jbrowse-plugin-msaview 5.4.0 → 5.6.0

package/dist/MsaViewPanel/model.js

@@ -1,9 +1,11 @@
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes';
-import { getSession } from '@jbrowse/core/util';
+import { getSession, isSessionWithAddSessionTrack, isSessionWithDeleteTrackConf, isSessionWithSessionTracks, } from '@jbrowse/core/util';
 import { addDisposer, getSnapshot, types } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
 import { MSAModelF } from 'react-msaview';
-import { autoLoadProteinDomains, launchBlastIfNeeded, launchOrthologsIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
+import { autoLoadProteinDomains, launchBlastIfNeeded, launchOrthologsIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, showDomainsOnGenomeIfAsked, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
+import { connectedDomains } from './connectedDomains';
+import { domainTrackConf } from './domainTrack';
 import { msaCoordToGenomeCoord, msaCoordToGenomeRegions, } from './msaCoordToGenomeCoord';
 import { resolveConnectedTranscriptIfNeeded } from './resolveConnectedTranscript';
 import { transcriptMap } from './transcriptMap';
@@ -106,6 +108,13 @@ export default function stateModelFactory() {
          * it false for the labeled toolbar.
          */
         embeddedMode: true,
+        /**
+         * #property
+         * a launch asking for the domains on the genome: once the connected
+         * view and the query row's domains are both there, the view adds the
+         * domain track and clears this
+         */
+        domainsOnGenome: types.stripDefault(types.boolean, false),
     }))
         .volatile(() => ({
         /**
@@ -205,6 +214,15 @@ export default function stateModelFactory() {
                 ...this.connectedClickHighlights,
             ];
         },
+        /**
+         * #getter
+         * cross-plugin contract: the query row's domains on the genome, with
+         * the color object every surface paints them through.
+         * jbrowse-plugin-protein3d reads it to draw them on the structure
+         */
+        get connectedDomains() {
+            return connectedDomains(self);
+        },
     }))
         .views(self => ({
         /**
@@ -396,6 +414,46 @@ export default function stateModelFactory() {
         setDomainsRequested(arg) {
             self.domainsRequested = arg;
         },
+        /**
+         * #action
+         */
+        setDomainsOnGenome(arg) {
+            self.domainsOnGenome = arg;
+        },
+        /**
+         * #action
+         * Add the query row's domains to the connected genome view as a session
+         * track, replacing the one an earlier call added.
+         */
+        showDomainsOnGenome() {
+            const session = getSession(self);
+            const { connectedView, connectedDomains, connectedFeature } = self;
+            const assemblyName = connectedView?.assemblyNames[0];
+            if (!connectedView ||
+                !assemblyName ||
+                connectedDomains.features.length === 0 ||
+                !isSessionWithAddSessionTrack(session)) {
+                return;
+            }
+            const feature = connectedFeature;
+            const label = [feature?.gene_name, feature?.gene, feature?.name].find((v) => typeof v === 'string' && v !== '');
+            const conf = domainTrackConf({
+                viewId: self.id,
+                assemblyName,
+                name: `${label ?? self.querySeqName} domains (from the alignment)`,
+                strand: self.mafRegion ? undefined : self.transcriptToMsaMap?.strand,
+                domains: connectedDomains,
+            });
+            const existing = isSessionWithSessionTracks(session)
+                ? session.sessionTracks.find(t => t.trackId === conf.trackId)
+                : undefined;
+            if (existing && isSessionWithDeleteTrackConf(session)) {
+                session.deleteTrackConf(existing);
+            }
+            if (session.addSessionTrackConf(conf)) {
+                void connectedView.launchTrack(conf.trackId);
+            }
+        },
         /**
          * #action
          */
@@ -477,6 +535,16 @@ export default function stateModelFactory() {
                             self.setZoomToBaseLevel(!self.zoomToBaseLevel);
                         },
                     },
+                    ...(self.connectedView && self.connectedDomains.features.length > 0
+                        ? [
+                            {
+                                label: 'Show domains on the genome',
+                                onClick: () => {
+                                    self.showDomainsOnGenome();
+                                },
+                            },
+                        ]
+                        : []),
                 ];
             },
         };
@@ -498,6 +566,7 @@ export default function stateModelFactory() {
                 launchOrthologsIfNeeded,
                 processInit,
                 autoLoadProteinDomains,
+                showDomainsOnGenomeIfAsked,
             ]) {
                 addDisposer(self, autorun(() => {
                     fn(self);

package/dist/MsaViewPanel/model.test.js

@@ -166,3 +166,97 @@ describe('returning to the import form', () => {
 test('the view asks react-msaview for its icon toolbar', () => {
     expect(view().embeddedMode).toBe(true);
 });
+// two CDS on the reverse strand, so residue 3's codon straddles the intron
+const reverseTranscript = {
+    refName: 'chr1',
+    strand: -1,
+    start: 100,
+    end: 208,
+    subfeatures: [
+        { type: 'CDS', start: 100, end: 107, phase: 0 },
+        { type: 'CDS', start: 200, end: 208, phase: 0 },
+    ],
+};
+describe('connectedDomains', () => {
+    function domainView() {
+        const model = stateModelFactory().create({
+            type: 'MsaView',
+            id: 'msaview1',
+            data: { msa: '>QUERY\nMKV-LA\n>Mouse\nMKVQLA' },
+            connectedFeature: reverseTranscript,
+        });
+        model.setAnnotations([
+            {
+                id: 'QUERY',
+                accession: 'cd1',
+                name: 'Hb beta-like',
+                description: '',
+                start: 1,
+                end: 5,
+            },
+            {
+                id: 'QUERY',
+                accession: 'cd2',
+                name: 'heme binding site',
+                description: '',
+                featureType: 'Site',
+                start: 2,
+                end: 4,
+            },
+            {
+                id: 'Mouse',
+                accession: 'cd1',
+                name: 'Hb beta-like',
+                description: '',
+                start: 1,
+                end: 6,
+            },
+        ]);
+        return model;
+    }
+    test('carries the query row domains in the colors the alignment draws', () => {
+        const model = domainView();
+        const fills = new Map([...model.featureColors].map(([a, c]) => [
+            `${a.id}:${a.accession}`,
+            c.fill,
+        ]));
+        expect(model.connectedDomains).toEqual({
+            features: [
+                {
+                    name: 'Hb beta-like',
+                    accession: 'cd1',
+                    kind: 'domain',
+                    regions: [
+                        { refName: 'chr1', start: 100, end: 107 },
+                        { refName: 'chr1', start: 200, end: 208 },
+                    ],
+                },
+                {
+                    name: 'heme binding site',
+                    accession: 'cd2',
+                    kind: 'site',
+                    regions: [
+                        { refName: 'chr1', start: 103, end: 107 },
+                        { refName: 'chr1', start: 200, end: 205 },
+                    ],
+                },
+            ],
+            color: {
+                field: 'accession',
+                domain: ['cd1', 'cd2'],
+                range: [fills.get('QUERY:cd1'), fills.get('QUERY:cd2')],
+                labels: ['Hb beta-like', 'heme binding site'],
+            },
+        });
+    });
+    test('follows the overlay and the legend filter', () => {
+        const model = domainView();
+        model.setFilter('cd2', false);
+        expect(model.connectedDomains.color.domain).toEqual(['cd1']);
+        model.setShowDomains(false);
+        expect(model.connectedDomains).toEqual({
+            features: [],
+            color: { field: 'accession', domain: [], range: [], labels: [] },
+        });
+    });
+});

package/dist/MsaViewPanel/msaCoordToGenomeCoord.d.ts

@@ -1,11 +1,10 @@
 import type { MafRegion } from './types';
-interface GenomeRegion {
+export interface GenomeRegion {
     refName: string;
     start: number;
     end: number;
 }
-interface CoordModel {
-    querySeqName: string;
+export interface SeqPosModel {
     transcriptToMsaMap: {
         refName: string;
         p2gCodon: Record<number, number[]>;
@@ -13,6 +12,9 @@ interface CoordModel {
     mafRegion?: MafRegion;
     /** transcript residues before the query row's first residue */
     querySeqOffset?: number;
+}
+interface CoordModel extends SeqPosModel {
+    querySeqName: string;
     /**
      * react-msaview's converter, which is the only thing that knows which columns
      * are on screen. `rows` carries the whole gapped alignment, so counting
@@ -22,6 +24,12 @@ interface CoordModel {
      */
     visibleColToSeqPos: (rowName: string, visibleCol: number) => number | undefined;
 }
+/**
+ * The genome regions under residue `ungappedPos` (0-based) of the query row,
+ * 0-based half-open: the codon, one region per contiguous piece, or one base
+ * in a MAF alignment.
+ */
+export declare function seqPosToGenomeRegions(model: SeqPosModel, ungappedPos: number): GenomeRegion[];
 /**
  * The genome regions covered by MSA column `coord` of the query row, in 0-based
  * half-open coordinates (what bpToPx and navTo take).

package/dist/MsaViewPanel/msaCoordToGenomeCoord.js

@@ -1,20 +1,11 @@
 import { getCodonRanges } from 'g2p_mapper';
 /**
- * The genome regions covered by MSA column `coord` of the query row, in 0-based
- * half-open coordinates (what bpToPx and navTo take).
- *
- * `coord` is a VISIBLE column -- what mouseCol and mouseClickCol carry.
- *
- * Usually one region -- one codon, or one base in a MAF alignment -- but a
- * codon split across an exon boundary yields one region per contiguous piece,
- * which is why this returns a list.
+ * The genome regions under residue `ungappedPos` (0-based) of the query row,
+ * 0-based half-open: the codon, one region per contiguous piece, or one base
+ * in a MAF alignment.
  */
-export function msaCoordToGenomeRegions({ model, coord: mouseCol, }) {
-    const { querySeqName, transcriptToMsaMap, mafRegion } = model;
-    const ungappedPos = model.visibleColToSeqPos(querySeqName, mouseCol);
-    if (ungappedPos === undefined) {
-        return [];
-    }
+export function seqPosToGenomeRegions(model, ungappedPos) {
+    const { transcriptToMsaMap, mafRegion } = model;
     if (mafRegion) {
         const genomePos = mafRegion.start + ungappedPos;
         return genomePos < mafRegion.end
@@ -40,6 +31,22 @@ export function msaCoordToGenomeRegions({ model, coord: mouseCol, }) {
     }
     return [];
 }
+/**
+ * The genome regions covered by MSA column `coord` of the query row, in 0-based
+ * half-open coordinates (what bpToPx and navTo take).
+ *
+ * `coord` is a VISIBLE column -- what mouseCol and mouseClickCol carry.
+ *
+ * Usually one region -- one codon, or one base in a MAF alignment -- but a
+ * codon split across an exon boundary yields one region per contiguous piece,
+ * which is why this returns a list.
+ */
+export function msaCoordToGenomeRegions({ model, coord: mouseCol, }) {
+    const ungappedPos = model.visibleColToSeqPos(model.querySeqName, mouseCol);
+    return ungappedPos === undefined
+        ? []
+        : seqPosToGenomeRegions(model, ungappedPos);
+}
 /**
  * A single region spanning the codon at MSA column `coord`, for navigation. For
  * a codon split across an exon boundary this spans the intervening intron.

package/dist/chunks/{LaunchMsaViewDialog-HGL6P4E4.js → LaunchMsaViewDialog-BG4MX2BW.js}

@@ -1,5 +1,5 @@
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+//# sourceMappingURL=LaunchMsaViewDialog-BG4MX2BW.js.map

package/dist/chunks/{chunk-2XCUSA22.js → chunk-4TEPHD3L.js}

@@ -1,3 +1,3 @@
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