jbrowse-plugin-mafviewer 1.2.3 → 1.2.4
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/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.d.ts +1 -1
- package/dist/BigMafAdapter/BigMafAdapter.d.ts +1 -1
- package/dist/BigMafAdapter/BigMafAdapter.js +50 -49
- package/dist/BigMafAdapter/BigMafAdapter.js.map +1 -1
- package/dist/LinearMafDisplay/components/ColorLegend.d.ts +2 -4
- package/dist/LinearMafDisplay/components/ColorLegend.js +2 -3
- package/dist/LinearMafDisplay/components/ColorLegend.js.map +1 -1
- package/dist/LinearMafDisplay/components/{ReactComponent.d.ts → LinearMafDisplayComponent.d.ts} +1 -1
- package/dist/LinearMafDisplay/components/{ReactComponent.js → LinearMafDisplayComponent.js} +2 -2
- package/dist/LinearMafDisplay/components/LinearMafDisplayComponent.js.map +1 -0
- package/dist/LinearMafDisplay/components/SetRowHeightDialog.js +38 -0
- package/dist/LinearMafDisplay/components/SetRowHeightDialog.js.map +1 -0
- package/dist/LinearMafDisplay/components/SvgWrapper.d.ts +1 -1
- package/dist/LinearMafDisplay/components/SvgWrapper.js.map +1 -1
- package/dist/LinearMafDisplay/components/Tree.d.ts +2 -1
- package/dist/LinearMafDisplay/components/Tree.js +2 -0
- package/dist/LinearMafDisplay/components/Tree.js.map +1 -1
- package/dist/LinearMafDisplay/components/YScaleBars.d.ts +1 -1
- package/dist/LinearMafDisplay/components/YScaleBars.js +1 -10
- package/dist/LinearMafDisplay/components/YScaleBars.js.map +1 -1
- package/dist/LinearMafDisplay/index.js +1 -1
- package/dist/LinearMafDisplay/index.js.map +1 -1
- package/dist/LinearMafDisplay/stateModel.d.ts +20 -19
- package/dist/LinearMafDisplay/stateModel.js +42 -7
- package/dist/LinearMafDisplay/stateModel.js.map +1 -1
- package/dist/LinearMafDisplay/types.d.ts +5 -3
- package/dist/LinearMafDisplay/types.js +1 -15
- package/dist/LinearMafDisplay/types.js.map +1 -1
- package/dist/LinearMafDisplay/util.d.ts +4 -0
- package/dist/LinearMafDisplay/util.js +16 -0
- package/dist/LinearMafDisplay/util.js.map +1 -0
- package/dist/LinearMafRenderer/LinearMafRenderer.d.ts +4 -4
- package/dist/LinearMafRenderer/LinearMafRenderer.js +8 -10
- package/dist/LinearMafRenderer/LinearMafRenderer.js.map +1 -1
- package/dist/LinearMafRenderer/makeImageData.js +18 -16
- package/dist/LinearMafRenderer/makeImageData.js.map +1 -1
- package/dist/MafAddTrackWorkflow/index.js +0 -1
- package/dist/MafAddTrackWorkflow/index.js.map +1 -1
- package/dist/MafTabixAdapter/MafTabixAdapter.d.ts +1 -1
- package/dist/MafTabixAdapter/MafTabixAdapter.js +6 -7
- package/dist/MafTabixAdapter/MafTabixAdapter.js.map +1 -1
- package/dist/MafTabixAdapter/configSchema.js +29 -1
- package/dist/MafTabixAdapter/configSchema.js.map +1 -1
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js +7 -20
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map +4 -4
- package/dist/util.d.ts +2 -2
- package/dist/util.js +5 -1
- package/dist/util.js.map +1 -1
- package/package.json +10 -10
- package/src/BigMafAdapter/BigMafAdapter.ts +52 -49
- package/src/LinearMafDisplay/components/ColorLegend.tsx +11 -7
- package/src/LinearMafDisplay/components/{ReactComponent.tsx → LinearMafDisplayComponent.tsx} +2 -2
- package/src/LinearMafDisplay/components/SetRowHeightDialog.tsx +83 -0
- package/src/LinearMafDisplay/components/SvgWrapper.tsx +1 -2
- package/src/LinearMafDisplay/components/Tree.tsx +5 -1
- package/src/LinearMafDisplay/components/YScaleBars.tsx +3 -21
- package/src/LinearMafDisplay/index.ts +1 -1
- package/src/LinearMafDisplay/stateModel.ts +49 -18
- package/src/LinearMafDisplay/types.ts +4 -24
- package/src/LinearMafDisplay/util.ts +27 -0
- package/src/LinearMafRenderer/LinearMafRenderer.ts +9 -14
- package/src/LinearMafRenderer/makeImageData.ts +18 -17
- package/src/MafAddTrackWorkflow/index.ts +0 -1
- package/src/MafTabixAdapter/MafTabixAdapter.ts +9 -7
- package/src/MafTabixAdapter/configSchema.ts +29 -1
- package/src/util.ts +6 -2
- package/dist/LinearMafDisplay/components/ReactComponent.js.map +0 -1
- package/dist/LinearMafDisplay/components/SetRowHeight.js +0 -36
- package/dist/LinearMafDisplay/components/SetRowHeight.js.map +0 -1
- package/src/LinearMafDisplay/components/SetRowHeight.tsx +0 -83
- /package/dist/LinearMafDisplay/components/{SetRowHeight.d.ts → SetRowHeightDialog.d.ts} +0 -0
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@@ -12,12 +12,11 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
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if (!this.getSubAdapter) {
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throw new Error('no getSubAdapter available');
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}
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const adapter = await this.getSubAdapter({
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...getSnapshot(this.config),
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type: 'BigBedAdapter',
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});
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return {
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adapter:
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adapter: (await this.getSubAdapter({
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...getSnapshot(this.config),
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type: 'BigBedAdapter',
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})).dataAdapter,
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};
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}
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async setupPre() {
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@@ -41,53 +40,55 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
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const { statusCallback = () => { } } = opts || {};
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return ObservableCreate(async (observer) => {
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const { adapter } = await this.setup();
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const features = await updateStatus('Downloading
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const
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if (
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const features = await updateStatus('Downloading alignments', statusCallback, () => firstValueFrom(adapter.getFeatures(query).pipe(toArray())));
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await updateStatus('Processing alignments', statusCallback, () => {
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for (const feature of features) {
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const maf = feature.get('mafBlock');
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const blocks = maf.split(';');
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let aln;
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const alns = [];
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const alignments = {};
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const blocks2 = [];
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for (const block of blocks) {
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if (block.startsWith('s')) {
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if (aln) {
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alns.push(block.split(/ +/)[6]);
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blocks2.push(block);
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}
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else {
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aln = block.split(/ +/)[6];
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alns.push(aln);
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blocks2.push(block);
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}
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}
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}
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for (let i = 0; i < blocks2.length; i++) {
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const elt = blocks2[i];
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const ad = elt.split(/ +/);
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const y = ad[1].split('.');
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const org = y[0];
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const chr = y[1];
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alignments[org] = {
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chr: chr,
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start: +ad[1],
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srcSize: +ad[2],
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strand: ad[3] === '+' ? 1 : -1,
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unknown: +ad[4],
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data: alns[i],
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};
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}
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observer.next(new SimpleFeature({
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id: feature.id(),
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data: {
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start: feature.get('start'),
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end: feature.get('end'),
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refName: feature.get('refName'),
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seq: alns[0],
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alignments: alignments,
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},
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}));
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}
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const elt = blocks2[i];
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const ad = elt.split(/ +/);
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const y = ad[1].split('.');
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const org = y[0];
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const chr = y[1];
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alignments[org] = {
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chr: chr,
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start: +ad[1],
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srcSize: +ad[2],
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strand: ad[3] === '+' ? 1 : -1,
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unknown: +ad[4],
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data: alns[i],
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};
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}
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observer.next(new SimpleFeature({
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id: feature.id(),
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data: {
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start: feature.get('start'),
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end: feature.get('end'),
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refName: feature.get('refName'),
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seq: alns[0],
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alignments: alignments,
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},
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}));
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}
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});
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observer.complete();
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});
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}
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@@ -1 +1 @@
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-
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declare const ColorLegend: ({ model, }: {
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const { labelWidth, canDisplayLabel, totalHeight, treeWidth, samples = [], rowHeight, svgFontSize, } = model;
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const boxHeight = Math.min(20, rowHeight);
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return (React.createElement(React.Fragment, null,
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React.createElement(RectBg, { y: 0, x: 0, width: labelWidth + 5 + treeWidth, height: totalHeight }),
|
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@@ -1 +1 @@
|
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1
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-
{"version":3,"file":"ColorLegend.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/ColorLegend.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;
|
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1
|
+
{"version":3,"file":"ColorLegend.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/ColorLegend.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,MAAM,MAAM,UAAU,CAAA;AAC7B,OAAO,IAAI,MAAM,QAAQ,CAAA;AAIzB,MAAM,WAAW,GAAG,QAAQ,CAAC,UAAU,EACrC,KAAK,GAGN;IACC,MAAM,EACJ,UAAU,EACV,eAAe,EACf,WAAW,EACX,SAAS,EACT,OAAO,GAAG,EAAE,EACZ,SAAS,EACT,WAAW,GACZ,GAAG,KAAK,CAAA;IACT,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,SAAS,CAAC,CAAA;IAEzC,OAAO,CACL;QACE,oBAAC,MAAM,IACL,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,UAAU,GAAG,CAAC,GAAG,SAAS,EACjC,MAAM,EAAE,WAAW,GACnB;QACF,oBAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI;QACtB,2BAAG,SAAS,EAAE,aAAa,SAAS,GAAG,CAAC,KAAK;YAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC,CAC5B,oBAAC,MAAM,IACL,GAAG,EAAE,GAAG,MAAM,CAAC,EAAE,IAAI,GAAG,EAAE,EAC1B,CAAC,EAAE,GAAG,GAAG,SAAS,EAClB,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,UAAU,GAAG,CAAC,EACrB,MAAM,EAAE,SAAS,EACjB,KAAK,EAAE,MAAM,CAAC,KAAK,GACnB,CACH,CAAC;YACD,eAAe;gBACd,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC,CAC3B,8BACE,GAAG,EAAE,GAAG,MAAM,CAAC,EAAE,IAAI,GAAG,EAAE,EAC1B,gBAAgB,EAAC,QAAQ,EACzB,QAAQ,EAAE,WAAW,EACrB,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,GAAG,GAAG,SAAS,GAAG,SAAS,GAAG,CAAC,IAEjC,MAAM,CAAC,KAAK,CACR,CACR,CAAC;gBACJ,CAAC,CAAC,IAAI,CACN,CACH,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,WAAW,CAAA"}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import React, { useRef, useState } from 'react';
|
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2
|
+
import { SanitizedHTML } from '@jbrowse/core/ui';
|
|
2
3
|
import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
|
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3
|
-
import SanitizedHTML from '@jbrowse/core/ui/SanitizedHTML';
|
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4
4
|
import { getContainingView, getEnv } from '@jbrowse/core/util';
|
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5
5
|
import { observer } from 'mobx-react';
|
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6
6
|
import { makeStyles } from 'tss-react/mui';
|
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@@ -47,4 +47,4 @@ const LinearMafDisplay = observer(function (props) {
|
|
|
47
47
|
.join('\n') })))) : null));
|
|
48
48
|
});
|
|
49
49
|
export default LinearMafDisplay;
|
|
50
|
-
//# sourceMappingURL=
|
|
50
|
+
//# sourceMappingURL=LinearMafDisplayComponent.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"LinearMafDisplayComponent.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/LinearMafDisplayComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE/C,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAChD,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,EAAE,iBAAiB,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAA;AAC9D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,UAAU,MAAM,cAAc,CAAA;AAKrC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,aAAa,EAAE,MAAM;KACtB;CACF,CAAC,CAAA;AAEF,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,KAE3C;IACC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAChE,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IAExC,MAAM,kBAAkB,GAAG,aAAa,CAAC,SAAS,CAChD,wBAAwB,CAC+B,CAAA;IACzD,MAAM,EAAE,0BAA0B,EAAE,GAAG,kBAAkB,CAAC,OAAO,CAAA;IAEjE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC9C,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC9C,MAAM,EAAE,KAAK,EAAE,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAEnE,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,KAAK,CAAC,EAAE;YACnB,MAAM,IAAI,GAAG,GAAG,CAAC,OAAO,EAAE,qBAAqB,EAAE,CAAA;YACjD,MAAM,GAAG,GAAG,IAAI,EAAE,GAAG,IAAI,CAAC,CAAA;YAC1B,MAAM,IAAI,GAAG,IAAI,EAAE,IAAI,IAAI,CAAC,CAAA;YAC5B,SAAS,CAAC,KAAK,CAAC,OAAO,GAAG,GAAG,CAAC,CAAA;YAC9B,SAAS,CAAC,KAAK,CAAC,OAAO,GAAG,IAAI,CAAC,CAAA;QACjC,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;YACjB,SAAS,CAAC,SAAS,CAAC,CAAA;YACpB,SAAS,CAAC,SAAS,CAAC,CAAA;QACtB,CAAC;QAED,oBAAC,0BAA0B,OAAK,KAAK,GAAI;QACzC,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,MAAM,IAAI,OAAO,CAAC,CAAC,CAAC,CACnB,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;YAClC,6BACE,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;oBACL,QAAQ,EAAE,UAAU;oBACpB,GAAG,EAAE,SAAS;iBACf;gBAED,8BACE,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,KAAK,EACT,EAAE,EAAE,MAAM,GAAG,SAAS,EACtB,EAAE,EAAE,MAAM,GAAG,SAAS,EACtB,MAAM,EAAC,OAAO,GACd;gBACF,8BAAM,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,EAAC,OAAO,GAAG,CAC9D;YACN,oBAAC,WAAW;gBACV,oBAAC,aAAa,IACZ,IAAI,EAAE,MAAM,CAAC,OAAO,CAClB,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,SAAS,CAAC,CAAC,IAAI,EAAE,CAC9C;yBACE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,GAAG,KAAK,OAAO,IAAI,GAAG,KAAK,IAAI,CAAC;yBAClD,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,IAAI,KAAK,EAAE,CAAC;yBACxC,IAAI,CAAC,IAAI,CAAC,GACb,CACU,CACV,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}
|
|
@@ -0,0 +1,38 @@
|
|
|
1
|
+
import React, { useState } from 'react';
|
|
2
|
+
import { Dialog } from '@jbrowse/core/ui';
|
|
3
|
+
import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
|
|
4
|
+
import { observer } from 'mobx-react';
|
|
5
|
+
import { makeStyles } from 'tss-react/mui';
|
|
6
|
+
const useStyles = makeStyles()({
|
|
7
|
+
root: {
|
|
8
|
+
width: 500,
|
|
9
|
+
},
|
|
10
|
+
});
|
|
11
|
+
const SetRowHeightDialog = observer(function (props) {
|
|
12
|
+
const { model, handleClose } = props;
|
|
13
|
+
const { classes } = useStyles();
|
|
14
|
+
const [rowHeight, setRowHeight] = useState(`${model.rowHeight}`);
|
|
15
|
+
const [rowProportion, setRowProportion] = useState(`${model.rowProportion}`);
|
|
16
|
+
return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Set row height" },
|
|
17
|
+
React.createElement("form", { onSubmit: event => {
|
|
18
|
+
event.preventDefault();
|
|
19
|
+
model.setRowProportion(+rowProportion);
|
|
20
|
+
model.setRowHeight(+rowHeight);
|
|
21
|
+
handleClose();
|
|
22
|
+
} },
|
|
23
|
+
React.createElement(DialogContent, { className: classes.root },
|
|
24
|
+
React.createElement(Typography, null, "Set row height and the proportion of the row height to use for drawing each row"),
|
|
25
|
+
React.createElement(TextField, { value: rowHeight, helperText: "Enter row height", autoFocus: true, onChange: event => {
|
|
26
|
+
setRowHeight(event.target.value);
|
|
27
|
+
} }),
|
|
28
|
+
React.createElement(TextField, { value: rowProportion, helperText: "Enter row proportion", onChange: event => {
|
|
29
|
+
setRowProportion(event.target.value);
|
|
30
|
+
} }),
|
|
31
|
+
React.createElement(DialogActions, null,
|
|
32
|
+
React.createElement(Button, { variant: "contained", color: "primary", type: "submit" }, "Submit"),
|
|
33
|
+
React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
|
|
34
|
+
handleClose();
|
|
35
|
+
} }, "Cancel"))))));
|
|
36
|
+
});
|
|
37
|
+
export default SetRowHeightDialog;
|
|
38
|
+
//# sourceMappingURL=SetRowHeightDialog.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"SetRowHeightDialog.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/SetRowHeightDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;CACF,CAAC,CAAA;AAEF,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,KAQ7C;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,GAAG,KAAK,CAAC,SAAS,EAAE,CAAC,CAAA;IAChE,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,GAAG,KAAK,CAAC,aAAa,EAAE,CAAC,CAAA;IAE5E,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BACE,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,KAAK,CAAC,cAAc,EAAE,CAAA;gBACtB,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC,CAAA;gBACtC,KAAK,CAAC,YAAY,CAAC,CAAC,SAAS,CAAC,CAAA;gBAC9B,WAAW,EAAE,CAAA;YACf,CAAC;YAED,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;gBACpC,oBAAC,UAAU,0FAGE;gBACb,oBAAC,SAAS,IACR,KAAK,EAAE,SAAS,EAChB,UAAU,EAAC,kBAAkB,EAC7B,SAAS,QACT,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBAClC,CAAC,GACD;gBACF,oBAAC,SAAS,IACR,KAAK,EAAE,aAAa,EACpB,UAAU,EAAC,sBAAsB,EACjC,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,gBAAgB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACtC,CAAC,GACD;gBACF,oBAAC,aAAa;oBACZ,oBAAC,MAAM,IAAC,OAAO,EAAC,WAAW,EAAC,KAAK,EAAC,SAAS,EAAC,IAAI,EAAC,QAAQ,aAEhD;oBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;4BACZ,WAAW,EAAE,CAAA;wBACf,CAAC,aAGM,CACK,CACF,CACX,CACA,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AACF,eAAe,kBAAkB,CAAA"}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import React from 'react';
|
|
2
|
-
import { LinearMafDisplayModel } from '../stateModel';
|
|
2
|
+
import type { LinearMafDisplayModel } from '../stateModel';
|
|
3
3
|
declare const SvgWrapper: ({ children, model, exportSVG, }: {
|
|
4
4
|
model: LinearMafDisplayModel;
|
|
5
5
|
children: React.ReactNode;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"SvgWrapper.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/SvgWrapper.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;
|
|
1
|
+
{"version":3,"file":"SvgWrapper.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/SvgWrapper.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EACpC,QAAQ,EACR,KAAK,EACL,SAAS,GAKV;IACC,IAAI,SAAS,EAAE,CAAC;QACd,OAAO,0CAAG,QAAQ,CAAI,CAAA;IACxB,CAAC;SAAM,CAAC;QACN,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;QAC7B,OAAO,CACL,6BACE,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,CAAC;gBACP,aAAa,EAAE,MAAM;gBACrB,MAAM,EAAE,WAAW;gBACnB,KAAK,EAAE,iBAAiB,CAAC,KAAK,CAAC,CAAC,KAAK;aACtC,IAEA,QAAQ,CACL,CACP,CAAA;IACH,CAAC;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}
|
|
@@ -11,7 +11,9 @@ const Tree = observer(function ({ model }) {
|
|
|
11
11
|
const { source, target } = link;
|
|
12
12
|
const sy = source.x;
|
|
13
13
|
const ty = target.x;
|
|
14
|
+
// @ts-expect-error
|
|
14
15
|
const tx = showBranchLen ? target.len : target.y;
|
|
16
|
+
// @ts-expect-error
|
|
15
17
|
const sx = showBranchLen ? source.len : source.y;
|
|
16
18
|
// 1d line intersection to check if line crosses block at all, this is
|
|
17
19
|
// an optimization that allows us to skip drawing most tree links
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"Tree.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/Tree.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;
|
|
1
|
+
{"version":3,"file":"Tree.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/Tree.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,IAAI,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAAoC;IACzE,MAAM;IACJ,2EAA2E;IAC3E,mBAAmB;IACnB,8DAA8D;IAC9D,SAAS,EAAE,UAAU,EAErB,SAAS,EACT,aAAa,GACd,GAAG,KAAK,CAAA;IAET,OAAO,CACL,0CACG,SAAS;QACR,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;YAChC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;YAC/B,MAAM,EAAE,GAAG,MAAM,CAAC,CAAE,CAAA;YACpB,MAAM,EAAE,GAAG,MAAM,CAAC,CAAE,CAAA;YACpB,mBAAmB;YACnB,MAAM,EAAE,GAAG,aAAa,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;YAChD,mBAAmB;YACnB,MAAM,EAAE,GAAG,aAAa,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;YAEhD,sEAAsE;YACtE,iEAAiE;YACjE,oBAAoB;YACpB,OAAO,CACL,oBAAC,KAAK,CAAC,QAAQ,IAAC,GAAG,EAAE,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC;gBAC7C,8BAAM,MAAM,EAAC,OAAO,EAAC,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,GAAI;gBACvD,8BAAM,MAAM,EAAC,OAAO,EAAC,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,GAAI,CACxC,CAClB,CAAA;QACH,CAAC,CAAC;QACJ,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,IAAI,CAAA"}
|
|
@@ -1,20 +1,11 @@
|
|
|
1
1
|
import React from 'react';
|
|
2
|
-
import { measureText } from '@jbrowse/core/util';
|
|
3
2
|
import { observer } from 'mobx-react';
|
|
4
3
|
import ColorLegend from './ColorLegend';
|
|
5
4
|
import SvgWrapper from './SvgWrapper';
|
|
6
|
-
import { max } from './util';
|
|
7
5
|
export const YScaleBars = observer(function (props) {
|
|
8
6
|
const { model } = props;
|
|
9
|
-
const { rowHeight, samples } = model;
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.map(width => (canDisplayLabel ? width : minWidth)) || [], 0);
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return (React.createElement(SvgWrapper, { ...props },
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React.createElement(ColorLegend, { model: model })));
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export default YScaleBars;
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//# sourceMappingURL=YScaleBars.js.map
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@@ -1 +1 @@
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1
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{"version":3,"file":"YScaleBars.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/YScaleBars.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,
|
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+
{"version":3,"file":"YScaleBars.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/YScaleBars.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,WAAW,MAAM,eAAe,CAAA;AACvC,OAAO,UAAU,MAAM,cAAc,CAAA;AAIrC,MAAM,CAAC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,KAI5C;IACC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,OAAO,CACL,oBAAC,UAAU,OAAK,KAAK;QACnB,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,GAAI,CAClB,CACd,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}
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@@ -1,5 +1,5 @@
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1
1
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import { DisplayType } from '@jbrowse/core/pluggableElementTypes';
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import ReactComponent from './components/
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import ReactComponent from './components/LinearMafDisplayComponent';
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3
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import configSchemaF from './configSchema';
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import stateModelFactory from './stateModel';
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|
export default function LinearMafDisplayF(pluginManager) {
|
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,OAAO,cAAc,MAAM,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,OAAO,cAAc,MAAM,wCAAwC,CAAA;AACnE,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAC1C,OAAO,iBAAiB,MAAM,cAAc,CAAA;AAE5C,MAAM,CAAC,OAAO,UAAU,iBAAiB,CAAC,aAA4B;IACpE,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,MAAM,UAAU,GAAG,iBAAiB,CAAC,YAAY,EAAE,aAAa,CAAC,CAAA;QACjE,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,kBAAkB;YACxB,YAAY;YACZ,UAAU;YACV,cAAc;YACd,QAAQ,EAAE,kBAAkB;YAC5B,SAAS,EAAE,UAAU;YACrB,WAAW,EAAE,aAAa;SAC3B,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}
|
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@@ -1,14 +1,9 @@
|
|
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1
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-
import type { NodeWithIdsAndLength } from './types';
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1
|
+
import type { NodeWithIdsAndLength, Sample } from './types';
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2
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import type PluginManager from '@jbrowse/core/PluginManager';
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import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
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import type { Instance } from 'mobx-state-tree';
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|
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interface Sample {
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|
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id: string;
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label: string;
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color?: string;
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}
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|
/**
|
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13
8
|
* #stateModel LinearMafDisplay
|
|
14
9
|
* extends LinearBasicDisplay
|
|
@@ -112,15 +107,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
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|
rendererTypeName: string;
|
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error: unknown;
|
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message: string | undefined;
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|
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} & import(
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|
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/**
|
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* #getter
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*/
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"mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
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|
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
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|
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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type: import("mobx-state-tree"
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|
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* #getter
|
|
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|
-
*/).ISimpleType<string>;
|
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|
+
type: import("mobx-state-tree").ISimpleType<string>;
|
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|
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
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|
}, {
|
|
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|
rendererTypeName: string;
|
|
@@ -216,7 +205,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
216
205
|
} & {
|
|
217
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|
addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
|
|
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207
|
deleteBlock(key: string): void;
|
|
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|
-
selectFeature(feature: import("@jbrowse/core/util").Feature): void
|
|
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|
+
selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
|
|
220
209
|
navToFeature(feature: import("@jbrowse/core/util").Feature): void;
|
|
221
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|
clearFeatureSelection(): void;
|
|
222
211
|
setFeatureIdUnderMouse(feature?: string): void;
|
|
@@ -290,10 +279,10 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
290
279
|
/**
|
|
291
280
|
* #getter
|
|
292
281
|
*/
|
|
293
|
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readonly samples: {
|
|
282
|
+
readonly samples: Sample[] | {
|
|
283
|
+
label: string | undefined;
|
|
284
|
+
color: string | undefined;
|
|
294
285
|
id: string;
|
|
295
|
-
label: string;
|
|
296
|
-
color?: string;
|
|
297
286
|
}[] | undefined;
|
|
298
287
|
/**
|
|
299
288
|
* #getter
|
|
@@ -335,6 +324,19 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
335
324
|
onClick: () => void;
|
|
336
325
|
subMenu?: undefined;
|
|
337
326
|
})[];
|
|
327
|
+
} & {
|
|
328
|
+
/**
|
|
329
|
+
* #getter
|
|
330
|
+
*/
|
|
331
|
+
readonly svgFontSize: number;
|
|
332
|
+
/**
|
|
333
|
+
* #getter
|
|
334
|
+
*/
|
|
335
|
+
readonly canDisplayLabel: boolean;
|
|
336
|
+
/**
|
|
337
|
+
* #getter
|
|
338
|
+
*/
|
|
339
|
+
readonly labelWidth: number;
|
|
338
340
|
} & {
|
|
339
341
|
afterCreate(): void;
|
|
340
342
|
} & {
|
|
@@ -431,4 +433,3 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
431
433
|
} & import("mobx-state-tree")._NotCustomized>;
|
|
432
434
|
export type LinearMafDisplayStateModel = ReturnType<typeof stateModelFactory>;
|
|
433
435
|
export type LinearMafDisplayModel = Instance<LinearMafDisplayStateModel>;
|
|
434
|
-
export {};
|
|
@@ -1,14 +1,15 @@
|
|
|
1
|
+
import { lazy } from 'react';
|
|
1
2
|
import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
|
|
2
|
-
import { getEnv, getSession } from '@jbrowse/core/util';
|
|
3
|
+
import { getEnv, getSession, max, measureText } from '@jbrowse/core/util';
|
|
3
4
|
import { getRpcSessionId } from '@jbrowse/core/util/tracks';
|
|
4
5
|
import { ascending } from 'd3-array';
|
|
5
6
|
import { cluster, hierarchy } from 'd3-hierarchy';
|
|
6
7
|
import deepEqual from 'fast-deep-equal';
|
|
7
8
|
import { autorun } from 'mobx';
|
|
8
9
|
import { addDisposer, isAlive, types } from 'mobx-state-tree';
|
|
9
|
-
import
|
|
10
|
-
import { maxLength, setBrLength } from './types';
|
|
10
|
+
import { maxLength, setBrLength } from './util';
|
|
11
11
|
import { normalize } from '../util';
|
|
12
|
+
const SetRowHeightDialog = lazy(() => import('./components/SetRowHeightDialog'));
|
|
12
13
|
/**
|
|
13
14
|
* #stateModel LinearMafDisplay
|
|
14
15
|
* extends LinearBasicDisplay
|
|
@@ -158,7 +159,19 @@ export default function stateModelFactory(configSchema, pluginManager) {
|
|
|
158
159
|
* #getter
|
|
159
160
|
*/
|
|
160
161
|
get samples() {
|
|
161
|
-
|
|
162
|
+
if (this.rowNames) {
|
|
163
|
+
const volatileSamplesMap = self.volatileSamples
|
|
164
|
+
? Object.fromEntries(self.volatileSamples.map(e => [e.id, e]))
|
|
165
|
+
: undefined;
|
|
166
|
+
return normalize(this.rowNames).map(r => ({
|
|
167
|
+
...r,
|
|
168
|
+
label: volatileSamplesMap?.[r.id]?.label || r.label,
|
|
169
|
+
color: volatileSamplesMap?.[r.id]?.color || r.color,
|
|
170
|
+
}));
|
|
171
|
+
}
|
|
172
|
+
else {
|
|
173
|
+
return self.volatileSamples;
|
|
174
|
+
}
|
|
162
175
|
},
|
|
163
176
|
/**
|
|
164
177
|
* #getter
|
|
@@ -267,13 +280,36 @@ export default function stateModelFactory(configSchema, pluginManager) {
|
|
|
267
280
|
},
|
|
268
281
|
};
|
|
269
282
|
})
|
|
283
|
+
.views(self => ({
|
|
284
|
+
/**
|
|
285
|
+
* #getter
|
|
286
|
+
*/
|
|
287
|
+
get svgFontSize() {
|
|
288
|
+
return Math.min(Math.max(self.rowHeight, 8), 14);
|
|
289
|
+
},
|
|
290
|
+
/**
|
|
291
|
+
* #getter
|
|
292
|
+
*/
|
|
293
|
+
get canDisplayLabel() {
|
|
294
|
+
return self.rowHeight >= 7;
|
|
295
|
+
},
|
|
296
|
+
/**
|
|
297
|
+
* #getter
|
|
298
|
+
*/
|
|
299
|
+
get labelWidth() {
|
|
300
|
+
const minWidth = 20;
|
|
301
|
+
return max(self.samples
|
|
302
|
+
?.map(s => measureText(s.label, this.svgFontSize))
|
|
303
|
+
.map(width => (this.canDisplayLabel ? width : minWidth)) || [], 0);
|
|
304
|
+
},
|
|
305
|
+
}))
|
|
270
306
|
.actions(self => ({
|
|
271
307
|
afterCreate() {
|
|
272
308
|
addDisposer(self, autorun(async () => {
|
|
273
309
|
try {
|
|
274
310
|
const { rpcManager } = getSession(self);
|
|
275
311
|
const sessionId = getRpcSessionId(self);
|
|
276
|
-
|
|
312
|
+
self.setSamples((await rpcManager.call(sessionId, 'MafGetSamples', {
|
|
277
313
|
sessionId,
|
|
278
314
|
adapterConfig: self.adapterConfig,
|
|
279
315
|
statusCallback: (message) => {
|
|
@@ -281,8 +317,7 @@ export default function stateModelFactory(configSchema, pluginManager) {
|
|
|
281
317
|
self.setMessage(message);
|
|
282
318
|
}
|
|
283
319
|
},
|
|
284
|
-
}));
|
|
285
|
-
self.setSamples(results);
|
|
320
|
+
})));
|
|
286
321
|
}
|
|
287
322
|
catch (e) {
|
|
288
323
|
console.error(e);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"stateModel.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/stateModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AAC7E,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;
|
|
1
|
+
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@@ -1,4 +1,3 @@
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-
import type { HierarchyNode } from 'd3-hierarchy';
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export interface NodeWithIds {
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id: string;
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name: string;
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@@ -13,5 +12,8 @@ export interface NodeWithIdsAndLength {
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noTree?: boolean;
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13
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length: number;
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}
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export
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-
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export interface Sample {
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id: string;
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label: string;
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color?: string;
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}
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@@ -1,16 +1,2 @@
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1
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-
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2
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-
// basically same as maxLength from https://observablehq.com/@d3/tree-of-life
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-
export function maxLength(d) {
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return ((d.data.length || 0) + (d.children ? max(d.children, maxLength) || 0 : 0));
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}
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// basically same as setRadius from https://observablehq.com/@d3/tree-of-life
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export function setBrLength(d, y0, k) {
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// @ts-expect-error
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d.len = (y0 += Math.max(d.data.length || 0, 0)) * k;
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if (d.children) {
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d.children.forEach(d => {
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setBrLength(d, y0, k);
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});
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}
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-
}
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export {};
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|
//# sourceMappingURL=types.js.map
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/types.ts"],"names":[],"mappings":"
|
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1
|
+
{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/types.ts"],"names":[],"mappings":""}
|