAC;QACvE,KAAK;QACL,OAAO,EAAE,eAAe;KACzB,CAAC,CAAA;IAEF,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE,MAAM,EAAE;QAC5C,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI;QAG1C,6BACE,KAAK,EAAE,EAAE,KAAK,EAAE,cAAc,GAAG,iBAAiB,EAAE,UAAU,EAAE,CAAC,EAAE,GACnE;QACF,6BACE,GAAG,EAAE,GAAG,iBACK,SAAS,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,EACtC,QAAQ,EAAE,CAAC,CAAC,EACZ,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,EAC1B,SAAS,EAAE,KAAK,CAAC,EAAE;gBACjB,IAAI,QAAQ,CAAC,KAAK,EAAE,KAAK,CAAC,EAAE,CAAC;oBAC3B,KAAK,CAAC,cAAc,EAAE,CAAA;gBACxB,CAAC;YACH,CAAC,EACD,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;oBAChB,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,OAAO,CAAC,CAAA;gBACjC,CAAC;YACH,CAAC,EACD,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;oBAChB,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,OAAO,CAAC,CAAA;gBACjC,CAAC;YACH,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,YAAY,EAAE,CAAA;YAChB,CAAC;YAED,oBAAC,KAAK,CAAC,cAAc,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI;YACnD,MAAM,CAAC,CAAC,CAAC,CACR,oBAAC,WAAW,IAAC,WAAW,EAAE,MAAM,CAAC,WAAW;gBAC1C,oBAAC,mBAAmB,IAClB,KAAK,EAAE,KAAK,EACZ,KAAK,EAAE,KAAK,EACZ,GAAG,EAAE,MAAM,CAAC,KAAK,GACjB,CACU,CACf,CAAC,CAAC,CAAC,IAAI,CACJ,CACF,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,KAAK,CAAA"}
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@@ -1,9 +1,8 @@
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1
1
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import React from 'react';
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2
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-
import Attributes from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes';
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3
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-
import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
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4
2
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import { Dialog } from '@jbrowse/core/ui';
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5
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-
import { DialogContent } from '@mui/material';
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3
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+
import { DialogContent, Typography } from '@mui/material';
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6
4
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import { observer } from 'mobx-react';
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5
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+
import MetadataTable, { isEmpty } from '../MetadataTable.js';
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7
6
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import SequenceTextArea from '../SequenceTextArea.js';
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8
7
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const MetadataDialog = observer(function ({ model, onClose, }) {
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8
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const { header } = model;
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@@ -11,9 +10,9 @@ const MetadataDialog = observer(function ({ model, onClose, }) {
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onClose();
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11
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}, open: true, title: "Metadata", maxWidth: "xl" },
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React.createElement(DialogContent, null,
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React.createElement(
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React.createElement(
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Object.values(header).every(isEmpty) ? (React.createElement(Typography, null, "This alignment has no metadata.")) : (React.createElement(MetadataTable, { record: header })),
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14
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+
React.createElement(Typography, { variant: "h6" }, "Sequences"),
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React.createElement(SequenceTextArea, { str: model.rows }))));
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});
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17
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export default MetadataDialog;
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19
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//# sourceMappingURL=MetadataDialog.js.map
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@@ -1 +1 @@
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-
{"version":3,"file":"MetadataDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/MetadataDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,
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1
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+
{"version":3,"file":"MetadataDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/MetadataDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,aAAa,EAAE,EAAE,OAAO,EAAE,MAAM,qBAAsB,CAAA;AAC7D,OAAO,gBAAgB,MAAM,wBAAyB,CAAA;AAItD,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACxB,OAAO,CACL,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;YACZ,OAAO,EAAE,CAAA;QACX,CAAC,EACD,IAAI,QACJ,KAAK,EAAC,UAAU,EAChB,QAAQ,EAAC,IAAI;QAEb,oBAAC,aAAa;YACX,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CACtC,oBAAC,UAAU,0CAA6C,CACzD,CAAC,CAAC,CAAC,CACF,oBAAC,aAAa,IAAC,MAAM,EAAE,MAAM,GAAI,CAClC;YACD,oBAAC,UAAU,IAAC,OAAO,EAAC,IAAI,gBAAuB;YAC/C,oBAAC,gBAAgB,IAAC,GAAG,EAAE,KAAK,CAAC,IAAI,GAAI,CACvB,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}
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@@ -1,5 +1,11 @@
|
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1
1
|
import React from 'react';
|
|
2
2
|
import type { MsaViewModel } from '../../model.ts';
|
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3
|
+
export declare function colorSchemeMenuItems(model: MsaViewModel): {
|
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4
|
+
readonly label: string;
|
|
5
|
+
readonly type: 'radio';
|
|
6
|
+
readonly checked: boolean;
|
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7
|
+
readonly onClick: () => void;
|
|
8
|
+
}[];
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3
9
|
declare const ColorSchemeMenu: ({ model }: {
|
|
4
10
|
model: MsaViewModel;
|
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5
11
|
}) => React.JSX.Element;
|