jbrowse-plugin-msaview 5.2.0 → 5.4.0

package/dist/chunks/{chunk-YOTSFJMU.js → chunk-GAY2PLS6.js}

@@ -1,2 +1,2 @@
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+//# sourceMappingURL=chunk-GAY2PLS6.js.map

package/dist/chunks/{chunk-YOTSFJMU.js.map → chunk-GAY2PLS6.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/Checkbox2.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/Checkbox2.tsx"],
   "sourcesContent": ["import React from 'react'\n\nimport { Checkbox, FormControlLabel } from '@mui/material'\n\nexport default function Checkbox2({\n  checked,\n  label,\n  disabled,\n  onChange,\n}: {\n  checked: boolean\n  label: string\n  disabled?: boolean\n  onChange: () => void\n}) {\n  return (\n    <div>\n      <FormControlLabel\n        control={\n          <Checkbox\n            disabled={disabled}\n            checked={checked}\n            onChange={() => {\n              onChange()\n            }}\n          />\n        }\n        label={label}\n      />\n    </div>\n  )\n}\n"],
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package/dist/chunks/chunk-JDQUBCHM.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-JDQUBCHM.js.map

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

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/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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+  "names": ["arrows", "keyboardControls", "selectCells", "mouseControls", "alignmentAriaLabel", "c"]
+}

package/dist/chunks/{chunk-IBBQUV2I.js → chunk-KSCGTF4R.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/{chunk-IBBQUV2I.js.map → chunk-KSCGTF4R.js.map}

@@ -1,6 +1,6 @@
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   "version": 3,
-  "sources": ["global-externals:@jbrowse/core/util", "global-externals:@mui/material/SvgIcon", "global-externals:react/jsx-runtime", "../../node_modules/.pnpm/@mui+icons-material@9.4.0_@mui+material@9.4.0_@emotion+react@11.14.0_@types+react@19.3._3766ec55733e6b150ee672ad270cc236/node_modules/@mui/icons-material/utils/createSvgIcon.mjs"],
+  "sources": ["global-externals:@jbrowse/core/util", "global-externals:@mui/material/SvgIcon", "global-externals:react/jsx-runtime", "../../node_modules/.pnpm/@mui+icons-material@9.5.0_@mui+material@9.5.0_@emotion+react@11.14.0_@types+react@19.3._abf953b0c56c79ebdc461ec953894a27/node_modules/@mui/icons-material/utils/createSvgIcon.mjs"],
   "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/util\"];", "module.exports = JBrowseExports[\"@mui/material/SvgIcon\"];", "module.exports = JBrowseExports[\"react/jsx-runtime\"];", "'use client';\n\nexport { createSvgIcon as default } from '@mui/material/SvgIcon';"],
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package/dist/chunks/{chunk-6YFCSBEE.js → chunk-NLAW2OYS.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=chunk-6YFCSBEE.js.map
+import{c as o,d as l}from"./chunk-KSCGTF4R.js";import{a as c}from"./chunk-BX4Z274Q.js";import{a}from"./chunk-J6KYLXRD.js";import{b as r}from"./chunk-FY3BTKY4.js";var e=r(a());var t=r(l(),1),n=(0,o.createSvgIcon)((0,t.jsx)("path",{d:"M19 19H5V5h7V3H5c-1.11 0-2 .9-2 2v14c0 1.1.89 2 2 2h14c1.1 0 2-.9 2-2v-7h-2zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3z"}),"OpenInNew");var i=r(c());function s(m){let{children:p,...f}=m;return e.default.createElement(i.Link,{...f,target:"_blank",rel:"noreferrer"},p," ",e.default.createElement(n,{fontSize:"small"}))}export{s as a};
+//# sourceMappingURL=chunk-NLAW2OYS.js.map

package/dist/chunks/{chunk-6YFCSBEE.js.map → chunk-NLAW2OYS.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../src/components/ExternalLink.tsx", "../../node_modules/.pnpm/@mui+icons-material@9.4.0_@mui+material@9.4.0_@emotion+react@11.14.0_@types+react@19.3._3766ec55733e6b150ee672ad270cc236/node_modules/@mui/icons-material/OpenInNew.mjs"],
+  "sources": ["../../src/components/ExternalLink.tsx", "../../node_modules/.pnpm/@mui+icons-material@9.5.0_@mui+material@9.5.0_@emotion+react@11.14.0_@types+react@19.3._abf953b0c56c79ebdc461ec953894a27/node_modules/@mui/icons-material/OpenInNew.mjs"],
   "sourcesContent": ["import React from 'react'\n\nimport OpenInNewIcon from '@mui/icons-material/OpenInNew'\nimport { Link } from '@mui/material'\n\nimport type { LinkProps } from '@mui/material'\n\nexport default function ExternalLink(props: LinkProps) {\n  const { children, ...rest } = props\n  return (\n    <Link {...rest} target=\"_blank\" rel=\"noreferrer\">\n      {children} <OpenInNewIcon fontSize=\"small\" />\n    </Link>\n  )\n}\n", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M19 19H5V5h7V3H5c-1.11 0-2 .9-2 2v14c0 1.1.89 2 2 2h14c1.1 0 2-.9 2-2v-7h-2zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3z\"\n}), 'OpenInNew');"],
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package/dist/chunks/{chunk-ZCT7RD24.js → chunk-QQKPT6EL.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=chunk-ZCT7RD24.js.map
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package/dist/chunks/{chunk-H6IQBAW7.js → chunk-WMDOEOAH.js}

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+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/MetadataTable.tsx", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/SequenceTextArea.tsx"],
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+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/version.ts"],
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package/dist/chunks/chunk-XXCNVFGP.js

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+`)[Symbol.iterator]();return oe(e)}var d=class extends u{MSA;constructor(e){let n=L(e);super(n.alns.map(t=>[t.id,t.seq])),this.MSA=n}getHeader(){return this.MSA.header}get seqConsensus(){return this.MSA.consensus}};function D(s){let e=s.split(`
+`).map(o=>o.trim()).filter(o=>!!o),n=[],t=[];for(let o of e)if(o.startsWith("SEQ"))n.push(o);else{if(o.startsWith("DATA"))continue;if(o.startsWith("//"))break;t.push(o)}let r=n.map(o=>{let[,c,i,a,f,l,p,x,R]=o.split(" ");return{species:c,protein:i,chr:a,start:+f,end:+l,strand:+p,geneId:x,unknown:R,seq:""}});for(let o of t)for(let c=0;c<n.length;c++)r[c].seq+=o[c];return r}function B(s){let e=s.split(`
+`).map(o=>o.trim()).filter(o=>!!o),n=[],t="";for(let o of e)if(o.startsWith("SEQ"))n.push(o);else{if(o.startsWith("DATA"))continue;if(o.startsWith("//"))break;t=o}let r=n.map(o=>{let[,c,i,a,f,l,p,x,R]=o.split(" ");return{species:c,protein:i,chr:a,start:+f,end:+l,strand:+p,geneId:x,unknown:R}});return{tree:t,seqs:r}}var h=class extends u{constructor(e){super(D(e).map(n=>[n.protein,n.seq]))}};var g=class extends u{colonNormalized=new Map;constructor(e){let n=w(e);super(n.map(t=>[t.id,t.seq]));for(let{id:t}of n)t.includes(":")&&this.colonNormalized.set(t.replaceAll(":","_"),t)}getRow(e){return this.rows.get(e)??this.rows.get(this.colonNormalized.get(e)??"")??""}};function q(s){return $(s,{postParenNumeric:"name"})}function U(){return{gf:Object.create(null),gc:Object.create(null),gs:Object.create(null),gr:Object.create(null),seqname:[],seqdata:Object.create(null)}}function E(s,e){if(s)return s;if(e)throw new Error("No format header: # STOCKHOLM 1.0");return U()}var W=/^# STOCKHOLM 1.0/,ie=/^\/\/\s*$/,ce=/^#=GF\s+(\S+)\s+(.*?)\s*$/,ae=/^#=GC\s+(\S+)\s+(.*?)\s*$/,fe=/^#=GS\s+(\S+)\s+(\S+)\s+(.*?)\s*$/,le=/^#=GR\s+(\S+)\s+(\S+)\s+(.*?)\s*$/,ue=/^\s*([^#\s]\S*)\s+(\S+)\s*$/,pe=/\S/;function M(s){return W.test(s)}function I(s,e){let n=e??{},t=[],r=null,o=!1,c=s.split(`
+`);for(let i of c){let a;if(W.test(i))r&&t.push(r),r=U(),o=!1;else if(ie.test(i))r&&t.push(r),r=null;else if(a=ce.exec(i)){r=E(r,!!n.strict);let f=a[1],l=r.gf[f]??=[];f==="NH"&&o&&l.length>0?l[l.length-1]+=a[2]:l.push(a[2]),o=f==="NH"}else if(a=ae.exec(i))r=E(r,!!n.strict),r.gc[a[1]]=(r.gc[a[1]]??"")+a[2];else if(a=fe.exec(i)){r=E(r,!!n.strict);let f=r.gs[a[2]]??=Object.create(null);(f[a[1]]??=[]).push(a[3])}else if(a=le.exec(i)){r=E(r,!!n.strict);let f=r.gr[a[2]]??=Object.create(null);f[a[1]]=(f[a[1]]??"")+a[3]}else if(a=ue.exec(i)){r=E(r,!!n.strict);let f=a[1],l=a[2];r.seqdata[f]===void 0&&(r.seqdata[f]="",r.seqname.push(f)),r.seqdata[f]+=l}else if(pe.test(i)&&n.strict)throw new Error("Malformed line")}return r&&t.push(r),t}var S=class extends u{data;MSA;constructor(e,n){let t=I(e),r=t[n]??t[0];if(!r)throw new Error("No alignments found in Stockholm file");super(r.seqname.map(o=>[o,r.seqdata[o]??""])),this.data=t,this.MSA=r}getMSA(){return this.MSA}get alignmentNames(){return this.data.map((e,n)=>e.gf.DE?.[0]??`Alignment ${n+1}`)}getHeader(){let e=this.MSA.gs.AC??{},n=this.MSA.gs.DR??{};return{General:this.MSA.gf,Accessions:Object.fromEntries(Object.entries(e).map(([t,r])=>[t,r[0]])),Dbxref:Object.fromEntries(Object.entries(n).map(([t,r])=>[t,r.join("; ")]))}}getRowData(e){return{name:e,accession:this.MSA.gs.AC?.[e]?.[0],dbxref:this.MSA.gs.DR?.[e]?.join("; ")}}getStructures(){let e=/PDB; +(\S+) +([^;\s]+); *(-?[0-9]+)-(-?[0-9]+)/,n=this.MSA.gs.DR??{},t={};for(let[r,o]of Object.entries(n))for(let c of o){let i=e.exec(c);i&&(t[r]??=[]).push({pdb:i[1].toLowerCase(),chain:i[2],startPos:+i[3],endPos:+i[4]})}return t}getTree(){let e=this.MSA.gf.NH?.[0];return e?T(q(e)):super.getTree()}get seqConsensus(){return this.MSA.gc.seq_cons}get secondaryStructureConsensus(){return this.MSA.gc.SS_cons}get tracks(){let{seq_cons:e,SS_cons:n,...t}=this.MSA.gc;return[{id:"seqConsensus",name:"Sequence consensus",data:e,customColorScheme:{}},{id:"secondaryStruct",name:"Secondary-structure",data:n,customColorScheme:v},...Object.entries(t).map(([r,o])=>({id:`gc-${r}`,name:r,data:o,customColorScheme:H(r)})),...Object.entries(this.MSA.gr).flatMap(([r,o])=>Object.entries(o).map(([c,i])=>({id:`gr-${c}-${r}`,name:`${c} ${r}`,data:i,customColorScheme:H(r),defaultOff:!0})))]}},v={"<":"lightblue","(":"lightblue","[":"lightblue","{":"lightblue",">":"pink",")":"pink","]":"pink","}":"pink"};function H(s){return s==="SS"||s.endsWith("_SS")?v:{}}var me=/^<(!doctype\s+html|html[\s>])/i,de=/^(CLUSTAL|MUSCLE|PROBCONS|MSAPROBS|Kalign)/i;function he(s,e=0,n){let t=s.replace(/^\uFEFF/,"").replaceAll(/\r\n?/g,`
+`).trimStart();if(me.test(t))throw new Error("Received an HTML page, not an alignment. Check that the URL points at the file itself");if(n==="stockholm")return new S(t,e);if(n==="a3m")return new m(t);if(n==="fasta")return new g(t);if(n==="emf")return new h(t);if(n==="clustal")return new d(t);if(M(t))return new S(t,e);if(C(t)){let o=O(t);return m.sniff(o)?new m(o):new g(o)}if(t.startsWith("SEQ"))return new h(t);if(de.test(t))return new d(t);let r=t.split(`
+`,1)[0].slice(0,80);throw new Error(r?`Unrecognized alignment format: expected FASTA, A3M, Stockholm, Clustal or EMF, but the first line reads "${r}"`:"The alignment file is empty")}function ge(s){return s.replaceAll(/[.-]/g,"")}function z(s){try{return decodeURIComponent(s)}catch{return s}}function Se(s){return s.replace(/^"(.*)"$/,"$1")}function xe(s){if(!s)return{};let e={};for(let n of s.split(";")){let t=n.indexOf("="),r=n.slice(0,t).trim(),o=n.slice(t+1);t!==-1&&r&&o&&(e[r]=o.split(",").map(c=>Se(z(c).trim())).join(" "))}return e}function K(s){if(!s)return[];let e=[];for(let n of s.split(`
+`)){let t=n.trim();if(t.startsWith("##FASTA"))break;t&&!t.startsWith("#")&&t.split("	").length>=8&&e.push(t)}return e.map(n=>{let t=n.split("	"),[r,o,c,i,a,f,l,p]=t,x=t[8];return{...xe(x),seq_id:z(r??""),source:o??"",type:c??"",start:Number(i)||0,end:Number(a)||0,score:Number(f)||0,strand:l??".",phase:p??"."}})}var Ae=new Set(["gene","CDS","pseudogene","mRNA","transcript","primary_transcript","ncRNA","tRNA","rRNA","snRNA","snoRNA","miRNA","lnc_RNA"]);function we({type:s,strand:e}){let n=e==="+"?1:e==="-"?-1:void 0;return Ae.has(s)?n:void 0}var qe=new Set(["seq_id","source","type","start","end","score","strand","phase"]);function Ee(s){let e=Object.entries(s).filter(([n,t])=>!qe.has(n)&&typeof t=="string");return e.length>0?Object.fromEntries(e):void 0}var Me=/^(\d{1,3})[\s,]+(\d{1,3})[\s,]+(\d{1,3})$/;function Ce(s){let e=s.color??s.colour??s.Color??s.Colour;if(!e)return;let n=Me.exec(e.trim());return n?`rgb(${n[1]},${n[2]},${n[3]})`:e.trim()}var Re=new Set(["polypeptide","nucleic_acid"]);function Q(s){return s.filter(e=>!Re.has(e.type)).map(e=>{let n=e.Name||e.ID||`${e.source}_${e.start}_${e.end}`,t=e.signature_desc||e.Name||n;return{id:e.seq_id,accession:n,name:t,description:e.description||e.Note||e.signature_desc||t,featureType:e.type,start:e.start,end:e.end,strand:we(e),color:Ce(e),attributes:Ee(e)}})}export{T as a,B as b,q as c,S as d,he as e,ge as f,K as g,Q as h,X as i};
+//# sourceMappingURL=chunk-XXCNVFGP.js.map

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

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/interProScanToAnnotations.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/gff/annotationsToGFF.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/gff/annotationTextToGFF.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/util.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/BaseMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/fastaRecords.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/A3mMSA.ts", "../../node_modules/.pnpm/clustal-js@2.0.19/node_modules/clustal-js/src/util.ts", "../../node_modules/.pnpm/clustal-js@2.0.19/node_modules/clustal-js/src/index.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/ClustalMSA.ts", "../../node_modules/.pnpm/emf-js@2.0.0/node_modules/emf-js/src/index.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/EmfMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/FastaMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/parseNewick.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/stockholmParser.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/StockholmMSA.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/msa/index.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/gff/parseGFF.ts", "../../node_modules/.pnpm/msa-parsers@9.1.0/node_modules/msa-parsers/src/gff/gffToAnnotations.ts"],
+  "sourcesContent": ["import type {\n  Annotation,\n  InterProScanResponse,\n  InterProScanResults,\n} from './types.ts'\n\n/**\n * Key each result by its xref id, which is the row name its annotations attach\n * to. A result without one is dropped rather than keyed `undefined`, which\n * would draw a phantom row's worth of annotations (and rather than throwing,\n * which would lose every other result over one malformed one).\n */\nexport function indexResultsByXref(results: InterProScanResults[]) {\n  return Object.fromEntries(\n    results\n      .map(r => [r.xref[0]?.id, r] as const)\n      .filter((e): e is [string, InterProScanResults] => e[0] !== undefined),\n  )\n}\n\n/**\n * Flatten InterProScan results, keyed by the row name they attach to, into one\n * annotation per signature location.\n *\n * An unintegrated signature has no InterPro `entry` -- MobiDBLite's disorder\n * calls, and many CDD, Pfam and PANTHER hits -- and falling back to the\n * signature's own accession and name is the difference between drawing those\n * and dropping them. Only a signature with no accession at all has nothing to\n * color, filter or label by, and is dropped.\n */\nexport function interProScanToAnnotations(\n  results: Record<string, InterProScanResults>,\n): Annotation[] {\n  return Object.entries(results).flatMap(([id, { matches }]) =>\n    matches.flatMap(({ signature, locations }) => {\n      const { entry } = signature\n      const accession = entry?.accession ?? signature.accession\n      if (!accession) {\n        return []\n      }\n      const name = entry?.name ?? signature.name ?? accession\n      return locations.map(({ start, end, strand }) => ({\n        id,\n        accession,\n        name,\n        description: entry?.description ?? signature.description ?? name,\n        start,\n        end,\n        strand,\n      }))\n    }),\n  )\n}\n\n/**\n * Flatten a whole InterProScan JSON response, resolving each result's row name\n * from its xref.\n */\nexport function interProScanResponseToAnnotations(\n  response: InterProScanResponse,\n): Annotation[] {\n  return interProScanToAnnotations(indexResultsByXref(response.results))\n}\n", "import type { Annotation } from '../types.ts'\n\n/**\n * Write annotations as GFF3, one line per annotation, in list order, with\n * optional `#` comment lines after the version directive saying where they came\n * from.\n *\n * The source column is always `InterProScan`: an Annotation records no source\n * of its own, and the viewer reads a precomputed-lookup GFF by the same rules\n * it reads a real InterProScan run's.\n */\nexport function annotationsToGFF(\n  annotations: Annotation[],\n  header: string[] = [],\n): string {\n  return [\n    '##gff-version 3',\n    ...header.map(line => `# ${line}`),\n    ...annotations.map(annotation => {\n      const { accession, name, description, featureType } = annotation\n      const { id, start, end, strand } = annotation\n      return [\n        id.replaceAll(/[%\\t\\n\\r]/g, encodeURIComponent),\n        'InterProScan',\n        // GFF-sourced annotations carry their original type; writing every\n        // feature back out as protein_match would turn an exon overlay into\n        // generic domains on the next read, losing the numbered-segment\n        // rendering and the gene arrowheads\n        featureType ?? 'protein_match',\n        start,\n        end,\n        '.',\n        strand === undefined ? '.' : strand > 0 ? '+' : '-',\n        '.',\n        [\n          `Name=${encodeURIComponent(accession)}`,\n          `signature_desc=${encodeURIComponent(name)}`,\n          `description=${encodeURIComponent(description)}`,\n        ].join(';'),\n      ].join('\\t')\n    }),\n  ].join('\\n')\n}\n", "import { interProScanResponseToAnnotations } from '../interProScanToAnnotations.ts'\nimport { annotationsToGFF } from './annotationsToGFF.ts'\n\nimport type { InterProScanResponse } from '../types.ts'\n\n/**\n * An annotation file's text as GFF3: GFF passes through, and the JSON an\n * InterProScan run returns converts, taking each result's row from its xref.\n */\nexport function annotationTextToGFF(text: string): string {\n  const trimmed = text.trimStart()\n  if (!trimmed.startsWith('{')) {\n    return text\n  }\n  const response: InterProScanResponse = JSON.parse(trimmed)\n  return annotationsToGFF(interProScanResponseToAnnotations(response))\n}\n", "import type { Node, NodeWithIds } from './types.ts'\n\n/**\n * Copy a parsed tree, giving every node a stable id derived from its path, and\n * falling back to that id for an unnamed node.\n *\n * Iterative, like the traversals in @gmod/newick and the Newick emitter in the\n * viewer's neighbor joining: a phylogeny can be a caterpillar whose depth equals\n * its leaf count, and the recursive form of this overflowed the stack somewhere\n * past 5000 deep -- which every tree reaches, since this is the last step of\n * parsing one.\n */\nexport function generateNodeIds(\n  tree: Node,\n  parent = 'node',\n  depth = 0,\n): NodeWithIds {\n  const withId = (node: Node, id: string): NodeWithIds => ({\n    ...node,\n    id,\n    name: node.name || id,\n    children: [],\n  })\n\n  const root = withId(tree, `${parent}-${depth}`)\n  const stack = [{ src: tree, out: root, depth }]\n  while (stack.length > 0) {\n    const { src, out, depth: d } = stack.pop()!\n    if (src.children) {\n      out.children = src.children.map((child, i) =>\n        withId(child, `${out.id}-${i}-${d + 1}`),\n      )\n      for (const [i, child] of src.children.entries()) {\n        stack.push({ src: child, out: out.children[i]!, depth: d + 1 })\n      }\n    }\n  }\n  return root\n}\n", "import type { MSATrack, NodeWithIds } from '../types.ts'\n\nexport default abstract class BaseMSA {\n  protected rows = new Map<string, string>()\n  private names: string[]\n  private width?: number\n\n  /**\n   * A repeated name keeps its first row: names index the rows, so listing the\n   * name twice would render a phantom duplicate row.\n   */\n  constructor(rows: Iterable<readonly [string, string]>) {\n    for (const [name, seq] of rows) {\n      if (!this.rows.has(name)) {\n        this.rows.set(name, seq)\n      }\n    }\n    this.names = [...this.rows.keys()]\n  }\n\n  getRow(name: string): string {\n    return this.rows.get(name) ?? ''\n  }\n\n  getNames(): string[] {\n    return this.names\n  }\n\n  /**\n   * Column count of the alignment: the length of its widest row, since a\n   * hand-edited fasta or some aligners leave rows short. The viewer's gap\n   * analysis counts columns the same way.\n   */\n  getWidth(): number {\n    this.width ??= this.getNames().reduce(\n      (max, name) => Math.max(max, this.getRow(name).length),\n      0,\n    )\n    return this.width\n  }\n\n  getTree(): NodeWithIds {\n    return {\n      id: 'root',\n      name: 'root',\n      noTree: true,\n      children: this.getNames().map(name => ({\n        id: name,\n        children: [],\n        name,\n      })),\n    }\n  }\n\n  getRowData(\n    _name: string,\n  ): { name?: string; accession?: string; dbxref?: string } | undefined {\n    return undefined\n  }\n\n  getStructures(): Record<string, unknown> {\n    return {}\n  }\n\n  getHeader(): Record<string, unknown> {\n    return {}\n  }\n\n  get alignmentNames(): string[] {\n    return []\n  }\n\n  get seqConsensus(): string | undefined {\n    return undefined\n  }\n\n  get secondaryStructureConsensus(): string | undefined {\n    return undefined\n  }\n\n  get tracks(): MSATrack[] {\n    return []\n  }\n}\n", "export interface FastaRecord {\n  id: string\n  seq: string\n}\n\n// a `>` record, optionally after `#` header lines such as ColabFold's `#8\\t1`\nexport function fastaSniff(text: string) {\n  return /^(#.*\\n)*>/.test(text)\n}\n\n/**\n * Split FASTA-style text (shared by the FASTA and A3M parsers) into records.\n *\n * A record starts at a `>` that begins a line, so a `>` inside a defline\n * (`x->y`, HGVS `c.1799T>A`) stays part of it, and anything before the first\n * record (ColabFold's `#8\\t1` header) is skipped. The id is the first word of\n * the defline, so `> name` reads as `name`, and a defline with no word names\n * its record `unnamed_N` after its position in the file. A repeated id keeps\n * the first record: ids index the row data, so emitting the id twice would\n * render a phantom duplicate row showing the last record's residues.\n */\nexport function splitFastaRecords(text: string): FastaRecord[] {\n  const records: FastaRecord[] = []\n  const seen = new Set<string>()\n  let current: { id: string; lines: string[] } | undefined\n\n  const flush = () => {\n    if (current && !seen.has(current.id)) {\n      seen.add(current.id)\n      records.push({\n        id: current.id,\n        seq: current.lines.join('').replaceAll(/\\s/g, ''),\n      })\n    }\n  }\n\n  let count = 0\n  for (const line of text.split('\\n')) {\n    if (line.startsWith('>')) {\n      flush()\n      count++\n      const id = /^>\\s*(\\S*)/.exec(line)![1] || `unnamed_${count}`\n      current = { id, lines: [] }\n    } else {\n      current?.lines.push(line)\n    }\n  }\n  flush()\n\n  return records\n}\n\nexport function toRecords(input: string | FastaRecord[]) {\n  return typeof input === 'string' ? splitFastaRecords(input) : input\n}\n", "import BaseMSA from './BaseMSA.ts'\nimport { fastaSniff, toRecords } from './fastaRecords.ts'\n\nimport type { FastaRecord } from './fastaRecords.ts'\n\n/**\n * A3M Format Parser\n *\n * The A3M format consists of aligned FASTA, in which alignments are shown with:\n * - Inserts as lowercase characters\n * - Matches as uppercase characters\n * - Deletions as '-'\n * - Gaps aligned to inserts as '.'\n *\n * Note that gaps aligned to inserts can be omitted in the A3M format.\n *\n * Example:\n * >query\n * ETESMKTVRIREKIKKFLGDRPRNTAEILEHINSTMRHGTTSQQLGNVLSKDKDIVKVGYIKRSGILSGGYDICEWATRNWVAEHCPEWTE\n * >seq1\n * ----MRTTRLRQKIKKFLNERGeANTTEILEHVNSTMRHGTTPQQLGNVLSKDKDILKVATTKRGGALSGRYEICVWTLRP-----------\n *\n * In the above, 'e' after 'G' in seq1 is a lowercase insert.\n *\n * @see https://yanglab.qd.sdu.edu.cn/trRosetta/msa_format.html\n */\n\nconst CODE_A = 65 // 'A'\nconst CODE_Z = 90 // 'Z'\nconst CODE_a = 97 // 'a'\nconst CODE_z = 122 // 'z'\nconst CODE_DASH = 45 // '-'\n\nfunction isLower(code: number): boolean {\n  return code >= CODE_a && code <= CODE_z\n}\n\nfunction isMatch(code: number): boolean {\n  return (code >= CODE_A && code <= CODE_Z) || code === CODE_DASH\n}\n\ninterface ParsedRow {\n  // one entry per match column, in order\n  matches: string[]\n  // inserts[k] is the run of insert residues sitting immediately BEFORE match\n  // column k, already uppercased; inserts[matches.length] holds the trailing\n  // run. An insert must never consume a match column, or a row that opens with\n  // an insert falls a column out of register with every other row.\n  inserts: string[]\n}\n\nfunction parseRow(seq: string): ParsedRow {\n  const matches: string[] = []\n  const inserts = ['']\n\n  for (const ch of seq) {\n    const code = ch.charCodeAt(0)\n    if (isMatch(code)) {\n      matches.push(ch)\n      inserts.push('')\n    } else if (isLower(code)) {\n      inserts[inserts.length - 1] += ch.toUpperCase()\n    }\n    // '.' is padding aligned to some other row's insert, and anything else is\n    // unrecognized -- neither carries alignment information\n  }\n\n  return { matches, inserts }\n}\n\nexport default class A3mMSA extends BaseMSA {\n  constructor(input: string | FastaRecord[]) {\n    const records = toRecords(input)\n    const expanded = expandA3M(records.map(r => r.seq))\n    super(records.map((r, i) => [r.id, expanded[i]!]))\n  }\n\n  static sniff(input: string | FastaRecord[]): boolean {\n    if (typeof input === 'string' && !fastaSniff(input)) {\n      return false\n    }\n\n    const seqs = toRecords(input)\n      .map(r => r.seq)\n      .filter(s => !!s)\n\n    if (seqs.length < 2) {\n      return false\n    }\n\n    // A true aligned FASTA (e.g. impg's fasta-aln output from soft-masked\n    // references) has all rows the same total length. A3M's defining feature is\n    // variable-length rows, since lowercase inserts live outside the fixed match\n    // grid. So equal-length rows are an alignment, not A3M, even when lowercase\n    // soft-masking is present.\n    if (new Set(seqs.map(s => s.length)).size === 1) {\n      return false\n    }\n\n    let hasLowercase = false\n    let matchCount: number | undefined\n    for (const seq of seqs) {\n      let matches = 0\n      for (let i = 0; i < seq.length; i++) {\n        const code = seq.charCodeAt(i)\n        if (isMatch(code)) {\n          matches++\n        } else if (isLower(code)) {\n          hasLowercase = true\n        }\n      }\n      if (matchCount !== undefined && matches !== matchCount) {\n        return false\n      }\n      matchCount = matches\n    }\n    return hasLowercase\n  }\n}\n\n/**\n * Expand A3M rows into a rectangular alignment: every insert slot is widened to\n * the longest insert any row places there, and rows without one are padded with\n * '.' so all rows stay in register.\n */\nfunction expandA3M(rawSeqs: string[]): string[] {\n  const rows = rawSeqs.map(parseRow)\n  // a loop, not Math.max(...): an a3m from an hhblits search routinely carries\n  // six figures of hits, and spreading one argument per row throws\n  // \"Maximum call stack size exceeded\" somewhere past ~125k of them\n  let numPositions = 0\n  for (const { matches } of rows) {\n    numPositions = Math.max(numPositions, matches.length)\n  }\n\n  // one insert slot before each match column, plus one trailing slot\n  const maxInserts = new Array<number>(numPositions + 1).fill(0)\n  for (const { inserts } of rows) {\n    for (const [pos, ins] of inserts.entries()) {\n      maxInserts[pos] = Math.max(maxInserts[pos]!, ins.length)\n    }\n  }\n\n  return rows.map(({ matches, inserts }) => {\n    const result: string[] = []\n    for (let pos = 0; pos <= numPositions; pos++) {\n      const ins = inserts[pos] ?? ''\n      result.push(ins, '.'.repeat(maxInserts[pos]! - ins.length))\n      if (pos < numPositions) {\n        // a row with fewer match columns than the widest is padded out\n        result.push(matches[pos] ?? '-')\n      }\n    }\n    return result.join('')\n  })\n}\n", "export function parseVersion(line: string) {\n  const res = /\\(?(\\d+(\\.\\d+)+)\\)?/.exec(line)\n  return res && res.length > 1 ? res[1] : ''\n}\nexport function parseHeader(info: string) {\n  const knownHeaders = ['CLUSTAL', 'PROBCONS', 'MUSCLE', 'MSAPROBS', 'Kalign']\n\n  if (!knownHeaders.some(l => info.startsWith(l))) {\n    console.warn(\n      `${info} is not a known CLUSTAL header: ${knownHeaders.join(\n        ',',\n      )}, proceeding but could indicate an issue`,\n    )\n  }\n  const version = parseVersion(info)\n  return { info, version }\n}\n\nexport function getFirstNonEmptyLine(arr: Iterator<string>): string {\n  // There should be two blank lines after the header line\n  let line = arr.next()\n  while (!line.done && line.value.trim() === '') {\n    line = arr.next()\n  }\n  return line.value!\n}\n\nexport function getSeqBounds(line: string) {\n  const fields = line.split(/\\s+/)\n  const temp = line.slice(fields[0]!.length)\n  const s = fields[0]!.length + temp.indexOf(fields[1]!)\n  const e = s + fields[1]!.length\n  return [s, e] as const\n}\n\n// Use the first block to get the sequence identifiers\nexport function parseBlock(arr: Iterator<string>) {\n  let line = getFirstNonEmptyLine(arr)\n  const block = []\n  let consensusLine = ''\n  if (!line) {\n    return undefined\n  }\n\n  while (line) {\n    if (line.startsWith(' ')) {\n      consensusLine = line\n    } else {\n      block.push(line)\n    }\n    line = arr.next().value\n  }\n  const [start, end] = getSeqBounds(block[0]!)\n  const fields = block.map(s => s.split(/\\s+/))\n  const ids = fields.map(s => s[0]!)\n  const seqs = block.map(s => s.slice(start, end))\n  let consensus = consensusLine.slice(start, end)\n\n  // handle if the consensus trailing whitespace got trimmed\n  const remainder = seqs[0]!.length - consensus.length\n  if (remainder) {\n    consensus += ' '.repeat(remainder)\n  }\n  return {\n    ids,\n    seqs,\n    consensus,\n  }\n}\n\nexport function parseBlocks(arr: Iterator<string>) {\n  let block\n  const res = parseBlock(arr)\n  if (res !== undefined) {\n    while ((block = parseBlock(arr))) {\n      for (let i = 0; i < block.seqs.length; i++) {\n        res.seqs[i] += block.seqs[i]!\n      }\n      res.consensus += block.consensus\n    }\n  }\n  return res\n}\n", "import { parsePairwiseBlocks } from './pairwise.ts'\nimport { parseBlocks, parseHeader, getFirstNonEmptyLine } from './util.ts'\n\nexport function parseClustalIter(arr: Iterator<string>) {\n  const line = getFirstNonEmptyLine(arr)\n  if (!line) {\n    throw new Error('Empty file received')\n  }\n  const header = parseHeader(line)\n\n  const res = parseBlocks(arr)\n  if (res === undefined) {\n    throw new Error('No blocks parsed')\n  }\n\n  const alns = res.seqs.map((n, index) => ({ id: res.ids[index]!, seq: n }))\n  const { consensus } = res\n  if (consensus.length !== alns[0]!.seq.length) {\n    throw new Error(\n      `Consensus length != sequence length. Con ${consensus.length} seq ${alns[0]!.seq.length}`,\n    )\n  }\n\n  return { consensus, alns, header }\n}\n\nexport interface Row {\n  id: string\n  seq: string\n}\n\nexport function parse(contents: string) {\n  const iter = contents.split('\\n')[Symbol.iterator]()\n  return parseClustalIter(iter)\n}\n\nexport function parsePairwise(contents: string) {\n  const filtered = contents\n    .split('\\n')\n    .filter(f => !f.startsWith('#'))\n    .join('\\n')\n\n  const res = parsePairwiseBlocks(filtered.split('\\n')[Symbol.iterator]())\n  if (res === undefined) {\n    throw new Error('No blocks parsed')\n  }\n\n  const alns = res.seqs.map((n, index) => ({ id: res.ids[index]!, seq: n }))\n  const { consensus } = res\n  const firstAln = alns[0]\n  if (!firstAln) {\n    throw new Error('No alignments found')\n  }\n  if (consensus.length !== firstAln.seq.length) {\n    throw new Error(\n      `Consensus length !== sequence length. Con ${consensus.length} seq ${firstAln.seq.length}`,\n    )\n  }\n  if (alns.length !== 2) {\n    throw new Error(\n      `Expected exactly 2 sequences in pairwise alignment, got ${alns.length}`,\n    )\n  }\n  return {\n    consensus,\n    alns: alns as [Row, Row],\n  }\n}\n", "import { parse } from 'clustal-js'\n\nimport BaseMSA from './BaseMSA.ts'\n\nexport default class ClustalMSA extends BaseMSA {\n  private MSA: ReturnType<typeof parse>\n\n  constructor(text: string) {\n    const msa = parse(text)\n    super(msa.alns.map(aln => [aln.id, aln.seq]))\n    this.MSA = msa\n  }\n\n  getHeader() {\n    return this.MSA.header\n  }\n\n  get seqConsensus() {\n    return this.MSA.consensus\n  }\n}\n", "export interface Row {\n  id: string\n  seq: string\n}\n\nexport function parseEmfAln(contents: string) {\n  const lines = contents\n    .split('\\n')\n    .map(f => f.trim())\n    .filter(f => !!f)\n  const seqs = []\n  const alns = []\n  for (const line of lines) {\n    if (line.startsWith('SEQ')) {\n      seqs.push(line)\n    } else if (line.startsWith('DATA')) {\n      continue\n    } else if (line.startsWith('//')) {\n      break\n    } else {\n      alns.push(line)\n    }\n  }\n  const arr = seqs.map(s => {\n    const [, species, protein, chr, start, end, strand, geneId, unknown] =\n      s.split(' ')\n    return {\n      species,\n      protein,\n      chr,\n      start: +start,\n      end: +end,\n      strand: +strand,\n      geneId,\n      unknown,\n      seq: '',\n    }\n  })\n  for (const aln of alns) {\n    for (let j = 0; j < seqs.length; j++) {\n      arr[j].seq += aln[j]\n    }\n  }\n  return arr\n}\n\nexport function parseEmfTree(contents: string) {\n  const lines = contents\n    .split('\\n')\n    .map(f => f.trim())\n    .filter(f => !!f)\n  const seqs = []\n  let tree = ''\n  for (const line of lines) {\n    if (line.startsWith('SEQ')) {\n      seqs.push(line)\n    } else if (line.startsWith('DATA')) {\n      continue\n    } else if (line.startsWith('//')) {\n      break\n    } else {\n      tree = line\n    }\n  }\n  const arr = seqs.map(s => {\n    const [, species, protein, chr, start, end, strand, geneId, unknown] =\n      s.split(' ')\n    return {\n      species,\n      protein,\n      chr,\n      start: +start,\n      end: +end,\n      strand: +strand,\n      geneId,\n      unknown,\n    }\n  })\n\n  return { tree, seqs: arr }\n}\n", "import { parseEmfAln } from 'emf-js'\n\nimport BaseMSA from './BaseMSA.ts'\n\nexport default class EmfMSA extends BaseMSA {\n  constructor(text: string) {\n    super(parseEmfAln(text).map(aln => [aln.protein, aln.seq]))\n  }\n}\n", "import BaseMSA from './BaseMSA.ts'\nimport { toRecords } from './fastaRecords.ts'\n\nimport type { FastaRecord } from './fastaRecords.ts'\n\nexport default class FastaMSA extends BaseMSA {\n  // Newick tools write a colon in a name as an underscore\n  private colonNormalized = new Map<string, string>()\n\n  constructor(input: string | FastaRecord[]) {\n    const records = toRecords(input)\n    super(records.map(r => [r.id, r.seq]))\n    for (const { id } of records) {\n      if (id.includes(':')) {\n        this.colonNormalized.set(id.replaceAll(':', '_'), id)\n      }\n    }\n  }\n\n  getRow(name: string) {\n    return (\n      this.rows.get(name) ??\n      this.rows.get(this.colonNormalized.get(name) ?? '') ??\n      ''\n    )\n  }\n}\n", "import { parseNewick } from '@gmod/newick'\n\nimport type { NewickNode } from '@gmod/newick'\n\n/**\n * Newick parsing for phylogenetic trees.\n *\n * `postParenNumeric: 'name'` is the whole reason this wrapper exists. A bare\n * number after a `)` is an internal node label in standard Newick -- typically a\n * bootstrap support value -- but `@gmod/hclust` reuses that slot for a cluster's\n * merge height, and the parser's default guesses between the two by whether the\n * tree carries any `:` branch length. Everything reaching this package is a\n * phylogeny (newick, the tree embedded in Stockholm `#=GF NH`, EMF, ASN.1), so\n * the guess is settled here instead: reading `((A,B)95,(C,D)80);` as lengths\n * would draw a phylogram scaled by support values.\n */\nexport default function parse(s: string): NewickNode {\n  return parseNewick(s, { postParenNumeric: 'name' })\n}\n", "/**\n * Stockholm format parser\n * Based on stockholm-js by Ian Holmes\n * Rewritten in TypeScript\n */\n\nexport interface StockholmData {\n  gf: Record<string, string[]>\n  gc: Record<string, string>\n  gs: Record<string, Record<string, string[]>>\n  gr: Record<string, Record<string, string>>\n  seqname: string[]\n  seqdata: Record<string, string>\n}\n\nfunction createStockholm(): StockholmData {\n  return {\n    gf: Object.create(null),\n    gc: Object.create(null),\n    gs: Object.create(null),\n    gr: Object.create(null),\n    seqname: [],\n    seqdata: Object.create(null),\n  }\n}\n\n// records before a \"# STOCKHOLM 1.0\" header are an error in strict mode,\n// otherwise they implicitly start a new alignment\nfunction ensureStock(\n  stock: StockholmData | null,\n  strict: boolean,\n): StockholmData {\n  if (stock) {\n    return stock\n  }\n  if (strict) {\n    throw new Error('No format header: # STOCKHOLM 1.0')\n  }\n  return createStockholm()\n}\n\nconst formatStartRegex = /^# STOCKHOLM 1.0/\nconst formatEndRegex = /^\\/\\/\\s*$/\nconst gfRegex = /^#=GF\\s+(\\S+)\\s+(.*?)\\s*$/\nconst gcRegex = /^#=GC\\s+(\\S+)\\s+(.*?)\\s*$/\nconst gsRegex = /^#=GS\\s+(\\S+)\\s+(\\S+)\\s+(.*?)\\s*$/\nconst grRegex = /^#=GR\\s+(\\S+)\\s+(\\S+)\\s+(.*?)\\s*$/\n// a sequence line is \"<name> <residues>\". The leading [^#\\s] guards against a\n// two-word comment (\"# note\") being taken as a sequence named '#'; every\n// meaningful '#' line is a #=GF/#=GC/#=GS/#=GR record already matched above.\nconst lineRegex = /^\\s*([^#\\s]\\S*)\\s+(\\S+)\\s*$/\nconst nonwhiteRegex = /\\S/\n\nexport function sniff(text: string): boolean {\n  return formatStartRegex.test(text)\n}\n\nexport function parseAll(\n  text: string,\n  opts?: { strict?: boolean },\n): StockholmData[] {\n  const options = opts ?? {}\n  const db: StockholmData[] = []\n  let stock: StockholmData | null = null\n  // one tree spans consecutive `#=GF NH` lines, so a `#=GF TN` naming the\n  // next tree, or any other #=GF line, ends it\n  let treeContinues = false\n\n  const lines = text.split('\\n')\n  for (const line of lines) {\n    let match: RegExpExecArray | null\n\n    if (formatStartRegex.test(line)) {\n      if (stock) {\n        db.push(stock)\n      }\n      stock = createStockholm()\n      treeContinues = false\n    } else if (formatEndRegex.test(line)) {\n      if (stock) {\n        db.push(stock)\n      }\n      stock = null\n    } else if ((match = gfRegex.exec(line))) {\n      stock = ensureStock(stock, !!options.strict)\n      const tag = match[1]!\n      const values = (stock.gf[tag] ??= [])\n      if (tag === 'NH' && treeContinues && values.length > 0) {\n        values[values.length - 1] += match[2]!\n      } else {\n        values.push(match[2]!)\n      }\n      treeContinues = tag === 'NH'\n    } else if ((match = gcRegex.exec(line))) {\n      stock = ensureStock(stock, !!options.strict)\n      stock.gc[match[1]!] = (stock.gc[match[1]!] ?? '') + match[2]!\n    } else if ((match = gsRegex.exec(line))) {\n      stock = ensureStock(stock, !!options.strict)\n      const byName = (stock.gs[match[2]!] ??= Object.create(null))\n      ;(byName[match[1]!] ??= []).push(match[3]!)\n    } else if ((match = grRegex.exec(line))) {\n      stock = ensureStock(stock, !!options.strict)\n      const byName = (stock.gr[match[2]!] ??= Object.create(null))\n      byName[match[1]!] = (byName[match[1]!] ?? '') + match[3]!\n    } else if ((match = lineRegex.exec(line))) {\n      stock = ensureStock(stock, !!options.strict)\n      const seqname = match[1]!\n      const seqdata = match[2]!\n      if (stock.seqdata[seqname] === undefined) {\n        stock.seqdata[seqname] = ''\n        stock.seqname.push(seqname)\n      }\n      stock.seqdata[seqname] += seqdata\n    } else if (nonwhiteRegex.test(line)) {\n      if (options.strict) {\n        throw new Error('Malformed line')\n      }\n    }\n  }\n\n  if (stock) {\n    db.push(stock)\n  }\n\n  return db\n}\n\nexport function parse(\n  text: string,\n  opts?: { strict?: boolean },\n): StockholmData {\n  const db = parseAll(text, opts)\n  if (db.length === 0) {\n    throw new Error('No alignments found')\n  }\n  if (db.length > 1) {\n    throw new Error('More than one alignment found')\n  }\n  return db[0]!\n}\n", "import { generateNodeIds } from '../util.ts'\nimport BaseMSA from './BaseMSA.ts'\nimport parseNewick from './parseNewick.ts'\nimport { parseAll } from './stockholmParser.ts'\n\nimport type { MSATrack, NodeWithIds } from '../types.ts'\nimport type { StockholmData } from './stockholmParser.ts'\n\nexport default class StockholmMSA extends BaseMSA {\n  private data: StockholmData[]\n  private MSA: StockholmData\n\n  constructor(text: string, currentAlignment: number) {\n    const res = parseAll(text)\n    const aln = res[currentAlignment] ?? res[0]\n    if (!aln) {\n      throw new Error('No alignments found in Stockholm file')\n    }\n    super(aln.seqname.map(name => [name, aln.seqdata[name] ?? '']))\n    this.data = res\n    this.MSA = aln\n  }\n\n  getMSA() {\n    return this.MSA\n  }\n\n  get alignmentNames() {\n    return this.data.map((aln, idx) => aln.gf.DE?.[0] ?? `Alignment ${idx + 1}`)\n  }\n\n  getHeader() {\n    const acEntries = this.MSA.gs.AC ?? {}\n    const drEntries = this.MSA.gs.DR ?? {}\n    return {\n      General: this.MSA.gf,\n      Accessions: Object.fromEntries(\n        Object.entries(acEntries).map(([k, v]) => [k, v[0]]),\n      ),\n      Dbxref: Object.fromEntries(\n        Object.entries(drEntries).map(([k, v]) => [k, v.join('; ')]),\n      ),\n    }\n  }\n\n  getRowData(rowName: string) {\n    return {\n      name: rowName,\n      accession: this.MSA.gs.AC?.[rowName]?.[0],\n      dbxref: this.MSA.gs.DR?.[rowName]?.join('; '),\n    }\n  }\n\n  getStructures() {\n    const pdbRegex = /PDB; +(\\S+) +([^;\\s]+); *(-?[0-9]+)-(-?[0-9]+)/\n    const drEntries = this.MSA.gs.DR ?? {}\n    const result: Record<\n      string,\n      { pdb: string; chain: string; startPos: number; endPos: number }[]\n    > = {}\n    for (const [id, drList] of Object.entries(drEntries)) {\n      for (const dr of drList) {\n        const match = pdbRegex.exec(dr)\n        if (match) {\n          ;(result[id] ??= []).push({\n            pdb: match[1]!.toLowerCase(),\n            chain: match[2]!,\n            startPos: +match[3]!,\n            endPos: +match[4]!,\n          })\n        }\n      }\n    }\n    return result\n  }\n\n  getTree(): NodeWithIds {\n    const tree = this.MSA.gf.NH?.[0]\n    return tree ? generateNodeIds(parseNewick(tree)) : super.getTree()\n  }\n\n  get seqConsensus() {\n    return this.MSA.gc.seq_cons\n  }\n\n  get secondaryStructureConsensus() {\n    return this.MSA.gc.SS_cons\n  }\n\n  /**\n   * One text track per `#=GC` line, and one per `#=GR` line that stays hidden\n   * until asked for: a Pfam seed carries a few per-row active-site lines, but\n   * an Rfam family carries a structure line for every row with a PDB entry.\n   */\n  get tracks(): MSATrack[] {\n    const { seq_cons, SS_cons, ...otherGc } = this.MSA.gc\n    return [\n      {\n        id: 'seqConsensus',\n        name: 'Sequence consensus',\n        data: seq_cons,\n        customColorScheme: {},\n      },\n      {\n        id: 'secondaryStruct',\n        name: 'Secondary-structure',\n        data: SS_cons,\n        customColorScheme: wussColors,\n      },\n      ...Object.entries(otherGc).map(([tag, data]) => ({\n        id: `gc-${tag}`,\n        name: tag,\n        data,\n        customColorScheme: structureColors(tag),\n      })),\n      ...Object.entries(this.MSA.gr).flatMap(([tag, byRow]) =>\n        Object.entries(byRow).map(([row, data]) => ({\n          id: `gr-${row}-${tag}`,\n          name: `${row} ${tag}`,\n          data,\n          customColorScheme: structureColors(tag),\n          defaultOff: true,\n        })),\n      ),\n    ]\n  }\n}\n\n// WUSS writes base-paired columns as open/close brackets of several nesting\n// types (<>, (), [], {}); coloring every open one way and every close the other\n// highlights each helix, including the tRNA acceptor stem written with parens\nconst wussColors: Record<string, string> = {\n  '<': 'lightblue',\n  '(': 'lightblue',\n  '[': 'lightblue',\n  '{': 'lightblue',\n  '>': 'pink',\n  ')': 'pink',\n  ']': 'pink',\n  '}': 'pink',\n}\n\n// `SS`, and Rfam's per-structure `2GIS_A_SS`\nfunction structureColors(tag: string) {\n  return tag === 'SS' || tag.endsWith('_SS') ? wussColors : {}\n}\n\nexport { sniff as stockholmSniff } from './stockholmParser.ts'\n", "import A3mMSA from './A3mMSA.ts'\nimport ClustalMSA from './ClustalMSA.ts'\nimport EmfMSA from './EmfMSA.ts'\nimport FastaMSA from './FastaMSA.ts'\nimport StockholmMSA, { stockholmSniff } from './StockholmMSA.ts'\nimport { fastaSniff, splitFastaRecords } from './fastaRecords.ts'\n\nexport { parseEmfTree } from 'emf-js'\nexport { default as parseNewick } from './parseNewick.ts'\n\nexport type MSAParserType =\n  | StockholmMSA\n  | A3mMSA\n  | FastaMSA\n  | EmfMSA\n  | ClustalMSA\n\nexport type MSAFormat = 'stockholm' | 'a3m' | 'fasta' | 'emf' | 'clustal'\n\nconst htmlPage = /^<(!doctype\\s+html|html[\\s>])/i\nconst clustalHeader = /^(CLUSTAL|MUSCLE|PROBCONS|MSAPROBS|Kalign)/i\n\n// A caller that knows the format, such as impg emitting fasta-aln, passes\n// `format` to skip sniffing, which cannot always tell FASTA from A3M\nexport function parseMSA(\n  input: string,\n  currentAlignment = 0,\n  format?: MSAFormat,\n): MSAParserType {\n  const text = input\n    .replace(/^\\uFEFF/, '')\n    .replaceAll(/\\r\\n?/g, '\\n')\n    .trimStart()\n  if (htmlPage.test(text)) {\n    throw new Error(\n      'Received an HTML page, not an alignment. Check that the URL points at the file itself',\n    )\n  }\n  if (format === 'stockholm') {\n    return new StockholmMSA(text, currentAlignment)\n  }\n  if (format === 'a3m') {\n    return new A3mMSA(text)\n  }\n  if (format === 'fasta') {\n    return new FastaMSA(text)\n  }\n  if (format === 'emf') {\n    return new EmfMSA(text)\n  }\n  if (format === 'clustal') {\n    return new ClustalMSA(text)\n  }\n  if (stockholmSniff(text)) {\n    return new StockholmMSA(text, currentAlignment)\n  }\n  if (fastaSniff(text)) {\n    const records = splitFastaRecords(text)\n    return A3mMSA.sniff(records) ? new A3mMSA(records) : new FastaMSA(records)\n  }\n  if (text.startsWith('SEQ')) {\n    return new EmfMSA(text)\n  }\n  if (clustalHeader.test(text)) {\n    return new ClustalMSA(text)\n  }\n  const firstLine = text.split('\\n', 1)[0]!.slice(0, 80)\n  throw new Error(\n    firstLine\n      ? `Unrecognized alignment format: expected FASTA, A3M, Stockholm, Clustal or EMF, but the first line reads \"${firstLine}\"`\n      : 'The alignment file is empty',\n  )\n}\n\n/**\n * Get ungapped sequence from an aligned row\n */\nexport function getUngappedSequence(alignedSeq: string): string {\n  return alignedSeq.replaceAll(/[.-]/g, '')\n}\n\nexport { default as A3mMSA } from './A3mMSA.ts'\nexport { default as ClustalMSA } from './ClustalMSA.ts'\nexport { default as EmfMSA } from './EmfMSA.ts'\nexport { default as FastaMSA } from './FastaMSA.ts'\nexport { default as StockholmMSA, stockholmSniff } from './StockholmMSA.ts'\n", "import type { GFFRecord } from '../types.ts'\n\n// decodeURIComponent throws on a stray '%' (common in unescaped GFF3 values);\n// fall back to the raw value rather than aborting the whole parse\nfunction safeDecode(val: string) {\n  try {\n    return decodeURIComponent(val)\n  } catch {\n    return val\n  }\n}\n\n// InterProScan quotes some of its values (Ontology_term=\"GO:0008652\",\n// Dbxref=\"InterPro:IPR001048\"), and the quotes are not part of the term\nfunction unquote(val: string) {\n  return val.replace(/^\"(.*)\"$/, '$1')\n}\n\nfunction parseAttributes(col9?: string): Record<string, string> {\n  if (!col9) {\n    return {}\n  }\n  const attributes: Record<string, string> = {}\n  for (const field of col9.split(';')) {\n    const eq = field.indexOf('=')\n    const key = field.slice(0, eq).trim()\n    const val = field.slice(eq + 1)\n    // split on comma (the GFF3 multi-value separator) BEFORE decoding, so a\n    // literal comma encoded as %2C survives the split and isn't mistaken\n    // for a separator\n    if (eq !== -1 && key && val) {\n      attributes[key] = val\n        .split(',')\n        .map(v => unquote(safeDecode(v).trim()))\n        .join(' ')\n    }\n  }\n  return attributes\n}\n\nexport function parseGFF(str?: string): GFFRecord[] {\n  if (!str) {\n    return []\n  }\n  const lines: string[] = []\n  for (const raw of str.split('\\n')) {\n    const line = raw.trim()\n    // InterProScan appends the sequences it scanned; every line past this is\n    // FASTA, and reading it as features gave rows named \">P51587\"\n    if (line.startsWith('##FASTA')) {\n      break\n    }\n    // a feature is nine tab-separated columns, eight of them mandatory; a\n    // FASTA line in a file that omitted the ##FASTA directive is one\n    if (line && !line.startsWith('#') && line.split('\\t').length >= 8) {\n      lines.push(line)\n    }\n  }\n  return lines.map(f => {\n    const parts = f.split('\\t')\n    const [seq_id, source, type, start, end, score, strand, phase] = parts\n    const col9 = parts[8]\n\n    // attributes first, so a column-9 key colliding with a core column (e.g.\n    // \"start=\") can't turn a number field into a string\n    return {\n      ...parseAttributes(col9),\n      seq_id: safeDecode(seq_id ?? ''),\n      source: source ?? '',\n      type: type ?? '',\n      start: Number(start) || 0,\n      end: Number(end) || 0,\n      score: Number(score) || 0,\n      strand: strand ?? '.',\n      phase: phase ?? '.',\n    }\n  })\n}\n", "import type { Annotation, GFFRecord } from '../types.ts'\n\n// Feature types drawn with an arrowhead for their strand. A prokaryotic GFF\n// writes each gene as a CDS row. Exon, UTR and domain features stay blocks,\n// since an exon is a segment of one transcript.\nconst GENE_LEVEL_TYPES = new Set([\n  'gene',\n  'CDS',\n  'pseudogene',\n  'mRNA',\n  'transcript',\n  'primary_transcript',\n  'ncRNA',\n  'tRNA',\n  'rRNA',\n  'snRNA',\n  'snoRNA',\n  'miRNA',\n  'lnc_RNA',\n])\n\n// +1/-1 for a stranded gene-level feature, undefined otherwise (which the\n// renderer draws as a plain block).\nfunction geneStrand({ type, strand }: GFFRecord): number | undefined {\n  const directional = strand === '+' ? 1 : strand === '-' ? -1 : undefined\n  return GENE_LEVEL_TYPES.has(type) ? directional : undefined\n}\n\n// The nine columns a feature line holds; every other key of a record came from\n// column 9\nconst GFF_COLUMNS = new Set([\n  'seq_id',\n  'source',\n  'type',\n  'start',\n  'end',\n  'score',\n  'strand',\n  'phase',\n])\n\nfunction attributesOf(record: GFFRecord) {\n  const entries = Object.entries(record).filter(\n    ([key, value]) => !GFF_COLUMNS.has(key) && typeof value === 'string',\n  ) as [string, string][]\n  return entries.length > 0 ? Object.fromEntries(entries) : undefined\n}\n\n// JBrowse and IGV read an RGB triple as well as a named or hex color, and the\n// attribute parser has already turned `255,0,0` into `255 0 0` by splitting on\n// the GFF3 multi-value comma\nconst RGB_TRIPLE = /^(\\d{1,3})[\\s,]+(\\d{1,3})[\\s,]+(\\d{1,3})$/\n\nfunction cssColor(record: GFFRecord) {\n  const value = (record.color ??\n    record.colour ??\n    record.Color ??\n    record.Colour) as string | undefined\n  if (!value) {\n    return undefined\n  }\n  const triple = RGB_TRIPLE.exec(value.trim())\n  return triple ? `rgb(${triple[1]},${triple[2]},${triple[3]})` : value.trim()\n}\n\n// InterProScan describes the sequence it scanned before listing the matches\n// against it. Those lines span the whole row and carry no signature, so they\n// would draw a full-width block labelled by an md5.\nconst WHOLE_SEQUENCE_TYPES = new Set(['polypeptide', 'nucleic_acid'])\n\n/**\n * Convert GFF records to annotations, one per record, in file order.\n *\n * InterProScan's own GFF3 output falls out of the same mapping: it writes\n * `Name` as the signature accession and `signature_desc` as its human-readable\n * name, with domain positions 1-based.\n */\nexport function gffToAnnotations(gffRecords: GFFRecord[]): Annotation[] {\n  return gffRecords\n    .filter(record => !WHOLE_SEQUENCE_TYPES.has(record.type))\n    .map(record => {\n      const accession =\n        (record.Name as string) ||\n        (record.ID as string) ||\n        `${record.source}_${record.start}_${record.end}`\n      const name =\n        (record.signature_desc as string) ||\n        (record.Name as string) ||\n        accession\n      return {\n        id: record.seq_id,\n        accession,\n        name,\n        // not Ontology_term: a GO id list is what the domain is annotated\n        // with, not what it is, and reading it first labelled every\n        // InterProScan domain \"GO:0003677 GO:0006281\"\n        description:\n          (record.description as string) ||\n          (record.Note as string) ||\n          (record.signature_desc as string) ||\n          name,\n        featureType: record.type,\n        start: record.start,\n        end: record.end,\n        strand: geneStrand(record),\n        color: cssColor(record),\n        attributes: attributesOf(record),\n      }\n    })\n}\n"],
+  "mappings": 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+}

package/dist/chunks/chunk-ZQSWX57C.js

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=chunk-ZQSWX57C.js.map

package/dist/chunks/chunk-ZQSWX57C.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/msa/legendRows.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/constants.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/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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+}

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