jbrowse-plugin-mafviewer 1.1.3 → 1.2.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.d.ts +5 -4
- package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js +103 -82
- package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js.map +1 -1
- package/dist/BgzipTaffyAdapter/util.d.ts +1 -0
- package/dist/BgzipTaffyAdapter/util.js +22 -0
- package/dist/BgzipTaffyAdapter/util.js.map +1 -0
- package/dist/BigMafAdapter/BigMafAdapter.d.ts +3 -2
- package/dist/BigMafAdapter/BigMafAdapter.js +4 -3
- package/dist/BigMafAdapter/BigMafAdapter.js.map +1 -1
- package/dist/LinearMafDisplay/components/ColorLegend.js +1 -1
- package/dist/LinearMafDisplay/components/ColorLegend.js.map +1 -1
- package/dist/LinearMafDisplay/components/ReactComponent.js +1 -1
- package/dist/LinearMafDisplay/components/ReactComponent.js.map +1 -1
- package/dist/LinearMafDisplay/components/SvgWrapper.js +2 -2
- package/dist/LinearMafDisplay/components/SvgWrapper.js.map +1 -1
- package/dist/LinearMafDisplay/components/YScaleBars.js +2 -2
- package/dist/LinearMafDisplay/components/YScaleBars.js.map +1 -1
- package/dist/LinearMafDisplay/renderSvg.d.ts +2 -2
- package/dist/LinearMafDisplay/renderSvg.js +0 -1
- package/dist/LinearMafDisplay/renderSvg.js.map +1 -1
- package/dist/LinearMafDisplay/stateModel.d.ts +19 -17
- package/dist/LinearMafDisplay/stateModel.js +17 -10
- package/dist/LinearMafDisplay/stateModel.js.map +1 -1
- package/dist/LinearMafRenderer/LinearMafRenderer.d.ts +8 -4
- package/dist/LinearMafRenderer/LinearMafRenderer.js +14 -148
- package/dist/LinearMafRenderer/LinearMafRenderer.js.map +1 -1
- package/dist/LinearMafRenderer/configSchema.d.ts +6 -1
- package/dist/LinearMafRenderer/configSchema.js +6 -1
- package/dist/LinearMafRenderer/configSchema.js.map +1 -1
- package/dist/LinearMafRenderer/makeImageData.d.ts +20 -0
- package/dist/LinearMafRenderer/makeImageData.js +144 -0
- package/dist/LinearMafRenderer/makeImageData.js.map +1 -0
- package/dist/LinearMafRenderer/util.d.ts +6 -1
- package/dist/LinearMafRenderer/util.js +17 -0
- package/dist/LinearMafRenderer/util.js.map +1 -1
- package/dist/MafAddTrackWorkflow/AddTrackWorkflow.d.ts +1 -1
- package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map +1 -1
- package/dist/MafTabixAdapter/MafTabixAdapter.d.ts +9 -6
- package/dist/MafTabixAdapter/MafTabixAdapter.js +74 -43
- package/dist/MafTabixAdapter/MafTabixAdapter.js.map +1 -1
- package/dist/MafTabixAdapter/configSchema.d.ts +7 -0
- package/dist/MafTabixAdapter/configSchema.js +7 -0
- package/dist/MafTabixAdapter/configSchema.js.map +1 -1
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js +7 -8
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map +4 -4
- package/package.json +2 -2
- package/src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts +123 -86
- package/src/BgzipTaffyAdapter/util.ts +25 -0
- package/src/BigMafAdapter/BigMafAdapter.ts +10 -4
- package/src/LinearMafDisplay/components/ColorLegend.tsx +1 -2
- package/src/LinearMafDisplay/components/ReactComponent.tsx +1 -1
- package/src/LinearMafDisplay/components/SvgWrapper.tsx +2 -2
- package/src/LinearMafDisplay/components/YScaleBars.tsx +3 -2
- package/src/LinearMafDisplay/renderSvg.tsx +5 -5
- package/src/LinearMafDisplay/stateModel.ts +30 -24
- package/src/LinearMafRenderer/LinearMafRenderer.ts +21 -176
- package/src/LinearMafRenderer/configSchema.ts +6 -1
- package/src/LinearMafRenderer/makeImageData.ts +211 -0
- package/src/LinearMafRenderer/util.ts +28 -1
- package/src/MafAddTrackWorkflow/AddTrackWorkflow.tsx +2 -1
- package/src/MafTabixAdapter/MafTabixAdapter.ts +92 -44
- package/src/MafTabixAdapter/configSchema.ts +7 -0
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@@ -1,12 +1,13 @@
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import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
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import { Feature, Region } from '@jbrowse/core/util';
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import type { IndexData } from './types';
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export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
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setupP?: Promise<IndexData>;
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getRefNames(): Promise<string[]>;
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setupPre(): Promise<IndexData>;
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setup(opts?: BaseOptions): Promise<IndexData>;
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readTaiFile(): Promise<IndexData>;
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getFeatures(query: Region): import("rxjs").Observable<Feature>;
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getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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getSamples(_query: Region): Promise<{
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samples: {
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id: string;
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@@ -15,6 +16,6 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
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}[];
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tree: Record<string, any> | undefined;
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}>;
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getLines(query: Region): Promise<
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getLines(query: Region, byteRanges: IndexData): Promise<Uint8Array<ArrayBuffer> | undefined>;
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freeResources(): void;
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}
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import { unzip } from '@gmod/bgzf-filehandle';
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import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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import { SimpleFeature } from '@jbrowse/core/util';
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import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
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import { SimpleFeature, updateStatus, } from '@jbrowse/core/util';
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import { openLocation } from '@jbrowse/core/util/io';
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import { ObservableCreate } from '@jbrowse/core/util/rxjs';
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import Long from 'long';
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@@ -8,13 +8,15 @@ import VirtualOffset from './virtualOffset';
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import parseNewick from '../parseNewick';
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import { normalize } from '../util';
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import { parseRowInstructions } from './rowInstructions';
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import { parseLineByLine } from './util';
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const toP = (s = 0) => +(+s).toFixed(1);
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export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
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setupP;
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async getRefNames() {
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const data = await this.setup();
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return Object.keys(data);
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}
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setupPre() {
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if (!this.setupP) {
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this.setupP = this.readTaiFile().catch((e) => {
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this.setupP = undefined;
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@@ -23,6 +25,10 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
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}
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return this.setupP;
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}
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setup(opts) {
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const { statusCallback = () => { } } = opts || {};
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return updateStatus('Downloading index', statusCallback, () => this.setupPre());
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}
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async readTaiFile() {
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const text = await openLocation(this.getConf('taiLocation')).readFile('utf8');
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const lines = text
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@@ -61,88 +67,103 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
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}
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return entries;
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}
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getFeatures(query) {
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getFeatures(query, opts) {
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const { statusCallback = () => { } } = opts || {};
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console.log(query.start, query.end, 'wtf');
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return ObservableCreate(async (observer) => {
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try {
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if (
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const byteRanges = await this.setup();
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const buffer = await updateStatus('Downloading alignments', statusCallback, () => this.getLines(query, byteRanges));
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if (buffer) {
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const alignments = {};
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const data = [];
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let a0;
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let j = 0;
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let b = 0;
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parseLineByLine(buffer, line => {
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if (j++ % 100 === 0) {
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statusCallback(`Processing ${toP(b / 1_000_000)}/${toP(buffer.length / 1_000_000)}Mb`);
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}
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b += line.length;
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if (line) {
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const [lineData, rowInstructions] = line.split(' ; ');
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if (rowInstructions) {
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for (const ins of parseRowInstructions(rowInstructions)) {
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if (ins.type === 'i') {
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data.splice(ins.row, 0, ins);
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if (!alignments[ins.asm]) {
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alignments[ins.asm] = {
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start: ins.start,
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strand: ins.strand,
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srcSize: ins.length,
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chr: ins.ref,
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data: '',
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};
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}
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const e = alignments[ins.asm];
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e.data += ' '.repeat(Math.max(0, j - e.data.length)); // catch it up
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}
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else if (ins.type === 's') {
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if (!alignments[ins.asm]) {
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alignments[ins.asm] = {
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start: ins.start,
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strand: ins.strand,
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srcSize: ins.length,
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chr: ins.ref,
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data: '',
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};
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}
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const e = alignments[ins.asm];
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e.data += ' '.repeat(Math.max(0, j - e.data.length)); // catch it up
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data[ins.row] = ins;
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}
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data.splice(ins.row, 1);
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// no gaps for now(?)
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// else if (ins.type === 'g') {
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// }
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// else if (ins.type === 'G') {
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// }
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}
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a0 = data[0];
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}
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// }
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const lineLen = lineData.length;
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for (let i = 0; i < lineLen; i++) {
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const letter = lineData[i];
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const r = data[i];
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if (r) {
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alignments[r.asm].data += letter;
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}
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else {
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// not sure why but chr22_KI270731v1_random.taf.gz ends up here
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}
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});
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if (a0) {
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const row0 = alignments[a0.asm];
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// see
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// https://github.com/ComparativeGenomicsToolkit/taffy/blob/f5a5354/docs/taffy_utilities.md#referenced-based-maftaf-and-indexing
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// for the significance of row[0]:
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//
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// "An anchor line in TAF is a column from which all sequence
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// lines "
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observer.next(new SimpleFeature({
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uniqueId: `${row0.start}-${row0.data.length}`,
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refName: query.refName,
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start: row0.start,
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alignments,
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seq: row0.data,
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}));
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observer.next(new SimpleFeature({
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uniqueId: `${row0.start}-${row0.data.length}`,
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start: row0.start,
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statusCallback('');
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observer.complete();
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}
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catch (e) {
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// TODO: cache processed large chunks
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async getLines(query, byteRanges) {
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nextEntry = nextEntry ?? records.at(-1);
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// we NEED at least a firstEntry (validate behavior?) because othrwise it fetches whole
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// file whn you request e.g. out of range region (e.g. taf in chr22:1-100
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// and you are at chr22:200-300)
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const buffer = await unzip(response);
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return
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.decode(buffer.slice(firstEntry.virtualOffset.dataPosition))
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.split('\n');
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}
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-
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|
|
1
|
+
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@@ -0,0 +1 @@
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1
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+
export declare function parseLineByLine<T>(buffer: Uint8Array, cb: (line: string) => T | undefined): T[];
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1
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export function parseLineByLine(buffer, cb) {
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let blockStart = 0;
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const entries = [];
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const decoder = new TextDecoder('utf8');
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while (blockStart < buffer.length) {
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const n = buffer.indexOf(10, blockStart);
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if (n === -1) {
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break;
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}
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const b = buffer.subarray(blockStart, n);
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|
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const line = decoder.decode(b).trim();
|
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if (line) {
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const entry = cb(line);
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if (entry) {
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entries.push(entry);
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}
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}
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blockStart = n + 1;
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}
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return entries;
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}
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//# sourceMappingURL=util.js.map
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@@ -0,0 +1 @@
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1
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+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/BgzipTaffyAdapter/util.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAC7B,MAAkB,EAClB,EAAmC;IAEnC,IAAI,UAAU,GAAG,CAAC,CAAA;IAClB,MAAM,OAAO,GAAQ,EAAE,CAAA;IACvB,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,MAAM,CAAC,CAAA;IACvC,OAAO,UAAU,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC;QAClC,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC,EAAE,EAAE,UAAU,CAAC,CAAA;QACxC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC;YACb,MAAK;QACP,CAAC;QACD,MAAM,CAAC,GAAG,MAAM,CAAC,QAAQ,CAAC,UAAU,EAAE,CAAC,CAAC,CAAA;QACxC,MAAM,IAAI,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QACrC,IAAI,IAAI,EAAE,CAAC;YACT,MAAM,KAAK,GAAG,EAAE,CAAC,IAAI,CAAC,CAAA;YACtB,IAAI,KAAK,EAAE,CAAC;gBACV,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACrB,CAAC;QACH,CAAC;QAED,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;IACpB,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC"}
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@@ -1,5 +1,6 @@
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|
1
1
|
import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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2
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-
import {
|
|
2
|
+
import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
|
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3
|
+
import type { Feature, Region } from '@jbrowse/core/util';
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3
4
|
export default class BigMafAdapter extends BaseFeatureDataAdapter {
|
|
4
5
|
setupP?: Promise<{
|
|
5
6
|
adapter: BaseFeatureDataAdapter;
|
|
@@ -12,7 +13,7 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
|
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|
12
13
|
}>;
|
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13
14
|
getRefNames(): Promise<string[]>;
|
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14
15
|
getHeader(): Promise<unknown>;
|
|
15
|
-
getFeatures(query: Region): import("rxjs").Observable<Feature>;
|
|
16
|
+
getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
|
|
16
17
|
getSamples(_query: Region): Promise<{
|
|
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18
|
samples: {
|
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|
id: string;
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
|
|
2
|
-
import { SimpleFeature } from '@jbrowse/core/util';
|
|
2
|
+
import { SimpleFeature, updateStatus } from '@jbrowse/core/util';
|
|
3
3
|
import { openLocation } from '@jbrowse/core/util/io';
|
|
4
4
|
import { ObservableCreate } from '@jbrowse/core/util/rxjs';
|
|
5
5
|
import { getSnapshot } from 'mobx-state-tree';
|
|
@@ -37,10 +37,11 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
|
|
|
37
37
|
const { adapter } = await this.setup();
|
|
38
38
|
return adapter.getHeader();
|
|
39
39
|
}
|
|
40
|
-
getFeatures(query) {
|
|
40
|
+
getFeatures(query, opts) {
|
|
41
|
+
const { statusCallback = () => { } } = opts || {};
|
|
41
42
|
return ObservableCreate(async (observer) => {
|
|
42
43
|
const { adapter } = await this.setup();
|
|
43
|
-
const features = await firstValueFrom(adapter.getFeatures(query).pipe(toArray()));
|
|
44
|
+
const features = await updateStatus('Downloading alignment', statusCallback, () => firstValueFrom(adapter.getFeatures(query).pipe(toArray())));
|
|
44
45
|
for (const feature of features) {
|
|
45
46
|
const maf = feature.get('mafBlock');
|
|
46
47
|
const blocks = maf.split(';');
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BigMafAdapter.js","sourceRoot":"","sources":["../../src/BigMafAdapter/BigMafAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAA;AAChF,OAAO,
|
|
1
|
+
{"version":3,"file":"BigMafAdapter.js","sourceRoot":"","sources":["../../src/BigMafAdapter/BigMafAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAA;AAChF,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AAChE,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAanC,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,sBAAsB;IACxD,MAAM,CAA+C;IAE5D,KAAK,CAAC,KAAK;QACT,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;QAC/C,CAAC;QACD,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC;YACvC,GAAG,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC;YAC3B,IAAI,EAAE,eAAe;SACtB,CAAC,CAAA;QACF,OAAO;YACL,OAAO,EAAE,OAAO,CAAC,WAAqC;SACvD,CAAA;IACH,CAAC;IACD,KAAK,CAAC,QAAQ;QACZ,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBAC9C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,SAAS,EAAE,CAAA;IAC5B,CAAC;IAED,WAAW,CAAC,KAAa,EAAE,IAAkB;QAC3C,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACtC,MAAM,QAAQ,GAAG,MAAM,YAAY,CACjC,uBAAuB,EACvB,cAAc,EACd,GAAG,EAAE,CAAC,cAAc,CAAC,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CACjE,CAAA;YACD,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;gBAC/B,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,UAAU,CAAW,CAAA;gBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;gBAC7B,IAAI,GAAuB,CAAA;gBAC3B,MAAM,IAAI,GAAG,EAAc,CAAA;gBAC3B,MAAM,UAAU,GAAG,EAAoC,CAAA;gBACvD,MAAM,OAAO,GAAG,EAAc,CAAA;gBAC9B,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;oBAC3B,IAAI,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC1B,IAAI,GAAG,EAAE,CAAC;4BACR,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAE,CAAC,CAAA;4BAChC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;wBACrB,CAAC;6BAAM,CAAC;4BACN,GAAG,GAAG,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;4BAC1B,IAAI,CAAC,IAAI,CAAC,GAAI,CAAC,CAAA;4BACf,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;wBACrB,CAAC;oBACH,CAAC;gBACH,CAAC;gBAED,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;oBACxC,MAAM,GAAG,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;oBACvB,MAAM,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;oBAC1B,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBAC3B,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;oBACjB,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;oBAEjB,UAAU,CAAC,GAAG,CAAC,GAAG;wBAChB,GAAG,EAAE,GAAG;wBACR,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;wBACd,OAAO,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;wBAChB,MAAM,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;wBAC9B,OAAO,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;wBAChB,IAAI,EAAE,IAAI,CAAC,CAAC,CAAE;qBACf,CAAA;gBACH,CAAC;gBACD,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,OAAO,CAAC,EAAE,EAAE;oBAChB,IAAI,EAAE;wBACJ,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;wBAC3B,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC;wBACvB,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC;wBAC/B,GAAG,EAAE,IAAI,CAAC,CAAC,CAAC;wBACZ,UAAU,EAAE,UAAU;qBACvB;iBACF,CAAC,CACH,CAAA;YACH,CAAC;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,MAAc;QAC7B,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACxC,MAAM,EAAE,GACN,KAAK,CAAC,GAAG,KAAK,gBAAgB;YAC5B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,MAAM,YAAY,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QAEhD,2EAA2E;QAC3E,OAAO;QACP,OAAO;YACL,OAAO,EAAE,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YAC3C,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;SACvC,CAAA;IACH,CAAC;IAED,aAAa,KAAU,CAAC;CACzB"}
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@@ -3,7 +3,7 @@ import { observer } from 'mobx-react';
|
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3
3
|
import RectBg from './RectBg';
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4
4
|
import Tree from './Tree';
|
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5
|
const ColorLegend = observer(function ({ model, labelWidth, svgFontSize, }) {
|
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|
-
const { totalHeight, treeWidth, samples, rowHeight } = model;
|
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+
const { totalHeight, treeWidth, samples = [], rowHeight } = model;
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|
const canDisplayLabel = rowHeight >= 8;
|
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const boxHeight = Math.min(20, rowHeight);
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|
return (React.createElement(React.Fragment, null,
|
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@@ -1 +1 @@
|
|
|
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;
|
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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;AAGrC,OAAO,MAAM,MAAM,UAAU,CAAA;AAC7B,OAAO,IAAI,MAAM,QAAQ,CAAA;AAEzB,MAAM,WAAW,GAAG,QAAQ,CAAC,UAAU,EACrC,KAAK,EACL,UAAU,EACV,WAAW,GAKZ;IACC,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,OAAO,GAAG,EAAE,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IACjE,MAAM,eAAe,GAAG,SAAS,IAAI,CAAC,CAAA;IACtC,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,CAAC,EAAE,GAAG,GAAG,SAAS,GAAG,SAAS,GAAG,CAAC,EAClC,gBAAgB,EAAC,QAAQ,EACzB,CAAC,EAAE,CAAC,EACJ,QAAQ,EAAE,WAAW,IAEpB,MAAM,CAAC,KAAK,CACR,CACR,CAAC;gBACJ,CAAC,CAAC,IAAI,CACN,CACH,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,WAAW,CAAA"}
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@@ -33,7 +33,7 @@ const LinearMafDisplay = observer(function (props) {
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} },
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34
|
React.createElement(BaseLinearDisplayComponent, { ...props }),
|
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React.createElement(YScaleBars, { model: model }),
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-
mouseY ? (React.createElement("div", { style: { position: 'relative' } },
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+
mouseY && sources ? (React.createElement("div", { style: { position: 'relative' } },
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|
React.createElement("svg", { className: classes.cursor, width: width, height: height, style: {
|
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|
position: 'absolute',
|
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39
39
|
top: scrollTop,
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ReactComponent.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/ReactComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE/C,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,aAAa,MAAM,gCAAgC,CAAA;AAC1D,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,CAAC,CAAC,CAAC,
|
|
1
|
+
{"version":3,"file":"ReactComponent.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/ReactComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE/C,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,aAAa,MAAM,gCAAgC,CAAA;AAC1D,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"}
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@@ -6,13 +6,13 @@ const SvgWrapper = observer(function ({ children, model, exportSVG, }) {
|
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6
6
|
return React.createElement(React.Fragment, null, children);
|
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7
7
|
}
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|
else {
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-
const {
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+
const { totalHeight } = model;
|
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10
10
|
return (React.createElement("svg", { style: {
|
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position: 'absolute',
|
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12
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top: 0,
|
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13
13
|
left: 0,
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14
|
pointerEvents: 'none',
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-
height:
|
|
15
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+
height: totalHeight,
|
|
16
16
|
width: getContainingView(model).width,
|
|
17
17
|
} }, children));
|
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18
18
|
}
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@@ -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;AAKrC,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,
|
|
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;AAKrC,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"}
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@@ -11,8 +11,8 @@ export const YScaleBars = observer(function (props) {
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const canDisplayLabel = rowHeight >= 8;
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const minWidth = 20;
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const labelWidth = max(samples
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-
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-
.map(width => (canDisplayLabel ? width : minWidth)));
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+
?.map(s => measureText(s.label, svgFontSize))
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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, labelWidth: labelWidth, svgFontSize: svgFontSize })));
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});
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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,WAAW,EAAE,MAAM,oBAAoB,CAAA;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,OAAO,WAAW,MAAM,eAAe,CAAA;AACvC,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,EAAE,GAAG,EAAE,MAAM,QAAQ,CAAA;AAE5B,MAAM,CAAC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,KAI5C;IACC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;IACxD,MAAM,eAAe,GAAG,SAAS,IAAI,CAAC,CAAA;IACtC,MAAM,QAAQ,GAAG,EAAE,CAAA;IAEnB,MAAM,UAAU,GAAG,GAAG,CACpB,OAAO;
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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,WAAW,EAAE,MAAM,oBAAoB,CAAA;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,OAAO,WAAW,MAAM,eAAe,CAAA;AACvC,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,EAAE,GAAG,EAAE,MAAM,QAAQ,CAAA;AAE5B,MAAM,CAAC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,KAI5C;IACC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;IACxD,MAAM,eAAe,GAAG,SAAS,IAAI,CAAC,CAAA;IACtC,MAAM,QAAQ,GAAG,EAAE,CAAA;IAEnB,MAAM,UAAU,GAAG,GAAG,CACpB,OAAO;QACL,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,EAAE,WAAW,CAAC,CAAC;SAC5C,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,EAC3D,CAAC,CACF,CAAA;IAED,OAAO,CACL,oBAAC,UAAU,OAAK,KAAK;QACnB,oBAAC,WAAW,IACV,KAAK,EAAE,KAAK,EACZ,UAAU,EAAE,UAAU,EACtB,WAAW,EAAE,WAAW,GACxB,CACS,CACd,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}
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@@ -1,4 +1,4 @@
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1
1
|
import React from 'react';
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2
|
-
import {
|
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3
|
-
import {
|
|
2
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+
import type { LinearMafDisplayModel } from './stateModel';
|
|
3
|
+
import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
|
|
4
4
|
export declare function renderSvg(self: LinearMafDisplayModel, opts: ExportSvgDisplayOptions, superRenderSvg: (opts: ExportSvgDisplayOptions) => Promise<React.ReactNode>): Promise<React.JSX.Element>;
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|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"renderSvg.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/renderSvg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;
|
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1
|
+
{"version":3,"file":"renderSvg.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/renderSvg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAEtD,OAAO,UAAU,MAAM,yBAAyB,CAAA;AAQhD,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,IAA2B,EAC3B,IAA6B,EAC7B,cAA2E;IAE3E,MAAM,EAAE,MAAM,EAAE,EAAE,EAAE,GAAG,IAAI,CAAA;IAC3B,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,iBAAiB,CAAC,IAAI,CAA0B,CAAA;IAC5E,MAAM,MAAM,GAAG,WAAW,EAAE,EAAE,CAAA;IAC9B,OAAO,CACL;QACE;YACE,kCAAU,EAAE,EAAE,MAAM;gBAClB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,GAAI,CACzC,CACN;QACP,2BAAG,QAAQ,EAAE,QAAQ,MAAM,GAAG;YAC5B,2BAAG,EAAE,EAAC,QAAQ,IAAE,MAAM,cAAc,CAAC,IAAI,CAAC,CAAK;YAC/C,2BAAG,SAAS,EAAE,aAAa,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,GAAG;gBAClD,oBAAC,UAAU,IAAC,KAAK,EAAE,IAAI,EAAE,WAAW,EAAC,MAAM,EAAC,SAAS,SAAG,CACtD,CACF,CACH,CACJ,CAAA;AACH,CAAC"}
|
|
@@ -1,9 +1,9 @@
|
|
|
1
|
-
import
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2
|
-
import
|
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3
|
-
import {
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|
4
|
-
import {
|
|
5
|
-
import {
|
|
6
|
-
import {
|
|
1
|
+
import type { NodeWithIdsAndLength } from './types';
|
|
2
|
+
import type PluginManager from '@jbrowse/core/PluginManager';
|
|
3
|
+
import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
|
|
4
|
+
import type { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
|
|
5
|
+
import type { HierarchyNode } from 'd3-hierarchy';
|
|
6
|
+
import type { Instance } from 'mobx-state-tree';
|
|
7
7
|
interface Sample {
|
|
8
8
|
id: string;
|
|
9
9
|
label: string;
|
|
@@ -25,9 +25,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
25
25
|
} & {
|
|
26
26
|
blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
|
|
27
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|
key: import("mobx-state-tree").ISimpleType<string>;
|
|
28
|
-
region: import("mobx-state-tree"
|
|
29
|
-
* #property
|
|
30
|
-
*/).IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
|
|
28
|
+
region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
|
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31
29
|
reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
32
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|
isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
33
31
|
isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
@@ -58,9 +56,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
58
56
|
setStatus(message: string): void;
|
|
59
57
|
setLoading(newStopToken: string): void;
|
|
60
58
|
setMessage(messageText: string): void;
|
|
61
|
-
setRendered(props: import("@jbrowse/plugin-linear-genome-view/dist/BaseLinearDisplay/models/serverSideRenderedBlock"
|
|
62
|
-
* #getter
|
|
63
|
-
*/).RenderedProps | undefined): void;
|
|
59
|
+
setRendered(props: import("@jbrowse/plugin-linear-genome-view/dist/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
|
|
64
60
|
setError(error: unknown): void;
|
|
65
61
|
reload(): void;
|
|
66
62
|
beforeDestroy(): void;
|
|
@@ -116,9 +112,15 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
116
112
|
rendererTypeName: string;
|
|
117
113
|
error: unknown;
|
|
118
114
|
message: string | undefined;
|
|
119
|
-
} & import(
|
|
115
|
+
} & import(
|
|
116
|
+
/**
|
|
117
|
+
* #getter
|
|
118
|
+
*/
|
|
119
|
+
"mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
120
120
|
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
121
|
-
type: import("mobx-state-tree"
|
|
121
|
+
type: import("mobx-state-tree" /**
|
|
122
|
+
* #getter
|
|
123
|
+
*/).ISimpleType<string>;
|
|
122
124
|
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
123
125
|
}, {
|
|
124
126
|
rendererTypeName: string;
|
|
@@ -236,11 +238,11 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
236
238
|
/**
|
|
237
239
|
* #volatile
|
|
238
240
|
*/
|
|
239
|
-
volatileSamples: Sample[];
|
|
241
|
+
volatileSamples: Sample[] | undefined;
|
|
240
242
|
/**
|
|
241
243
|
* #volatile
|
|
242
244
|
*/
|
|
243
|
-
|
|
245
|
+
volatileTree: any;
|
|
244
246
|
} & {
|
|
245
247
|
/**
|
|
246
248
|
* #action
|
|
@@ -292,7 +294,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
|
|
|
292
294
|
id: string;
|
|
293
295
|
label: string;
|
|
294
296
|
color?: string;
|
|
295
|
-
}[];
|
|
297
|
+
}[] | undefined;
|
|
296
298
|
/**
|
|
297
299
|
* #getter
|
|
298
300
|
*/
|