jbrowse-plugin-protein3d 0.0.3 → 0.0.5

package/dist/ProteinView/model.js

@@ -1,12 +1,11 @@
 import { autorun } from 'mobx';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes';
-import { ElementId, Region } from '@jbrowse/core/util/types/mst';
-import { addDisposer, cast, types } from 'mobx-state-tree';
-import { SimpleFeature, getSession, } from '@jbrowse/core/util';
-// locals
-import { checkHovered, invertMap, toStr } from './util';
-import { launchPairwiseAlignment } from './launchRemotePairwiseAlignment';
-import { structureSeqVsTranscriptSeqMap, genomeToTranscriptSeqMapping, structurePositionToAlignmentMap, transcriptPositionToAlignmentMap, } from '../mappings';
+import { ElementId } from '@jbrowse/core/util/types/mst';
+import { addDisposer, types } from 'mobx-state-tree';
+import { addStructureFromData } from './addStructureFromData';
+import { addStructureFromURL } from './addStructureFromURL';
+import Structure from './structureModel';
+import highlightResidue from './highlightResidue';
 /**
  * #stateModel Protein3dViewPlugin
  * extends
@@ -25,50 +24,16 @@ function stateModelFactory() {
         type: types.literal('ProteinView'),
         /**
          * #property
-         * url to structure file
          */
-        url: types.maybe(types.string),
+        structures: types.array(Structure),
         /**
          * #property
-         * full string for structure data
          */
-        data: types.maybe(types.string),
-        /**
-         * #property
-         */
-        clickGenomeHighlights: types.array(Region),
-        /**
-         * #property
-         */
-        hoverGenomeHighlights: types.array(Region),
-        /**
-         * #property
-         */
-        showControls: true,
+        showControls: false,
         /**
          * #property
          */
         height: types.optional(types.number, 650),
-        /**
-         * #property
-         */
-        feature: types.frozen(),
-        /**
-         * #property
-         */
-        seq1: types.maybe(types.string),
-        /**
-         * #property
-         */
-        seq2: types.maybe(types.string),
-        /**
-         * #property
-         */
-        alignment: types.frozen(),
-        /**
-         * #property
-         */
-        connectedViewId: types.maybe(types.string),
         /**
          * #property
          */
@@ -86,48 +51,29 @@ function stateModelFactory() {
         /**
          * #volatile
          */
-        error: undefined,
-        /**
-         * #volatile
-         */
-        clickPosition: undefined,
+        progress: '',
         /**
          * #volatile
          */
-        hoverPosition: undefined,
+        error: undefined,
         /**
          * #volatile
          */
-        progress: '',
-    }))
-        .views(self => ({
-        /**
-         * #getter
-         */
-        get connectedView() {
-            const { views } = getSession(self);
-            return views.find(f => f.id === self.connectedViewId);
-        },
+        molstarPluginContext: undefined,
     }))
         .actions(self => ({
         /**
          * #action
          */
-        setShowAlignment(f) {
-            self.showAlignment = f;
-        },
-        /**
-         * #action
-         */
-        setHoveredPosition(arg) {
-            self.hoverPosition = arg;
+        setHeight(n) {
+            self.height = n;
+            return n;
         },
         /**
          * #action
          */
-        setSeqs(str1, str2) {
-            self.seq1 = str1;
-            self.seq2 = str2;
+        setShowAlignment(f) {
+            self.showAlignment = f;
         },
         /**
          * #action
@@ -135,54 +81,12 @@ function stateModelFactory() {
         setShowControls(arg) {
             self.showControls = arg;
         },
-        /**
-         * #action
-         */
-        setProgress(str) {
-            self.progress = str;
-        },
-        /**
-         * #action
-         */
-        setClickedPosition(arg) {
-            self.clickPosition = arg;
-        },
-        /**
-         * #action
-         */
-        setClickGenomeHighlights(r) {
-            self.clickGenomeHighlights = cast(r);
-        },
-        /**
-         * #action
-         */
-        clearClickGenomeHighlights() {
-            self.clickGenomeHighlights = cast([]);
-        },
-        /**
-         * #action
-         */
-        setHoverGenomeHighlights(r) {
-            self.hoverGenomeHighlights = cast(r);
-        },
-        /**
-         * #action
-         */
-        clearHoverGenomeHighlights() {
-            self.hoverGenomeHighlights = cast([]);
-        },
         /**
          * #action
          */
         setError(e) {
             self.error = e;
         },
-        /**
-         * #action
-         */
-        setAlignment(r) {
-            self.alignment = r;
-        },
         /**
          * #action
          */
@@ -195,152 +99,64 @@ function stateModelFactory() {
         setZoomToBaseLevel(arg) {
             self.zoomToBaseLevel = arg;
         },
-    }))
-        .views(self => ({
-        /**
-         * #getter
-         */
-        get structureSeqToTranscriptSeqPosition() {
-            return self.alignment
-                ? structureSeqVsTranscriptSeqMap(self.alignment)
-                    .structureSeqToTranscriptSeqPosition
-                : undefined;
-        },
-        /**
-         * #getter
-         */
-        get transcriptSeqToStructureSeqPosition() {
-            return self.alignment
-                ? structureSeqVsTranscriptSeqMap(self.alignment)
-                    .transcriptSeqToStructureSeqPosition
-                : undefined;
-        },
-        /**
-         * #getter
-         */
-        get structurePositionToAlignmentMap() {
-            return self.alignment
-                ? structurePositionToAlignmentMap(self.alignment)
-                : undefined;
-        },
         /**
-         * #getter
-         */
-        get transcriptPositionToAlignmentMap() {
-            return self.alignment
-                ? transcriptPositionToAlignmentMap(self.alignment)
-                : undefined;
-        },
-        /**
-         * #getter
-         */
-        get alignmentToTranscriptPosition() {
-            return this.transcriptPositionToAlignmentMap
-                ? invertMap(this.transcriptPositionToAlignmentMap)
-                : undefined;
-        },
-        /**
-         * #getter
-         */
-        get alignmentToStructurePosition() {
-            return this.structurePositionToAlignmentMap
-                ? invertMap(this.structurePositionToAlignmentMap)
-                : undefined;
-        },
-        /**
-         * #getter
-         */
-        get clickString() {
-            const r = self.clickPosition;
-            return r ? toStr(r) : '';
-        },
-        /**
-         * #getter
-         */
-        get hoverString() {
-            const r = self.hoverPosition;
-            return r ? toStr(r) : '';
-        },
-        /**
-         * #getter
-         */
-        get genomeToTranscriptSeqMapping() {
-            return self.feature
-                ? genomeToTranscriptSeqMapping(new SimpleFeature(self.feature))
-                : undefined;
-        },
-        /**
-         * #getter
+         * #action
          */
-        get structureSeqHoverPos() {
-            return self.hoverPosition?.structureSeqPos;
-        },
-        get exactMatch() {
-            const r1 = self.seq1?.replaceAll('*', '');
-            const r2 = self.seq2?.replaceAll('*', '');
-            return r1 === r2;
+        setMolstarPluginContext(p) {
+            self.molstarPluginContext = p;
         },
     }))
         .actions(self => ({
         afterAttach() {
-            // pairwise align transcript sequence to structure residues
             addDisposer(self, autorun(async () => {
-                try {
-                    const { seq1, seq2, exactMatch } = self;
-                    if (!!self.alignment || !seq1 || !seq2) {
-                        return;
-                    }
-                    const r1 = seq1.replaceAll('*', '');
-                    const r2 = seq2.replaceAll('*', '');
-                    if (!exactMatch) {
-                        const alignment = await launchPairwiseAlignment({
-                            seq1: r1,
-                            seq2: r2,
-                            algorithm: 'emboss_needle',
-                            onProgress: arg => self.setProgress(arg),
-                        });
-                        self.setAlignment(alignment.alignment);
-                        // showHighlight when we are
-                        self.setShowHighlight(true);
-                        self.setShowAlignment(true);
-                    }
-                    else {
-                        let consensus = '';
-                        // eslint-disable-next-line @typescript-eslint/prefer-for-of
-                        for (let i = 0; i < r1.length; i++) {
-                            consensus += '|';
+                const { structures, molstarPluginContext } = self;
+                if (molstarPluginContext) {
+                    for (const structure of structures) {
+                        try {
+                            const { model } = structure.data
+                                ? await addStructureFromData({
+                                    data: structure.data,
+                                    plugin: molstarPluginContext,
+                                })
+                                : structure.url
+                                    ? await addStructureFromURL({
+                                        url: structure.url,
+                                        plugin: molstarPluginContext,
+                                    })
+                                    : { model: undefined };
+                            const sequences = model?.obj?.data.sequence.sequences.map(s => {
+                                let seq = '';
+                                const arr = s.sequence.label.toArray();
+                                // eslint-disable-next-line unicorn/no-for-loop,@typescript-eslint/prefer-for-of
+                                for (let i = 0; i < arr.length; i++) {
+                                    seq += arr[i];
+                                }
+                                return seq;
+                            });
+                            structure.setSequences(sequences);
+                        }
+                        catch (e) {
+                            self.setError(e);
+                            console.error(e);
                         }
-                        self.setAlignment({
-                            consensus,
-                            alns: [
-                                { id: 'seq1', seq: r1 },
-                                { id: 'seq2', seq: r2 },
-                            ],
-                        });
                     }
                 }
-                catch (e) {
-                    console.error(e);
-                    self.setError(e);
-                }
             }));
-            // convert hover over the genome to structure position
             addDisposer(self, autorun(() => {
-                const { hovered } = getSession(self);
-                const { transcriptSeqToStructureSeqPosition, genomeToTranscriptSeqMapping, connectedView, } = self;
-                if (!connectedView?.initialized ||
-                    !genomeToTranscriptSeqMapping ||
-                    !checkHovered(hovered)) {
-                    return undefined;
-                }
-                const pos = genomeToTranscriptSeqMapping.g2p[hovered.hoverPosition.coord];
-                const c0 = pos
-                    ? transcriptSeqToStructureSeqPosition?.[pos]
-                    : undefined;
-                if (c0 !== undefined) {
-                    self.setHoveredPosition({
-                        structureSeqPos: c0,
-                    });
+                const { structures, molstarPluginContext } = self;
+                if (molstarPluginContext) {
+                    for (const [i, s0] of structures.entries()) {
+                        const structure = molstarPluginContext.managers.structure.hierarchy.current
+                            .structures[i]?.cell.obj?.data;
+                        const pos = s0.structureSeqHoverPos;
+                        if (structure && pos !== undefined) {
+                            highlightResidue({
+                                structure,
+                                plugin: molstarPluginContext,
+                                selectedResidue: pos,
+                            });
+                        }
+                    }
                 }
             }));
         },

package/dist/ProteinView/model.js.map

@@ -1 +1 @@
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package/dist/ProteinView/proteinToGenomeMapping.d.ts

@@ -1,13 +1,13 @@
-import { JBrowsePluginProteinViewModel } from './model';
+import { JBrowsePluginProteinStructureModel } from './model';
 export declare function proteinToGenomeMapping({ model, structureSeqPos, }: {
     structureSeqPos: number;
-    model: JBrowsePluginProteinViewModel;
-}): number[] | undefined;
+    model: JBrowsePluginProteinStructureModel;
+}): readonly [number, number] | undefined;
 export declare function clickProteinToGenome({ model, structureSeqPos, }: {
     structureSeqPos: number;
-    model: JBrowsePluginProteinViewModel;
+    model: JBrowsePluginProteinStructureModel;
 }): Promise<undefined>;
 export declare function hoverProteinToGenome({ model, structureSeqPos, }: {
-    structureSeqPos: number;
-    model: JBrowsePluginProteinViewModel;
+    structureSeqPos?: number;
+    model: JBrowsePluginProteinStructureModel;
 }): void;

package/dist/ProteinView/proteinToGenomeMapping.js

@@ -1,7 +1,7 @@
 import { getSession } from '@jbrowse/core/util';
 export function proteinToGenomeMapping({ model, structureSeqPos, }) {
-    const { genomeToTranscriptSeqMapping, alignment, structureSeqToTranscriptSeqPosition, } = model;
-    if (!genomeToTranscriptSeqMapping || !alignment) {
+    const { genomeToTranscriptSeqMapping, pairwiseAlignment, structureSeqToTranscriptSeqPosition, } = model;
+    if (!genomeToTranscriptSeqMapping || !pairwiseAlignment) {
         return undefined;
     }
     const { p2g, strand } = genomeToTranscriptSeqMapping;
@@ -20,13 +20,12 @@ export function proteinToGenomeMapping({ model, structureSeqPos, }) {
 export async function clickProteinToGenome({ model, structureSeqPos, }) {
     const session = getSession(model);
     const result = proteinToGenomeMapping({ structureSeqPos, model });
-    const { genomeToTranscriptSeqMapping, zoomToBaseLevel } = model;
+    const { connectedView, genomeToTranscriptSeqMapping, zoomToBaseLevel } = model;
     const { assemblyManager } = session;
     if (!genomeToTranscriptSeqMapping || result === undefined) {
         return undefined;
     }
     const [s1, s2] = result;
-    const lgv = session.views[0];
     const { strand, refName } = genomeToTranscriptSeqMapping;
     model.setClickGenomeHighlights([
         {
@@ -36,34 +35,36 @@ export async function clickProteinToGenome({ model, structureSeqPos, }) {
             end: s2,
         },
     ]);
-    if (!zoomToBaseLevel) {
-        const assembly = assemblyManager.get(lgv.assemblyNames[0]);
-        const r = assembly?.getCanonicalRefName(refName) ?? refName;
-        lgv.centerAt(s1, r);
-    }
-    else {
-        await lgv.navToLocString(`${refName}:${s1}-${s2}${strand === -1 ? '[rev]' : ''}`);
+    if (connectedView) {
+        if (zoomToBaseLevel) {
+            await connectedView.navToLocString(`${refName}:${s1}-${s2}${strand === -1 ? '[rev]' : ''}`);
+        }
+        else {
+            const assembly = assemblyManager.get(connectedView.assemblyNames[0]);
+            connectedView.centerAt(s1, assembly?.getCanonicalRefName(refName) ?? refName);
+        }
     }
 }
 export function hoverProteinToGenome({ model, structureSeqPos, }) {
-    const session = getSession(model);
-    const result = proteinToGenomeMapping({ structureSeqPos, model });
-    const { genomeToTranscriptSeqMapping } = model;
-    if (!genomeToTranscriptSeqMapping || !result) {
-        return;
+    if (structureSeqPos === undefined) {
+        model.setHoverGenomeHighlights([]);
     }
-    if (!result) {
-        session.notify('Genome position not found');
+    else {
+        const mappedGenomeCoordinate = proteinToGenomeMapping({
+            structureSeqPos,
+            model,
+        });
+        const { genomeToTranscriptSeqMapping } = model;
+        if (genomeToTranscriptSeqMapping && mappedGenomeCoordinate) {
+            model.setHoverGenomeHighlights([
+                {
+                    assemblyName: 'hg38',
+                    refName: genomeToTranscriptSeqMapping.refName,
+                    start: mappedGenomeCoordinate[0],
+                    end: mappedGenomeCoordinate[1],
+                },
+            ]);
+        }
     }
-    const [s1, s2] = result;
-    const { refName } = genomeToTranscriptSeqMapping;
-    model.setHoverGenomeHighlights([
-        {
-            assemblyName: 'hg38',
-            refName,
-            start: s1,
-            end: s2,
-        },
-    ]);
 }
 //# sourceMappingURL=proteinToGenomeMapping.js.map

package/dist/ProteinView/proteinToGenomeMapping.js.map

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package/dist/ProteinView/selectResidue.js

@@ -3,7 +3,7 @@ import { getMolstarStructureSelection } from './util';
 export default function selectResidue({ structure, selectedResidue, plugin, }) {
     const sel = getMolstarStructureSelection({ structure, selectedResidue });
     const loci = StructureSelection.toLociWithSourceUnits(sel);
-    plugin?.managers.interactivity.lociSelects.select({
+    plugin.managers.interactivity.lociSelects.select({
         loci,
     });
 }

package/dist/ProteinView/selectResidue.js.map

@@ -1 +1 @@
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+{"version":3,"file":"selectResidue.js","sourceRoot":"","sources":["../../src/ProteinView/selectResidue.ts"],"names":[],"mappings":"AACA,OAAO,EAAa,kBAAkB,EAAE,MAAM,iCAAiC,CAAA;AAC/E,OAAO,EAAE,4BAA4B,EAAE,MAAM,QAAQ,CAAA;AAErD,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,EACpC,SAAS,EACT,eAAe,EACf,MAAM,GAKP;IACC,MAAM,GAAG,GAAG,4BAA4B,CAAC,EAAE,SAAS,EAAE,eAAe,EAAE,CAAC,CAAA;IACxE,MAAM,IAAI,GAAG,kBAAkB,CAAC,qBAAqB,CAAC,GAAG,CAAC,CAAA;IAC1D,MAAM,CAAC,QAAQ,CAAC,aAAa,CAAC,WAAW,CAAC,MAAM,CAAC;QAC/C,IAAI;KACL,CAAC,CAAA;AACJ,CAAC"}