npm - @platforma-sdk/ui-vue - Versions diffs - 1.41.19 → 1.42.0 - Mend

@platforma-sdk/ui-vue 1.41.19 → 1.42.0

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package/dist/components/PlMultiSequenceAlignment/data.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"data.js","sources":["../../../src/components/PlMultiSequenceAlignment/data.ts"],"sourcesContent":["import { isJsonEqual } from '@milaboratories/helpers';\nimport type { ListOptionNormalized } from '@milaboratories/uikit';\nimport {\n type CalculateTableDataRequest,\n type CanonicalizedJson,\n canonicalizeJson,\n createRowSelectionColumn,\n ensureError,\n getAxisId,\n getRawPlatformaInstance,\n isLabelColumn,\n isLinkerColumn,\n type JoinEntry,\n matchAxisId,\n parseJson,\n type PColumnIdAndSpec,\n type PFrameHandle,\n type PlMultiSequenceAlignmentColorSchemeOption,\n type PlMultiSequenceAlignmentSettings,\n type PlSelectionModel,\n type PObjectId,\n type PTableColumnId,\n type PTableSorting,\n pTableValue,\n} from '@platforma-sdk/model';\nimport { ref, watch } from 'vue';\nimport {\n chemicalPropertiesColorMap,\n colorizeSequencesByChemicalProperties,\n} from './chemical-properties';\nimport {\n colorizeSequencesByMarkup,\n type Markup,\n markupAlignedSequence,\n markupColors,\n parseMarkup,\n} from './markup';\nimport { multiSequenceAlignment } from './multi-sequence-alignment';\nimport { getResidueCounts } from './residue-counts';\nimport type { ColorMap, ResidueCounts } from './types';\n\nconst getPFrameDriver = () => getRawPlatformaInstance().pFrameDriver;\n\nexport const sequenceLimit = 1000;\n\nexport const useSequenceColumnsOptions = refreshOnDeepChange(\n getSequenceColumnsOptions,\n);\n\nexport const useLabelColumnsOptions = refreshOnDeepChange(\n getLabelColumnsOptions,\n);\n\nexport const useMarkupColumnsOptions = refreshOnDeepChange(\n getMarkupColumnsOptions,\n);\n\nexport const useMultipleAlignmentData = refreshOnDeepChange(\n getMultipleAlignmentData,\n);\n\nasync function getSequenceColumnsOptions({\n pFrame,\n sequenceColumnPredicate,\n}: {\n pFrame: PFrameHandle \| undefined;\n sequenceColumnPredicate: (column: PColumnIdAndSpec) => boolean;\n}): Promise<OptionsWithDefaults<PObjectId> \| undefined> {\n if (!pFrame) return;\n\n const pFrameDriver = getPFrameDriver();\n const columns = await pFrameDriver.listColumns(pFrame);\n const options = columns\n .filter((column) => sequenceColumnPredicate(column))\n .map(({ spec, columnId }) => ({\n label: spec.annotations?.['pl7.app/label'] ?? 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'Unlabelled axis',\n );\n }\n\n const { hits: compatibleColumns } = await pFrameDriver.findColumns(pFrame, {\n columnFilter: {},\n compatibleWith: Array.from(\n sequenceColumnsAxes.keys(),\n (axisIdJson) => parseJson(axisIdJson),\n ),\n strictlyCompatible: false,\n });\n\n for (const { columnId, spec } of compatibleColumns) {\n const columnIdJson = canonicalizeJson({ type: 'column', id: columnId });\n if (optionMap.has(columnIdJson)) continue;\n optionMap.set(\n columnIdJson,\n spec.annotations?.['pl7.app/label'] ?? 'Unlabelled column',\n );\n }\n\n const options = Array.from(optionMap).map(\n ([value, label]) => ({ label, value: parseJson(value) }),\n );\n\n const defaults = options\n .filter(({ value }) => {\n if (value.type === 'axis') return true;\n const column = columns.find(({ columnId }) => columnId === value.id);\n return column && isLabelColumn(column.spec);\n })\n .map(({ value }) => value);\n return { options, defaults };\n}\n\nasync function getMarkupColumnsOptions({\n pFrame,\n sequenceColumnIds,\n}: {\n pFrame: PFrameHandle \| undefined;\n sequenceColumnIds: PObjectId[] \| undefined;\n}): Promise<ListOptionNormalized<PObjectId>[] \| undefined> {\n if (!pFrame \|\| sequenceColumnIds?.length !== 1) return;\n\n const pFrameDriver = getPFrameDriver();\n const columns = await pFrameDriver.listColumns(pFrame);\n const sequenceColumn = columns.find((column) =>\n column.columnId === sequenceColumnIds[0],\n );\n if (!sequenceColumn) {\n throw new Error(\n `Couldn't find sequence column (ID: \\`${sequenceColumnIds[0]}\\`).`,\n );\n }\n return columns\n .filter((column) =>\n column.spec.annotations?.['pl7.app/sequence/isAnnotation'] === 'true'\n && isJsonEqual(sequenceColumn.spec.axesSpec, column.spec.axesSpec)\n && Object.entries(sequenceColumn.spec.domain ?? {}).every((\n [key, value],\n ) => column.spec.domain?.[key] === value),\n ).map(({ columnId, spec }) => ({\n value: columnId,\n label: spec.annotations?.['pl7.app/label'] ?? 'Unlabelled column',\n }));\n}\n\nasync function getMultipleAlignmentData({\n pframe,\n sequenceColumnIds,\n labelColumnIds,\n markupColumnId,\n selection,\n colorScheme,\n alignmentParams,\n}: {\n pframe: PFrameHandle \| undefined;\n sequenceColumnIds: PObjectId[] \| undefined;\n labelColumnIds: PTableColumnId[] \| undefined;\n markupColumnId: PObjectId \| undefined;\n selection: PlSelectionModel \| undefined;\n colorScheme: PlMultiSequenceAlignmentColorSchemeOption;\n alignmentParams: PlMultiSequenceAlignmentSettings['alignmentParams'];\n}): Promise<MultipleAlignmentData \| undefined> {\n if (!pframe \|\| !sequenceColumnIds?.length \|\| !labelColumnIds) return;\n\n const pFrameDriver = getPFrameDriver();\n const columns = await pFrameDriver.listColumns(pframe);\n const linkerColumns = columns.filter((column) => isLinkerColumn(column.spec));\n\n const filterColumn = createRowSelectionColumn({ selection });\n\n // inner join of sequence columns\n let primaryEntry: JoinEntry<PObjectId> = {\n type: 'inner',\n entries: sequenceColumnIds.map((column) => ({\n type: 'column',\n column,\n })),\n };\n\n // if we have linkers, left join them\n if (linkerColumns.length > 0) {\n primaryEntry = {\n type: 'outer',\n primary: primaryEntry,\n secondary: linkerColumns.map(({ columnId }) => ({\n type: 'column',\n column: columnId,\n })),\n };\n }\n\n // inner join with filters\n if (filterColumn) {\n primaryEntry = {\n type: 'inner',\n entries: [\n primaryEntry,\n {\n type: 'inlineColumn',\n column: filterColumn,\n },\n ],\n };\n }\n\n // left join with labels\n const secondaryEntry: JoinEntry<PObjectId>[] = labelColumnIds\n .flatMap((column) => {\n if (column.type !== 'column') return [];\n return { type: 'column', column: column.id };\n });\n\n // and markup\n if (markupColumnId) {\n secondaryEntry.push({ type: 'column', column: markupColumnId });\n }\n\n const sorting: PTableSorting[] = Array.from(\n new Set(sequenceColumnIds.flatMap((id) => {\n const column = columns.find(({ columnId }) => columnId === id);\n if (!column) {\n throw new Error(`Couldn't find sequence column (ID: ${id})`);\n }\n return column.spec.axesSpec\n .map((spec) => canonicalizeJson(getAxisId(spec)));\n })),\n )\n .sort()\n .map((id) => ({\n column: { type: 'axis', id: parseJson(id) },\n ascending: true,\n naAndAbsentAreLeastValues: true,\n }));\n\n const request: CalculateTableDataRequest<PObjectId> = {\n src: {\n type: 'outer',\n primary: primaryEntry,\n secondary: secondaryEntry,\n },\n filters: [],\n sorting,\n };\n\n const table = await pFrameDriver.calculateTableData(\n pframe,\n JSON.parse(JSON.stringify(request)),\n {\n offset: 0,\n // +1 is a hack to check whether the selection is over the limit\n length: sequenceLimit + 1,\n },\n );\n\n let rowCount = table?.[0].data.data.length ?? 0;\n let exceedsLimit = false;\n if (rowCount > sequenceLimit) {\n rowCount = sequenceLimit;\n exceedsLimit = true;\n }\n\n const sequenceColumns = sequenceColumnIds.map((columnId) => {\n const column = table.find(({ spec }) => spec.id === columnId);\n if (!column) {\n throw new Error(`Couldn't find sequence column (ID: \\`${columnId}\\`).`);\n }\n return column;\n });\n\n const labelColumns = labelColumnIds.map((labelColumn) => {\n const column = table.find(({ spec }) => {\n if (labelColumn.type === 'axis' && spec.type === 'axis') {\n return isJsonEqual(labelColumn.id, spec.id);\n }\n if (labelColumn.type === 'column' && spec.type === 'column') {\n return labelColumn.id === spec.id;\n }\n });\n if (!column) {\n throw new Error(`Couldn't find label column (ID: \\`${labelColumn}\\`).`);\n }\n return column;\n });\n\n const markupColumn = markupColumnId\n && table.find(({ spec }) => spec.id === markupColumnId);\n\n const alignedSequences = await Promise.all(\n sequenceColumns.map((column) =>\n multiSequenceAlignment(\n Array.from(\n { length: rowCount },\n (_, row) =>\n pTableValue(column.data, row, { na: '', absent: '' })?.toString()\n ?? 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'Unlabelled column',\n }))\n .toArray();\n}\n\nasync function getMultipleAlignmentData({\n pframe,\n sequenceColumnIds,\n labelColumnIds,\n selection,\n colorScheme,\n alignmentParams,\n}: {\n pframe: PFrameHandle \| undefined;\n sequenceColumnIds: PObjectId[] \| undefined;\n labelColumnIds: PTableColumnId[] \| undefined;\n selection: PlSelectionModel \| undefined;\n colorScheme: PlMultiSequenceAlignmentColorSchemeOption;\n alignmentParams: PlMultiSequenceAlignmentSettings['alignmentParams'];\n}): Promise<MultipleAlignmentData \| undefined> {\n if (!pframe \|\| !sequenceColumnIds?.length \|\| !labelColumnIds) return;\n\n const pFrameDriver = getPFrameDriver();\n const columns = await pFrameDriver.listColumns(pframe);\n const linkerColumns = columns.filter((column) => isLinkerColumn(column.spec));\n\n const filterColumn = createRowSelectionColumn({ selection });\n\n // inner join of sequence columns\n let primaryEntry: JoinEntry<PObjectId> = {\n type: 'inner',\n entries: sequenceColumnIds.map((column) => ({\n type: 'column',\n column,\n })),\n };\n\n // if we have linkers, left join them\n if (linkerColumns.length > 0) {\n primaryEntry = {\n type: 'outer',\n primary: primaryEntry,\n secondary: linkerColumns.map(({ columnId }) => ({\n type: 'column',\n column: columnId,\n })),\n };\n }\n\n // inner join with filters\n if (filterColumn) {\n primaryEntry = {\n type: 'inner',\n entries: [\n primaryEntry,\n {\n type: 'inlineColumn',\n column: filterColumn,\n },\n ],\n };\n }\n\n // left join with labels\n const secondaryEntry: JoinEntry<PObjectId>[] = labelColumnIds\n .flatMap((column) => {\n if (column.type !== 'column') return [];\n return { type: 'column', column: column.id };\n });\n\n // and markup\n if (colorScheme.type === 'markup') {\n secondaryEntry.push({ type: 'column', column: colorScheme.columnId });\n }\n\n const sorting: PTableSorting[] = Array.from(\n new Set(\n sequenceColumnIds.values().flatMap((id) => {\n const column = columns.find(({ columnId }) => columnId === id);\n if (!column) {\n throw new Error(`Couldn't find sequence column (ID: ${id})`);\n }\n return column.spec.axesSpec\n .map((spec) => canonicalizeJson(getAxisId(spec)));\n }),\n ),\n )\n .sort()\n .map((id) => ({\n column: { type: 'axis', id: parseJson(id) },\n ascending: true,\n naAndAbsentAreLeastValues: true,\n }));\n\n const request: CalculateTableDataRequest<PObjectId> = {\n src: {\n type: 'outer',\n primary: primaryEntry,\n secondary: secondaryEntry,\n },\n filters: [],\n sorting,\n };\n\n const table = await pFrameDriver.calculateTableData(\n pframe,\n JSON.parse(JSON.stringify(request)),\n {\n offset: 0,\n // +1 is a hack to check whether the selection is over the limit\n length: sequenceLimit + 1,\n },\n );\n\n let rowCount = table?.[0].data.data.length ?? 0;\n let exceedsLimit = false;\n if (rowCount > sequenceLimit) {\n rowCount = sequenceLimit;\n exceedsLimit = true;\n }\n\n const sequenceColumns = sequenceColumnIds.map((columnId) => {\n const column = table.find(({ spec }) => spec.id === columnId);\n if (!column) {\n throw new Error(`Couldn't find sequence column (ID: \\`${columnId}\\`).`);\n }\n return column;\n });\n\n const labelColumns = labelColumnIds.map((labelColumn) => {\n const column = table.find(({ spec }) => {\n if (labelColumn.type === 'axis' && spec.type === 'axis') {\n return isJsonEqual(labelColumn.id, spec.id);\n }\n if (labelColumn.type === 'column' && spec.type === 'column') {\n return labelColumn.id === spec.id;\n }\n });\n if (!column) {\n throw new Error(`Couldn't find label column (ID: \\`${labelColumn}\\`).`);\n }\n return column;\n });\n\n const alignedSequences = await Promise.all(\n sequenceColumns.map((column) =>\n multiSequenceAlignment(\n Array.from(\n { length: rowCount },\n (_, row) =>\n pTableValue(column.data, row, { na: '', absent: '' })?.toString()\n ?? 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package/dist/components/PlMultiSequenceAlignment/markup.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import { ColorMap } from './types';
+import { HighlightLegend } from './types';
 export type Markup = {
     id: string;
     start: number;
@@ -6,10 +6,12 @@ export type Markup = {
 }[];
 export declare function parseMarkup(row: string): Markup;
 export declare function markupAlignedSequence(alignedSequence: string, markup: Markup): Markup;
-export declare function colorizeSequencesByMarkup({ markupRows, columnCount, colorMap }: {
+export declare function highlightByMarkup({ markupRows, columnCount, labels }: {
     markupRows: Markup[];
     columnCount: number;
-    colorMap: ColorMap;
-}): Promise<Blob>;
-export declare const markupColors: string[];
+    labels: Record<string, string>;
+}): {
+    blob: Blob;
+    legend: HighlightLegend;
+};
 //# sourceMappingURL=markup.d.ts.map

package/dist/components/PlMultiSequenceAlignment/markup.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"markup.d.ts","sourceRoot":"","sources":["../../../src/components/PlMultiSequenceAlignment/markup.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,SAAS,CAAC;AAE/C,MAAM,MAAM,MAAM,GAAG;IAAE,EAAE,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,EAAE,CAAC;AAErE,wBAAgB,WAAW,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAmB/C;AAED,wBAAgB,qBAAqB,CACnC,eAAe,EAAE,MAAM,EACvB,MAAM,EAAE,MAAM,GACb,MAAM,CAkBR;AAED,wBAAgB,iBAAiB,CAC/B,EAAE,UAAU,EAAE,WAAW,EAAE,MAAM,EAAE,EAAE;IACnC,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAChC,GACA;IAAE,IAAI,EAAE,IAAI,CAAC;IAAC,MAAM,EAAE,eAAe,CAAA;CAAE,CA4CzC"}

package/dist/components/PlMultiSequenceAlignment/markup.js CHANGED Viewed

@@ -1,40 +1,62 @@
-function l(e) {
-  return Array.from(e.matchAll(
+function E(o) {
+  return Array.from(o.matchAll(
     /(?<id>[^:]*):(?<start>[0-9A-Za-z]*)(?:\+(?<length>[0-9A-Za-z]*))?\|?/g
-  )).map((o) => {
-    const n = o.groups, s = Number.parseInt(n.start, 36), t = n.length ? Number.parseInt(n.length, 36) : 0;
+  )).map((l) => {
+    const r = l.groups, n = Number.parseInt(r.start, 36), t = r.length ? Number.parseInt(r.length, 36) : 0;
     return {
-      id: n.id,
-      start: s,
+      id: r.id,
+      start: n,
       length: t
     };
   });
 }
-function i(e, o) {
-  const n = e.split("").reduce(
-    (t, r, F) => (r !== "-" && t.push(F), t),
+function f(o, l) {
+  const r = o.split("").reduce(
+    (t, a, e) => (a !== "-" && t.push(e), t),
     []
   );
-  return o.map((t) => {
-    const r = n[t.start], F = n[t.start + t.length - 1] + 1;
+  return l.map((t) => {
+    const a = r[t.start], e = r[t.start + t.length - 1] + 1;
     return {
       id: t.id,
-      start: r,
-      length: F - r
+      start: a,
+      length: e - a
     };
   });
 }
-function E({ markupRows: e, columnCount: o, colorMap: n }) {
-  var r;
-  const s = new OffscreenCanvas(o, e.length), t = s.getContext("2d");
-  for (const [F, u] of e.entries())
-    for (const c of u) {
-      const a = (r = n[c.id]) == null ? void 0 : r.color;
-      a && (t.fillStyle = a, t.fillRect(c.start, F, c.length, 1));
+function C({ markupRows: o, columnCount: l, labels: r }) {
+  const n = /* @__PURE__ */ new Map();
+  for (const [e, F] of o.entries())
+    for (const { id: s, start: u, length: c } of F) {
+      let i = n.get(s);
+      i || n.set(s, i = []), i.push({ row: e, start: u, length: c });
     }
-  return s.convertToBlob();
+  const t = Object.fromEntries(
+    Object.entries(r).filter(([e]) => n.has(e)).map(([e, F], s) => [
+      e,
+      {
+        label: F,
+        color: g[s % g.length]
+      }
+    ])
+  );
+  return { blob: new Blob(
+    function* () {
+      yield `<svg xmlns="http://www.w3.org/2000/svg" viewBox="${`0 0 ${l} ${o.length * 2}`}" stroke-width="2" preserveAspectRatio="none">`;
+      for (const [F, s] of n) {
+        const { color: u } = t[F];
+        yield `<path stroke="${u}" d="`;
+        let c = 0, i = 0;
+        for (const { row: d, start: p, length: h } of s)
+          yield `m${p - c},${d * 2 + 1 - i}h${h}`, c = p + h, i = d * 2 + 1;
+        yield '"/>';
+      }
+      yield "</svg>";
+    }().toArray(),
+    { type: "image/svg+xml" }
+  ), legend: t };
 }
-const C = [
+const g = [
   "#E5F2FF",
   "#FFE8E8",
   "#F0EBFF",
@@ -53,9 +75,8 @@ const C = [
   "#DEEEEF"
 ];
 export {
-  E as colorizeSequencesByMarkup,
-  i as markupAlignedSequence,
-  C as markupColors,
-  l as parseMarkup
+  C as highlightByMarkup,
+  f as markupAlignedSequence,
+  E as parseMarkup
 };
 //# sourceMappingURL=markup.js.map

package/dist/components/PlMultiSequenceAlignment/markup.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"markup.js","sources":["../../../src/components/PlMultiSequenceAlignment/markup.ts"],"sourcesContent":["import type { ~~ColorMap~~ } from './types';\n\nexport type Markup = { id: string; start: number; length: number }[];\n\nexport function parseMarkup(row: string): Markup {\n return Array.from(row.matchAll(\n /(?<id>[^:]):(?<start>[0-9A-Za-z])(?:\\+(?<length>[0-9A-Za-z]*))?\\\|?/g,\n )).map((match) => {\n const matchGroups = match.groups as {\n id: string;\n start: string;\n length: string \| undefined;\n };\n const start = Number.parseInt(matchGroups.start, 36);\n const length = matchGroups.length\n ? Number.parseInt(matchGroups.length, 36)\n : 0;\n return {\n id: matchGroups.id,\n start,\n length,\n };\n });\n}\n\nexport function markupAlignedSequence(\n alignedSequence: string,\n markup: Markup,\n): Markup {\n const indexMap = alignedSequence.split('').reduce<number[]>(\n (acc, char, index) => {\n if (char !== '-') acc.push(index);\n return acc;\n },\n [],\n );\n const adjusted = markup.map((segment) => {\n const start = indexMap[segment.start];\n const end = indexMap[segment.start + segment.length - 1] + 1;\n return {\n id: segment.id,\n start: start,\n length: end - start,\n };\n });\n return adjusted;\n}\n\nexport function ~~colorizeSequencesByMarkup~~(\n { markupRows, columnCount, ~~colorMap~~ }: {\n markupRows: Markup[];\n columnCount: number;\n ~~colorMap~~: ~~ColorMap;\~~n },\n): ~~Promise<~~Blob> {\n const ~~canvas~~ = ~~new~~ ~~OffscreenCanvas(columnCount,~~ ~~markupRows.~~length);\n ~~const~~ ~~context~~ = ~~canvas.getContext~~(~~'2d'~~)~~!;\~~n for (const [~~rowIndex~~, markup] of markupRows.entries()) {\n for (const ~~segment~~ of markup) {\n ~~const~~ ~~color~~ = ~~colorMap[segment~~.id~~]?.color~~;\n if (!~~color~~) ~~continue~~;\n ~~context~~.~~fillStyle~~ = ~~color~~;\n ~~context~~.~~fillRect~~(~~segment~~.~~start~~, ~~rowIndex~~, ~~segment~~.length, 1);\n }\n }\n ~~return~~ ~~canvas~~.~~convertToBlob~~();\n}\n\~~nexport~~ ~~const~~ markupColors = [\n '#E5F2FF',\n '#FFE8E8',\n '#F0EBFF',\n '#FFFFE3',\n '#E5F7E5',\n '#FEEAFE',\n '#FDEED6',\n '#E8FDFE',\n '#CCDFF2',\n '#F2CCCD',\n '#D5CCF2',\n '#F2F2CC',\n '#CCF2CC',\n '#F2CCF2',\n '#EFDDBF',\n '#DEEEEF',\n];\n\nif (import.meta.vitest) {\n const { test, expect } = import.meta.vitest;\n test('annotateAlignedRow', () => {\n const alignedSequence\n = 'EVRLVESGGALVQPGGSLRLSCVAASGFTFINNWVTWVRQAPGKGLEWVANIKEDGSQKYYVDSVKGRFTISRDNAEKSVYLQMSSLRVDDTAVYYCAR------------GRAV----D---QWGQGTLVTVSS';\n // 0 10 20 30 40 50 60 70 80 90 100 110 120 130\n // EVRLVESGGALVQPGGSLRLSCVAASGFTFINNWVTWVRQAPGKGLEWVANIKEDGSQKYYVDSVKGRFTISRDNAEKSVYLQMSSLRVDDTAVYYCARGRAVDQWGQGTLVTVSS\n const markup = [\n { id: '1', start: 0, length: 99 },\n { id: '2', start: 99, length: 3 },\n { id: '3', start: 102, length: 14 },\n ];\n const alignedMarkup = markupAlignedSequence(alignedSequence, markup);\n expect(alignedMarkup).toEqual([\n { id: '1', start: 0, length: 99 },\n { id: '2', start: 111, length: 3 },\n { id: '3', start: 114, length: 21 },\n ]);\n });\n}\n"],"names":["parseMarkup","row","match","matchGroups","start","length","markupAlignedSequence","alignedSequence","markup","indexMap","acc","char","index","segment","end","~~colorizeSequencesByMarkup~~","markupRows","columnCount","~~colorMap~~","_a","~~canvas~~","~~context~~","~~rowIndex~~","~~color~~","markupColors"],"mappings":"AAIO,SAASA,EAAYC,GAAqB;AACxC,SAAA,MAAM,KAAKA,EAAI;AAAA,IACpB;AAAA,EAAA,CACD,EAAE,IAAI,CAACC,MAAU;AAChB,UAAMC,IAAcD,EAAM,QAKpBE,IAAQ,OAAO,SAASD,EAAY,OAAO,EAAE,GAC7CE,IAASF,EAAY,SACvB,OAAO,SAASA,EAAY,QAAQ,EAAE,IACtC;AACG,WAAA;AAAA,MACL,IAAIA,EAAY;AAAA,MAChB,OAAAC;AAAA,MACA,QAAAC;AAAA,IACF;AAAA,EAAA,CACD;AACH;AAEgB,SAAAC,EACdC,GACAC,GACQ;AACR,QAAMC,IAAWF,EAAgB,MAAM,EAAE,EAAE;AAAA,IACzC,CAACG,GAAKC,GAAMC,OACND,MAAS,OAASD,EAAA,KAAKE,CAAK,GACzBF;AAAA,IAET,CAAA;AAAA,EACF;AAUO,SATUF,EAAO,IAAI,CAACK,MAAY;AACjC,UAAAT,IAAQK,EAASI,EAAQ,KAAK,GAC9BC,IAAML,EAASI,EAAQ,QAAQA,EAAQ,SAAS,CAAC,IAAI;AACpD,WAAA;AAAA,MACL,IAAIA,EAAQ;AAAA,MACZ,OAAAT;AAAA,MACA,QAAQU,IAAMV;AAAA,IAChB;AAAA,EAAA,CACD;AAEH;AAEO,SAASW,EACd,EAAE,YAAAC,GAAY,aAAAC,GAAa,~~UAAAC~~,~~KAKZ~~;~~AAlDV~~,~~MAAAC~~;~~AAmDL~~,~~QAAMC~~,IAAS,IAAI,~~gBAAgBH~~,~~GAAaD~~,~~EAAW~~,MAAM,~~GAC3DK~~,~~IAAUD~~,~~EAAO~~,~~WAAW~~,IAAI;~~AACtC~~,~~aAAW~~,~~CAACE~~,~~GAAUd~~,~~CAAM~~,~~KAAKQ~~,EAAW;~~AAC1C~~,~~eAAWH~~,~~KAAWL~~,~~GAAQ~~;~~AAC5B~~,~~YAAMe~~,~~KAAQJ~~,~~IAAAD~~,~~EAASL~~,~~EAAQ~~,EAAE,~~MAAnB~~,~~gBAAAM~~,~~EAAsB~~;~~AACpC~~,~~MAAKI~~,~~MACLF~~,~~EAAQ~~,~~YAAYE~~,~~GACpBF~~,~~EAAQ~~,~~SAASR~~,~~EAAQ~~,~~OAAOS~~,~~GAAUT~~,~~EAAQ~~,~~QAAQ~~,~~CAAC~~;AAAA,~~IAAA~~;~~AAG/D~~,~~SAAOO~~,~~EAAO~~,~~cAAc~~;~~AAC9B~~;~~AAEO~~,~~MAAMI~~,IAAe;AAAA,~~EAC1B~~;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACF;"}
1	+ {"version":3,"file":"markup.js","sources":["../../../src/components/PlMultiSequenceAlignment/markup.ts"],"sourcesContent":["import type { HighlightLegend } from './types';\n\nexport type Markup = { id: string; start: number; length: number }[];\n\nexport function parseMarkup(row: string): Markup {\n return Array.from(row.matchAll(\n /(?<id>[^:]):(?<start>[0-9A-Za-z])(?:\\+(?<length>[0-9A-Za-z]))?\\\|?/g,\n )).map((match) => {\n const matchGroups = match.groups as {\n id: string;\n start: string;\n length: string \| undefined;\n };\n const start = Number.parseInt(matchGroups.start, 36);\n const length = matchGroups.length\n ? Number.parseInt(matchGroups.length, 36)\n : 0;\n return {\n id: matchGroups.id,\n start,\n length,\n };\n });\n}\n\nexport function markupAlignedSequence(\n alignedSequence: string,\n markup: Markup,\n): Markup {\n const indexMap = alignedSequence.split('').reduce<number[]>(\n (acc, char, index) => {\n if (char !== '-') acc.push(index);\n return acc;\n },\n [],\n );\n const adjusted = markup.map((segment) => {\n const start = indexMap[segment.start];\n const end = indexMap[segment.start + segment.length - 1] + 1;\n return {\n id: segment.id,\n start: start,\n length: end - start,\n };\n });\n return adjusted;\n}\n\nexport function highlightByMarkup(\n { markupRows, columnCount, labels }: {\n markupRows: Markup[];\n columnCount: number;\n labels: Record<string, string>;\n },\n): { blob: Blob; legend: HighlightLegend } {\n const linesById: Map<string, {\n row: number;\n start: number;\n length: number;\n }[]> = new Map();\n for (const [row, markup] of markupRows.entries()) {\n for (const { id, start, length } of markup) {\n let bucket = linesById.get(id);\n if (!bucket) linesById.set(id, bucket = []);\n bucket.push({ row, start, length });\n }\n }\n const legend: HighlightLegend = Object.fromEntries(\n Object.entries(labels)\n .filter(([id]) => linesById.has(id))\n .map(([id, label], index) => [\n id,\n {\n label,\n color: markupColors[index % markupColors.length],\n },\n ]),\n );\n const blob = new Blob(\n (function() {\n const viewBox = `0 0 ${columnCount} ${markupRows.length * 2}`;\n yield `<svg xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"${viewBox}\" stroke-width=\"2\" preserveAspectRatio=\"none\">`;\n for (const [id, lines] of linesById) {\n const { color } = legend[id];\n yield `<path stroke=\"${color}\" d=\"`;\n let x = 0, y = 0;\n for (const { row, start, length } of lines) {\n yield `m${start - x},${row * 2 + 1 - y}h${length}`;\n x = start + length;\n y = row * 2 + 1;\n }\n yield '\"/>';\n }\n yield '</svg>';\n })().toArray(),\n { type: 'image/svg+xml' },\n );\n return { blob, legend };\n}\n\nconst markupColors = [\n '#E5F2FF',\n '#FFE8E8',\n '#F0EBFF',\n '#FFFFE3',\n '#E5F7E5',\n '#FEEAFE',\n '#FDEED6',\n '#E8FDFE',\n '#CCDFF2',\n '#F2CCCD',\n '#D5CCF2',\n '#F2F2CC',\n '#CCF2CC',\n '#F2CCF2',\n '#EFDDBF',\n '#DEEEEF',\n];\n\nif (import.meta.vitest) {\n const { test, expect } = import.meta.vitest;\n test('annotateAlignedRow', () => {\n const alignedSequence\n = 'EVRLVESGGALVQPGGSLRLSCVAASGFTFINNWVTWVRQAPGKGLEWVANIKEDGSQKYYVDSVKGRFTISRDNAEKSVYLQMSSLRVDDTAVYYCAR------------GRAV----D---QWGQGTLVTVSS';\n // 0 10 20 30 40 50 60 70 80 90 100 110 120 130\n // EVRLVESGGALVQPGGSLRLSCVAASGFTFINNWVTWVRQAPGKGLEWVANIKEDGSQKYYVDSVKGRFTISRDNAEKSVYLQMSSLRVDDTAVYYCARGRAVDQWGQGTLVTVSS\n const markup = [\n { id: '1', start: 0, length: 99 },\n { id: '2', start: 99, length: 3 },\n { id: '3', start: 102, length: 14 },\n ];\n const alignedMarkup = markupAlignedSequence(alignedSequence, markup);\n expect(alignedMarkup).toEqual([\n { id: '1', start: 0, length: 99 },\n { id: '2', start: 111, length: 3 },\n { id: '3', start: 114, length: 21 },\n ]);\n });\n}\n"],"names":["parseMarkup","row","match","matchGroups","start","length","markupAlignedSequence","alignedSequence","markup","indexMap","acc","char","index","segment","end","highlightByMarkup","markupRows","columnCount","labels","linesById","id","bucket","legend","label","markupColors","lines","color","x","y"],"mappings":"AAIO,SAASA,EAAYC,GAAqB;AACxC,SAAA,MAAM,KAAKA,EAAI;AAAA,IACpB;AAAA,EAAA,CACD,EAAE,IAAI,CAACC,MAAU;AAChB,UAAMC,IAAcD,EAAM,QAKpBE,IAAQ,OAAO,SAASD,EAAY,OAAO,EAAE,GAC7CE,IAASF,EAAY,SACvB,OAAO,SAASA,EAAY,QAAQ,EAAE,IACtC;AACG,WAAA;AAAA,MACL,IAAIA,EAAY;AAAA,MAChB,OAAAC;AAAA,MACA,QAAAC;AAAA,IACF;AAAA,EAAA,CACD;AACH;AAEgB,SAAAC,EACdC,GACAC,GACQ;AACR,QAAMC,IAAWF,EAAgB,MAAM,EAAE,EAAE;AAAA,IACzC,CAACG,GAAKC,GAAMC,OACND,MAAS,OAASD,EAAA,KAAKE,CAAK,GACzBF;AAAA,IAET,CAAA;AAAA,EACF;AAUO,SATUF,EAAO,IAAI,CAACK,MAAY;AACjC,UAAAT,IAAQK,EAASI,EAAQ,KAAK,GAC9BC,IAAML,EAASI,EAAQ,QAAQA,EAAQ,SAAS,CAAC,IAAI;AACpD,WAAA;AAAA,MACL,IAAIA,EAAQ;AAAA,MACZ,OAAAT;AAAA,MACA,QAAQU,IAAMV;AAAA,IAChB;AAAA,EAAA,CACD;AAEH;AAEO,SAASW,EACd,EAAE,YAAAC,GAAY,aAAAC,GAAa,QAAAC,KAKc;AACnC,QAAAC,wBAIK,IAAI;AACf,aAAW,CAAClB,GAAKO,CAAM,KAAKQ,EAAW;AACrC,eAAW,EAAE,IAAAI,GAAI,OAAAhB,GAAO,QAAAC,EAAA,KAAYG,GAAQ;AACtC,UAAAa,IAASF,EAAU,IAAIC,CAAE;AAC7B,MAAKC,KAAQF,EAAU,IAAIC,GAAIC,IAAS,EAAE,GAC1CA,EAAO,KAAK,EAAE,KAAApB,GAAK,OAAAG,GAAO,QAAAC,GAAQ;AAAA,IAAA;AAGtC,QAAMiB,IAA0B,OAAO;AAAA,IACrC,OAAO,QAAQJ,CAAM,EAClB,OAAO,CAAC,CAACE,CAAE,MAAMD,EAAU,IAAIC,CAAE,CAAC,EAClC,IAAI,CAAC,CAACA,GAAIG,CAAK,GAAGX,MAAU;AAAA,MAC3BQ;AAAA,MACA;AAAA,QACE,OAAAG;AAAA,QACA,OAAOC,EAAaZ,IAAQY,EAAa,MAAM;AAAA,MAAA;AAAA,IAElD,CAAA;AAAA,EACL;AAoBO,SAAA,EAAE,MAnBI,IAAI;AAAA,IACd,aAAY;AAEX,YAAM,oDADU,OAAOP,CAAW,IAAID,EAAW,SAAS,CAAC,EACM;AACjE,iBAAW,CAACI,GAAIK,CAAK,KAAKN,GAAW;AACnC,cAAM,EAAE,OAAAO,EAAA,IAAUJ,EAAOF,CAAE;AAC3B,cAAM,iBAAiBM,CAAK;AACxB,YAAAC,IAAI,GAAGC,IAAI;AACf,mBAAW,EAAE,KAAA3B,GAAK,OAAAG,GAAO,QAAAC,EAAA,KAAYoB;AAC7B,gBAAA,IAAIrB,IAAQuB,CAAC,IAAI1B,IAAM,IAAI,IAAI2B,CAAC,IAAIvB,CAAM,IAChDsB,IAAIvB,IAAQC,GACZuB,IAAI3B,IAAM,IAAI;AAEV,cAAA;AAAA,MAAA;AAEF,YAAA;AAAA,IACR,EAAA,EAAK,QAAQ;AAAA,IACb,EAAE,MAAM,gBAAgB;AAAA,EAC1B,GACe,QAAAqB,EAAO;AACxB;AAEA,MAAME,IAAe;AAAA,EACnB;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACF;"}

package/dist/components/PlMultiSequenceAlignment/types.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-export type ColorMap = Record<string, {
+export type HighlightLegend = Record<string, {
     label: string;
     color: string;
 }>;

package/dist/components/PlMultiSequenceAlignment/types.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/lib/ui/uikit/dist/components/PlAccordion/{ExpandTransition.vue.js → ExpandTransition.vue2.js} RENAMED Viewed

@@ -24,4 +24,4 @@ const f = /* @__PURE__ */ n({
 export {
   f as default
 };
-//# sourceMappingURL=ExpandTransition.vue.js.map
+//# sourceMappingURL=ExpandTransition.vue2.js.map

package/dist/lib/ui/uikit/dist/components/PlAccordion/ExpandTransition.vue2.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"ExpandTransition.vue2.js","sources":["../../../../../../../../../lib/ui/uikit/src/components/PlAccordion/ExpandTransition.vue"],"sourcesContent":["<script lang=\"ts\" setup>\nconst onStart = (el: Element) => {\n el.classList.add('expand-collapse-fix');\n (el as HTMLElement).style.setProperty('--component-height', el.scrollHeight + 'px');\n};\n\nconst onAfter = (el: Element) => {\n (el as HTMLElement).style.removeProperty('--component-height');\n el.classList.remove('expand-collapse-fix');\n};\n</script>\n\n<template>\n <Transition name=\"expand-collapse\" @enter=\"onStart\" @leave=\"onStart\" @after-enter=\"onAfter\" @after-leave=\"onAfter\">\n <slot/>\n </Transition>\n</template>\n\n<style>\n.expand-collapse-fix {\n overflow: hidden;\n}\n\n.expand-collapse-enter-active,\n.expand-collapse-leave-active {\n transition:\n height 0.2s ease-in-out,\n opacity 0.2s ease-in-out;\n height: var(--component-height);\n}\n\n.expand-collapse-enter-from,\n.expand-collapse-leave-to {\n opacity: 0.5;\n height: 0;\n}\n</style>\n"],"names":["onStart","el","onAfter"],"mappings":";;;;AACMA,UAAAA,IAAU,CAACC,MAAgB;AAC5BA,QAAA,UAAU,IAAI,qBAAqB,GACrCA,EAAmB,MAAM,YAAY,sBAAsBA,EAAG,eAAe,IAAI;AAAA,IAAA,GAG9EC,IAAU,CAACD,MAAgB;AAC9BA,QAAmB,MAAM,eAAe,oBAAoB,GAC1DA,EAAA,UAAU,OAAO,qBAAqB;AAAA,IAC3C;;;;;;;;;;;;;;;"}

package/dist/lib/ui/uikit/dist/components/PlAccordion/PlAccordionSection.vue2.js CHANGED Viewed

@@ -2,7 +2,7 @@ import { defineComponent as x, mergeModels as g, inject as d, toRef as u, useMod
 import { uniqueId as w } from "../../lib/util/helpers/dist/index.js";
 import B from "../PlIcon16/PlIcon16.vue.js";
 import N from "../PlSectionSeparator/PlSectionSeparator.vue.js";
-import _ from "./ExpandTransition.vue.js";
+import _ from "./ExpandTransition.vue2.js";
 (function() {
   try {
     if (typeof document < "u") {