@jbrowse/plugin-gff3 3.0.1 → 3.0.2

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Files changed (5) hide show
  1. package/dist/Gff3TabixAdapter/Gff3TabixAdapter.d.ts +11 -7
  2. package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js +43 -22
  3. package/esm/Gff3TabixAdapter/Gff3TabixAdapter.d.ts +11 -7
  4. package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js +43 -22
  5. package/package.json +4 -4
package/dist/Gff3TabixAdapter/Gff3TabixAdapter.d.ts CHANGED
@@ -1,17 +1,21 @@
1
1
  import { TabixIndexedFile } from '@gmod/tabix';
2
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  import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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- import type PluginManager from '@jbrowse/core/PluginManager';
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- import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
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  import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
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- import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
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  import type { Feature } from '@jbrowse/core/util/simpleFeature';
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  import type { Region } from '@jbrowse/core/util/types';
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  export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
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- protected gff: TabixIndexedFile;
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- protected dontRedispatch: string[];
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- constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
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+ private configured?;
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+ private configurePre;
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+ protected configurePre2(): Promise<{
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+ gff: TabixIndexedFile;
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+ dontRedispatch: string[];
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+ }>;
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+ configure(opts?: BaseOptions): Promise<{
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+ gff: TabixIndexedFile;
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+ dontRedispatch: string[];
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+ }>;
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  getRefNames(opts?: BaseOptions): Promise<string[]>;
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- getHeader(): Promise<string>;
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+ getHeader(opts?: BaseOptions): Promise<string>;
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  getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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  private getFeaturesHelper;
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  private parseLine;
package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js CHANGED
@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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  };
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  Object.defineProperty(exports, "__esModule", { value: true });
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  const tabix_1 = require("@gmod/tabix");
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- const configuration_1 = require("@jbrowse/core/configuration");
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  const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
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+ const util_1 = require("@jbrowse/core/util");
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  const io_1 = require("@jbrowse/core/util/io");
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  const range_1 = require("@jbrowse/core/util/range");
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  const rxjs_1 = require("@jbrowse/core/util/rxjs");
@@ -13,50 +13,71 @@ const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeatur
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  const gff_nostream_1 = require("gff-nostream");
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  const featureData_1 = require("../featureData");
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  class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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- constructor(config, getSubAdapter, pluginManager) {
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- super(config, getSubAdapter, pluginManager);
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- const gffGzLocation = (0, configuration_1.readConfObject)(config, 'gffGzLocation');
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- const indexType = (0, configuration_1.readConfObject)(config, ['index', 'indexType']);
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- const location = (0, configuration_1.readConfObject)(config, ['index', 'location']);
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- const dontRedispatch = (0, configuration_1.readConfObject)(config, 'dontRedispatch');
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- this.dontRedispatch = dontRedispatch || ['chromosome', 'contig', 'region'];
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- this.gff = new tabix_1.TabixIndexedFile({
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+ async configurePre(_opts) {
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+ const gffGzLocation = this.getConf('gffGzLocation');
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+ const indexType = this.getConf(['index', 'indexType']);
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+ const loc = this.getConf(['index', 'location']);
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+ const dontRedispatch = this.getConf('dontRedispatch') || [
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+ 'chromosome',
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+ 'contig',
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+ 'region',
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+ ];
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+ const gff = new tabix_1.TabixIndexedFile({
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  filehandle: (0, io_1.openLocation)(gffGzLocation, this.pluginManager),
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- csiFilehandle: indexType === 'CSI'
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- ? (0, io_1.openLocation)(location, this.pluginManager)
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- : undefined,
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- tbiFilehandle: indexType !== 'CSI'
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- ? (0, io_1.openLocation)(location, this.pluginManager)
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- : undefined,
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+ csiFilehandle: indexType === 'CSI' ? (0, io_1.openLocation)(loc, this.pluginManager) : undefined,
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+ tbiFilehandle: indexType !== 'CSI' ? (0, io_1.openLocation)(loc, this.pluginManager) : undefined,
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  chunkCacheSize: 50 * 2 ** 20,
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  renameRefSeqs: (n) => n,
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  });
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+ return {
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+ gff,
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+ dontRedispatch,
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+ header: await gff.getHeader(),
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+ };
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+ }
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+ async configurePre2() {
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+ if (!this.configured) {
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+ this.configured = this.configurePre().catch((e) => {
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+ this.configured = undefined;
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+ throw e;
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+ });
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+ }
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+ return this.configured;
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+ }
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+ async configure(opts) {
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+ const { statusCallback = () => { } } = opts || {};
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+ return (0, util_1.updateStatus)('Downloading index', statusCallback, () => this.configurePre2());
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  }
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  async getRefNames(opts = {}) {
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- return this.gff.getReferenceSequenceNames(opts);
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+ const { gff } = await this.configure(opts);
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+ return gff.getReferenceSequenceNames(opts);
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  }
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- async getHeader() {
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- return this.gff.getHeader();
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+ async getHeader(opts = {}) {
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+ const { gff } = await this.configure(opts);
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+ return gff.getHeader();
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  }
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  getFeatures(query, opts = {}) {
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  return (0, rxjs_1.ObservableCreate)(async (observer) => {
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- const metadata = await this.gff.getMetadata();
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+ const { gff } = await this.configure(opts);
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+ const metadata = await gff.getMetadata();
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  await this.getFeaturesHelper(query, opts, metadata, observer, true);
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  }, opts.stopToken);
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  }
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  async getFeaturesHelper(query, opts, metadata, observer, allowRedispatch, originalQuery = query) {
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  var _a, _b;
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+ const { statusCallback = () => { } } = opts;
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  try {
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  const lines = [];
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- await this.gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
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+ const { dontRedispatch, gff } = await this.configure(opts);
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+ await (0, util_1.updateStatus)('Downloading features', statusCallback, () => gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
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  lines.push(this.parseLine(metadata.columnNumbers, line, fileOffset));
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- });
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+ }));
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  if (allowRedispatch && lines.length) {
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  let minStart = Number.POSITIVE_INFINITY;
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  let maxEnd = Number.NEGATIVE_INFINITY;
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  for (const line of lines) {
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  const featureType = line.fields[2];
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- if (!this.dontRedispatch.includes(featureType)) {
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+ if (!dontRedispatch.includes(featureType)) {
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  const start = line.start - 1;
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  if (start < minStart) {
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  minStart = start;
package/esm/Gff3TabixAdapter/Gff3TabixAdapter.d.ts CHANGED
@@ -1,17 +1,21 @@
1
1
  import { TabixIndexedFile } from '@gmod/tabix';
2
2
  import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
3
- import type PluginManager from '@jbrowse/core/PluginManager';
4
- import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
5
3
  import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
6
- import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
7
4
  import type { Feature } from '@jbrowse/core/util/simpleFeature';
8
5
  import type { Region } from '@jbrowse/core/util/types';
9
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  export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
10
- protected gff: TabixIndexedFile;
11
- protected dontRedispatch: string[];
12
- constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
7
+ private configured?;
8
+ private configurePre;
9
+ protected configurePre2(): Promise<{
10
+ gff: TabixIndexedFile;
11
+ dontRedispatch: string[];
12
+ }>;
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+ configure(opts?: BaseOptions): Promise<{
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+ gff: TabixIndexedFile;
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+ dontRedispatch: string[];
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+ }>;
13
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  getRefNames(opts?: BaseOptions): Promise<string[]>;
14
- getHeader(): Promise<string>;
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+ getHeader(opts?: BaseOptions): Promise<string>;
15
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  getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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  private getFeaturesHelper;
17
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  private parseLine;
package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js CHANGED
@@ -1,6 +1,6 @@
1
1
  import { TabixIndexedFile } from '@gmod/tabix';
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- import { readConfObject } from '@jbrowse/core/configuration';
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  import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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+ import { updateStatus } from '@jbrowse/core/util';
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  import { openLocation } from '@jbrowse/core/util/io';
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  import { doesIntersect2 } from '@jbrowse/core/util/range';
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  import { ObservableCreate } from '@jbrowse/core/util/rxjs';
@@ -8,50 +8,71 @@ import SimpleFeature from '@jbrowse/core/util/simpleFeature';
8
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  import { parseStringSync } from 'gff-nostream';
9
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  import { featureData } from '../featureData';
10
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  export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
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- constructor(config, getSubAdapter, pluginManager) {
12
- super(config, getSubAdapter, pluginManager);
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- const gffGzLocation = readConfObject(config, 'gffGzLocation');
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- const indexType = readConfObject(config, ['index', 'indexType']);
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- const location = readConfObject(config, ['index', 'location']);
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- const dontRedispatch = readConfObject(config, 'dontRedispatch');
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- this.dontRedispatch = dontRedispatch || ['chromosome', 'contig', 'region'];
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- this.gff = new TabixIndexedFile({
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+ async configurePre(_opts) {
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+ const gffGzLocation = this.getConf('gffGzLocation');
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+ const indexType = this.getConf(['index', 'indexType']);
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+ const loc = this.getConf(['index', 'location']);
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+ const dontRedispatch = this.getConf('dontRedispatch') || [
16
+ 'chromosome',
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+ 'contig',
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+ 'region',
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+ ];
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+ const gff = new TabixIndexedFile({
19
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  filehandle: openLocation(gffGzLocation, this.pluginManager),
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- csiFilehandle: indexType === 'CSI'
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- ? openLocation(location, this.pluginManager)
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- : undefined,
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- tbiFilehandle: indexType !== 'CSI'
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- ? openLocation(location, this.pluginManager)
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- : undefined,
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+ csiFilehandle: indexType === 'CSI' ? openLocation(loc, this.pluginManager) : undefined,
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+ tbiFilehandle: indexType !== 'CSI' ? openLocation(loc, this.pluginManager) : undefined,
26
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  chunkCacheSize: 50 * 2 ** 20,
27
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  renameRefSeqs: (n) => n,
28
26
  });
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+ return {
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+ gff,
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+ dontRedispatch,
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+ header: await gff.getHeader(),
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+ };
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+ }
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+ async configurePre2() {
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+ if (!this.configured) {
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+ this.configured = this.configurePre().catch((e) => {
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+ this.configured = undefined;
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+ throw e;
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+ });
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+ }
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+ return this.configured;
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+ }
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+ async configure(opts) {
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+ const { statusCallback = () => { } } = opts || {};
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+ return updateStatus('Downloading index', statusCallback, () => this.configurePre2());
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  }
30
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  async getRefNames(opts = {}) {
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- return this.gff.getReferenceSequenceNames(opts);
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+ const { gff } = await this.configure(opts);
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+ return gff.getReferenceSequenceNames(opts);
32
49
  }
33
- async getHeader() {
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- return this.gff.getHeader();
50
+ async getHeader(opts = {}) {
51
+ const { gff } = await this.configure(opts);
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+ return gff.getHeader();
35
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  }
36
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  getFeatures(query, opts = {}) {
37
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  return ObservableCreate(async (observer) => {
38
- const metadata = await this.gff.getMetadata();
56
+ const { gff } = await this.configure(opts);
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+ const metadata = await gff.getMetadata();
39
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  await this.getFeaturesHelper(query, opts, metadata, observer, true);
40
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  }, opts.stopToken);
41
60
  }
42
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  async getFeaturesHelper(query, opts, metadata, observer, allowRedispatch, originalQuery = query) {
43
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  var _a, _b;
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+ const { statusCallback = () => { } } = opts;
44
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  try {
45
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  const lines = [];
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- await this.gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
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+ const { dontRedispatch, gff } = await this.configure(opts);
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+ await updateStatus('Downloading features', statusCallback, () => gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
47
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  lines.push(this.parseLine(metadata.columnNumbers, line, fileOffset));
48
- });
69
+ }));
49
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  if (allowRedispatch && lines.length) {
50
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  let minStart = Number.POSITIVE_INFINITY;
51
72
  let maxEnd = Number.NEGATIVE_INFINITY;
52
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  for (const line of lines) {
53
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  const featureType = line.fields[2];
54
- if (!this.dontRedispatch.includes(featureType)) {
75
+ if (!dontRedispatch.includes(featureType)) {
55
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  const start = line.start - 1;
56
77
  if (start < minStart) {
57
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  minStart = start;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-gff3",
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- "version": "3.0.1",
3
+ "version": "3.0.2",
4
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  "description": "JBrowse 2 gff3.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -39,8 +39,8 @@
39
39
  "@flatten-js/interval-tree": "^1.0.15",
40
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  "@gmod/bgzf-filehandle": "^2.0.1",
41
41
  "@gmod/tabix": "^2.0.0",
42
- "@jbrowse/core": "^3.0.1",
43
- "@jbrowse/plugin-linear-genome-view": "^3.0.1",
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+ "@jbrowse/core": "^3.0.2",
43
+ "@jbrowse/plugin-linear-genome-view": "^3.0.2",
44
44
  "@mui/material": "^6.0.0",
45
45
  "gff-nostream": "^1.3.3",
46
46
  "mobx": "^6.0.0",
@@ -53,5 +53,5 @@
53
53
  "distModule": "esm/index.js",
54
54
  "srcModule": "src/index.ts",
55
55
  "module": "esm/index.js",
56
- "gitHead": "aa2f1d1a89d2361c7fd1a93fe29506fa4554f5cc"
56
+ "gitHead": "c01a35edcb2612e94661af8793f09c95c0b13c75"
57
57
  }