jbrowse-plugin-graphgenomeviewer 4.7.0 → 5.0.0

package/dist/chunks/chunk-BZOIENU5.js

@@ -0,0 +1,2 @@
+import{a as w,b as N,c as H,d as R}from"./chunk-2H7GDQ3R.js";function j(e){if(typeof e!="object"||e===null)return!1;let n=e;return typeof n.horizontalScroll=="function"&&typeof n.zoomTo=="function"&&"coarseDynamicBlocks"in n&&"dynamicBlocks"in n}function P(e){return e.reduce((n,t)=>n&&n.end-n.start>=t.end-t.start?n:t,void 0)}function Q(e,n){let t=P(e.dynamicBlocks.contentBlocks.filter(s=>s.refName===n.refName&&s.assemblyName===n.assemblyName)),{bpPerPx:r}=e;if(!t||!(r>0))return;let o=t.offsetPx-e.offsetPx;return t.reversed?{scale:-1/r,translateX:o+t.end/r}:{scale:1/r,translateX:o-t.start/r}}function U(e){let n=P(e.dynamicBlocks.contentBlocks),t=n?.displayedRegionIndex===void 0?void 0:e.displayedRegions[n.displayedRegionIndex];return n&&e.bpPerPx>0?{refName:n.refName,assemblyName:n.assemblyName,start:n.start,end:n.end,bpPerPx:e.bpPerPx,span:e.bpPerPx*e.width,regionStart:t?.start??n.start,regionEnd:t?.end??n.end}:void 0}function C(e,n,t=!0){let r=e.end-e.start,o=t?Math.max(0,Math.min(e.span,(n-r)/2)):0,s=Math.max(e.regionStart,Math.floor(e.start-o)),i=Math.min(e.regionEnd,Math.ceil(e.end+o)),a=i-s-n;return a>0&&(s+=Math.floor(a/2),i-=Math.ceil(a/2)),{refName:e.refName,assemblyName:e.assemblyName,start:s,end:i}}function Y(e,n,t=!0){if(e?.refName!==n.refName||e.assemblyName!==n.assemblyName)return!1;if(t)return e.start<=n.start+1&&n.end<=e.end+1;let r=C(n,1/0,!1);return Math.abs(e.start-r.start)<1&&Math.abs(e.end-r.end)<1}var d={absent:[244,244,244],reference:[200,200,200],partial:[224,204,150],variant:[[132,166,200],[64,116,168],[33,82,132],[14,46,86]]},h=40,L=4,T=3,D=14,I=9,_=16384,B=["absent: no contig covers the bin","reference-like","partial: contigs cover under 90% of the bin","diverges"],$=["1 excursion","2\u20133 excursions","4\u201315 excursions","16+ excursions"],Z="SNPs and indels under 50 bp are not shown";function A(e){let n=e&3;return n===w?d.absent:n===N?d.reference:n===H?d.partial:d.variant[e>>2]}function ee(e){let n=e&3;return n===R?`diverges \u226550 bp, ${$[e>>2]}`:B[n]}function ne(e,n,t){let r=new Set([...e.reference,...e.pinned]),o=e.pinned.filter(f=>!e.reference.includes(f)),s=n?e.rows.flatMap((f,u)=>r.has(u)?[]:[u]):[],i=h+L,a=Math.max(0,t-i),l=o.length>0&&s.length>0?T:0,m=o.length===0?0:Math.min(D,(s.length>0?a*.4:a)/o.length),c=i+o.length*m+l;return{rows:[...o,...s],pinnedCount:o.length,pinnedHeight:m,restHeight:s.length>0?Math.max(0,t-c)/s.length:0,rowsTop:i,restTop:c}}function W(e,n){return n<e.pinnedCount?e.rowsTop+n*e.pinnedHeight:e.restTop+(n-e.pinnedCount)*e.restHeight}function te(e,n){let{pinnedCount:t,pinnedHeight:r,restHeight:o,rowsTop:s,restTop:i}=e,a=s+t*r,l=n>=s&&n<a?Math.floor((n-s)/r):n>=i&&o>0?t+Math.floor((n-i)/o):void 0;return l!==void 0&&l<e.rows.length?e.rows[l]:void 0}function re(e,n){let{bins:t}=e,r=0,o=t.length-1;for(;r<o;){let i=r+o+1>>1;t[i].start<=n?r=i:o=i-1}let s=t[r];return s&&s.start<=n&&n<s.end?r:void 0}function oe(e){let n=e.rows.length,t=new Set(e.reference);return e.bins.map((r,o)=>{let s=[0,0,0,0,0,0];for(let i=0;i<n;i++)if(!t.has(i)){let a=e.cells[o*n+i],l=a&3;l===R?s[2+(a>>2)]+=1:l===w?s[0]+=1:l===H&&(s[1]+=1)}return s})}function se(e,n){let t=e.bins[n],[r,o,s,i]=t.classes;return{span:`${t.start.toLocaleString()}\u2013${t.end.toLocaleString()}`,classes:`${o} reference-like, ${i} diverge \u226550 bp, ${s} partial, ${r} absent`,excursions:`${t.excursions.toLocaleString()} excursions, ${t.variants.toLocaleString()} of 50 bp or more, longest ${t.longestExcursion.toLocaleString()} bp`}}function S(e,n){let t=document.createElement("canvas");return t.width=Math.max(1,e),t.height=Math.max(1,n),t}function F(e){let n=[],t=0;return e.bins.forEach((r,o)=>{o>0&&r.start!==e.bins[o-1].end&&(n.push([t,o]),t=o)}),e.bins.length>0&&n.push([t,e.bins.length]),n}function O(e,n,t,r,o){let s=e.bins.length;if(n.length===0||s===0||r<=0)return;let i=S(s,n.length),a=i.getContext("2d"),l=a.createImageData(s,n.length),m=e.rows.length;n.forEach((g,p)=>{for(let b=0;b<s;b++){let[x,y,k]=A(e.cells[b*m+g]),v=(p*s+b)*4;l.data[v]=x,l.data[v+1]=y,l.data[v+2]=k,l.data[v+3]=255}}),a.putImageData(l,0,0);let c=Math.max(1,Math.round(r*o)),f=S(s,c),u=f.getContext("2d");return u.imageSmoothingEnabled=n.length>c,u.imageSmoothingQuality="high",u.drawImage(i,0,0,s,c),{image:f,top:t,height:r}}function ie(e,n,t){let{rows:r,pinnedCount:o,pinnedHeight:s,restHeight:i}=n;return[O(e,r.slice(0,o),n.rowsTop,o*s,t),O(e,r.slice(o),n.restTop,(r.length-o)*i,t)].filter(a=>a!==void 0)}function M(e,n,t){let r=e.xOf(n),o=e.xOf(t);return{left:Math.min(r,o),width:Math.abs(o-r),reversed:o<r}}function V(e,n,t,r){for(let[o,s]of F(n)){let{left:i,width:a,reversed:l}=M(r,n.bins[o].start,n.bins[s-1].end);if(!(i+a<0||i>r.width)){e.imageSmoothingEnabled=s-o>a*r.dpr;for(let{image:m,top:c,height:f}of t)e.save(),l&&(e.translate(2*i+a,0),e.scale(-1,1)),e.drawImage(m,o,0,s-o,m.height,i,c,a,f),e.restore()}}}function X(e,n,t,r){let o=n.rows.length-n.reference.length,s=Math.max(1,...n.bins.map(a=>a.variants)),i=[[175,175,175],d.partial,...d.variant];n.bins.forEach((a,l)=>{let m=M(r,a.start,a.end),{left:c}=m,f=Math.max(m.width,1/r.dpr);if(!(c+f<0||c>r.width))if(t){let u=h;for(let g of[5,4,3,2,1,0]){let p=h*t[l][g]/Math.max(1,o);if(p>0){let[b,x,y]=i[g];e.fillStyle=`rgb(${b},${x},${y})`,e.fillRect(c,u-p,f,p),u-=p}}}else{let u=h*a.variants/s,[g,p,b]=d.variant[1];e.fillStyle=`rgb(${g},${p},${b})`,e.fillRect(c,h-u,f,u)}})}function z(e,n,t){if(!(t.pinnedHeight<I)){e.font=`${Math.min(11,t.pinnedHeight-2)}px sans-serif`,e.textBaseline="middle";for(let r=0;r<t.pinnedCount;r++){let o=n.rows[t.rows[r]],s=W(t,r),i=e.measureText(o).width;e.fillStyle="rgba(255,255,255,0.8)",e.fillRect(2,s+1,i+6,t.pinnedHeight-2),e.fillStyle="#222",e.fillText(o,5,s+t.pinnedHeight/2)}}}function E(e){return e>=1e6?`${+(e/1e6).toFixed(1)} Mb`:`${+(e/1e3).toFixed(1)} kb`}function G(e){let n=e.rows.length-e.reference.length;return e.bin<=_?`haplotypes diverging \u226550 bp, of ${n} \xB7 ${E(e.bin)} bins`:`excursions \u226550 bp per ${E(e.bin)} bin, all ${n} haplotypes`}function K(e,n){let t=G(n);e.font="10px sans-serif",e.textBaseline="top";let r=e.measureText(t).width;e.fillStyle="rgba(255,255,255,0.8)",e.fillRect(2,1,r+6,13),e.fillStyle="#444",e.fillText(t,5,2)}function ae(e,n,t,r,o,s){e.clearRect(0,0,s.width,s.height),X(e,n,t,s),V(e,n,o,s),z(e,n,r),K(e,n)}export{j as a,Q as b,U as c,C as d,Y as e,_ as f,Z as g,ee as h,ne as i,te as j,re as k,oe as l,se as m,ie as n,ae as o};
+//# sourceMappingURL=chunk-BZOIENU5.js.map

package/dist/chunks/chunk-BZOIENU5.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/GraphGenomeView/host.ts", "../../src/HaplotypeOverview/draw.ts"],
+  "sourcesContent": ["import type { SubgraphRegion } from '../GetSubgraph'\n\n// The members of a LinearGenomeView a hosted pane reads and drives.\n// Structural, because this plugin takes no runtime dependency on the LGV\n// plugin (see hoverSync/index.tsx).\nexport interface HostBlock {\n  refName: string\n  assemblyName: string\n  start: number\n  end: number\n  offsetPx: number\n  reversed?: boolean\n  displayedRegionIndex?: number\n}\n\nexport interface LinearHost {\n  id: string\n  initialized: boolean\n  bpPerPx: number\n  offsetPx: number\n  width: number\n  displayedRegions: readonly { start: number; end: number }[]\n  dynamicBlocks: { contentBlocks: readonly HostBlock[] }\n  coarseDynamicBlocks: readonly HostBlock[]\n  horizontalScroll: (distance: number) => number\n  zoomTo: (bpPerPx: number, offset?: number) => number\n  navTo?: (loc: {\n    refName: string\n    assemblyName: string\n    start: number\n    end: number\n  }) => void\n  // whether the view's body is mounted, which an off-screen view's is not\n  effectiveBodyMounted?: boolean\n  hasVisibleContent?: boolean\n}\n\nexport function isLinearHost(view: unknown): view is LinearHost {\n  if (typeof view !== 'object' || view === null) {\n    return false\n  }\n  const v = view as Record<string, unknown>\n  return (\n    typeof v.horizontalScroll === 'function' &&\n    typeof v.zoomTo === 'function' &&\n    'coarseDynamicBlocks' in v &&\n    'dynamicBlocks' in v\n  )\n}\n\nfunction widest(blocks: readonly HostBlock[]) {\n  return blocks.reduce<HostBlock | undefined>(\n    (best, b) => (best && best.end - best.start >= b.end - b.start ? best : b),\n    undefined,\n  )\n}\n\nexport interface HostWindow {\n  refName: string\n  assemblyName: string\n  start: number\n  end: number\n  bpPerPx: number\n  // the view's width in bp, which the margin is sized by: a block at a contig\n  // end is clipped, the zoom is not\n  span: number\n  regionStart: number\n  regionEnd: number\n}\n\n// x is reference bp on an anchored layout, so the graph shows what the linear\n// view shows when one bp is as many px in both and the cut's refName sits at\n// the same screen x. Undefined when the linear view shows no block of that\n// refName, which is a re-cut's job rather than the frame's. A reversed block\n// runs bp right to left, which only the tube map's connectors can draw.\nexport function hostFrame(view: LinearHost, region: SubgraphRegion) {\n  const block = widest(\n    view.dynamicBlocks.contentBlocks.filter(\n      b =>\n        b.refName === region.refName && b.assemblyName === region.assemblyName,\n    ),\n  )\n  const { bpPerPx } = view\n  if (!block || !(bpPerPx > 0)) {\n    return undefined\n  }\n  const left = block.offsetPx - view.offsetPx\n  return block.reversed\n    ? { scale: -1 / bpPerPx, translateX: left + block.end / bpPerPx }\n    : { scale: 1 / bpPerPx, translateX: left - block.start / bpPerPx }\n}\n\n// Read off the LIVE blocks even when the coarse ones woke the caller: those\n// name where the window was half a second ago (SyntenyFollow/CLAUDE.md).\nexport function hostWindow(view: LinearHost): HostWindow | undefined {\n  const block = widest(view.dynamicBlocks.contentBlocks)\n  const displayed =\n    block?.displayedRegionIndex === undefined\n      ? undefined\n      : view.displayedRegions[block.displayedRegionIndex]\n  return block && view.bpPerPx > 0\n    ? {\n        refName: block.refName,\n        assemblyName: block.assemblyName,\n        start: block.start,\n        end: block.end,\n        bpPerPx: view.bpPerPx,\n        span: view.bpPerPx * view.width,\n        regionStart: displayed?.start ?? block.start,\n        regionEnd: displayed?.end ?? block.end,\n      }\n    : undefined\n}\n\n// The window plus one window-width each side, clamped to the displayed\n// region, with the margins narrowed until the whole cut fits under `capBp`.\nexport function hostCut(\n  window: HostWindow,\n  capBp: number,\n  margins = true,\n): SubgraphRegion {\n  const visible = window.end - window.start\n  const margin = margins\n    ? Math.max(0, Math.min(window.span, (capBp - visible) / 2))\n    : 0\n  let start = Math.max(window.regionStart, Math.floor(window.start - margin))\n  let end = Math.min(window.regionEnd, Math.ceil(window.end + margin))\n  // Rounding outward can put a cut a base or two past the cap, which the load\n  // refuses whole; trim it back rather than lose the cut.\n  const over = end - start - capBp\n  if (over > 0) {\n    start += Math.floor(over / 2)\n    end -= Math.ceil(over / 2)\n  }\n  return {\n    refName: window.refName,\n    assemblyName: window.assemblyName,\n    start,\n    end,\n  }\n}\n\n// With margins, a cut holds while the window is inside it; without, only the\n// window itself does, since the drawing is the window.\nexport function cutHolds(\n  cut: SubgraphRegion | undefined,\n  window: HostWindow,\n  margins = true,\n) {\n  if (\n    cut?.refName !== window.refName ||\n    cut.assemblyName !== window.assemblyName\n  ) {\n    return false\n  }\n  // to the base, since a cut trimmed to its cap can end a base inside the window\n  if (margins) {\n    return cut.start <= window.start + 1 && window.end <= cut.end + 1\n  }\n  const exact = hostCut(window, Infinity, false)\n  return (\n    Math.abs(cut.start - exact.start) < 1 && Math.abs(cut.end - exact.end) < 1\n  )\n}\n", "import {\n  OVERVIEW_ABSENT,\n  OVERVIEW_PARTIAL,\n  OVERVIEW_REFERENCE,\n  OVERVIEW_VARIANT,\n} from '@gmod/gbz-base'\n\nimport type { HaplotypeOverviewData } from '../GetHaplotypeOverview'\n\ntype Rgb = readonly [number, number, number]\n\n// The variant track's colours: reference grey, so the two tracks read alike,\n// and variant cells deepening with how many variant marks the bin holds\nexport const PALETTE = {\n  absent: [244, 244, 244],\n  reference: [200, 200, 200],\n  partial: [224, 204, 150],\n  variant: [\n    [132, 166, 200],\n    [64, 116, 168],\n    [33, 82, 132],\n    [14, 46, 86],\n  ],\n} as const satisfies Record<string, Rgb | readonly Rgb[]>\n\nexport const DENSITY_PX = 40\nconst GAP_PX = 4\nconst PIN_GAP_PX = 3\nconst PIN_ROW_PX = 14\nconst LABEL_MIN_PX = 9\n// Past 16 kb bins nearly every bin holds a 50 bp excursion for most\n// haplotypes, so the density row counts variant excursions instead of\n// haplotypes per class\nexport const FINE_BIN_BP = 16_384\n\n// \"Diverges\" rather than \"variant\": only excursions of 50 bp or more and\n// rearrangements count, so a haplotype full of SNPs is reference-like\nconst CLASS_NAMES = [\n  'absent: no contig covers the bin',\n  'reference-like',\n  'partial: contigs cover under 90% of the bin',\n  'diverges',\n]\nconst MARK_BUCKETS = [\n  '1 excursion',\n  '2\u20133 excursions',\n  '4\u201315 excursions',\n  '16+ excursions',\n]\nexport const NOT_SHOWN = 'SNPs and indels under 50 bp are not shown'\n\nexport function cellColor(cell: number): Rgb {\n  const klass = cell & 3\n  return klass === OVERVIEW_ABSENT\n    ? PALETTE.absent\n    : klass === OVERVIEW_REFERENCE\n      ? PALETTE.reference\n      : klass === OVERVIEW_PARTIAL\n        ? PALETTE.partial\n        : PALETTE.variant[cell >> 2]!\n}\n\nexport function cellLabel(cell: number) {\n  const klass = cell & 3\n  return klass === OVERVIEW_VARIANT\n    ? `diverges \u226550 bp, ${MARK_BUCKETS[cell >> 2]}`\n    : CLASS_NAMES[klass]!\n}\n\nexport interface OverviewLayout {\n  rows: number[]\n  pinnedCount: number\n  pinnedHeight: number\n  restHeight: number\n  rowsTop: number\n  restTop: number\n}\n\n// The track's lanes first, at a height their labels fit when there is room,\n// then every other haplotype unless only the lanes are wanted, sharing what\n// is left. The reference sample's rows never draw.\nexport function overviewLayout(\n  data: Pick<HaplotypeOverviewData, 'rows' | 'pinned' | 'reference'>,\n  allRows: boolean,\n  height: number,\n): OverviewLayout {\n  const skip = new Set([...data.reference, ...data.pinned])\n  const pinned = data.pinned.filter(row => !data.reference.includes(row))\n  const rest = allRows\n    ? data.rows.flatMap((_, row) => (skip.has(row) ? [] : [row]))\n    : []\n  const rowsTop = DENSITY_PX + GAP_PX\n  const available = Math.max(0, height - rowsTop)\n  const gap = pinned.length > 0 && rest.length > 0 ? PIN_GAP_PX : 0\n  const pinnedHeight =\n    pinned.length === 0\n      ? 0\n      : Math.min(\n          PIN_ROW_PX,\n          (rest.length > 0 ? available * 0.4 : available) / pinned.length,\n        )\n  const restTop = rowsTop + pinned.length * pinnedHeight + gap\n  return {\n    rows: [...pinned, ...rest],\n    pinnedCount: pinned.length,\n    pinnedHeight,\n    restHeight:\n      rest.length > 0 ? Math.max(0, height - restTop) / rest.length : 0,\n    rowsTop,\n    restTop,\n  }\n}\n\nexport function rowTop(layout: OverviewLayout, index: number) {\n  return index < layout.pinnedCount\n    ? layout.rowsTop + index * layout.pinnedHeight\n    : layout.restTop + (index - layout.pinnedCount) * layout.restHeight\n}\n\n// The haplotype row under y, or undefined over the density row or a gap\nexport function rowAt(layout: OverviewLayout, y: number) {\n  const { pinnedCount, pinnedHeight, restHeight, rowsTop, restTop } = layout\n  const pinnedEnd = rowsTop + pinnedCount * pinnedHeight\n  const index =\n    y >= rowsTop && y < pinnedEnd\n      ? Math.floor((y - rowsTop) / pinnedHeight)\n      : y >= restTop && restHeight > 0\n        ? pinnedCount + Math.floor((y - restTop) / restHeight)\n        : undefined\n  return index !== undefined && index < layout.rows.length\n    ? layout.rows[index]\n    : undefined\n}\n\n// The bin holding bp, or undefined between fragments and past either end\nexport function binAt(data: Pick<HaplotypeOverviewData, 'bins'>, bp: number) {\n  const { bins } = data\n  let lo = 0\n  let hi = bins.length - 1\n  while (lo < hi) {\n    const mid = (lo + hi + 1) >> 1\n    if (bins[mid]!.start <= bp) {\n      lo = mid\n    } else {\n      hi = mid - 1\n    }\n  }\n  const bin = bins[lo]\n  return bin && bin.start <= bp && bp < bin.end ? lo : undefined\n}\n\n// Per bin, the haplotypes that are not the reference counted by what the\n// density row stacks: absent, partial, and variant in each mark bucket\nexport function densityCounts(data: HaplotypeOverviewData) {\n  const height = data.rows.length\n  const reference = new Set(data.reference)\n  return data.bins.map((_, b) => {\n    const counts = [0, 0, 0, 0, 0, 0]\n    for (let row = 0; row < height; row++) {\n      if (!reference.has(row)) {\n        const cell = data.cells[b * height + row]!\n        const klass = cell & 3\n        if (klass === OVERVIEW_VARIANT) {\n          counts[2 + (cell >> 2)]! += 1\n        } else if (klass === OVERVIEW_ABSENT) {\n          counts[0]! += 1\n        } else if (klass === OVERVIEW_PARTIAL) {\n          counts[1]! += 1\n        }\n      }\n    }\n    return counts\n  })\n}\n\nexport function describeBin(data: HaplotypeOverviewData, b: number) {\n  const bin = data.bins[b]!\n  const [absent, reference, partial, variant] = bin.classes\n  return {\n    span: `${bin.start.toLocaleString()}\u2013${bin.end.toLocaleString()}`,\n    classes: `${reference} reference-like, ${variant} diverge \u226550 bp, ${partial} partial, ${absent} absent`,\n    excursions: `${bin.excursions.toLocaleString()} excursions, ${bin.variants.toLocaleString()} of 50 bp or more, longest ${bin.longestExcursion.toLocaleString()} bp`,\n  }\n}\n\ninterface Frame {\n  // screen x of a bp on the overview's contig\n  xOf: (bp: number) => number\n  width: number\n  height: number\n  dpr: number\n}\n\nfunction makeCanvas(width: number, height: number) {\n  const canvas = document.createElement('canvas')\n  canvas.width = Math.max(1, width)\n  canvas.height = Math.max(1, height)\n  return canvas\n}\n\n// Consecutive bins with no gap between them, which one image can stretch over\nfunction contiguousRuns(data: HaplotypeOverviewData) {\n  const runs: [number, number][] = []\n  let first = 0\n  data.bins.forEach((bin, b) => {\n    if (b > 0 && bin.start !== data.bins[b - 1]!.end) {\n      runs.push([first, b])\n      first = b\n    }\n  })\n  if (data.bins.length > 0) {\n    runs.push([first, data.bins.length])\n  }\n  return runs\n}\n\nexport interface RowImage {\n  image: HTMLCanvasElement\n  top: number\n  height: number\n}\n\n// One image per group of rows, built once per overview and layout: a pixel\n// per cell, scaled to the group's device height with smoothing only when\n// rows outnumber pixels\nfunction rowImage(\n  data: HaplotypeOverviewData,\n  rows: number[],\n  top: number,\n  height: number,\n  dpr: number,\n): RowImage | undefined {\n  const cols = data.bins.length\n  if (rows.length === 0 || cols === 0 || height <= 0) {\n    return undefined\n  }\n  const cells = makeCanvas(cols, rows.length)\n  const cellsCtx = cells.getContext('2d')!\n  const pixels = cellsCtx.createImageData(cols, rows.length)\n  const stride = data.rows.length\n  rows.forEach((row, y) => {\n    for (let b = 0; b < cols; b++) {\n      const [r, g, bl] = cellColor(data.cells[b * stride + row]!)\n      const o = (y * cols + b) * 4\n      pixels.data[o] = r\n      pixels.data[o + 1] = g\n      pixels.data[o + 2] = bl\n      pixels.data[o + 3] = 255\n    }\n  })\n  cellsCtx.putImageData(pixels, 0, 0)\n  const devHeight = Math.max(1, Math.round(height * dpr))\n  const image = makeCanvas(cols, devHeight)\n  const ctx = image.getContext('2d')!\n  ctx.imageSmoothingEnabled = rows.length > devHeight\n  ctx.imageSmoothingQuality = 'high'\n  ctx.drawImage(cells, 0, 0, cols, devHeight)\n  return { image, top, height }\n}\n\nexport function rowImages(\n  data: HaplotypeOverviewData,\n  layout: OverviewLayout,\n  dpr: number,\n) {\n  const { rows, pinnedCount, pinnedHeight, restHeight } = layout\n  return [\n    rowImage(\n      data,\n      rows.slice(0, pinnedCount),\n      layout.rowsTop,\n      pinnedCount * pinnedHeight,\n      dpr,\n    ),\n    rowImage(\n      data,\n      rows.slice(pinnedCount),\n      layout.restTop,\n      (rows.length - pinnedCount) * restHeight,\n      dpr,\n    ),\n  ].filter(image => image !== undefined)\n}\n\n// The screen span of bp [start, end), which runs right to left on a\n// reversed block\nfunction screenSpan(frame: Frame, start: number, end: number) {\n  const a = frame.xOf(start)\n  const b = frame.xOf(end)\n  return { left: Math.min(a, b), width: Math.abs(b - a), reversed: b < a }\n}\n\n// Each run of bins stretched to its bp, smoothed only when bins outnumber\n// pixels, and mirrored on a reversed block\nfunction blitRows(\n  ctx: CanvasRenderingContext2D,\n  data: HaplotypeOverviewData,\n  images: RowImage[],\n  frame: Frame,\n) {\n  for (const [first, end] of contiguousRuns(data)) {\n    const { left, width, reversed } = screenSpan(\n      frame,\n      data.bins[first]!.start,\n      data.bins[end - 1]!.end,\n    )\n    if (left + width < 0 || left > frame.width) {\n      continue\n    }\n    ctx.imageSmoothingEnabled = end - first > width * frame.dpr\n    for (const { image, top, height } of images) {\n      ctx.save()\n      if (reversed) {\n        ctx.translate(2 * left + width, 0)\n        ctx.scale(-1, 1)\n      }\n      ctx.drawImage(\n        image,\n        first,\n        0,\n        end - first,\n        image.height,\n        left,\n        top,\n        width,\n        height,\n      )\n      ctx.restore()\n    }\n  }\n}\n\nfunction drawDensity(\n  ctx: CanvasRenderingContext2D,\n  data: HaplotypeOverviewData,\n  counts: number[][] | undefined,\n  frame: Frame,\n) {\n  const total = data.rows.length - data.reference.length\n  const most = Math.max(1, ...data.bins.map(bin => bin.variants))\n  const stack: Rgb[] = [[175, 175, 175], PALETTE.partial, ...PALETTE.variant]\n  data.bins.forEach((bin, b) => {\n    const span = screenSpan(frame, bin.start, bin.end)\n    const { left } = span\n    const width = Math.max(span.width, 1 / frame.dpr)\n    if (left + width < 0 || left > frame.width) {\n      return\n    }\n    if (counts) {\n      let y = DENSITY_PX\n      for (const i of [5, 4, 3, 2, 1, 0]) {\n        const h = (DENSITY_PX * counts[b]![i]!) / Math.max(1, total)\n        if (h > 0) {\n          const [r, g, bl] = stack[i]!\n          ctx.fillStyle = `rgb(${r},${g},${bl})`\n          ctx.fillRect(left, y - h, width, h)\n          y -= h\n        }\n      }\n    } else {\n      const h = (DENSITY_PX * bin.variants) / most\n      const [r, g, bl] = PALETTE.variant[1]\n      ctx.fillStyle = `rgb(${r},${g},${bl})`\n      ctx.fillRect(left, DENSITY_PX - h, width, h)\n    }\n  })\n}\n\nfunction drawLabels(\n  ctx: CanvasRenderingContext2D,\n  data: HaplotypeOverviewData,\n  layout: OverviewLayout,\n) {\n  if (layout.pinnedHeight < LABEL_MIN_PX) {\n    return\n  }\n  ctx.font = `${Math.min(11, layout.pinnedHeight - 2)}px sans-serif`\n  ctx.textBaseline = 'middle'\n  for (let i = 0; i < layout.pinnedCount; i++) {\n    const label = data.rows[layout.rows[i]!]!\n    const y = rowTop(layout, i)\n    const w = ctx.measureText(label).width\n    ctx.fillStyle = 'rgba(255,255,255,0.8)'\n    ctx.fillRect(2, y + 1, w + 6, layout.pinnedHeight - 2)\n    ctx.fillStyle = '#222'\n    ctx.fillText(label, 5, y + layout.pinnedHeight / 2)\n  }\n}\n\nfunction formatBp(bp: number) {\n  return bp >= 1_000_000\n    ? `${+(bp / 1_000_000).toFixed(1)} Mb`\n    : `${+(bp / 1000).toFixed(1)} kb`\n}\n\n// What the density band counts, which changes with the bin size\nexport function densityLabel(data: HaplotypeOverviewData) {\n  const haplotypes = data.rows.length - data.reference.length\n  return data.bin <= FINE_BIN_BP\n    ? `haplotypes diverging \u226550 bp, of ${haplotypes} \u00B7 ${formatBp(data.bin)} bins`\n    : `excursions \u226550 bp per ${formatBp(data.bin)} bin, all ${haplotypes} haplotypes`\n}\n\nfunction drawDensityLabel(\n  ctx: CanvasRenderingContext2D,\n  data: HaplotypeOverviewData,\n) {\n  const label = densityLabel(data)\n  ctx.font = '10px sans-serif'\n  ctx.textBaseline = 'top'\n  const w = ctx.measureText(label).width\n  ctx.fillStyle = 'rgba(255,255,255,0.8)'\n  ctx.fillRect(2, 1, w + 6, 13)\n  ctx.fillStyle = '#444'\n  ctx.fillText(label, 5, 2)\n}\n\n// The density band from per-class counts at bins up to FINE_BIN_BP, from\n// excursion counts past them (undefined counts)\nexport function drawOverview(\n  ctx: CanvasRenderingContext2D,\n  data: HaplotypeOverviewData,\n  counts: number[][] | undefined,\n  layout: OverviewLayout,\n  images: RowImage[],\n  frame: Frame,\n) {\n  ctx.clearRect(0, 0, frame.width, frame.height)\n  drawDensity(ctx, data, counts, frame)\n  blitRows(ctx, data, images, frame)\n  drawLabels(ctx, data, layout)\n  drawDensityLabel(ctx, data)\n}\n"],
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+}

package/dist/chunks/{chunk-UTWFU4X6.js → chunk-H54W6OQQ.js}

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