@jbrowse/plugin-sequence 3.5.0 → 3.6.0

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Files changed (9) hide show
  1. package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts +1 -3
  2. package/dist/DivSequenceRenderer/components/DivSequenceRendering.js +16 -13
  3. package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js +8 -1
  4. package/dist/LinearReferenceSequenceDisplay/model.d.ts +1 -0
  5. package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts +1 -3
  6. package/esm/DivSequenceRenderer/components/DivSequenceRendering.js +16 -13
  7. package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js +8 -1
  8. package/esm/LinearReferenceSequenceDisplay/model.d.ts +1 -0
  9. package/package.json +5 -5
package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts CHANGED
@@ -1,7 +1,6 @@
1
1
  import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
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  import type { Feature, Region } from '@jbrowse/core/util';
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- import type { Theme } from '@mui/material';
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- declare const DivSequenceRendering: ({ exportSVG, features, regions, colorByCDS, bpPerPx, rowHeight, sequenceHeight, theme, showForward, showReverse, showTranslation, }: {
3
+ declare const DivSequenceRendering: ({ exportSVG, features, regions, colorByCDS, bpPerPx, rowHeight, sequenceHeight, showForward, showReverse, showTranslation, }: {
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  exportSVG?: {
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  rasterizeLayers: boolean;
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  };
@@ -12,7 +11,6 @@ declare const DivSequenceRendering: ({ exportSVG, features, regions, colorByCDS,
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  rowHeight: number;
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  sequenceHeight: number;
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  config: AnyConfigurationModel;
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- theme?: Theme;
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  showForward?: boolean;
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  showReverse?: boolean;
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  showTranslation?: boolean;
package/dist/DivSequenceRenderer/components/DivSequenceRendering.js CHANGED
@@ -2,14 +2,15 @@
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  Object.defineProperty(exports, "__esModule", { value: true });
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  const jsx_runtime_1 = require("react/jsx-runtime");
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  const react_1 = require("react");
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- const ui_1 = require("@jbrowse/core/ui");
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  const util_1 = require("@jbrowse/core/util");
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+ const material_1 = require("@mui/material");
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  const mobx_react_1 = require("mobx-react");
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- function Translation({ codonTable, seq, frame, width, bpPerPx, colorByCDS, region, seqStart, height, y, reverse = false, theme, }) {
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+ function Translation({ codonTable, seq, frame, width, bpPerPx, colorByCDS, region, seqStart, height, y, reverse = false, }) {
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  var _a, _b;
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  const normalizedFrame = Math.abs(frame) - 1;
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  const seqFrame = seqStart % 3;
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  const frameShift = (normalizedFrame - seqFrame + 3) % 3;
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+ const theme = (0, material_1.useTheme)();
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  const frameShiftAdjustedSeqLength = seq.length - frameShift;
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  const multipleOfThreeLength = frameShiftAdjustedSeqLength - (frameShiftAdjustedSeqLength % 3);
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  const seqSliced = seq.slice(frameShift, frameShift + multipleOfThreeLength);
@@ -28,25 +29,26 @@ function Translation({ codonTable, seq, frame, width, bpPerPx, colorByCDS, regio
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  const frameOffset = frameShift / bpPerPx;
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  const startOffset = (region.start - seqStart) / bpPerPx;
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  const offset = frameOffset - startOffset;
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+ const dark = theme.palette.mode === 'dark' ? 'dark' : 'main';
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  const defaultFill = colorByCDS
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- ? (_a = theme === null || theme === void 0 ? void 0 : theme.palette.framesCDS.at(frame)) === null || _a === void 0 ? void 0 : _a.main
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- : (_b = theme === null || theme === void 0 ? void 0 : theme.palette.frames.at(frame)) === null || _b === void 0 ? void 0 : _b.main;
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+ ? (_a = theme.palette.framesCDS.at(frame)) === null || _a === void 0 ? void 0 : _a[dark]
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+ : (_b = theme.palette.frames.at(frame)) === null || _b === void 0 ? void 0 : _b[dark];
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  return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("rect", { x: 0, y: y, width: width, height: height, fill: defaultFill }), translated.map((element, index) => {
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  const x = region.reversed
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  ? width - (index + 1) * codonWidth - offset
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  : codonWidth * index + offset;
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  const { letter, codon } = element;
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  const codonFill = util_1.defaultStarts.includes(codon)
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- ? theme === null || theme === void 0 ? void 0 : theme.palette.startCodon
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+ ? theme.palette.startCodon
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  : util_1.defaultStops.includes(codon)
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- ? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
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+ ? theme.palette.stopCodon
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  : undefined;
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  return !(renderLetter || codonFill) ? null : ((0, jsx_runtime_1.jsxs)(react_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("rect", { x: x, y: y, width: renderLetter
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  ? codonWidth
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  : codonWidth + 0.7, height: height, stroke: renderLetter ? '#555' : 'none', fill: codonFill || 'none' }), renderLetter ? ((0, jsx_runtime_1.jsx)("text", { x: x + codonWidth / 2, fontSize: height - 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", children: letter })) : null] }, `${index}-${letter}`));
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  })] }));
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  }
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- function Sequence({ bpPerPx, region, feature, sequenceType, theme, height, seq, y, }) {
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+ function Sequence({ bpPerPx, region, feature, sequenceType, height, seq, y, }) {
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  const render = 1 / bpPerPx >= 12;
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  const s = feature.get('start');
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  const e = feature.get('end');
@@ -54,18 +56,19 @@ function Sequence({ bpPerPx, region, feature, sequenceType, theme, height, seq,
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  const reverse = region.reversed;
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  const len = e - s;
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  const w = Math.max((rightPx - leftPx) / len, 0.8);
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+ const theme = (0, material_1.useTheme)();
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  return ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: seq.split('').map((letter, index) => {
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  const color = sequenceType === 'dna'
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  ?
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  theme.palette.bases[letter.toUpperCase()]
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  : undefined;
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+ const dark = theme.palette.mode === 'dark';
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  const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
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- return ((0, jsx_runtime_1.jsxs)(react_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("rect", { x: x, y: y, width: w, height: height, fill: color ? color.main : '#aaa', stroke: render ? '#555' : 'none' }), render ? ((0, jsx_runtime_1.jsx)("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fontSize: height - 2, fill: color ? theme.palette.getContrastText(color.main) : 'black', children: letter })) : null] }, `${letter}-${index}`));
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+ return ((0, jsx_runtime_1.jsxs)(react_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("rect", { x: x, y: y, width: w, height: height, fill: color ? (dark ? color.dark : color.main) : '#aaa', stroke: render ? '#555' : 'none' }), render ? ((0, jsx_runtime_1.jsx)("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fontSize: height - 2, fill: color ? theme.palette.getContrastText(color.main) : 'black', children: letter })) : null] }, `${letter}-${index}`));
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  }) }));
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  }
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- function SequenceSVG({ regions, width, theme: configTheme, colorByCDS, features = new Map(), showReverse = true, showForward = true, showTranslation = true, sequenceType = 'dna', bpPerPx, rowHeight, }) {
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+ function SequenceSVG({ regions, width, colorByCDS, features = new Map(), showReverse = true, showForward = true, showTranslation = true, sequenceType = 'dna', bpPerPx, rowHeight, }) {
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  const region = regions[0];
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- const theme = (0, ui_1.createJBrowseTheme)(configTheme);
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  const codonTable = (0, util_1.generateCodonTable)(util_1.defaultCodonTable);
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  const [feature] = [...features.values()];
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  if (!feature) {
@@ -82,7 +85,7 @@ function SequenceSVG({ regions, width, theme: configTheme, colorByCDS, features
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  const [topFrames, bottomFrames] = region.reversed
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  ? [reverseFrames.toReversed(), forwardFrames.toReversed()]
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  : [forwardFrames, reverseFrames];
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- return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [topFrames.map(index => ((0, jsx_runtime_1.jsx)(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), theme: theme, height: rowHeight, reverse: region.reversed }, `translation-${index}`))), showForward && showSequence ? ((0, jsx_runtime_1.jsx)(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? (0, util_1.complement)(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null, showReverse && showSequence ? ((0, jsx_runtime_1.jsx)(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : (0, util_1.complement)(seq), bpPerPx: bpPerPx, theme: theme })) : null, bottomFrames.map(index => ((0, jsx_runtime_1.jsx)(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), theme: theme, height: rowHeight, reverse: !region.reversed }, `rev-translation-${index}`)))] }));
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+ return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [topFrames.map(index => ((0, jsx_runtime_1.jsx)(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), height: rowHeight, reverse: region.reversed }, `translation-${index}`))), showForward && showSequence ? ((0, jsx_runtime_1.jsx)(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? (0, util_1.complement)(seq) : seq, bpPerPx: bpPerPx })) : null, showReverse && showSequence ? ((0, jsx_runtime_1.jsx)(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : (0, util_1.complement)(seq), bpPerPx: bpPerPx })) : null, bottomFrames.map(index => ((0, jsx_runtime_1.jsx)(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), height: rowHeight, reverse: !region.reversed }, `rev-translation-${index}`)))] }));
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  }
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  function Wrapper({ exportSVG, width, totalHeight, children, }) {
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  return exportSVG ? (children) : ((0, jsx_runtime_1.jsx)("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
@@ -92,9 +95,9 @@ function Wrapper({ exportSVG, width, totalHeight, children, }) {
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  userSelect: 'none',
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  }, children: children }));
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  }
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- const DivSequenceRendering = (0, mobx_react_1.observer)(function ({ exportSVG, features, regions, colorByCDS, bpPerPx, rowHeight, sequenceHeight, theme, showForward, showReverse, showTranslation, }) {
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+ const DivSequenceRendering = (0, mobx_react_1.observer)(function ({ exportSVG, features, regions, colorByCDS, bpPerPx, rowHeight, sequenceHeight, showForward, showReverse, showTranslation, }) {
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  const region = regions[0];
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  const width = Math.ceil((region.end - region.start) / bpPerPx);
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- return ((0, jsx_runtime_1.jsx)(Wrapper, { exportSVG: exportSVG, totalHeight: sequenceHeight, width: width, children: (0, jsx_runtime_1.jsx)(SequenceSVG, { width: width, showReverse: showReverse, showForward: showForward, theme: theme, showTranslation: showTranslation, colorByCDS: colorByCDS, bpPerPx: bpPerPx, rowHeight: rowHeight, features: features, regions: regions }) }));
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+ return ((0, jsx_runtime_1.jsx)(Wrapper, { exportSVG: exportSVG, totalHeight: sequenceHeight, width: width, children: (0, jsx_runtime_1.jsx)(SequenceSVG, { width: width, showReverse: showReverse, showForward: showForward, showTranslation: showTranslation, colorByCDS: colorByCDS, bpPerPx: bpPerPx, rowHeight: rowHeight, features: features, regions: regions }) }));
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  });
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  exports.default = DivSequenceRendering;
package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js CHANGED
@@ -79,7 +79,14 @@ class IndexedFastaAdapter extends BaseAdapter_1.BaseSequenceAdapter {
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  end: chunkStart + chunkSize,
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  };
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  (0, stopToken_1.checkStopToken)(stopToken);
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- chunks.push(await this.seqCache.get(JSON.stringify(r), { ...r, fasta }));
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+ const res = await this.seqCache.get(JSON.stringify(r), {
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+ ...r,
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+ fasta,
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+ });
86
+ if (!res) {
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+ break;
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+ }
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+ chunks.push(res);
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  }
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  const seq = chunks
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  .filter(f => !!f)
package/dist/LinearReferenceSequenceDisplay/model.d.ts CHANGED
@@ -184,6 +184,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  readonly renderDelay: number;
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  readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
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  readonly selectedFeatureId: string | undefined;
187
+ copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
187
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  } & {
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  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
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  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
package/esm/DivSequenceRenderer/components/DivSequenceRendering.d.ts CHANGED
@@ -1,7 +1,6 @@
1
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  import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
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  import type { Feature, Region } from '@jbrowse/core/util';
3
- import type { Theme } from '@mui/material';
4
- declare const DivSequenceRendering: ({ exportSVG, features, regions, colorByCDS, bpPerPx, rowHeight, sequenceHeight, theme, showForward, showReverse, showTranslation, }: {
3
+ declare const DivSequenceRendering: ({ exportSVG, features, regions, colorByCDS, bpPerPx, rowHeight, sequenceHeight, showForward, showReverse, showTranslation, }: {
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4
  exportSVG?: {
6
5
  rasterizeLayers: boolean;
7
6
  };
@@ -12,7 +11,6 @@ declare const DivSequenceRendering: ({ exportSVG, features, regions, colorByCDS,
12
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  rowHeight: number;
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  sequenceHeight: number;
14
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  config: AnyConfigurationModel;
15
- theme?: Theme;
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  showForward?: boolean;
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  showReverse?: boolean;
18
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  showTranslation?: boolean;
package/esm/DivSequenceRenderer/components/DivSequenceRendering.js CHANGED
@@ -1,13 +1,14 @@
1
1
  import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
2
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  import { Fragment } from 'react';
3
- import { createJBrowseTheme } from '@jbrowse/core/ui';
4
3
  import { bpSpanPx, complement, defaultCodonTable, defaultStarts, defaultStops, generateCodonTable, revcom, } from '@jbrowse/core/util';
4
+ import { useTheme } from '@mui/material';
5
5
  import { observer } from 'mobx-react';
6
- function Translation({ codonTable, seq, frame, width, bpPerPx, colorByCDS, region, seqStart, height, y, reverse = false, theme, }) {
6
+ function Translation({ codonTable, seq, frame, width, bpPerPx, colorByCDS, region, seqStart, height, y, reverse = false, }) {
7
7
  var _a, _b;
8
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  const normalizedFrame = Math.abs(frame) - 1;
9
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  const seqFrame = seqStart % 3;
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  const frameShift = (normalizedFrame - seqFrame + 3) % 3;
11
+ const theme = useTheme();
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  const frameShiftAdjustedSeqLength = seq.length - frameShift;
12
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  const multipleOfThreeLength = frameShiftAdjustedSeqLength - (frameShiftAdjustedSeqLength % 3);
13
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  const seqSliced = seq.slice(frameShift, frameShift + multipleOfThreeLength);
@@ -26,25 +27,26 @@ function Translation({ codonTable, seq, frame, width, bpPerPx, colorByCDS, regio
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  const frameOffset = frameShift / bpPerPx;
27
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  const startOffset = (region.start - seqStart) / bpPerPx;
28
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  const offset = frameOffset - startOffset;
30
+ const dark = theme.palette.mode === 'dark' ? 'dark' : 'main';
29
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  const defaultFill = colorByCDS
30
- ? (_a = theme === null || theme === void 0 ? void 0 : theme.palette.framesCDS.at(frame)) === null || _a === void 0 ? void 0 : _a.main
31
- : (_b = theme === null || theme === void 0 ? void 0 : theme.palette.frames.at(frame)) === null || _b === void 0 ? void 0 : _b.main;
32
+ ? (_a = theme.palette.framesCDS.at(frame)) === null || _a === void 0 ? void 0 : _a[dark]
33
+ : (_b = theme.palette.frames.at(frame)) === null || _b === void 0 ? void 0 : _b[dark];
32
34
  return (_jsxs(_Fragment, { children: [_jsx("rect", { x: 0, y: y, width: width, height: height, fill: defaultFill }), translated.map((element, index) => {
33
35
  const x = region.reversed
34
36
  ? width - (index + 1) * codonWidth - offset
35
37
  : codonWidth * index + offset;
36
38
  const { letter, codon } = element;
37
39
  const codonFill = defaultStarts.includes(codon)
38
- ? theme === null || theme === void 0 ? void 0 : theme.palette.startCodon
40
+ ? theme.palette.startCodon
39
41
  : defaultStops.includes(codon)
40
- ? theme === null || theme === void 0 ? void 0 : theme.palette.stopCodon
42
+ ? theme.palette.stopCodon
41
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  : undefined;
42
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  return !(renderLetter || codonFill) ? null : (_jsxs(Fragment, { children: [_jsx("rect", { x: x, y: y, width: renderLetter
43
45
  ? codonWidth
44
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  : codonWidth + 0.7, height: height, stroke: renderLetter ? '#555' : 'none', fill: codonFill || 'none' }), renderLetter ? (_jsx("text", { x: x + codonWidth / 2, fontSize: height - 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", children: letter })) : null] }, `${index}-${letter}`));
45
47
  })] }));
46
48
  }
47
- function Sequence({ bpPerPx, region, feature, sequenceType, theme, height, seq, y, }) {
49
+ function Sequence({ bpPerPx, region, feature, sequenceType, height, seq, y, }) {
48
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  const render = 1 / bpPerPx >= 12;
49
51
  const s = feature.get('start');
50
52
  const e = feature.get('end');
@@ -52,18 +54,19 @@ function Sequence({ bpPerPx, region, feature, sequenceType, theme, height, seq,
52
54
  const reverse = region.reversed;
53
55
  const len = e - s;
54
56
  const w = Math.max((rightPx - leftPx) / len, 0.8);
57
+ const theme = useTheme();
55
58
  return (_jsx(_Fragment, { children: seq.split('').map((letter, index) => {
56
59
  const color = sequenceType === 'dna'
57
60
  ?
58
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  theme.palette.bases[letter.toUpperCase()]
59
62
  : undefined;
63
+ const dark = theme.palette.mode === 'dark';
60
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  const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
61
- return (_jsxs(Fragment, { children: [_jsx("rect", { x: x, y: y, width: w, height: height, fill: color ? color.main : '#aaa', stroke: render ? '#555' : 'none' }), render ? (_jsx("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fontSize: height - 2, fill: color ? theme.palette.getContrastText(color.main) : 'black', children: letter })) : null] }, `${letter}-${index}`));
65
+ return (_jsxs(Fragment, { children: [_jsx("rect", { x: x, y: y, width: w, height: height, fill: color ? (dark ? color.dark : color.main) : '#aaa', stroke: render ? '#555' : 'none' }), render ? (_jsx("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fontSize: height - 2, fill: color ? theme.palette.getContrastText(color.main) : 'black', children: letter })) : null] }, `${letter}-${index}`));
62
66
  }) }));
63
67
  }
64
- function SequenceSVG({ regions, width, theme: configTheme, colorByCDS, features = new Map(), showReverse = true, showForward = true, showTranslation = true, sequenceType = 'dna', bpPerPx, rowHeight, }) {
68
+ function SequenceSVG({ regions, width, colorByCDS, features = new Map(), showReverse = true, showForward = true, showTranslation = true, sequenceType = 'dna', bpPerPx, rowHeight, }) {
65
69
  const region = regions[0];
66
- const theme = createJBrowseTheme(configTheme);
67
70
  const codonTable = generateCodonTable(defaultCodonTable);
68
71
  const [feature] = [...features.values()];
69
72
  if (!feature) {
@@ -80,7 +83,7 @@ function SequenceSVG({ regions, width, theme: configTheme, colorByCDS, features
80
83
  const [topFrames, bottomFrames] = region.reversed
81
84
  ? [reverseFrames.toReversed(), forwardFrames.toReversed()]
82
85
  : [forwardFrames, reverseFrames];
83
- return (_jsxs(_Fragment, { children: [topFrames.map(index => (_jsx(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), theme: theme, height: rowHeight, reverse: region.reversed }, `translation-${index}`))), showForward && showSequence ? (_jsx(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? complement(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null, showReverse && showSequence ? (_jsx(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : complement(seq), bpPerPx: bpPerPx, theme: theme })) : null, bottomFrames.map(index => (_jsx(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), theme: theme, height: rowHeight, reverse: !region.reversed }, `rev-translation-${index}`)))] }));
86
+ return (_jsxs(_Fragment, { children: [topFrames.map(index => (_jsx(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), height: rowHeight, reverse: region.reversed }, `translation-${index}`))), showForward && showSequence ? (_jsx(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? complement(seq) : seq, bpPerPx: bpPerPx })) : null, showReverse && showSequence ? (_jsx(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : complement(seq), bpPerPx: bpPerPx })) : null, bottomFrames.map(index => (_jsx(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), height: rowHeight, reverse: !region.reversed }, `rev-translation-${index}`)))] }));
84
87
  }
85
88
  function Wrapper({ exportSVG, width, totalHeight, children, }) {
86
89
  return exportSVG ? (children) : (_jsx("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
@@ -90,9 +93,9 @@ function Wrapper({ exportSVG, width, totalHeight, children, }) {
90
93
  userSelect: 'none',
91
94
  }, children: children }));
92
95
  }
93
- const DivSequenceRendering = observer(function ({ exportSVG, features, regions, colorByCDS, bpPerPx, rowHeight, sequenceHeight, theme, showForward, showReverse, showTranslation, }) {
96
+ const DivSequenceRendering = observer(function ({ exportSVG, features, regions, colorByCDS, bpPerPx, rowHeight, sequenceHeight, showForward, showReverse, showTranslation, }) {
94
97
  const region = regions[0];
95
98
  const width = Math.ceil((region.end - region.start) / bpPerPx);
96
- return (_jsx(Wrapper, { exportSVG: exportSVG, totalHeight: sequenceHeight, width: width, children: _jsx(SequenceSVG, { width: width, showReverse: showReverse, showForward: showForward, theme: theme, showTranslation: showTranslation, colorByCDS: colorByCDS, bpPerPx: bpPerPx, rowHeight: rowHeight, features: features, regions: regions }) }));
99
+ return (_jsx(Wrapper, { exportSVG: exportSVG, totalHeight: sequenceHeight, width: width, children: _jsx(SequenceSVG, { width: width, showReverse: showReverse, showForward: showForward, showTranslation: showTranslation, colorByCDS: colorByCDS, bpPerPx: bpPerPx, rowHeight: rowHeight, features: features, regions: regions }) }));
97
100
  });
98
101
  export default DivSequenceRendering;
package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js CHANGED
@@ -74,7 +74,14 @@ export default class IndexedFastaAdapter extends BaseSequenceAdapter {
74
74
  end: chunkStart + chunkSize,
75
75
  };
76
76
  checkStopToken(stopToken);
77
- chunks.push(await this.seqCache.get(JSON.stringify(r), { ...r, fasta }));
77
+ const res = await this.seqCache.get(JSON.stringify(r), {
78
+ ...r,
79
+ fasta,
80
+ });
81
+ if (!res) {
82
+ break;
83
+ }
84
+ chunks.push(res);
78
85
  }
79
86
  const seq = chunks
80
87
  .filter(f => !!f)
package/esm/LinearReferenceSequenceDisplay/model.d.ts CHANGED
@@ -184,6 +184,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
184
184
  readonly renderDelay: number;
185
185
  readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
186
186
  readonly selectedFeatureId: string | undefined;
187
+ copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
187
188
  } & {
188
189
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
189
190
  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-sequence",
3
- "version": "3.5.0",
3
+ "version": "3.6.0",
4
4
  "description": "JBrowse 2 sequence adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -39,9 +39,9 @@
39
39
  "@gmod/abortable-promise-cache": "^3.0.1",
40
40
  "@gmod/indexedfasta": "^4.0.0",
41
41
  "@gmod/twobit": "^6.0.0",
42
- "@jbrowse/core": "^3.5.0",
43
- "@jbrowse/plugin-linear-genome-view": "^3.5.0",
44
- "@jbrowse/plugin-wiggle": "^3.5.0",
42
+ "@jbrowse/core": "^3.6.0",
43
+ "@jbrowse/plugin-linear-genome-view": "^3.6.0",
44
+ "@jbrowse/plugin-wiggle": "^3.6.0",
45
45
  "@mui/material": "^7.0.0",
46
46
  "mobx": "^6.0.0",
47
47
  "mobx-react": "^9.0.0",
@@ -57,5 +57,5 @@
57
57
  "distModule": "esm/index.js",
58
58
  "srcModule": "src/index.ts",
59
59
  "module": "esm/index.js",
60
- "gitHead": "8a8aa0aab2229dece106a5715a767e649e2fe92b"
60
+ "gitHead": "133a68815ab348d156c18d83cffc997356c3cfbb"
61
61
  }