jbrowse-plugin-msaview 5.2.0 → 5.3.0

package/dist/chunks/{chunk-F3EC6OCO.js → chunk-NWHZOZMG.js}

@@ -1,2 +1,2 @@
 function n(c,o){let t=URL.createObjectURL(c),e=document.createElement("a");e.href=t,e.download=o,e.click(),setTimeout(()=>{URL.revokeObjectURL(t)},4e4)}export{n as a};
-//# sourceMappingURL=chunk-F3EC6OCO.js.map
+//# sourceMappingURL=chunk-NWHZOZMG.js.map

package/dist/chunks/{chunk-F3EC6OCO.js.map → chunk-NWHZOZMG.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/vendor/fileSaver.ts"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/vendor/fileSaver.ts"],
   "sourcesContent": ["export function saveAs(blob: Blob, name: string) {\n  const url = URL.createObjectURL(blob)\n  const a = document.createElement('a')\n  a.href = url\n  a.download = name\n  a.click()\n  setTimeout(() => {\n    URL.revokeObjectURL(url)\n  }, 40_000)\n}\n"],
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   "names": ["saveAs", "blob", "name", "url", "a"]

package/dist/chunks/chunk-OVAXNTPN.js

@@ -0,0 +1,2 @@
+function c(t){let o=t.length>1;return t.flatMap(r=>[...o?[{key:r.id,label:r.title}]:[],...r.entries.map(e=>({key:`${r.id}:${e.id}`,label:e.label,color:e.color,hint:e.id}))])}var G=new Set(["exon","CDS","five_prime_UTR","three_prime_UTR","UTR","intron"]),z=["#9fb6d4","#d4dcea"],O=!0,B=!1,P=["both","horizontal","vertical"],X="both",y=8,k=5,Z=9;function A(t){return Math.min(Math.max(6,t-3),18)}var U=A(16),Y=.2,I=1,$=80,J=!0,j="maeditor",q=!0,K=!0,Q=!1,V=70,tt=160,et=10,ot=.3,rt=!0,nt=["branchLength","input","ladderize","ladderizeReverse"],at="branchLength",it=!0,st=!0,lt=!1,ct=!1,ht=120,pt=500,xt=.25,dt="#fff3c4",ut=.6,ft=5e4,gt=56,g=22,mt=200,D=1e3,wt=D+1;var h=8,R=16,_=12,Tt=12,E=7,v=360,C=h+_+6;function M(t){let o=t.reduce((e,n)=>Math.max(e,n.label.length),0),r=C+h+o*E;return Math.min(v,Math.max(120,r))}function N(t){return h*2+t.length*R}function bt(t,o){let{scrollX:r,scrollY:e,totalWidth:n,totalHeight:a,effectiveTreeAreaWidth:m,rowPanelsWidth:w,rowPanelsHeaderHeight:H,totalTrackAreaHeight:S,minimapHeight:L,msaAreaHeight:p,msaCanvasWidth:x,showHorizontalScrollbar:T,treeOverviewHeight:b,treeScaleBar:W}=t,i=o.includeTracks?S:0,l=o.exportType==="viewport"&&!!o.includeMinimap&&T,d=c(t.legends),u=d.length>0?M(d):0,s=Math.max(l?L:0,H,b+(W?g:0)),f=m+w;return o.exportType==="entire"?{width:n+f,msaAreaWidth:n,height:a+i+s,contentHeight:a,trackHeight:i,topHeight:s,offsetX:0,offsetY:0,includeMinimap:l,legendWidth:u}:{width:x+f,msaAreaWidth:x,height:p+s+i,contentHeight:p,trackHeight:i,topHeight:s,offsetX:-r,offsetY:-e,includeMinimap:l,legendWidth:u}}function Wt(t,o){let{width:r,height:e,legendWidth:n,topHeight:a}=o;return{width:r+n,height:n>0?Math.max(e,a+N(c(t.legends))):e}}export{c as a,G as b,z as c,O as d,B as e,P as f,X as g,y as h,k as i,Z as j,A as k,U as l,Y as m,I as n,$ as o,J as p,j as q,q as r,K as s,Q as t,V as u,tt as v,et as w,ot as x,rt as y,nt as z,at as A,it as B,st as C,lt as D,ct as E,ht as F,pt as G,xt as H,dt as I,ut as J,ft as K,gt as L,g as M,mt as N,D as O,wt as P,h as Q,R,_ as S,Tt as T,E as U,C as V,N as W,bt as X,Wt as Y};
+//# sourceMappingURL=chunk-OVAXNTPN.js.map

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

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/msa/legendRows.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/constants.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/exportLayout.ts"],
+  "sourcesContent": ["import type { Legend } from '../../types.ts'\n\nexport interface LegendRow {\n  key: string\n  label: string\n  color?: string\n  hint?: string\n}\n\n// the legends flattened into the rows both the overlay and the export stack\n// top to bottom. A title row separates one legend from the next, and a lone\n// legend needs no title.\nexport function legendRows(legends: Legend[]): LegendRow[] {\n  const titled = legends.length > 1\n  return legends.flatMap(legend => [\n    ...(titled ? [{ key: legend.id, label: legend.title }] : []),\n    ...legend.entries.map(entry => ({\n      key: `${legend.id}:${entry.id}`,\n      label: entry.label,\n      color: entry.color,\n      hint: entry.id,\n    })),\n  ])\n}\n", "import type { TreeOrder } from './types.ts'\n\n// Main model defaults\nexport const defaultRowHeight = 16\nexport const defaultColWidth = 12\nexport const defaultHeight = 550\nexport const defaultScrollX = 0\nexport const defaultScrollY = 0\nexport const defaultCurrentAlignment = 0\n// Only a hidden overlay is stored, so a link that never mentions it opens\n// showing its annotations.\nexport const defaultShowDomains = true\nexport const defaultShowDomainLegend = true\nexport const defaultHideGaps = true\nexport const defaultAllowedGappyness = 100\nexport const defaultSubFeatureRows = false\n// height of one sub-row when subFeatureRows is on, unless the row has more\n// lanes than fit at this height (see renderBoxFeatureCanvasBlock)\nexport const subFeatureRowHeight = 4\n// height of the bar the overlay draws under a row in letter-color mode\nexport const domainUnderlineHeight = 3\n\n// Feature types that are ordinal segments of one transcript. The overlay\n// alternates two shades across them and labels them by number, where a domain\n// type gets its own hue and legend row.\nexport const segmentFeatureTypes = new Set([\n  'exon',\n  'CDS',\n  'five_prime_UTR',\n  'three_prime_UTR',\n  'UTR',\n  'intron',\n])\n\n// the two shades alternated across adjacent segments (exons)\nexport const segmentShades = ['#9fb6d4', '#d4dcea']\nexport const defaultDrawMsaLetters = true\nexport const defaultScrollZoom = false\n\n// Which cell dimensions a wheel zoom scales. 'horizontal' holds the row height,\n// which fixes the label and letter font size while the columns compress.\n// 'vertical' does the reverse.\nexport const scrollZoomAxes = ['both', 'horizontal', 'vertical'] as const\nexport type ScrollZoomAxis = (typeof scrollZoomAxes)[number]\nexport const defaultScrollZoomAxis: ScrollZoomAxis = 'both'\n\n// Cell size floors for drawing residue letters and tree labels. Below these a\n// 500px block holds thousands of glyphs, and fillText dominates every zoom\n// frame. A sprite atlas measured slower.\nexport const minLetterRowHeight = 8\nexport const minLetterColWidth = 5\n\n// A feature span draws its label at two pixels under its height, capped at 11,\n// so a span shorter than this holds no readable text: an underline bar, a\n// sub-row band or a features panel over small rows\nexport const minFeatureLabelHeight = 9\n\nexport function fontSizeFor(rowHeight: number) {\n  return Math.min(Math.max(6, rowHeight - 3), 18)\n}\n\n// The fitted tree area measures the tip labels and the clade labels at the\n// font a default row draws, so a vertical zoom leaves the alignment in place.\n// A larger font ellipsizes the labels.\nexport const labelFitFontSize = fontSizeFor(defaultRowHeight)\n\n// Zoom limits, px per cell. maxCellSize caps both smooth zoom and the stepwise\n// zoom-in buttons (which otherwise grow unbounded). minColWidth/minRowHeight are\n// the smooth-zoom floors.\nexport const minColWidth = 0.2\nexport const minRowHeight = 1\nexport const maxCellSize = 80\n\n// MSA model defaults\nexport const defaultBgColor = true\nexport const defaultColorSchemeName = 'maeditor'\nexport const defaultShowColumnStats = true\n\n// Tree model defaults\nexport const defaultDrawLabels = true\nexport const defaultLabelsAlignRight = false\n// The fitted tree area gives the tree pxPerTreeDepth per level of its depth,\n// between minTreeWidth and maxFitTreeWidth, beside the widest label, and takes\n// at most maxTreeAreaShare of a view with an alignment. Where the share binds,\n// the tree keeps minTreeWidth and the labels ellipsize.\nexport const minTreeWidth = 70\nexport const maxFitTreeWidth = 160\nexport const pxPerTreeDepth = 10\nexport const maxTreeAreaShare = 0.3\nexport const defaultShowBranchLen = true\nexport const treeOrders = [\n  'branchLength',\n  'input',\n  'ladderize',\n  'ladderizeReverse',\n] as const satisfies readonly TreeOrder[]\nexport const defaultTreeOrder: TreeOrder = 'branchLength'\nexport const defaultDrawTree = true\nexport const defaultDrawNodeBubbles = true\nexport const defaultDrawNodeLabels = false\nexport const defaultShowTreeOverview = false\nexport const defaultOverviewHeight = 120\n\n// Neighbor joining does not run above this many rows. The distance matrix is\n// O(n^2*L) and the join loop O(n^3), both on the main thread with no progress\n// and no cancel: 400 rows measured 1.5s, 800 rows 10s, and 1600 would be about\n// seventy. See agent-docs/reference/neighbor-joining-scaling.md.\nexport const maxNeighborJoiningRows = 500\n\n// The opacity a `rowTint` encoding draws its scale's color at, so the residues\n// under the wash stay readable. A color the producer already gave an alpha\n// keeps it.\nexport const rowTintAlpha = 0.25\n\n// The fill a `clades` record with the `highlight` mark draws behind its rows,\n// and the opacity a producer's own color takes when it carries none.\nexport const cladeHighlightColor = '#fff3c4'\nexport const cladeHighlightAlpha = 0.6\n\n// The largest inline document a snapshot carries by default, which keeps a\n// jbrowse session small. A larger pasted or locally-opened file stays in the\n// live model and out of the snapshot, and `unshareableData` warns using the\n// same number. `MSAModelF({ maxInlineSnapshotBytes })` sets another; the demo\n// app's links hold far more.\nexport const maxInlineSnapshotBytes = 50_000\n\n// Height of the band the `rowPanels` headers draw in, above the strips in the\n// top area beside the tree ruler and the minimap. A panel wider than the band\n// is tall writes its header across, where it has more room.\nexport const rowPanelHeaderHeight = 56\n\n// Height of the branch-length scale bar above the tree.\nexport const treeScaleBarHeight = 22\n\n// Width of a `features` row panel that names none, wide enough for a gene\n// neighborhood of a few arrows to read.\nexport const defaultFeaturePanelWidth = 200\n\n// The alignment's overlay canvas draws the mouseover, the persisted highlights\n// and the row tints over the residues, and the legend key floats above that,\n// so a tint reaching the top right corner leaves the key readable.\nexport const msaOverlayZIndex = 1000\nexport const legendZIndex = msaOverlayZIndex + 1\n", "import { legendRows } from './components/msa/legendRows.ts'\nimport { treeScaleBarHeight } from './constants.ts'\n\nimport type { LegendRow } from './components/msa/legendRows.ts'\nimport type { MsaViewModel } from './model.ts'\nimport type { Theme } from '@mui/material'\n\nexport interface ExportSvgOptions {\n  theme: Theme\n  includeMinimap?: boolean\n  includeTracks?: boolean\n  exportType: 'entire' | 'viewport'\n}\n\n// legend geometry, shared by the width calculation and the renderer so the\n// reserved column on the right exactly fits the drawn legends\nexport const LEGEND_PAD = 8\nexport const LEGEND_ROW_H = 16\nexport const LEGEND_SWATCH = 12\nexport const LEGEND_FONT = 12\nexport const LEGEND_CHAR_W = 7\n\nexport const LEGEND_MAX_W = 360\nexport const LEGEND_TEXT_X = LEGEND_PAD + LEGEND_SWATCH + 6\n\nexport function getLegendWidth(rows: LegendRow[]) {\n  const maxLen = rows.reduce((a, r) => Math.max(a, r.label.length), 0)\n  const w = LEGEND_TEXT_X + LEGEND_PAD + maxLen * LEGEND_CHAR_W\n  return Math.min(LEGEND_MAX_W, Math.max(120, w))\n}\n\nexport function legendHeight(rows: LegendRow[]) {\n  return LEGEND_PAD * 2 + rows.length * LEGEND_ROW_H\n}\n\n// resolved sizes/offsets (in svg user units) for the chosen export, shared by\n// every layer; 'entire' renders the whole alignment unscrolled, 'viewport'\n// mirrors the live scroll position\nexport interface Layout {\n  width: number\n  msaAreaWidth: number\n  height: number\n  contentHeight: number\n  trackHeight: number\n  // the band the minimap, the row panel headers and the tree overview stacked\n  // on the scale bar share across the top\n  topHeight: number\n  offsetX: number\n  offsetY: number\n  includeMinimap: boolean\n  legendWidth: number\n}\n\nexport function getLayout(model: MsaViewModel, opts: ExportSvgOptions): Layout {\n  const {\n    scrollX,\n    scrollY,\n    totalWidth,\n    totalHeight,\n    effectiveTreeAreaWidth,\n    rowPanelsWidth,\n    rowPanelsHeaderHeight,\n    totalTrackAreaHeight,\n    minimapHeight,\n    msaAreaHeight,\n    msaCanvasWidth,\n    showHorizontalScrollbar,\n    treeOverviewHeight,\n    treeScaleBar,\n  } = model\n  const trackHeight = opts.includeTracks ? totalTrackAreaHeight : 0\n  // the minimap reflects the live viewport scroll position, so it's only\n  // meaningful for a viewport export, never for the entire alignment -- and\n  // only when the live view shows one at all, since a minimap over an alignment\n  // that already fits marks a viewport wider than the bar\n  const includeMinimap =\n    opts.exportType === 'viewport' &&\n    !!opts.includeMinimap &&\n    showHorizontalScrollbar\n  const rows = legendRows(model.legends)\n  const legendWidth = rows.length > 0 ? getLegendWidth(rows) : 0\n  const topHeight = Math.max(\n    includeMinimap ? minimapHeight : 0,\n    rowPanelsHeaderHeight,\n    treeOverviewHeight + (treeScaleBar ? treeScaleBarHeight : 0),\n  )\n  const gutterWidth = effectiveTreeAreaWidth + rowPanelsWidth\n\n  // width stays content-only; the legend occupies an extra column added at the\n  // svg root in MsaSvg. The viewport export takes the alignment canvas's own\n  // size rather than the widget's -- the widget box also covers the header, the\n  // resize handle and the scrollbars, and rendering that box exports rows and\n  // columns the scrollbars hide on screen\n  return opts.exportType === 'entire'\n    ? {\n        width: totalWidth + gutterWidth,\n        msaAreaWidth: totalWidth,\n        height: totalHeight + trackHeight + topHeight,\n        contentHeight: totalHeight,\n        trackHeight,\n        topHeight,\n        offsetX: 0,\n        offsetY: 0,\n        includeMinimap,\n        legendWidth,\n      }\n    : {\n        width: msaCanvasWidth + gutterWidth,\n        msaAreaWidth: msaCanvasWidth,\n        height: msaAreaHeight + topHeight + trackHeight,\n        contentHeight: msaAreaHeight,\n        trackHeight,\n        topHeight,\n        offsetX: -scrollX,\n        offsetY: -scrollY,\n        includeMinimap,\n        legendWidth,\n      }\n}\n\n/**\n * the exported page's size: the layout plus the legend column, and as tall as\n * the legend where the key outgrows a short alignment\n */\nexport function exportPageSize(model: MsaViewModel, layout: Layout) {\n  const { width, height, legendWidth, topHeight } = layout\n  return {\n    width: width + legendWidth,\n    height:\n      legendWidth > 0\n        ? Math.max(height, topHeight + legendHeight(legendRows(model.legends)))\n        : height,\n  }\n}\n"],
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+  "names": ["legendRows", "legends", "titled", "legend", "entry", "segmentFeatureTypes", "segmentShades", "defaultDrawMsaLetters", "defaultScrollZoom", "scrollZoomAxes", "defaultScrollZoomAxis", "minLetterRowHeight", "minLetterColWidth", "minFeatureLabelHeight", "fontSizeFor", "rowHeight", "labelFitFontSize", "minColWidth", "minRowHeight", "maxCellSize", "defaultBgColor", "defaultColorSchemeName", "defaultShowColumnStats", "defaultDrawLabels", "defaultLabelsAlignRight", "minTreeWidth", "maxFitTreeWidth", "pxPerTreeDepth", "maxTreeAreaShare", "defaultShowBranchLen", "treeOrders", "defaultTreeOrder", "defaultDrawTree", "defaultDrawNodeBubbles", "defaultDrawNodeLabels", "defaultShowTreeOverview", "defaultOverviewHeight", "maxNeighborJoiningRows", "rowTintAlpha", "cladeHighlightColor", "cladeHighlightAlpha", "maxInlineSnapshotBytes", "rowPanelHeaderHeight", "treeScaleBarHeight", "defaultFeaturePanelWidth", "msaOverlayZIndex", "legendZIndex", "LEGEND_PAD", "LEGEND_ROW_H", "LEGEND_SWATCH", "LEGEND_FONT", "LEGEND_CHAR_W", "LEGEND_MAX_W", "LEGEND_TEXT_X", "getLegendWidth", "rows", "maxLen", "a", "r", "w", "legendHeight", "getLayout", "model", "opts", "scrollX", "scrollY", "totalWidth", "totalHeight", "effectiveTreeAreaWidth", "rowPanelsWidth", "rowPanelsHeaderHeight", "totalTrackAreaHeight", "minimapHeight", "msaAreaHeight", "msaCanvasWidth", "showHorizontalScrollbar", "treeOverviewHeight", "treeScaleBar", "trackHeight", "includeMinimap", "legendRows", "legendWidth", "topHeight", "treeScaleBarHeight", "gutterWidth", "exportPageSize", "layout", "width", "height"]
+}

package/dist/chunks/chunk-TSHN6J7U.js

@@ -0,0 +1,2 @@
+var o=["ArrowLeft","ArrowRight","ArrowUp","ArrowDown"],l=[{label:"Arrow keys",action:"Scroll one cell",keys:o},{label:"Shift + arrow keys",action:"Scroll one page",keys:o,shiftKey:!0},{label:"+ and -",action:"Zoom in and out",keys:["+","=","-"]},{label:"Home and End",action:"Jump to the first and last column",keys:["Home","End"]},{label:"Escape",action:"Clear the selection",keys:["Escape"]}],a={label:"Shift + drag",action:"Select a block of cells"},t=[{label:"Drag",action:"Pan the alignment"},{label:"Wheel",action:"Scroll, or zoom as set in Alignment settings \u2192 Mouse wheel"},{label:"Ctrl + wheel",action:"Zoom at the cursor"},a,{label:"Drag along a track",action:"Select a range of columns across every row"},{label:"Click a tree node",action:"Collapse, rotate, reroot or show only that clade"},{label:"Click the tree overview",action:"Show only the clade under the pointer"},{label:"Drag a divider",action:"Resize the tree area or a track"}],r=["Alignment",...[...l,a].map(e=>`${e.label}: ${e.action}`)].join(". ");export{l as a,t as b,r as c};
+//# sourceMappingURL=chunk-TSHN6J7U.js.map

package/dist/chunks/chunk-TSHN6J7U.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/controls.ts"],
+  "sourcesContent": ["export interface Control {\n  label: string\n  action: string\n}\n\nexport interface KeyControl extends Control {\n  keys: string[]\n  shiftKey?: boolean\n}\n\nconst arrows = ['ArrowLeft', 'ArrowRight', 'ArrowUp', 'ArrowDown']\n\nexport const keyboardControls: KeyControl[] = [\n  { label: 'Arrow keys', action: 'Scroll one cell', keys: arrows },\n  {\n    label: 'Shift + arrow keys',\n    action: 'Scroll one page',\n    keys: arrows,\n    shiftKey: true,\n  },\n  { label: '+ and -', action: 'Zoom in and out', keys: ['+', '=', '-'] },\n  {\n    label: 'Home and End',\n    action: 'Jump to the first and last column',\n    keys: ['Home', 'End'],\n  },\n  { label: 'Escape', action: 'Clear the selection', keys: ['Escape'] },\n]\n\nconst selectCells: Control = {\n  label: 'Shift + drag',\n  action: 'Select a block of cells',\n}\n\nexport const mouseControls: Control[] = [\n  { label: 'Drag', action: 'Pan the alignment' },\n  {\n    label: 'Wheel',\n    action: 'Scroll, or zoom as set in Alignment settings \u2192 Mouse wheel',\n  },\n  { label: 'Ctrl + wheel', action: 'Zoom at the cursor' },\n  selectCells,\n  {\n    label: 'Drag along a track',\n    action: 'Select a range of columns across every row',\n  },\n  {\n    label: 'Click a tree node',\n    action: 'Collapse, rotate, reroot or show only that clade',\n  },\n  {\n    label: 'Click the tree overview',\n    action: 'Show only the clade under the pointer',\n  },\n  { label: 'Drag a divider', action: 'Resize the tree area or a track' },\n]\n\nexport const alignmentAriaLabel = [\n  'Alignment',\n  ...[...keyboardControls, selectCells].map(c => `${c.label}: ${c.action}`),\n].join('. ')\n"],
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+}

package/dist/chunks/{chunk-H6IQBAW7.js → chunk-WAPIOD25.js}

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+//# sourceMappingURL=chunk-WAPIOD25.js.map

package/dist/chunks/{chunk-H6IQBAW7.js.map → chunk-WAPIOD25.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/MetadataTable.tsx", "../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/SequenceTextArea.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/MetadataTable.tsx", "../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/SequenceTextArea.tsx"],
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package/dist/chunks/chunk-XVNCZQMR.js

@@ -0,0 +1,2 @@
+import{j as m,p as l,q as h,u as p}from"./chunk-A63PUWQZ.js";var g="ncbiblast";function f(e){return(e.hits??[]).map(t=>{let n=Number.parseInt(t.hit_uni_ox??"",10);return{accession:t.hit_acc??"unknown",id:t.hit_id??t.hit_acc??"unknown",sciname:t.hit_uni_os??t.hit_os??"unknown",taxid:Number.isNaN(n)?void 0:n,title:t.hit_uni_de??t.hit_desc,sequence:(t.hit_hsps?.[0]?.hsp_hseq??"").replaceAll("-","")}})}function E(e){return`https://www.ebi.ac.uk/jdispatcher/sss/${g}/summary?jobId=${e}`}async function w({query:e,blastDatabase:t,maxHits:n,onProgress:r,onRid:s,signal:i}){let a=String(h(n??l)),o=await m({tool:g,label:"BLAST",params:{program:"blastp",stype:"protein",database:t,sequence:e,alignments:a,scores:a},onProgress:r,onRid:s,signal:i});return{rid:o.jobId,hits:f(JSON.parse(await o.result("json")))}}var R=({database:e,...t})=>w({blastDatabase:e,...t});var u="hmmer3_phmmer";function O(e){return`https://www.ebi.ac.uk/jdispatcher/sss/${u}/summary?jobId=${e}`}function H(e){return e.startsWith(`${u}-`)}function x({rf:e,query:t}){let n=0,r=Array.from(e,s=>s==="x"?t[n++]??"-":"-").join("");if(n!==t.length)throw new Error(`phmmer alignment has ${n} match columns for a query of ${t.length} residues, so the query row cannot be placed`);return r}function _(e){let t=(e??"").replace("[subseq from] ","");if(t.includes("^|^")){let s=t.split("^|^"),i=s[6];return{id:s[0]||void 0,sciname:s[5]||"unknown",taxid:i&&/^\d+$/.test(i)?Number.parseInt(i,10):void 0,title:s[2]||void 0}}let n=/OS=(.*?)\s+(?:OX|GN|PE|SV)=/.exec(t)?.[1],r=/OX=(\d+)/.exec(t)?.[1];return{id:void 0,sciname:n??"unknown",taxid:r?Number.parseInt(r,10):void 0,title:t.split(" OS=")[0]||void 0}}function S(e){let t=e.lastIndexOf("/"),n=t===-1?void 0:/^\d+-\d+$/.exec(e.slice(t+1))?.[0],r=n===void 0?e:e.slice(0,t),s=r.split("|");return s.length===3?{accession:s[1],id:s[2],range:n}:{accession:r,id:r,range:n}}function y({stockholm:e,query:t}){let{gc:n,gs:r,seqdata:s,seqname:i}=new p(e,0).getMSA(),a=n.RF;if(!a)throw new Error("phmmer alignment has no #=GC RF line");return{queryRow:x({rf:a,query:t}),rows:i.map(o=>{let{id:d,...b}=_(r.DE?.[o]?.[0]),c=S(o);return{...c,id:c.id===c.accession&&d?d:c.id,...b,aligned:(s[o]??"").replaceAll(".","-").toUpperCase()}})}}async function B({query:e,database:t,maxHits:n,onProgress:r,onRid:s,signal:i}){let a=await m({tool:u,label:"phmmer",params:{database:t,sequence:e,alignView:"true",...n?{nhits:String(n)}:{}},onProgress:r,onRid:s,signal:i});return{rid:a.jobId,...y({stockholm:await a.result("sto"),query:e})}}function q(e){return e.map(({aligned:t,...n})=>({...n,sequence:t}))}var I=async({database:e,...t})=>{let{rows:n,queryRow:r,rid:s}=await B({database:e,...t});return{rid:s,queryRow:r,hits:q(n)}};export{E as a,R as b,O as c,H as d,I as e};
+//# sourceMappingURL=chunk-XVNCZQMR.js.map

package/dist/chunks/{chunk-ZCT7RD24.js.map → chunk-XVNCZQMR.js.map}

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["../../src/utils/ebiBlast.ts", "../../src/utils/phmmer.ts"],
   "sourcesContent": ["import {\n  defaultMaxHits,\n  snapBlastHitCount,\n} from '../LaunchMsaView/components/BlastQuery/consts'\nimport { runEbiJob } from './ebiJobDispatcher'\n\nimport type { BlastDatabase } from '../LaunchMsaView/components/BlastQuery/consts'\nimport type { SearchBackend, SearchHit } from './homologSearch'\n\nconst TOOL = 'ncbiblast'\n\n/**\n * The subset of EBI's ncbiblast JSON result this plugin reads. The service\n * returns a great deal more per hit (urls, bit scores, e-values, the match\n * string); only what the MSA rows are built from is typed here.\n */\ninterface EbiBlastJson {\n  hits?: {\n    hit_acc?: string\n    hit_id?: string\n    hit_desc?: string\n    /** the UniProt fields are absent on hits from non-UniProt databases */\n    hit_os?: string\n    hit_uni_de?: string\n    hit_uni_os?: string\n    /** NCBI taxon id, delivered as a string */\n    hit_uni_ox?: string\n    hit_hsps?: { hsp_hseq?: string }[]\n  }[]\n}\n\n/**\n * EBI's hits as search hits. BLAST's alignments are pairwise, one hit at a\n * time, so the gaps come back off and an aligner gets bare sequences. Exported\n * for testing against a captured response: nothing else in CI would notice if\n * EBI renamed a field.\n */\nexport function normalizeEbiBlastHits(result: EbiBlastJson): SearchHit[] {\n  return (result.hits ?? []).map(hit => {\n    const taxid = Number.parseInt(hit.hit_uni_ox ?? '', 10)\n    return {\n      accession: hit.hit_acc ?? 'unknown',\n      id: hit.hit_id ?? hit.hit_acc ?? 'unknown',\n      sciname: hit.hit_uni_os ?? hit.hit_os ?? 'unknown',\n      taxid: Number.isNaN(taxid) ? undefined : taxid,\n      // hit_uni_de is the bare protein name; hit_desc repeats it with the\n      // OS=/OX=/GN= suffix that makeId already covers with real columns\n      title: hit.hit_uni_de ?? hit.hit_desc,\n      sequence: (hit.hit_hsps?.[0]?.hsp_hseq ?? '').replaceAll('-', ''),\n    }\n  })\n}\n\n/**\n * Human-facing link to a job, shown while it runs and on error \u2014 so it has to\n * be EBI's own results UI, not the REST result endpoint, which does not exist\n * yet at the moment the link is on screen.\n */\nexport function ebiBlastResultUrl(jobId: string) {\n  return `https://www.ebi.ac.uk/jdispatcher/sss/${TOOL}/summary?jobId=${jobId}`\n}\n\nexport async function queryEbiBlast({\n  query,\n  blastDatabase,\n  maxHits,\n  onProgress,\n  onRid,\n  signal,\n}: {\n  query: string\n  blastDatabase: BlastDatabase\n  /** rounded up to a count EBI accepts */\n  maxHits?: number\n  onProgress: (arg: string) => void\n  onRid: (arg: string) => void\n  signal?: AbortSignal\n}) {\n  const hitCount = String(snapBlastHitCount(maxHits ?? defaultMaxHits))\n  const job = await runEbiJob({\n    tool: TOOL,\n    label: 'BLAST',\n    params: {\n      program: 'blastp',\n      stype: 'protein',\n      database: blastDatabase,\n      sequence: query,\n      alignments: hitCount,\n      scores: hitCount,\n    },\n    onProgress,\n    onRid,\n    signal,\n  })\n  return {\n    rid: job.jobId,\n    hits: normalizeEbiBlastHits(\n      JSON.parse(await job.result('json')) as EbiBlastJson,\n    ),\n  }\n}\n\nexport const searchEbiBlast: SearchBackend = ({ database, ...request }) =>\n  queryEbiBlast({ blastDatabase: database as BlastDatabase, ...request })\n", "import { StockholmMSA } from 'msa-parsers'\n\nimport { runEbiJob } from './ebiJobDispatcher'\n\nimport type { PhmmerDatabase } from '../LaunchMsaView/components/BlastQuery/consts'\nimport type { SearchBackend, SearchHit } from './homologSearch'\n\nconst TOOL = 'hmmer3_phmmer'\n\nexport interface PhmmerRow {\n  accession: string\n  id: string\n  sciname: string\n  taxid?: number\n  title?: string\n  /** the matched envelope on the target, e.g. '503-912', absent if unparseable */\n  range?: string\n  /** the row as phmmer aligned it, uppercased with '.' inserts turned into '-' */\n  aligned: string\n}\n\nexport interface PhmmerAlignment {\n  rows: PhmmerRow[]\n  /**\n   * the query, placed into the same columns. phmmer does not put the query in\n   * its own output, so this is derived \u2014 see buildQueryRow.\n   */\n  queryRow: string\n}\n\n/**\n * Human-facing link to a job, shown while it runs and on error.\n *\n * The category has to be sss: jdispatcher serves its shell with a 200 for any\n * category, so /pfa/ and /psa/ look fine to a fetch and render \"Page Not Found\"\n * in a browser.\n */\nexport function phmmerResultUrl(jobId: string) {\n  return `https://www.ebi.ac.uk/jdispatcher/sss/${TOOL}/summary?jobId=${jobId}`\n}\n\n/** EBI job ids are prefixed with the tool that made them */\nexport function isPhmmerJobId(jobId: string) {\n  return jobId.startsWith(`${TOOL}-`)\n}\n\n/**\n * phmmer aligns every hit to a profile built from the query, one match state\n * per query residue, and marks those columns 'x' in #=GC RF. So the query's own\n * row is exactly recoverable: walk RF, consume a query residue at each match\n * column, gap everywhere else.\n *\n * This is the one piece of real logic here rather than a library call, and it\n * is checked hard: if the match columns do not account for the query exactly,\n * the columns and the query have drifted apart, and a query row that is off by\n * even one residue would silently mis-map every column to the genome. Throwing\n * is much better than drawing that.\n */\nfunction buildQueryRow({ rf, query }: { rf: string; query: string }) {\n  let consumed = 0\n  const row = Array.from(rf, c =>\n    c === 'x' ? (query[consumed++] ?? '-') : '-',\n  ).join('')\n  if (consumed !== query.length) {\n    throw new Error(\n      `phmmer alignment has ${consumed} match columns for a query of ${query.length} residues, so the query row cannot be placed`,\n    )\n  }\n  return row\n}\n\n/**\n * '[subseq from] Albumin OS=Homo sapiens OX=9606 GN=ALB PE=1 SV=2' is what a\n * UniProt target's #=GS DE looks like. The representative-proteome databases\n * (rp15..rp75) write the same facts as caret-pipe fields instead --\n * 'P53_HUMAN^|^DNHU53^|^Cellular tumor antigen p53^|^...^|^Homo sapiens^|^9606^|^Euk/mammal^|^40674'\n * -- so both grammars are read. Hits from the non-UniProt databases phmmer\n * also offers (PDB, AlphaFold, MEROPS...) carry neither, so every field here\n * is optional.\n */\nfunction parseDescription(de: string | undefined) {\n  const text = (de ?? '').replace('[subseq from] ', '')\n  if (text.includes('^|^')) {\n    const fields = text.split('^|^')\n    const ox = fields[6]\n    return {\n      id: fields[0] || undefined,\n      sciname: fields[5] || 'unknown',\n      taxid: ox && /^\\d+$/.test(ox) ? Number.parseInt(ox, 10) : undefined,\n      title: fields[2] || undefined,\n    }\n  }\n  const sciname = /OS=(.*?)\\s+(?:OX|GN|PE|SV)=/.exec(text)?.[1]\n  const ox = /OX=(\\d+)/.exec(text)?.[1]\n  return {\n    id: undefined,\n    sciname: sciname ?? 'unknown',\n    taxid: ox ? Number.parseInt(ox, 10) : undefined,\n    title: text.split(' OS=')[0] || undefined,\n  }\n}\n\n/**\n * Target names look like 'sp|P02768|ALBU_HUMAN/1-609' for UniProt databases and\n * like anything at all for the others, so an unrecognized name becomes its own\n * accession rather than being dropped.\n */\nfunction parseName(name: string) {\n  const slash = name.lastIndexOf('/')\n  const range =\n    slash === -1 ? undefined : /^\\d+-\\d+$/.exec(name.slice(slash + 1))?.[0]\n  const bare = range === undefined ? name : name.slice(0, slash)\n  const parts = bare.split('|')\n  return parts.length === 3\n    ? { accession: parts[1]!, id: parts[2]!, range }\n    : { accession: bare, id: bare, range }\n}\n\n/**\n * Exported for testing against a captured .sto \u2014 the annotation names (RF, the\n * DE line's OS=/OX=) are the whole risk in this mapping, and nothing else in CI\n * would notice if HMMER or EBI changed one.\n */\nexport function parsePhmmerAlignment({\n  stockholm,\n  query,\n}: {\n  stockholm: string\n  query: string\n}): PhmmerAlignment {\n  const { gc, gs, seqdata, seqname } = new StockholmMSA(stockholm, 0).getMSA()\n  const rf = gc.RF\n  if (!rf) {\n    throw new Error('phmmer alignment has no #=GC RF line')\n  }\n\n  return {\n    queryRow: buildQueryRow({ rf, query }),\n    rows: seqname.map(name => {\n      const { id, ...description } = parseDescription(gs.DE?.[name]?.[0])\n      const parsed = parseName(name)\n      return {\n        ...parsed,\n        // the rp databases name a row by bare accession and put the mnemonic\n        // id in the description instead\n        id: parsed.id === parsed.accession && id ? id : parsed.id,\n        ...description,\n        // insert columns come back lowercase with '.' for gaps; the MSA renderer\n        // looks colors up by the literal letter, so lowercase would draw\n        // uncolored. The insert columns stay visible as gaps in the query row.\n        aligned: (seqdata[name] ?? '').replaceAll('.', '-').toUpperCase(),\n      }\n    }),\n  }\n}\n\nexport async function queryPhmmer({\n  query,\n  database,\n  maxHits,\n  onProgress,\n  onRid,\n  signal,\n}: {\n  query: string\n  database: PhmmerDatabase\n  /** EBI's `nhits`, 100 when omitted */\n  maxHits?: number\n  onProgress: (arg: string) => void\n  onRid: (arg: string) => void\n  signal?: AbortSignal\n}) {\n  const job = await runEbiJob({\n    tool: TOOL,\n    label: 'phmmer',\n    params: {\n      database,\n      sequence: query,\n      // the alignment is the whole point of using phmmer here\n      alignView: 'true',\n      ...(maxHits ? { nhits: String(maxHits) } : {}),\n    },\n    onProgress,\n    onRid,\n    signal,\n  })\n  return {\n    rid: job.jobId,\n    ...parsePhmmerAlignment({ stockholm: await job.result('sto'), query }),\n  }\n}\n\n/** phmmer's rows as search hits: the aligned row is the hit's sequence. */\nexport function toSearchHits(rows: PhmmerRow[]): SearchHit[] {\n  return rows.map(({ aligned, ...rest }) => ({ ...rest, sequence: aligned }))\n}\n\n/**\n * phmmer as a search backend. 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 }

package/dist/chunks/{dist-CMWKVHC7.js → dist-GXYZN4ZR.js}

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r=this.__parsedFont(),i=this.__closestGroupOrSvg(),n=this.__createElement("text",{"font-family":r.fontFamily,"font-size":r.fontSize,"font-style":m("font-style",r.fontStyle),"font-weight":m("font-weight",r.fontWeight),x:e,y:s,"text-anchor":x(this.textAlign),"dominant-baseline":m("dominant-baseline",v(this.textBaseline))},!0);n.appendChild(this.__document.createTextNode(t)),this.__currentElement=n,this.__applyTransformation(n),this.__applyStyleToCurrentElement("fill"),i.appendChild(n)}measureText(t){return this.__ctx.font=this.font,this.__ctx.measureText(t)}arc(t,e,s,r,i,n){if(r===i)return;r=r%(2*Math.PI),i=i%(2*Math.PI),r===i&&(i=(i+2*Math.PI-.001*(n?-1:1))%(2*Math.PI));let a=t+s*Math.cos(i),_=e+s*Math.sin(i),f=t+s*Math.cos(r),u=e+s*Math.sin(r),l=n?0:1,c=i-r;c<0&&(c+=2*Math.PI);let g=n?c>Math.PI?0:1:c>Math.PI?1:0,{x:y,y:S}=this.__getTransformScale(),p=this.__matrixTransform(a,_);this.lineTo(f,u),this.__addPathCommand(`A ${s*y} ${s*S} 0 ${g} ${l} ${p.x} ${p.y}`),this.__currentPosition={x:a,y:_}}setLineDash(t){this.lineDash=t.length>0?t.join(","):null}setTransform(t,e,s,r,i,n){this.__transformMatrix=t instanceof DOMMatrix?new DOMMatrix([t.a,t.b,t.c,t.d,t.e,t.f]):new DOMMatrix([t,e,s,r,i,n])}getTransform(){let{a:t,b:e,c:s,d:r,e:i,f:n}=this.__transformMatrix;return new DOMMatrix([t,e,s,r,i,n])}resetTransform(){this.setTransform(1,0,0,1,0,0)}scale(t,e){e===void 0&&(e=t),!(isNaN(t)||isNaN(e)||!isFinite(t)||!isFinite(e))&&this.setTransform(this.getTransform().scale(t,e))}translate(t,e){this.setTransform(this.getTransform().translate(t,e))}__matrixTransform(t,e){return new DOMPoint(t,e).matrixTransform(this.__transformMatrix)}__getTransformScale(){return{x:Math.hypot(this.__transformMatrix.a,this.__transformMatrix.b),y:Math.hypot(this.__transformMatrix.c,this.__transformMatrix.d)}}};export{d as Context};
-//# sourceMappingURL=dist-CMWKVHC7.js.map
+import"./chunk-FY3BTKY4.js";function S(_){let t={left:"start",right:"end",center:"middle",start:"start",end:"end"};return t[_]||t.start}function b(_){let t={alphabetic:"alphabetic",hanging:"hanging",top:"text-before-edge",bottom:"text-after-edge",middle:"central"};return t[_]||t.alphabetic}var v={"font-style":"normal","font-weight":"normal","dominant-baseline":"alphabetic"};function c(_,t){return t===v[_]?void 0:t}var h={strokeStyle:{svgAttr:"stroke",canvas:"#000000",svg:"none",apply:"stroke"},fillStyle:{svgAttr:"fill",canvas:"#000000",svg:null,apply:"fill"},lineWidth:{svgAttr:"stroke-width",canvas:1,svg:1,apply:"stroke"},font:{canvas:"10px sans-serif"},textAlign:{canvas:"start"},textBaseline:{canvas:"alphabetic"},lineDash:{svgAttr:"stroke-dasharray",canvas:null,svg:null,apply:"stroke"}},T=/rgba\(\s*(\d*\.?\d+)\s*,\s*(\d*\.?\d+)\s*,\s*(\d*\.?\d+)\s*,\s*(\d?\.?\d*)\s*\)/i,u=class{width;height;canvas;__document;__ctx;__canvas;__root;__currentElement;__styleStack;__groupStack;__currentDefaultPath;__currentPosition;__transformMatrix;__transformMatrixStack;__fontCache=new Map;strokeStyle;fillStyle;lineWidth;font;textAlign;textBaseline;lineDash;constructor(t,e,s={}){this.width=t,this.height=e,this.canvas=this,this.__document=s.document||document,s.ctx?this.__ctx=s.ctx:(this.__canvas=this.__document.createElement("canvas"),this.__ctx=this.__canvas.getContext("2d")),this.__setDefaultStyles(),this.__styleStack=[this.__getStyleState()],this.__groupStack=[],this.__root=this.__document.createElementNS("http://www.w3.org/2000/svg","svg"),this.__root.setAttribute("version","1.1"),this.__root.setAttribute("xmlns","http://www.w3.org/2000/svg"),this.__root.setAttribute("width",String(t)),this.__root.setAttribute("height",String(e)),this.__currentElement=this.__document.createElementNS("http://www.w3.org/2000/svg","g"),this.__root.appendChild(this.__currentElement),this.__currentDefaultPath="",this.__currentPosition={},this.__transformMatrix=new DOMMatrix,this.resetTransform()}__createElement(t,e={},s){let r=this.__document.createElementNS("http://www.w3.org/2000/svg",t);s&&(r.setAttribute("fill","none"),r.setAttribute("stroke","none"));for(let i of Object.keys(e)){let n=e[i];n!=null&&r.setAttribute(i,n)}return r}__setDefaultStyles(){for(let t of Object.keys(h))this[t]=h[t].canvas}__applyStyleState(t){for(let e of Object.keys(t))this[e]=t[e]}__getStyleState(){let t={};for(let e of Object.keys(h))t[e]=this[e];return t}__applyTransformation(t,e){let{a:s,b:r,c:i,d:n,e:a,f:o}=e||this.getTransform();if(s===1&&r===0&&i===0&&n===1&&t.hasAttribute("x")&&t.hasAttribute("y")){a!==0&&t.setAttribute("x",String(Number(t.getAttribute("x"))+a)),o!==0&&t.setAttribute("y",String(Number(t.getAttribute("y"))+o));return}t.setAttribute("transform",`matrix(${s} ${r} ${i} ${n} ${a} ${o})`)}__applyStyleToCurrentElement(t){let e=this.__currentElement;for(let s of Object.keys(h)){let r=h[s],i=this[s];if(!r.apply?.includes(t)||r.svg===i)continue;let n=(r.svgAttr==="stroke"||r.svgAttr==="fill")&&typeof i=="string"&&i.includes("rgba")?T.exec(i):null;if(n)e.setAttribute(r.svgAttr,`rgb(${n[1]},${n[2]},${n[3]})`),e.setAttribute(`${r.svgAttr}-opacity`,n[4]);else if(s==="lineWidth"){let a=this.__getTransformScale();e.setAttribute(r.svgAttr,String(i*Math.max(a.x,a.y)))}else e.setAttribute(r.svgAttr,i)}t==="fill"&&e.getAttribute("stroke")==="none"&&e.removeAttribute("stroke")}__closestGroupOrSvg(t){return t=t||this.__currentElement,t.nodeName==="g"||t.nodeName==="svg"?t:this.__closestGroupOrSvg(t.parentNode)}getSvg(){return this.__root}save(){let t=this.__createElement("g"),e=this.__closestGroupOrSvg();this.__groupStack.push(e),e.appendChild(t),this.__currentElement=t,this.__styleStack.push(this.__getStyleState()),this.__transformMatrixStack||(this.__transformMatrixStack=[]),this.__transformMatrixStack.push(this.getTransform())}restore(){this.__currentElement=this.__groupStack.pop(),this.__currentElement||(this.__currentElement=this.__root.childNodes[0]),this.__applyStyleState(this.__styleStack.pop()),this.__transformMatrixStack&&this.__transformMatrixStack.length>0&&this.setTransform(this.__transformMatrixStack.pop())}beginPath(){this.__currentDefaultPath="",this.__currentPosition={};let t=this.__createElement("path",{},!0);this.__closestGroupOrSvg().appendChild(t),this.__currentElement=t}__applyCurrentDefaultPath(){this.__currentElement.nodeName==="path"&&this.__currentElement.setAttribute("d",this.__currentDefaultPath)}__addPathCommand(t){this.__currentDefaultPath+=" ",this.__currentDefaultPath+=t}moveTo(t,e){this.__currentElement.nodeName!=="path"&&this.beginPath(),this.__currentPosition={x:t,y:e};let s=this.__matrixTransform(t,e);this.__addPathCommand(`M ${s.x} ${s.y}`)}closePath(){this.__currentDefaultPath&&this.__addPathCommand("Z")}lineTo(t,e){this.__currentPosition={x:t,y:e};let s=this.__matrixTransform(t,e);this.__addPathCommand(this.__currentDefaultPath.includes("M")?`L ${s.x} ${s.y}`:`M ${s.x} ${s.y}`)}quadraticCurveTo(t,e,s,r){this.__currentPosition={x:s,y:r};let i=this.__matrixTransform(t,e),n=this.__matrixTransform(s,r);this.__addPathCommand(`Q ${i.x} ${i.y} ${n.x} ${n.y}`)}__applyPaintOrder(t,e){let s=this.__currentElement;s.nodeName==="path"&&s.hasAttribute(e)&&s.getAttribute(e)!=="none"&&s.setAttribute("paint-order",t)}stroke(){this.__applyPaintOrder("fill stroke markers","fill"),this.__applyCurrentDefaultPath(),this.__applyStyleToCurrentElement("stroke")}fill(){this.__applyPaintOrder("stroke fill markers","stroke"),this.__applyCurrentDefaultPath(),this.__applyStyleToCurrentElement("fill")}fillRect(t,e,s,r){let i=this.__createElement("rect",{x:t,y:e,width:s,height:r},!0);this.__closestGroupOrSvg().appendChild(i),this.__currentElement=i,this.__applyTransformation(i),this.__applyStyleToCurrentElement("fill")}strokeRect(t,e,s,r){let i=this.__createElement("rect",{x:t,y:e,width:s,height:r},!0);this.__closestGroupOrSvg().appendChild(i),this.__currentElement=i,this.__applyTransformation(i),this.__applyStyleToCurrentElement("stroke")}__parsedFont(){let t=this.__fontCache.get(this.font);if(t)return t;let e=document.createElement("span");return e.setAttribute("style",`font:${this.font}`),this.__fontCache.set(this.font,e.style),e.style}fillText(t,e,s){let r=this.__parsedFont(),i=this.__closestGroupOrSvg(),n=this.__createElement("text",{"font-family":r.fontFamily,"font-size":r.fontSize,"font-style":c("font-style",r.fontStyle),"font-weight":c("font-weight",r.fontWeight),x:e,y:s,"text-anchor":S(this.textAlign),"dominant-baseline":c("dominant-baseline",b(this.textBaseline))},!0);n.appendChild(this.__document.createTextNode(t)),this.__currentElement=n,this.__applyTransformation(n),this.__applyStyleToCurrentElement("fill"),i.appendChild(n)}measureText(t){return this.__ctx.font=this.font,this.__ctx.measureText(t)}arc(t,e,s,r,i,n){if(r===i)return;r=r%(2*Math.PI),i=i%(2*Math.PI),r===i&&(i=(i+2*Math.PI-.001*(n?-1:1))%(2*Math.PI));let a=t+s*Math.cos(i),o=e+s*Math.sin(i),m=t+s*Math.cos(r),p=e+s*Math.sin(r),d=n?0:1,l=i-r;l<0&&(l+=2*Math.PI);let g=n?l>Math.PI?0:1:l>Math.PI?1:0,{x:y,y:x}=this.__getTransformScale(),f=this.__matrixTransform(a,o);this.lineTo(m,p),this.__addPathCommand(`A ${s*y} ${s*x} 0 ${g} ${d} ${f.x} ${f.y}`),this.__currentPosition={x:a,y:o}}setLineDash(t){this.lineDash=t.length>0?t.join(","):null}setTransform(t,e,s,r,i,n){this.__transformMatrix=t instanceof DOMMatrix?new DOMMatrix([t.a,t.b,t.c,t.d,t.e,t.f]):new DOMMatrix([t,e,s,r,i,n])}getTransform(){let{a:t,b:e,c:s,d:r,e:i,f:n}=this.__transformMatrix;return new DOMMatrix([t,e,s,r,i,n])}resetTransform(){this.setTransform(1,0,0,1,0,0)}scale(t,e){e===void 0&&(e=t),!(isNaN(t)||isNaN(e)||!isFinite(t)||!isFinite(e))&&this.setTransform(this.getTransform().scale(t,e))}translate(t,e){this.setTransform(this.getTransform().translate(t,e))}__matrixTransform(t,e){return new DOMPoint(t,e).matrixTransform(this.__transformMatrix)}__getTransformScale(){return{x:Math.hypot(this.__transformMatrix.a,this.__transformMatrix.b),y:Math.hypot(this.__transformMatrix.c,this.__transformMatrix.d)}}};export{u as Context};
+//# sourceMappingURL=dist-GXYZN4ZR.js.map

package/dist/chunks/{dist-CMWKVHC7.js.map → dist-GXYZN4ZR.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+svgcanvas@9.0.0/node_modules/@jbrowse/svgcanvas/src/index.ts"],
-  "sourcesContent": ["/**\n * SVGCanvas v2.0.3\n * Draw on SVG using Canvas's 2D Context API.\n *\n * Licensed under the MIT license:\n * http://www.opensource.org/licenses/mit-license.php\n *\n * Original Authors: Kerry Liu, Zeno Zeng\n * Copyright (c) 2014 Gliffy Inc.\n * Copyright (c) 2021 Zeno Zeng\n *\n * Vendored, converted to ESM/TypeScript, and cut down to the calls the\n * renderers make: rectangles, paths, arcs and glyphs.\n */\n\n/* eslint-disable @typescript-eslint/no-explicit-any */\n\nfunction getTextAnchor(textAlign: string): string {\n  const mapping: Record<string, string> = {\n    left: 'start',\n    right: 'end',\n    center: 'middle',\n    start: 'start',\n    end: 'end',\n  }\n  return mapping[textAlign] || mapping.start!\n}\n\nfunction getDominantBaseline(textBaseline: string): string {\n  const mapping: Record<string, string> = {\n    alphabetic: 'alphabetic',\n    hanging: 'hanging',\n    top: 'text-before-edge',\n    bottom: 'text-after-edge',\n    middle: 'central',\n  }\n  return mapping[textBaseline] || mapping.alphabetic!\n}\n\n/**\n * SVG's initial values for text presentation attributes. Omitting them from\n * every glyph takes ~22% off a sequence-logo figure.\n */\nconst TEXT_ATTR_DEFAULTS: Record<string, string> = {\n  'font-style': 'normal',\n  'font-weight': 'normal',\n  // the initial value is `auto`, which resolves to the alphabetic baseline\n  'dominant-baseline': 'alphabetic',\n}\n\nfunction omitDefault(attr: string, value: string | undefined) {\n  return value === TEXT_ATTR_DEFAULTS[attr] ? undefined : value\n}\n\nconst STYLES: Record<string, any> = {\n  strokeStyle: {\n    svgAttr: 'stroke',\n    canvas: '#000000',\n    svg: 'none',\n    apply: 'stroke',\n  },\n  fillStyle: {\n    svgAttr: 'fill',\n    canvas: '#000000',\n    svg: null,\n    apply: 'fill',\n  },\n  lineWidth: {\n    svgAttr: 'stroke-width',\n    canvas: 1,\n    svg: 1,\n    apply: 'stroke',\n  },\n  font: {\n    canvas: '10px sans-serif',\n  },\n  textAlign: {\n    canvas: 'start',\n  },\n  textBaseline: {\n    canvas: 'alphabetic',\n  },\n  // null on both sides so the canvas and svg defaults compare equal and strokes\n  // carry no empty stroke-dasharray\n  lineDash: {\n    svgAttr: 'stroke-dasharray',\n    canvas: null,\n    svg: null,\n    apply: 'stroke',\n  },\n}\n\nconst rgbaRegex =\n  /rgba\\(\\s*(\\d*\\.?\\d+)\\s*,\\s*(\\d*\\.?\\d+)\\s*,\\s*(\\d*\\.?\\d+)\\s*,\\s*(\\d?\\.?\\d*)\\s*\\)/i\n\ninterface ContextOptions {\n  document?: Document\n  ctx?: CanvasRenderingContext2D\n}\n\nexport class Context {\n  width: number\n  height: number\n  canvas: Context\n\n  __document: Document\n  __ctx: CanvasRenderingContext2D\n  __canvas?: HTMLCanvasElement\n  __root: SVGSVGElement\n  __currentElement: SVGElement\n  __styleStack: any[]\n  __groupStack: SVGElement[]\n  __currentDefaultPath: string\n  __currentPosition: { x?: number; y?: number }\n  __transformMatrix: DOMMatrix\n  __transformMatrixStack?: DOMMatrix[]\n  // parsed fonts keyed by `font` string; each parse costs a DOM element and a\n  // CSS parse, and exports ask per glyph\n  __fontCache = new Map<string, CSSStyleDeclaration>()\n\n  strokeStyle: any\n  fillStyle: any\n  lineWidth: any\n  font: any\n  textAlign: any\n  textBaseline: any\n  lineDash: any\n\n  constructor(width: number, height: number, options: ContextOptions = {}) {\n    this.width = width\n    this.height = height\n    this.canvas = this\n    this.__document = options.document || document\n\n    if (options.ctx) {\n      this.__ctx = options.ctx\n    } else {\n      this.__canvas = this.__document.createElement('canvas')\n      this.__ctx = this.__canvas.getContext('2d')!\n    }\n\n    this.__setDefaultStyles()\n    this.__styleStack = [this.__getStyleState()]\n    this.__groupStack = []\n\n    this.__root = this.__document.createElementNS(\n      'http://www.w3.org/2000/svg',\n      'svg',\n    )\n    this.__root.setAttribute('version', '1.1')\n    this.__root.setAttribute('xmlns', 'http://www.w3.org/2000/svg')\n    this.__root.setAttribute('width', String(width))\n    this.__root.setAttribute('height', String(height))\n\n    this.__currentElement = this.__document.createElementNS(\n      'http://www.w3.org/2000/svg',\n      'g',\n    )\n    this.__root.appendChild(this.__currentElement)\n\n    this.__currentDefaultPath = ''\n    this.__currentPosition = {}\n    this.__transformMatrix = new DOMMatrix()\n\n    this.resetTransform()\n  }\n\n  __createElement(\n    elementName: string,\n    properties: Record<string, any> = {},\n    resetFill?: boolean,\n  ): SVGElement {\n    const element = this.__document.createElementNS(\n      'http://www.w3.org/2000/svg',\n      elementName,\n    )\n    if (resetFill) {\n      // placeholders: fill()/stroke() overwrite their own attribute, and\n      // __applyStyleToCurrentElement drops the other when it is the svg default\n      element.setAttribute('fill', 'none')\n      element.setAttribute('stroke', 'none')\n    }\n    for (const key of Object.keys(properties)) {\n      // __applyText passes optional attributes through unconditionally; skipping\n      // unset ones keeps an invalid text-decoration=\"undefined\" (~28 bytes) off\n      // every glyph\n      const value = properties[key]\n      if (value !== undefined && value !== null) {\n        element.setAttribute(key, value)\n      }\n    }\n    return element\n  }\n\n  __setDefaultStyles() {\n    for (const key of Object.keys(STYLES)) {\n      ;(this as any)[key] = STYLES[key].canvas\n    }\n  }\n\n  __applyStyleState(styleState: Record<string, any>) {\n    for (const key of Object.keys(styleState)) {\n      ;(this as any)[key] = styleState[key]\n    }\n  }\n\n  __getStyleState(): Record<string, any> {\n    const styleState: Record<string, any> = {}\n    for (const key of Object.keys(STYLES)) {\n      styleState[key] = (this as any)[key]\n    }\n    return styleState\n  }\n\n  /**\n   * A pure translation folds into the element's x/y, saving ~35 bytes per\n   * glyph. Any other transform, such as a sequence-logo letter's scale, is\n   * written as a matrix.\n   */\n  __applyTransformation(element: SVGElement, matrix?: DOMMatrix) {\n    const { a, b, c, d, e, f } = matrix || this.getTransform()\n    if (\n      a === 1 &&\n      b === 0 &&\n      c === 0 &&\n      d === 1 &&\n      element.hasAttribute('x') &&\n      element.hasAttribute('y')\n    ) {\n      if (e !== 0) {\n        element.setAttribute('x', String(Number(element.getAttribute('x')) + e))\n      }\n      if (f !== 0) {\n        element.setAttribute('y', String(Number(element.getAttribute('y')) + f))\n      }\n      return\n    }\n    element.setAttribute('transform', `matrix(${a} ${b} ${c} ${d} ${e} ${f})`)\n  }\n\n  __applyStyleToCurrentElement(type: string) {\n    const currentElement = this.__currentElement\n\n    for (const key of Object.keys(STYLES)) {\n      const style = STYLES[key]\n      const value = (this as any)[key]\n      if (!style.apply?.includes(type) || style.svg === value) {\n        continue\n      }\n      const matches =\n        (style.svgAttr === 'stroke' || style.svgAttr === 'fill') &&\n        typeof value === 'string' &&\n        value.includes('rgba')\n          ? rgbaRegex.exec(value)\n          : null\n      if (matches) {\n        // SVG has no rgba(); the alpha goes in the -opacity attribute\n        currentElement.setAttribute(\n          style.svgAttr,\n          `rgb(${matches[1]},${matches[2]},${matches[3]})`,\n        )\n        currentElement.setAttribute(`${style.svgAttr}-opacity`, matches[4]!)\n      } else if (key === 'lineWidth') {\n        const scale = this.__getTransformScale()\n        currentElement.setAttribute(\n          style.svgAttr,\n          String(value * Math.max(scale.x, scale.y)),\n        )\n      } else {\n        currentElement.setAttribute(style.svgAttr, value)\n      }\n    }\n\n    // svg defaults stroke to none, so a fill drops stroke=\"none\". Fill defaults\n    // to black, so a stroked element keeps fill=\"none\".\n    if (type === 'fill' && currentElement.getAttribute('stroke') === 'none') {\n      currentElement.removeAttribute('stroke')\n    }\n  }\n\n  __closestGroupOrSvg(node?: SVGElement): SVGElement {\n    node = node || this.__currentElement\n    if (node.nodeName === 'g' || node.nodeName === 'svg') {\n      return node\n    }\n    return this.__closestGroupOrSvg(node.parentNode as SVGElement)\n  }\n\n  getSvg(): SVGSVGElement {\n    return this.__root\n  }\n\n  save() {\n    const group = this.__createElement('g')\n    const parent = this.__closestGroupOrSvg()\n    this.__groupStack.push(parent)\n    parent.appendChild(group)\n    this.__currentElement = group\n    this.__styleStack.push(this.__getStyleState())\n    if (!this.__transformMatrixStack) {\n      this.__transformMatrixStack = []\n    }\n    this.__transformMatrixStack.push(this.getTransform())\n  }\n\n  restore() {\n    this.__currentElement = this.__groupStack.pop()!\n    if (!this.__currentElement) {\n      this.__currentElement = this.__root.childNodes[0] as SVGElement\n    }\n    this.__applyStyleState(this.__styleStack.pop())\n    if (this.__transformMatrixStack && this.__transformMatrixStack.length > 0) {\n      this.setTransform(this.__transformMatrixStack.pop()!)\n    }\n  }\n\n  beginPath() {\n    this.__currentDefaultPath = ''\n    this.__currentPosition = {}\n    const path = this.__createElement('path', {}, true)\n    this.__closestGroupOrSvg().appendChild(path)\n    this.__currentElement = path\n  }\n\n  __applyCurrentDefaultPath() {\n    if (this.__currentElement.nodeName === 'path') {\n      this.__currentElement.setAttribute('d', this.__currentDefaultPath)\n    }\n  }\n\n  __addPathCommand(command: string) {\n    this.__currentDefaultPath += ' '\n    this.__currentDefaultPath += command\n  }\n\n  moveTo(x: number, y: number) {\n    if (this.__currentElement.nodeName !== 'path') {\n      this.beginPath()\n    }\n    this.__currentPosition = { x, y }\n    const p = this.__matrixTransform(x, y)\n    this.__addPathCommand(`M ${p.x} ${p.y}`)\n  }\n\n  closePath() {\n    if (this.__currentDefaultPath) {\n      this.__addPathCommand('Z')\n    }\n  }\n\n  lineTo(x: number, y: number) {\n    this.__currentPosition = { x, y }\n    const p = this.__matrixTransform(x, y)\n    this.__addPathCommand(\n      this.__currentDefaultPath.includes('M')\n        ? 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+  "sources": ["../../node_modules/.pnpm/@jbrowse+svgcanvas@9.1.0/node_modules/@jbrowse/svgcanvas/src/index.ts"],
+  "sourcesContent": ["/**\n * SVGCanvas v2.0.3\n * Draw on SVG using Canvas's 2D Context API.\n *\n * Licensed under the MIT license:\n * http://www.opensource.org/licenses/mit-license.php\n *\n * Original Authors: Kerry Liu, Zeno Zeng\n * Copyright (c) 2014 Gliffy Inc.\n * Copyright (c) 2021 Zeno Zeng\n *\n * Vendored, converted to ESM/TypeScript, and cut down to the calls the\n * renderers make: rectangles, paths, arcs and glyphs.\n */\n\n/* eslint-disable @typescript-eslint/no-explicit-any */\n\nfunction getTextAnchor(textAlign: string): string {\n  const mapping: Record<string, string> = {\n    left: 'start',\n    right: 'end',\n    center: 'middle',\n    start: 'start',\n    end: 'end',\n  }\n  return mapping[textAlign] || mapping.start!\n}\n\nfunction getDominantBaseline(textBaseline: string): string {\n  const mapping: Record<string, string> = {\n    alphabetic: 'alphabetic',\n    hanging: 'hanging',\n    top: 'text-before-edge',\n    bottom: 'text-after-edge',\n    middle: 'central',\n  }\n  return mapping[textBaseline] || mapping.alphabetic!\n}\n\n/**\n * SVG's initial values for text presentation attributes. Omitting them from\n * every glyph takes ~22% off a sequence-logo figure.\n */\nconst TEXT_ATTR_DEFAULTS: Record<string, string> = {\n  'font-style': 'normal',\n  'font-weight': 'normal',\n  // the initial value is `auto`, which resolves to the alphabetic baseline\n  'dominant-baseline': 'alphabetic',\n}\n\nfunction omitDefault(attr: string, value: string | undefined) {\n  return value === TEXT_ATTR_DEFAULTS[attr] ? undefined : value\n}\n\nconst STYLES: Record<string, any> = {\n  strokeStyle: {\n    svgAttr: 'stroke',\n    canvas: '#000000',\n    svg: 'none',\n    apply: 'stroke',\n  },\n  fillStyle: {\n    svgAttr: 'fill',\n    canvas: '#000000',\n    svg: null,\n    apply: 'fill',\n  },\n  lineWidth: {\n    svgAttr: 'stroke-width',\n    canvas: 1,\n    svg: 1,\n    apply: 'stroke',\n  },\n  font: {\n    canvas: '10px sans-serif',\n  },\n  textAlign: {\n    canvas: 'start',\n  },\n  textBaseline: {\n    canvas: 'alphabetic',\n  },\n  // null on both sides so the canvas and svg defaults compare equal and strokes\n  // carry no empty stroke-dasharray\n  lineDash: {\n    svgAttr: 'stroke-dasharray',\n    canvas: null,\n    svg: null,\n    apply: 'stroke',\n  },\n}\n\nconst rgbaRegex =\n  /rgba\\(\\s*(\\d*\\.?\\d+)\\s*,\\s*(\\d*\\.?\\d+)\\s*,\\s*(\\d*\\.?\\d+)\\s*,\\s*(\\d?\\.?\\d*)\\s*\\)/i\n\ninterface ContextOptions {\n  document?: Document\n  ctx?: CanvasRenderingContext2D\n}\n\nexport class Context {\n  width: number\n  height: number\n  canvas: Context\n\n  __document: Document\n  __ctx: CanvasRenderingContext2D\n  __canvas?: HTMLCanvasElement\n  __root: SVGSVGElement\n  __currentElement: SVGElement\n  __styleStack: any[]\n  __groupStack: SVGElement[]\n  __currentDefaultPath: string\n  __currentPosition: { x?: number; y?: number }\n  __transformMatrix: DOMMatrix\n  __transformMatrixStack?: DOMMatrix[]\n  // parsed fonts keyed by `font` string; each parse costs a DOM element and a\n  // CSS parse, and exports ask per glyph\n  __fontCache = new Map<string, CSSStyleDeclaration>()\n\n  strokeStyle: any\n  fillStyle: any\n  lineWidth: any\n  font: any\n  textAlign: any\n  textBaseline: any\n  lineDash: any\n\n  constructor(width: number, height: number, options: ContextOptions = {}) {\n    this.width = width\n    this.height = height\n    this.canvas = this\n    this.__document = options.document || document\n\n    if (options.ctx) {\n      this.__ctx = options.ctx\n    } else {\n      this.__canvas = this.__document.createElement('canvas')\n      this.__ctx = this.__canvas.getContext('2d')!\n    }\n\n    this.__setDefaultStyles()\n    this.__styleStack = [this.__getStyleState()]\n    this.__groupStack = []\n\n    this.__root = this.__document.createElementNS(\n      'http://www.w3.org/2000/svg',\n      'svg',\n    )\n    this.__root.setAttribute('version', '1.1')\n    this.__root.setAttribute('xmlns', 'http://www.w3.org/2000/svg')\n    this.__root.setAttribute('width', String(width))\n    this.__root.setAttribute('height', String(height))\n\n    this.__currentElement = this.__document.createElementNS(\n      'http://www.w3.org/2000/svg',\n      'g',\n    )\n    this.__root.appendChild(this.__currentElement)\n\n    this.__currentDefaultPath = ''\n    this.__currentPosition = {}\n    this.__transformMatrix = new DOMMatrix()\n\n    this.resetTransform()\n  }\n\n  __createElement(\n    elementName: string,\n    properties: Record<string, any> = {},\n    resetFill?: boolean,\n  ): SVGElement {\n    const element = this.__document.createElementNS(\n      'http://www.w3.org/2000/svg',\n      elementName,\n    )\n    if (resetFill) {\n      // placeholders: fill()/stroke() overwrite their own attribute, and\n      // __applyStyleToCurrentElement drops the other when it is the svg default\n      element.setAttribute('fill', 'none')\n      element.setAttribute('stroke', 'none')\n    }\n    for (const key of Object.keys(properties)) {\n      // __applyText passes optional attributes through unconditionally; skipping\n      // unset ones keeps an invalid text-decoration=\"undefined\" (~28 bytes) off\n      // every glyph\n      const value = properties[key]\n      if (value !== undefined && value !== null) {\n        element.setAttribute(key, value)\n      }\n    }\n    return element\n  }\n\n  __setDefaultStyles() {\n    for (const key of Object.keys(STYLES)) {\n      ;(this as any)[key] = STYLES[key].canvas\n    }\n  }\n\n  __applyStyleState(styleState: Record<string, any>) {\n    for (const key of Object.keys(styleState)) {\n      ;(this as any)[key] = styleState[key]\n    }\n  }\n\n  __getStyleState(): Record<string, any> {\n    const styleState: Record<string, any> = {}\n    for (const key of Object.keys(STYLES)) {\n      styleState[key] = (this as any)[key]\n    }\n    return styleState\n  }\n\n  /**\n   * A pure translation folds into the element's x/y, saving ~35 bytes per\n   * glyph. Any other transform, such as a sequence-logo letter's scale, is\n   * written as a matrix.\n   */\n  __applyTransformation(element: SVGElement, matrix?: DOMMatrix) {\n    const { a, b, c, d, e, f } = matrix || this.getTransform()\n    if (\n      a === 1 &&\n      b === 0 &&\n      c === 0 &&\n      d === 1 &&\n      element.hasAttribute('x') &&\n      element.hasAttribute('y')\n    ) {\n      if (e !== 0) {\n        element.setAttribute('x', String(Number(element.getAttribute('x')) + e))\n      }\n      if (f !== 0) {\n        element.setAttribute('y', String(Number(element.getAttribute('y')) + f))\n      }\n      return\n    }\n    element.setAttribute('transform', `matrix(${a} ${b} ${c} ${d} ${e} ${f})`)\n  }\n\n  __applyStyleToCurrentElement(type: string) {\n    const currentElement = this.__currentElement\n\n    for (const key of Object.keys(STYLES)) {\n      const style = STYLES[key]\n      const value = (this as any)[key]\n      if (!style.apply?.includes(type) || style.svg === value) {\n        continue\n      }\n      const matches =\n        (style.svgAttr === 'stroke' || style.svgAttr === 'fill') &&\n        typeof value === 'string' &&\n        value.includes('rgba')\n          ? rgbaRegex.exec(value)\n          : null\n      if (matches) {\n        // SVG has no rgba(); the alpha goes in the -opacity attribute\n        currentElement.setAttribute(\n          style.svgAttr,\n          `rgb(${matches[1]},${matches[2]},${matches[3]})`,\n        )\n        currentElement.setAttribute(`${style.svgAttr}-opacity`, matches[4]!)\n      } else if (key === 'lineWidth') {\n        const scale = this.__getTransformScale()\n        currentElement.setAttribute(\n          style.svgAttr,\n          String(value * Math.max(scale.x, scale.y)),\n        )\n      } else {\n        currentElement.setAttribute(style.svgAttr, value)\n      }\n    }\n\n    // svg defaults stroke to none, so a fill drops stroke=\"none\". Fill defaults\n    // to black, so a stroked element keeps fill=\"none\".\n    if (type === 'fill' && currentElement.getAttribute('stroke') === 'none') {\n      currentElement.removeAttribute('stroke')\n    }\n  }\n\n  __closestGroupOrSvg(node?: SVGElement): SVGElement {\n    node = node || this.__currentElement\n    if (node.nodeName === 'g' || node.nodeName === 'svg') {\n      return node\n    }\n    return this.__closestGroupOrSvg(node.parentNode as SVGElement)\n  }\n\n  getSvg(): SVGSVGElement {\n    return this.__root\n  }\n\n  save() {\n    const group = this.__createElement('g')\n    const parent = this.__closestGroupOrSvg()\n    this.__groupStack.push(parent)\n    parent.appendChild(group)\n    this.__currentElement = group\n    this.__styleStack.push(this.__getStyleState())\n    if (!this.__transformMatrixStack) {\n      this.__transformMatrixStack = []\n    }\n    this.__transformMatrixStack.push(this.getTransform())\n  }\n\n  restore() {\n    this.__currentElement = this.__groupStack.pop()!\n    if (!this.__currentElement) {\n      this.__currentElement = this.__root.childNodes[0] as SVGElement\n    }\n    this.__applyStyleState(this.__styleStack.pop())\n    if (this.__transformMatrixStack && this.__transformMatrixStack.length > 0) {\n      this.setTransform(this.__transformMatrixStack.pop()!)\n    }\n  }\n\n  beginPath() {\n    this.__currentDefaultPath = ''\n    this.__currentPosition = {}\n    const path = this.__createElement('path', {}, true)\n    this.__closestGroupOrSvg().appendChild(path)\n    this.__currentElement = path\n  }\n\n  __applyCurrentDefaultPath() {\n    if (this.__currentElement.nodeName === 'path') {\n      this.__currentElement.setAttribute('d', this.__currentDefaultPath)\n    }\n  }\n\n  __addPathCommand(command: string) {\n    this.__currentDefaultPath += ' '\n    this.__currentDefaultPath += command\n  }\n\n  moveTo(x: number, y: number) {\n    if (this.__currentElement.nodeName !== 'path') {\n      this.beginPath()\n    }\n    this.__currentPosition = { x, y }\n    const p = this.__matrixTransform(x, y)\n    this.__addPathCommand(`M ${p.x} ${p.y}`)\n  }\n\n  closePath() {\n    if (this.__currentDefaultPath) {\n      this.__addPathCommand('Z')\n    }\n  }\n\n  lineTo(x: number, y: number) {\n    this.__currentPosition = { x, y }\n    const p = this.__matrixTransform(x, y)\n    this.__addPathCommand(\n      this.__currentDefaultPath.includes('M')\n        ? `L ${p.x} ${p.y}`\n        : `M ${p.x} ${p.y}`,\n    )\n  }\n\n  quadraticCurveTo(cpx: number, cpy: number, x: number, y: number) {\n    this.__currentPosition = { x, y }\n    const cp = this.__matrixTransform(cpx, cpy)\n    const p = this.__matrixTransform(x, y)\n    this.__addPathCommand(`Q ${cp.x} ${cp.y} ${p.x} ${p.y}`)\n  }\n\n  // paint-order matters only on an element with both fill and stroke: the\n  // collapsed-clade triangle\n  __applyPaintOrder(order: string, other: string) {\n    const current = this.__currentElement\n    if (\n      current.nodeName === 'path' &&\n      current.hasAttribute(other) &&\n      current.getAttribute(other) !== 'none'\n    ) {\n      current.setAttribute('paint-order', order)\n    }\n  }\n\n  stroke() {\n    this.__applyPaintOrder('fill stroke markers', 'fill')\n    this.__applyCurrentDefaultPath()\n    this.__applyStyleToCurrentElement('stroke')\n  }\n\n  fill() {\n    this.__applyPaintOrder('stroke fill markers', 'stroke')\n    this.__applyCurrentDefaultPath()\n    this.__applyStyleToCurrentElement('fill')\n  }\n\n  // A fill covering the whole context paints over what is under it, as on a\n  // canvas; it does not clear the drawing.\n  fillRect(x: number, y: number, width: number, height: number) {\n    const rect = this.__createElement('rect', { x, y, width, height }, true)\n    this.__closestGroupOrSvg().appendChild(rect)\n    this.__currentElement = rect\n    this.__applyTransformation(rect)\n    this.__applyStyleToCurrentElement('fill')\n  }\n\n  strokeRect(x: number, y: number, width: number, height: number) {\n    const rect = this.__createElement('rect', { x, y, width, height }, true)\n    this.__closestGroupOrSvg().appendChild(rect)\n    this.__currentElement = rect\n    this.__applyTransformation(rect)\n    this.__applyStyleToCurrentElement('stroke')\n  }\n\n  __parsedFont() {\n    const hit = this.__fontCache.get(this.font)\n    if (hit) {\n      return hit\n    }\n    const el = document.createElement('span')\n    el.setAttribute('style', `font:${this.font}`)\n    this.__fontCache.set(this.font, el.style)\n    return el.style\n  }\n\n  fillText(text: string, x: number, y: number) {\n    const style = this.__parsedFont()\n    const parent = this.__closestGroupOrSvg()\n    const textElement = this.__createElement(\n      'text',\n      {\n        'font-family': style.fontFamily,\n        'font-size': style.fontSize,\n        'font-style': omitDefault('font-style', style.fontStyle),\n        'font-weight': omitDefault('font-weight', style.fontWeight),\n        x,\n        y,\n        'text-anchor': getTextAnchor(this.textAlign),\n        'dominant-baseline': omitDefault(\n          'dominant-baseline',\n          getDominantBaseline(this.textBaseline),\n        ),\n      },\n      true,\n    )\n\n    textElement.appendChild(this.__document.createTextNode(text))\n    this.__currentElement = textElement\n    this.__applyTransformation(textElement)\n    this.__applyStyleToCurrentElement('fill')\n    parent.appendChild(textElement)\n  }\n\n  measureText(text: string): TextMetrics {\n    this.__ctx.font = this.font\n    return this.__ctx.measureText(text)\n  }\n\n  arc(\n    x: number,\n    y: number,\n    radius: number,\n    startAngle: number,\n    endAngle: number,\n    counterClockwise?: boolean,\n  ) {\n    if (startAngle === endAngle) {\n      return\n    }\n    startAngle = startAngle % (2 * Math.PI)\n    endAngle = endAngle % (2 * Math.PI)\n    if (startAngle === endAngle) {\n      endAngle =\n        (endAngle + 2 * Math.PI - 0.001 * (counterClockwise ? -1 : 1)) %\n        (2 * Math.PI)\n    }\n    const endX = x + radius * Math.cos(endAngle)\n    const endY = y + radius * Math.sin(endAngle)\n    const startX = x + radius * Math.cos(startAngle)\n    const startY = y + radius * Math.sin(startAngle)\n    const sweepFlag = counterClockwise ? 0 : 1\n    let diff = endAngle - startAngle\n    if (diff < 0) {\n      diff += 2 * Math.PI\n    }\n    const largeArcFlag = counterClockwise\n      ? diff > Math.PI\n        ? 0\n        : 1\n      : diff > Math.PI\n        ? 1\n        : 0\n\n    const { x: scaleX, y: scaleY } = this.__getTransformScale()\n    const end = this.__matrixTransform(endX, endY)\n\n    this.lineTo(startX, startY)\n    this.__addPathCommand(\n      `A ${radius * scaleX} ${radius * scaleY} 0 ${largeArcFlag} ${sweepFlag} ${end.x} ${end.y}`,\n    )\n    this.__currentPosition = { x: endX, y: endY }\n  }\n\n  setLineDash(dashArray: number[]) {\n    this.lineDash = dashArray.length > 0 ? dashArray.join(',') : null\n  }\n\n  setTransform(\n    a: number | DOMMatrix,\n    b?: number,\n    c?: number,\n    d?: number,\n    e?: number,\n    f?: number,\n  ) {\n    this.__transformMatrix =\n      a instanceof DOMMatrix\n        ? new DOMMatrix([a.a, a.b, a.c, a.d, a.e, a.f])\n        : new DOMMatrix([a, b!, c!, d!, e!, f!])\n  }\n\n  getTransform(): DOMMatrix {\n    const { a, b, c, d, e, f } = this.__transformMatrix\n    return new DOMMatrix([a, b, c, d, e, f])\n  }\n\n  resetTransform() {\n    this.setTransform(1, 0, 0, 1, 0, 0)\n  }\n\n  scale(x: number, y?: number) {\n    if (y === undefined) {\n      y = x\n    }\n    if (isNaN(x) || isNaN(y) || !isFinite(x) || !isFinite(y)) {\n      return\n    }\n    this.setTransform(this.getTransform().scale(x, y))\n  }\n\n  translate(x: number, y: number) {\n    this.setTransform(this.getTransform().translate(x, y))\n  }\n\n  __matrixTransform(x: number, y: number): DOMPoint {\n    return new DOMPoint(x, y).matrixTransform(this.__transformMatrix)\n  }\n\n  __getTransformScale(): { x: number; y: number } {\n    return {\n      x: Math.hypot(this.__transformMatrix.a, this.__transformMatrix.b),\n      y: Math.hypot(this.__transformMatrix.c, this.__transformMatrix.d),\n    }\n  }\n}\n"],
+  "mappings": 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 }

package/dist/chunks/dist-N4ZJK63Q.js

@@ -0,0 +1,2 @@
+import{a as d,b as e,c as f,d as g,e as h,f as i,g as j,h as k,i as l,j as m,k as n}from"./chunk-CSCUNTGJ.js";import"./chunk-TSHN6J7U.js";import"./chunk-NWHZOZMG.js";import"./chunk-DEFUNIWW.js";import"./chunk-FCWXYIFC.js";import"./chunk-YUKJI2AH.js";import"./chunk-K55ZVN73.js";import"./chunk-IBBQUV2I.js";import{K as b,Z as c}from"./chunk-L6CBIH6H.js";import{G as a}from"./chunk-OVAXNTPN.js";import"./chunk-73KAPCJ2.js";import"./chunk-JF6CW6MO.js";import"./chunk-CVLB4VFP.js";import"./chunk-DNFD5II2.js";import"./chunk-BX4Z274Q.js";import"./chunk-J6KYLXRD.js";import"./chunk-FY3BTKY4.js";export{b as CHAR_WIDTH_RATIO,h as MSAModelF,g as MSAView,k as MSAViewer,m as defineMsaElement,f as expandSpec,d as installHeadlessRenderEnv,a as maxNeighborJoiningRows,l as mount,c as renderToSvg,e as residueLabel,i as resolveTheme,n as useMsaSvgFigure,j as viewerSnapshot};
+//# sourceMappingURL=dist-N4ZJK63Q.js.map