jbrowse-plugin-graphgenomeviewer 8.0.0 → 8.0.2

package/dist/chunks/renderSvg-YNA5VK6A.js

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+import{A as N,C as I,d as H,g as _,h as A,i as W,k as X,l as j,m as z,n as F,s as O,t as E,v as Y,x as J,y as K}from"./chunk-JOYKGTDE.js";import{Db as R,Fb as B,Nb as D,q as S,r as M}from"./chunk-ZGTG74GE.js";import"./chunk-XWCLYB5C.js";import"./chunk-XB5KC2EZ.js";import{o as P}from"./chunk-2V75YPTT.js";import"./chunk-CJAV55QB.js";import"./chunk-FY7X6253.js";import"./chunk-X7YIGIYW.js";import"./chunk-JMRW3IGK.js";import"./chunk-5RHNR3TH.js";import"./chunk-IKJZPPOA.js";import"./chunk-3WG3GF2A.js";import"./chunk-NIEZKWQV.js";import{a as k,b as e,c as f}from"./chunk-JMBDTNUR.js";var m=JBrowseExports["@jbrowse/display-kit/renderDisplaySvg"],rt=t=>m!=null&&t in Object(m)?m[t]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+t+"' from '@jbrowse/display-kit/renderDisplaySvg' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:t});var U=rt("renderDisplaySvg");var dt=m&&m.__esModule?m.default:m;var w=JBrowseExports["@jbrowse/core/util/paintLayer"],ot=t=>w!=null&&t in Object(w)?w[t]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+t+"' from '@jbrowse/core/util/paintLayer' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:t}),C=ot("PaintLayer"),yt=w&&w.__esModule?w.default:w;var L={fontFamily:"sans-serif",fontSize:11},Z=16,at=2,V=t=>t;function q({model:t,lift:a,drawPaths:i,width:n,height:r,rasterize:l}){let o=t.buildDrawing(a,i);if(!o)return null;let s=l?at:1,c=l?void 0:R(n,r),y=c?.canvas??document.createElement("canvas");c||(y.width=Math.round(n*s),y.height=Math.round(r*s));let{scaleX:b,scaleY:x,translateX:d,translateY:g}=t.screenTransform,h=new B(y);return h.uploadGeometry(o.batch),h.updateTransform({scaleX:b*s,scaleY:x*s,translateX:d*s,translateY:g*s,dpr:s}),h.render([0,0,0,0]),c?e("svg",{width:n,height:r,overflow:"hidden",children:e("g",{dangerouslySetInnerHTML:{__html:c.markup()}})}):e("image",{width:n,height:r,href:y.toDataURL("image/png")})}function it(t,a,i,n){let r=n?0:E,l=t.toUpperCase();return{key:a,width:l.length*P,height:i+r,draw:o=>e("text",{fontFamily:"sans-serif",fontSize:9.5,fontWeight:600,letterSpacing:"0.06em",x:o,y:r,fill:O,children:l},a)}}function $(t,a,i=Z,n){if(!t.swatch)return{key:t.key,width:t.label.length*P,height:i,draw:c=>e("text",{...L,x:c,y:0,fill:"#666",children:t.label},t.key)};let r=t.swatch,l=n??_(r),o=n===void 0?0:n+5,s=(t.strong??"")+t.label;return{key:t.key,width:Math.max(l+5+s.length*P,o+(t.under?.length??0)*P),height:t.under?i*2:i,draw:c=>f("g",{...L,children:[e(F,{swatch:r,x:c+(l-_(r))/2,id:a}),f("text",{x:c+l+5,y:0,children:[t.strong?e("tspan",{fontWeight:"bold",children:t.strong}):null,t.label]}),t.under?e("text",{x:c+o,y:i,children:t.under}):null]},t.key)}}function st({model:t,idPrefix:a}){let i=z(t);if(i.length===0)return null;let n=i.flatMap(p=>p.rows),r=W(n),l=A(n),o=i.flatMap(({testid:p,rows:u,heading:v,spaced:G},tt)=>[...v?[it(v,`${p}-heading`,r,tt===0)]:[],...G?[{key:`${p}-gap`,width:0,height:E,draw:()=>null}]:[],...u.map((et,nt)=>$(et,`${a}-${p}-${nt}`,r,l))]),s=6,c=o.reduce((p,u)=>Math.max(p,u.width),-1/0)+s*2,y=o.reduce((p,u)=>p+u.height,0)+s,x=t.paneWidth-D-c+s,d=D+t.referenceStripZonePx,g=[],h=d+s/2+r/2+4;for(let p of o)g.push({row:p,y:h}),h+=p.height;return f("g",{"data-testid":"graph-svg-keys",children:[e("rect",{x:x-s,y:d,width:c,height:y,rx:3,fill:"#fff"}),g.map(({row:p,y:u})=>e("g",{transform:`translate(0 ${u})`,children:p.draw(x)},p.key))]})}function Q({x:t,y:a,text:i,fontSize:n,anchor:r,bold:l}){let o=i.length*n*.56+6,s=r==="middle"?t-o/2:t-3;return f(k,{children:[e("rect",{x:s,y:a-n*.65,width:o,height:n*1.3,rx:3,fill:"#fff",fillOpacity:.8}),e("text",{x:t,y:a+n*.35,textAnchor:r,fontSize:n,fontWeight:l?600:void 0,fill:"#18181c",children:i})]})}function lt({model:t}){return e("g",{fontFamily:L.fontFamily,children:t.overlayLabels.sizes.map(({key:a,text:i,x:n,y:r,kind:l,leader:o})=>f("g",{children:[o?e("line",{x1:o.arcX,y1:o.arcY,x2:o.labelX,y2:o.labelY,stroke:"#18181c"}):null,e(Q,{x:n,y:r,text:i,fontSize:10,anchor:"middle",bold:l==="deletion"})]},a))})}function pt({model:t}){return e("g",{fontFamily:L.fontFamily,children:t.visibleRowLabels.map(({label:a,y:i,top:n})=>e(Q,{x:10,y:n,text:a,fontSize:11,anchor:"start"},i))})}function ct({model:t,rasterize:a,idPrefix:i}){let n=t.facetPanels,r=t.facetGrid,l=t.facetPlacement;if(!n||!r||!l)return null;let{columns:o,width:s,height:c}=r,y=r.total+S+14,b=j(t).map((d,g)=>$(d,`${i}-facet-key-${g}`)),x=b.map((d,g)=>b.slice(0,g).reduce((h,p)=>h+p.width+14,6));return f(k,{children:[e("g",{transform:`translate(0 ${y})`,children:b.map((d,g)=>d.draw(x[g]))}),n.map((d,g)=>{let h=l.cells[g],p=h%o*(s+S),u=Math.floor(h/o)*(M+c+S),v=d.walks[0],G=$(X(t,v),`${i}-facet-${g}`);return f("g",{transform:`translate(${p} ${u})`,children:[e("g",{transform:`translate(0 ${Z-2})`,children:G.draw(6)}),e("g",{transform:`translate(0 ${M})`,children:e(q,{model:t,lift:d,drawPaths:!1,width:s,height:c,rasterize:a})})]},v.name)})]})}function T({model:t,rasterize:a=!1,idPrefix:i}){let n=t.paneWidth,r=t.canvasHeight,l=!!t.layoutResult?.tubeMap,o={rasterizeLayers:a};return f("g",{"data-testid":"graph-pane-svg",children:[t.facetPanels?e(ct,{model:t,rasterize:a,idPrefix:i}):l?e(C,{width:n,height:r,opts:o,paint:s=>{N(V(s),t,{highlightNode:null})}}):e(q,{model:t,lift:t.drawnHighlight,drawPaths:t.effectiveDrawPaths,width:n,height:r,rasterize:a}),t.facetPanels?null:f(k,{children:[e(H,{model:t}),e(Y,{model:t}),e(lt,{model:t}),e(J,{model:t}),e(I,{model:t,vector:!0}),e(pt,{model:t})]}),t.referenceStripShown?e(C,{width:n,height:r,opts:o,paint:s=>{K(V(s),t,{lit:void 0,dpr:1})}}):null,t.facetPanels?null:e(st,{model:t,idPrefix:i})]})}function gt({model:t,opts:a}){return e(T,{model:t,rasterize:!!a?.rasterizeLayers,idPrefix:`graph-${t.id}`})}function At(t,a){return U(t,a,gt)}export{At as renderGraphTrackSvg};
+//# sourceMappingURL=renderSvg-YNA5VK6A.js.map

package/dist/chunks/renderSvg-YNA5VK6A.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["host:@jbrowse/display-kit/renderDisplaySvg", "host:@jbrowse/core/util/paintLayer", "../../src/GraphGenomeView/components/PaneSvg.tsx", "../../src/LinearGraphDisplay/renderSvg.tsx"],
+  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/display-kit/renderDisplaySvg\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-kit/renderDisplaySvg\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const SvgLegend = /* @__PURE__ */ read(\"SvgLegend\")\nexport const SvgPinnedHighlight = /* @__PURE__ */ read(\"SvgPinnedHighlight\")\nexport const SvgYAxis = /* @__PURE__ */ read(\"SvgYAxis\")\nexport const renderDisplaySvg = /* @__PURE__ */ read(\"renderDisplaySvg\")\nexport const svgLegendGutterWidth = /* @__PURE__ */ read(\"svgLegendGutterWidth\")\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/core/util/paintLayer\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/core/util/paintLayer\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const PaintLayer = /* @__PURE__ */ read(\"PaintLayer\")\nexport default host && host.__esModule ? host.default : host", "import { FACET_GAP_PX, FACET_TITLE_PX } from '@jbrowse/bandage-core/facetGrid'\nimport { LEGEND_INSET_PX } from '@jbrowse/bandage-core/labelLayout'\nimport { LABEL_CHAR_PX } from '@jbrowse/bandage-core/overlayLabels'\nimport { Canvas2DRenderer } from '@jbrowse/bandage-core/renderer/Canvas2DRenderer'\nimport { svgCanvas } from '@jbrowse/bandage-core/renderer/svgCanvas'\nimport { PaintLayer } from '@jbrowse/core/util/paintLayer'\n\nimport BubbleHalos from './BubbleHalos'\nimport GenePins from './GenePins'\nimport LabelLayer from './LabelLayer'\nimport { SvgSwatch } from './LegendSwatch'\nimport { paintReferenceStrip } from './ReferenceStripOverlay'\nimport { paintTubeMap } from './TubeMapOverlay'\nimport WalkRowsOverlay from './WalkRowsOverlay'\nimport { HEADING_GAP_PX, HEADING_INK } from './legendStyles'\nimport {\n  facetKeyRows,\n  legendSections,\n  rowPitch,\n  swatchColumn,\n  swatchWidth,\n  walkKeyRow,\n} from '../legendSections'\n\nimport type { LegendRow } from '../legendSections'\nimport type { GraphPaneModel } from '../model'\nimport type { WalkLift } from '@jbrowse/bandage-core/walkHighlight'\nimport type { Ctx2D } from '@jbrowse/core/util/paintLayer'\n\nconst FONT = { fontFamily: 'sans-serif', fontSize: 11 }\nconst ROW_PX = 16\nconst RASTER_SCALE = 2\n\nconst asCanvasCtx = (ctx: Ctx2D) => ctx as CanvasRenderingContext2D\n\n// The drawing's nodes and edges through the pane's own transform, so the\n// export lines up with the linear view's ruler wherever the screen does\nfunction Body({\n  model,\n  lift,\n  drawPaths,\n  width,\n  height,\n  rasterize,\n}: {\n  model: GraphPaneModel\n  lift: WalkLift | undefined\n  drawPaths: boolean\n  width: number\n  height: number\n  rasterize: boolean\n}) {\n  const built = model.buildDrawing(lift, drawPaths)\n  if (!built) {\n    return null\n  }\n  const k = rasterize ? RASTER_SCALE : 1\n  const vector = rasterize ? undefined : svgCanvas(width, height)\n  const canvas = vector?.canvas ?? document.createElement('canvas')\n  if (!vector) {\n    canvas.width = Math.round(width * k)\n    canvas.height = Math.round(height * k)\n  }\n  const { scaleX, scaleY, translateX, translateY } = model.screenTransform\n  const renderer = new Canvas2DRenderer(canvas)\n  renderer.uploadGeometry(built.batch)\n  renderer.updateTransform({\n    scaleX: scaleX * k,\n    scaleY: scaleY * k,\n    translateX: translateX * k,\n    translateY: translateY * k,\n    dpr: k,\n  })\n  renderer.render([0, 0, 0, 0])\n  return vector ? (\n    <svg width={width} height={height} overflow=\"hidden\">\n      <g dangerouslySetInnerHTML={{ __html: vector.markup() }} />\n    </svg>\n  ) : (\n    <image width={width} height={height} href={canvas.toDataURL('image/png')} />\n  )\n}\n\ninterface KeyRow {\n  key: string\n  width: number\n  height: number\n  draw: (left: number) => React.ReactNode\n}\n\n// A group's name in small capitals, a gap below the rows before it\nfunction svgHeading(\n  heading: string,\n  key: string,\n  pitch: number,\n  first: boolean,\n): KeyRow {\n  const gap = first ? 0 : HEADING_GAP_PX\n  const text = heading.toUpperCase()\n  return {\n    key,\n    width: text.length * LABEL_CHAR_PX,\n    height: pitch + gap,\n    draw: left => (\n      <text\n        key={key}\n        fontFamily=\"sans-serif\"\n        fontSize={9.5}\n        fontWeight={600}\n        letterSpacing=\"0.06em\"\n        x={left}\n        y={gap}\n        fill={HEADING_INK}\n      >\n        {text}\n      </text>\n    ),\n  }\n}\n\n// A legend row as the screen lays it out: its swatch, then its words, the\n// line under it if any; a note is grey words alone. A `column` is the slot\n// every swatch of the key is centred in.\nfunction svgRow(\n  row: LegendRow,\n  id: string,\n  pitch = ROW_PX,\n  column?: number,\n): KeyRow {\n  if (!row.swatch) {\n    return {\n      key: row.key,\n      width: row.label.length * LABEL_CHAR_PX,\n      height: pitch,\n      draw: left => (\n        <text key={row.key} {...FONT} x={left} y={0} fill=\"#666\">\n          {row.label}\n        </text>\n      ),\n    }\n  }\n  const swatch = row.swatch\n  const sw = column ?? swatchWidth(swatch)\n  const indent = column === undefined ? 0 : column + 5\n  const words = (row.strong ?? '') + row.label\n  return {\n    key: row.key,\n    width: Math.max(\n      sw + 5 + words.length * LABEL_CHAR_PX,\n      indent + (row.under?.length ?? 0) * LABEL_CHAR_PX,\n    ),\n    height: row.under ? pitch * 2 : pitch,\n    draw: left => (\n      <g key={row.key} {...FONT}>\n        <SvgSwatch\n          swatch={swatch}\n          x={left + (sw - swatchWidth(swatch)) / 2}\n          id={id}\n        />\n        <text x={left + sw + 5} y={0}>\n          {row.strong ? <tspan fontWeight=\"bold\">{row.strong}</tspan> : null}\n          {row.label}\n        </text>\n        {row.under ? (\n          <text x={left + indent} y={pitch}>\n            {row.under}\n          </text>\n        ) : null}\n      </g>\n    ),\n  }\n}\n\n// The screen's legend panel, section by section\nfunction Keys({\n  model,\n  idPrefix,\n}: {\n  model: GraphPaneModel\n  idPrefix: string\n}) {\n  const sections = legendSections(model)\n  if (sections.length === 0) {\n    return null\n  }\n  const all = sections.flatMap(section => section.rows)\n  const pitch = rowPitch(all)\n  const column = swatchColumn(all)\n  const rows = sections.flatMap(({ testid, rows, heading, spaced }, s) => [\n    ...(heading\n      ? [svgHeading(heading, `${testid}-heading`, pitch, s === 0)]\n      : []),\n    ...(spaced\n      ? [\n          {\n            key: `${testid}-gap`,\n            width: 0,\n            height: HEADING_GAP_PX,\n            draw: () => null,\n          },\n        ]\n      : []),\n    ...rows.map((row, i) =>\n      svgRow(row, `${idPrefix}-${testid}-${i}`, pitch, column),\n    ),\n  ])\n  const pad = 6\n  const boxWidth =\n    rows.reduce((max, r) => Math.max(max, r.width), -Infinity) + pad * 2\n  const boxHeight = rows.reduce((sum, r) => sum + r.height, 0) + pad\n  const right = model.paneWidth - LEGEND_INSET_PX\n  const left = right - boxWidth + pad\n  const top = LEGEND_INSET_PX + model.referenceStripZonePx\n  const placed: { row: KeyRow; y: number }[] = []\n  let y = top + pad / 2 + pitch / 2 + 4\n  for (const row of rows) {\n    placed.push({ row, y })\n    y += row.height\n  }\n  return (\n    <g data-testid=\"graph-svg-keys\">\n      <rect\n        x={left - pad}\n        y={top}\n        width={boxWidth}\n        height={boxHeight}\n        rx={3}\n        fill=\"#fff\"\n      />\n      {placed.map(({ row, y }) => (\n        <g key={row.key} transform={`translate(0 ${y})`}>\n          {row.draw(left)}\n        </g>\n      ))}\n    </g>\n  )\n}\n\n// Words on a pale rounded backing, as the screen's labels sit\nfunction Chip({\n  x,\n  y,\n  text,\n  fontSize,\n  anchor,\n  bold,\n}: {\n  x: number\n  y: number\n  text: string\n  fontSize: number\n  anchor: 'start' | 'middle'\n  bold?: boolean\n}) {\n  const w = text.length * fontSize * 0.56 + 6\n  const left = anchor === 'middle' ? x - w / 2 : x - 3\n  return (\n    <>\n      <rect\n        x={left}\n        y={y - fontSize * 0.65}\n        width={w}\n        height={fontSize * 1.3}\n        rx={3}\n        fill=\"#fff\"\n        fillOpacity={0.8}\n      />\n      <text\n        x={x}\n        y={y + fontSize * 0.35}\n        textAnchor={anchor}\n        fontSize={fontSize}\n        fontWeight={bold ? 600 : undefined}\n        fill=\"#18181c\"\n      >\n        {text}\n      </text>\n    </>\n  )\n}\n\n// The node and deletion lengths written on the drawing, with their leaders\nfunction SizeLabels({ model }: { model: GraphPaneModel }) {\n  return (\n    <g fontFamily={FONT.fontFamily}>\n      {model.overlayLabels.sizes.map(({ key, text, x, y, kind, leader }) => (\n        <g key={key}>\n          {leader ? (\n            <line\n              x1={leader.arcX}\n              y1={leader.arcY}\n              x2={leader.labelX}\n              y2={leader.labelY}\n              stroke=\"#18181c\"\n            />\n          ) : null}\n          <Chip\n            x={x}\n            y={y}\n            text={text}\n            fontSize={10}\n            anchor=\"middle\"\n            bold={kind === 'deletion'}\n          />\n        </g>\n      ))}\n    </g>\n  )\n}\n\nfunction RowLabels({ model }: { model: GraphPaneModel }) {\n  return (\n    <g fontFamily={FONT.fontFamily}>\n      {model.visibleRowLabels.map(({ label, y, top }) => (\n        <Chip\n          key={y}\n          x={10}\n          y={top}\n          text={label}\n          fontSize={11}\n          anchor=\"start\"\n        />\n      ))}\n    </g>\n  )\n}\n\n// Each lifted walk in a panel of its own, its key as the panel's title\nfunction Facets({\n  model,\n  rasterize,\n  idPrefix,\n}: {\n  model: GraphPaneModel\n  rasterize: boolean\n  idPrefix: string\n}) {\n  const panels = model.facetPanels\n  const grid = model.facetGrid\n  const place = model.facetPlacement\n  if (!panels || !grid || !place) {\n    return null\n  }\n  const { columns, width, height } = grid\n  const keyY = grid.total + FACET_GAP_PX + 14\n  const key = facetKeyRows(model).map((row, i) =>\n    svgRow(row, `${idPrefix}-facet-key-${i}`),\n  )\n  const keyX = key.map((_, i) =>\n    key.slice(0, i).reduce((x, row) => x + row.width + 14, 6),\n  )\n  return (\n    <>\n      <g transform={`translate(0 ${keyY})`}>\n        {key.map((row, i) => row.draw(keyX[i]!))}\n      </g>\n      {panels.map((lift, i) => {\n        const cell = place.cells[i]!\n        const x = (cell % columns) * (width + FACET_GAP_PX)\n        const y =\n          Math.floor(cell / columns) * (FACET_TITLE_PX + height + FACET_GAP_PX)\n        const walk = lift.walks[0]!\n        const title = svgRow(walkKeyRow(model, walk), `${idPrefix}-facet-${i}`)\n        return (\n          <g key={walk.name} transform={`translate(${x} ${y})`}>\n            <g transform={`translate(0 ${ROW_PX - 2})`}>{title.draw(6)}</g>\n            <g transform={`translate(0 ${FACET_TITLE_PX})`}>\n              <Body\n                model={model}\n                lift={lift}\n                drawPaths={false}\n                width={width}\n                height={height}\n                rasterize={rasterize}\n              />\n            </g>\n          </g>\n        )\n      })}\n    </>\n  )\n}\n\n// The pane as the screen draws it, for the linear view's SVG export: the\n// canvas's ink, the tube map and reference strip painters, and the SVG\n// overlays the screen mounts over them. Hover and selection are left out.\nexport default function PaneSvg({\n  model,\n  rasterize = false,\n  idPrefix,\n}: {\n  model: GraphPaneModel\n  rasterize?: boolean\n  idPrefix: string\n}) {\n  const width = model.paneWidth\n  const height = model.canvasHeight\n  const tubeMap = !!model.layoutResult?.tubeMap\n  const opts = { rasterizeLayers: rasterize }\n  return (\n    <g data-testid=\"graph-pane-svg\">\n      {model.facetPanels ? (\n        <Facets model={model} rasterize={rasterize} idPrefix={idPrefix} />\n      ) : tubeMap ? (\n        <PaintLayer\n          width={width}\n          height={height}\n          opts={opts}\n          paint={ctx => {\n            paintTubeMap(asCanvasCtx(ctx), model, { highlightNode: null })\n          }}\n        />\n      ) : (\n        <Body\n          model={model}\n          lift={model.drawnHighlight}\n          drawPaths={model.effectiveDrawPaths}\n          width={width}\n          height={height}\n          rasterize={rasterize}\n        />\n      )}\n      {/* in the screen's stacking order, bottom first */}\n      {model.facetPanels ? null : (\n        <>\n          <BubbleHalos model={model} />\n          <GenePins model={model} />\n          <SizeLabels model={model} />\n          <LabelLayer model={model} />\n          <WalkRowsOverlay model={model} vector />\n          <RowLabels model={model} />\n        </>\n      )}\n      {model.referenceStripShown ? (\n        <PaintLayer\n          width={width}\n          height={height}\n          opts={opts}\n          paint={ctx => {\n            paintReferenceStrip(asCanvasCtx(ctx), model, {\n              lit: undefined,\n              dpr: 1,\n            })\n          }}\n        />\n      ) : null}\n      {model.facetPanels ? null : <Keys model={model} idPrefix={idPrefix} />}\n    </g>\n  )\n}\n", "import { renderDisplaySvg } from '@jbrowse/display-kit/renderDisplaySvg'\n\nimport PaneSvg from '../GraphGenomeView/components/PaneSvg'\n\nimport type { LinearGraphDisplayModel } from './model'\nimport type { LgvSvgBodyProps } from '@jbrowse/display-kit/renderDisplaySvg'\nimport type { ExportSvgDisplayOptions } from '@jbrowse/display-kit/types'\n\nfunction GraphTrackSvgBody({\n  model,\n  opts,\n}: LgvSvgBodyProps<LinearGraphDisplayModel>) {\n  return (\n    <PaneSvg\n      model={model}\n      rasterize={!!opts?.rasterizeLayers}\n      idPrefix={`graph-${model.id}`}\n    />\n  )\n}\n\nexport function renderGraphTrackSvg(\n  model: LinearGraphDisplayModel,\n  opts?: ExportSvgDisplayOptions,\n) {\n  return renderDisplaySvg(model, opts, GraphTrackSvgBody)\n}\n"],
+  "mappings": 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+}

package/dist/jbrowse-plugin-graphgenomeviewer.esm.js

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ye=JBrowseExports["@jbrowse/core/svg/svgReady"],Ai=e=>ye!=null&&e in Object(ye)?ye[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/svg/svgReady' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var Sa=Ai("computeSvgReady");var Fm=ye&&ye.__esModule?ye.default:ye;var ct=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var xa=ct&&ct.__esModule?ct.default:ct;var fe=JBrowseExports["@jbrowse/display-kit/plotMenu"],Pi=e=>fe!=null&&e in Object(fe)?fe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/plotMenu' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),Ra=Pi("editPlotMenuItems");var Vm=fe&&fe.__esModule?fe.default:fe;var we=JBrowseExports["@jbrowse/render-core/displayPhase"],Ta=e=>we!=null&&e in 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La({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>Ga({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted&&t.geometryPainted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({writeGrammar(o){for(let[r,n]of Object.entries(o))Vo(t,r,n)},setSubgraphContext(o){t.subgraphContext=o,t.dense=void 0},setSubgraphHaplotypes(o){t.subgraphHaplotypes=o,t.dense=void 0},setDense(o){t.dense=o},setHaplotypeNames(o){t.haplotypeNames=o},setMaxRegionBp(o){t.maxRegionBp=o},cut(){let o=t.cutRegion,r=t.sourceAdapter;if(!o||!r)return;let n=t.offReference(o);if(n){t.clearGraph(),t.setError(new Error(n));return}let a=t.cutTier==="coarse";return t.cutFoldBp=Math.round(no*(t.settledWindow?.bpPerPx??t.host?.bpPerPx??0)),t.cutSubgraph(r,o,{...t.cutOptions,tier:a?"coarse":void 0},t.cutFoldBp)}})).actions(t=>({recutAt(o){let r=t.tierAt(o.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=un(o,t.capFor(r),Q(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=Q(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||ro(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&cn(t.cutRegion,o,r)&&!t.foldDrifted(o.bpPerPx))return!1;let n=t.recutAt(o),a=t.recuts;return Promise.resolve(n).then(()=>{V(t)&&t.recuts===a&&St(t.error)&&this.refuseDenseCut(o)}),!0},refuseDenseCut(o){t.setDense(o),t.cutRegion=void 0,this.settleOn(t.settledWindow??o)},recut(){t.cutRegion?t.cut():t.settledWindow&&this.settleOn(t.settledWindow)},relayoutFrom(o){let r=t.host?Re(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||Q(o).cutMargins!==Q(t.chosenLayoutMode).cutMargins)?t.recutAt(r):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(o,r){try{let n=await x(t).rpcManager.call(ae(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});V(t)&&!r?.aborted&&t.setHaplotypeNames(n)}catch(n){r?.aborted||console.warn("[LinearGraphDisplay] no haplotype names",n)}}})).actions(t=>({stretchWithHost(o,r){let n=t.layoutBounds;if(!n||!t.followsHostView)return;t.viewportOwner==="fit"&&(t.viewportOwner="user");let a=o.bpPerPx/r.bpPerPx,i=t.translateY+t.scaleY*(n.minY+n.h/2);t.scale*=a,t.translateX=a*(t.translateX+o.offsetPx)-r.offsetPx,t.translateY=i-a*(i-t.translateY)}})).actions(t=>({forceLoad(){let o=t.settledWindow;o&&(t.setMaxRegionBp(Math.ceil(o.end-o.start)),t.settleOn(o))},afterAttach(){t.cutRegion&&!t.graph&&t.cut();let o;L(t,()=>{o?.abort()}),L(t,C(()=>{let n=t.sourceAdapter;return n&&nr(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new 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Vi=W("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:F("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:_("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:F("/path/to/graph.tier.links.bed.gz"),linksIndex:_("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),ji=W("RgfaTabixAdapter",{segmentsLocation:F("/path/to/graph.segs.bed.gz"),segmentsIndex:_("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:F("/path/to/graph.links.bed.gz"),linksIndex:_("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:F(""),walksIndex:_("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Me.stepBudget},walkByteBudget:{type:"integer",defaultValue:Me.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:Vi},{explicitlyTyped:!0,preProcessSnapshot:Hi}),Ca=ji;function so(e){e.addAdapterType(()=>new Z({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:Ca,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-HN2NLJJW.js").then(t=>t.default)}))}var Wi=["LinearMultiSampleVariantDisplay"],Oi=[{label:"Auto",value:"auto"},{label:"50 bp",value:50},{label:"1 kb",value:1e3},{label:"10 kb",value:1e4}];function Di(e,t){return e?`Pinned to ${Ze(e)}${t===void 0?"":` \xB7 ${t} form${t===1?"":"s"}`}`:"Not pinned"}function _i(e,t){let o=x(e),r=t.flatMap(n=>n?[Gn(n)]:[]);for(let{message:n}of[...o.snackbarMessages??[]])r.some(a=>n.startsWith(a))&&o.removeSnackbarMessage?.(n)}function zi(e){return e.props({formsPinned:M.maybe(M.frozen()),formsFloorBp:M.maybe(M.frozen())}).views(t=>({get configuredAdapter(){return Ho(t.parentTrack.configuration,"adapter")},get walkForms(){return this.configuredAdapter.type==="WalkFormsAdapter"}})).views(t=>({get adapterConfig(){let o=t.configuredAdapter;return t.walkForms?{...o,...t.formsPinned?{pinned:t.formsPinned}:{},...t.formsFloorBp===void 0?{}:{floorBp:t.formsFloorBp}}:o},get formsWindow(){return Rn(this.adapterConfig.pinned)},get formsFloor(){return Tn(this.adapterConfig.floorBp)},get formsCount(){return t.sourcesBase?.reduce((o,r)=>o+(Number(r.forms)||1),0)},get visibleWindow(){let o=vo(t),r=dn(o)?Re(o):void 0;return r&&r.end>r.start?{refName:r.refName,start:Math.max(0,Math.floor(r.start)),end:Math.ceil(r.end)}:void 0}})).volatile(()=>({warnedWindow:void 0})).actions(t=>{let{setSources:o}=t,r=()=>{_i(t,[t.warnedWindow,t.formsWindow])};return{setFormsPinned(n){r(),t.formsPinned=n},setFormsFloorBp(n){r(),t.formsFloorBp=n},setSources(n,a){t.walkForms&&(r(),t.warnedWindow=t.formsWindow),o?.(n,a)}}}).views(t=>{let{trackMenuItems:o}=t;return{formsMenuItems(){let r=t.formsWindow,n=t.visibleWindow;return[{label:Di(r,t.formsCount),disabled:!0,onClick:()=>{}},{label:"Re-pin to visible region",helpText:"Cut the forms from the region the view 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Panning and zooming leave the forms alone",disabled:!n||r!==void 0&&Ze(n)===Ze(r),onClick:()=>{n&&t.setFormsPinned(n)}},{label:"Hide changes under",subMenu:Oi.map(({label:a,value:i})=>({label:a,type:"radio",checked:t.formsFloor===i,onClick:()=>{t.setFormsFloorBp(i)}}))}]},trackMenuItems(){return t.walkForms?[...o(),...this.formsMenuItems()]:o()}}})}function po(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof rt&&Wi.includes(t.name)&&t.extendStateModel(zi),t))}var $i=W("WalkFormsAdapter",{walksLocation:F("/path/to/graph.walks.bed.gz"),walksIndex:_("WalkFormsWalksIndex"),pinned:{type:"frozen",defaultValue:{}},floorBp:{type:"frozen",defaultValue:"auto"},exclude:{type:"stringArray",defaultValue:[]},maxForms:{type:"integer",defaultValue:Ln},walkByteBudget:{type:"integer",defaultValue:1e6}},{explicitlyTyped:!0,preProcessSnapshot:Se}),Ba=$i;function uo(e){e.addAdapterType(()=>new Z({name:"WalkFormsAdapter",displayName:"Walk-file structural forms 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Yi=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Ui(e){return yt(e).toLowerCase().endsWith(".gbz.db")}function Xi(e){let t=e.adapter;return t?.type!==void 0&&mn.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function qi(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Wo(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function Ki(e,t,o){let r=n=>Ko({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&Ui(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(qo(e))return r("RgfaTabixAdapter");if(yt(e).endsWith(jo)&&(t!==void 0||_o(e)))return r("RgfaTabixWalks")}}function mo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Xi),e.addToExtensionPoint("Core-preProcessTrackConfig",qi),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>Ki(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>Yi.has(o)?"GraphTrack":t(o,r))}function lo(e){let t;if(B(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function Qi(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function Ea(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Fa(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>B(o)&&Array.isArray(o.displays)?o.displays.filter(r=>B(r)&&r.type==="LinearGraphDisplay"):[])}function Na(e,t,o){let r=[],n=xe(e),a=new Set(n.map(i=>B(i)?i.id:void 0));for(let i of n){if(B(i)&&i.id===t)for(let s of Fa(i)){let p=lo(s.hoverHighlight);p&&Ea(p,o)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:p})}for(let s of B(i)?[...Fa(i),...i.type==="GraphGenomeView"?[i]:[]]:[])(Array.isArray(s.assemblyHoverHighlights)?s.assemblyHoverHighlights:[]).forEach((u,m)=>{let S=lo(u);S?.assemblyName!==void 0&&o?.includes(S.assemblyName)&&r.push({key:`${typeof s.id=="string"?s.id:"graph"}-${m}`,region:S})});if(B(i)&&i.type==="GraphGenomeView"&&Qi(i,t,a)){let s=lo(i.hoverHighlight);s&&Ea(s,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Zi=Mn()(e=>({highlight:{height:"100%",position:"absolute",background:Je(e.palette.primary.main,.08),borderLeft:`1px solid ${Je(e.palette.primary.main,.4)}`,borderRight:`1px solid ${Je(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),es=Mt(function({model:t,region:o}){let{classes:r}=Zi(),n=t.getHighlightCoords(o);return n?E("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),ts=Mt(function({model:t}){let{views:o}=x(t);return E(Bo,{children:Na([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>E(es,{model:t,region:n},`graph-hover-${r}`))})}),Ha=ts;var os="LinearGenomeView-TracksContainerComponent";function go(e){e.contributeToExtensionPoint(os,({model:t})=>E(Ha,{model:t},"graphgenomeview-hover-highlight"))}function rs(e){return e.views(t=>({get adapterConfig(){return ln(t,t.parentTrack.configuration)}}))}function ho(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof rt&&eo.includes(t.name)&&t.extendStateModel(rs),t))}var Va="GraphGenomeView";var ja="8.0.0";var bo=class extends vn{constructor(){super(...arguments);this.name=Va;this.version=ja}install(o){Zt(o),ao(o),to(o),oo(o),go(o),so(o),io(o),jt(o),co(o),uo(o),po(o),Ot(o),mo(o),ho(o),o.addRpcMethod(()=>new Oe(o)),o.addRpcMethod(()=>new We(o)),o.addRpcMethod(()=>new je(o)),o.addRpcMethod(()=>new Ve(o))}configure(o){try{Ao(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:tt,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{bo as default};
+`);return[{type:"radio",label:"Every sample",checked:o===void 0,onClick:()=>{e.setWalkRowSamples(void 0)}},...t.length>0?[{type:"radio",label:"Where walk and call disagree",checked:r(t),onClick:()=>{e.setWalkRowSamples(t)}}]:[],{type:"radio",label:"Choose samples...",checked:o!==void 0&&!r(t),onClick:()=>{x(e).queueDialog(n=>[Mr,{model:e,onClose:n}])}}]},walkRowGroupMenuItems(){let t=e.walkRowGroups?e.walkRowGroupBy?.field:void 0;return ee([{value:void 0,label:"None"},...e.walkRowGroupFields.map(o=>({value:o,label:o}))],t,o=>{e.setWalkRowGroupBy(o===void 0?void 0:{field:o})})},tubeMapPanelMenuItems(){let{graph:t,walkRowSampleTable:o}=e,{field:r}=e.facetSetting,n=r===""?e.walkRowGroupBy?.field:void 0,a=i=>!!t&&qe(t,i).length>1;return[...ee(en.map(i=>({value:i.field,label:i.label,disabled:i.field!==""&&!a({by:i.field})})),n?void 0:r,i=>{e.setFacet(i),i===""&&e.setWalkRowGroupBy(void 0)}),...ee(e.walkRowGroupFields.map(i=>({value:i,label:`By 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rows",checked:e.walkRibbons,onClick:()=>{e.setLayer("walkRibbons",!e.walkRibbons)}},{type:"checkbox",label:"Letter shared blocks",checked:e.layerSet.has("walkBlocks"),onClick:()=>{e.setLayer("walkBlocks",!e.layerSet.has("walkBlocks"))}},{type:"checkbox",label:"Order rows by shared sequence",checked:e.walkRowOrder==="shared",onClick:()=>{e.setWalkRowOrder(e.walkRowOrder==="shared"?void 0:"shared")}}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars&&e.walkRowGroupFields.length>0?[{label:"Group by...",subMenu:this.walkRowGroupMenuItems()}]:[]]},showMenuItems(){let t=(o,r)=>({type:"checkbox",label:o,checked:e.layerSet.has(r),onClick:()=>{e.setLayer(r,!e.layerSet.has(r))}});return[t("Show bubble halos","bubbles"),t("Show deletion edges","deletions"),{label:"Hover highlight",subMenu:ee(Le.map(o=>({value:o,label:o[0].toUpperCase()+o.slice(1)})),e.chosenHover,e.setHover)},t("Show genes on the backbone","genes"),...e.referenceStripApplies?[t("Show reference 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dt=ba.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Ie(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&ir(o),n=x(e);return r===void 0?void 0:pr(Ee(n,r),Ee(n,t.assemblyName))},cutChangedFrom(t){return e.cutsWholeWalks!==e.cutsWholeWalksIn(t)||t==="walkrows"!=(e.chosenLayoutMode==="walkrows")}})).views(e=>({get cutOptions(){return{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...e.chosenLayoutMode==="walkrows"?{walkRows:!0}:{},...e.cutsWholeWalks?{snarls:"overlapping"}:{},...e.expandedWalks.length>0?{expand:e.expandedWalks}:{}}}}));var ya={scale:["scale","type"],domain:["scale","domain"],range:["scale","range"],labels:["scale","names"],scheme:["scale","scheme"],reverse:["scale","reverse"],domainMin:["scale","domainMin"],domainMax:["scale","domainMax"],domainMid:["scale","domainMid"],domainQuantile:["scale","domainQuantile"],unknown:["scale","unknown"],title:["legend","title"],descending:["legend","descending"]};function Ti(e){return Object.entries(e).some(([t,o])=>t in ya&&!(t==="scale"&&B(o)))}function Kt(e){if(typeof e=="string")return{value:e};if(!B(e)||!Ti(e))return e;let t={},o={scale:{},legend:{}};for(let[r,n]of Object.entries(e)){let a=ya[r];!a||r==="scale"&&B(n)?t[r]=n:n!==void 0&&(o[a[0]][a[1]]=r==="scale"&&n==="categorical"?"ordinal":n)}for(let r of["scale","legend"])if(Object.keys(o[r]).length>0){let n=t[r];t[r]={...o[r],...B(n)?n:{}}}return t}var fa={color:e=>({encoding:{color:Kt(e)}})};function Qt(){return M.compose("GraphGenomeView",Wn,dt,M.model({type:M.literal("GraphGenomeView"),gfaLocation:M.maybe(M.frozen()),loadedRegion:M.maybe(M.frozen()),loadedTrackId:M.optional(M.string,""),layoutMode:Gt(Ue),color:M.maybe(M.frozen()),size:M.maybe(M.frozen()),layers:M.maybe(M.frozen()),facet:M.maybe(M.frozen()),rows:M.maybe(M.frozen()),hover:Gt(Le)})).preProcessSnapshot(e=>e.color===void 0?e:{...e,color:Kt(e.color)}).views(e=>({get grammar(){return{layoutMode:e.layoutMode,encoding:{color:e.color},size:e.size,layers:e.layers,facet:e.facet,rows:e.rows,hover:e.hover}}})).actions(e=>({writeGrammar({encoding:t,...o}){Object.assign(e,t?{...o,color:t.color}:o)}})).volatile(()=>({widthMeasured:!1})).actions(e=>{let t=e.setWidth;return{setWidth(o){t(o),e.widthMeasured=!0}}}).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get paneMeasured(){return e.widthMeasured},get sourceTrack(){return e.loadedTrackId?e.sessionTrack(e.loadedTrackId):void 0},get canRetryLoad(){return 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eo=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function Li(e){let t=e.getElementTypesInGroup("display"),o=n=>t.find(a=>a.name===n),r=n=>n&&Object.assign(Object.create(n),{adapterCapabilities:["headerLanes"]});return[o("LinearGraphDisplay"),o("LinearBasicDisplay"),...eo.map(n=>r(o(n)))].filter(n=>n!==void 0)}function to(e){e.addTrackType(()=>{let t=W("GraphTrack",{},{baseConfiguration:En(e),explicitIdentifier:"trackId"}),o=new In({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:Fn(e,"GraphTrack",t)});for(let r of Li(e))o.addDisplayType(r);return o})}function oo(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:o,...r}=t;return o.addView("GraphGenomeView",r),t})}var ct=JBrowseExports["@jbrowse/core/pluggableElementTypes/DisplayType"];var wa=ct&&ct.__esModule?ct.default:ct;var be=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],vi=e=>be!=null&&e in 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ye=JBrowseExports["@jbrowse/core/svg/svgReady"],Ai=e=>ye!=null&&e in Object(ye)?ye[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/svg/svgReady' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var Sa=Ai("computeSvgReady");var Fm=ye&&ye.__esModule?ye.default:ye;var ut=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var xa=ut&&ut.__esModule?ut.default:ut;var fe=JBrowseExports["@jbrowse/display-kit/plotMenu"],Pi=e=>fe!=null&&e in Object(fe)?fe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/plotMenu' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),Ra=Pi("editPlotMenuItems");var Vm=fe&&fe.__esModule?fe.default:fe;var we=JBrowseExports["@jbrowse/render-core/displayPhase"],Ta=e=>we!=null&&e in Object(we)?we[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/displayPhase' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),Ga=Ta("computeActivityPhase"),La=Ta("computeDisplayPhase");var Wm=we&&we.__esModule?we.default:we;function ro(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let o=e.end-e.start;return t.end-t.start>=o&&t.end>e.start-o&&t.start<e.end+o}var Ci=new Set(["scale","translateX","translateY"]);function Bi(e){return Object.fromEntries(Object.keys(Pr.properties).filter(t=>!Ci.has(t)).map(t=>[t,e[t]]))}var no=10;function Ii(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/no:void 0}var Ei=oe(()=>import("./chunks/GraphTrackSettingsDialog-7M3Q635V.js"));function va(e){return M.compose("LinearGraphDisplay",Cn,xa(),dt,M.model({type:M.literal("LinearGraphDisplay"),configuration:No(e),layoutEngine:rr(Qo,"stress"),cutRegion:M.maybe(M.frozen()),coarseCut:M.optional(M.boolean,!1)})).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0,cutFoldBp:0})).views(t=>({get grammar(){return{layoutMode:te(t,"layoutMode"),encoding:te(t,"encoding"),size:te(t,"size"),layers:te(t,"layers"),facet:te(t,"facet"),rows:te(t,"rows"),hover:te(t,"hover")}},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get trackHaplotypes(){let o=t.sourceAdapter,r=t.sourceTrack;return(o&&Ie(o))??(r&&Lt(r))},get coarseAboveBpPerPx(){return Ii(t.sourceAdapter?.coarse)}})).views(t=>({tierAt(o){let r=t.coarseAboveBpPerPx;return r!==void 0&&o>r?"coarse":"fine"},capFor(o){return o==="coarse"?1/0:t.maxRegionBp},foldDrifted(o){let 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La({renderError:t.renderError,regionTooLarge:t.regionTooLarge,error:t.error},()=>Ga({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({writeGrammar(o){for(let[r,n]of Object.entries(o))Vo(t,r,n)},setSubgraphContext(o){t.subgraphContext=o,t.dense=void 0},setSubgraphHaplotypes(o){t.subgraphHaplotypes=o,t.dense=void 0},setDense(o){t.dense=o},setHaplotypeNames(o){t.haplotypeNames=o},setMaxRegionBp(o){t.maxRegionBp=o},cut(){let o=t.cutRegion,r=t.sourceAdapter;if(!o||!r)return;let n=t.offReference(o);if(n){t.clearGraph(),t.setError(new Error(n));return}let a=t.cutTier==="coarse";return t.cutFoldBp=Math.round(no*(t.settledWindow?.bpPerPx??t.host?.bpPerPx??0)),t.cutSubgraph(r,o,{...t.cutOptions,tier:a?"coarse":void 0},t.cutFoldBp)}})).actions(t=>({recutAt(o){let r=t.tierAt(o.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=cn(o,t.capFor(r),Q(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=Q(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||ro(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&un(t.cutRegion,o,r)&&!t.foldDrifted(o.bpPerPx))return!1;let n=t.recutAt(o),a=t.recuts;return Promise.resolve(n).then(()=>{V(t)&&t.recuts===a&&St(t.error)&&this.refuseDenseCut(o)}),!0},refuseDenseCut(o){t.setDense(o),t.cutRegion=void 0,this.settleOn(t.settledWindow??o)},recut(){t.cutRegion?t.cut():t.settledWindow&&this.settleOn(t.settledWindow)},relayoutFrom(o){let r=t.host?Re(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||Q(o).cutMargins!==Q(t.chosenLayoutMode).cutMargins)?t.recutAt(r):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(o,r){try{let n=await x(t).rpcManager.call(ae(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});V(t)&&!r?.aborted&&t.setHaplotypeNames(n)}catch(n){r?.aborted||console.warn("[LinearGraphDisplay] no haplotype names",n)}}})).actions(t=>({stretchWithHost(o,r){let n=t.layoutBounds;if(!n||!t.followsHostView)return;t.viewportOwner==="fit"&&(t.viewportOwner="user");let a=o.bpPerPx/r.bpPerPx,i=t.translateY+t.scaleY*(n.minY+n.h/2);t.scale*=a,t.translateX=a*(t.translateX+o.offsetPx)-r.offsetPx,t.translateY=i-a*(i-t.translateY)}})).actions(t=>({forceLoad(){let o=t.settledWindow;o&&(t.setMaxRegionBp(Math.ceil(o.end-o.start)),t.settleOn(o))},afterAttach(){t.cutRegion&&!t.graph&&t.cut();let o;L(t,()=>{o?.abort()}),L(t,C(()=>{let n=t.sourceAdapter;return n&&nr(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new 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graph",checked:s?s.length===0:!n&&!a,onClick:()=>{p([])}},...n||a?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${a?.length} assemblies`,checked:s===void 0,onClick:()=>{p(void 0)}}]:[],{type:"radio",label:"Chosen in Graph settings...",checked:(s?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){x(t).queueDialog(o=>[Ei,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-YNA5VK6A.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();pt(o,{label:"Graph genome view",icon:tt,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!St(t.error)?"The track could not cut a graph here":t.isLoading&&!t.hasGraph?"The track is still cutting its graph":"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:Sn,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:xn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...Ra(t)]}}))}function ao(e){e.addDisplayType(()=>{let t=Ma();return Object.assign(new wa({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:va(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:oe(()=>import("./chunks/LinearGraphDisplay-BAEMS5WG.js"))}),{adapterCapabilities:["getSubgraph"]})})}function Fi(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:Pe(t,o,r)}:e}var Ni=W("MinigraphBubbleAdapter",{bubblesLocation:F("/path/to/graph.bb.bed.gz"),index:_("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Fi}),Aa=Ni;function io(e){e.addAdapterType(()=>new Z({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:Aa,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-G25V6MZL.js").then(t=>t.default)}))}function Pa(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:o},segmentsIndex:Pe(`${t}.segs.bed.gz`,o,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:o},linksIndex:Pe(`${t}.links.bed.gz`,o,r)}:e}function Hi(e){let{coarse:t,baseUri:o,csi:r}=e;return Se(Pa(typeof t=="object"&&t!==null?{...e,coarse:Pa({baseUri:o,csi:r,...t})}:e))}var Vi=W("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:F("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:_("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:F("/path/to/graph.tier.links.bed.gz"),linksIndex:_("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),ji=W("RgfaTabixAdapter",{segmentsLocation:F("/path/to/graph.segs.bed.gz"),segmentsIndex:_("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:F("/path/to/graph.links.bed.gz"),linksIndex:_("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:F(""),walksIndex:_("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Me.stepBudget},walkByteBudget:{type:"integer",defaultValue:Me.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:Vi},{explicitlyTyped:!0,preProcessSnapshot:Hi}),Ca=ji;function so(e){e.addAdapterType(()=>new Z({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:Ca,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-JPTUWO2Z.js").then(t=>t.default)}))}var Wi=["LinearMultiSampleVariantDisplay"],Oi=[{label:"Auto",value:"auto"},{label:"50 bp",value:50},{label:"1 kb",value:1e3},{label:"10 kb",value:1e4}];function Di(e,t){return e?`Pinned to ${Ze(e)}${t===void 0?"":` \xB7 ${t} form${t===1?"":"s"}`}`:"Not pinned"}function _i(e,t){let o=x(e),r=t.flatMap(n=>n?[Gn(n)]:[]);for(let{message:n}of[...o.snackbarMessages??[]])r.some(a=>n.startsWith(a))&&o.removeSnackbarMessage?.(n)}function zi(e){return e.props({formsPinned:M.maybe(M.frozen()),formsFloorBp:M.maybe(M.frozen())}).views(t=>({get configuredAdapter(){return Ho(t.parentTrack.configuration,"adapter")},get walkForms(){return this.configuredAdapter.type==="WalkFormsAdapter"}})).views(t=>({get adapterConfig(){let o=t.configuredAdapter;return t.walkForms?{...o,...t.formsPinned?{pinned:t.formsPinned}:{},...t.formsFloorBp===void 0?{}:{floorBp:t.formsFloorBp}}:o},get formsWindow(){return Rn(this.adapterConfig.pinned)},get formsFloor(){return Tn(this.adapterConfig.floorBp)},get formsCount(){return t.sourcesBase?.reduce((o,r)=>o+(Number(r.forms)||1),0)},get visibleWindow(){let o=vo(t),r=dn(o)?Re(o):void 0;return r&&r.end>r.start?{refName:r.refName,start:Math.max(0,Math.floor(r.start)),end:Math.ceil(r.end)}:void 0}})).volatile(()=>({warnedWindow:void 0})).actions(t=>{let{setSources:o}=t,r=()=>{_i(t,[t.warnedWindow,t.formsWindow])};return{setFormsPinned(n){r(),t.formsPinned=n},setFormsFloorBp(n){r(),t.formsFloorBp=n},setSources(n,a){t.walkForms&&(r(),t.warnedWindow=t.formsWindow),o?.(n,a)}}}).views(t=>{let{trackMenuItems:o}=t;return{formsMenuItems(){let r=t.formsWindow,n=t.visibleWindow;return[{label:Di(r,t.formsCount),disabled:!0,onClick:()=>{}},{label:"Re-pin to visible region",helpText:"Cut the forms from the region the view shows. Panning and zooming leave the forms alone",disabled:!n||r!==void 0&&Ze(n)===Ze(r),onClick:()=>{n&&t.setFormsPinned(n)}},{label:"Hide changes under",subMenu:Oi.map(({label:a,value:i})=>({label:a,type:"radio",checked:t.formsFloor===i,onClick:()=>{t.setFormsFloorBp(i)}}))}]},trackMenuItems(){return t.walkForms?[...o(),...this.formsMenuItems()]:o()}}})}function po(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof rt&&Wi.includes(t.name)&&t.extendStateModel(zi),t))}var $i=W("WalkFormsAdapter",{walksLocation:F("/path/to/graph.walks.bed.gz"),walksIndex:_("WalkFormsWalksIndex"),pinned:{type:"frozen",defaultValue:{}},floorBp:{type:"frozen",defaultValue:"auto"},exclude:{type:"stringArray",defaultValue:[]},maxForms:{type:"integer",defaultValue:Ln},walkByteBudget:{type:"integer",defaultValue:1e6}},{explicitlyTyped:!0,preProcessSnapshot:Se}),Ba=$i;function co(e){e.addAdapterType(()=>new Z({name:"WalkFormsAdapter",displayName:"Walk-file structural forms adapter",configSchema:Ba,adapterMetadata:{category:"Variant adapters"},getAdapterClass:()=>import("./chunks/WalkFormsAdapter-PBN7BJZW.js").then(t=>t.default)}))}var Ji=W("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:F("/path/to/graph.walks.bed.gz"),walksIndex:_("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:Me.stepBudget},walkByteBudget:{type:"integer",defaultValue:Me.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:F(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Se}),Ia=Ji;function uo(e){e.addAdapterType(()=>new Z({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:Ia,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-27WDE5JF.js").then(t=>t.default)}))}var Yi=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function Ui(e){return yt(e).toLowerCase().endsWith(".gbz.db")}function Xi(e){let t=e.adapter;return t?.type!==void 0&&mn.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function qi(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Wo(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function Ki(e,t,o){let r=n=>Ko({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&Ui(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(qo(e))return r("RgfaTabixAdapter");if(yt(e).endsWith(jo)&&(t!==void 0||_o(e)))return r("RgfaTabixWalks")}}function mo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Xi),e.addToExtensionPoint("Core-preProcessTrackConfig",qi),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>Ki(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>Yi.has(o)?"GraphTrack":t(o,r))}function lo(e){let t;if(B(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function Qi(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function Ea(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Fa(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>B(o)&&Array.isArray(o.displays)?o.displays.filter(r=>B(r)&&r.type==="LinearGraphDisplay"):[])}function Na(e,t,o){let r=[],n=xe(e),a=new Set(n.map(i=>B(i)?i.id:void 0));for(let i of n){if(B(i)&&i.id===t)for(let s of Fa(i)){let p=lo(s.hoverHighlight);p&&Ea(p,o)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:p})}for(let s of B(i)?[...Fa(i),...i.type==="GraphGenomeView"?[i]:[]]:[])(Array.isArray(s.assemblyHoverHighlights)?s.assemblyHoverHighlights:[]).forEach((c,m)=>{let S=lo(c);S?.assemblyName!==void 0&&o?.includes(S.assemblyName)&&r.push({key:`${typeof s.id=="string"?s.id:"graph"}-${m}`,region:S})});if(B(i)&&i.type==="GraphGenomeView"&&Qi(i,t,a)){let s=lo(i.hoverHighlight);s&&Ea(s,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Zi=Mn()(e=>({highlight:{height:"100%",position:"absolute",background:Je(e.palette.primary.main,.08),borderLeft:`1px solid ${Je(e.palette.primary.main,.4)}`,borderRight:`1px solid ${Je(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),es=Mt(function({model:t,region:o}){let{classes:r}=Zi(),n=t.getHighlightCoords(o);return n?E("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),ts=Mt(function({model:t}){let{views:o}=x(t);return E(Bo,{children:Na([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>E(es,{model:t,region:n},`graph-hover-${r}`))})}),Ha=ts;var os="LinearGenomeView-TracksContainerComponent";function go(e){e.contributeToExtensionPoint(os,({model:t})=>E(Ha,{model:t},"graphgenomeview-hover-highlight"))}function rs(e){return e.views(t=>({get adapterConfig(){return ln(t,t.parentTrack.configuration)}}))}function ho(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof rt&&eo.includes(t.name)&&t.extendStateModel(rs),t))}var Va="GraphGenomeView";var ja="8.0.2";var bo=class extends vn{constructor(){super(...arguments);this.name=Va;this.version=ja}install(o){Zt(o),ao(o),to(o),oo(o),go(o),so(o),io(o),jt(o),uo(o),co(o),po(o),Ot(o),mo(o),ho(o),o.addRpcMethod(()=>new Oe(o)),o.addRpcMethod(()=>new We(o)),o.addRpcMethod(()=>new je(o)),o.addRpcMethod(()=>new Ve(o))}configure(o){try{Ao(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:tt,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{bo as default};
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