Fixes bug on URL highlight param in which refName aliases were not wo…

…rking (#4275)
GMOD · Mar 8, 2024 · 72d6402 · 72d6402
1 parent 67d5877
commit 72d6402
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Showing 3 changed files with 37 additions and 6 deletions.
diff --git a/plugins/linear-genome-view/src/LaunchLinearGenomeView/index.ts b/plugins/linear-genome-view/src/LaunchLinearGenomeView/index.ts
@@ -61,11 +61,16 @@ export default (pluginManager: PluginManager) => {
           view.setHideHeader(!nav)
         }
         if (highlight !== undefined) {
-          const location = parseLocString(highlight, refName =>
+          const parsedLocString = parseLocString(highlight, refName =>
             isValidRefName(refName, assembly),
           ) as Required<ParsedLocString>
+
+          const location = {
+            ...parsedLocString,
+            assemblyName: assembly,
+          }
+
           if (location?.start !== undefined && location?.end !== undefined) {
-            location.assemblyName = assembly
             view.setHighlight(location)
           }
         }

diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/Highlight.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/Highlight.tsx
@@ -40,6 +40,7 @@ const Highlight = observer(function Highlight({ model }: { model: LGV }) {
   const color = useTheme().palette.quaternary?.main ?? 'goldenrod'
 
   const session = getSession(model) as SessionWithWidgets
+  const { assemblyManager } = session
 
   const dismissHighlight = () => {
     model.setHighlight(undefined)
@@ -95,7 +96,14 @@ const Highlight = observer(function Highlight({ model }: { model: LGV }) {
       : undefined
   }
 
-  const h = mapCoords(model.highlight)
+  const asm = assemblyManager.get(model.highlight?.assemblyName)
+
+  const h = mapCoords({
+    ...model.highlight,
+    refName:
+      asm?.getCanonicalRefName(model.highlight.refName) ??
+      model.highlight.refName,
+  })
 
   return (
     <>
@@ -108,7 +116,11 @@ const Highlight = observer(function Highlight({ model }: { model: LGV }) {
           }}
         >
           <Tooltip title={'Highlighted from URL parameter'} arrow>
-            <IconButton ref={anchorEl} onClick={() => setOpen(true)}>
+            <IconButton
+              ref={anchorEl}
+              onClick={() => setOpen(true)}
+              style={{ zIndex: 4 }}
+            >
               <LinkIcon
                 fontSize="small"
                 sx={{

diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/OverviewHighlight.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/OverviewHighlight.tsx
@@ -2,7 +2,11 @@ import React from 'react'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 import { colord } from '@jbrowse/core/util/colord'
-import { ParsedLocString } from '@jbrowse/core/util'
+import {
+  ParsedLocString,
+  SessionWithWidgets,
+  getSession,
+} from '@jbrowse/core/util'
 import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel'
 
 // locals
@@ -32,6 +36,9 @@ const OverviewHighlight = observer(function OverviewHighlight({
   const { classes } = useStyles()
   const { cytobandOffset } = model
 
+  const session = getSession(model) as SessionWithWidgets
+  const { assemblyManager } = session
+
   // coords
   const mapCoords = (r: Required<ParsedLocString>) => {
     const s = overview.bpToPx({
@@ -56,7 +63,14 @@ const OverviewHighlight = observer(function OverviewHighlight({
     return null
   }
 
-  const h = mapCoords(model.highlight)
+  const asm = assemblyManager.get(model.highlight?.assemblyName)
+
+  const h = mapCoords({
+    ...model.highlight,
+    refName:
+      asm?.getCanonicalRefName(model.highlight.refName) ??
+      model.highlight.refName,
+  })
 
   return (
     <>