jbrowse-plugin-mafviewer 1.2.1 → 1.2.3
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/README.md +6 -1
- package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.d.ts +11 -2
- package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js +123 -94
- package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.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/RectBg.js +1 -1
- package/dist/LinearMafDisplay/stateModel.d.ts +10 -0
- package/dist/LinearMafDisplay/stateModel.js +30 -10
- package/dist/LinearMafDisplay/stateModel.js.map +1 -1
- package/dist/LinearMafRenderer/LinearMafRenderer.js +1 -1
- package/dist/LinearMafRenderer/LinearMafRenderer.js.map +1 -1
- package/dist/LinearMafRenderer/makeImageData.js +25 -9
- package/dist/LinearMafRenderer/makeImageData.js.map +1 -1
- package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js +1 -1
- package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map +1 -1
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js +8 -7
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map +4 -4
- package/package.json +2 -1
- package/src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts +135 -99
- package/src/LinearMafDisplay/components/ColorLegend.tsx +2 -2
- package/src/LinearMafDisplay/components/RectBg.tsx +1 -1
- package/src/LinearMafDisplay/stateModel.ts +30 -10
- package/src/LinearMafRenderer/LinearMafRenderer.ts +1 -1
- package/src/LinearMafRenderer/makeImageData.ts +38 -9
- package/src/MafAddTrackWorkflow/AddTrackWorkflow.tsx +9 -11
package/README.md
CHANGED
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@@ -94,7 +94,12 @@ can use nhLocation or samples array on adapter
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### Example BgzipTaffyAdapter config
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-
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Note: TAF files are actually significantly slower and has known bugs...will
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update once fixed
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This notice will be removed it it is improved
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As with other adapters, you can use nhLocation or samples array on adapter
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```json
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{
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@@ -1,9 +1,18 @@
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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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import type { IndexData, OrganismRecord } from './types';
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export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
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setupP?: Promise<IndexData>;
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private cache;
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getRefNames(): Promise<string[]>;
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getChunk(buffer: Uint8Array, opts?: BaseOptions): Promise<{
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uniqueId: string;
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start: number;
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end: number;
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strand: number;
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alignments: Record<string, OrganismRecord>;
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seq: string;
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} | undefined>;
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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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@@ -16,6 +25,6 @@ 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, byteRanges: IndexData): Promise<
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getLines(query: Region, byteRanges: IndexData): Promise<unknown>;
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freeResources(): void;
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}
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@@ -1,8 +1,10 @@
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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, updateStatus, } from '@jbrowse/core/util';
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import QuickLRU from '@jbrowse/core/util/QuickLRU';
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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 AbortablePromiseCache from 'abortable-promise-cache';
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import Long from 'long';
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import VirtualOffset from './virtualOffset';
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import parseNewick from '../parseNewick';
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@@ -12,10 +14,116 @@ 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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cache = new AbortablePromiseCache({
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cache: new QuickLRU({ maxSize: 50 }),
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// @ts-expect-error
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fill: async ({ nextEntry, firstEntry }, signal, statusCallback) => {
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const file = openLocation(this.getConf('tafGzLocation'));
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const response = await file.read(nextEntry.virtualOffset.blockPosition -
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firstEntry.virtualOffset.blockPosition, firstEntry.virtualOffset.blockPosition);
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const buffer = await unzip(response);
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const slice = buffer.slice(firstEntry.virtualOffset.dataPosition);
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return this.getChunk(slice, {
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statusCallback: statusCallback,
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signal,
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});
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},
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});
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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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async getChunk(buffer, opts) {
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const { statusCallback = () => { } } = opts || {};
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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 - 1)); // 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 - 1)); // catch it up
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data[ins.row] = ins;
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}
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else if (ins.type === 'd') {
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data.splice(ins.row, 1);
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}
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// no gaps for now(?)
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// else if (ins.type === 'g') {
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// console.log('g??')
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// } else if (ins.type === 'G') {
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// console.log('G??')
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// }
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}
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if (!a0) {
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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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}
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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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// coordinates can be deduced without scanning backwards to previous
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// lines "
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return {
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uniqueId: `${row0.start}-${row0.data.length}`,
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start: row0.start,
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end: row0.start + row0.data.length,
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strand: row0.strand,
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alignments,
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seq: row0.data,
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};
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}
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return undefined;
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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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return ObservableCreate(async (observer) => {
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try {
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const byteRanges = await this.setup();
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const
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if (
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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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else if (ins.type === 'd') {
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data.splice(ins.row, 1);
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}
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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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if (!a0) {
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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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}
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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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// coordinates can be deduced without scanning backwards to previous
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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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end: row0.start + row0.data.length,
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strand: row0.strand,
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alignments,
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seq: row0.data,
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}));
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}
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const feat = await updateStatus('Downloading alignments', statusCallback, () => this.getLines(query, byteRanges));
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if (feat) {
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observer.next(
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// @ts-expect-error
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new SimpleFeature({
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...feat,
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refName: query.refName,
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}));
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}
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else {
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console.error('no feature found');
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}
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statusCallback('');
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observer.complete();
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}
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// TODO: cache processed large chunks
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async getLines(query, byteRanges) {
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const file = openLocation(this.getConf('tafGzLocation'));
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const records = byteRanges[query.refName];
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if (records) {
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let firstEntry;
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@@ -211,10 +240,10 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
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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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if (firstEntry && nextEntry) {
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return this.cache.get(`${JSON.stringify(nextEntry)}_${JSON.stringify(firstEntry)}`, {
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nextEntry,
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firstEntry,
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});
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}
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}
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return undefined;
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|
-
{"version":3,"file":"BgzipTaffyAdapter.js","sourceRoot":"","sources":["../../src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAGL,aAAa,EACb,YAAY,GACb,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,IAAI,MAAM,MAAM,CAAA;AAEvB,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAC3C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,oBAAoB,EAAE,MAAM,mBAAmB,CAAA;AACxD,OAAO,EAAE,eAAe,EAAE,MAAM,QAAQ,CAAA;
|
|
1
|
+
{"version":3,"file":"BgzipTaffyAdapter.js","sourceRoot":"","sources":["../../src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAGL,aAAa,EACb,YAAY,GACb,MAAM,oBAAoB,CAAA;AAC3B,OAAO,QAAQ,MAAM,6BAA6B,CAAA;AAClD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,OAAO,IAAI,MAAM,MAAM,CAAA;AAEvB,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAC3C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,oBAAoB,EAAE,MAAM,mBAAmB,CAAA;AACxD,OAAO,EAAE,eAAe,EAAE,MAAM,QAAQ,CAAA;AAcxC,MAAM,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAA;AAEvC,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,sBAAsB;IAC5D,MAAM,CAAqB;IAE1B,KAAK,GAAG,IAAI,qBAAqB,CAAC;QACxC,KAAK,EAAE,IAAI,QAAQ,CAAC,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC;QACpC,mBAAmB;QACnB,IAAI,EAAE,KAAK,EAAE,EAAE,SAAS,EAAE,UAAU,EAAE,EAAE,MAAM,EAAE,cAAc,EAAE,EAAE;YAChE,MAAM,IAAI,GAAG,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAC,CAAA;YACxD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,IAAI,CAC9B,SAAS,CAAC,aAAa,CAAC,aAAa;gBACnC,UAAU,CAAC,aAAa,CAAC,aAAa,EACxC,UAAU,CAAC,aAAa,CAAC,aAAa,CACvC,CAAA;YACD,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,QAAQ,CAAC,CAAA;YACpC,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,aAAa,CAAC,YAAY,CAAC,CAAA;YACjE,OAAO,IAAI,CAAC,QAAQ,CAAC,KAAK,EAAE;gBAC1B,cAAc,EAAE,cAAuC;gBACvD,MAAM;aACP,CAAC,CAAA;QACJ,CAAC;KACF,CAAC,CAAA;IAEF,KAAK,CAAC,WAAW;QACf,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC/B,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IAC1B,CAAC;IAED,KAAK,CAAC,QAAQ,CAAC,MAAkB,EAAE,IAAkB;QACnD,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,UAAU,GAAG,EAAoC,CAAA;QACvD,MAAM,IAAI,GAAG,EAAa,CAAA;QAC1B,IAAI,EAAO,CAAA;QACX,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,eAAe,CAAC,MAAM,EAAE,IAAI,CAAC,EAAE;YAC7B,IAAI,CAAC,EAAE,GAAG,GAAG,KAAK,CAAC,EAAE,CAAC;gBACpB,cAAc,CACZ,cAAc,GAAG,CAAC,CAAC,GAAG,SAAS,CAAC,IAAI,GAAG,CAAC,MAAM,CAAC,MAAM,GAAG,SAAS,CAAC,IAAI,CACvE,CAAA;YACH,CAAC;YACD,CAAC,IAAI,IAAI,CAAC,MAAM,CAAA;YAChB,IAAI,IAAI,EAAE,CAAC;gBACT,MAAM,CAAC,QAAQ,EAAE,eAAe,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBACrD,IAAI,eAAe,EAAE,CAAC;oBACpB,KAAK,MAAM,GAAG,IAAI,oBAAoB,CAAC,eAAe,CAAC,EAAE,CAAC;wBACxD,IAAI,GAAG,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;4BACrB,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;4BAC5B,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gCACzB,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG;oCACpB,KAAK,EAAE,GAAG,CAAC,KAAK;oCAChB,MAAM,EAAE,GAAG,CAAC,MAAM;oCAClB,OAAO,EAAE,GAAG,CAAC,MAAM;oCACnB,GAAG,EAAE,GAAG,CAAC,GAAG;oCACZ,IAAI,EAAE,EAAE;iCACT,CAAA;4BACH,CAAC;4BACD,MAAM,CAAC,GAAG,UAAU,CAAC,GAAG,CAAC,GAAG,CAAE,CAAA;4BAC9B,CAAC,CAAC,IAAI,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA,CAAC,cAAc;wBACzE,CAAC;6BAAM,IAAI,GAAG,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;4BAC5B,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gCACzB,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG;oCACpB,KAAK,EAAE,GAAG,CAAC,KAAK;oCAChB,MAAM,EAAE,GAAG,CAAC,MAAM;oCAClB,OAAO,EAAE,GAAG,CAAC,MAAM;oCACnB,GAAG,EAAE,GAAG,CAAC,GAAG;oCACZ,IAAI,EAAE,EAAE;iCACT,CAAA;4BACH,CAAC;4BACD,MAAM,CAAC,GAAG,UAAU,CAAC,GAAG,CAAC,GAAG,CAAE,CAAA;4BAC9B,CAAC,CAAC,IAAI,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA,CAAC,cAAc;4BACvE,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,GAAG,CAAA;wBACrB,CAAC;6BAAM,IAAI,GAAG,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;4BAC5B,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;wBACzB,CAAC;wBAED,qBAAqB;wBACrB,+BAA+B;wBAC/B,uBAAuB;wBACvB,iCAAiC;wBACjC,uBAAuB;wBACvB,IAAI;oBACN,CAAC;oBACD,IAAI,CAAC,EAAE,EAAE,CAAC;wBACR,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;oBACd,CAAC;gBACH,CAAC;gBACD,MAAM,OAAO,GAAG,QAAS,CAAC,MAAM,CAAA;gBAEhC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE,CAAC;oBACjC,MAAM,MAAM,GAAG,QAAS,CAAC,CAAC,CAAC,CAAA;oBAC3B,MAAM,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;oBAEjB,IAAI,CAAC,EAAE,CAAC;wBACN,UAAU,CAAC,CAAC,CAAC,GAAG,CAAE,CAAC,IAAI,IAAI,MAAM,CAAA;oBACnC,CAAC;yBAAM,CAAC;wBACN,+DAA+D;oBACjE,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC,CAAC,CAAA;QACF,IAAI,EAAE,EAAE,CAAC;YACP,MAAM,IAAI,GAAG,UAAU,CAAC,EAAE,CAAC,GAAG,CAAE,CAAA;YAEhC,MAAM;YACN,gIAAgI;YAChI,kCAAkC;YAClC,EAAE;YACF,6DAA6D;YAC7D,oEAAoE;YACpE,UAAU;YACV,OAAO;gBACL,QAAQ,EAAE,GAAG,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;gBAC7C,KAAK,EAAE,IAAI,CAAC,KAAK;gBACjB,GAAG,EAAE,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM;gBAClC,MAAM,EAAE,IAAI,CAAC,MAAM;gBACnB,UAAU;gBACV,GAAG,EAAE,IAAI,CAAC,IAAI;aACf,CAAA;QACH,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACpD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IACD,KAAK,CAAC,IAAkB;QACtB,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI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@@ -12,7 +12,7 @@ const ColorLegend = observer(function ({ model, labelWidth, svgFontSize, }) {
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12
12
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React.createElement("g", { transform: `translate(${treeWidth + 5},0)` },
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13
13
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samples.map((sample, idx) => (React.createElement(RectBg, { key: `${sample.id}-${idx}`, y: idx * rowHeight, x: 0, width: labelWidth + 5, height: boxHeight, color: sample.color }))),
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14
14
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canDisplayLabel
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15
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-
? samples.map((sample, idx) => (React.createElement("text", { key: `${sample.id}-${idx}`, y: idx * rowHeight + rowHeight / 2
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15
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+
? samples.map((sample, idx) => (React.createElement("text", { key: `${sample.id}-${idx}`, dominantBaseline: "middle", fontSize: svgFontSize, x: 2, y: idx * rowHeight + rowHeight / 2 }, sample.label)))
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16
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: null)));
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17
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});
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18
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export default ColorLegend;
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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;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,
|
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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;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,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"}
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@@ -320,10 +320,20 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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* #method
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*/
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trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
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type: string;
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subMenu: {
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}[];
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checked?: undefined;
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onClick?: undefined;
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} | {
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label: string;
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type: string;
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checked: boolean;
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|
onClick: () => void;
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+
subMenu?: undefined;
|
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|
})[];
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|
} & {
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afterCreate(): void;
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@@ -200,7 +200,7 @@ export default function stateModelFactory(configSchema, pluginManager) {
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const s = superRenderProps();
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return {
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...s,
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-
notReady: !self.volatileSamples
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+
notReady: (!self.volatileSamples && !self.volatileTree) || super.notReady,
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|
config: rendererConfig,
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samples,
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rowHeight,
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@@ -216,16 +216,36 @@ export default function stateModelFactory(configSchema, pluginManager) {
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|
return [
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|
...superTrackMenuItems(),
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{
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-
label: 'Set
|
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-
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-
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-
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-
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-
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-
|
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+
label: 'Set feature height',
|
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|
+
type: 'subMenu',
|
|
221
|
+
subMenu: [
|
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|
+
{
|
|
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|
+
label: 'Normal',
|
|
224
|
+
onClick: () => {
|
|
225
|
+
self.setRowHeight(15);
|
|
226
|
+
self.setRowProportion(0.8);
|
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|
},
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227
|
-
|
|
228
|
-
|
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|
+
},
|
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|
+
{
|
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|
+
label: 'Compact',
|
|
231
|
+
onClick: () => {
|
|
232
|
+
self.setRowHeight(8);
|
|
233
|
+
self.setRowProportion(0.9);
|
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234
|
+
},
|
|
235
|
+
},
|
|
236
|
+
{
|
|
237
|
+
label: 'Manually set height',
|
|
238
|
+
onClick: () => {
|
|
239
|
+
getSession(self).queueDialog(handleClose => [
|
|
240
|
+
SetRowHeightDialog,
|
|
241
|
+
{
|
|
242
|
+
model: self,
|
|
243
|
+
handleClose,
|
|
244
|
+
},
|
|
245
|
+
]);
|
|
246
|
+
},
|
|
247
|
+
},
|
|
248
|
+
],
|
|
229
249
|
},
|
|
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250
|
{
|
|
231
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|
label: 'Show all letters',
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
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;AACvD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAC3D,OAAO,EAAE,SAAS,EAAE,MAAM,UAAU,CAAA;AACpC,OAAO,EAAE,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,SAAS,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAE7D,OAAO,kBAAkB,MAAM,2BAA2B,CAAA;AAC1D,OAAO,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAChD,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAkBnC;;;GAGG;AACH,MAAM,CAAC,OAAO,UAAU,iBAAiB,CACvC,YAAwC,EACxC,aAA4B;IAE5B,MAAM,kBAAkB,GAAG,aAAa,CAAC,SAAS,CAChD,wBAAwB,CAC+B,CAAA;IACzD,MAAM,EAAE,iBAAiB,EAAE,GAAG,kBAAkB,CAAC,OAAO,CAAA;IAExD,OAAO,KAAK;SACT,OAAO,CACN,kBAAkB,EAClB,iBAAiB,EACjB,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,kBAAkB,CAAC;QACvC;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD;;WAEG;QACH,SAAS,EAAE,EAAE;QACb;;WAEG;QACH,aAAa,EAAE,GAAG;QAClB;;WAEG;QACH,cAAc,EAAE,KAAK;QACrB;;WAEG;QACH,iBAAiB,EAAE,IAAI;QAEvB;;WAEG;QACH,aAAa,EAAE,KAAK;QAEpB;;WAEG;QACH,aAAa,EAAE,EAAE;KAClB,CAAC,CACH;SACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf;;WAEG;QACH,aAAa,EAAE,IAAI;QACnB;;WAEG;QACH,eAAe,EAAE,SAAiC;QAClD;;WAEG;QACH,YAAY,EAAE,SAAgB;KAC/B,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,YAAY,CAAC,CAAS;YACpB,IAAI,CAAC,SAAS,GAAG,CAAC,CAAA;QACpB,CAAC;QACD;;WAEG;QACH,gBAAgB,CAAC,CAAS;YACxB,IAAI,CAAC,aAAa,GAAG,CAAC,CAAA;QACxB,CAAC;QACD;;WAEG;QACH,iBAAiB,CAAC,CAAU;YAC1B,IAAI,CAAC,cAAc,GAAG,CAAC,CAAA;QACzB,CAAC;QACD;;WAEG;QACH,oBAAoB,CAAC,CAAU;YAC7B,IAAI,CAAC,iBAAiB,GAAG,CAAC,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,UAAU,CAAC,EAAE,OAAO,EAAE,IAAI,EAAwC;YAChE,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,IAAI,CAAC,eAAe,CAAC,EAAE,CAAC;gBAC9C,IAAI,CAAC,eAAe,GAAG,OAAO,CAAA;YAChC,CAAC;YACD,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,YAAY,CAAC,EAAE,CAAC;gBACxC,IAAI,CAAC,YAAY,GAAG,IAAI,CAAA;YAC1B,CAAC;QACH,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,mBAAmB,CAAA;QAC5B,CAAC;QAED;;WAEG;QACH,IAAI,cAAc;YAChB,MAAM,UAAU,GAAG,OAAO,CAAC,IAAI,EAAE,CAAC,UAAU,CAAC,CAAC,IAAI,EAAE,CAAA;YACpD,MAAM,MAAM,GAAG,UAA6C,CAAA;YAE5D,OAAO,IAAI,CAAC,YAAY,CAAC,YAAY,CAAC,MAAM,CAC1C;gBACE,GAAG,MAAM;gBACT,IAAI,EAAE,mBAAmB;aAC1B,EACD,MAAM,CAAC,IAAI,CAAC,CACb,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SAEF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,IAAI;YACN,OAAO,IAAI,CAAC,YAAY;gBACtB,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC;oBAC3C,yEAAyE;qBACxE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;qBAC9B,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,CAAC;gBACtE,CAAC,CAAC,SAAS,CAAA;QACf,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;;WAGG;QACH,IAAI,SAAS;YACX,MAAM,CAAC,GAAG,IAAI,CAAC,IAAI,CAAA;YACnB,IAAI,CAAC,EAAE,CAAC;gBACN,MAAM,KAAK,GAAG,IAAI,CAAC,aAAa,CAAA;gBAChC,MAAM,KAAK,GAAG,OAAO,EAAe;qBACjC,IAAI,CAAC,CAAC,IAAI,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC;qBAC/B,UAAU,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAA;gBACtB,KAAK,CAAC,CAAC,CAAC,CAAA;gBACR,WAAW,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,EAAE,KAAK,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA;gBACzD,OAAO,CAAwC,CAAA;YACjD,CAAC;iBAAM,CAAC;gBACN,OAAO,SAAS,CAAA;YAClB,CAAC;QACH,CAAC;QACD;;WAEG;QACH,IAAI,OAAO;YACT,OAAO,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,eAAe,CAAA;QACxE,CAAC;QACD;;WAEG;QACH,IAAI,WAAW;YACb,OAAO,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA;QAChE,CAAC;QACD;;WAEG;QACH,IAAI,MAAM;YACR,OAAO,IAAI,CAAC,IAAI,EAAE,MAAM,EAAE,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,IAAI,QAAQ;YACV,OAAO,IAAI,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAC3C,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM;QACJ,6DAA6D;QAC7D,cAAc,EAAE,mBAAmB;QACnC,6DAA6D;QAC7D,WAAW,EAAE,gBAAgB,GAC9B,GAAG,IAAI,CAAA;QACR,OAAO;YACL;;eAEG;YACH,IAAI,SAAS;gBACX,OAAO,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAAA;YAChD,CAAC;YACD;;eAEG;YACH,WAAW;gBACT,MAAM,EACJ,cAAc,EACd,cAAc,EACd,OAAO,EACP,SAAS,EACT,aAAa,EACb,iBAAiB,GAClB,GAAG,IAAI,CAAA;gBACR,MAAM,CAAC,GAAG,gBAAgB,EAAE,CAAA;gBAC5B,OAAO;oBACL,GAAG,CAAC;oBACJ,QAAQ,EACN,CAAC,CAAC,IAAI,CAAC,eAAe,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,IAAI,KAAK,CAAC,QAAQ;oBACjE,MAAM,EAAE,cAAc;oBACtB,OAAO;oBACP,SAAS;oBACT,aAAa;oBACb,cAAc;oBACd,iBAAiB;iBAClB,CAAA;YACH,CAAC;YACD;;eAEG;YACH,cAAc;gBACZ,OAAO;oBACL,GAAG,mBAAmB,EAAE;oBACxB;wBACE,KAAK,EAAE,oBAAoB;wBAC3B,IAAI,EAAE,SAAS;wBACf,OAAO,EAAE;4BACP;gCACE,KAAK,EAAE,QAAQ;gCACf,OAAO,EAAE,GAAG,EAAE;oCACZ,IAAI,CAAC,YAAY,CAAC,EAAE,CAAC,CAAA;oCACrB,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAA;gCAC5B,CAAC;6BACF;4BACD;gCACE,KAAK,EAAE,SAAS;gCAChB,OAAO,EAAE,GAAG,EAAE;oCACZ,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;oCACpB,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAA;gCAC5B,CAAC;6BACF;4BACD;gCACE,KAAK,EAAE,qBAAqB;gCAC5B,OAAO,EAAE,GAAG,EAAE;oCACZ,UAAU,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;wCAC1C,kBAAkB;wCAClB;4CACE,KAAK,EAAE,IAAI;4CACX,WAAW;yCACZ;qCACF,CAAC,CAAA;gCACJ,CAAC;6BACF;yBACF;qBACF;oBACD;wBACE,KAAK,EAAE,kBAAkB;wBACzB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,IAAI,CAAC,cAAc;wBAC5B,OAAO,EAAE,GAAG,EAAE;4BACZ,IAAI,CAAC,iBAAiB,CAAC,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;wBAC9C,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,iCAAiC;wBACxC,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,CAAC,IAAI,CAAC,iBAAiB;wBAChC,OAAO,EAAE,GAAG,EAAE;4BACZ,IAAI,CAAC,oBAAoB,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAA;wBACpD,CAAC;qBACF;iBACF,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,WAAW;YACT,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,KAAK,IAAI,EAAE;gBACjB,IAAI,CAAC;oBACH,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;oBACvC,MAAM,SAAS,GAAG,eAAe,CAAC,IAAI,CAAC,CAAA;oBAEvC,MAAM,OAAO,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,CACpC,SAAS,EACT,eAAe,EACf;wBACE,SAAS;wBACT,aAAa,EAAE,IAAI,CAAC,aAAa;wBACjC,cAAc,EAAE,CAAC,OAAe,EAAE,EAAE;4BAClC,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;gCAClB,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAA;4BAC1B,CAAC;wBACH,CAAC;qBACF,CACF,CAAQ,CAAA;oBACT,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAA;gBAC1B,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;oBAChB,UAAU,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;gBACzC,CAAC;YACH,CAAC,CAAC,CACH,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,6DAA6D;QAC7D,MAAM,EAAE,SAAS,EAAE,cAAc,EAAE,GAAG,IAAI,CAAA;QAC1C,OAAO;YACL;;eAEG;YACH,KAAK,CAAC,SAAS,CAAC,IAA6B;gBAC3C,MAAM,EAAE,SAAS,EAAE,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,CAAA;gBACjD,OAAO,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,cAAc,CAAC,CAAA;YAC9C,CAAC;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}
|
|
@@ -15,7 +15,7 @@ export default class LinearMafRenderer extends FeatureRendererType {
|
|
|
15
15
|
async render(renderProps) {
|
|
16
16
|
const { statusCallback = () => { }, regions, bpPerPx, samples, rowHeight, } = renderProps;
|
|
17
17
|
const region = regions[0];
|
|
18
|
-
const height = samples.length *
|
|
18
|
+
const height = samples.length * rowHeight + 100;
|
|
19
19
|
const width = (region.end - region.start) / bpPerPx;
|
|
20
20
|
const features = await this.getFeatures(renderProps);
|
|
21
21
|
const res = await renderToAbstractCanvas(width, height, renderProps, async (ctx) => {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"LinearMafRenderer.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/LinearMafRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,qCAAqC,CAAA;AAEzE,OAAO,EAEL,sBAAsB,EACtB,YAAY,GACb,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAe/C,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,mBAAmB;IAChE,iBAAiB,CAAC,MAAc;QAC9B,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QAC7B,MAAM,WAAW,GAAG,CAAC,CAAA;QAErB,OAAO;YACL,sEAAsE;YACtE,GAAI,MAAsC;YAC1C,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,WAAW,EAAE,CAAC,CAAC,CAAC;YACnD,GAAG,EAAE,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC;SAClC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,MAAM,CAAC,WAAuB;QAClC,MAAM,EACJ,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EACzB,OAAO,EACP,OAAO,EACP,OAAO,EACP,SAAS,GACV,GAAG,WAAW,CAAA;QACf,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,
|
|
1
|
+
{"version":3,"file":"LinearMafRenderer.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/LinearMafRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,qCAAqC,CAAA;AAEzE,OAAO,EAEL,sBAAsB,EACtB,YAAY,GACb,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAe/C,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,mBAAmB;IAChE,iBAAiB,CAAC,MAAc;QAC9B,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QAC7B,MAAM,WAAW,GAAG,CAAC,CAAA;QAErB,OAAO;YACL,sEAAsE;YACtE,GAAI,MAAsC;YAC1C,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,WAAW,EAAE,CAAC,CAAC,CAAC;YACnD,GAAG,EAAE,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC;SAClC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,MAAM,CAAC,WAAuB;QAClC,MAAM,EACJ,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EACzB,OAAO,EACP,OAAO,EACP,OAAO,EACP,SAAS,GACV,GAAG,WAAW,CAAA;QACf,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,SAAS,GAAG,GAAG,CAAA;QAC/C,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QACnD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,WAAW,CAAC,CAAA;QACpD,MAAM,GAAG,GAAG,MAAM,sBAAsB,CACtC,KAAK,EACL,MAAM,EACN,WAAW,EACX,KAAK,EAAC,GAAG,EAAC,EAAE;YACV,MAAM,YAAY,CAAC,qBAAqB,EAAE,cAAc,EAAE,GAAG,EAAE;gBAC7D,aAAa,CAAC;oBACZ,GAAG;oBACH,UAAU,EAAE;wBACV,GAAG,WAAW;wBACd,QAAQ;qBACT;iBACF,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YACF,OAAO,SAAS,CAAA;QAClB,CAAC,CACF,CAAA;QACD,MAAM,OAAO,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC;YACjC,GAAG,WAAW;YACd,GAAG,GAAG;YACN,KAAK;YACL,MAAM;SACP,CAAC,CAAA;QACF,OAAO;YACL,GAAG,OAAO;YACV,GAAG,GAAG;YACN,QAAQ,EAAE,IAAI,GAAG,EAAE;YACnB,KAAK;YACL,MAAM;YACN,uBAAuB,EAAE,IAAI;SAC9B,CAAA;IACH,CAAC;CACF"}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { createJBrowseTheme } from '@jbrowse/core/ui';
|
|
2
|
-
import { featureSpanPx } from '@jbrowse/core/util';
|
|
2
|
+
import { featureSpanPx, measureText } from '@jbrowse/core/util';
|
|
3
3
|
import { fillRect, getCharWidthHeight, getColorBaseMap, getContrastBaseMap, } from './util';
|
|
4
4
|
export function makeImageData({ ctx, renderArgs, }) {
|
|
5
5
|
const { regions, bpPerPx, rowHeight, showAllLetters, theme: configTheme, mismatchRendering, samples, rowProportion, features, } = renderArgs;
|
|
@@ -52,7 +52,7 @@ export function makeImageData({ ctx, renderArgs, }) {
|
|
|
52
52
|
if (seq[i] !== '-') {
|
|
53
53
|
const c = alignment[i];
|
|
54
54
|
const l = leftPx + scale * o;
|
|
55
|
-
if (seq[i] === c && c !== '-') {
|
|
55
|
+
if (seq[i] === c && c !== '-' && c !== ' ') {
|
|
56
56
|
fillRect(ctx, l, offset + t, scale + f, h, canvasWidth);
|
|
57
57
|
}
|
|
58
58
|
o++;
|
|
@@ -117,8 +117,6 @@ export function makeImageData({ ctx, renderArgs, }) {
|
|
|
117
117
|
continue;
|
|
118
118
|
}
|
|
119
119
|
const t = rowHeight * row;
|
|
120
|
-
ctx.beginPath();
|
|
121
|
-
ctx.fillStyle = 'purple';
|
|
122
120
|
for (let i = 0, o = 0; i < alignment.length; i++) {
|
|
123
121
|
let ins = '';
|
|
124
122
|
while (seq[i] === '-') {
|
|
@@ -129,15 +127,33 @@ export function makeImageData({ ctx, renderArgs, }) {
|
|
|
129
127
|
}
|
|
130
128
|
if (ins.length > 0) {
|
|
131
129
|
const l = leftPx + scale * o - 1;
|
|
132
|
-
|
|
133
|
-
|
|
134
|
-
|
|
135
|
-
|
|
130
|
+
if (ins.length > 10) {
|
|
131
|
+
const txt = `${ins.length}`;
|
|
132
|
+
if (bpPerPx > 10) {
|
|
133
|
+
fillRect(ctx, l - 1, t, 2, h, canvasWidth, 'purple');
|
|
134
|
+
}
|
|
135
|
+
else if (h > charHeight) {
|
|
136
|
+
const rwidth = measureText(txt);
|
|
137
|
+
const padding = 5;
|
|
138
|
+
fillRect(ctx, l - rwidth / 2 - padding, t, rwidth + 2 * padding, h, canvasWidth, 'purple');
|
|
139
|
+
ctx.fillStyle = 'white';
|
|
140
|
+
ctx.fillText(txt, l - rwidth / 2, t + h);
|
|
141
|
+
}
|
|
142
|
+
else {
|
|
143
|
+
const padding = 2;
|
|
144
|
+
fillRect(ctx, l - padding, t, 2 * padding, h, canvasWidth, 'purple');
|
|
145
|
+
}
|
|
146
|
+
}
|
|
147
|
+
else {
|
|
148
|
+
fillRect(ctx, l, offset + t, 1, h, canvasWidth, 'purple');
|
|
149
|
+
if (bpPerPx < 0.2 && rowHeight > 5) {
|
|
150
|
+
fillRect(ctx, l - 2, offset + t, 5, 1, canvasWidth);
|
|
151
|
+
fillRect(ctx, l - 2, offset + t + h - 1, 5, 1, canvasWidth);
|
|
152
|
+
}
|
|
136
153
|
}
|
|
137
154
|
}
|
|
138
155
|
o++;
|
|
139
156
|
}
|
|
140
|
-
ctx.fill();
|
|
141
157
|
}
|
|
142
158
|
}
|
|
143
159
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"makeImageData.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/makeImageData.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAA;AACrD,OAAO,EAAW,aAAa,EAAE,MAAM,oBAAoB,CAAA;
|
|
1
|
+
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