Refname renaming fix for breakpoint split view

GMOD · Dec 3, 2023 · f7dd8e3 · f7dd8e3
1 parent 1c08a12
commit f7dd8e3
Show file tree

Hide file tree

Showing 8 changed files with 65 additions and 48 deletions.
diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx
@@ -31,7 +31,7 @@ const AlignmentConnections = observer(function ({
   const session = getSession(model)
   const snap = getSnapshot(model)
   const { assemblyManager } = session
-  const assembly = assemblyManager.get(views[0].assemblyNames[0])
+  const asm = assemblyManager.get(views[0].assemblyNames[0])
   useNextFrame(snap)
   const allFeatures = model.getTrackFeatures(trackId)
   const hasPaired = useMemo(() => hasPairedReads(allFeatures), [allFeatures])
@@ -59,7 +59,7 @@ const AlignmentConnections = observer(function ({
     yOffset = rect.top
   }
 
-  if (!assembly) {
+  if (!asm) {
     return null
   }
 
@@ -86,20 +86,15 @@ const AlignmentConnections = observer(function ({
           if (!showIntraviewLinks && level1 === level2) {
             return null
           }
-          const f1ref = assembly.getCanonicalRefName(f1.get('refName'))
-          const f2ref = assembly.getCanonicalRefName(f2.get('refName'))
-
-          if (!f1ref || !f2ref) {
-            throw new Error(`unable to find ref for ${f1ref || f2ref}`)
-          }
-
+          const f1ref = f1.get('refName')
+          const f2ref = f2.get('refName')
           const s1 = f1.get('strand')
           const s2 = f2.get('strand')
           const p1 = c1[s1 === -1 ? LEFT : RIGHT]
           const sn1 = s2 === -1
           const p2 = hasPaired ? c2[sn1 ? LEFT : RIGHT] : c2[sn1 ? RIGHT : LEFT]
-          const x1 = getPxFromCoordinate(views[level1], f1ref, p1)
-          const x2 = getPxFromCoordinate(views[level2], f2ref, p2)
+          const x1 = getPxFromCoordinate(views[level1], f1ref, p1, asm)
+          const x2 = getPxFromCoordinate(views[level2], f2ref, p2, asm)
           const reversed1 = views[level1].pxToBp(x1).reversed
           const reversed2 = views[level2].pxToBp(x2).reversed
           const tracks = views.map(v => v.getTrack(trackId))

diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/components/Breakends.tsx b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/Breakends.tsx
@@ -37,9 +37,9 @@ const Breakends = observer(function ({
   const [mouseoverElt, setMouseoverElt] = useState<string>()
   const snap = getSnapshot(model)
   useNextFrame(snap)
-  const assembly = assemblyManager.get(views[0].assemblyNames[0])
+  const asm = assemblyManager.get(views[0].assemblyNames[0])
 
-  if (!assembly) {
+  if (!asm) {
     return null
   }
 
@@ -69,15 +69,10 @@ const Breakends = observer(function ({
           if (!c1 || !c2) {
             return null
           }
-          const f1origref = f1.get('refName')
-          const f2origref = f2.get('refName')
-          const f1ref = assembly.getCanonicalRefName(f1origref)
-          const f2ref = assembly.getCanonicalRefName(f2origref)
-          if (!f1ref || !f2ref) {
-            throw new Error(`unable to find ref for ${f1ref || f2ref}`)
-          }
-          const x1 = getPxFromCoordinate(views[level1], f1ref, c1[LEFT])
-          const x2 = getPxFromCoordinate(views[level2], f2ref, c2[LEFT])
+          const f1ref = f1.get('refName')
+          const f2ref = f2.get('refName')
+          const x1 = getPxFromCoordinate(views[level1], f1ref, c1[LEFT], asm)
+          const x2 = getPxFromCoordinate(views[level2], f2ref, c2[LEFT], asm)
           const reversed1 = views[level1].pxToBp(x1).reversed
           const reversed2 = views[level2].pxToBp(x2).reversed
 

diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/components/Translocations.tsx b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/Translocations.tsx
@@ -80,13 +80,14 @@ const Translocations = observer(function ({
           const end2 = info.END[0]
           const [myDirection, mateDirection] = info.STRANDS[0].split('')
 
-          const r = getPxFromCoordinate(views[level2], chr2, end2)
+          const r = getPxFromCoordinate(views[level2], chr2, end2, assembly)
           if (r) {
             const c2: LayoutRecord = [r, 0, r + 1, 0]
             const x1 = getPxFromCoordinate(
               views[level1],
               f1.get('refName'),
               c1[LEFT],
+              assembly,
             )
             const x2 = r
             const reversed1 = views[level1].pxToBp(x1).reversed
@@ -99,21 +100,11 @@ const Translocations = observer(function ({
             const y2 =
               yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
               yOffset
-
-            const path = [
-              'M', // move to
-              x1 - 20 * (myDirection === '+' ? 1 : -1) * (reversed1 ? -1 : 1),
-              y1,
-              'L', // line to
-              x1,
-              y1,
-              'L', // line to
-              x2,
-              y2,
-              'L', // line to
-              x2 - 20 * (mateDirection === '+' ? 1 : -1) * (reversed2 ? -1 : 1),
-              y2,
-            ].join(' ')
+            const foot1 =
+              x1 - 20 * (myDirection === '+' ? 1 : -1) * (reversed1 ? -1 : 1)
+            const foot2 =
+              x2 - 20 * (mateDirection === '+' ? 1 : -1) * (reversed2 ? -1 : 1)
+            const path = `M ${foot1} ${y1} L ${x1} ${y1} L ${x2} ${y2} L ${foot2} ${y2}`
             ret.push(
               <path
                 d={path}

diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/util.ts b/plugins/breakpoint-split-view/src/BreakpointSplitView/util.ts
@@ -4,6 +4,7 @@ import { clamp } from '@jbrowse/core/util'
 
 // locals
 import { LayoutRecord } from './model'
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 
 type LGV = LinearGenomeViewModel
 
@@ -34,8 +35,18 @@ function heightFromSpecificLevel(
     : views[level].trackRefs[trackId]?.getBoundingClientRect().top || 0
 }
 
-export function getPxFromCoordinate(view: LGV, refName: string, coord: number) {
-  return (view.bpToPx({ refName, coord })?.offsetPx || 0) - view.offsetPx
+export function getPxFromCoordinate(
+  view: LGV,
+  refName: string,
+  coord: number,
+  asm: Assembly,
+) {
+  return (
+    (view.bpToPx({
+      refName: asm.getCanonicalRefName(refName) || refName,
+      coord,
+    })?.offsetPx || 0) - view.offsetPx
+  )
 }
 
 // get's the yposition of a layout record in a track

diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.ts
@@ -3,7 +3,11 @@ import { assembleLocString } from '@jbrowse/core/util'
 
 // locals
 import LocString from './components/LocString'
-import { launchBreakpointSplitView, launchLGV } from './util'
+import {
+  launchBreakpointSplitView,
+  launchLinearGenomeView,
+  launchLinearGenomeViewWithEndFocus,
+} from './util'
 import { SpreadsheetModel } from '../models/Spreadsheet'
 
 type Row = Record<string, unknown>
@@ -84,13 +88,19 @@ export function parseVcfBuffer(buffer: Buffer) {
           }) => [
             {
               label: 'Launch linear genome view',
-              onClick: () => launchLGV({ model, value: row.loc as string }),
+              onClick: () =>
+                launchLinearGenomeView({ model, value: row.loc as string }),
             },
             {
               label: 'Launch breakpoint split view',
               onClick: () =>
                 launchBreakpointSplitView({ model, row, vcfParser }),
             },
+            {
+              label: 'Launch linear genome view focused on ends of SV',
+              onClick: () =>
+                launchLinearGenomeViewWithEndFocus({ model, row, vcfParser }),
+            },
           ],
         },
       },

diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/util.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/util.ts
@@ -18,7 +18,7 @@ export function parseStrand(strand: string) {
   }
 }
 
-export async function launchLGV({
+export async function launchLinearGenomeView({
   model,
   value,
 }: {
@@ -62,10 +62,28 @@ export async function launchBreakpointSplitView({
       assemblyName,
       session,
     )
+    const v = getParent<{ width: number }>(model)
+    snap.views[0].offsetPx -= v.width / 2 + 100
+    snap.views[1].offsetPx -= v.width / 2 + 100
 
     session.addView('BreakpointSplitView', snap)
   } catch (e) {
     console.error(e)
     getSession(model).notify(`${e}`, 'error')
   }
 }
+
+export async function launchLinearGenomeViewWithEndFocus({
+  model,
+  value,
+}: {
+  model: SpreadsheetModel
+  value: string
+}) {
+  try {
+    await locationLinkClick(model, value)
+  } catch (e) {
+    console.error(e)
+    getSession(model).notify(`${e}`, 'error')
+  }
+}
diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/Spreadsheet.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/models/Spreadsheet.tsx
@@ -74,7 +74,6 @@ function stateModelFactory() {
         const { data, widths } = self
         return data?.columns.map(m => {
           const res = data.CustomComponents?.[m]
-          console.log({ self })
           return {
             field: m,
             width: widths[m],

diff --git a/plugins/variants/src/VariantFeatureWidget/BreakendPanel.tsx b/plugins/variants/src/VariantFeatureWidget/BreakendPanel.tsx
@@ -22,12 +22,10 @@ export default function BreakendPanel(props: {
   const session = getSession(model)
   const { pluginManager } = getEnv(session)
   const [breakpointDialog, setBreakpointDialog] = useState(false)
-  let viewType: BreakpointSplitViewType | undefined
+  let viewType
 
   try {
-    viewType = pluginManager.getViewType(
-      'BreakpointSplitView',
-    ) as BreakpointSplitViewType
+    viewType = pluginManager.getViewType('BreakpointSplitView')
   } catch (e) {
     // ignore
   }