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Merge pull request #1951 from GMOD/breakpoint_split_view_fix
Fix breakpoint split view demo
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273 changes: 135 additions & 138 deletions
273
plugins/breakpoint-split-view/src/components/AlignmentConnections.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,153 +1,150 @@ | ||
| import React, { useState } from 'react' | ||
| import Path from 'svg-path-generator' | ||
| import { BreakpointViewModel } from '../model' | ||
| import { observer } from 'mobx-react' | ||
| import { getSnapshot } from 'mobx-state-tree' | ||
| import { getSession } from '@jbrowse/core/util' | ||
| import { yPos, useNextFrame, getPxFromCoordinate } from '../util' | ||
| import { BreakpointViewModel } from '../model' | ||
|
|
||
| const [LEFT, , RIGHT] = [0, 1, 2, 3] | ||
|
|
||
| // eslint-disable-next-line @typescript-eslint/no-explicit-any | ||
| export default (pluginManager: any) => { | ||
| const { jbrequire } = pluginManager | ||
| const { getSession } = jbrequire('@jbrowse/core/util') | ||
| const { observer } = jbrequire('mobx-react') | ||
| const React = jbrequire('react') | ||
| const { useState } = jbrequire('react') | ||
| const { getSnapshot } = jbrequire('mobx-state-tree') | ||
| const AlignmentConnections = observer( | ||
| ({ | ||
| model, | ||
| trackConfigId, | ||
| parentRef, | ||
| }: { | ||
| model: BreakpointViewModel | ||
| trackConfigId: string | ||
| parentRef: React.RefObject<SVGSVGElement> | ||
| }) => { | ||
| const { views, showIntraviewLinks } = model | ||
| const { assemblyManager } = getSession(model) | ||
|
|
||
| return observer( | ||
| ({ | ||
| model, | ||
| trackConfigId, | ||
| parentRef: ref, | ||
| }: { | ||
| model: BreakpointViewModel | ||
| height: number | ||
| trackConfigId: string | ||
| parentRef: React.RefObject<SVGSVGElement> | ||
| }) => { | ||
| const { views, showIntraviewLinks } = model | ||
| const { assemblyManager } = getSession(model) | ||
| const session = getSession(model) | ||
| const snap = getSnapshot(model) | ||
| useNextFrame(snap) | ||
| const assembly = assemblyManager.get(views[0].assemblyNames[0]) | ||
| if (!assembly) { | ||
| return null | ||
| } | ||
|
|
||
| const session = getSession(model) | ||
| const snap = getSnapshot(model) | ||
| useNextFrame(snap) | ||
| const assembly = assemblyManager.get(views[0].assemblyNames[0]) | ||
| if (!assembly) { | ||
| return null | ||
| } | ||
| const totalFeatures = model.getTrackFeatures(trackConfigId) | ||
| const features = model.hasPairedReads(trackConfigId) | ||
| ? model.getBadlyPairedAlignments(trackConfigId) | ||
| : model.getMatchedAlignmentFeatures(trackConfigId) | ||
| const layoutMatches = model.getMatchedFeaturesInLayout( | ||
| trackConfigId, | ||
| features, | ||
| ) | ||
| layoutMatches.forEach(m => { | ||
| m.sort((a, b) => a.feature.get('clipPos') - b.feature.get('clipPos')) | ||
| }) | ||
| const [mouseoverElt, setMouseoverElt] = useState<string>() | ||
|
|
||
| const totalFeatures = model.getTrackFeatures(trackConfigId) | ||
| const features = model.hasPairedReads(trackConfigId) | ||
| ? model.getBadlyPairedAlignments(trackConfigId) | ||
| : model.getMatchedAlignmentFeatures(trackConfigId) | ||
| const layoutMatches = model.getMatchedFeaturesInLayout( | ||
| trackConfigId, | ||
| features, | ||
| ) | ||
| layoutMatches.forEach(m => { | ||
| m.sort((a, b) => a.feature.get('clipPos') - b.feature.get('clipPos')) | ||
| }) | ||
| const [mouseoverElt, setMouseoverElt] = useState() | ||
| let yOffset = 0 | ||
| if (parentRef.current) { | ||
| const rect = parentRef.current.getBoundingClientRect() | ||
| yOffset = rect.top | ||
| } | ||
| return ( | ||
| <g | ||
| stroke="#333" | ||
| fill="none" | ||
| data-testid={ | ||
| layoutMatches.length ? `${trackConfigId}-loaded` : trackConfigId | ||
| } | ||
| > | ||
| {layoutMatches.map(chunk => { | ||
| const ret = [] | ||
| // we follow a path in the list of chunks, not from top to bottom, just in series | ||
| // following x1,y1 -> x2,y2 | ||
| for (let i = 0; i < chunk.length - 1; i += 1) { | ||
| const { layout: c1, feature: f1, level: level1 } = chunk[i] | ||
| const { layout: c2, feature: f2, level: level2 } = chunk[i + 1] | ||
|
|
||
| let yOffset = 0 | ||
| if (ref.current) { | ||
| const rect = ref.current.getBoundingClientRect() | ||
| yOffset = rect.top | ||
| } | ||
| return ( | ||
| <g | ||
| stroke="#333" | ||
| fill="none" | ||
| data-testid={ | ||
| layoutMatches.length ? `${trackConfigId}-loaded` : trackConfigId | ||
| } | ||
| > | ||
| {layoutMatches.map(chunk => { | ||
| const ret = [] | ||
| // we follow a path in the list of chunks, not from top to bottom, just in series | ||
| // following x1,y1 -> x2,y2 | ||
| for (let i = 0; i < chunk.length - 1; i += 1) { | ||
| const { layout: c1, feature: f1, level: level1 } = chunk[i] | ||
| const { layout: c2, feature: f2, level: level2 } = chunk[i + 1] | ||
| if (!c1 || !c2) { | ||
| console.warn('received null layout for a overlay feature') | ||
| return null | ||
| } | ||
|
|
||
| if (!c1 || !c2) { | ||
| console.warn('received null layout for a overlay feature') | ||
| return null | ||
| } | ||
| // disable rendering connections in a single level | ||
| if (!showIntraviewLinks && level1 === level2) { | ||
| return null | ||
| } | ||
| const f1origref = f1.get('refName') | ||
| const f2origref = f2.get('refName') | ||
| const f1ref = assembly.getCanonicalRefName(f1origref) | ||
| const f2ref = assembly.getCanonicalRefName(f2origref) | ||
|
|
||
| // disable rendering connections in a single level | ||
| 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 x1 = getPxFromCoordinate( | ||
| views[level1], | ||
| f1ref, | ||
| c1[f1.get('strand') === -1 ? LEFT : RIGHT], | ||
| ) | ||
| const x2 = getPxFromCoordinate( | ||
| views[level2], | ||
| f2ref, | ||
| c2[f2.get('strand') === -1 ? RIGHT : LEFT], | ||
| ) | ||
| const reversed1 = views[level1].pxToBp(x1).reversed | ||
| const reversed2 = views[level2].pxToBp(x2).reversed | ||
| if (!f1ref || !f2ref) { | ||
| throw new Error(`unable to find ref for ${f1ref || f2ref}`) | ||
| } | ||
| const x1 = getPxFromCoordinate( | ||
| views[level1], | ||
| f1ref, | ||
| c1[f1.get('strand') === -1 ? LEFT : RIGHT], | ||
| ) | ||
| const x2 = getPxFromCoordinate( | ||
| views[level2], | ||
| f2ref, | ||
| c2[f2.get('strand') === -1 ? RIGHT : LEFT], | ||
| ) | ||
| const reversed1 = views[level1].pxToBp(x1).reversed | ||
| const reversed2 = views[level2].pxToBp(x2).reversed | ||
|
|
||
| const tracks = views.map(v => v.getTrack(trackConfigId)) | ||
| const tracks = views.map(v => v.getTrack(trackConfigId)) | ||
|
|
||
| const y1 = | ||
| yPos(trackConfigId, level1, views, tracks, c1) - yOffset | ||
| const y2 = | ||
| yPos(trackConfigId, level2, views, tracks, c2) - yOffset | ||
| const y1 = yPos(trackConfigId, level1, views, tracks, c1) - yOffset | ||
| const y2 = yPos(trackConfigId, level2, views, tracks, c2) - yOffset | ||
|
|
||
| // possible todo: use totalCurveHeight to possibly make alternative squiggle if the S is too small | ||
| const path = Path() | ||
| .moveTo(x1, y1) | ||
| .curveTo( | ||
| x1 + 200 * f1.get('strand') * (reversed1 ? -1 : 1), | ||
| y1, | ||
| x2 - 200 * f2.get('strand') * (reversed2 ? -1 : 1), | ||
| y2, | ||
| x2, | ||
| y2, | ||
| ) | ||
| .end() | ||
| const id = `${f1.id()}-${f2.id()}` | ||
| ret.push( | ||
| <path | ||
| d={path} | ||
| key={id} | ||
| data-testid="r1" | ||
| strokeWidth={mouseoverElt === id ? 5 : 1} | ||
| onClick={() => { | ||
| const featureWidget = session.addWidget( | ||
| 'BreakpointAlignmentsWidget', | ||
| 'breakpointAlignments', | ||
| { | ||
| featureData: { | ||
| feature1: ( | ||
| totalFeatures.get(f1.id()) || { toJSON: () => {} } | ||
| ).toJSON(), | ||
| feature2: ( | ||
| totalFeatures.get(f2.id()) || { toJSON: () => {} } | ||
| ).toJSON(), | ||
| }, | ||
| }, | ||
| ) | ||
| session.showWidget(featureWidget) | ||
| }} | ||
| onMouseOver={() => setMouseoverElt(id)} | ||
| onMouseOut={() => setMouseoverElt(undefined)} | ||
| />, | ||
| // possible todo: use totalCurveHeight to possibly make alternative | ||
| // squiggle if the S is too small | ||
| const path = Path() | ||
| .moveTo(x1, y1) | ||
| .curveTo( | ||
| x1 + 200 * f1.get('strand') * (reversed1 ? -1 : 1), | ||
| y1, | ||
| x2 - 200 * f2.get('strand') * (reversed2 ? -1 : 1), | ||
| y2, | ||
| x2, | ||
| y2, | ||
| ) | ||
| } | ||
| return ret | ||
| })} | ||
| </g> | ||
| ) | ||
| }, | ||
| ) | ||
| } | ||
| .end() | ||
| const id = `${f1.id()}-${f2.id()}` | ||
| ret.push( | ||
| <path | ||
| d={path} | ||
| key={id} | ||
| data-testid="r1" | ||
| strokeWidth={mouseoverElt === id ? 5 : 1} | ||
| onClick={() => { | ||
| const featureWidget = session.addWidget?.( | ||
| 'BreakpointAlignmentsWidget', | ||
| 'breakpointAlignments', | ||
| { | ||
| featureData: { | ||
| feature1: ( | ||
| totalFeatures.get(f1.id()) || { toJSON: () => {} } | ||
| ).toJSON(), | ||
| feature2: ( | ||
| totalFeatures.get(f2.id()) || { toJSON: () => {} } | ||
| ).toJSON(), | ||
| }, | ||
| }, | ||
| ) | ||
| session.showWidget?.(featureWidget) | ||
| }} | ||
| onMouseOver={() => setMouseoverElt(id)} | ||
| onMouseOut={() => setMouseoverElt(undefined)} | ||
| />, | ||
| ) | ||
| } | ||
| return ret | ||
| })} | ||
| </g> | ||
| ) | ||
| }, | ||
| ) | ||
|
|
||
| export default AlignmentConnections |
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