@jbrowse/plugin-wiggle 2.16.0 → 2.16.1

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Files changed (9) hide show
  1. package/dist/BigWigAdapter/BigWigAdapter.js +2 -1
  2. package/dist/BigWigAdapter/configSchema.d.ts +8 -0
  3. package/dist/BigWigAdapter/configSchema.js +8 -0
  4. package/dist/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js +52 -44
  5. package/esm/BigWigAdapter/BigWigAdapter.js +2 -1
  6. package/esm/BigWigAdapter/configSchema.d.ts +8 -0
  7. package/esm/BigWigAdapter/configSchema.js +8 -0
  8. package/esm/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js +52 -44
  9. package/package.json +2 -2
package/dist/BigWigAdapter/BigWigAdapter.js CHANGED
@@ -44,10 +44,11 @@ class BigWigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  return (0, rxjs_1.ObservableCreate)(async (observer) => {
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  statusCallback('Downloading bigwig data');
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  const source = this.getConf('source');
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+ const resolutionMultiplier = this.getConf('resolutionMultiplier');
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  const { bigwig } = await this.setup(opts);
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  const feats = await bigwig.getFeatures(refName, start, end, {
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  ...opts,
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- basesPerSpan: bpPerPx / resolution,
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+ basesPerSpan: (bpPerPx / resolution) * resolutionMultiplier,
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  });
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  for (const data of feats) {
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  if (source) {
package/dist/BigWigAdapter/configSchema.d.ts CHANGED
@@ -17,5 +17,13 @@ declare const BigWigAdapter: import("@jbrowse/core/configuration/configurationSc
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  defaultValue: string;
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  description: string;
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  };
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+ /**
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+ * #slot
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+ */
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+ resolutionMultiplier: {
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+ type: string;
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+ defaultValue: number;
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+ description: string;
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+ };
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  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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  export default BigWigAdapter;
package/dist/BigWigAdapter/configSchema.js CHANGED
@@ -24,5 +24,13 @@ const BigWigAdapter = (0, configuration_1.ConfigurationSchema)('BigWigAdapter',
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  defaultValue: '',
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  description: 'Used for multiwiggle',
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  },
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+ /**
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+ * #slot
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+ */
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+ resolutionMultiplier: {
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+ type: 'number',
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+ defaultValue: 1,
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+ description: 'Initial resolution multiplier',
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+ },
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  }, { explicitlyTyped: true });
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  exports.default = BigWigAdapter;
package/dist/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js CHANGED
@@ -30,9 +30,6 @@ const mui_1 = require("tss-react/mui");
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  const util_1 = require("@jbrowse/core/util");
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  const tracks_1 = require("@jbrowse/core/util/tracks");
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  const useStyles = (0, mui_1.makeStyles)()(theme => ({
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- textbox: {
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- width: '100%',
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- },
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  paper: {
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  margin: theme.spacing(),
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  padding: theme.spacing(),
@@ -43,6 +40,16 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
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  display: 'block',
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  },
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  }));
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+ // on electron, use path to LocalFileLocation, on web, use the BlobLocation
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+ function makeFileLocation(file) {
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+ const { webUtils } = window.require('electron');
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+ return util_1.isElectron
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+ ? {
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+ localPath: webUtils.getPathForFile(file),
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+ locationType: 'LocalPathLocation',
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+ }
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+ : (0, tracks_1.storeBlobLocation)({ blob: file });
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+ }
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  function MultiWiggleWidget({ model }) {
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  const { classes } = useStyles();
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  const [val, setVal] = (0, react_1.useState)('');
@@ -51,64 +58,65 @@ function MultiWiggleWidget({ model }) {
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  react_1.default.createElement("ul", null,
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  react_1.default.createElement("li", null, "Enter list of URLs for bigwig files in the textbox"),
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  react_1.default.createElement("li", null, "Or, use the button below the text box to select files from your computer")),
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- react_1.default.createElement(material_1.TextField, { multiline: true, rows: 10, value: val, onChange: event => {
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+ react_1.default.createElement(material_1.TextField, { multiline: true, fullWidth: true, rows: 10, value: val, placeholder: "Paste list of URLs here, or use file selector below", variant: "outlined", onChange: event => {
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  setVal(event.target.value);
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- }, placeholder: 'Paste list of URLs here, or use file selector below', variant: "outlined", className: classes.textbox }),
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+ } }),
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  react_1.default.createElement(material_1.Button, { variant: "outlined", component: "label" },
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  "Choose Files from your computer",
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  react_1.default.createElement("input", { type: "file", hidden: true, multiple: true, onChange: ({ target }) => {
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  const res = [...(target.files || [])].map(file => ({
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  type: 'BigWigAdapter',
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- bigWigLocation: util_1.isElectron
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- ? {
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- localPath: file.path,
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- locationType: 'LocalPathLocation',
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- }
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- : (0, tracks_1.storeBlobLocation)({ blob: file }),
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+ bigWigLocation: makeFileLocation(file),
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  source: file.name,
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  }));
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  setVal(JSON.stringify(res, null, 2));
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  } })),
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- react_1.default.createElement(material_1.TextField, { value: trackName, onChange: event => {
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+ react_1.default.createElement(material_1.TextField, { value: trackName, helperText: "Track name", onChange: event => {
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  setTrackName(event.target.value);
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- }, helperText: "Track name" }),
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+ } }),
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  react_1.default.createElement(material_1.Button, { variant: "contained", className: classes.submit, onClick: () => {
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  var _a;
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  const session = (0, util_1.getSession)(model);
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- const trackId = [
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- `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
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- session.adminMode ? '' : '-sessionTrack',
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- ].join('');
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- // allow list of bigwigs in JSON format or line-by-line
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- let bigWigs;
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  try {
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- bigWigs = JSON.parse(val);
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+ const trackId = [
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+ `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
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+ session.adminMode ? '' : '-sessionTrack',
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+ ].join('');
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+ // allow list of bigwigs in JSON format or line-by-line
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+ let bigWigs;
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+ try {
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+ bigWigs = JSON.parse(val);
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+ }
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+ catch (e) {
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+ bigWigs = val
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+ .split(/\n|\r\n|\r/)
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+ .map(f => f.trim())
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+ .filter(f => !!f);
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+ }
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+ const obj = typeof bigWigs[0] === 'string'
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+ ? { bigWigs }
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+ : { subadapters: bigWigs };
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+ if ((0, util_1.isSessionWithAddTracks)(session)) {
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+ session.addTrackConf({
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+ trackId,
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+ type: 'MultiQuantitativeTrack',
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+ name: trackName,
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+ assemblyNames: [model.assembly],
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+ adapter: {
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+ type: 'MultiWiggleAdapter',
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+ ...obj,
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+ },
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+ });
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+ (_a = model.view) === null || _a === void 0 ? void 0 : _a.showTrack(trackId);
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+ }
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+ model.clearData();
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+ if ((0, util_1.isSessionModelWithWidgets)(session)) {
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+ session.hideWidget(model);
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+ }
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  }
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  catch (e) {
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- bigWigs = val
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- .split(/\n|\r\n|\r/)
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- .map(f => f.trim())
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- .filter(f => !!f);
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- }
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- const obj = typeof bigWigs[0] === 'string'
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- ? { bigWigs }
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- : { subadapters: bigWigs };
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- if ((0, util_1.isSessionWithAddTracks)(session)) {
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- session.addTrackConf({
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- trackId,
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- type: 'MultiQuantitativeTrack',
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- name: trackName,
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- assemblyNames: [model.assembly],
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- adapter: {
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- type: 'MultiWiggleAdapter',
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- ...obj,
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- },
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- });
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- (_a = model.view) === null || _a === void 0 ? void 0 : _a.showTrack(trackId);
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- }
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- model.clearData();
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- if ((0, util_1.isSessionModelWithWidgets)(session)) {
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- session.hideWidget(model);
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+ console.error(e);
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+ session.notifyError(`${e}`, e);
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  }
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  } }, "Submit"),
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  react_1.default.createElement("p", null, "Additional notes: "),
package/esm/BigWigAdapter/BigWigAdapter.js CHANGED
@@ -42,10 +42,11 @@ class BigWigAdapter extends BaseFeatureDataAdapter {
42
42
  return ObservableCreate(async (observer) => {
43
43
  statusCallback('Downloading bigwig data');
44
44
  const source = this.getConf('source');
45
+ const resolutionMultiplier = this.getConf('resolutionMultiplier');
45
46
  const { bigwig } = await this.setup(opts);
46
47
  const feats = await bigwig.getFeatures(refName, start, end, {
47
48
  ...opts,
48
- basesPerSpan: bpPerPx / resolution,
49
+ basesPerSpan: (bpPerPx / resolution) * resolutionMultiplier,
49
50
  });
50
51
  for (const data of feats) {
51
52
  if (source) {
package/esm/BigWigAdapter/configSchema.d.ts CHANGED
@@ -17,5 +17,13 @@ declare const BigWigAdapter: import("@jbrowse/core/configuration/configurationSc
17
17
  defaultValue: string;
18
18
  description: string;
19
19
  };
20
+ /**
21
+ * #slot
22
+ */
23
+ resolutionMultiplier: {
24
+ type: string;
25
+ defaultValue: number;
26
+ description: string;
27
+ };
20
28
  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
21
29
  export default BigWigAdapter;
package/esm/BigWigAdapter/configSchema.js CHANGED
@@ -22,5 +22,13 @@ const BigWigAdapter = ConfigurationSchema('BigWigAdapter', {
22
22
  defaultValue: '',
23
23
  description: 'Used for multiwiggle',
24
24
  },
25
+ /**
26
+ * #slot
27
+ */
28
+ resolutionMultiplier: {
29
+ type: 'number',
30
+ defaultValue: 1,
31
+ description: 'Initial resolution multiplier',
32
+ },
25
33
  }, { explicitlyTyped: true });
26
34
  export default BigWigAdapter;
package/esm/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js CHANGED
@@ -4,9 +4,6 @@ import { makeStyles } from 'tss-react/mui';
4
4
  import { getSession, isElectron, isSessionModelWithWidgets, isSessionWithAddTracks, } from '@jbrowse/core/util';
5
5
  import { storeBlobLocation } from '@jbrowse/core/util/tracks';
6
6
  const useStyles = makeStyles()(theme => ({
7
- textbox: {
8
- width: '100%',
9
- },
10
7
  paper: {
11
8
  margin: theme.spacing(),
12
9
  padding: theme.spacing(),
@@ -17,6 +14,16 @@ const useStyles = makeStyles()(theme => ({
17
14
  display: 'block',
18
15
  },
19
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  }));
17
+ // on electron, use path to LocalFileLocation, on web, use the BlobLocation
18
+ function makeFileLocation(file) {
19
+ const { webUtils } = window.require('electron');
20
+ return isElectron
21
+ ? {
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+ localPath: webUtils.getPathForFile(file),
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+ locationType: 'LocalPathLocation',
24
+ }
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+ : storeBlobLocation({ blob: file });
26
+ }
20
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  export default function MultiWiggleWidget({ model }) {
21
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  const { classes } = useStyles();
22
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  const [val, setVal] = useState('');
@@ -25,64 +32,65 @@ export default function MultiWiggleWidget({ model }) {
25
32
  React.createElement("ul", null,
26
33
  React.createElement("li", null, "Enter list of URLs for bigwig files in the textbox"),
27
34
  React.createElement("li", null, "Or, use the button below the text box to select files from your computer")),
28
- React.createElement(TextField, { multiline: true, rows: 10, value: val, onChange: event => {
35
+ React.createElement(TextField, { multiline: true, fullWidth: true, rows: 10, value: val, placeholder: "Paste list of URLs here, or use file selector below", variant: "outlined", onChange: event => {
29
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  setVal(event.target.value);
30
- }, placeholder: 'Paste list of URLs here, or use file selector below', variant: "outlined", className: classes.textbox }),
37
+ } }),
31
38
  React.createElement(Button, { variant: "outlined", component: "label" },
32
39
  "Choose Files from your computer",
33
40
  React.createElement("input", { type: "file", hidden: true, multiple: true, onChange: ({ target }) => {
34
41
  const res = [...(target.files || [])].map(file => ({
35
42
  type: 'BigWigAdapter',
36
- bigWigLocation: isElectron
37
- ? {
38
- localPath: file.path,
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- locationType: 'LocalPathLocation',
40
- }
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- : storeBlobLocation({ blob: file }),
43
+ bigWigLocation: makeFileLocation(file),
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  source: file.name,
43
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  }));
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  setVal(JSON.stringify(res, null, 2));
45
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  } })),
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- React.createElement(TextField, { value: trackName, onChange: event => {
48
+ React.createElement(TextField, { value: trackName, helperText: "Track name", onChange: event => {
47
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  setTrackName(event.target.value);
48
- }, helperText: "Track name" }),
50
+ } }),
49
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  React.createElement(Button, { variant: "contained", className: classes.submit, onClick: () => {
50
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  var _a;
51
53
  const session = getSession(model);
52
- const trackId = [
53
- `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
54
- session.adminMode ? '' : '-sessionTrack',
55
- ].join('');
56
- // allow list of bigwigs in JSON format or line-by-line
57
- let bigWigs;
58
54
  try {
59
- bigWigs = JSON.parse(val);
55
+ const trackId = [
56
+ `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
57
+ session.adminMode ? '' : '-sessionTrack',
58
+ ].join('');
59
+ // allow list of bigwigs in JSON format or line-by-line
60
+ let bigWigs;
61
+ try {
62
+ bigWigs = JSON.parse(val);
63
+ }
64
+ catch (e) {
65
+ bigWigs = val
66
+ .split(/\n|\r\n|\r/)
67
+ .map(f => f.trim())
68
+ .filter(f => !!f);
69
+ }
70
+ const obj = typeof bigWigs[0] === 'string'
71
+ ? { bigWigs }
72
+ : { subadapters: bigWigs };
73
+ if (isSessionWithAddTracks(session)) {
74
+ session.addTrackConf({
75
+ trackId,
76
+ type: 'MultiQuantitativeTrack',
77
+ name: trackName,
78
+ assemblyNames: [model.assembly],
79
+ adapter: {
80
+ type: 'MultiWiggleAdapter',
81
+ ...obj,
82
+ },
83
+ });
84
+ (_a = model.view) === null || _a === void 0 ? void 0 : _a.showTrack(trackId);
85
+ }
86
+ model.clearData();
87
+ if (isSessionModelWithWidgets(session)) {
88
+ session.hideWidget(model);
89
+ }
60
90
  }
61
91
  catch (e) {
62
- bigWigs = val
63
- .split(/\n|\r\n|\r/)
64
- .map(f => f.trim())
65
- .filter(f => !!f);
66
- }
67
- const obj = typeof bigWigs[0] === 'string'
68
- ? { bigWigs }
69
- : { subadapters: bigWigs };
70
- if (isSessionWithAddTracks(session)) {
71
- session.addTrackConf({
72
- trackId,
73
- type: 'MultiQuantitativeTrack',
74
- name: trackName,
75
- assemblyNames: [model.assembly],
76
- adapter: {
77
- type: 'MultiWiggleAdapter',
78
- ...obj,
79
- },
80
- });
81
- (_a = model.view) === null || _a === void 0 ? void 0 : _a.showTrack(trackId);
82
- }
83
- model.clearData();
84
- if (isSessionModelWithWidgets(session)) {
85
- session.hideWidget(model);
92
+ console.error(e);
93
+ session.notifyError(`${e}`, e);
86
94
  }
87
95
  } }, "Submit"),
88
96
  React.createElement("p", null, "Additional notes: "),
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-wiggle",
3
- "version": "2.16.0",
3
+ "version": "2.16.1",
4
4
  "description": "JBrowse 2 wiggle adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -65,5 +65,5 @@
65
65
  "distModule": "esm/index.js",
66
66
  "srcModule": "src/index.ts",
67
67
  "module": "esm/index.js",
68
- "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
68
+ "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
69
69
  }