Fix mouseover at 0

GMOD · Aug 23, 2024 · a660be2 · a660be2
1 parent 82bc2b9
commit a660be2
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Showing 6 changed files with 34 additions and 50 deletions.
diff --git a/src/ProteinView/components/ProteinAlignment.tsx b/src/ProteinView/components/ProteinAlignment.tsx
@@ -17,10 +17,10 @@ const ProteinAlignment = observer(function ({
   model: JBrowsePluginProteinStructureModel
 }) {
   const {
-    structureSeqHoverPos,
     alignment,
-    structurePositionToAlignmentMap,
     alignmentToStructurePosition,
+    structurePositionToAlignmentMap,
+    structureSeqHoverPos,
     showHighlight,
   } = model
   if (!alignment) {

diff --git a/src/ProteinView/components/ProteinView.tsx b/src/ProteinView/components/ProteinView.tsx
@@ -1,21 +1,13 @@
 import React, { useEffect } from 'react'
 import { observer } from 'mobx-react'
 import { ErrorMessage, ResizeHandle } from '@jbrowse/core/ui'
-import { PluginContext } from 'molstar/lib/mol-plugin/context'
 
 // locals
 import { JBrowsePluginProteinViewModel } from '../model'
 import ProteinViewHeader from './ProteinViewHeader'
 
 // hooks
 import useProteinView from '../useProteinView'
-import useProteinViewClickBehavior from '../useProteinViewClickBehavior'
-import useProteinViewHoverBehavior from '../useProteinViewHoverBehavior'
-
-// utils
-import selectResidue from '../selectResidue'
-import highlightResidue from '../highlightResidue'
-import clearSelection from '../clearSelection'
 
 // css
 import css from '../css/molstar'

diff --git a/src/ProteinView/model.ts b/src/ProteinView/model.ts
@@ -9,11 +9,6 @@ import { addStructureFromData } from './addStructureFromData'
 import { addStructureFromURL } from './addStructureFromURL'
 import Structure from './structureModel'
 import highlightResidue from './highlightResidue'
-import {
-  StructureElement,
-  StructureProperties,
-} from 'molstar/lib/mol-model/structure'
-import { clickProteinToGenome } from './proteinToGenomeMapping'
 
 /**
  * #stateModel Protein3dViewPlugin

diff --git a/src/ProteinView/proteinToGenomeMapping.ts b/src/ProteinView/proteinToGenomeMapping.ts
@@ -77,24 +77,19 @@ export function hoverProteinToGenome({
   structureSeqPos: number
   model: JBrowsePluginProteinStructureModel
 }) {
-  const session = getSession(model)
-  const result = proteinToGenomeMapping({ structureSeqPos, model })
+  const mappedGenomeCoordinate = proteinToGenomeMapping({
+    structureSeqPos,
+    model,
+  })
   const { genomeToTranscriptSeqMapping } = model
-  if (!genomeToTranscriptSeqMapping) {
-    return
-  }
-  if (!result) {
-    session.notify('Genome position not found')
-    return
+  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,
-    },
-  ])
 }
diff --git a/src/ProteinView/structureModel.ts b/src/ProteinView/structureModel.ts
@@ -364,9 +364,11 @@ const Structure = types
           ) {
             const { hoverPosition } = hovered
             const pos = genomeToTranscriptSeqMapping.g2p[hoverPosition.coord]
-            const c0 = pos
-              ? transcriptSeqToStructureSeqPosition?.[pos]
-              : undefined
+            const c0 =
+              pos === undefined
+                ? undefined
+                : transcriptSeqToStructureSeqPosition?.[pos]
+
             if (c0 !== undefined) {
               self.setHoveredPosition({
                 structureSeqPos: c0,

diff --git a/yarn.lock b/yarn.lock
@@ -1850,7 +1850,7 @@ browserslist@^4.23.1, browserslist@^4.23.3:
     node-releases "^2.0.18"
     update-browserslist-db "^1.1.0"
 
-bs-logger@0.x:
+bs-logger@^0.2.6:
   version "0.2.6"
   resolved "https://registry.yarnpkg.com/bs-logger/-/bs-logger-0.2.6.tgz#eb7d365307a72cf974cc6cda76b68354ad336bd8"
   integrity sha512-pd8DCoxmbgc7hyPKOvxtqNcjYoOsABPQdcCUjGp3d42VR2CX1ORhk2A87oqqu5R1kk+76nsxZupkmyd+MVtCog==
@@ -4207,7 +4207,7 @@ locate-path@^6.0.0:
   dependencies:
     p-locate "^5.0.0"
 
-lodash.memoize@4.x:
+lodash.memoize@^4.1.2:
   version "4.1.2"
   resolved "https://registry.yarnpkg.com/lodash.memoize/-/lodash.memoize-4.1.2.tgz#bcc6c49a42a2840ed997f323eada5ecd182e0bfe"
   integrity sha512-t7j+NzmgnQzTAYXcsHYLgimltOV1MXHtlOWf6GjL9Kj8GK5FInw5JotxvbOs+IvV1/Dzo04/fCGfLVs7aXb4Ag==
@@ -4253,7 +4253,7 @@ make-dir@^4.0.0:
   dependencies:
     semver "^7.5.3"
 
-make-error@1.x, make-error@^1.1.1:
+make-error@^1.1.1, make-error@^1.3.6:
   version "1.3.6"
   resolved "https://registry.yarnpkg.com/make-error/-/make-error-1.3.6.tgz#2eb2e37ea9b67c4891f684a1394799af484cf7a2"
   integrity sha512-s8UhlNe7vPKomQhC1qFelMokr/Sc3AgNbso3n74mVPA5LTZwkB9NlXf4XPamLxJE8h0gh73rM94xvwRT2CVInw==
@@ -5493,7 +5493,7 @@ semver@^6.3.0, semver@^6.3.1:
   resolved "https://registry.yarnpkg.com/semver/-/semver-6.3.1.tgz#556d2ef8689146e46dcea4bfdd095f3434dffcb4"
   integrity sha512-BR7VvDCVHO+q2xBEWskxS6DJE1qRnb7DxzUrogb71CWoSficBxYsiAGd+Kl0mmq/MprG9yArRkyrQxTO6XjMzA==
 
-semver@^7.5.3, semver@^7.5.4, semver@^7.6.0, semver@^7.6.1:
+semver@^7.5.3, semver@^7.5.4, semver@^7.6.0, semver@^7.6.1, semver@^7.6.3:
   version "7.6.3"
   resolved "https://registry.yarnpkg.com/semver/-/semver-7.6.3.tgz#980f7b5550bc175fb4dc09403085627f9eb33143"
   integrity sha512-oVekP1cKtI+CTDvHWYFUcMtsK/00wmAEfyqKfNdARm8u1wNVhSgaX7A8d4UuIlUI5e84iEwOhs7ZPYRmzU9U6A==
@@ -5969,19 +5969,19 @@ ts-api-utils@^1.3.0:
   integrity sha512-UQMIo7pb8WRomKR1/+MFVLTroIvDVtMX3K6OUir8ynLyzB8Jeriont2bTAtmNPa1ekAgN7YPDyf6V+ygrdU+eQ==
 
 ts-jest@^29.1.2:
-  version "29.2.4"
-  resolved "https://registry.yarnpkg.com/ts-jest/-/ts-jest-29.2.4.tgz#38ccf487407d7a63054a72689f6f99b075e296e5"
-  integrity sha512-3d6tgDyhCI29HlpwIq87sNuI+3Q6GLTTCeYRHCs7vDz+/3GCMwEtV9jezLyl4ZtnBgx00I7hm8PCP8cTksMGrw==
+  version "29.2.5"
+  resolved "https://registry.yarnpkg.com/ts-jest/-/ts-jest-29.2.5.tgz#591a3c108e1f5ebd013d3152142cb5472b399d63"
+  integrity sha512-KD8zB2aAZrcKIdGk4OwpJggeLcH1FgrICqDSROWqlnJXGCXK4Mn6FcdK2B6670Xr73lHMG1kHw8R87A0ecZ+vA==
   dependencies:
-    bs-logger "0.x"
+    bs-logger "^0.2.6"
     ejs "^3.1.10"
-    fast-json-stable-stringify "2.x"
+    fast-json-stable-stringify "^2.1.0"
     jest-util "^29.0.0"
     json5 "^2.2.3"
-    lodash.memoize "4.x"
-    make-error "1.x"
-    semver "^7.5.3"
-    yargs-parser "^21.0.1"
+    lodash.memoize "^4.1.2"
+    make-error "^1.3.6"
+    semver "^7.6.3"
+    yargs-parser "^21.1.1"
 
 ts-node@^10.3.0:
   version "10.9.2"
@@ -6429,7 +6429,7 @@ yaml@^1.10.0:
   resolved "https://registry.yarnpkg.com/yaml/-/yaml-1.10.2.tgz#2301c5ffbf12b467de8da2333a459e29e7920e4b"
   integrity sha512-r3vXyErRCYJ7wg28yvBY5VSoAF8ZvlcW9/BwUzEtUsjvX/DKs24dIkuwjtuprwJJHsbyUbLApepYTR1BN4uHrg==
 
-yargs-parser@^21.0.1, yargs-parser@^21.1.1:
+yargs-parser@^21.1.1:
   version "21.1.1"
   resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-21.1.1.tgz#9096bceebf990d21bb31fa9516e0ede294a77d35"
   integrity sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw==