jbrowse-plugin-protein3d 0.0.3 → 0.0.4

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 +51,28 @@ 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;
         },
         /**
          * #action
          */
-        setSeqs(str1, str2) {
-            self.seq1 = str1;
-            self.seq2 = str2;
+        setShowAlignment(f) {
+            self.showAlignment = f;
         },
         /**
          * #action
@@ -135,54 +80,12 @@ 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 +98,64 @@ 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 @@
-{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/ProteinView/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,aAAa,EAAE,MAAM,qCAAqC,CAAA;AACnE,OAAO,EAAE,SAAS,EAAE,MAAM,EAAE,MAAM,8BAA8B,CAAA;AAEhE,OAAO,EAAY,WAAW,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACpE,OAAO,EACL,aAAa,EAEb,UAAU,GACX,MAAM,oBAAoB,CAAA;AAI3B,SAAS;AACT,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,KAAK,EAAE,MAAM,QAAQ,CAAA;AACvD,OAAO,EAAE,uBAAuB,EAAE,MAAM,iCAAiC,CAAA;AACzE,OAAO,EACL,8BAA8B,EAC9B,4BAA4B,EAC5B,+BAA+B,EAC/B,gCAAgC,GACjC,MAAM,aAAa,CAAA;AAKpB;;;;GAIG;AACH,SAAS,iBAAiB;IACxB,OAAO,KAAK;SACT,OAAO,CACN,aAAa,EACb,aAAa,EACb,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,EAAE,EAAE,SAAS;QACb;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,aAAa,CAAC;QAClC;;;WAGG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC9B;;;WAGG;QACH,IAAI,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC/B;;WAEG;QACH,qBAAqB,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC1C;;WAEG;QACH,qBAAqB,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC1C;;WAEG;QACH,YAAY,EAAE,IAAI;QAClB;;WAEG;QACH,MAAM,EAAE,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC;QACzC;;WAEG;QACH,OAAO,EAAE,KAAK,CAAC,MAAM,EAA2B;QAChD;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC/B;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC/B;;WAEG;QACH,SAAS,EAAE,KAAK,CAAC,MAAM,EAAgD;QAEvE;;WAEG;QACH,eAAe,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC1C;;WAEG;QACH,aAAa,EAAE,KAAK;QACpB;;WAEG;QACH,eAAe,EAAE,IAAI;QACrB;;WAEG;QACH,aAAa,EAAE,KAAK;KACrB,CAAC,CACH;SACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf;;WAEG;QACH,KAAK,EAAE,SAAoB;QAC3B;;WAEG;QACH,aAAa,EAAE,SAMF;QACb;;WAEG;QACH,aAAa,EAAE,SAMF;QACb;;WAEG;QACH,QAAQ,EAAE,EAAE;KACb,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,aAAa;YACf,MAAM,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAClC,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,IAAI,CAAC,eAAe,CAAa,CAAA;QACnE,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,gBAAgB,CAAC,CAAU;YACzB,IAAI,CAAC,aAAa,GAAG,CAAC,CAAA;QACxB,CAAC;QACD;;WAEG;QACH,kBAAkB,CAAC,GAIlB;YACC,IAAI,CAAC,aAAa,GAAG,GAAG,CAAA;QAC1B,CAAC;QACD;;WAEG;QACH,OAAO,CAAC,IAAa,EAAE,IAAa;YAClC,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;YAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAClB,CAAC;QACD;;WAEG;QACH,eAAe,CAAC,GAAY;YAC1B,IAAI,CAAC,YAAY,GAAG,GAAG,CAAA;QACzB,CAAC;QACD;;WAEG;QACH,WAAW,CAAC,GAAW;YACrB,IAAI,CAAC,QAAQ,GAAG,GAAG,CAAA;QACrB,CAAC;QACD;;WAEG;QACH,kBAAkB,CAAC,GAIlB;YACC,IAAI,CAAC,aAAa,GAAG,GAAG,CAAA;QAC1B,CAAC;QACD;;WAEG;QACH,wBAAwB,CAAC,CAAY;YACnC,IAAI,CAAC,qBAAqB,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACtC,CAAC;QACD;;WAEG;QACH,0BAA0B;YACxB,IAAI,CAAC,qBAAqB,GAAG,IAAI,CAAC,EAAE,CAAC,CAAA;QACvC,CAAC;QACD;;WAEG;QACH,wBAAwB,CAAC,CAAY;YACnC,IAAI,CAAC,qBAAqB,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACtC,CAAC;QACD;;WAEG;QACH,0BAA0B;YACxB,IAAI,CAAC,qBAAqB,GAAG,IAAI,CAAC,EAAE,CAAC,CAAA;QACvC,CAAC;QACD;;WAEG;QACH,QAAQ,CAAC,CAAU;YACjB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QAChB,CAAC;QACD;;WAEG;QACH,YAAY,CAAC,CAAoC;YAC/C,IAAI,CAAC,SAAS,GAAG,CAAC,CAAA;QACpB,CAAC;QACD;;WAEG;QACH,gBAAgB,CAAC,GAAY;YAC3B,IAAI,CAAC,aAAa,GAAG,GAAG,CAAA;QAC1B,CAAC;QACD;;WAEG;QACH,kBAAkB,CAAC,GAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,GAAG,CAAA;QAC5B,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,mCAAmC;YACrC,OAAO,IAAI,CAAC,SAAS;gBACnB,CAAC,CAAC,8BAA8B,CAAC,IAAI,CAAC,SAAS,CAAC;qBAC3C,mCAAmC;gBACxC,CAAC,CAAC,SAAS,CAAA;QACf,CAAC;QACD;;WAEG;QACH,IAAI,mCAAmC;YACrC,OAAO,IAAI,CAAC,SAAS;gBACnB,CAAC,CAAC,8BAA8B,CAAC,IAAI,CAAC,SAAS,CAAC;qBAC3C,mCAAmC;gBACxC,CAAC,CAAC,SAAS,CAAA;QACf,CAAC;QACD;;WAEG;QACH,IAAI,+BAA+B;YACjC,OAAO,IAAI,CAAC,SAAS;gBACnB,CAAC,CAAC,+BAA+B,CAAC,IAAI,CAAC,SAAS,CAAC;gBACjD,CAAC,CAAC,SAAS,CAAA;QACf,CAAC;QACD;;WAEG;QACH,IAAI,gCAAgC;YAClC,OAAO,IAAI,CAAC,SAAS;gBACnB,CAAC,CAAC,gCAAgC,CAAC,IAAI,CAAC,SAAS,CAAC;gBAClD,CAAC,CAAC,SAAS,CAAA;QACf,CAAC;QACD;;WAEG;QACH,IAAI,6BAA6B;YAC/B,OAAO,IAAI,CAAC,gCAAgC;gBAC1C,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,gCAAgC,CAAC;gBAClD,CAAC,CAAC,SAAS,CAAA;QACf,CAAC;QACD;;WAEG;QACH,IAAI,4BAA4B;YAC9B,OAAO,IAAI,CAAC,+BAA+B;gBACzC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,+BAA+B,CAAC;gBACjD,CAAC,CAAC,SAAS,CAAA;QACf,CAAC;QACD;;WAEG;QACH,IAAI,WAAW;YACb,MAAM,CAAC,GAAG,IAAI,CAAC,aAAa,CAAA;YAC5B,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAC1B,CAAC;QACD;;WAEG;QACH,IAAI,WAAW;YACb,MAAM,CAAC,GAAG,IAAI,CAAC,aAAa,CAAA;YAC5B,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAC1B,CAAC;QACD;;WAEG;QACH,IAAI,4BAA4B;YAC9B,OAAO,IAAI,CAAC,OAAO;gBACjB,CAAC,CAAC,4BAA4B,CAAC,IAAI,aAAa,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;gBAC/D,CAAC,CAAC,SAAS,CAAA;QACf,CAAC;QACD;;WAEG;QACH,IAAI,oBAAoB;YACtB,OAAO,IAAI,CAAC,aAAa,EAAE,eAAe,CAAA;QAC5C,CAAC;QAED,IAAI,UAAU;YACZ,MAAM,EAAE,GAAG,IAAI,CAAC,IAAI,EAAE,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;YACzC,MAAM,EAAE,GAAG,IAAI,CAAC,IAAI,EAAE,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;YACzC,OAAO,EAAE,KAAK,EAAE,CAAA;QAClB,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,WAAW;YACT,2DAA2D;YAC3D,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,KAAK,IAAI,EAAE;gBACjB,IAAI,CAAC;oBACH,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,UAAU,EAAE,GAAG,IAAI,CAAA;oBACvC,IAAI,CAAC,CAAC,IAAI,CAAC,SAAS,IAAI,CAAC,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;wBACvC,OAAM;oBACR,CAAC;oBACD,MAAM,EAAE,GAAG,IAAI,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;oBACnC,MAAM,EAAE,GAAG,IAAI,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;oBACnC,IAAI,CAAC,UAAU,EAAE,CAAC;wBAChB,MAAM,SAAS,GAAG,MAAM,uBAAuB,CAAC;4BAC9C,IAAI,EAAE,EAAE;4BACR,IAAI,EAAE,EAAE;4BACR,SAAS,EAAE,eAAe;4BAC1B,UAAU,EAAE,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC;yBACzC,CAAC,CAAA;wBACF,IAAI,CAAC,YAAY,CAAC,SAAS,CAAC,SAAS,CAAC,CAAA;wBAEtC,4BAA4B;wBAC5B,IAAI,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;wBAC3B,IAAI,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;oBAC7B,CAAC;yBAAM,CAAC;wBACN,IAAI,SAAS,GAAG,EAAE,CAAA;wBAClB,4DAA4D;wBAC5D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;4BACnC,SAAS,IAAI,GAAG,CAAA;wBAClB,CAAC;wBACD,IAAI,CAAC,YAAY,CAAC;4BAChB,SAAS;4BACT,IAAI,EAAE;gCACJ,EAAE,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,EAAE,EAAE;gCACvB,EAAE,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,EAAE,EAAE;6BACxB;yBACF,CAAC,CAAA;oBACJ,CAAC;gBACH,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;oBAChB,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;gBAClB,CAAC;YACH,CAAC,CAAC,CACH,CAAA;YAED,sDAAsD;YACtD,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,MAAM,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;gBACpC,MAAM,EACJ,mCAAmC,EACnC,4BAA4B,EAC5B,aAAa,GACd,GAAG,IAAI,CAAA;gBACR,IACE,CAAC,aAAa,EAAE,WAAW;oBAC3B,CAAC,4BAA4B;oBAC7B,CAAC,YAAY,CAAC,OAAO,CAAC,EACtB,CAAC;oBACD,OAAO,SAAS,CAAA;gBAClB,CAAC;gBAED,MAAM,GAAG,GACP,4BAA4B,CAAC,GAAG,CAAC,OAAO,CAAC,aAAa,CAAC,KAAK,CAAC,CAAA;gBAC/D,MAAM,EAAE,GAAG,GAAG;oBACZ,CAAC,CAAC,mCAAmC,EAAE,CAAC,GAAG,CAAC;oBAC5C,CAAC,CAAC,SAAS,CAAA;gBACb,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;oBACrB,IAAI,CAAC,kBAAkB,CAAC;wBACtB,eAAe,EAAE,EAAE;qBACpB,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC,CAAC,CACH,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AAED,eAAe,iBAAiB,CAAA"}
+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/ProteinView/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,aAAa,EAAE,MAAM,qCAAqC,CAAA;AACnE,OAAO,EAAE,SAAS,EAAE,MAAM,8BAA8B,CAAA;AACxD,OAAO,EAAY,WAAW,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAI9D,OAAO,EAAE,oBAAoB,EAAE,MAAM,wBAAwB,CAAA;AAC7D,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAA;AAC3D,OAAO,SAAS,MAAM,kBAAkB,CAAA;AACxC,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AAEjD;;;;GAIG;AACH,SAAS,iBAAiB;IACxB,OAAO,KAAK;SACT,OAAO,CACN,aAAa,EACb,aAAa,EACb,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,EAAE,EAAE,SAAS;QACb;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,aAAa,CAAC;QAClC;;WAEG;QACH,UAAU,EAAE,KAAK,CAAC,KAAK,CAAC,SAAS,CAAC;QAElC;;WAEG;QACH,YAAY,EAAE,KAAK;QACnB;;WAEG;QACH,MAAM,EAAE,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC;QAEzC;;WAEG;QACH,aAAa,EAAE,KAAK;QACpB;;WAEG;QACH,eAAe,EAAE,IAAI;QACrB;;WAEG;QACH,aAAa,EAAE,KAAK;KACrB,CAAC,CACH;SACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf;;WAEG;QACH,QAAQ,EAAE,EAAE;QACZ;;WAEG;QACH,KAAK,EAAE,SAAoB;QAC3B;;WAEG;QACH,oBAAoB,EAAE,SAAsC;KAC7D,CAAC,CAAC;SAEF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,SAAS,CAAC,CAAS;YACjB,IAAI,CAAC,MAAM,GAAG,CAAC,CAAA;QACjB,CAAC;QACD;;WAEG;QACH,gBAAgB,CAAC,CAAU;YACzB,IAAI,CAAC,aAAa,GAAG,CAAC,CAAA;QACxB,CAAC;QAED;;WAEG;QACH,eAAe,CAAC,GAAY;YAC1B,IAAI,CAAC,YAAY,GAAG,GAAG,CAAA;QACzB,CAAC;QAED;;WAEG;QACH,QAAQ,CAAC,CAAU;YACjB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QAChB,CAAC;QAED;;WAEG;QACH,gBAAgB,CAAC,GAAY;YAC3B,IAAI,CAAC,aAAa,GAAG,GAAG,CAAA;QAC1B,CAAC;QACD;;WAEG;QACH,kBAAkB,CAAC,GAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,GAAG,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,uBAAuB,CAAC,CAAiB;YACvC,IAAI,CAAC,oBAAoB,GAAG,CAAC,CAAA;QAC/B,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,WAAW;YACT,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,KAAK,IAAI,EAAE;gBACjB,MAAM,EAAE,UAAU,EAAE,oBAAoB,EAAE,GAAG,IAAI,CAAA;gBACjD,IAAI,oBAAoB,EAAE,CAAC;oBACzB,KAAK,MAAM,SAAS,IAAI,UAAU,EAAE,CAAC;wBACnC,IAAI,CAAC;4BACH,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,IAAI;gCAC9B,CAAC,CAAC,MAAM,oBAAoB,CAAC;oCACzB,IAAI,EAAE,SAAS,CAAC,IAAI;oCACpB,MAAM,EAAE,oBAAoB;iCAC7B,CAAC;gCACJ,CAAC,CAAC,SAAS,CAAC,GAAG;oCACb,CAAC,CAAC,MAAM,mBAAmB,CAAC;wCACxB,GAAG,EAAE,SAAS,CAAC,GAAG;wCAClB,MAAM,EAAE,oBAAoB;qCAC7B,CAAC;oCACJ,CAAC,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;4BAE1B,MAAM,SAAS,GAAG,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,GAAG,CACvD,CAAC,CAAC,EAAE;gCACF,IAAI,GAAG,GAAG,EAAE,CAAA;gCACZ,MAAM,GAAG,GAAG,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,EAAE,CAAA;gCACtC,gFAAgF;gCAChF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;oCACpC,GAAG,IAAI,GAAG,CAAC,CAAC,CAAE,CAAA;gCAChB,CAAC;gCACD,OAAO,GAAG,CAAA;4BACZ,CAAC,CACF,CAAA;4BACD,SAAS,CAAC,YAAY,CAAC,SAAS,CAAC,CAAA;wBACnC,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;4BAChB,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAClB,CAAC;oBACH,CAAC;gBACH,CAAC;YACH,CAAC,CAAC,CACH,CAAA;YAED,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,MAAM,EAAE,UAAU,EAAE,oBAAoB,EAAE,GAAG,IAAI,CAAA;gBACjD,IAAI,oBAAoB,EAAE,CAAC;oBACzB,KAAK,MAAM,CAAC,CAAC,EAAE,EAAE,CAAC,IAAI,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC;wBAC3C,MAAM,SAAS,GACb,oBAAoB,CAAC,QAAQ,CAAC,SAAS,CAAC,SAAS,CAAC,OAAO;6BACtD,UAAU,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,EAAE,IAAI,CAAA;wBAClC,MAAM,GAAG,GAAG,EAAE,CAAC,oBAAoB,CAAA;wBACnC,IAAI,SAAS,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;4BACnC,gBAAgB,CAAC;gCACf,SAAS;gCACT,MAAM,EAAE,oBAAoB;gCAC5B,eAAe,EAAE,GAAG;6BACrB,CAAC,CAAA;wBACJ,CAAC;oBACH,CAAC;gBACH,CAAC;YACH,CAAC,CAAC,CACH,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AAED,eAAe,iBAAiB,CAAA"}

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

@@ -1 +1 @@
-{"version":3,"file":"proteinToGenomeMapping.js","sourceRoot":"","sources":["../../src/ProteinView/proteinToGenomeMapping.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAM/C,MAAM,UAAU,sBAAsB,CAAC,EACrC,KAAK,EACL,eAAe,GAIhB;IACC,MAAM,EACJ,4BAA4B,EAC5B,SAAS,EACT,mCAAmC,GACpC,GAAG,KAAK,CAAA;IACT,IAAI,CAAC,4BAA4B,IAAI,CAAC,SAAS,EAAE,CAAC;QAChD,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,4BAA4B,CAAA;IACpD,MAAM,EAAE,GAAG,mCAAmC,EAAE,CAAC,eAAe,CAAC,CAAA;IACjE,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;QACrB,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,EAAE,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAClB,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;QACrB,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,MAAM,GAAG,GAAG,KAAK,GAAG,CAAC,GAAG,MAAM,CAAA;IAC9B,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAA;AACrD,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,oBAAoB,CAAC,EACzC,KAAK,EACL,eAAe,GAIhB;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,MAAM,GAAG,sBAAsB,CAAC,EAAE,eAAe,EAAE,KAAK,EAAE,CAAC,CAAA;IACjE,MAAM,EAAE,4BAA4B,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IAC/D,MAAM,EAAE,eAAe,EAAE,GAAG,OAAO,CAAA;IACnC,IAAI,CAAC,4BAA4B,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;QAC1D,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,CAAC,EAAE,EAAE,EAAE,CAAC,GAAG,MAAM,CAAA;IACvB,MAAM,GAAG,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,CAA0B,CAAA;IACrD,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,4BAA4B,CAAA;IACxD,KAAK,CAAC,wBAAwB,CAAC;QAC7B;YACE,YAAY,EAAE,MAAM;YACpB,OAAO;YACP,KAAK,EAAE,EAAE;YACT,GAAG,EAAE,EAAE;SACR;KACF,CAAC,CAAA;IAEF,IAAI,CAAC,eAAe,EAAE,CAAC;QACrB,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAAA;QAC1D,MAAM,CAAC,GAAG,QAAQ,EAAE,mBAAmB,CAAC,OAAO,CAAC,IAAI,OAAO,CAAA;QAC3D,GAAG,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;IACrB,CAAC;SAAM,CAAC;QACN,MAAM,GAAG,CAAC,cAAc,CACtB,GAAG,OAAO,IAAI,EAAE,IAAI,EAAE,GAAG,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CACxD,CAAA;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,EACnC,KAAK,EACL,eAAe,GAIhB;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,MAAM,GAAG,sBAAsB,CAAC,EAAE,eAAe,EAAE,KAAK,EAAE,CAAC,CAAA;IACjE,MAAM,EAAE,4BAA4B,EAAE,GAAG,KAAK,CAAA;IAC9C,IAAI,CAAC,4BAA4B,IAAI,CAAC,MAAM,EAAE,CAAC;QAC7C,OAAM;IACR,CAAC;IACD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAO,CAAC,MAAM,CAAC,2BAA2B,CAAC,CAAA;IAC7C,CAAC;IACD,MAAM,CAAC,EAAE,EAAE,EAAE,CAAC,GAAG,MAAM,CAAA;IACvB,MAAM,EAAE,OAAO,EAAE,GAAG,4BAA4B,CAAA;IAChD,KAAK,CAAC,wBAAwB,CAAC;QAC7B;YACE,YAAY,EAAE,MAAM;YACpB,OAAO;YACP,KAAK,EAAE,EAAE;YACT,GAAG,EAAE,EAAE;SACR;KACF,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"proteinToGenomeMapping.js","sourceRoot":"","sources":["../../src/ProteinView/proteinToGenomeMapping.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAK/C,MAAM,UAAU,sBAAsB,CAAC,EACrC,KAAK,EACL,eAAe,GAIhB;IACC,MAAM,EACJ,4BAA4B,EAC5B,iBAAiB,EACjB,mCAAmC,GACpC,GAAG,KAAK,CAAA;IACT,IAAI,CAAC,4BAA4B,IAAI,CAAC,iBAAiB,EAAE,CAAC;QACxD,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,4BAA4B,CAAA;IACpD,MAAM,EAAE,GAAG,mCAAmC,EAAE,CAAC,eAAe,CAAC,CAAA;IACjE,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;QACrB,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,EAAE,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAClB,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;QACrB,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,MAAM,GAAG,GAAG,KAAK,GAAG,CAAC,GAAG,MAAM,CAAA;IAC9B,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,CAAU,CAAA;AAC9D,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,oBAAoB,CAAC,EACzC,KAAK,EACL,eAAe,GAIhB;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,MAAM,GAAG,sBAAsB,CAAC,EAAE,eAAe,EAAE,KAAK,EAAE,CAAC,CAAA;IACjE,MAAM,EAAE,aAAa,EAAE,4BAA4B,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IAC9E,MAAM,EAAE,eAAe,EAAE,GAAG,OAAO,CAAA;IACnC,IAAI,CAAC,4BAA4B,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;QAC1D,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,CAAC,EAAE,EAAE,EAAE,CAAC,GAAG,MAAM,CAAA;IACvB,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,4BAA4B,CAAA;IACxD,KAAK,CAAC,wBAAwB,CAAC;QAC7B;YACE,YAAY,EAAE,MAAM;YACpB,OAAO;YACP,KAAK,EAAE,EAAE;YACT,GAAG,EAAE,EAAE;SACR;KACF,CAAC,CAAA;IACF,IAAI,aAAa,EAAE,CAAC;QAClB,IAAI,eAAe,EAAE,CAAC;YACpB,MAAM,aAAa,CAAC,cAAc,CAChC,GAAG,OAAO,IAAI,EAAE,IAAI,EAAE,GAAG,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CACxD,CAAA;QACH,CAAC;aAAM,CAAC;YACN,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,CAAE,CAAC,CAAA;YACrE,aAAa,CAAC,QAAQ,CACpB,EAAE,EACF,QAAQ,EAAE,mBAAmB,CAAC,OAAO,CAAC,IAAI,OAAO,CAClD,CAAA;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,EACnC,KAAK,EACL,eAAe,GAIhB;IACC,IAAI,eAAe,KAAK,SAAS,EAAE,CAAC;QAClC,KAAK,CAAC,wBAAwB,CAAC,EAAE,CAAC,CAAA;IACpC,CAAC;SAAM,CAAC;QACN,MAAM,sBAAsB,GAAG,sBAAsB,CAAC;YACpD,eAAe;YACf,KAAK;SACN,CAAC,CAAA;QACF,MAAM,EAAE,4BAA4B,EAAE,GAAG,KAAK,CAAA;QAC9C,IAAI,4BAA4B,IAAI,sBAAsB,EAAE,CAAC;YAC3D,KAAK,CAAC,wBAAwB,CAAC;gBAC7B;oBACE,YAAY,EAAE,MAAM;oBACpB,OAAO,EAAE,4BAA4B,CAAC,OAAO;oBAC7C,KAAK,EAAE,sBAAsB,CAAC,CAAC,CAAC;oBAChC,GAAG,EAAE,sBAAsB,CAAC,CAAC,CAAC;iBAC/B;aACF,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;AACH,CAAC"}

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 @@
-{"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,EAAE,QAAQ,CAAC,aAAa,CAAC,WAAW,CAAC,MAAM,CAAC;QAChD,IAAI;KACL,CAAC,CAAA;AACJ,CAAC"}
+{"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"}