jbrowse-plugin-protein3d 0.0.3 → 0.0.5

package/src/mappings.test.ts

@@ -1,22 +1,24 @@
+import { expect, test } from 'vitest'
 import {
   genomeToTranscriptSeqMapping,
   structureSeqVsTranscriptSeqMap,
 } from './mappings'
 import { SimpleFeature } from '@jbrowse/core/util'
-import { feature, alignment } from './test_data/gene'
+import { feature, pairwiseAlignment } from './test_data/gene'
 
 test('test', () => {
-  const ret = structureSeqVsTranscriptSeqMap(alignment)
+  const ret = structureSeqVsTranscriptSeqMap(pairwiseAlignment)
   expect(ret).toMatchSnapshot()
 })
 
 test('mapping', () => {
+  // @ts-expect-error
   const res = genomeToTranscriptSeqMapping(new SimpleFeature(feature))
   const { p2g } = res
-  const aln = structureSeqVsTranscriptSeqMap(alignment)
+  const aln = structureSeqVsTranscriptSeqMap(pairwiseAlignment)
 
   // expected position in sequence
-  const s2 = alignment.alns[1].seq
+  const s2 = pairwiseAlignment.alns[1].seq
   expect(s2[392]).toBe('M')
   expect(s2[393]).toBe('K')
   expect(s2[394]).toBe('A')
@@ -24,7 +26,7 @@ test('mapping', () => {
   // maps the 392 position in the "pdb version of the protein" to the 0th
   // position in the genome version of the protein, and then maps that back to
   // the genome
-  const p0 = aln.structureSeqToTranscriptSeqPosition[392]!
+  const p0 = aln.transcriptSeqToStructureSeqPosition[392]!
   const g0 = p2g[p0]
   expect(p0).toBe(0)
   expect(g0).toBe(51_296_155)

package/src/mappings.ts

@@ -1,30 +1,27 @@
 import { Feature } from '@jbrowse/core/util'
 import { genomeToTranscriptSeqMapping as g2p } from 'g2p_mapper'
-
-export interface Alignment {
-  alns: {
-    id: string
-    seq: string
-  }[]
+export interface AlignmentRow {
+  id: string
+  seq: string
+}
+export interface PairwiseAlignment {
+  consensus: string
+  alns: readonly [AlignmentRow, AlignmentRow]
 }
 
-export function structureSeqVsTranscriptSeqMap(alignment: Alignment) {
-  const structureSeq = alignment.alns[0].seq
-  const transcriptSeq = alignment.alns[1].seq
+export function structureSeqVsTranscriptSeqMap(
+  pairwiseAlignment: PairwiseAlignment,
+) {
+  const structureSeq = pairwiseAlignment.alns[1].seq
+  const transcriptSeq = pairwiseAlignment.alns[0].seq
   if (structureSeq.length !== transcriptSeq.length) {
     throw new Error('mismatched length')
   }
 
   let j = 0
   let k = 0
-  const structureSeqToTranscriptSeqPosition = {} as Record<
-    string,
-    number | undefined
-  >
-  const transcriptSeqToStructureSeqPosition = {} as Record<
-    string,
-    number | undefined
-  >
+  const structureSeqToTranscriptSeqPosition = {} as Record<string, number>
+  const transcriptSeqToStructureSeqPosition = {} as Record<string, number>
 
   // eslint-disable-next-line unicorn/no-for-loop
   for (let i = 0; i < structureSeq.length; i++) {
@@ -48,15 +45,18 @@ export function structureSeqVsTranscriptSeqMap(alignment: Alignment) {
       j++
     }
   }
+
   return {
     structureSeqToTranscriptSeqPosition,
     transcriptSeqToStructureSeqPosition,
   }
 }
 
-export function structurePositionToAlignmentMap(alignment: Alignment) {
-  const structureSeq = alignment.alns[0].seq
-  const structurePositionToAlignment = {} as Record<string, number | undefined>
+export function structurePositionToAlignmentMap(
+  pairwiseAlignment: PairwiseAlignment,
+) {
+  const structureSeq = pairwiseAlignment.alns[1].seq
+  const structurePositionToAlignment = {} as Record<string, number>
 
   for (let i = 0, j = 0; i < structureSeq.length; i++) {
     if (structureSeq[i] !== '-') {
@@ -68,9 +68,11 @@ export function structurePositionToAlignmentMap(alignment: Alignment) {
   return structurePositionToAlignment
 }
 
-export function transcriptPositionToAlignmentMap(alignment: Alignment) {
-  const transcriptSeq = alignment.alns[1].seq
-  const transcriptPositionToAlignment = {} as Record<string, number | undefined>
+export function transcriptPositionToAlignmentMap(
+  pairwiseAlignment: PairwiseAlignment,
+) {
+  const transcriptSeq = pairwiseAlignment.alns[0].seq
+  const transcriptPositionToAlignment = {} as Record<string, number>
 
   for (let i = 0, j = 0; i < transcriptSeq.length; i++) {
     if (transcriptSeq[i] !== '-') {

package/src/test_data/gene.ts

@@ -586,9 +586,9 @@ export const feature = {
   uniqueId: '590611027-offset-601794870-0',
   parentId: '590611027-offset-601794870',
   __jbrowsefmt: {},
-}
+} as const
 
-export const alignment = {
+export const pairwiseAlignment = {
   consensus:
     '                                                                                                                                                                                                                                                                                                                                                                                                        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ',
   alns: [
@@ -601,4 +601,4 @@ export const alignment = {
       seq: '--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNPISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIITKAEEMLEKGPENEYSVDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALLELALLLMEQDRNEEAIKLLESAKQNYKNYSMESRTHFRIQAATLQAKSSLENSSRSMVSSVSL*',
     },
   ],
-}
+} as const

package/dist/ProteinView/components/Header.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../../src/ProteinView/components/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AAEtE,QAAQ;AACR,OAAO,QAAQ,MAAM,0BAA0B,CAAA;AAC/C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AAIvD,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AACjD,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAElD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAC3C,KAAK,GAGN;IACC,MAAM,EAAE,SAAS,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC1C,OAAO,CACL;QACE,oBAAC,qBAAqB,IAAC,KAAK,EAAE,KAAK,GAAI;QACtC,aAAa,CAAC,CAAC,CAAC,CACf,SAAS,CAAC,CAAC,CAAC,CACV,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI,CACnC,CAAC,CAAC,CAAC,CACF,oBAAC,eAAe,IAAC,OAAO,EAAC,4BAA4B,GAAG,CACzD,CACF,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,qBAAqB,GAAG,QAAQ,CAAC,UAAU,EAC/C,KAAK,GAGN;IACC,MAAM,EACJ,aAAa,EACb,WAAW,EACX,WAAW,EACX,aAAa,EACb,eAAe,GAChB,GAAG,KAAK,CAAA;IACT,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,kCACG;YACC,WAAW,CAAC,CAAC,CAAC,UAAU,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE;YAC1C,WAAW,CAAC,CAAC,CAAC,UAAU,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE;SAC3C,CAAC,IAAI,CAAC,GAAG,CAAC,CACN;QACP,8BAAM,KAAK,EAAE,EAAE,QAAQ,EAAE,CAAC,EAAE,GAAI;QAChC,oBAAC,mBAAmB,IAClB,SAAS,EAAE;gBACT;oBACE,KAAK,EAAE,8BAA8B;oBACrC,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,aAAa;oBACtB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC;iBACtD;gBACD;oBACE,KAAK,EAAE,sCAAsC;oBAC7C,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,aAAa;oBACtB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC;iBACtD;gBACD;oBACE,KAAK,EAAE,6BAA6B;oBACpC,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,eAAe;oBACxB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC,eAAe,CAAC;iBAC1D;aACF;YAED,oBAAC,QAAQ,OAAG,CACQ,CAClB,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}

package/dist/ProteinView/loadStructureFromData.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"loadStructureFromData.js","sourceRoot":"","sources":["../../src/ProteinView/loadStructureFromData.ts"],"names":[],"mappings":"AAQA,qIAAqI;AACrI,MAAM,CAAC,KAAK,UAAU,qBAAqB,CAAC,EAC1C,IAAI,EACJ,MAAM,GAAG,KAAK,EACd,OAAO,EACP,MAAM,GAMP;IACC,MAAM,MAAM,CAAC,KAAK,EAAE,CAAA;IAEpB,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC;QAC/C,IAAI;QACJ,KAAK,EAAE,OAAO,EAAE,SAAS;KAC1B,CAAC,CAAA;IAEF,MAAM,UAAU,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,eAAe,CAChE,KAAK,EACL,MAAM,CACP,CAAA;IACD,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;IACrE,MAAM,GAAG,GAAG,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK;SAC7D,OAAO,EAAE;QACV,mBAAmB;SAClB,IAAI,CAAC,EAAE,CAAC,CAAA;IAEX,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,SAAS,CAAC,WAAW,CACnD,UAAU,EACV,YAAY,EACZ;QACE,uBAAuB,EAAE,IAAI;QAC7B,0BAA0B,EAAE,OAAO,EAAE,oBAAoB;KAC1D,CACF,CAAA;IAED,OAAO,EAAE,GAAG,EAAE,GAAa,EAAE,CAAA;AAC/B,CAAC"}

package/dist/ProteinView/loadStructureFromURL.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"loadStructureFromURL.js","sourceRoot":"","sources":["../../src/ProteinView/loadStructureFromURL.ts"],"names":[],"mappings":"AAQA,4HAA4H;AAC5H,MAAM,CAAC,KAAK,UAAU,oBAAoB,CAAC,EACzC,GAAG,EACH,MAAM,GAAG,OAAO,EAChB,QAAQ,EACR,OAAO,EACP,MAAM,GAOP;IACC,MAAM,MAAM,CAAC,KAAK,EAAE,CAAA;IAEpB,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,QAAQ,CAC9C,EAAE,GAAG,EAAE,QAAQ,EAAE,EACjB,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,EAAE,CAC7B,CAAA;IAED,MAAM,UAAU,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,eAAe,CAChE,IAAI,EACJ,MAAM,CACP,CAAA;IACD,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;IACrE,MAAM,GAAG,GAAG,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK;SAC7D,OAAO,EAAE;QACV,mBAAmB;SAClB,IAAI,CAAC,EAAE,CAAC,CAAA;IAEX,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,SAAS,CAAC,WAAW,CACnD,UAAU,EACV,YAAY,EACZ;QACE,uBAAuB,EAAE,IAAI;QAC7B,0BAA0B,EAAE,OAAO,EAAE,oBAAoB;KAC1D,CACF,CAAA;IAED,OAAO,EAAE,GAAG,EAAE,GAAa,EAAE,CAAA;AAC/B,CAAC"}

package/dist/ProteinView/useProteinViewClickBehavior.d.ts

@@ -1,8 +0,0 @@
-import { PluginContext } from 'molstar/lib/mol-plugin/context';
-import { JBrowsePluginProteinViewModel } from './model';
-export default function useProteinViewClickActionBehavior({ plugin, model, }: {
-    plugin?: PluginContext;
-    model: JBrowsePluginProteinViewModel;
-}): {
-    error: unknown;
-};

package/dist/ProteinView/useProteinViewClickBehavior.js

@@ -1,34 +0,0 @@
-import { useEffect, useState } from 'react';
-import { getSession } from '@jbrowse/core/util';
-import { clickProteinToGenome } from './proteinToGenomeMapping';
-import { StructureElement, StructureProperties as Props, } from 'molstar/lib/mol-model/structure';
-export default function useProteinViewClickActionBehavior({ plugin, model, }) {
-    const [error, setError] = useState();
-    const session = getSession(model);
-    useEffect(() => {
-        if (!plugin) {
-            return;
-        }
-        plugin.behaviors.interaction.click.subscribe(event => {
-            if (StructureElement.Loci.is(event.current.loci)) {
-                const loc = StructureElement.Loci.getFirstLocation(event.current.loci);
-                if (loc) {
-                    const pos = Props.residue.auth_seq_id(loc);
-                    const code = Props.atom.label_comp_id(loc);
-                    const chain = Props.chain.auth_asym_id(loc);
-                    model.setHoveredPosition({
-                        structureSeqPos: pos - 1,
-                        code,
-                        chain,
-                    });
-                    clickProteinToGenome({ model, structureSeqPos: pos - 1 }).catch(e => {
-                        console.error(e);
-                        setError(e);
-                    });
-                }
-            }
-        });
-    }, [plugin, session, model]);
-    return { error };
-}
-//# sourceMappingURL=useProteinViewClickBehavior.js.map

package/dist/ProteinView/useProteinViewClickBehavior.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"useProteinViewClickBehavior.js","sourceRoot":"","sources":["../../src/ProteinView/useProteinViewClickBehavior.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC3C,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAK/C,OAAO,EAAE,oBAAoB,EAAE,MAAM,0BAA0B,CAAA;AAC/D,OAAO,EACL,gBAAgB,EAChB,mBAAmB,IAAI,KAAK,GAC7B,MAAM,iCAAiC,CAAA;AAExC,MAAM,CAAC,OAAO,UAAU,iCAAiC,CAAC,EACxD,MAAM,EACN,KAAK,GAIN;IACC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAM;QACR,CAAC;QACD,MAAM,CAAC,SAAS,CAAC,WAAW,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,EAAE;YACnD,IAAI,gBAAgB,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;gBACjD,MAAM,GAAG,GAAG,gBAAgB,CAAC,IAAI,CAAC,gBAAgB,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;gBACtE,IAAI,GAAG,EAAE,CAAC;oBACR,MAAM,GAAG,GAAG,KAAK,CAAC,OAAO,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;oBAC1C,MAAM,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;oBAC1C,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;oBAC3C,KAAK,CAAC,kBAAkB,CAAC;wBACvB,eAAe,EAAE,GAAG,GAAG,CAAC;wBACxB,IAAI;wBACJ,KAAK;qBACN,CAAC,CAAA;oBAEF,oBAAoB,CAAC,EAAE,KAAK,EAAE,eAAe,EAAE,GAAG,GAAG,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;wBAClE,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;oBACb,CAAC,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;QACH,CAAC,CAAC,CAAA;IACJ,CAAC,EAAE,CAAC,MAAM,EAAE,OAAO,EAAE,KAAK,CAAC,CAAC,CAAA;IAC5B,OAAO,EAAE,KAAK,EAAE,CAAA;AAClB,CAAC"}

package/dist/ProteinView/useProteinViewHoverBehavior.d.ts

@@ -1,6 +0,0 @@
-import { PluginContext } from 'molstar/lib/mol-plugin/context';
-import { JBrowsePluginProteinViewModel } from './model';
-export default function useProteinViewClickActionBehavior({ plugin, model, }: {
-    plugin?: PluginContext;
-    model: JBrowsePluginProteinViewModel;
-}): void;

package/dist/ProteinView/useProteinViewHoverBehavior.js

@@ -1,31 +0,0 @@
-import { useEffect } from 'react';
-import { getSession } from '@jbrowse/core/util';
-import { StructureElement, StructureProperties as Props, } from 'molstar/lib/mol-model/structure';
-import { hoverProteinToGenome } from './proteinToGenomeMapping';
-export default function useProteinViewClickActionBehavior({ plugin, model, }) {
-    const session = getSession(model);
-    useEffect(() => {
-        if (!plugin) {
-            return;
-        }
-        plugin.behaviors.interaction.hover.subscribe(event => {
-            if (StructureElement.Loci.is(event.current.loci)) {
-                const loc = StructureElement.Loci.getFirstLocation(event.current.loci);
-                if (loc) {
-                    // example code for this label
-                    // https://github.com/molstar/molstar/blob/60550cfea1f62a50a764d5714307d6d1049be71d/src/mol-theme/label.ts#L255-L264
-                    const structureSeqPos = Props.residue.auth_seq_id(loc);
-                    const code = Props.atom.label_comp_id(loc);
-                    const chain = Props.chain.auth_asym_id(loc);
-                    model.setHoveredPosition({
-                        structureSeqPos: structureSeqPos - 1,
-                        code,
-                        chain,
-                    });
-                    hoverProteinToGenome({ model, structureSeqPos: structureSeqPos - 1 });
-                }
-            }
-        });
-    }, [plugin, session, model]);
-}
-//# sourceMappingURL=useProteinViewHoverBehavior.js.map

package/dist/ProteinView/useProteinViewHoverBehavior.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"useProteinViewHoverBehavior.js","sourceRoot":"","sources":["../../src/ProteinView/useProteinViewHoverBehavior.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AACjC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAK/C,OAAO,EACL,gBAAgB,EAChB,mBAAmB,IAAI,KAAK,GAC7B,MAAM,iCAAiC,CAAA;AACxC,OAAO,EAAE,oBAAoB,EAAE,MAAM,0BAA0B,CAAA;AAE/D,MAAM,CAAC,OAAO,UAAU,iCAAiC,CAAC,EACxD,MAAM,EACN,KAAK,GAIN;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAM;QACR,CAAC;QACD,MAAM,CAAC,SAAS,CAAC,WAAW,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,EAAE;YACnD,IAAI,gBAAgB,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;gBACjD,MAAM,GAAG,GAAG,gBAAgB,CAAC,IAAI,CAAC,gBAAgB,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;gBACtE,IAAI,GAAG,EAAE,CAAC;oBACR,8BAA8B;oBAC9B,oHAAoH;oBACpH,MAAM,eAAe,GAAG,KAAK,CAAC,OAAO,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;oBACtD,MAAM,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;oBAC1C,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;oBAC3C,KAAK,CAAC,kBAAkB,CAAC;wBACvB,eAAe,EAAE,eAAe,GAAG,CAAC;wBACpC,IAAI;wBACJ,KAAK;qBACN,CAAC,CAAA;oBACF,oBAAoB,CAAC,EAAE,KAAK,EAAE,eAAe,EAAE,eAAe,GAAG,CAAC,EAAE,CAAC,CAAA;gBACvE,CAAC;YACH,CAAC;QACH,CAAC,CAAC,CAAA;IACJ,CAAC,EAAE,CAAC,MAAM,EAAE,OAAO,EAAE,KAAK,CAAC,CAAC,CAAA;AAC9B,CAAC"}

package/src/ProteinView/useProteinViewClickBehavior.ts

@@ -1,48 +0,0 @@
-import { useEffect, useState } from 'react'
-import { getSession } from '@jbrowse/core/util'
-import { PluginContext } from 'molstar/lib/mol-plugin/context'
-
-// local
-import { JBrowsePluginProteinViewModel } from './model'
-import { clickProteinToGenome } from './proteinToGenomeMapping'
-import {
-  StructureElement,
-  StructureProperties as Props,
-} from 'molstar/lib/mol-model/structure'
-
-export default function useProteinViewClickActionBehavior({
-  plugin,
-  model,
-}: {
-  plugin?: PluginContext
-  model: JBrowsePluginProteinViewModel
-}) {
-  const [error, setError] = useState<unknown>()
-  const session = getSession(model)
-  useEffect(() => {
-    if (!plugin) {
-      return
-    }
-    plugin.behaviors.interaction.click.subscribe(event => {
-      if (StructureElement.Loci.is(event.current.loci)) {
-        const loc = StructureElement.Loci.getFirstLocation(event.current.loci)
-        if (loc) {
-          const pos = Props.residue.auth_seq_id(loc)
-          const code = Props.atom.label_comp_id(loc)
-          const chain = Props.chain.auth_asym_id(loc)
-          model.setHoveredPosition({
-            structureSeqPos: pos - 1,
-            code,
-            chain,
-          })
-
-          clickProteinToGenome({ model, structureSeqPos: pos - 1 }).catch(e => {
-            console.error(e)
-            setError(e)
-          })
-        }
-      }
-    })
-  }, [plugin, session, model])
-  return { error }
-}

package/src/ProteinView/useProteinViewHoverBehavior.ts

@@ -1,44 +0,0 @@
-import { useEffect } from 'react'
-import { getSession } from '@jbrowse/core/util'
-import { PluginContext } from 'molstar/lib/mol-plugin/context'
-
-// local
-import { JBrowsePluginProteinViewModel } from './model'
-import {
-  StructureElement,
-  StructureProperties as Props,
-} from 'molstar/lib/mol-model/structure'
-import { hoverProteinToGenome } from './proteinToGenomeMapping'
-
-export default function useProteinViewClickActionBehavior({
-  plugin,
-  model,
-}: {
-  plugin?: PluginContext
-  model: JBrowsePluginProteinViewModel
-}) {
-  const session = getSession(model)
-  useEffect(() => {
-    if (!plugin) {
-      return
-    }
-    plugin.behaviors.interaction.hover.subscribe(event => {
-      if (StructureElement.Loci.is(event.current.loci)) {
-        const loc = StructureElement.Loci.getFirstLocation(event.current.loci)
-        if (loc) {
-          // example code for this label
-          // https://github.com/molstar/molstar/blob/60550cfea1f62a50a764d5714307d6d1049be71d/src/mol-theme/label.ts#L255-L264
-          const structureSeqPos = Props.residue.auth_seq_id(loc)
-          const code = Props.atom.label_comp_id(loc)
-          const chain = Props.chain.auth_asym_id(loc)
-          model.setHoveredPosition({
-            structureSeqPos: structureSeqPos - 1,
-            code,
-            chain,
-          })
-          hoverProteinToGenome({ model, structureSeqPos: structureSeqPos - 1 })
-        }
-      }
-    })
-  }, [plugin, session, model])
-}