jbrowse-plugin-graphgenomeviewer 8.3.7 → 8.3.9

package/src/GraphGenomeView/walkRowSpans.ts

@@ -14,6 +14,14 @@ import type { MarkContext2D, SpanChannels } from '@jbrowse/render-core/marks'
 
 type Rgb = [number, number, number]
 
+type SpanKind = 'bars' | 'gaps' | 'hairlines'
+
+const SPAN_KINDS: SpanKind[] = ['bars', 'gaps', 'hairlines']
+
+// the numbers in a CSS colour, `1e-7` among them, as `${hue}` may print one
+const cssNumbers = (css: string) =>
+  (css.match(/-?\d*\.?\d+(?:e[-+]?\d+)?/gi) ?? []).map(Number)
+
 // The colours runPaint writes: `#rrggbb`, `rgb(r, g, b)` and
 // `hsl(h, s%, l%)`
 export function cssRgb(css: string): Rgb {
@@ -21,7 +29,7 @@ export function cssRgb(css: string): Rgb {
     const v = Number.parseInt(css.slice(1), 16)
     return [(v >> 16) & 0xff, (v >> 8) & 0xff, v & 0xff]
   }
-  const [a = 0, b = 0, c = 0] = css.match(/[\d.]+/g)!.map(Number)
+  const [a = 0, b = 0, c = 0] = cssNumbers(css)
   return css.startsWith('hsl')
     ? (hslToRgb(a, b / 100, c / 100).map(v => v * 255) as Rgb)
     : [a, b, c]
@@ -30,14 +38,19 @@ export function cssRgb(css: string): Rgb {
 const abgr = ([r, g, b]: Rgb) =>
   packAbgr(Math.round(r), Math.round(g), Math.round(b), 255)
 
-const cssAbgr = new Map<string, number>()
-function packCss(css: string) {
-  let v = cssAbgr.get(css)
-  if (v === undefined) {
-    v = abgr(cssRgb(css))
-    cssAbgr.set(css, v)
+const packCss = (css: string) => abgr(cssRgb(css))
+
+// packCss remembering each colour it packed, for one cut's runs
+function cssPacker() {
+  const packed = new Map<string, number>()
+  return (css: string) => {
+    let v = packed.get(css)
+    if (v === undefined) {
+      v = packCss(css)
+      packed.set(css, v)
+    }
+    return v
   }
-  return v
 }
 
 /**
@@ -50,14 +63,15 @@ export function runPieces(
   run: WalkRun,
   ramp: { start: number; end: number } | undefined,
   pxPerBp: number,
+  pack = packCss,
 ): [number, number, number][] {
   const end = run.start + run.bp
   const paint = runPaint(run, ramp)
   if ('fill' in paint) {
-    return [[run.start, end, packCss(paint.fill)]]
+    return [[run.start, end, pack(paint.fill)]]
   }
   const stops = paint.stops.map(cssRgb)
-  const hues = paint.stops.map(css => Number(/[\d.]+/.exec(css)![0]))
+  const hues = paint.stops.map(css => cssNumbers(css)[0]!)
   const hueSpan = Math.abs(hues.at(-1)! - hues[0]!)
   const n = Math.max(
     1,
@@ -79,11 +93,13 @@ export function runPieces(
   return pieces
 }
 
+type ColoredSpans = SpanChannels & { color: Uint32Array }
+
 export interface WalkRowSpans {
-  bars: SpanChannels & { color: Uint32Array }
-  gaps: SpanChannels & { color: Uint32Array }
+  bars: ColoredSpans
+  gaps: ColoredSpans
   // gaps of bases the graph lacks, which draw as a hairline
-  hairlines: SpanChannels & { color: Uint32Array }
+  hairlines: ColoredSpans
   // where each drawn row's spans start in `bars`, `gaps` and `hairlines`
   barRows: Uint32Array
   gapRows: Uint32Array
@@ -102,11 +118,7 @@ function channels(capacity: number) {
   }
 }
 
-function slice<T extends SpanChannels & { color: Uint32Array }>(
-  c: T,
-  a: number,
-  b: number,
-) {
+function slice(c: ColoredSpans, a: number, b: number) {
   return {
     x: c.x.subarray(a, b),
     x2: c.x2.subarray(a, b),
@@ -116,6 +128,13 @@ function slice<T extends SpanChannels & { color: Uint32Array }>(
   }
 }
 
+const kindOf = (run: WalkRun): SpanKind =>
+  !run.gap
+    ? 'bars'
+    : gapStyle(run.cause).px === MISSING_PX
+      ? 'hairlines'
+      : 'gaps'
+
 /**
  * Each row's runs as `walkRowsTree` coalesces and colours them at
  * `pxPerBp`, as span channels: `x`/`x2` in bp along the row, `row` its index
@@ -127,49 +146,51 @@ export function walkRowSpans(
   pxPerBp: number,
   ramp?: { start: number; end: number },
 ): WalkRowSpans {
+  const pack = cssPacker()
   const pieces = rows.map(r =>
     coalesceRuns(r.runs, pxPerBp).map(run => ({
-      gap: run.gap,
-      hairline: run.gap && gapStyle(run.cause).px === MISSING_PX,
-      pieces: runPieces(run, ramp, pxPerBp),
+      kind: kindOf(run),
+      pieces: runPieces(run, ramp, pxPerBp, pack),
     })),
   )
-  let total = 0
+  const totals = { bars: 0, gaps: 0, hairlines: 0 }
   for (const runs of pieces) {
     for (const run of runs) {
-      total += run.pieces.length
+      totals[run.kind] += run.pieces.length
     }
   }
-  const bars = channels(total)
-  const gaps = channels(total)
-  const hairlines = channels(total)
-  const barRows = new Uint32Array(rows.length + 1)
-  const gapRows = new Uint32Array(rows.length + 1)
-  const hairlineRows = new Uint32Array(rows.length + 1)
+  const spans = {
+    bars: channels(totals.bars),
+    gaps: channels(totals.gaps),
+    hairlines: channels(totals.hairlines),
+  }
+  const starts = {
+    bars: new Uint32Array(rows.length + 1),
+    gaps: new Uint32Array(rows.length + 1),
+    hairlines: new Uint32Array(rows.length + 1),
+  }
   let longest = 1
   pieces.forEach((runs, row) => {
     for (const run of runs) {
-      const c = run.hairline ? hairlines : run.gap ? gaps : bars
+      const c = spans[run.kind]
       for (const [x, x2, color] of run.pieces) {
         const i = c.count++
         c.x[i] = x
         c.x2[i] = x2
         c.row[i] = row
         c.color[i] = color
-        longest = Math.max(longest, c.x2[i])
+        longest = Math.max(longest, x2)
       }
     }
-    barRows[row + 1] = bars.count
-    gapRows[row + 1] = gaps.count
-    hairlineRows[row + 1] = hairlines.count
+    for (const kind of SPAN_KINDS) {
+      starts[kind][row + 1] = spans[kind].count
+    }
   })
   return {
-    bars: slice(bars, 0, bars.count),
-    gaps: slice(gaps, 0, gaps.count),
-    hairlines: slice(hairlines, 0, hairlines.count),
-    barRows,
-    gapRows,
-    hairlineRows,
+    ...spans,
+    barRows: starts.bars,
+    gapRows: starts.gaps,
+    hairlineRows: starts.hairlines,
     longest,
   }
 }

package/src/version.ts

@@ -1 +1 @@
-export const version = '8.3.7'
+export const version = '8.3.9'

package/dist/chunks/chunk-6YK4U5LT.js

@@ -1,4 +0,0 @@
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e.drawnGraph?.nodes??[])t.set(n.id,n.length);return t},get nodeCount(){return e.graph?.nodes.length??0},get edgeCount(){return e.graph?.edges.length??0},get pathCount(){return e.graph?.paths?.length??0},get legendAtRest(){return e.hoveredNode===null&&e.hoveredRowWalks.length===0},get hasGraph(){return e.graph!==void 0},get geometryPainted(){return uo(e)},get paintSuperseded(){return!this.geometryPainted},get showLoading(){return e.error===void 0&&(e.isLoading||e.hasPendingSource||e.graph!==void 0&&!this.geometryPainted)},get canCancelLoad(){return e.isLoading&&!e.layoutResult},get usesLayoutEngine(){return e.graph?Ut(e.chosenLayoutMode,e.graph):!1},get anchorPaths(){return e.graph?.anchorPaths??[]},get walkChoices(){let t=e.graph?.paths;return t?.length?ve(t):[]},get effectiveDrawPaths(){return e.drawPaths&&Xe(e.graph?.paths?.length??0)},get activeReferencePath(){return e.graph?.referencePath},get rampDomain(){let t=e.openBubbles.at(-1);return 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t=this.walkLift?.referenceDomain;return t&&{...t,name:e.graphRegion?.refName}},get walkLabels(){return je(this.walkChoices)},walkLabel(t){return this.walkLabels.get(t)??t},get liftPaintsOffReference(){return!!this.walkLift?.walks.some(t=>t.encoding.field!=="walk"&&[...t.colors.values()].includes(ro))},get liftedWalksLabel(){let t=this.walkLift?.walks??[];return t.length===1?this.walkLabel(t[0].name):"these walks"},get effectiveColorScheme(){return e.layoutResult?.tubeMap&&(this.tubeMapReads||e.chosenColorScheme==="auto")?"uniform":Oe(e.chosenColorScheme,e.graph)},get tubeMapReads(){let t=e.layoutResult;return!t?.tubeMapPanels&&(t?.tubeMap?.layout.reads.length??0)>0},get colorSchemeLock(){return this.walkLift?{value:"By walk",why:"Each highlighted haplotype colours its own lane: set it under Haplotypes, Color highlighted..."}:this.tubeMapReads?{value:"By strand",why:"Reads take the reds and blues, so the tube map leaves its nodes clear"}:void 0},get nodePositions(){return e.layoutResult?.nodePositions},get labelsNodeSizes(){return!e.layoutResult?.tubeMap&&!this.walkLift},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get deletionRoutes(){return e.layoutResult?.deletionRoutes},get stranded(){return e.layoutResult?.stranded},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get derivedBubbles(){return e.graph?kt(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>kt(He(t,pe(n)),n).filter(o=>!o.covering)):[]},get openBubble(){return e.openBubbles.at(-1)},get openBubbleFocus(){let t=this.openBubble,{graph:n}=e;if(!t||!n)return;let o=new Set(pe(t)),r=new Set(n.nodes.filter(s=>o.has(s.name)).map(s=>s.id)),a=new Set;return n.edges.forEach((s,i)=>{r.has(s.from)&&r.has(s.to)&&a.add(i)}),{walks:[],nodeIds:r,edgeIndexes:a,names:new Set}},get drawnHighlight(){return e.walkLift??this.openBubbleFocus},bubbleIsOpen(t){return e.openBubbles.some(n=>ot(n,t))},bubbleFaded({bubble:t,nodeIds:n}){let o=e.walkLift,r=this.openBubbleFocus;return o?!n.some(a=>o.nodeIds.has(a)):!!r&&!this.bubbleIsOpen(t)&&!n.every(a=>r.nodeIds.has(a))}})).views(e=>({get bubbles(){let t=e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles,n=new Set(t.map(rt));return[...t,...e.openBubbleInsides.flat().filter(o=>!n.has(rt(o))&&n.add(rt(o)))]},get foldNote(){let t=e.foldedBelowBp;return t===void 0?void 0:`variants under ${Xn(t)} folded into the reference`}})).views(e=>({get cutHaplotypes(){},get sourceAdapter(){let t=e.sourceTrack;return t?ir(e,t):void 0},get sourceTrackId(){return e.sourceTrack?.trackId},get sessionTracks(){let t=U(e);return t.tracks.map(n=>({trackId:n.trackId,name:_n(n,t),adapterType:ze(n).type,assemblies:Qt(t,n)}))}})).views(e=>({get assemblyTrackChoices(){let t=e.graphRegion,n=t&&Zt(U(e),t.assemblyName);return 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t=e.sourceAdapter?.samplesTsvLocation;return t&&In(t)?t:void 0},get walkRowGroupFields(){return Mo(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=Eo(t,n),r=(e.graph?.paths??[]).map(a=>de(a.name).name).filter(a=>a!==e.graph?.referencePath);return{field:t,valueOf:o,palette:To(r.map(o)),unvalued:r.some(a=>o(a)==="")}},get tableGroupBy(){let t=e.walkRowGroupBy,n=e.walkRowSampleTable;return t&&n&&this.walkRowGroupFields.includes(t.field)?{groupBy:t,table:n}:void 0},get tubeMapPanelSplit(){let{field:t,sort:n}=e.facetSetting,o=this.tableGroupBy;return t!==""?{by:t,sort:n}:o?{by:"column",...o.groupBy,table:o.table}:void 0},get keptCohortRows(){let t=this.cohortWalkRows,n=t&&Me(t.rows,e.walkRowSamples);if(!t||!n||e.walkRowOrder!=="shared")return n;let o=[t.reference,...n];return wn(o).filter(r=>r>0).map(r=>o[r])},get walkRowGroups(){let t=this.keptCohortRows,n=this.tableGroupBy;return t&&n?Lo(t,n.table,n.groupBy):void 0},get walkRowBars(){let t=this.cohortWalkRows,n=this.keptCohortRows;return t&&n?{...t,rows:this.walkRowGroups?.rows??n}:void 0},get walkRowRibbons(){let t=this.walkRowBars;if(!e.walkRibbons||!e.rowVisitsNeeded||!t)return;let n=[t.reference,...t.rows];return bn(n,ye(n))},get sharedBlocks(){let t=this.walkRowBars;if(!e.layerSet.has("walkBlocks")||!e.rowVisitsNeeded||!t)return;let n=[t.reference,...t.rows];return yn(n,ye(n))},get drawsNodes(){return Y(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Ae(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=[...e.backboneGenes??[],...e.ownGeneFeatures??[]];return e.showGenes&&this.drawsNodes&&e.graph&&n.length>0&&t?Ce(e.graph,n,t):[]},get bubbleHalos(){Ae(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=e.showBubbles?e.bubbles:e.hoveredBubble?[e.hoveredBubble]:[];return n.length===0||!this.drawsNodes||!e.graph||!t?[]:dn(e.graph,n,t,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"?e.drawnReferenceRamp:void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get axisScale(){return Ze(e.scale,e.pixelRows)},get scaleX(){return this.axisScale.scaleX},get scaleY(){return this.axisScale.scaleY}})).views(e=>({get screenTransform(){return{scaleX:e.scaleX,scaleY:e.scaleY,translateX:e.translateX,translateY:e.translateY}},toScreen(t){return{x:t.x*e.scaleX+e.translateX,y:t.y*e.scaleY+e.translateY}},get deletionDrawing(){return e.graph?Ve(e.graph,e.allDeletions,e.showDeletionEdges):void 0},get deletions(){return this.deletionDrawing?.shown??[]},get deletionEdgeIndexes(){return this.deletionDrawing?.bypassed},get hiddenEdgeIndexes(){return this.deletionDrawing?.hidden},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get paintsNodeColors(){return e.drawsNodes||!!e.layoutResult?.tubeMap},get referenceRampDrawsOffReference(){return!!e.referenceRamp&&this.paintsNodeColors&&!!e.drawnGraph?.nodes.some(t=>!A(t))},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?kn(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeColorKind(){let t=e.layoutResult,n=e.drawnGraph?.paths??[],o=e.tubeMapReads;return t?.tubeMap?e.tubeMapColoring&&!o?"value":t.tubeMapPanels?"role":this.tubeMapNodeColors?"tinted":!o&&(!Xe(n.length)||n.some(r=>r.members))?"role":"path":void 0},tubeColorsOf(t,n){let o=t.paths??[],r=this.tubeColorKind,a=e.tubeMapColoring;return r==="value"&&a?Go(o,t.referencePath,a.valueOf,a.palette):r==="tinted"?Xt(o,t.referencePath,Ao):r==="role"?Xt(o,t.referencePath):n},fadeUnhovered(t,n,o){let r=new Set(e.hoveredRowWalks);return r.size>0?t.map((a,s)=>{let i=n[s]?.name??"";return r.has(i)||o!==void 0&&de(i).name===o?a:et}):t},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap,n=e.drawnGraph;return t&&n?this.fadeUnhovered(this.tubeColorsOf(n,t.pathColors),n.paths??[]):void 0},nodeSpan(t){return Ur(t,e.nodeById,e.nodeNeighbors)},get hoverDrawing(){let t=e.hoveredPanel;return(t===null?void 0:e.layoutResult?.tubeMapPanels?.[t]?.result.tubeMap)??e.layoutResult?.tubeMap},get hoverGraph(){return this.hoverDrawing?.graph??e.drawnGraph},get hoverNodeById(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeById:t&&Kr(t)},get hoverNeighbors(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeNeighbors:t&&te(t)}})).views(e=>({get pathLegend(){let t=e.drawnGraph?.paths;return(e.layoutResult?.tubeMap?e.tubeColorKind==="path":e.drawPaths)&&t&&Xe(t.length)&&!t.some(o=>o.members)?ve(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble;return t!==null?Ur(t,e.hoverNodeById,e.hoverNeighbors):n&&!n.offReference?{start:n.start,end:n.end}:void 0},get hoverHighlight(){let t=e.graphRegion,n=this.hoveredSpan;return 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