jbrowse-plugin-msaview 2.4.0 → 2.4.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map +1 -1
- package/dist/AddHighlightModel/MsaToGenomeHighlight.js +6 -5
- package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map +1 -1
- package/dist/AddHighlightModel/util.d.ts +4 -1
- package/dist/AddHighlightModel/util.js +4 -1
- package/dist/AddHighlightModel/util.js.map +1 -1
- package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.d.ts +2 -0
- package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js +8 -4
- package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js.map +1 -1
- package/dist/MsaViewPanel/afterCreateAutoruns.js +9 -4
- package/dist/MsaViewPanel/afterCreateAutoruns.js.map +1 -1
- package/dist/MsaViewPanel/model.d.ts +5 -0
- package/dist/MsaViewPanel/model.js +16 -3
- package/dist/MsaViewPanel/model.js.map +1 -1
- package/dist/MsaViewPanel/util.d.ts +11 -0
- package/dist/MsaViewPanel/util.js +11 -3
- package/dist/MsaViewPanel/util.js.map +1 -1
- package/dist/jbrowse-plugin-msaview.umd.production.min.js +23 -23
- package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
- package/dist/utils/ncbiBlast.js +6 -6
- package/dist/utils/ncbiBlast.js.map +1 -1
- package/dist/utils/taxonomyNames.js +0 -3
- package/dist/utils/taxonomyNames.js.map +1 -1
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/package.json +1 -1
- package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx +2 -5
- package/src/AddHighlightModel/MsaToGenomeHighlight.tsx +6 -6
- package/src/AddHighlightModel/util.ts +7 -2
- package/src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts +10 -4
- package/src/MsaViewPanel/afterCreateAutoruns.ts +8 -2
- package/src/MsaViewPanel/model.ts +17 -4
- package/src/MsaViewPanel/util.ts +27 -2
- package/src/utils/ncbiBlast.ts +9 -6
- package/src/utils/taxonomyNames.ts +0 -2
- package/src/version.ts +1 -1
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"GenomeMouseoverHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/GenomeMouseoverHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAIpD,MAAM,wBAAwB,GAAG,QAAQ,CAAC,UAAU,EAClD,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAC5C,MAAM,UAAU,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAAC,CAAA;IACxD,OAAO,UAAU,IAAI,gBAAgB,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAC/C,oBAAC,gCAAgC,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,OAAO,GAAI,CACrE,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,MAAM,gCAAgC,GAAG,QAAQ,CAAC,UAAU,EAC1D,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,
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{"version":3,"file":"GenomeMouseoverHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/GenomeMouseoverHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAIpD,MAAM,wBAAwB,GAAG,QAAQ,CAAC,UAAU,EAClD,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAC5C,MAAM,UAAU,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAAC,CAAA;IACxD,OAAO,UAAU,IAAI,gBAAgB,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAC/C,oBAAC,gCAAgC,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,OAAO,GAAI,CACrE,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,MAAM,gCAAgC,GAAG,QAAQ,CAAC,UAAU,EAC1D,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,aAAa,CAAA;IAEhD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC,CAAA;IACrD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAA;IAE1C,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;QAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,QAAQ,CAAA;QACxD,OAAO,6BAAK,SAAS,EAAE,OAAO,CAAC,SAAS,EAAE,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GAAI,CAAA;IACtE,CAAC;IAED,OAAO,IAAI,CAAA;AACb,CAAC,CAAC,CAAA;AAEF,eAAe,wBAAwB,CAAA"}
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@@ -2,6 +2,7 @@ import React from 'react';
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import { getSession } from '@jbrowse/core/util';
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import { observer } from 'mobx-react';
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import { hasHoverPosition, useStyles } from './util';
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import { getCanonicalRefName } from '../MsaViewPanel/util';
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const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({ model, }) {
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const { views, hovered } = getSession(model);
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const msaView = views.find(f => f.type === 'MsaView');
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@@ -14,13 +15,13 @@ const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({ model, })
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const MsaToGenomeHighlightRenderer = observer(function ({ model, highlights, }) {
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const { classes } = useStyles();
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const { assemblyManager } = getSession(model);
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const assembly = assemblyManager.get(model.assemblyNames[0]);
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const { offsetPx } = model;
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if (!assembly) {
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return null;
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}
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return (React.createElement(React.Fragment, null, highlights.map((r, idx) => {
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const refName =
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const refName = getCanonicalRefName({
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assemblyManager,
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assemblyNames: model.assemblyNames,
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refName: r.refName,
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});
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const s = model.bpToPx({ refName, coord: r.start });
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const e = model.bpToPx({ refName, coord: r.end });
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if (s && e) {
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@@ -1 +1 @@
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-
{"version":3,"file":"MsaToGenomeHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/MsaToGenomeHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;
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{"version":3,"file":"MsaToGenomeHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/MsaToGenomeHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AACpD,OAAO,EAAE,mBAAmB,EAAE,MAAM,sBAAsB,CAAA;AAO1D,MAAM,oBAAoB,GAAG,QAAQ,CAAC,SAAS,qBAAqB,CAAC,EACnE,KAAK,GAGN;IACC,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAC5C,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAEvC,CAAA;IACb,MAAM,UAAU,GAAG,OAAO,EAAE,mBAAmB,CAAA;IAE/C,6EAA6E;IAC7E,6CAA6C;IAC7C,OAAO,CAAC,gBAAgB,CAAC,OAAO,CAAC,IAAI,UAAU,EAAE,MAAM,CAAC,CAAC,CAAC,CACxD,oBAAC,4BAA4B,IAC3B,KAAK,EAAE,KAAK,EACZ,UAAU,EAAE,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,GAClC,CACH,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,0DAA0D;AAC1D,MAAM,4BAA4B,GAAG,QAAQ,CAAC,UAAU,EACtD,KAAK,EACL,UAAU,GAIX;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAE1B,OAAO,CACL,0CACG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;QACzB,MAAM,OAAO,GAAG,mBAAmB,CAAC;YAClC,eAAe;YACf,aAAa,EAAE,KAAK,CAAC,aAAa;YAClC,OAAO,EAAE,CAAC,CAAC,OAAO;SACnB,CAAC,CAAA;QACF,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAA;QACnD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;YAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,QAAQ,CAAA;YACxD,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,EAC9C,SAAS,EAAE,OAAO,CAAC,SAAS,EAC5B,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GACtB,CACH,CAAA;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,oBAAoB,CAAA"}
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export declare function hasHoverPosition(hovered: unknown): hovered is {
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hoverPosition:
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hoverPosition: {
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};
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export declare const useStyles: (params: void, muiStyleOverridesParams?: {
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import { makeStyles } from 'tss-react/mui';
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export function hasHoverPosition(hovered) {
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return !!hovered &&
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export const useStyles = makeStyles()({
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highlight: {
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{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/AddHighlightModel/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,UAAU,gBAAgB,CAC9B,OAAgB;IAEhB,OAAO,CAAC,CAAC,OAAO,
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{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/AddHighlightModel/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,UAAU,gBAAgB,CAC9B,OAAgB;IAEhB,OAAO,CACL,CAAC,CAAC,OAAO;QACT,OAAO,OAAO,KAAK,QAAQ;QAC3B,eAAe,IAAI,OAAO;QAC1B,CAAC,CAAC,OAAO,CAAC,aAAa,CACxB,CAAA;AACH,CAAC;AAED,MAAM,CAAC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IACpC,SAAS,EAAE;QACT,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,qBAAqB;QACjC,MAAM,EAAE,6BAA6B;QACrC,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,EAAE;QACV,SAAS,EAAE,QAAQ;QACnB,aAAa,EAAE,MAAM;QACrB,QAAQ,EAAE,QAAQ;KACnB;CACF,CAAC,CAAA"}
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@@ -6,6 +6,8 @@ export default class BgzipFastaMsaAdapter extends BaseAdapter {
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configurePre(): Promise<BaseFeatureDataAdapter>;
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getMSARefs(): Promise<string[]>;
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getMsaRegex(): RegExp;
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refNameToMsaId(refName: string): string;
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getMsaRegex() {
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return new RegExp(this.getConf('msaRegex'));
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}
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return refName.split(this.getMsaRegex())[0];
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}
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const
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const list = new Set(refNames.map(name => name.split(re)[0]));
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const list = new Set(refNames.map(name => this.refNameToMsaId(name)));
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async getMSA(id) {
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const rows = refNames.filter(refName =>
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const rows = refNames.filter(refName => this.refNameToMsaId(refName) === id);
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{"version":3,"file":"BgzipFastaMsaAdapter.js","sourceRoot":"","sources":["../../src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EAAE,WAAW,EAAE,MAAM,yCAAyC,CAAA;AACrE,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAI9C,MAAM,CAAC,OAAO,OAAO,oBAAqB,SAAQ,WAAW;IAK3D,KAAK,CAAC,YAAY;QAChB,MAAM,aAAa,GAAG,IAAI,CAAC,aAAa,CAAA;QACxC,IAAI,aAAa,EAAE,CAAC;YAClB,MAAM,OAAO,GAAG,MAAM,aAAa,CAAC;gBAClC,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC;gBAC9B,IAAI,EAAE,mBAAmB;aAC1B,CAAC,CAAA;YAEF,OAAO,OAAO,CAAC,WAAqC,CAAA;QACtD,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;QACtC,CAAC;IACH,CAAC;IACD,SAAS;QACP,IAAI,CAAC,UAAU,KAAK,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;YAC3D,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;YAC3B,MAAM,CAAC,CAAA;QACT,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,UAAU;QACd,IAAI,CAAC,SAAS,KAAK,IAAI,CAAC,SAAS,EAAE;aAChC,IAAI,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC;aACtC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;YACpB,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;YAC1B,MAAM,CAAC,CAAA;QACT,CAAC,CAAC,CAAA;QACJ,OAAO,IAAI,CAAC,SAAS,CAAA;IACvB,CAAC;IAED,
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{"version":3,"file":"BgzipFastaMsaAdapter.js","sourceRoot":"","sources":["../../src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EAAE,WAAW,EAAE,MAAM,yCAAyC,CAAA;AACrE,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAI9C,MAAM,CAAC,OAAO,OAAO,oBAAqB,SAAQ,WAAW;IAK3D,KAAK,CAAC,YAAY;QAChB,MAAM,aAAa,GAAG,IAAI,CAAC,aAAa,CAAA;QACxC,IAAI,aAAa,EAAE,CAAC;YAClB,MAAM,OAAO,GAAG,MAAM,aAAa,CAAC;gBAClC,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC;gBAC9B,IAAI,EAAE,mBAAmB;aAC1B,CAAC,CAAA;YAEF,OAAO,OAAO,CAAC,WAAqC,CAAA;QACtD,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;QACtC,CAAC;IACH,CAAC;IACD,SAAS;QACP,IAAI,CAAC,UAAU,KAAK,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;YAC3D,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;YAC3B,MAAM,CAAC,CAAA;QACT,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,UAAU;QACd,IAAI,CAAC,SAAS,KAAK,IAAI,CAAC,SAAS,EAAE;aAChC,IAAI,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC;aACtC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;YACpB,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;YAC1B,MAAM,CAAC,CAAA;QACT,CAAC,CAAC,CAAA;QACJ,OAAO,IAAI,CAAC,SAAS,CAAA;IACvB,CAAC;IAED,WAAW;QACT,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC,CAAA;IAC7C,CAAC;IAED,cAAc,CAAC,OAAe;QAC5B,OAAO,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,CAAE,CAAA;IAC9C,CAAC;IAED,KAAK,CAAC,UAAU;QACd,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,UAAU,EAAE,CAAA;QACxC,MAAM,IAAI,GAAG,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACrE,OAAO,CAAC,GAAG,IAAI,CAAC,CAAA;IAClB,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,EAAU;QACrB,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,WAAW,EAAE,CAAA;QAC5C,MAAM,IAAI,GAAG,QAAQ,CAAC,MAAM,CAAC,OAAO,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,OAAO,CAAC,KAAK,EAAE,CAAC,CAAA;QAC5E,OAAO,cAAc,CACnB,OAAO;aACJ,4BAA4B,CAC3B,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YACnB,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,aAAa;YAClB,YAAY,EAAE,EAAE;SACjB,CAAC,CAAC,CACJ;aACA,IAAI,CAAC,OAAO,EAAE,CAAC,CACnB,CAAA;IACH,CAAC;CACF"}
|
|
@@ -32,16 +32,18 @@ export function loadStoredData(self) {
|
|
|
32
32
|
}
|
|
33
33
|
}
|
|
34
34
|
export function storeDataToIndexedDB(self) {
|
|
35
|
-
const { rows, dataStoreId } = self;
|
|
36
|
-
if (rows.length > 0 && !dataStoreId) {
|
|
35
|
+
const { rows, dataStoreId, isStoringData } = self;
|
|
36
|
+
if (rows.length > 0 && !dataStoreId && !isStoringData) {
|
|
37
37
|
if (self.msaFilehandle || self.treeFilehandle) {
|
|
38
38
|
return;
|
|
39
39
|
}
|
|
40
40
|
const msaData = self.data.msa;
|
|
41
41
|
const treeData = self.data.tree;
|
|
42
42
|
if (msaData || treeData) {
|
|
43
|
-
//
|
|
44
|
-
|
|
43
|
+
// mark as storing synchronously so re-runs of this autorun (e.g. when
|
|
44
|
+
// data observables change while the write is pending) don't kick off a
|
|
45
|
+
// duplicate write and leave an orphan IndexedDB entry
|
|
46
|
+
self.setIsStoringData(true);
|
|
45
47
|
(async () => {
|
|
46
48
|
try {
|
|
47
49
|
const newId = generateDataStoreId();
|
|
@@ -57,6 +59,9 @@ export function storeDataToIndexedDB(self) {
|
|
|
57
59
|
catch (e) {
|
|
58
60
|
console.error('Failed to store MSA data to IndexedDB:', e);
|
|
59
61
|
}
|
|
62
|
+
finally {
|
|
63
|
+
self.setIsStoringData(false);
|
|
64
|
+
}
|
|
60
65
|
})();
|
|
61
66
|
}
|
|
62
67
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"afterCreateAutoruns.js","sourceRoot":"","sources":["../../src/MsaViewPanel/afterCreateAutoruns.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAC/C,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,eAAe,EACf,YAAY,GACb,MAAM,gBAAgB,CAAA;AACvB,OAAO,EACL,wBAAwB,EACxB,eAAe,GAChB,MAAM,uBAAuB,CAAA;AAC9B,OAAO,EAAE,4BAA4B,EAAE,MAAM,QAAQ,CAAA;AAIrD,MAAM,UAAU,cAAc,CAAC,IAA+B;IAC5D,MAAM,EAAE,WAAW,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IAClC,IAAI,WAAW,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACrC,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,CAAA;gBAC/B,MAAM,UAAU,GAAG,MAAM,eAAe,CAAC,WAAW,CAAC,CAAA;gBACrD,IAAI,UAAU,EAAE,CAAC;oBACf,IAAI,UAAU,CAAC,GAAG,EAAE,CAAC;wBACnB,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,GAAG,CAAC,CAAA;oBAC7B,CAAC;oBACD,IAAI,UAAU,CAAC,IAAI,EAAE,CAAC;wBACpB,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;oBAC/B,CAAC;gBACH,CAAC;YACH,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,yCAAyC,EAAE,CAAC,CAAC,CAAA;YAC7D,CAAC;oBAAS,CAAC;gBACT,IAAI,CAAC,oBAAoB,CAAC,KAAK,CAAC,CAAA;YAClC,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,IAA+B;IAClE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;
|
|
1
|
+
{"version":3,"file":"afterCreateAutoruns.js","sourceRoot":"","sources":["../../src/MsaViewPanel/afterCreateAutoruns.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAC/C,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,eAAe,EACf,YAAY,GACb,MAAM,gBAAgB,CAAA;AACvB,OAAO,EACL,wBAAwB,EACxB,eAAe,GAChB,MAAM,uBAAuB,CAAA;AAC9B,OAAO,EAAE,4BAA4B,EAAE,MAAM,QAAQ,CAAA;AAIrD,MAAM,UAAU,cAAc,CAAC,IAA+B;IAC5D,MAAM,EAAE,WAAW,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IAClC,IAAI,WAAW,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACrC,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,CAAA;gBAC/B,MAAM,UAAU,GAAG,MAAM,eAAe,CAAC,WAAW,CAAC,CAAA;gBACrD,IAAI,UAAU,EAAE,CAAC;oBACf,IAAI,UAAU,CAAC,GAAG,EAAE,CAAC;wBACnB,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,GAAG,CAAC,CAAA;oBAC7B,CAAC;oBACD,IAAI,UAAU,CAAC,IAAI,EAAE,CAAC;wBACpB,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;oBAC/B,CAAC;gBACH,CAAC;YACH,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,yCAAyC,EAAE,CAAC,CAAC,CAAA;YAC7D,CAAC;oBAAS,CAAC;gBACT,IAAI,CAAC,oBAAoB,CAAC,KAAK,CAAC,CAAA;YAClC,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,IAA+B;IAClE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;IACjD,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,IAAI,CAAC,aAAa,EAAE,CAAC;QACtD,IAAI,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,cAAc,EAAE,CAAC;YAC9C,OAAM;QACR,CAAC;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,CAAA;QAC7B,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAA;QAE/B,IAAI,OAAO,IAAI,QAAQ,EAAE,CAAC;YACxB,sEAAsE;YACtE,uEAAuE;YACvE,sDAAsD;YACtD,IAAI,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAE1B;YAAA,CAAC,KAAK,IAAI,EAAE;gBACX,IAAI,CAAC;oBACH,MAAM,KAAK,GAAG,mBAAmB,EAAE,CAAA;oBACnC,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,KAAK,EAAE;wBACxC,GAAG,EAAE,OAAO;wBACZ,IAAI,EAAE,QAAQ;wBACd,YAAY,EAAE,IAAI,CAAC,IAAI,CAAC,YAAY;qBACrC,CAAC,CAAA;oBACF,IAAI,OAAO,EAAE,CAAC;wBACZ,IAAI,CAAC,cAAc,CAAC,KAAK,CAAC,CAAA;oBAC5B,CAAC;gBACH,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,OAAO,CAAC,KAAK,CAAC,wCAAwC,EAAE,CAAC,CAAC,CAAA;gBAC5D,CAAC;wBAAS,CAAC;oBACT,IAAI,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAA;gBAC9B,CAAC;YACH,CAAC,CAAC,EAAE,CAAA;QACN,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,mBAAmB,CAAC,IAA+B;IACjE,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;QACrB,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,IAAI,CAAC,WAAW,CAAC,kBAAkB,CAAC,CAAA;gBACpC,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;gBACxB,MAAM,IAAI,GAAG,MAAM,aAAa,CAAC,EAAE,IAAI,EAAE,CAAC,CAAA;gBAC1C,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;gBAClB,IAAI,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;YAChC,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;gBAChB,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAClB,CAAC;oBAAS,CAAC;gBACT,IAAI,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YACtB,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC;AACH,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,IAA+B;IACzD,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IACrB,IAAI,IAAI,EAAE,CAAC;QACT,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;gBACxB,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,IAAI,CAAA;gBAEjE,IAAI,MAAM,EAAE,CAAC;oBACX,MAAM,EAAE,GAAG,4BAA4B,CAAC,MAAM,CAAC,CAAA;oBAC/C,IAAI,EAAE,EAAE,CAAC;wBACP,IAAI,CAAC,YAAY,CAAC,EAAE,CAAC,CAAA;wBACrB,IAAI,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;oBAC/B,CAAC;gBACH,CAAC;gBAED,IAAI,YAAY,EAAE,CAAC;oBACjB,IAAI,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;gBACpC,CAAC;gBAED,IAAI,OAAO,EAAE,CAAC;oBACZ,IAAI,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;gBACtB,CAAC;qBAAM,IAAI,MAAM,EAAE,CAAC;oBAClB,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,CAAA;oBACpC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;wBACjB,MAAM,IAAI,KAAK,CAAC,wBAAwB,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;oBAC5D,CAAC;oBACD,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAA;oBAClC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;gBACnB,CAAC;gBAED,IAAI,QAAQ,EAAE,CAAC;oBACb,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;gBACxB,CAAC;qBAAM,IAAI,OAAO,EAAE,CAAC;oBACnB,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,OAAO,CAAC,CAAA;oBACrC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;wBACjB,MAAM,IAAI,KAAK,CAAC,yBAAyB,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;oBAC7D,CAAC;oBACD,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAA;oBAClC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;gBACpB,CAAC;gBAED,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;YACzB,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;gBAChB,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAClB,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC;AACH,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,IAA+B;IACpE,MAAM,EAAE,QAAQ,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;IACxC,MAAM,EAAE,GACN,QAAQ,KAAK,SAAS;QACpB,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,qBAAqB,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,CAAA;IAC7D,MAAM,EAAE,GACN,aAAa,KAAK,SAAS;QACzB,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,qBAAqB,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,aAAa,EAAE,CAAC,CAAA;IAElE,IAAI,CAAC,sBAAsB,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,UAAU,4BAA4B,CAAC,IAA+B;IAC1E,MAAM,EAAE,QAAQ,EAAE,qBAAqB,EAAE,GAAG,IAAI,CAAA;IAChD,IAAI,qBAAqB,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvC,OAAM;IACR,CAAC;IAED,KAAK,MAA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@@ -614,6 +614,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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progress: string;
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error: unknown;
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loadingStoredData: boolean;
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617
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+
isStoringData: boolean;
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|
} & {
|
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619
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/**
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* #method
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* #action
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*/
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setLoadingStoredData(arg: boolean): void;
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+
/**
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715
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+
* #action
|
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+
*/
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+
setIsStoringData(arg: boolean): void;
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|
/**
|
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714
719
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* #action
|
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715
720
|
*/
|
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@@ -10,6 +10,7 @@ import { genomeToMSA } from './genomeToMSA';
|
|
|
10
10
|
import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
|
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11
11
|
import { buildAlignmentMaps, runPairwiseAlignment } from './pairwiseAlignment';
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12
12
|
import { getProteinViews, ungappedToGappedPosition, } from './structureConnection';
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13
|
+
import { getCanonicalRefName } from './util';
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13
14
|
const ConnectStructureDialog = lazy(() => import('./components/ConnectStructureDialog'));
|
|
14
15
|
/**
|
|
15
16
|
* #stateModel MsaViewPlugin
|
|
@@ -85,6 +86,10 @@ export default function stateModelFactory() {
|
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85
86
|
* #volatile
|
|
86
87
|
*/
|
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87
88
|
loadingStoredData: false,
|
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89
|
+
/**
|
|
90
|
+
* #volatile
|
|
91
|
+
*/
|
|
92
|
+
isStoringData: false,
|
|
88
93
|
}))
|
|
89
94
|
.views(self => ({
|
|
90
95
|
/**
|
|
@@ -252,6 +257,12 @@ export default function stateModelFactory() {
|
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252
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|
setLoadingStoredData(arg) {
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253
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|
self.loadingStoredData = arg;
|
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|
},
|
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|
+
/**
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|
+
* #action
|
|
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|
+
*/
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263
|
+
setIsStoringData(arg) {
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|
+
self.isStoringData = arg;
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+
},
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|
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|
/**
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|
* #action
|
|
257
268
|
*/
|
|
@@ -266,9 +277,11 @@ export default function stateModelFactory() {
|
|
|
266
277
|
connectedView.navTo(r2);
|
|
267
278
|
}
|
|
268
279
|
else {
|
|
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|
-
const r =
|
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|
-
|
|
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|
-
|
|
280
|
+
const r = getCanonicalRefName({
|
|
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|
+
assemblyManager,
|
|
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|
+
assemblyNames: connectedView.assemblyNames,
|
|
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|
+
refName: r2.refName,
|
|
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|
+
});
|
|
272
285
|
connectedView.centerAt(r2.start, r);
|
|
273
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|
}
|
|
274
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|
},
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/MsaViewPanel/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,EAAE,aAAa,EAAE,MAAM,qCAAqC,CAAA;AACnE,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AACnE,OAAO,EAAE,4BAA4B,EAAE,MAAM,YAAY,CAAA;AACzD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAEzC,OAAO,EACL,qBAAqB,EACrB,4BAA4B,EAC5B,mBAAmB,EACnB,cAAc,EACd,wBAAwB,EACxB,WAAW,EACX,UAAU,EACV,oBAAoB,EACpB,sBAAsB,GACvB,MAAM,uBAAuB,CAAA;AAC9B,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAA;AAC3C,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,MAAM,qBAAqB,CAAA;AAC9E,OAAO,EACL,eAAe,EACf,wBAAwB,GACzB,MAAM,uBAAuB,CAAA;
|
|
1
|
+
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@@ -6,6 +6,16 @@ export declare function checkHovered(hovered: unknown): hovered is {
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refName: string;
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};
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interface AssemblyManagerLike {
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export declare function getCanonicalRefName({ assemblyManager, assemblyNames, refName, }: {
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assemblyManager: AssemblyManagerLike;
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}): string;
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/**
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* Extracts UniProt ID from an AlphaFold URL
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* Examples:
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@@ -13,3 +23,4 @@ export declare function checkHovered(hovered: unknown): hovered is {
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* - https://alphafold.ebi.ac.uk/files/msa/AF-P12345-F1-msa_v6.a3m -> P12345
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*/
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export declare function getUniprotIdFromAlphaFoldUrl(url: string): string | undefined;
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export {};
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1
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export function checkHovered(hovered) {
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-
return (
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hovered
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return (!!hovered &&
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typeof hovered === 'object' &&
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'hoverFeature' in hovered &&
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'hoverPosition' in hovered
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!!hovered.hoverPosition);
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}
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export function getCanonicalRefName({ assemblyManager, assemblyNames, refName, }) {
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const assemblyName = assemblyNames?.[0];
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if (assemblyName) {
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return (assemblyManager.get(assemblyName)?.getCanonicalRefName(refName) ?? refName);
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}
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return refName;
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}
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/**
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* Extracts UniProt ID from an AlphaFold URL
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/MsaViewPanel/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,YAAY,CAAC,OAAgB;IAI3C,OAAO,CACL,OAAO,OAAO,KAAK,QAAQ;QAC3B,OAAO,
|
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1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/MsaViewPanel/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,YAAY,CAAC,OAAgB;IAI3C,OAAO,CACL,CAAC,CAAC,OAAO;QACT,OAAO,OAAO,KAAK,QAAQ;QAC3B,cAAc,IAAI,OAAO;QACzB,eAAe,IAAI,OAAO;QAC1B,CAAC,CAAC,OAAO,CAAC,aAAa,CACxB,CAAA;AACH,CAAC;AAQD,MAAM,UAAU,mBAAmB,CAAC,EAClC,eAAe,EACf,aAAa,EACb,OAAO,GAKR;IACC,MAAM,YAAY,GAAG,aAAa,EAAE,CAAC,CAAC,CAAC,CAAA;IACvC,IAAI,YAAY,EAAE,CAAC;QACjB,OAAO,CACL,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,mBAAmB,CAAC,OAAO,CAAC,IAAI,OAAO,CAC3E,CAAA;IACH,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,4BAA4B,CAAC,GAAW;IACtD,MAAM,KAAK,GAAG,qBAAqB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IAC7C,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA;AACnB,CAAC"}
|