No specialized multi-step bezier

GMOD · Sep 11, 2024 · 4f4cabb · 4f4cabb
1 parent c381714
commit 4f4cabb
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Showing 4 changed files with 94 additions and 104 deletions.
diff --git a/packages/sv-core/src/BreakendMultiLevelOptionDialog.tsx b/packages/sv-core/src/BreakendMultiLevelOptionDialog.tsx
@@ -1,10 +1,10 @@
 import React, { useState } from 'react'
 import { observer } from 'mobx-react'
-import { Button, DialogActions, DialogContent, TextField } from '@mui/material'
+import { Button, DialogActions, DialogContent } from '@mui/material'
 import { getSnapshot } from 'mobx-state-tree'
 import { Dialog } from '@jbrowse/core/ui'
 import { when } from 'mobx'
-import { getSession, Feature, useLocalStorage } from '@jbrowse/core/util'
+import { getSession, Feature } from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 
@@ -85,6 +85,7 @@ const BreakendMultiLevelOptionDialog = observer(function ({
       <DialogActions>
         <Button
           onClick={() => {
+            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             ;(async () => {
               const session = getSession(model)
               try {
@@ -100,7 +101,6 @@ const BreakendMultiLevelOptionDialog = observer(function ({
                     assembly: asm,
                   })
 
-
                 const viewTracks = getSnapshot(view.tracks) as Track[]
                 const breakpointSplitView = session.addView(
                   'BreakpointSplitView',

diff --git a/packages/sv-core/src/BreakendSingleLevelOptionDialog.tsx b/packages/sv-core/src/BreakendSingleLevelOptionDialog.tsx
@@ -90,56 +90,58 @@ const BreakendSingleLevelOptionDialog = observer(function ({
         <Button
           onClick={() => {
             const session = getSession(model)
-            try {
-              console.log({ assemblyName })
-              const assembly = session.assemblyManager.get(assemblyName)
-              const w = +windowSize
-              if (Number.isNaN(w)) {
-                throw new Error('windowSize not a number')
-              }
-              const { refName, pos, mateRefName, matePos } =
-                // @ts-expect-error
-                viewType.getBreakendCoveringRegions({ feature, assembly })
+            // eslint-disable-next-line @typescript-eslint/no-floating-promises
+            ;(async () => {
+              try {
+                const assembly = session.assemblyManager.get(assemblyName)
+                const w = +windowSize
+                if (Number.isNaN(w)) {
+                  throw new Error('windowSize not a number')
+                }
+                const { refName, pos, mateRefName, matePos } =
+                  // @ts-expect-error
+                  viewType.getBreakendCoveringRegions({ feature, assembly })
 
-              const breakpointSplitView = session.addView(
-                'BreakpointSplitView',
-                {
-                  type: 'BreakpointSplitView',
-                  displayName: `${
-                    feature.get('name') || feature.get('id') || 'breakend'
-                  } split detail`,
-                  views: [
-                    {
-                      type: 'LinearGenomeView',
-                      tracks: stripIds(getSnapshot(view.tracks)),
-                    },
-                  ],
-                },
-              ) as unknown as { views: LinearGenomeViewModel[] }
+                const breakpointSplitView = session.addView(
+                  'BreakpointSplitView',
+                  {
+                    type: 'BreakpointSplitView',
+                    displayName: `${
+                      feature.get('name') || feature.get('id') || 'breakend'
+                    } split detail`,
+                    views: [
+                      {
+                        type: 'LinearGenomeView',
+                        tracks: stripIds(getSnapshot(view.tracks)),
+                      },
+                    ],
+                  },
+                ) as unknown as { views: LinearGenomeViewModel[] }
 
-              breakpointSplitView.views[0]!.navToLocations(
-                gatherOverlaps(
-                  [
-                    {
-                      refName,
-                      start: Math.max(0, pos - w),
-                      end: pos + w,
-                      assemblyName,
-                    },
-                    {
-                      refName: mateRefName,
-                      start: Math.max(0, matePos - w),
-                      end: matePos + w,
-                      assemblyName,
-                    },
-                  ],
-                  w,
-                ),
-              )
-            } catch (e) {
-              console.error(e)
-              session.notify(`${e}`)
-            }
+                await breakpointSplitView.views[0]!.navToLocations(
+                  gatherOverlaps(
+                    [
+                      {
+                        refName,
+                        start: Math.max(0, pos - w),
+                        end: pos + w,
+                        assemblyName,
+                      },
+                      {
+                        refName: mateRefName,
+                        start: Math.max(0, matePos - w),
+                        end: matePos + w,
+                        assemblyName,
+                      },
+                    ],
+                    w,
+                  ),
+                )
+              } catch (e) {
+                console.error(e)
+                session.notify(`${e}`)
+              }
+            })()
             handleClose()
           }}
           variant="contained"

diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx
@@ -10,7 +10,12 @@ import {
   getMatchedAlignmentFeatures,
   hasPairedReads,
 } from './util'
-import { yPos, useNextFrame, getPxFromCoordinate } from '../util'
+import {
+  yPos,
+  useNextFrame,
+  getPxFromCoordinate,
+  heightFromSpecificLevel,
+} from '../util'
 import { BreakpointViewModel } from '../model'
 import {
   getLongReadOrientationAbnormal,
@@ -37,7 +42,8 @@ const AlignmentConnections = observer(function ({
   const session = getSession(model)
   const snap = getSnapshot(model)
   const { assemblyManager } = session
-  const assembly = assemblyManager.get(views[0]!.assemblyNames[0]!)
+  const v0 = views[0]
+  const assembly = v0 ? assemblyManager.get(v0.assemblyNames[0]!) : undefined
   useNextFrame(snap)
   const allFeatures = model.getTrackFeatures(trackId)
   const hasPaired = useMemo(() => hasPairedReads(allFeatures), [allFeatures])
@@ -128,60 +134,42 @@ const AlignmentConnections = observer(function ({
             yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
             yOffset
           const sameLevel = level1 === level2
-          const trackHeight =
-            sameLevel && isAbnormal ? tracks[level1].displays[0].height / 2 : 0
+          const abnormalSpecialRenderFlag = sameLevel && isAbnormal
+          const trackHeight = abnormalSpecialRenderFlag
+            ? tracks[level1].displays[0].height
+            : 0
           const pf1 = hasPaired ? -1 : 1
+          const y0 = heightFromSpecificLevel(
+            views,
+            trackId,
+            level1,
+            getTrackYPosOverride,
+          )
 
           // possible todo: use totalCurveHeight to possibly make alternative
           // squiggle if the S is too small
-          const path = isAbnormal
-            ? [
-                'M',
-                x1,
-                y1,
-                'C',
-
-                // first bezier x,y
-                x1 + 100 * f1.get('strand') * rf1,
-                y1,
-
-                // second bezier x,y
-                x1 + 100 * f1.get('strand') * rf1,
-                y1 + 100,
-
-                // third bezier x,y
-                x2 - 100 * f2.get('strand') * rf2 * pf1,
-                y2 + 100,
-
-                // bezier continuation
-                'S',
-
-                // first bezier x,y
-                x2 - 100 * f2.get('strand') * rf2 * pf1,
-                y2 + 100,
-
-                // second bezier x,y
-                x2,
-                y2,
-              ].join(' ')
-            : [
-                'M',
-                x1,
-                y1,
-                'C',
-
-                // first bezier x,y
-                x1 + 200 * f1.get('strand') * rf1,
-                y1,
-
-                // second bezier x,y
-                x2 - 200 * f2.get('strand') * rf2 * pf1,
-                y2,
-
-                // third bezier x,y
-                x2,
-                y2,
-              ].join(' ')
+          const path = [
+            'M',
+            x1,
+            y1,
+            'C',
+
+            // first bezier x,y
+            x1 + 200 * f1.get('strand') * rf1,
+            abnormalSpecialRenderFlag
+              ? Math.min(y0 - yOffset + trackHeight, y1 + trackHeight)
+              : y1,
+
+            // second bezier x,y
+            x2 - 200 * f2.get('strand') * rf2 * pf1,
+            abnormalSpecialRenderFlag
+              ? Math.min(y0 - yOffset + trackHeight, y2 + trackHeight)
+              : y2,
+
+            // third bezier x,y
+            x2,
+            y2,
+          ].join(' ')
           const id = `${f1.id()}-${f2.id()}`
           ret.push(
             <path

diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/util.ts b/plugins/breakpoint-split-view/src/BreakpointSplitView/util.ts
@@ -23,7 +23,7 @@ function cheight(chunk: LayoutRecord) {
   return chunk[BOTTOM] - chunk[TOP]
 }
 
-function heightFromSpecificLevel(
+export function heightFromSpecificLevel(
   views: LGV[],
   trackId: string,
   level: number,