jbrowse-plugin-graphgenomeviewer 4.1.1 → 4.3.0

package/src/GraphGenomeView/model.ts

@@ -40,6 +40,11 @@ import {
 } from '@jbrowse/bandage-core/layout/walkRowDraw'
 import { walkRowsExtent } from '@jbrowse/bandage-core/layout/walkRowLayout'
 import { walkRows } from '@jbrowse/bandage-core/layout/walkRows'
+import {
+  segmentAt,
+  stripMarks,
+  walkStripFrame,
+} from '@jbrowse/bandage-core/layout/walkStrip'
 import {
   LAYOUT_MODES,
   LAYOUT_MODE_VALUES,
@@ -47,6 +52,7 @@ import {
   modeUsesLayoutEngine,
 } from '@jbrowse/bandage-core/layoutModes'
 import { NODE_WIDTH_VALUES, nodeInk } from '@jbrowse/bandage-core/nodeWidths'
+import { LABEL_CHAR_PX } from '@jbrowse/bandage-core/overlayLabels'
 import {
   anchorFromPaths,
   chooseReferencePath,
@@ -297,6 +303,25 @@ const VIEWPORT_DEBOUNCE_MS = 150
 const VIEWPORT_PANES_BUILT = 1
 // How many walk rows read their haplotype's genes, the first rows down
 const WALK_GENE_ROWS = 40
+// The most of the pane's height the strip of walk rows under a node layout
+// takes; past it rows shrink, down to a dense overview
+const WALK_STRIP_CEILING = 260
+
+// The rows a sample filter keeps, in the order it names them
+function filterSamples<R extends { sample: string; label: string }>(
+  rows: R[],
+  samples: string[] | undefined,
+) {
+  return samples
+    ? rows
+        .filter(r => samples.includes(r.sample))
+        .sort(
+          (a, b) =>
+            samples.indexOf(a.sample) - samples.indexOf(b.sample) ||
+            a.label.localeCompare(b.label),
+        )
+    : rows
+}
 
 // What the canvas draws under the tube map, whose ink is all TubeMapOverlay's
 const EMPTY_BATCH: RenderBatch = {
@@ -494,7 +519,7 @@ export function GraphPaneMixin() {
         // with a label that opens it. Off by default: on a base-level cut
         // every SNP's halo is a blob.
         showBubbles: types.optional(types.boolean, false),
-        showDeletionEdges: types.optional(types.boolean, false),
+        showDeletionEdges: types.optional(types.boolean, true),
         // The session's genes drawn onto the backbone: exons along the nodes
         // that carry them, names pinned at their midpoints. See genes/.
         showGenes: types.optional(types.boolean, true),
@@ -517,6 +542,9 @@ export function GraphPaneMixin() {
         // Samples whose walks the walk rows show, by the name before the
         // haplotype number; undefined shows every walk the cut holds.
         walkRowSamples: types.maybe(types.frozen<string[]>()),
+        // Walk rows in a strip under a layout that draws nodes, linked to the
+        // drawing: a node's passes tick each bar, a bar's point lights its node
+        walkStrip: types.optional(types.boolean, false),
         // Walks lifted out of the drawing, each a layer with a lane of its own
         // and the rest fading, coloured by the encoding it states or by the
         // default one. See walkEncoding.ts. Empty lifts none.
@@ -622,6 +650,8 @@ export function GraphPaneMixin() {
       // whether the pointer is over this pane, whose own hit test then says
       // what it is on
       pointerInPane: false,
+      // the strip point the pointer is over, which lights its node above
+      stripHover: null as { row: string; offset: number } | null,
       hoveredEdge: null as number | null,
       selectedNode: null as string | null,
       viewportDirty: 0,
@@ -966,6 +996,9 @@ export function GraphPaneMixin() {
       get alleleDeletions() {
         return self.layoutResult?.alleleDeletions ?? []
       },
+      get deletionRoutes() {
+        return self.layoutResult?.deletionRoutes
+      },
       // Whether the current layout states y in screen px rather than in the same
       // units as x (LayoutResult.pixelRows). Everything that has to put the two
       // axes in one expression reads this through scaleX/scaleY.
@@ -1157,16 +1190,7 @@ export function GraphPaneMixin() {
         if (!bars) {
           return undefined
         }
-        const samples = self.walkRowSamples
-        const rows = samples
-          ? bars.rows
-              .filter(r => samples.includes(r.sample))
-              .sort(
-                (a, b) =>
-                  samples.indexOf(a.sample) - samples.indexOf(b.sample) ||
-                  a.label.localeCompare(b.label),
-              )
-          : bars.rows
+        const rows = filterSamples(bars.rows, self.walkRowSamples)
         const [reference, ...paired] = withCalls(
           [bars.reference, ...rows],
           repeat?.calls,
@@ -1608,8 +1632,7 @@ export function GraphPaneMixin() {
       // open: the span of its contig the bar covers, on the session assembly
       // its haplotype names (the cut's own assembly for the reference row).
       // The label names the haplotype when no assembly is loaded for it.
-      walkRowLaunchTarget(index: number) {
-        const bars = self.walkRowBars
+      walkRowLaunchTarget(index: number, bars = self.walkRowBars) {
         const row = bars ? [bars.reference, ...bars.rows][index] : undefined
         if (!row?.axis) {
           return undefined
@@ -1740,6 +1763,76 @@ export function GraphPaneMixin() {
         return isLinearHost(view) ? view : undefined
       },
     }))
+    .views(self => ({
+      // Whether the strip of walk rows sits under the drawing: asked for, on a
+      // standalone view whose layout draws nodes, for a graph with walks, and
+      // not while a bubble is popped
+      get walkStripShown() {
+        return (
+          self.walkStrip &&
+          !self.host &&
+          self.modeDrawsNodes &&
+          !self.layoutResult?.tubeMap &&
+          !self.walkRowBars &&
+          self.popStack.length === 0 &&
+          (self.graph?.paths?.length ?? 0) > 1
+        )
+      },
+      // The strip's rows: the cut's, with the sample filter and no repeat
+      // pick, which the Repeat menu only offers in walk rows
+      get walkStripRows() {
+        const graph = self.graph
+        const bars =
+          graph && this.walkStripShown
+            ? walkRows(graph, self.graphRegion)
+            : undefined
+        return bars
+          ? { ...bars, rows: filterSamples(bars.rows, self.walkRowSamples) }
+          : undefined
+      },
+      get walkStripFrame() {
+        const bars = this.walkStripRows
+        if (!bars) {
+          return undefined
+        }
+        const longest = Math.max(
+          ...[bars.reference, ...bars.rows].map(r => r.label.length),
+        )
+        return walkStripFrame(bars, {
+          width: self.paneWidth,
+          maxHeight: WALK_STRIP_CEILING,
+          labelPx: longest * LABEL_CHAR_PX + 16,
+        })
+      },
+      // Whether a cut must follow every snarl a walk leaves the window by, so
+      // walks come back whole: walk rows measure them, and so does the strip
+      get cutsWholeWalks() {
+        return (
+          layoutModeByValue(self.chosenLayoutMode).wholeWalks ||
+          (self.walkStrip && !self.host)
+        )
+      },
+      // Where each walk passes the hovered node, or the selected one
+      get walkStripMarks() {
+        const bars = this.walkStripRows
+        const id = self.hoveredNode ?? self.selectedNode
+        const node = id === null ? undefined : self.nodeById?.get(id)
+        return bars && node && self.graph
+          ? stripMarks(self.graph, [bars.reference, ...bars.rows], node)
+          : []
+      },
+      // Where the drawing has the node a strip point lights, for the ring
+      // that finds it in a hairball
+      get walkStripLocator() {
+        const id = self.stripHover ? self.hoveredNode : null
+        return id === null
+          ? undefined
+          : nodeAnchor(self.nodePositions?.[id], p => ({
+              x: p.x * self.scaleX + self.translateX,
+              y: p.y * self.scaleY + self.translateY,
+            }))
+      },
+    }))
     .views(self => ({
       // Whether the drawing's x is reference bp a host can place. Walk rows
       // put the backbone at its bp too, but their bars are lengths, so the
@@ -2212,6 +2305,7 @@ export function GraphPaneMixin() {
           // `deletions` is and for the same reason — see `referenceRamp`.
           referenceRamp: self.referenceRamp,
           deletions: self.deletionEdgeIndexes,
+          deletionRoutes: self.deletionRoutes,
           hiddenEdges: self.hiddenEdgeIndexes,
           // passed so the shared edge-curve cache can tell a drag from a pan
           version: self.positionsVersion,
@@ -2598,6 +2692,26 @@ export function GraphPaneMixin() {
       setPointerInPane(inside: boolean) {
         self.pointerInPane = inside
       },
+      setWalkStrip(show: boolean) {
+        self.walkStrip = show
+        self.stripHover = null
+      },
+      // The pointer over the strip: the node under it becomes the hovered
+      // node, so the drawing, the tooltip and a linked linear view follow
+      setStripHover(hover: { row: string; offset: number } | null) {
+        self.stripHover = hover
+        const bars = self.walkStripRows
+        const frame = self.walkStripFrame
+        const row =
+          hover && bars
+            ? [bars.reference, ...bars.rows].find(r => r.name === hover.row)
+            : undefined
+        const node =
+          row && frame && self.graph
+            ? segmentAt(self.graph, row, hover!.offset, frame.scaleX)
+            : undefined
+        self.hoveredNode = node ?? null
+      },
       setLegendSize(size: { width: number; height: number }) {
         self.legendSize = size
       },
@@ -2658,12 +2772,10 @@ export function GraphPaneMixin() {
                   // the assembly to load to open this node on its own
                   // coordinates
                   contributingHaplotype: nodeOwnLocation(node)?.haplotype,
-                  // Every assembly that traverses it, which is a different
-                  // question and one only a path GFA can answer. Absent on an
-                  // rGFA rather than approximated, so the two are never
-                  // confused: there `contributingAssembly` is first-seen, not
-                  // carriage.
-                  carriedBy: node.samples?.join(', '),
+                  // Every haplotype whose path visits it, which only a path
+                  // GFA records. Absent on an rGFA, where
+                  // `contributingAssembly` is the first-seen assembly alone.
+                  samples: node.samples?.join(', '),
                   ...(region && span
                     ? {
                         refName: region.refName,
@@ -4041,6 +4153,18 @@ export function GraphPaneMixin() {
               self.setShowGenes(!self.showGenes)
             },
           },
+          ...(self.modeDrawsNodes && (self.graph?.paths?.length ?? 0) > 1
+            ? [
+                {
+                  type: 'checkbox' as const,
+                  label: 'Walk rows under the graph',
+                  checked: self.walkStrip,
+                  onClick: () => {
+                    self.setWalkStrip(!self.walkStrip)
+                  },
+                },
+              ]
+            : []),
           ...(self.referenceStripApplies
             ? [
                 {

package/src/GraphGenomeView/viewModel.ts

@@ -2,7 +2,8 @@ import { layoutModeByValue } from '@jbrowse/bandage-core/layoutModes'
 import { readConfObject } from '@jbrowse/core/configuration'
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'
 import { getSession } from '@jbrowse/core/util'
-import { types } from '@jbrowse/mobx-state-tree'
+import { addDisposer, types } from '@jbrowse/mobx-state-tree'
+import { reaction } from 'mobx'
 
 import { GraphPaneMixin, MAX_GRAPH_REGION_BP, formatSpanBp } from './model'
 import {
@@ -134,7 +135,7 @@ export default function stateModelFactory() {
             return self.cutSubgraph(readConfObject(track, 'adapter'), region, {
               hops: self.subgraphContext,
               haplotypes: self.subgraphHaplotypes,
-              ...(layoutModeByValue(self.chosenLayoutMode).wholeWalks
+              ...(self.cutsWholeWalks
                 ? { snarls: 'overlapping' as const }
                 : {}),
             })
@@ -147,13 +148,14 @@ export default function stateModelFactory() {
       retryLoad() {
         void self.load()
       },
-      // walk rows measures whole walks, which a GBZ cut only follows when
-      // asked, so entering or leaving it cuts the track again
+      // walk rows, and the strip of them under a node layout, measure whole
+      // walks, which a GBZ cut only follows when asked, so a change in whether
+      // the drawing needs them cuts the track again; the strip's toggle does
+      // the same (afterAttach)
       switchLayout(mode: LayoutModeValue) {
-        const from = layoutModeByValue(self.chosenLayoutMode)
+        const before = self.cutsWholeWalks
         self.setLayoutMode(mode)
-        return self.loadedTrackId &&
-          layoutModeByValue(mode).wholeWalks !== from.wholeWalks
+        return self.loadedTrackId && self.cutsWholeWalks !== before
           ? self.load()
           : self.recomputeLayout()
       },
@@ -164,6 +166,20 @@ export default function stateModelFactory() {
         if (!self.graph) {
           void self.load()
         }
+        addDisposer(
+          self,
+          reaction(
+            () => self.walkStrip,
+            () => {
+              if (
+                self.loadedTrackId &&
+                !layoutModeByValue(self.chosenLayoutMode).wholeWalks
+              ) {
+                void self.load()
+              }
+            },
+          ),
+        )
       },
     }))
 }

package/src/RgfaTabixAdapter/RgfaTabixAdapter.test.ts

@@ -203,7 +203,7 @@ test('getFeatures carries SM:Z: onto the feature', async () => {
   const private1199 = features.find(f => f.get('name') === '196827')!
   expect(private1199.get('end') - private1199.get('start')).toBe(1199)
   expect(private1199.get('samples')).toEqual(['K12.1'])
-  expect(private1199.get('carriers')).toBe(1)
+  expect(private1199.get('sampleCount')).toBe(1)
 
   const core = features.find(f => f.get('name') === '196843')!
   expect(core.get('samples')).toEqual([
@@ -213,10 +213,10 @@ test('getFeatures carries SM:Z: onto the feature', async () => {
     'NCTC86.1',
     'IAI39.1',
   ])
-  expect(core.get('carriers')).toBe(5)
+  expect(core.get('sampleCount')).toBe(5)
 })
 
-// The other half of the same fixture: the graph route reads carriage off the
+// The other half of the same fixture: the graph route reads the samples off the
 // synthesized S-line, and rgfaBed.test.ts asserts that from a hand-written row.
 // This is the same claim against a real indexed file.
 test('getSubgraph keeps the tag on the S-line it synthesizes', async () => {
@@ -226,16 +226,16 @@ test('getSubgraph keeps the tag on the S-line it synthesizes', async () => {
   )
 })
 
-// An rGFA has no sixth column, so the attribute is absent rather than 0 — a
-// color expression reading `carriers` on such a track gets undefined, not a
-// claim that nothing carries the segment.
-test('getFeatures omits carriage on a graph that states none', async () => {
+// An rGFA has no sixth column, so the attribute is absent rather than 0: a
+// color expression reading `sampleCount` on such a track gets undefined, not a
+// count of zero.
+test('getFeatures omits samples on a graph that records none', async () => {
   const features = await firstValueFrom(
     makeAdapter().getFeatures(k12).pipe(toArray()),
   )
   expect(features.length).toBeGreaterThan(0)
   expect(features.every(f => f.get('samples') === undefined)).toBe(true)
-  expect(features.every(f => f.get('carriers') === undefined)).toBe(true)
+  expect(features.every(f => f.get('sampleCount') === undefined)).toBe(true)
 })
 
 // Minigraph-Cactus writes PanSN stable names, so HPRC release 2 calls the

package/src/RgfaTabixAdapter/RgfaTabixAdapter.ts

@@ -124,11 +124,10 @@ export default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAd
             signal,
             lineCallback: line => {
               const segment = parseSegmentLine(line)
-              // `samples` is who, `carriers` is how many, and the second is not
-              // just a convenience: a lane colored by carriage is a jexl
-              // expression in a config, where counting a list means relying on
-              // jexl resolving `.length` through a member access on an array.
-              // The count is the axis the color reads, so the index states it.
+              // `samples` lists the haplotypes whose paths visit the segment and
+              // `sampleCount` counts them. A lane's color reads the count, and
+              // a count in jexl would otherwise rely on `.length` resolving
+              // through a member access on an array.
               const samples = segmentSamples(segment)
               observer.next(
                 new SimpleFeature({
@@ -140,7 +139,7 @@ export default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAd
                   type: 'segment',
                   rank: segment.rank,
                   stableName: segment.refName,
-                  ...(samples && { samples, carriers: samples.length }),
+                  ...(samples && { samples, sampleCount: samples.length }),
                 }),
               )
             },

package/src/RgfaTabixAdapter/rgfaBed.test.ts

@@ -119,15 +119,15 @@ test('a valid tag beside a malformed one keeps only the valid one', () => {
   )
 })
 
-test('segmentSamples reads the carriers off the tag column', () => {
+test('segmentSamples reads the samples off the tag column', () => {
   const segment = parseSegmentLine(
     'K12#1#chr\t1004477\t1004500\ts119690\t0\tSM:Z:K12.1,Sakai.1,NCTC86.1',
   )
   expect(segmentSamples(segment)).toEqual(['K12.1', 'Sakai.1', 'NCTC86.1'])
 })
 
-// Undefined, not [], so a lane can tell a graph that states nothing about
-// carriage apart from a segment nothing carries.
+// Undefined, not [], so a lane can tell a graph that records no samples from a
+// segment no path visits.
 test('segmentSamples is undefined when the column says nothing', () => {
   expect(segmentSamples(parseSegmentLine(RGFA_SEG))).toBeUndefined()
   expect(segmentSamples(parseSegmentLine(TAGGED_SEG))).toBeUndefined()
@@ -148,11 +148,11 @@ test('segmentSamples finds the tag beside other tags', () => {
   expect(segmentSamples(segment)).toEqual(['HG002.1', 'HG002.2'])
 })
 
-// The whole carriage chain in one test, because it spans three files and each
+// The whole samples chain in one test, because it spans three files and each
 // half is covered on its own: a segs.bed SM:Z: column -> the synthesized S-line
-// -> the GFA parser -> GraphNode.samples, which is what model.ts renders as
-// `carriedBy` in the node popup. An indexed cut has no P/W lines, so this tag is
-// the only statement of carriage it can carry, and nothing else asserts that it
+// -> the GFA parser -> GraphNode.samples, which model.ts renders as `samples`
+// in the node popup. An indexed cut has no P/W lines, so this tag is its only
+// record of which haplotypes visit a segment, and nothing else asserts that it
 // survives the round trip.
 test('SM:Z: on a segs row reaches GraphNode.samples', async () => {
   const { parseGFA } = await import('@jbrowse/bandage-core/gfa-core/index')

package/src/version.ts

@@ -1 +1 @@
-export const version = '4.1.1'
+export const version = '4.3.0'

package/dist/chunks/chunk-ECKLYJWP.js

@@ -1,2 +0,0 @@
-import{b as R,g as ie}from"./chunk-7BKUWQE5.js";import{a as se,b as ce}from"./chunk-KULNKXPT.js";import{a as Re}from"./chunk-FY3BTKY4.js";var jt=Re((Kn,Oe)=>{Oe.exports=JBrowseExports["tss-react/mui"]});function Kt(e){let t=n=>Math.round(n*100)/100;return e.map((n,r)=>`${r?"L":"M"}${t(n.x)},${t(n.y)}`).join("")}function ue(e,t,n,r,a){let o=Math.hypot(r-t,n-e);if(o===0)return[n,r];let s=(n-e)/o,c=(r-t)/o;return[n+a*s,r+a*c]}function j(e,t){let n=1-t,r=n*n*n,a=3*n*n*t,o=3*n*t*t,s=t*t*t;return{x:r*e.x0+a*e.cx0+o*e.cx1+s*e.x1,y:r*e.y0+a*e.cy0+o*e.cy1+s*e.y1}}function he(e){let t=e[Math.floor(e.length/2)];return t?j(t,.5):void 0}function xe(e){let t=1/0,n=1/0,r=-1/0,a=-1/0;for(let o of e)t=Math.min(t,o.x0,o.cx0,o.cx1,o.x1),r=Math.max(r,o.x0,o.cx0,o.cx1,o.x1),n=Math.min(n,o.y0,o.cy0,o.cy1,o.y1),a=Math.max(a,o.y0,o.cy0,o.cy1,o.y1);return{minX:t,minY:n,maxX:r,maxY:a}}function De(e,t,n){let r=j(e,t),a=j(e,n),o=(n-t)/3,s=de(e,t),c=de(e,n);return{x0:r.x,y0:r.y,cx0:r.x+s.x*o,cy0:r.y+s.y*o,cx1:a.x-c.x*o,cy1:a.y-c.y*o,x1:a.x,y1:a.y}}function de(e,t){let n=1-t,r=3*n*n,a=6*n*t,o=3*t*t;return{x:r*(e.cx0-e.x0)+a*(e.cx1-e.cx0)+o*(e.x1-e.cx1),y:r*(e.cy0-e.y0)+a*(e.cy1-e.cy0)+o*(e.y1-e.cy1)}}function Jt(e,t){let n=[];for(let r of e){let a=Math.hypot(r.cx0-r.x0,r.cy0-r.y0)+Math.hypot(r.cx1-r.cx0,r.cy1-r.cy0)+Math.hypot(r.x1-r.cx1,r.y1-r.cy1),o=Math.max(3,Math.round(a/t)|1);for(let s=0;s<o;s+=2)n.push([De(r,s/o,(s+1)/o)])}return n}function Qt(e,t,n){let r=new Array(e.length);for(let a=0;a<e.length;a++){let o=e[a];r[a]={x0:o.x0+t,y0:o.y0+n,cx0:o.cx0+t,cy0:o.cy0+n,cx1:o.cx1+t,cy1:o.cy1+n,x1:o.x1+t,y1:o.y1+n}}return r}function W(e,t){let n=e.length-1;return t==="end"?{at:e[n],inward:e[n-1]}:{at:e[0],inward:e[1]}}var He=.5,Xe=80;function me(e){let t=1/0,n=-1/0;for(let r of e)t=Math.min(t,r.x),n=Math.max(n,r.x);return{min:t,max:n}}function le(e,t){return Math.max(0,t.min-e,e-t.max)}function pe(e,t,n){let r=le(e[0].x,t),a=le(e[e.length-1].x,t);return r===a?n:r<a?"start":"end"}function ke(e,t){return{from:pe(e,me(t),"end"),to:pe(t,me(e),"start")}}var Fe=.75,ze=1.15,$e=.35,We=60;function Ye(e,t,n,r,a,o){let s=Math.hypot(n-e,r-t),c=s===0?1:(n-e)/s,u=s===0?0:(r-t)/s,d=0,f=1/0,b=-1/0;for(let l of a){let p=l.x-e,x=l.y-t,y=p*-u+x*c;Math.abs(y)>Math.abs(d)&&(d=y);let A=p*c+x*u;f=Math.min(f,A),b=Math.max(b,A)}let i=a.length?b-f:0,h=Math.max(Math.abs(d)*ze/Fe,i*$e),m=o===void 0?h:Math.min(h,o);return d<0?-m:m}function be({scaleX:e,scaleY:t}){return t/e}var Ue=3;function Y(e,t,n){let r=t.x-e.x,a=(t.y-e.y)*n,o=Math.hypot(r,a);return o===0?void 0:{x:r/o,y:a/o}}function Zt(e,t,n,r,a=Ue){let o=be(r),s=Y(e[e.length-1],t[0],o)??Y(e[0],e.at(-1),o)??Y(t[0],t.at(-1),o)??{x:1,y:0},c=[];for(let u=0;u<n;u++){let d=(u-(n-1)/2)*a;c.push({x:-s.y*d,y:s.x*d/o})}return c}function U(e,t){return e.map(n=>({x:n.x,y:n.y*t}))}function je(e,t){for(let n of e)n.y0/=t,n.cy0/=t,n.cy1/=t,n.y1/=t;return e}var Ve=12,qe=40;function fe(e,t){let n=0;for(let o=1;o<e.length;o++)n+=Math.hypot(e[o].x-e[o-1].x,e[o].y-e[o-1].y);let r=n*t;return Math.min(qe,Math.max(Ve,r/2))/Math.max(t,Number.EPSILON)}function en(e){return e.from!==e.to?!1:e.fromStrand&&e.toStrand&&e.fromStrand!==e.toStrand?e.fromStrand==="+"?"end":"start":!0}function Ke(e,t,n,r){let{at:a,inward:o}=e,s=o?a.x-o.x:1,c=o?a.y-o.y:0,u=Math.hypot(s,c)||1,d=s/u,f=c/u,b=a.x+n,i=a.y+r,h=b+d*t/3,m=i+f*t/3,l=b+d*t,p=i+f*t,x=-f*t/2,y=d*t/2;return[{x0:b,y0:i,cx0:h,cy0:m,cx1:l+x,cy1:p+y,x1:l,y1:p},{x0:l,y0:p,cx0:l-x,cy0:p-y,cx1:h,cy1:m,x1:b,y1:i}]}function V(e,t,n,r,a,o,s=[],c){let u=o.scaleX,d=be(o),f=c??(o.pixelRows?We:void 0);if(d!==1)return je(V(U(e,d),U(t,d),n,r,a*d,{scaleX:u,scaleY:u},U(s,d),f===void 0?void 0:f*d),d);if(typeof n=="string")return Ke(W(e,n),fe(e,u),r,a);let b=n?{from:"end",to:"start"}:ke(e,t),i=W(e,b.from),h=W(t,b.to),m=i.at,l=h.at,p=m.x+r,x=m.y+a,y=l.x+r,A=l.y+a;if(n){let L=1,N=0;if(i.inward){let I=m.x-i.inward.x,O=m.y-i.inward.y,C=Math.hypot(I,O);C>0&&(L=I/C,N=O/C)}let g=fe(e,u),E=-N,M=L,S=(m.x+l.x)/2+r+E*g,_=(m.y+l.y)/2+a+M*g,G=p+L*g,w=x+N*g,P=y-L*g,B=A-N*g;return[{x0:p,y0:x,cx0:G,cy0:w,cx1:G+E*g,cy1:w+M*g,x1:S,y1:_},{x0:S,y0:_,cx0:P+E*g,cy0:B+M*g,cx1:P,cy1:B,x1:y,y1:A}]}else{let L=i.inward??{x:m.x-(l.x-m.x),y:m.y-(l.y-m.y)},N=h.inward??{x:l.x-(m.x-l.x),y:l.y-(m.y-l.y)},g=Math.hypot(y-p,A-x),E=(te,ne,Ce,Ie)=>{let re=ne.x-te.x,oe=ne.y-te.y,ae=Math.hypot(re,oe),Te=ae===0?0:(Ce*re+Ie*oe)/ae;return Math.max(0,Math.min(g*He,Xe,Te*.5))},M=l.x-m.x,S=l.y-m.y,[_,G]=ue(L.x,L.y,m.x,m.y,E(L,m,M,S)),[w,P]=ue(N.x,N.y,l.x,l.y,E(N,l,-M,-S)),B=s.length?Ye(p,x,y,A,s,f):0,I=g===0?1:g,O=(y-p)/I,C=(A-x)/I,J=-C*B,Q=O*B,Z=O*Math.abs(B),ee=C*Math.abs(B);return[{x0:p,y0:x,cx0:_+r+J-Z,cy0:G+a+Q-ee,cx1:w+r+J+Z,cy1:P+a+Q+ee,x1:y,y1:A}]}}var Je=1;function Qe(e,t){return t.flatMap(n=>e[n]??[])}function ye(e,t,n){let r=e[t.from],a=e[t.to];return r?.length&&a?.length?V(r,a,t.from===t.to,0,0,n,Qe(e,t.bypassed)):void 0}function Ze(e){let t=new Map;for(let n of e.nodes)if(R(n)){let r=t.get(n.stable.refName);r?r.push(n):t.set(n.stable.refName,[n])}for(let n of t.values())n.sort((r,a)=>r.stable.start-a.stable.start);return t}function et(e,t,n){let r=[];if(e)for(let a=ie(e,t);a<e.length;a++){let o=e[a];if(o.stable.start>=n)break;o.stable.start+o.length<=n&&r.push(o.id)}return r}function tt(e,t,n,r){let{fromStrand:a,toStrand:o}=e;if(a===void 0||o===void 0)return!0;let s=a===(t.stable.strand??"+"),c=o===(n.stable.strand??"+");return r?s&&c:!s&&!c}function on(e){let t=new Map(e.nodes.map(a=>[a.id,a])),n=Ze(e),r=[];for(let a=0;a<e.edges.length;a++){let o=e.edges[a],s=t.get(o.from),c=t.get(o.to);if(s!==void 0&&c!==void 0&&R(s)&&R(c)&&s.stable.refName===c.stable.refName){let u=s.stable.start<=c.stable.start,[d,f]=u?[s,c]:[c,s],b=d.stable.start+d.length,i=f.stable.start,h=i-b;if(h>=Je&&tt(o,s,c,u)){let m=d.stable.refName;r.push({edgeIndex:a,from:o.from,to:o.to,refName:m,start:b,end:i,bp:h,bypassed:et(n.get(m),b,i)})}}}return r}function v(e){return e.endsWith("-")?"-":"+"}function ge(e){return e==="+"?"-":"+"}function nt(e){let t=(e.fromStrand??v(e.from))===v(e.from)?"end":"start",n=(e.toStrand??v(e.to))===v(e.to)?"start":"end";return{from:t,to:n}}function cn(e){let t=e.edges.map(nt),n=new Map,r=(i,h,m)=>{let l=`${i}|${h}`,p=n.get(l);p?p.push(m):n.set(l,[m])};e.edges.forEach((i,h)=>{r(i.from,t[h].from,h),r(i.to,t[h].to,h)});let a=i=>{let h=n.get(`${i}|end`);if(h?.length!==1)return;let m=h[0],l=e.edges[m];return l.from===i&&l.to!==i&&t[m].from==="end"&&t[m].to==="start"&&n.get(`${l.to}|start`)?.length===1?m:void 0},o=new Set,s=new Map,c=new Map;for(let i of e.nodes){let h=n.get(`${i.id}|start`),m=h?.length===1?e.edges[h[0]].from:void 0;if(s.has(i.id)||m!==void 0&&a(m)===h[0])continue;let l=[i.id];for(;;){let p=a(l.at(-1)),x=p===void 0?void 0:e.edges[p].to;if(x===void 0||s.has(x))break;o.add(p),l.push(x)}for(let p of l)s.set(p,i.id);l.length>1&&c.set(i.id,l)}for(let i of e.nodes)s.has(i.id)||s.set(i.id,i.id);let u=new Map(e.nodes.map(i=>[i.id,i])),d=[];for(let i of e.nodes){if(s.get(i.id)!==i.id)continue;let h=c.get(i.id);if(!h){d.push(i);continue}let m=h.map(x=>u.get(x)),l=m.filter(R),p=l.length?l.reduce((x,y)=>x.stable.start<=y.stable.start?x:y):m[0];d.push({id:i.id,name:i.name,length:m.reduce((x,y)=>x+y.length,0),depth:i.depth,stable:p.stable})}let f=new Set,b=[];return e.edges.forEach((i,h)=>{let m=s.get(i.from),l=s.get(i.to),p=t[h],x=`${m}|${p.from}>${l}|${p.to}`;o.has(h)||f.has(x)||(f.add(x),b.push({from:m,to:l,...p.from==="start"?{fromStrand:ge(v(m))}:{},...p.to==="end"?{toStrand:ge(v(l))}:{}}))}),{graph:{...e,nodes:d,edges:b,paths:void 0,pathVisits:void 0},runs:c}}function un(e,t,n){let r={...e};for(let[a,o]of t){let s=e[a];if(!s?.length)continue;delete r[a];let c=K(s),u=c.at(-1),d=o.map(i=>Math.max(n(i),0)),f=d.reduce((i,h)=>i+h,0)||o.length,b=0;o.forEach((i,h)=>{let m=f?d[h]/f*u:u/o.length,l=h===o.length-1?u:b+m;r[i]=Le(s,c,b,l),b=l})}return r}function dn(e,t,n){if(e.length===0)return[];let r=K(e),a=r.at(-1);return Le(e,r,t*a,n*a)}function Ne(e){let t=K(e);return q(e,t,t.at(-1)/2)}function K(e){let t=[0];for(let n=1;n<e.length;n++)t.push(t[n-1]+Math.hypot(e[n].x-e[n-1].x,e[n].y-e[n-1].y));return t}function q(e,t,n){if(n<=0)return{...e[0]};let r=1;for(;r<t.length&&t[r]<n;)r++;if(r>=t.length)return{...e.at(-1)};let a=t[r]-t[r-1],o=a>0?(n-t[r-1])/a:0,s=e[r-1],c=e[r];return{x:s.x+(c.x-s.x)*o,y:s.y+(c.y-s.y)*o}}function Le(e,t,n,r){let a=[q(e,t,n)];for(let o=0;o<e.length;o++)t[o]>n&&t[o]<r&&a.push({...e[o]});return a.push(q(e,t,r)),a}function rt(e){return e.length*6.2+8}function ot(e,t){return e.x0<t.x1&&e.x1>t.x0&&e.y0<t.y1&&e.y1>t.y0}function Me(e,t){return e.x1<=0||e.x0>=t.width||e.y1<=0||e.y0>=t.height}function at(e,t){return e.x0>=0&&e.x1<=t.width&&e.y0>=0&&e.y1<=t.height}function st(e,t=[]){let n=[...t];return r=>Me(r,e)||n.some(a=>ot(a,r))?!1:(n.push(r),!0)}function ln(e,t,n){let r=[],o=(s,c)=>{let u=rt(c),d=s.y>t.height/2?-1:1;for(let f=0;f<=(s.stack??0);f++){let b=s.y+d*f*19,i={x0:s.x-u/2,x1:s.x+u/2,y0:b-11-4,y1:b+4};if(Me(i,t))return;if(at(i,t)&&n(i))return{...s,text:c,y:b,w:u}}};for(let s of e){let c=o(s,s.text)??(s.fallback===void 0?void 0:o(s,s.fallback));c&&r.push(c)}return r}var ct=26,it=4e4,ut=8,dt=8,mt=5.7,lt=6,pt=13,H=3,X=2;function z(e){return(e.length*mt+lt+H)/2}var T=(pt+H)/2,ft=z("1 bp");function k(e,t,n){return{x0:t-e,x1:t+e,y0:n-T,y1:n+T}}function yn(e,t){return{x0:6,x1:6+e.length*6.2+8+H,y0:t-8-H/2,y1:t+8+H/2}}function F(e,t,n){return n<t?e:Math.min(Math.max(e,t),n)}function _e(e){return String(e).replace(/\B(?=(\d{3})+$)/g,",")}function Be(e){return e>=1e6?`${+(e/1e6).toFixed(1)} Mb`:e>=1e3?`${+(e/1e3).toFixed(1)} kb`:`${e} bp`}function Ae(e){return`${Be(e)} del`}function ht(e,t,n,r){let a=e[0],o=e[e.length-1],s=(t.x-(a.x0+o.x1)/2)*n,c=(t.y-(a.y0+o.y1)/2)*r,u=Math.hypot(s,c);return u===0?{x:0,y:-1}:{x:s/u,y:c/u}}function xt(e,t){return Math.abs(t.x)*(e.x1-e.x0)/2+Math.abs(t.y)*(e.y1-e.y0)/2}function bt(e,t){let n=(e.x1-e.x0)/2,r=(e.y1-e.y0)/2;return Math.min(t.x===0?1/0:n/Math.abs(t.x),t.y===0?1/0:r/Math.abs(t.y))}function yt(e,t,n){let r=0;for(let a=1;a<e.length;a++){let o=e[a-1],s=e[a];r+=Math.hypot((s.x-o.x)*t,(s.y-o.y)*n)}return r}function gt(e,t){let n=1/0,r=1/0,a=-1/0,o=-1/0;for(let s of e)for(let c of t[s]??[])n=Math.min(n,c.x),a=Math.max(a,c.x),r=Math.min(r,c.y),o=Math.max(o,c.y);return n===1/0?void 0:{minX:n,minY:r,maxX:a,maxY:o}}var Ee=new WeakMap;function Nt(e,t){let n=Ee.get(e);if(n?.nodeLengths===t)return n.order;let r=Object.entries(e).filter(([a,o])=>o.length>0&&t.has(a)).sort(([a],[o])=>t.get(o)-t.get(a));return Ee.set(e,{nodeLengths:t,order:r}),r}var Se=new WeakMap;function Lt(e,t,n,r){let{scaleX:a,scaleY:o}=n,s=Se.get(e);if(s?.deletions===t&&s.scaleX===a&&s.scaleY===o&&s.version===r)return s.arcs;let c=[];for(let u of[...t].sort((d,f)=>f.bp-d.bp)){let d=ye(e,u,n),f=d?he(d):void 0;if(d&&f){let{minX:b,minY:i,maxX:h,maxY:m}=xe(d);c.push({deletion:u,curves:d,apex:f,extent:Math.max((h-b)*a,(m-i)*o)})}}return Se.set(e,{deletions:t,scaleX:a,scaleY:o,version:r,arcs:c}),c}function gn({nodePositions:e,nodeLengths:t,deletions:n,alleleDeletions:r,axis:a,translateX:o,translateY:s,width:c,height:u,version:d=0}){let{scaleX:f,scaleY:b}=a,i=[],h=[];for(let{deletion:p,curves:x,apex:y,extent:A}of Lt(e,n,a,d))if(A>=ct){let L=Ae(p.bp),N=z(L),g=k(N,0,0),E=y.x*f+o,M=y.y*b+s,S=A>=N*2/X,_=ht(x,y,f,b),G=xt(g,_)+dt,w=S?E:F(E+_.x*G,N,c-N),P=S?M:F(M+_.y*G,T,u-T),B=Math.hypot(w-E,P-M),I;if(B>0){let O={x:(w-E)/B,y:(P-M)/B},C=bt(g,O);I={arcX:E,arcY:M,labelX:w-O.x*C,labelY:P-O.y*C}}i.push({label:{key:`del:${p.edgeIndex}`,text:L,x:w,y:P,kind:"deletion",leader:I},box:k(N,w,P)})}let m=new Set,l=[...r??[]].sort((p,x)=>x.bp-p.bp);for(let p of l){let x=gt(p.nodeIds,e);if(!x)continue;let y=Math.max(x.minX*f+o,0),A=Math.min(x.maxX*f+o,c),L=Math.max(x.minY*b+s,0),N=Math.min(x.maxY*b+s,u);if(A<y||N<L)continue;let g=Math.max(A-y,N-L),E=Ae(p.bp),M=z(E);if(g>=M*2/X){for(let G of p.nodeIds)m.add(G);let S=F((y+A)/2,M,c-M),_=F((L+N)/2,T,u-T);i.push({label:{key:`alleledel:${p.nodeIds.join(",")}`,text:E,x:S,y:_,kind:"deletion"},box:k(M,S,_)})}}for(let[p,x]of Nt(e,t)){if(m.has(p))continue;let{x:y,y:A}=Ne(x),L=A*b+s;if(L+T<=0||L-T>=u)continue;let N=yt(x,f,b);if(N<ft*2/X)continue;let g=Be(t.get(p)),E=z(g);if(N>=E*2/X){let M=y*f+o;h.push({label:{key:`node:${p}`,text:g,x:M,y:L,kind:"node"},box:k(E,M,L)})}}return{deletions:i,nodes:h}}function Nn(e,t){return Math.max(ut,Math.floor(e*t/it))}function Ln(e,t,n=1/0){let r=[];for(let{label:a,box:o}of e){if(r.length>=n)break;t(o)&&r.push(a)}return r}var At=/:(\d+)-\d+$/;function $(e){let t=At.exec(e);return t?{name:e.slice(0,t.index),start:+t[1]}:{name:e,start:0}}function Sn(e,t){let n=[],r=new Map;for(let a of e){let o=se(a.name),s=a.start;for(let c of a.steps){let u={path:a.name,sample:o,start:s,strand:c.strand},d=r.get(c.id);d?d.push(u):r.set(c.id,[u]),s+=t(c.id)}n.push({name:a.name,sample:o,start:a.start,length:s-a.start})}return{anchorPaths:n,pathVisits:r}}function Et(e,t){return e.find(r=>r.sample===t||r.name===t)??e[0]}var St=1;function _t(e,t,n){let r=e;if(t&&t.length>0){let a=t.find(o=>o.path===n)??t[0];r={...e,stable:{refName:a.path,start:a.start,rank:a.path===n?0:St,strand:a.strand},samples:[...new Set(t.map(o=>o.sample))].sort()}}return r}function Bt(e,t){let{anchorPaths:n,pathVisits:r}=e,a=n&&r?Et(n,t):void 0;return a&&r?{...e,nodes:e.nodes.map(o=>_t(o,r.get(o.name),a.name)),anchoredBy:"paths",referencePath:a.name}:e}function _n(e,t){return e.anchoredBy==="tags"?e:Bt(e,t)}function Bn(e,t){if(!e.anchorPaths)return;let n=new Map(e.nodes.map(o=>[o.id,o.length])),r=(o,s=o.length)=>{let c=0;for(let u=0;u<s;u++)c+=n.get(o[u])??0;return c},a=new Map;for(let o of e.paths??[]){let s=$(o.name).name;a.set(s,[...a.get(s)??[],o])}return e.anchorPaths.map(o=>{let s=a.get(o.name),c=s?.length===1?s[0]:void 0,u=c&&t.get(c.name);return c&&u?{...o,start:o.start+r(c.nodeIds,u.first),length:r(u.nodeIds)}:o})}function Cn(e){let t=0;for(let n=0;n<e.length;n++)t=e.charCodeAt(n)+((t<<5)-t);return Math.abs(t%360)}function wt(e,t){return e*360/t}var Pt=.7,Gt=.5,Ot=16;function In(e){return e>0&&e<=Ot}function Ct(e,t){return`hsl(${wt(e,t)}, ${Pt*100}%, ${Gt*100}%)`}function Tn(e,t){return`hsl(0, 0%, ${t>1?25+45*e/(t-1):45}%)`}function It(e){let t=$(e).name.split("#"),n=t.join("#");if(t.length>=3&&ce(t[0])){let r=t.slice(2).join("#");return[r,r,n]}return[t[0],t.slice(0,2).join("#"),n]}function Tt(e,t){let{start:n}=$(e);return t.map(r=>`${r} @${_e(n)}`)}function Rn(e,t){let n=new Map;e.forEach((u,d)=>{n.has(u.name)||n.set(u.name,d)});let r=[...n].map(([u,d])=>({name:u,i:d})),a=r.map(u=>It(u.name)),o=[0,1,2].flatMap(u=>[r.map((d,f)=>a[f][u]),r.map((d,f)=>Tt(d.name,a[f])[u])]),c=o.find(u=>new Set(u).size===r.length)??o.at(-1);return r.map(({name:u,i:d},f)=>({name:u,label:c[f],color:t?.[d]??Ct(d,e.length)}))}function Dn(e,t){return Math.max(e.nodeLengthPerMegabase*t/1e6,e.minimumNodeLength)}function Rt(e,t=5){let r=e.nodes.reduce((o,s)=>o+s.length,0)/1e6,a=Math.max(e.nodes.length*40,500);return{nodeLengthPerMegabase:r>0?a/r:1e4,minimumNodeLength:Math.max(5,t),edgeLength:5,nodeSegmentLength:20}}var D={power:1,effect:1};function vt(e){return e.power===1&&e.effect===1}function Dt(e,t){let n=e.nodes.length,r=e.nodes.reduce((s,c)=>s+c.length,0),a=n>0?r/n:0,o=n>0?Math.max(n*40,500)/n:40;return s=>{if(a<=0)return o;let c=(s/a)**t.power;return Math.max(o*((c-1)*t.effect+1),5)}}var we=1e3,Ht={law:D,minNodeLength:0};function Hn(e,t=Ht){let{law:n,minNodeLength:r}=t,a=Rt(e,r);if(vt(n))return{nodes:e.nodes,opts:a};let o=Dt(e,n);return{nodes:e.nodes.map(s=>({...s,length:Math.round(o(s.length)*we)})),opts:{...a,nodeLengthPerMegabase:1e6/we,minimumNodeLength:5}}}var Pe=[{value:"auto",label:"Proportional",description:"Bandage's own scale: a node draws proportional to its length, so a 1 bp allele is a speck.",law:D,minNodeFactor:0},{value:"open",label:"Open bubbles",description:"Give every allele a drawn length, so a bubble reads as two arms rather than a knot.",law:D,minNodeFactor:2.5},{value:"wide",label:"Wide bubbles",description:"As open, spread further. Best on a window of a dozen bubbles.",law:D,minNodeFactor:10},{value:"compress",label:"Compress lengths",description:"Pull the longest and shortest nodes towards the graph\u2019s mean, so a cut spanning kb and bp fits one pane.",law:{power:.5,effect:.5},minNodeFactor:0}],Fn=Pe.map(e=>e.value);function zn(e){let t=Pe.find(n=>n.value===e);return{law:t?.law??D,minNodeLength:(t?.minNodeFactor??0)*40}}var kt=[{value:"auto",label:"Auto"},{value:"uniform",label:"Uniform"},{value:"random",label:"Random"},{value:"rainbow",label:"Rainbow"},{value:"depth",label:"Depth"},{value:"node-length",label:"Node Length"},{value:"stable-rank",label:"Stable rank"},{value:"reference-position",label:"Reference position"},{value:"grey",label:"Grey"}],Wn=kt.map(e=>e.value);function Yn(e,t){return e!=="auto"?e:t?.anchoredBy?"reference-position":"uniform"}var Ft=[{value:"depth",label:"By depth",description:"Thicker the more paths carry a node, on the square root of its depth against the mean. A graph with one depth everywhere draws uniform."},{value:"uniform",label:"Uniform",description:"Every node the same thickness."}],jn=Ft.map(e=>e.value),zt=.3,Ge=3;function $t(e){let t=0,n=0;for(let r of e.nodes)t+=r.depth*r.length,n+=r.length;return n>0?t/n:0}function Wt(e,t){return!(t>0)||!(e.depth>0)?1:Math.min(Ge,Math.max(zt,Math.sqrt(e.depth/t)))}function Yt(e,t,n,r){return t*(n==="depth"?Wt(e,r):1)}function Ut(e,t){return e*(t==="depth"?Ge:1)}function Vn(e,t,n,r){let a=e?$t(e):0;return{maxHalfWidthPx:Ut(n,r)/2,halfWidthPx:o=>{let s=t?.get(o);return s?Yt(s,n,r,a)/2:n/2}}}export{$ as a,Sn as b,Et as c,Bt as d,_n as e,Bn as f,Kt as g,xe as h,Jt as i,Qt as j,be as k,Zt as l,en as m,V as n,Qe as o,on as p,cn as q,un as r,dn as s,st as t,ln as u,yn as v,_e as w,Be as x,gn as y,Nn as z,Ln as A,Cn as B,wt as C,Pt as D,Gt as E,Ot as F,In as G,Ct as H,Tn as I,Rn as J,Dn as K,Hn as L,Pe as M,Fn as N,zn as O,kt as P,Wn as Q,Yn as R,Ft as S,jn as T,$t as U,Yt as V,Vn as W,jt as X};
-//# sourceMappingURL=chunk-ECKLYJWP.js.map