@jbrowse/plugin-gff3 3.0.5 → 3.2.0

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Files changed (7) hide show
  1. package/dist/Gff3Adapter/Gff3Adapter.js +10 -6
  2. package/dist/Gff3Adapter/configSchema.js +18 -2
  3. package/dist/Gff3TabixAdapter/configSchema.js +24 -2
  4. package/esm/Gff3Adapter/Gff3Adapter.js +11 -7
  5. package/esm/Gff3Adapter/configSchema.js +18 -2
  6. package/esm/Gff3TabixAdapter/configSchema.js +24 -2
  7. package/package.json +4 -4
package/dist/Gff3Adapter/Gff3Adapter.js CHANGED
@@ -45,7 +45,7 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  }
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  }
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  if (i++ % 10000 === 0) {
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- statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
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+ statusCallback(`Loading ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
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  }
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  blockStart = n + 1;
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  }
@@ -55,13 +55,14 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  if (!this.calculatedIntervalTreeMap[refName]) {
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  sc === null || sc === void 0 ? void 0 : sc('Parsing GFF data');
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  const intervalTree = new interval_tree_1.default();
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- (0, gff_nostream_1.parseStringSync)(lines)
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+ for (const obj of (0, gff_nostream_1.parseStringSync)(lines)
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  .flat()
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  .map((f, i) => new simpleFeature_1.default({
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  data: (0, featureData_1.featureData)(f),
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  id: `${this.id}-${refName}-${i}`,
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- }))
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- .forEach(obj => intervalTree.insert([obj.get('start'), obj.get('end')], obj));
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+ }))) {
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+ intervalTree.insert([obj.get('start'), obj.get('end')], obj);
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+ }
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  this.calculatedIntervalTreeMap[refName] = intervalTree;
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  }
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  return this.calculatedIntervalTreeMap[refName];
@@ -95,9 +96,12 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  try {
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  const { start, end, refName } = query;
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  const { intervalTreeMap } = await this.loadData(opts);
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- (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([start, end]).forEach(f => {
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+ for (const f of ((_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([
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+ start,
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+ end,
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+ ])) || []) {
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  observer.next(f);
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- });
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+ }
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  observer.complete();
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  }
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  catch (e) {
package/dist/Gff3Adapter/configSchema.js CHANGED
@@ -5,7 +5,23 @@ function x() { }
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  const Gff3Adapter = (0, configuration_1.ConfigurationSchema)('Gff3Adapter', {
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  gffLocation: {
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  type: 'fileLocation',
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- defaultValue: { uri: '/path/to/my.gff', locationType: 'UriLocation' },
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+ defaultValue: {
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+ uri: '/path/to/my.gff',
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+ locationType: 'UriLocation',
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+ },
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  },
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- }, { explicitlyTyped: true });
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+ }, {
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+ explicitlyTyped: true,
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+ preProcessSnapshot: snap => {
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+ return snap.uri
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+ ? {
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+ ...snap,
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+ gffLocation: {
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+ uri: snap.uri,
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+ baseUri: snap.baseUri,
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+ },
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+ }
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+ : snap;
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+ },
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+ });
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  exports.default = Gff3Adapter;
package/dist/Gff3TabixAdapter/configSchema.js CHANGED
@@ -6,7 +6,10 @@ function x() { }
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  const Gff3TabixAdapter = (0, configuration_1.ConfigurationSchema)('Gff3TabixAdapter', {
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  gffGzLocation: {
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  type: 'fileLocation',
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- defaultValue: { uri: '/path/to/my.gff.gz', locationType: 'UriLocation' },
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+ defaultValue: {
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+ uri: '/path/to/my.gff.gz',
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+ locationType: 'UriLocation',
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+ },
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  },
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  index: (0, configuration_1.ConfigurationSchema)('Gff3TabixIndex', {
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  indexType: {
@@ -26,5 +29,24 @@ const Gff3TabixAdapter = (0, configuration_1.ConfigurationSchema)('Gff3TabixAdap
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  type: 'stringArray',
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  defaultValue: ['chromosome', 'region', 'contig'],
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  },
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- }, { explicitlyTyped: true });
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+ }, {
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+ explicitlyTyped: true,
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+ preProcessSnapshot: snap => {
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+ return snap.uri
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+ ? {
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+ ...snap,
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+ gffGzLocation: {
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+ uri: snap.uri,
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+ baseUri: snap.baseUri,
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+ },
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+ index: {
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+ location: {
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+ uri: snap.uri,
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+ baseUri: snap.baseUri,
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+ },
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+ },
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+ }
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+ : snap;
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+ },
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+ });
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  exports.default = Gff3TabixAdapter;
package/esm/Gff3Adapter/Gff3Adapter.js CHANGED
@@ -1,6 +1,6 @@
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  import IntervalTree from '@flatten-js/interval-tree';
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  import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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- import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
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+ import { fetchAndMaybeUnzip, getProgressDisplayStr } 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 SimpleFeature from '@jbrowse/core/util/simpleFeature';
@@ -40,7 +40,7 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
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  }
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  }
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  if (i++ % 10000 === 0) {
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- statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
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+ statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
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  }
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  blockStart = n + 1;
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  }
@@ -50,13 +50,14 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
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  if (!this.calculatedIntervalTreeMap[refName]) {
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  sc === null || sc === void 0 ? void 0 : sc('Parsing GFF data');
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  const intervalTree = new IntervalTree();
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- parseStringSync(lines)
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+ for (const obj of parseStringSync(lines)
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  .flat()
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  .map((f, i) => new SimpleFeature({
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  data: featureData(f),
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  id: `${this.id}-${refName}-${i}`,
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- }))
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- .forEach(obj => intervalTree.insert([obj.get('start'), obj.get('end')], obj));
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+ }))) {
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+ intervalTree.insert([obj.get('start'), obj.get('end')], obj);
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+ }
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  this.calculatedIntervalTreeMap[refName] = intervalTree;
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  }
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  return this.calculatedIntervalTreeMap[refName];
@@ -90,9 +91,12 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
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  try {
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  const { start, end, refName } = query;
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  const { intervalTreeMap } = await this.loadData(opts);
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- (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([start, end]).forEach(f => {
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+ for (const f of ((_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([
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+ start,
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+ end,
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+ ])) || []) {
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  observer.next(f);
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- });
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+ }
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  observer.complete();
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  }
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  catch (e) {
package/esm/Gff3Adapter/configSchema.js CHANGED
@@ -3,7 +3,23 @@ function x() { }
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  const Gff3Adapter = ConfigurationSchema('Gff3Adapter', {
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  gffLocation: {
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  type: 'fileLocation',
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- defaultValue: { uri: '/path/to/my.gff', locationType: 'UriLocation' },
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+ defaultValue: {
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+ uri: '/path/to/my.gff',
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+ locationType: 'UriLocation',
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+ },
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  },
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- }, { explicitlyTyped: true });
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+ }, {
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+ explicitlyTyped: true,
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+ preProcessSnapshot: snap => {
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+ return snap.uri
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+ ? {
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+ ...snap,
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+ gffLocation: {
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+ uri: snap.uri,
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+ baseUri: snap.baseUri,
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+ },
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+ }
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+ : snap;
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+ },
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+ });
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  export default Gff3Adapter;
package/esm/Gff3TabixAdapter/configSchema.js CHANGED
@@ -4,7 +4,10 @@ function x() { }
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  const Gff3TabixAdapter = ConfigurationSchema('Gff3TabixAdapter', {
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  gffGzLocation: {
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  type: 'fileLocation',
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- defaultValue: { uri: '/path/to/my.gff.gz', locationType: 'UriLocation' },
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+ defaultValue: {
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+ uri: '/path/to/my.gff.gz',
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+ locationType: 'UriLocation',
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+ },
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  },
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  index: ConfigurationSchema('Gff3TabixIndex', {
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  indexType: {
@@ -24,5 +27,24 @@ const Gff3TabixAdapter = ConfigurationSchema('Gff3TabixAdapter', {
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  type: 'stringArray',
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  defaultValue: ['chromosome', 'region', 'contig'],
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  },
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- }, { explicitlyTyped: true });
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+ }, {
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+ explicitlyTyped: true,
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+ preProcessSnapshot: snap => {
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+ return snap.uri
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+ ? {
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+ ...snap,
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+ gffGzLocation: {
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+ uri: snap.uri,
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+ baseUri: snap.baseUri,
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+ },
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+ index: {
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+ location: {
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+ uri: snap.uri,
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+ baseUri: snap.baseUri,
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+ },
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+ },
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+ }
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+ : snap;
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+ },
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+ });
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  export default Gff3TabixAdapter;
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-gff3",
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- "version": "3.0.5",
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+ "version": "3.2.0",
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  "description": "JBrowse 2 gff3.",
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  "keywords": [
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  "jbrowse",
@@ -39,8 +39,8 @@
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  "@flatten-js/interval-tree": "^1.0.15",
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  "@gmod/bgzf-filehandle": "^2.0.1",
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  "@gmod/tabix": "^2.0.0",
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- "@jbrowse/core": "^3.0.5",
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- "@jbrowse/plugin-linear-genome-view": "^3.0.5",
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+ "@jbrowse/core": "^3.2.0",
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+ "@jbrowse/plugin-linear-genome-view": "^3.2.0",
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  "@mui/material": "^6.0.0",
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  "gff-nostream": "^1.3.3",
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  "mobx": "^6.0.0",
@@ -53,5 +53,5 @@
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  "distModule": "esm/index.js",
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  "srcModule": "src/index.ts",
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  "module": "esm/index.js",
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- "gitHead": "a03749efe19e51609922272b845a331897346789"
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+ "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
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  }