LASFD: Navigate to prev / next exon

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts

@@ -10,21 +10,24 @@ import {
   isSessionModelWithWidgets,
 } from '@jbrowse/core/util'
 import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import SkipNextRoundedIcon from '@mui/icons-material/SkipNextRounded'
-import SkipPreviousRoundedIcon from '@mui/icons-material/SkipPreviousRounded'
 import { alpha } from '@mui/material'
 
 import { type OntologyRecord } from '../../OntologyManager'
 import { MergeExons, MergeTranscripts, SplitExon } from '../../components'
-import { type ApolloSessionModel } from '../../session'
 import {
   type MousePosition,
   type MousePositionWithFeature,
   containsSelectedFeature,
+  getAdjacentExons,
   getMinAndMaxPx,
   getOverlappingEdge,
+  getStreamIcon,
+  isCDSFeature,
+  isExonFeature,
   isMousePositionWithFeature,
+  isTranscriptFeature,
   navToFeatureCenter,
+  selectFeatureAndOpenWidget,
 } from '../../util'
 import { getRelatedFeatures } from '../../util/annotationFeatureUtils'
 import { type LinearApolloDisplay } from '../stateModel'
@@ -696,45 +699,6 @@ function getRowForFeature(
   return
 }
 
-function selectFeatureAndOpenWidget(
-  stateModel: LinearApolloDisplayMouseEvents,
-  feature: AnnotationFeature,
-) {
-  if (stateModel.apolloDragging) {
-    return
-  }
-  stateModel.setSelectedFeature(feature)
-  const { session } = stateModel
-  const { apolloDataStore } = session
-  const { featureTypeOntology } = apolloDataStore.ontologyManager
-  if (!featureTypeOntology) {
-    throw new Error('featureTypeOntology is undefined')
-  }
-
-  let containsCDSOrExon = false
-  for (const [, child] of feature.children ?? []) {
-    if (
-      featureTypeOntology.isTypeOf(child.type, 'CDS') ||
-      featureTypeOntology.isTypeOf(child.type, 'exon')
-    ) {
-      containsCDSOrExon = true
-      break
-    }
-  }
-  if (
-    (featureTypeOntology.isTypeOf(feature.type, 'transcript') ||
-      featureTypeOntology.isTypeOf(feature.type, 'pseudogenic_transcript')) &&
-    containsCDSOrExon
-  ) {
-    stateModel.showFeatureDetailsWidget(feature, [
-      'ApolloTranscriptDetails',
-      'apolloTranscriptDetails',
-    ])
-  } else {
-    stateModel.showFeatureDetailsWidget(feature)
-  }
-}
-
 function onMouseDown(
   stateModel: LinearApolloDisplay,
   currentMousePosition: MousePositionWithFeature,
@@ -859,131 +823,6 @@ function getDraggableFeatureInfo(
   return
 }
 
-function isTranscriptFeature(
-  feature: AnnotationFeature,
-  session: ApolloSessionModel,
-): boolean {
-  const { featureTypeOntology } = session.apolloDataStore.ontologyManager
-  if (!featureTypeOntology) {
-    throw new Error('featureTypeOntology is undefined')
-  }
-  return (
-    featureTypeOntology.isTypeOf(feature.type, 'transcript') ||
-    featureTypeOntology.isTypeOf(feature.type, 'pseudogenic_transcript')
-  )
-}
-
-function isExonFeature(
-  feature: AnnotationFeature,
-  session: ApolloSessionModel,
-): boolean {
-  const { featureTypeOntology } = session.apolloDataStore.ontologyManager
-  if (!featureTypeOntology) {
-    throw new Error('featureTypeOntology is undefined')
-  }
-  return featureTypeOntology.isTypeOf(feature.type, 'exon')
-}
-
-function isCDSFeature(
-  feature: AnnotationFeature,
-  session: ApolloSessionModel,
-): boolean {
-  const { featureTypeOntology } = session.apolloDataStore.ontologyManager
-  if (!featureTypeOntology) {
-    throw new Error('featureTypeOntology is undefined')
-  }
-  return featureTypeOntology.isTypeOf(feature.type, 'CDS')
-}
-
-interface AdjacentExons {
-  upstream: AnnotationFeature | undefined
-  downstream: AnnotationFeature | undefined
-}
-
-function getAdjacentExons(
-  currentExon: AnnotationFeature,
-  display: LinearApolloDisplayMouseEvents,
-  mousePosition: MousePositionWithFeature,
-  session: ApolloSessionModel,
-): AdjacentExons {
-  const lgv = getContainingView(
-    display as BaseDisplayModel,
-  ) as unknown as LinearGenomeViewModel
-
-  // Genomic coords of current view
-  const viewGenomicLeft = mousePosition.bp - lgv.bpPerPx * mousePosition.x
-  const viewGenomicRight = viewGenomicLeft + lgv.coarseTotalBp
-  if (!currentExon.parent) {
-    return { upstream: undefined, downstream: undefined }
-  }
-  const transcript = currentExon.parent
-  if (!transcript.children) {
-    throw new Error(`Error getting children of ${transcript._id}`)
-  }
-  const { featureTypeOntology } = session.apolloDataStore.ontologyManager
-  if (!featureTypeOntology) {
-    throw new Error('featureTypeOntology is undefined')
-  }
-
-  let exons = []
-  for (const [, child] of transcript.children) {
-    if (featureTypeOntology.isTypeOf(child.type, 'exon')) {
-      exons.push(child)
-    }
-  }
-  const adjacentExons: AdjacentExons = {
-    upstream: undefined,
-    downstream: undefined,
-  }
-  exons = exons.sort((a, b) => (a.min < b.min ? -1 : 1))
-  for (const exon of exons) {
-    if (exon.min > viewGenomicRight) {
-      adjacentExons.downstream = exon
-      break
-    }
-  }
-  exons = exons.sort((a, b) => (a.min > b.min ? -1 : 1))
-  for (const exon of exons) {
-    if (exon.max < viewGenomicLeft) {
-      adjacentExons.upstream = exon
-      break
-    }
-  }
-  if (transcript.strand === -1) {
-    const newUpstream = adjacentExons.downstream
-    adjacentExons.downstream = adjacentExons.upstream
-    adjacentExons.upstream = newUpstream
-  }
-  return adjacentExons
-}
-
-function getStreamIcon(
-  strand: 1 | -1 | undefined,
-  isUpstream: boolean,
-  isFlipped: boolean | undefined,
-) {
-  // This is the icon you would use for strand=1, downstream, straight
-  // (non-flipped) view
-  let icon = SkipNextRoundedIcon
-
-  if (strand === -1) {
-    icon = SkipPreviousRoundedIcon
-  }
-  if (isUpstream) {
-    icon =
-      icon === SkipPreviousRoundedIcon
-        ? SkipNextRoundedIcon
-        : SkipPreviousRoundedIcon
-  }
-  if (isFlipped) {
-    icon =
-      icon === SkipPreviousRoundedIcon
-        ? SkipNextRoundedIcon
-        : SkipPreviousRoundedIcon
-  }
-  return icon
-}
-
 function getContextMenuItems(
   display: LinearApolloDisplayMouseEvents,
   mousePosition: MousePositionWithFeature,

packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts

@@ -2,13 +2,16 @@ import {
   type AnnotationFeature,
   type TranscriptPartCoding,
 } from '@apollo-annotation/mst'
+import { type BaseDisplayModel } from '@jbrowse/core/pluggableElementTypes'
 import { type MenuItem } from '@jbrowse/core/ui'
 import {
   type AbstractSessionModel,
+  getContainingView,
   getFrame,
   intersection2,
   measureText,
 } from '@jbrowse/core/util'
+import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { alpha } from '@mui/material'
 import equal from 'fast-deep-equal/es6'
 import { getSnapshot } from 'mobx-state-tree'
@@ -18,12 +21,19 @@ import { FilterTranscripts } from '../../components/FilterTranscripts'
 import {
   type MousePosition,
   type MousePositionWithFeature,
+  getAdjacentExons,
   getContextMenuItemsForFeature,
   getMinAndMaxPx,
   getOverlappingEdge,
   getRelatedFeatures,
+  getStreamIcon,
+  isCDSFeature,
+  isExonFeature,
   isMousePositionWithFeature,
+  // isTranscriptFeature,
   isSelectedFeature,
+  navToFeatureCenter,
+  selectFeatureAndOpenWidget,
 } from '../../util'
 import { type LinearApolloSixFrameDisplay } from '../stateModel'
 import { type LinearApolloSixFrameDisplayMouseEvents } from '../stateModel/mouseEvents'
@@ -848,18 +858,62 @@ function getContextMenuItems(
   }
   if (isMousePositionWithFeature(mousePosition)) {
     const { bp, feature } = mousePosition
-    for (const relatedFeature of getRelatedFeatures(feature, bp)) {
-      const featureID: string | undefined = relatedFeature.attributes
+    let featuresUnderClick = getRelatedFeatures(feature, bp)
+    if (isCDSFeature(feature, session)) {
+      featuresUnderClick = getRelatedFeatures(feature, bp, true)
+    }
+
+    for (const feature of featuresUnderClick) {
+      const featureID: string | undefined = feature.attributes
         .get('gff_id')
         ?.toString()
       if (featureID && filteredTranscripts.includes(featureID)) {
         continue
       }
       const contextMenuItemsForFeature = getContextMenuItemsForFeature(
         display,
-        relatedFeature,
+        feature,
       )
-      if (featureTypeOntology.isTypeOf(relatedFeature.type, 'exon')) {
+      if (isExonFeature(feature, session)) {
+        const adjacentExons = getAdjacentExons(
+          feature,
+          display,
+          mousePosition,
+          session,
+        )
+        const lgv = getContainingView(
+          display as BaseDisplayModel,
+        ) as unknown as LinearGenomeViewModel
+        if (adjacentExons.upstream) {
+          const exon = adjacentExons.upstream
+          contextMenuItemsForFeature.push({
+            label: 'Go to upstream exon',
+            icon: getStreamIcon(
+              feature.strand,
+              true,
+              lgv.displayedRegions.at(0)?.reversed,
+            ),
+            onClick: () => {
+              lgv.navTo(navToFeatureCenter(exon, 0.1, lgv.totalBp))
+              selectFeatureAndOpenWidget(display, exon)
+            },
+          })
+        }
+        if (adjacentExons.downstream) {
+          const exon = adjacentExons.downstream
+          contextMenuItemsForFeature.push({
+            label: 'Go to downstream exon',
+            icon: getStreamIcon(
+              feature.strand,
+              false,
+              lgv.displayedRegions.at(0)?.reversed,
+            ),
+            onClick: () => {
+              lgv.navTo(navToFeatureCenter(exon, 0.1, lgv.totalBp))
+              selectFeatureAndOpenWidget(display, exon)
+            },
+          })
+        }
         contextMenuItemsForFeature.push(
           {
             label: 'Merge exons',
@@ -874,7 +928,7 @@ function getContextMenuItems(
                       doneCallback()
                     },
                     changeManager,
-                    sourceFeature: relatedFeature,
+                    sourceFeature: feature,
                     sourceAssemblyId: currentAssemblyId,
                     selectedFeature,
                     setSelectedFeature: (feature?: AnnotationFeature) => {
@@ -898,7 +952,7 @@ function getContextMenuItems(
                       doneCallback()
                     },
                     changeManager,
-                    sourceFeature: relatedFeature,
+                    sourceFeature: feature,
                     sourceAssemblyId: currentAssemblyId,
                     selectedFeature,
                     setSelectedFeature: (feature?: AnnotationFeature) => {
@@ -911,7 +965,7 @@ function getContextMenuItems(
           },
         )
       }
-      if (featureTypeOntology.isTypeOf(relatedFeature.type, 'gene')) {
+      if (featureTypeOntology.isTypeOf(feature.type, 'gene')) {
         contextMenuItemsForFeature.push({
           label: 'Filter alternate transcripts',
           onClick: () => {
@@ -922,7 +976,7 @@ function getContextMenuItems(
                   handleClose: () => {
                     doneCallback()
                   },
-                  sourceFeature: relatedFeature,
+                  sourceFeature: feature,
                   filteredTranscripts: getSnapshot(filteredTranscripts),
                   onUpdate: (forms: string[]) => {
                     display.updateFilteredTranscripts(forms)
@@ -934,7 +988,7 @@ function getContextMenuItems(
         })
       }
       menuItems.push({
-        label: relatedFeature.type,
+        label: feature.type,
         subMenu: contextMenuItemsForFeature,
       })
     }