chromosomix 0.17.0 → 0.18.0

package/dist/assets/{workspace-DxOEjrSc.js → workspace-ZYKuBclx.js}

@@ -1,17 +1,15 @@
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xo(n,t){const e=Object.keys(n);return e.length===Object.keys(t).length&&e.every(s=>n[s]===t[s])}const So=100;function mt(n,t){return`${n}\0${t}`}const $o=8;function Zt(n,t){return`${n}\0${t}`}function Mo(n,t,e,s,i,o){const r=t===void 0||t.length===0?n:`${n}\0${t.join("\0")}`,a=e===void 0?r:`${r}\0${e.base}:${e.rungs}`,l=s===void 0?a:`${a}\0contacts:${s.contacts}:${s.seed??""}:${s.alpha??""}`,c=i===void 0?l:`${l}\0edit:${Rs(i)}`;return o===void 0?c:`${c}\0coarsen:${o}`}function _e(n){return Sn(n.label)}function Eo(n){return{line:n.line,notes:n.notes??[],detail:n.detail??[]}}class To{host;makeClient;client=null;mounted=null;states=new Map;results=new Map;history=new Map;resultTargets=new Map;queue=[];current=null;held=new Map;listeners=new Set;lastNotifiedAt=0;trailing=null;destroyed=!1;constructor(t,e=()=>new Fs){this.host=t,this.makeClient=e}stateOf(t){return this.states.get(t)??{status:"idle"}}holdFile(t,e,s){const i=Zt(t,e);s===null?this.held.delete(i):this.held.set(i,s)}heldFile(t,e){return this.held.get(Zt(t,e))}resultOf(t,e){const s=e??this.homeOf(t);return this.results.get(mt(s,t))??null}homeOf(t){const e=this.host.task?.(t)??St(t);return e!==void 0&&!nt(e)?J:this.host.targetMap?.()??J}runsOf(t,e){const s=e??this.homeOf(t),i=mt(s,t),o=this.results.get(i),r=this.history.get(i)??[];return o===void 0?[...r]:[o,...r]}resultsFor(t){const e=this.host.allTargets?.()??[],s=new Set,i=[];for(const o of e){const r=this.results.get(mt(o.map,t));r!==void 0&&(s.add(o.map),i.push({target:o,result:r}))}for(const[o,r]of this.results){const a=this.resultTargets.get(o);a===void 0||s.has(a.map)||o===mt(a.map,t)&&i.push({target:a,result:r})}return i}subscribe(t){return this.listeners.add(t),()=>{this.listeners.delete(t)}}get busy(){return this.current!==null||this.queue.length>0}run(t,e){this.queueOne(t,e,null)}runAll(t,e,s){if(!nt(t)){this.queueOne(t,e,null);return}if(s.length!==0){if(s.length===1){this.queueOne(t,e,null,s[0]);return}this.cancel(t.id),s.forEach((i,o)=>{this.queueOne(t,e,{at:o,of:s.length},i)})}}queueOne(t,e,s,i){if(this.destroyed)return;const o=this.host.context(t);if(o===null){this.refuse(t,s,"nothing is open");return}const r=t.mapless===!0?De(o,"sequences"):o.framing??(t.venue==="annotations"?De(o):null);if(r===null){this.refuse(t,s,"this view has no contact map to run against");return}const a=nt(t)?i??this.hostTarget(r,t):{...this.hostTarget(r,t),map:J};if(s===null){if(this.current?.task.id===t.id&&this.current.target.map===a.map)return;const l=this.queue.find(c=>c.task.id===t.id&&c.target.map===a.map);if(l!==void 0){l.params=e,l.framing=r;return}}this.queue.push({task:t,params:e,framing:r,target:a,batch:s,cancelled:!1,running:null}),this.setState(t.id,{status:"queued"}),this.pump()}targets(){return this.host.allTargets?.()??[]}async readyTargets(){return await this.host.allTargetsReady?.()??this.targets()}targetCount(){return this.host.targetCount?.()??this.targets().length}target(){const t=this.host.targetMap?.();return t===void 0?null:this.targets().find(e=>e.map===t)??null}hostTarget(t,e){const s=this.host.source(e);return{map:this.host.targetMap?.()??J,uri:s?.uri??t.uri,...s===null?{}:{source:s.source},...s?.cells===void 0?{}:{cells:s.cells},...s?.binning===void 0?{}:{binning:s.binning},...s?.orientation===void 0?{}:{orientation:s.orientation},...s?.pairsStats===void 0?{}:{pairsStats:s.pairsStats},...s?.resample===void 0?{}:{resample:s.resample},...s?.edit===void 0?{}:{edit:s.edit},label:s?.label??t.uri}}cancel(t){let e=0;for(let i=this.queue.length-1;i>=0;i--)this.queue[i].task.id===t&&(this.queue.splice(i,1),e++);const s=this.current;if(s===null||s.task.id!==t){e>0&&this.setState(t,{status:"cancelled"});return}s.cancelled=!0,s.running?.handle.cancel()}destroy(){this.destroyed=!0;for(const t of this.queue)this.setState(t.task.id,{status:"cancelled"});this.queue.length=0,this.current!==null&&(this.current.cancelled=!0,this.setState(this.current.task.id,{status:"cancelled"})),this.trailing!==null&&(clearTimeout(this.trailing),this.trailing=null),this.client?.terminate(),this.client=null,this.mounted=null,this.listeners.clear()}pump(){if(this.current!==null||this.destroyed)return;const t=this.queue.shift();t!==void 0&&(this.current=t,this.execute(t).finally(()=>{this.current=null,this.pump()}))}batchOf(t){return t.batch===null?{}:{batch:{at:t.batch.at,of:t.batch.of,label:t.target.label}}}async execute(t){const e=performance.now();let s=null;const i=this.recordStart(t);let o=null;this.setState(t.task.id,{status:"running",done:0,total:0,note:"starting",startedAt:e,...this.batchOf(t)});try{const r=this.plan(t.task,t.params),a=this.ensureClient();r.some(c=>c.task.venue!=="annotations")&&await this.mount(t,a,e);const l={};for(let c=0;c<r.length;c++){if(s=r[c],t.cancelled)throw ze();const u=s.task.id===t.task.id,d=this.results.get(mt(t.target.map,s.task.id));if(!u&&d!==void 0&&Yn(d.provenance,{params:s.params,framing:t.framing})){l[s.task.id]=d;continue}const f=await this.runStep(t,a,s,r,c,l,e);if(t.cancelled)throw ze();const m=mt(t.target.map,s.task.id),h=this.results.get(m);if(h!==void 0&&h!==f){const 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That gesture normally zooms; while this is lit it names this locus instead, once."}):null,c=()=>{i.replaceChildren(...(this.context.genomes??[]).map(f=>p("option",{value:f.name})),...this.context.contigs.map(f=>p("option",{value:f.name})))},u=()=>this.commit(t.key,o.value.trim());o.addEventListener("change",u),o.addEventListener("keydown",f=>{f.key==="Enter"&&u()});const d=()=>{if(l!==null){const f=Le();l.setAttribute("aria-pressed",String(f)),l.textContent=f?"pointing…":"pick on map",r.classList.toggle("hidden",!f),r.textContent=f?"Shift-drag along either axis of the map. Escape to stop.":""}document.activeElement!==o&&(o.value=X(this.params[t.key],""))};if(a){let f=Ie();this.teardown.push(ci(()=>{const m=Ie();m!==null&&m!==f&&(f=m,this.commit(t.key,m.whole===!0?m.contig:ye(m))),d()}))}return c(),d(),{spec:t,wrapper:this.wrap(t,this.labelled(t,p("div",{class:"param-locus"},o,i,...l===null?[]:[l]),e),r),shown:!1,sync:d,refill:()=>{c(),d()}}}fileControl(t){const e=`${this.id}-${t.key}-label`,s=`${this.id}-${t.key}`,i=p("span",{class:"ann-drop-label"}),o=p("span",{class:"ann-drop-hint"}),r=p("div",{class:"ann-drop param-drop",attrs:{tabindex:"0",role:"button","aria-labelledby":e}},i,o),a=tt("x","Forget this file",()=>this.chooseFile(t,null),{class:"btn btn-icon param-drop-forget"}),l=p("input",{class:"input param-address",type:"text",attrs:{id:s,"aria-label":`${t.label}: address`},...t.placeholder===void 0?{}:{placeholder:t.placeholder}}),c=p("p",{class:"hint param-file-note hidden"}),u=g=>{c.textContent=g,c.classList.toggle("hidden",g==="")},d=g=>{if(!hn(t,g.name)){u(`${g.name} is not a ${t.accept.join(" or ")} file.`);return}u(""),this.chooseFile(t,{value:g.name,source:{kind:"local",file:g},size:g.size})},f=()=>{fi({multiple:!1}).then(g=>{g.length>0&&d(g[0])})};r.addEventListener("click",f),r.addEventListener("keydown",g=>{g.key!=="Enter"&&g.key!==" "||(g.preventDefault(),f())}),r.addEventListener("dragover",g=>{!ui(g)&&!Ne(g)||(g.preventDefault(),r.classList.add("over"))}),r.addEventListener("dragleave",g=>{g.relatedTarget instanceof Node&&r.contains(g.relatedTarget)||r.classList.remove("over")}),r.addEventListener("drop",g=>{if(g.preventDefault(),g.stopPropagation(),r.classList.remove("over"),Ne(g)){di(g).then(b=>{if(b===null)return;const S=b.name??b.uri.split(/[\\/]/).pop()??b.uri;if(!hn(t,S)){u(`${S} is not a ${t.accept.join(" or ")} file.`);return}u(""),this.chooseFile(t,{value:b.source.kind==="local"?b.source.file.name:b.uri,source:b.source,name:S,...b.source.kind==="local"?{size:b.source.file.size}:{}})});return}const w=hi(g.dataTransfer);w.length>0&&d(w[0])});const m=()=>{const g=l.value.trim();if(g!==""&&!Ct(g)){u("An address starts with https:// or s3:// — a file on this computer is dropped above.");return}u(""),this.shelf.set(t.key,null),this.commit(t.key,g)};l.addEventListener("change",m),l.addEventListener("keydown",g=>{g.key==="Enter"&&(g.preventDefault(),m())});const h=()=>{const g=X(this.params[t.key],"").trim(),w=this.shelf.get(t.key),b=w!==void 0&&w.value===g&&g!==""&&!Ct(g),S=w!==void 0&&w.value===g&&Ct(g);r.classList.toggle("is-held",b||S),b||S?(i.textContent=w.name??(b?g:g.split(/[\\/]/).pop()??g),o.textContent=w.size===void 0?"drop or click to choose another":`${z.bytes(w.size)} · drop or click to choose another`):(i.textContent=t.prompt,o.textContent=t.accept.join(" or ")),a.classList.toggle("hidden",!(b||S)),document.activeElement!==l&&(l.value=b||S?"":g)};h();const y=p("div",{class:"param-file"},p("div",{class:"param-file-row"},r,a),l);return{spec:t,wrapper:this.wrap(t,this.named(t,y,e),c),shown:!1,sync:h}}chooseFile(t,e){this.shelf.set(t.key,e);const s=e?.value??"";if(me(this.params[t.key],s)){for(const i of this.controls)i.sync();this.options.onChange(this.value);return}this.commit(t.key,s)}textControl(t){const e=`${this.id}-${t.key}`,s=p("input",{class:"input",type:"text",attrs:{id:e},...t.placeholder===void 0?{}:{placeholder:t.placeholder},style:{width:"100%"}}),i=()=>this.commit(t.key,s.value.trim());s.addEventListener("change",i),s.addEventListener("keydown",r=>{r.key==="Enter"&&(r.preventDefault(),i())});const o=()=>{document.activeElement!==s&&(s.value=X(this.params[t.key],""))};return o(),{spec:t,wrapper:this.wrap(t,this.labelled(t,s,e)),shown:!1,sync:o}}seedControl(t){const e=`${this.id}-${t.key}`,s=p("input",{class:"input input-num input-step",type:"number",attrs:{id:e,size:"1",step:"1",min:"0"}}),i=()=>fn(this.params[t.key],t.default),o=()=>{const l=Number(s.value);if(!Number.isFinite(l)){s.value=String(i());return}const c=Math.max(0,Math.trunc(l));s.value=String(c),this.commit(t.key,c)};s.addEventListener("change",o),s.addEventListener("keydown",l=>{l.key==="Enter"&&o()});const r=tt("rotate-cw","Roll a new seed — the same seed gives the same numbers, a new one resamples",()=>{const l=Ia(i());s.value=String(l),this.commit(t.key,l)},{class:"btn btn-icon",size:14}),a=()=>{document.activeElement!==s&&(s.value=String(i()))};return a(),{spec:t,wrapper:this.wrap(t,this.labelled(t,p("div",{class:"plot-icon-row"},s,r),e)),shown:!1,sync:a}}}const wt="\0all-maps",pe="chromosomix:analysis-drawer:width",Pa=380,Ba=.75,qa=.95,za=300;let Ra=0;function _a(){try{const n=window.localStorage.getItem(pe);if(n===null)return null;const t=Number(n);return Number.isFinite(t)&&t>0?t:null}catch{return null}}function pn(n){try{n===null?window.localStorage.removeItem(pe):window.localStorage.setItem(pe,String(Math.round(n)))}catch{}}function Da(n){if(n===null)return!0;const t=typeof n;return t==="number"||t==="string"||t==="boolean"?!0:Array.isArray(n)&&n.every(e=>typeof e=="string")}function kt(n){return n===null?"":n.memoryKey??n.uri}function Va(n,t){const e={...Ht(n.params)},s=Fn(t,n.id);if(s===null)return e;for(const i of n.params){const o=s[i.key];Da(o)&&(e[i.key]=o)}return e}function Wa(n){const t=[n.note.replace(/\.\s*$/,"")];return n.requests!==null&&n.requests>0&&t.push(`${z.int(n.requests)} request${n.requests===1?"":"s"}`),n.bytes!==null&&n.bytes>0&&t.push(z.bytes(n.bytes)),t.join(" · ")}function Ga(n,t){return Yn(n,{params:n.params,framing:t})}function Ha(n){return n instanceof HTMLTextAreaElement||n instanceof HTMLSelectElement?!0:n instanceof HTMLInputElement?!["button","checkbox","radio","range","submit","reset"].includes(n.type):n.isContentEditable}function ge(n){return Mi(n.provenance.createdAt)}function Ka(n,t,e){if(n===t)return"The run on screen";const s=[];for(const o of e.params){const r=n.provenance.params[o.key],a=t.provenance.params[o.key];Ft(r)!==Ft(a)&&s.push(`${o.label}: ${Ft(r)} (latest: ${Ft(a)})`)}const i=`Finished ${ge(n)}.`;return s.length===0?`${i} The same parameters as the latest run.`:`${i} ${s.join(" · ")}`}function Ft(n){return n==null||n===""?"—":Array.isArray(n)?n.length===0?"—":n.join(", "):String(n)}function gn(n){return n.mapless===!0?"the sequences chosen":"the loaded tracks"}function Ya(n){switch(n.status){case"running":return[p("span",{class:"analysis-spinner",attrs:{"aria-hidden":"true"}}),n.note===""?"working":n.note];case"queued":return["waiting for the job in front of it"];case"failed":return[p("span",{class:"inline-error",text:n.message})];default:return[]}}function be(n){const t=n.getBoundingClientRect();return{width:Math.max(1,Math.round(t.width)),height:Math.max(1,Math.round(t.height))}}function ne(n){const t=be(n.el),e=Ti(za),s=document.createElement("canvas");s.width=Math.max(1,Math.round(t.width*e)),s.height=Math.max(1,Math.round(t.height*e));const i=s.getContext("2d");if(i===null)throw new Error("The browser would not give this page a canvas.");return i.setTransform(e,0,0,e,0,0),n.draw(i,t),s}function bn(n){return n.toLowerCase().replace(/[^a-z0-9]+/g,"-").replace(/^-+|-+$/g,"")||"figure"}function Pt(n,t,e,s){return $t(t.task,n,e).replace(/\.tsv$/,`.${s}`)}class Ua{constructor(t){this.options=t;const e=`analysis-drawer-${Ra++}`;this.titleEl.id=`${e}-title`,this.recomputeButton=I("recompute here",()=>this.run(),{class:"btn btn-quiet",title:"Take a new snapshot of the framing and run again. The result on screen is a record of the view it was computed from, so it is left as it is until this finishes."}),this.runButton=I("run",()=>this.run(),{class:"btn"}),this.runAllButton=I("run on all maps",()=>this.runAll(),{class:"btn hidden",title:"Run this task once per map on screen, one after another. Each result is filed against the map it was measured from, so a batch leaves a row per panel."}),this.cancelButton=I("cancel",()=>this.cancel(),{class:"btn"}),this.cliButton=I("copy CLI command",()=>this.copyCliCommand(),{class:"btn"}),this.progressEl=p("div",{class:"analysis-progress"},this.progressFill),this.recordEl=p("div",{class:"plot-icon-row hidden"},this.recordNote,I("copy provenance",()=>this.copyProvenance(),{class:"btn",title:"The task, its version, every parameter, the framing, the file and the build — the same lines every export carries at its head."}),this.cliButton),this.el=p("div",{class:"analysis-drawer collapsed",attrs:{role:"region","aria-labelledby":this.titleEl.id}},p("div",{class:"analysis-drawer-head"},this.titleEl,this.framingEl,this.recomputeButton,tt("x","Close the drawer. Anything running keeps running — the panel row says so.",()=>this.close(),{class:"btn-close",size:14})),p("div",{class:"analysis-drawer-body"},this.formSlot,p("div",{class:"analysis-run"},this.runButton,this.runAllButton,this.cancelButton,this.costEl,this.progressEl),this.noteEl,this.recordEl,this.notesEl,this.mapsEl,this.runsEl,this.outputsEl,this.statusEl),this.handle()),this.unsubscribe=t.runner.subscribe(()=>this.refresh()),window.addEventListener("keydown",this.onKeyDown)}el;titleEl=p("h2",{class:"analysis-drawer-title"});framingEl=p("span",{class:"analysis-framing"});recomputeButton;formSlot=p("div",{class:"analysis-form"});runButton;runAllButton;cancelButton;costEl=p("span",{class:"analysis-cost"});progressFill=p("div",{class:"analysis-progress-fill"});progressEl;noteEl=p("div",{class:"analysis-note hidden"});recordEl;recordNote=p("span",{class:"analysis-note"});notesEl=p("ul",{class:"analysis-notes hidden"});outputsEl=p("div",{style:{display:"flex",flexDirection:"column",gap:"0.8rem"}});mapsEl=p("div",{class:"analysis-maps hidden"});runsEl=p("div",{class:"analysis-runs hidden"});statusEl=p("div",{class:"analysis-note hidden"});unsubscribe;current=null;form=null;params={};figures=[];surfaceSlots=[];drawn=null;cliButton;chosenMap=new Map;chosenRun=new Map;combined=!1;across=null;width=_a();show(t){if(t!==null&&this.current!==null&&t.id===this.current.id){this.refresh();return}if(this.teardown(),this.current=t,t===null){this.el.classList.add("collapsed");return}this.params=Ht(t.params),this.el.classList.remove("collapsed"),this.paintWidth(),this.refresh()}get task(){return this.current}get isOpen(){return this.current!==null}context(){return this.options.context(this.current??void 0)}paintRun(t,e){if(!nt(t)){this.runButton.replaceChildren("run"),this.runButton.title=`Run ${t.title} on ${gn(t)}`+(e<2?".":" — it reads no map, so it runs once, whichever map is starred.");return}const s=e<2?null:this.options.runner.target();if(s===null){this.runButton.replaceChildren("run"),this.runButton.title=`Run ${t.title} on the open map.`;return}this.runButton.replaceChildren("run on ",se("star",{size:12,class:"run-star"})),this.runButton.title=`Run ${t.title} on ${s.label} — the starred map, which is the one every task measures. Move the star in a panel’s heading to measure another, or run on all of them.`}refresh(){const t=this.current;if(t===null)return;const e=this.context();this.titleEl.textContent=t.title,this.syncForm(t,e);const s=this.options.runner.resultsFor(t.id);this.syncMaps(t,s);const i=this.chosenMap.get(t.id),o=i===wt&&s.length>1,r=i===void 0||i===wt?void 0:i,a=r===void 0?[]:this.options.runner.runsOf(t.id,r),l=o?[]:a.length>0?a:this.options.runner.runsOf(t.id),c=Math.min(Math.max(0,this.chosenRun.get(t.id)??0),Math.max(0,l.length-1)),u=o?null:l[c]??null;this.syncRuns(t,l,c),o?this.syncCombined(s):this.syncOutputs(u),this.syncFraming(u??s[0]?.result??null),this.syncRun(t,e)}relayout(){this.current!==null&&this.paintWidth()}destroy(){this.unsubscribe(),window.removeEventListener("keydown",this.onKeyDown),this.teardown(),this.el.remove()}onKeyDown=t=>{if(t.key!=="Escape"||t.defaultPrevented||this.current===null)return;const e=document.activeElement;e instanceof HTMLElement&&this.el.contains(e)&&Ha(e)||(t.preventDefault(),this.close())};close(){this.show(null),this.options.onClose()}teardown(){this.form?.destroy(),this.form=null,this.clearFigures(),this.outputsEl.replaceChildren(),this.notesEl.replaceChildren(),this.notesEl.classList.add("hidden"),this.recordEl.classList.add("hidden"),this.formSlot.replaceChildren(),this.setStatus(""),this.drawn=null,this.params={}}setStatus(t){this.statusEl.textContent=t,this.statusEl.classList.toggle("hidden",t==="")}clearFigures(){for(const t of this.figures)t.destroy();this.figures=[]}handle(){return vi({side:"right",what:"Analysis drawer",width:()=>this.widthNow(),resize:t=>{this.width=t,this.paintWidth()},commit:()=>pn(this.widthNow()),reset:()=>{this.width=null,pn(null),this.paintWidth()}})}bodyWidth(){const e=(this.el.closest(".app-body")??this.el.parentElement)?.getBoundingClientRect().width??0;return e>0?e:window.innerWidth}widthNow(){const t=this.bodyWidth(),e=Math.round(t*qa),s=Math.min(Pa,e);return Math.max(s,Math.min(e,this.width??Math.round(t*Ba)))}paintWidth(){this.el.style.width=`${this.widthNow()}px`}syncForm(t,e){if(e===null)return;if(this.form!==null){this.form.setContext(e);return}this.params=Va(t,kt(e));const s=this.options.runner,i=new Fa({specs:t.params,context:e,value:this.params,onChange:o=>this.onParams(o),files:{get:o=>s.heldFile(t.id,o),set:(o,r)=>s.holdFile(t.id,o,r)}});this.form=i,this.params=i.value,this.formSlot.replaceChildren(i.el)}onParams(t){this.params=t;const e=this.current,s=this.context();e===null||s===null||(ie(kt(s),e.id,t),this.syncRun(e,s))}blockedFor(t){return nt(t)?this.options.blocked?.()??null:null}run(){const t=this.current;t!==null&&this.blockedFor(t)===null&&(this.setStatus(""),this.chosenRun.delete(t.id),this.options.runner.run(t,this.seeded(t)),this.refresh())}seeded(t){const e=this.context();return e===null?this.params:(ie(kt(e),t.id,this.params),wi(t.params,e,this.params))}runAll(){const t=this.current;t!==null&&this.blockedFor(t)===null&&(this.setStatus(""),this.chosenRun.delete(t.id),this.runAllButton.disabled=!0,this.options.runner.readyTargets().then(e=>{this.current===t&&this.options.runner.runAll(t,this.seeded(t),e)}).finally(()=>this.refresh()))}cancel(){this.current!==null&&this.options.runner.cancel(this.current.id)}syncRun(t,e){const s=this.options.runner.stateOf(t.id),i=s.status==="running"||s.status==="queued",o=e===null?null:t.estimate(e,this.params),r=this.blockedFor(t),a=r!==null?r:e===null?"This view has no contact map to run against.":o!==null&&o.refusal!==void 0&&o.refusal!==""?o.refusal:null;this.runButton.disabled=i||a!==null;const l=this.options.runner.targetCount();this.paintRun(t,l),this.runAllButton.classList.toggle("hidden",l<2||!nt(t)),this.runAllButton.disabled=i||a!==null,this.runAllButton.textContent=`run on all ${l} maps`,a!==null?(this.costEl.className="analysis-refusal",this.costEl.textContent=a):(this.costEl.className=o!==null&&o.class==="scan"?"analysis-cost is-scan":"analysis-cost",this.costEl.textContent=o===null?"":Wa(o)),this.cancelButton.classList.toggle("hidden",!i),this.cancelButton.title=`Stop this job. ${bs(t.venue)}`;const c=s.status==="running"&&s.total>0;this.progressEl.classList.toggle("hidden",!c),c&&s.status==="running"&&(this.progressFill.style.width=`${Math.min(100,s.done/s.total*100).toFixed(1)}%`);const u=Ya(s);this.noteEl.replaceChildren(...u),this.noteEl.classList.toggle("hidden",u.length===0)}syncMaps(t,e){if(e.length<2){this.mapsEl.classList.add("hidden"),this.mapsEl.replaceChildren(),this.chosenMap.delete(t.id);return}const s=[...e.map(a=>a.target.map),wt],i=this.chosenMap.get(t.id)??s[0],o=a=>{this.chosenMap.set(t.id,a),this.chosenRun.delete(t.id),this.drawn=null,this.refresh()},r=a=>{const l=s.indexOf(i);o(s[(l+a+s.length)%s.length])};this.mapsEl.classList.remove("hidden"),this.mapsEl.replaceChildren(tt("chevron-left","The previous map",()=>r(-1),{class:"btn-quiet"}),...e.map(a=>I(a.target.label,()=>o(a.target.map),{class:`btn btn-quiet analysis-map${a.target.map===i?" is-on":""}`,title:`The result measured on ${a.target.label}`})),I("all maps",()=>o(wt),{class:`btn btn-quiet analysis-map${i===wt?" is-on":""}`,title:"Every map’s curves on one axis and every map’s tables as one — the comparison the deck was opened for"}),tt("chevron-right","The next map",()=>r(1),{class:"btn-quiet"}))}syncRuns(t,e,s){if(e.length<2){this.runsEl.classList.add("hidden"),this.runsEl.replaceChildren();return}const i=l=>{this.chosenRun.set(t.id,Math.max(0,Math.min(e.length-1,l))),this.drawn=null,this.refresh()},o=I("older",()=>i(s+1),{class:"btn btn-quiet",title:"The run before this one, with the figures it produced"});o.disabled=s>=e.length-1;const r=I("newer",()=>i(s-1),{class:"btn btn-quiet",title:"Back towards the most recent run"});r.disabled=s<=0;const a=I("latest",()=>i(0),{class:"btn btn-quiet",title:"The most recent run of this task"});a.disabled=s===0,this.runsEl.classList.remove("hidden"),this.runsEl.replaceChildren(se("rotate-cw",{size:13,class:"analysis-runs-mark"}),o,p("span",{class:"analysis-run-at",text:s===0?`latest of ${e.length} runs`:`run ${e.length-s} of ${e.length} · ${ge(e[s])}`,title:Ka(e[s],e[0],t)}),r,a)}syncCombined(t){this.drawn=null,this.combined=!0,this.clearFigures(),this.setStatus(""),this.notesEl.classList.add("hidden"),this.recordEl.classList.remove("hidden"),this.recordNote.textContent=`${t.length} maps, together`;const{outputs:e,perMapOnly:s}=Io(t.map(a=>({label:a.target.label,result:a.result})),a=>a.kind==="curve"?a:a.kind==="profile"?Ei(a):null),i=t.map(a=>({label:a.target.label,provenance:a.target.uri===""||a.target.uri===a.result.provenance.framing.uri?a.result.provenance:{...a.result.provenance,framing:{...a.result.provenance.framing,uri:a.target.uri}}}));this.across=i;const o=i[0];o!==void 0&&this.paintCli(o.provenance);const r=e.map(a=>this.combinedBlock(a,i));s.length>0&&r.push(p("p",{class:"analysis-elsewhere",text:`${s.join(", ")} ${s.length===1?"is":"are"} one picture per map rather than one across them — a pileup averaged over four libraries would be a fifth thing nobody asked for. They are on the tabs above.`})),r.length===0&&r.push(p("p",{class:"analysis-elsewhere",text:"Nothing this task produces can be drawn across maps. Its tabs are above."})),this.outputsEl.replaceChildren(...r),this.paintWidth()}combinedBlock(t,e){const s=sn({output:t,task:`${this.current?.id??"task"}:combined`,uri:kt(this.context()),extras:[I("TSV",()=>this.saveCombinedTsv(t,e),{class:"btn",title:"The numbers of every map as one table, with each map’s provenance above them — the file, the framing and the settings every row was measured with."})],onPng:i=>void this.savePngPlain(i,t.label),onPdf:i=>void this.savePdfPlain(i,t.label),onCopy:i=>this.copyPng(i,t.label)});return this.figures.push(s),s.el}saveCombinedTsv(t,e){const s=j(new Date),i=new Blob([po(t,e)],{type:"text/tab-separated-values"});st(i,$t(this.current?.id??"task",t,s))}syncFraming(t){const e=this.options.framing();if(this.current!==null&&!nt(this.current)){const s=gn(this.current);this.framingEl.className="analysis-framing",this.framingEl.textContent=t===null?`reads ${s}, not the map`:`from ${s}, not the map`,this.framingEl.title="",this.recomputeButton.classList.add("hidden");return}if(t!==null){const s=t.provenance,i=e!==null&&!Ga(s,e);this.framingEl.className=i?"analysis-framing is-stale":"analysis-framing",this.framingEl.textContent=i?`from ${s.framing.label} — the view has moved since`:`from ${s.framing.label}`,this.framingEl.title=s.framing.label,this.recomputeButton.classList.toggle("hidden",!i);return}this.framingEl.className="analysis-framing",this.framingEl.textContent=e===null?"no contact map in this view":`will run on ${e.label}`,this.framingEl.title=e?.label??"",this.recomputeButton.classList.add("hidden")}syncOutputs(t){if(t===this.drawn&&!this.combined)return;if(this.combined=!1,this.across=null,this.drawn=t,this.clearFigures(),this.setStatus(""),t===null){this.outputsEl.replaceChildren(),this.notesEl.replaceChildren(),this.notesEl.classList.add("hidden"),this.recordEl.classList.add("hidden");return}const e=t.provenance;this.recordEl.classList.remove("hidden"),this.recordNote.textContent=`computed in ${In(t.ms)} at ${ge(t)}`,this.recordNote.title=e.createdAt,this.paintCli(e),this.notesEl.replaceChildren(...t.notes.map(s=>p("li",{text:s}))),this.notesEl.classList.toggle("hidden",t.notes.length===0),this.outputsEl.replaceChildren(...t.outputs.length===0?[p("p",{class:"analysis-elsewhere",text:t.notes.length===0?"This run produced no output, and said nothing about why. That is a bug — please report it.":"No output was produced. The reason is above."})]:this.outputBlocks(t.outputs,e))}outputBlocks(t,e){const s=[];let i=null;const o=()=>{i!==null&&(s.push(this.elsewhere(i.where,i.items,e)),i=null)};for(const r of t){const a=this.elsewhereOf(r);a===null?(o(),s.push(this.block(r,e))):i!==null&&i.where===a?i.items.push(r):(o(),i={where:a,items:[r]})}return o(),s}elsewhereOf(t){return t.kind==="intervals"?t.entryKind==="structure"?"structure":this.options.hasLanes()?"overlay":"loose":t.kind==="profile"&&this.options.hasLanes()?"lane":null}block(t,e){const s=sn({output:t,task:this.current?.id??"task",uri:kt(this.context()),extras:[...t.kind==="profile"?this.profileButtons(t,e):[],this.tsvButton(t,e)],onPng:i=>void this.savePng(i,t,e),onPdf:i=>void this.savePdf(i,t,e),onCopy:i=>this.copyPng(i,t.label)});return this.figures.push(s),s.el}profileButtons(t,e){const s=i=>{this.options.writeProfile(t,e,i).catch(o=>{this.setStatus(o instanceof Error?o.message:String(o))})};return[I("bigWig",()=>s("bigwig"),{class:"btn",title:"Written here, byte for byte — no bedGraphToBigWig step. What IGV, deepTools and pyBigWig open."}),I("bedGraph",()=>s("bedgraph"),{class:"btn",title:"One line per bin that has a value; bins with none are omitted, never written as 0."})]}elsewhere(t,e,s){const i=e.length>1,o=t==="lane"?i?`${z.int(e.length)} tracks added to the Tracks card in the Annotations panel, marked *.`:"Added to the Tracks card in the Annotations panel, marked *.":t==="structure"?"Added to the Structures card in the Annotations panel, and shown in the deck’s structure cell (add one from the deck’s bar if none is open).":t==="overlay"&&this.context()?.hasMap===!1?i?`${z.int(e.length)} sets added to the Tracks card in the Annotations panel as 1D tracks, marked *.`:"Added to the Tracks card in the Annotations panel as a 1D track, marked *.":t==="overlay"?i?`${z.int(e.length)} sets added to the Tracks card in the Annotations panel, marked *.`:"Added to the Tracks card in the Annotations panel, marked *.":"This file carries no annotation layer, so there is no overlay to draw these on. Take them as a BED, which this app reads back on any file that has one.";return p("div",{class:"analysis-elsewhere"},p("span",{text:o}),...e.map(r=>p("div",{class:"plot-icon-row"},p("span",{class:"analysis-elsewhere-name",text:r.label,title:r.label}),...r.kind==="intervals"?[this.bedButton(r,s)]:[],...r.kind==="intervals"&&r.entryKind==="structure"?[this.pdbButton(r,s)]:[],this.tsvButton(r,s))).flatMap((r,a)=>{const l=e[a];if(l.kind!=="intervals"||l.entryKind==="structure")return[r];const c=p("div",{class:"analysis-surfaces"});return this.surfaceSlots.push({slot:c,output:l}),this.fillSurface(c,l),[r,c]}))}fillSurfaces(){this.surfaceSlots=this.surfaceSlots.filter(({slot:t})=>t.isConnected);for(const{slot:t,output:e}of this.surfaceSlots)t.contains(document.activeElement)||this.fillSurface(t,e)}fillSurface(t,e){const s=this.options.surfaces?.(e)??null;t.replaceChildren(...s===null?[]:[s])}bedButton(t,e){const s=t.entryKind==="structure",i=s?"bed3d":t.payload.kind==="pairs"?"BEDPE":"BED";return I(i,()=>this.saveIntervals(t,e),{class:"btn",title:s?"The model as a bed3d — chrom, start, end, x, y, z — which this app and g3dtools read back":`The called intervals as a ${i} — what bedtools reads, and what this app reads back`})}saveIntervals(t,e){const s=j(new Date),i={label:t.label,file:e.framing.label,created:e.createdAt},o=t.payload,r=t.entryKind==="structure"&&o.kind==="features",a=r&&o.kind==="features"?On(o.data,i):oe(o,i),l=r?"bed3d":o.kind==="pairs"?"bedpe":"bed";st(new Blob([a],{type:"text/plain"}),Pt(t,e,s,l))}pdbButton(t,e){const s=t.payload,i=s.kind==="features"?ki(s.data):"This output holds no model.",o=I("PDB",()=>this.savePdb(t,e),{class:"btn",title:i??"The model as a PDB — an atom per bead, a chain per sequence, bonds along the fibre — which PyMOL and ChimeraX open and this app reads back"});return o.disabled=i!==null,o}savePdb(t,e){const s=t.payload;if(s.kind!=="features")return;const i=xi(s.data,{label:t.label,file:e.framing.label,created:e.createdAt});st(new Blob([i],{type:"text/plain"}),Pt(t,e,j(new Date),"pdb"))}tsvButton(t,e){return I("TSV",()=>this.saveTsv(t,e),{class:"btn",title:"The numbers as a table, with the provenance above them — what makes a figure checkable by the person reading it."})}saveTsv(t,e){const s=j(new Date),i=new Blob([re(t,e)],{type:"text/tab-separated-values"});st(i,$t(e.task,t,s))}copyPng(t,e){let s;try{s=ne(t)}catch(i){this.setStatus(i instanceof Error?i.message:String(i));return}Si(Ut(s)).then(()=>{this.setStatus(""),$i(`Copied ${e} · ${s.width} × ${s.height} px`)},i=>this.setStatus(`${e} could not be copied: ${i instanceof Error?i.message:String(i)}`))}async savePngPlain(t,e){const s=await pt(`${bn(e)}-${j(new Date)}.png`,"image/png");if(s!==null)try{await s.write(await Ut(ne(t))),this.setStatus("")}catch(i){this.setStatus(i instanceof Error?i.message:String(i))}}async savePdfPlain(t,e){const s=new Date,i=await pt(`${bn(e)}-${j(s)}.pdf`,"application/pdf");if(i!==null)try{const o=be(t.el),r=new Oe(o.width,o.height);t.draw(r.ctx,o);const a=await r.toBlob({title:e,created:s});await i.write(a),this.setStatus("")}catch(o){this.setStatus(o instanceof Error?o.message:String(o))}}async savePng(t,e,s){const i=await pt(Pt(e,s,j(new Date),"png"),"image/png");if(i!==null)try{await i.write(await Ut(ne(t))),this.setStatus("")}catch(o){this.setStatus(o instanceof Error?o.message:String(o))}}async savePdf(t,e,s){const i=new Date,o=await pt(Pt(e,s,j(i),"pdf"),"application/pdf");if(o!==null)try{const r=be(t.el),a=new Oe(r.width,r.height);t.draw(a.ctx,r);const l=await a.toBlob({title:e.label,created:i});await o.write(l),this.setStatus("")}catch(r){this.setStatus(r instanceof Error?r.message:String(r))}}paintCli(t){const e=St(t.task)===void 0;this.cliButton.disabled=e,this.cliButton.title=e?`This build does not have the task ${t.task}, so it cannot write its flags.`:"The same run as a chromosomix command line — the file, the window, the balancing and every parameter — for the other two hundred files."}shownProvenances(){return this.drawn!==null?[{label:null,provenance:this.drawn.provenance}]:(this.across??[]).map(t=>({label:t.label,provenance:t.provenance}))}copyCliCommand(){const t=this.shownProvenances(),e=t[0];if(e===void 0)return;const s=St(e.provenance.task);if(s===void 0)return;const o=t.map(({label:a,provenance:l})=>{const c=qn({task:s,provenance:l,context:this.options.context(s)}).text;return a===null?c:`# ${a}
+`;return this.block.length=0,t}}function*tt(n){for(const t of n)yield`${t}
+`}function ro(n){return n===null?"":typeof n=="number"?R(n):typeof n=="boolean"?n?"true":"false":Array.isArray(n)?n.join(","):String(n)}function ft(n){const{framing:t,params:e}=n,s=[`# chromosomix ${N(n.app)}`,`# created: ${N(n.createdAt)}`,`# file: ${N(t.uri)}`,`# task: ${N(n.task)} v${R(n.taskVersion)}`,`# framing: ${N(t.label)}`];for(const i of Object.keys(e).sort())s.push(`# param ${N(i)}: ${N(ro(e[i]))}`);return s}function*ao(n){const[t]=n.extent;yield*tt([`# output: ${N(n.label)}${n.unit===""?"":` (${N(n.unit)})`}`,`# binsize: ${R(n.binsize)}`,D(["bin","start","end","value"])]);const{binsize:e,values:s}=n,i=new Gn;for(let r=0;r<s.length;r++){const a=t+r,l=a*e,c=i.push(`${a}	${l}	${l+e}	${R(s[r])}`);c!==void 0&&(yield c)}const o=i.flush();o!==void 0&&(yield o)}function lo(n){const t=[`# output: ${N(n.label)}`,`# x: ${N(n.xLabel)}  y: ${N(n.yLabel)}`],e=[N(n.xLabel)===""?"x":N(n.xLabel)];let s=0,i=new Float64Array(0);for(const r of n.series){const a=N(r.name);e.push(a),r.low!==void 0&&r.high!==void 0&&e.push(`${a}_low`,`${a}_high`),r.y.length>s&&(s=r.y.length,i=r.x),r.n!==void 0&&t.push(`# n ${a}: ${R(r.n)}`)}t.push(D(e));const o=n.xTicks;for(let r=0;r<s;r++){const a=o?.[r],l=[a!==void 0?N(a):r<i.length?R(i[r]):""];for(const c of n.series){const u=r<c.y.length;l.push(u?R(c.y[r]):""),c.low!==void 0&&c.high!==void 0&&l.push(u?R(c.low[r]):"",u?R(c.high[r]):"")}t.push(D(l))}return t}function co(n){const t=[`# output: ${N(n.label)}`,`# x: ${N(n.xLabel)}  y: ${N(n.yLabel)}`];for(const r of n.stats??[])t.push(`# ${N(r.label)}: ${Wn(r.value,r.digits??4)}`);const e=(r,a)=>r.length===a&&a>0;for(const[r,a,l]of[["x",n.xTicks,n.ncols],["y",n.yTicks,n.nrows]])a.length===0||e(a,l)||t.push(`# ${r} ticks, evenly spaced across the axis: ${a.map(N).join(", ")}`);const s=(r,a,l)=>e(r,l)?N(r[a]):String(a),i=[N(n.yLabel)];for(let r=0;r<n.ncols;r++)i.push(s(n.xTicks,r,n.ncols));t.push(D(i));for(let r=0;r<n.nrows;r++){const a=[s(n.yTicks,r,n.nrows)];for(let l=0;l<n.ncols;l++)a.push(R(n.values[r*n.ncols+l]));t.push(D(a))}const o=[...(n.margins?.top??[]).map(r=>["top",r]),...(n.margins?.right??[]).map(r=>["right",r])];if(o.length>0){const r=Math.max(...o.map(([,a])=>a.values.length));t.push(""),t.push("# aggregate profiles along the edges: top runs along x, right runs down y"),t.push(D(["edge","track",...Array.from({length:r},(a,l)=>String(l))]));for(const[a,l]of o){const c=[a,N(l.name)];for(const u of l.values)c.push(R(u));t.push(D(c))}}return t}function uo(n){const t=[`# output: ${N(n.label)}`,`# columns: ${n.columns.map(e=>`${N(e.label)}${e.coordinate==="start"?" (0-based)":""}`).join(", ")}`,D(n.columns.map(e=>N(e.key)))];for(const e of n.rows)t.push(D(n.columns.map(s=>{const i=e[s.key];return i==null?"":typeof i=="number"?s.kind==="number"?Wn(i,s.digits,s.scientific===!0):R(i):N(i)})));return t}function ho(n){return n>0?"+":n<0?"-":"."}function fo(n){const t=[`# output: ${N(n.label)}`];if(n.payload.kind==="features"){const s=n.payload.data;t.push(D(["chrom","start","end","name","score","strand","detail"]));for(let i=0;i<s.length;i++)t.push(D([N(s.contigs[s.contig[i]]??""),String(s.start[i]),String(s.end[i]),N(s.name[i]??""),R(s.score[i]),ho(s.strand[i]),N(s.detail[i]??"")]));return t}const e=n.payload.data;t.push(D(["chrom1","start1","end1","chrom2","start2","end2","name","score","detail"]));for(let s=0;s<e.length;s++)t.push(D([N(e.contigs[e.contig1[s]]??""),String(e.start1[s]),String(e.end1[s]),N(e.contigs[e.contig2[s]]??""),String(e.start2[s]),String(e.end2[s]),N(e.name[s]??""),R(e.score[s]),N(e.detail[s]??"")]));return t}function mo(n,t,e,s,i){const o=[...ft(i),`# output: ${N(n)}${t===""?"":` (${N(t)})`}`,D(["chrom","start","end","value"])],r=new Map;for(const a of e){const l=r.get(a.contig);l===void 0?r.set(a.contig,[a]):l.push(a)}for(const a of s){const l=r.get(a.name);if(l===void 0)continue;const c=[];for(const u of l)for(let d=0;d<u.starts.length;d+=1){const f=u.values[d];if(!Number.isFinite(f))continue;const m=Math.max(0,u.starts[d]),h=Math.min(a.length,u.ends[d]);h>m&&c.push([m,h,f])}c.sort((u,d)=>u[0]-d[0]);for(const[u,d,f]of c)o.push(D([N(a.name),String(u),String(d),R(f)]))}return tt(o)}function*ae(n,t){yield*tt(ft(t)),yield*Kn(n)}function*po(n,t){yield*tt(Hn(t)),yield*Kn(n)}function Hn(n){const t=[],e=n[0]?.provenance.app;e!==void 0&&t.push(`# chromosomix ${N(e)}`),t.push(`# maps: ${R(n.length)}`);for(const s of n){t.push(`# map: ${N(s.label)}`);for(const i of ft(s.provenance).slice(1))t.push(`#   ${i.slice(2)}`)}return t}function Kn(n){switch(n.kind){case"profile":return ao(n);case"curve":return tt(lo(n));case"matrix":return tt(co(n));case"table":return tt(uo(n));case"intervals":return tt(fo(n))}}function Mt(n,t,e){const s=_t(n),i=t.id===""?"":_t(t.id);return`${[...i===""||i===s?[s]:[s,i],e].join("-")}.tsv`}const go=[xn,Os].filter(n=>n!=="").join(" ");function bo(n,t,e){return{task:n.id,taskVersion:n.version,params:t,framing:e,app:go,createdAt:new Date().toISOString()}}function Re(n){const{task:t,provenance:e,context:s,where:i}=n,o=qn({task:t,provenance:e,context:s}),r=ft(e),a=i===void 0?{}:{where:i},l=o.text.split(`
+`);return{kind:"run",line:l[l.length-1],shell:!0,notes:l.slice(0,-1),detail:r,...a}}function Yn(n,t){return yo(n.params,t.params)&&wo(n.framing,t.framing)}function yo(n,t){const e=Object.keys(n);if(e.length!==Object.keys(t).length)return!1;for(const s of e)if(!(s in t)||!vo(n[s],t[s]))return!1;return!0}function vo(n,t){return Array.isArray(n)||Array.isArray(t)?!Array.isArray(n)||!Array.isArray(t)||n.length!==t.length?!1:n.every((e,s)=>e===t[s]):Object.is(n,t)}function wo(n,t){return n.uri===t.uri&&n.rows[0]===t.rows[0]&&n.rows[1]===t.rows[1]&&n.cols[0]===t.cols[0]&&n.cols[1]===t.cols[1]&&n.binsize===t.binsize&&n.binsPerCell===t.binsPerCell&&n.balance===t.balance&&n.value===t.value&&n.level===t.level&&(n.contacts??null)===(t.contacts??null)&&(n.edit??null)===(t.edit??null)&&(n.coarsen??null)===(t.coarsen??null)&&ko(n.circular??[],t.circular??[])&&xo(n.origins??{},t.origins??{})}function ko(n,t){if(n.length!==t.length)return!1;const e=new Set(n);return t.every(s=>e.has(s))}function xo(n,t){const e=Object.keys(n);return e.length===Object.keys(t).length&&e.every(s=>n[s]===t[s])}const So=100;function pt(n,t){return`${n}\0${t}`}const $o=8;function Xt(n,t){return`${n}\0${t}`}function Mo(n,t,e,s,i,o){const r=t===void 0||t.length===0?n:`${n}\0${t.join("\0")}`,a=e===void 0?r:`${r}\0${e.base}:${e.rungs}`,l=s===void 0?a:`${a}\0contacts:${s.contacts}:${s.seed??""}:${s.alpha??""}`,c=i===void 0?l:`${l}\0edit:${Rs(i)}`;return o===void 0?c:`${c}\0coarsen:${o}`}function _e(n){return Sn(n.label)}function Eo(n){return{line:n.line,notes:n.notes??[],detail:n.detail??[]}}class To{host;makeClient;client=null;mounted=null;states=new Map;results=new Map;history=new Map;resultTargets=new Map;queue=[];current=null;held=new Map;listeners=new Set;lastNotifiedAt=0;trailing=null;destroyed=!1;constructor(t,e=()=>new Fs){this.host=t,this.makeClient=e}stateOf(t){return this.states.get(t)??{status:"idle"}}holdFile(t,e,s){const i=Xt(t,e);s===null?this.held.delete(i):this.held.set(i,s)}heldFile(t,e){return this.held.get(Xt(t,e))}resultOf(t,e){const s=e??this.homeOf(t);return this.results.get(pt(s,t))??null}homeOf(t){const e=this.host.task?.(t)??$t(t);return e!==void 0&&!st(e)?J:this.host.targetMap?.()??J}runsOf(t,e){const s=e??this.homeOf(t),i=pt(s,t),o=this.results.get(i),r=this.history.get(i)??[];return o===void 0?[...r]:[o,...r]}resultsFor(t){const e=this.host.allTargets?.()??[],s=new Set,i=[];for(const o of e){const r=this.results.get(pt(o.map,t));r!==void 0&&(s.add(o.map),i.push({target:o,result:r}))}for(const[o,r]of this.results){const a=this.resultTargets.get(o);a===void 0||s.has(a.map)||o===pt(a.map,t)&&i.push({target:a,result:r})}return i}subscribe(t){return this.listeners.add(t),()=>{this.listeners.delete(t)}}get busy(){return this.current!==null||this.queue.length>0}run(t,e){this.queueOne(t,e,null)}runAll(t,e,s){if(!st(t)){this.queueOne(t,e,null);return}if(s.length!==0){if(s.length===1){this.queueOne(t,e,null,s[0]);return}this.cancel(t.id),s.forEach((i,o)=>{this.queueOne(t,e,{at:o,of:s.length},i)})}}queueOne(t,e,s,i){if(this.destroyed)return;const o=this.host.context(t);if(o===null){this.refuse(t,s,"nothing is open");return}const r=t.mapless===!0?De(o,"sequences"):o.framing??(t.venue==="annotations"?De(o):null);if(r===null){this.refuse(t,s,"this view has no contact map to run against");return}const a=st(t)?i??this.hostTarget(r,t):{...this.hostTarget(r,t),map:J};if(s===null){if(this.current?.task.id===t.id&&this.current.target.map===a.map)return;const l=this.queue.find(c=>c.task.id===t.id&&c.target.map===a.map);if(l!==void 0){l.params=e,l.framing=r;return}}this.queue.push({task:t,params:e,framing:r,target:a,batch:s,cancelled:!1,running:null}),this.setState(t.id,{status:"queued"}),this.pump()}targets(){return this.host.allTargets?.()??[]}async readyTargets(){return await this.host.allTargetsReady?.()??this.targets()}targetCount(){return this.host.targetCount?.()??this.targets().length}target(){const t=this.host.targetMap?.();return t===void 0?null:this.targets().find(e=>e.map===t)??null}hostTarget(t,e){const s=this.host.source(e);return{map:this.host.targetMap?.()??J,uri:s?.uri??t.uri,...s===null?{}:{source:s.source},...s?.cells===void 0?{}:{cells:s.cells},...s?.binning===void 0?{}:{binning:s.binning},...s?.orientation===void 0?{}:{orientation:s.orientation},...s?.pairsStats===void 0?{}:{pairsStats:s.pairsStats},...s?.resample===void 0?{}:{resample:s.resample},...s?.edit===void 0?{}:{edit:s.edit},label:s?.label??t.uri}}cancel(t){let e=0;for(let i=this.queue.length-1;i>=0;i--)this.queue[i].task.id===t&&(this.queue.splice(i,1),e++);const 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t=this.bodyWidth(),e=Math.round(t*qa),s=Math.min(Pa,e);return Math.max(s,Math.min(e,this.width??Math.round(t*Ba)))}paintWidth(){this.el.style.width=`${this.widthNow()}px`}syncForm(t,e){if(e===null)return;if(this.form!==null){this.form.setContext(e);return}this.params=Va(t,xt(e));const s=this.options.runner,i=new Fa({specs:t.params,context:e,value:this.params,onChange:o=>this.onParams(o),files:{get:o=>s.heldFile(t.id,o),set:(o,r)=>s.holdFile(t.id,o,r)}});this.form=i,this.params=i.value,this.formSlot.replaceChildren(i.el)}onParams(t){this.params=t;const e=this.current,s=this.context();e===null||s===null||(oe(xt(s),e.id,t),this.syncRun(e,s))}blockedFor(t){return st(t)?this.options.blocked?.()??null:null}run(){const t=this.current;t!==null&&this.blockedFor(t)===null&&(this.setStatus(""),this.chosenRun.delete(t.id),this.options.runner.run(t,this.seeded(t)),this.refresh())}seeded(t){const e=this.context();return e===null?this.params:(oe(xt(e),t.id,this.params),wi(t.params,e,this.params))}runAll(){const t=this.current;t!==null&&this.blockedFor(t)===null&&(this.setStatus(""),this.chosenRun.delete(t.id),this.runAllButton.disabled=!0,this.options.runner.readyTargets().then(e=>{this.current===t&&this.options.runner.runAll(t,this.seeded(t),e)}).finally(()=>this.refresh()))}cancel(){this.current!==null&&this.options.runner.cancel(this.current.id)}syncRun(t,e){const s=this.options.runner.stateOf(t.id),i=s.status==="running"||s.status==="queued",o=e===null?null:t.estimate(e,this.params),r=this.blockedFor(t),a=r!==null?r:e===null?"This view has no contact map to run against.":o!==null&&o.refusal!==void 0&&o.refusal!==""?o.refusal:null;this.runButton.disabled=i||a!==null;const l=this.options.runner.targetCount();this.paintRun(t,l),this.runAllButton.classList.toggle("hidden",l<2||!st(t)),this.runAllButton.disabled=i||a!==null,this.runAllButton.textContent=`run on all ${l} maps`,a!==null?(this.costEl.className="analysis-refusal",this.costEl.textContent=a):(this.costEl.className=o!==null&&o.class==="scan"?"analysis-cost is-scan":"analysis-cost",this.costEl.textContent=o===null?"":Wa(o)),this.cancelButton.classList.toggle("hidden",!i),this.cancelButton.title=`Stop this job. ${bs(t.venue)}`;const c=s.status==="running"&&s.total>0;this.progressEl.classList.toggle("hidden",!c),c&&s.status==="running"&&(this.progressFill.style.width=`${Math.min(100,s.done/s.total*100).toFixed(1)}%`);const u=Ya(s);this.noteEl.replaceChildren(...u),this.noteEl.classList.toggle("hidden",u.length===0)}syncMaps(t,e){if(e.length<2){this.mapsEl.classList.add("hidden"),this.mapsEl.replaceChildren(),this.chosenMap.delete(t.id);return}const s=[...e.map(a=>a.target.map),kt],i=this.chosenMap.get(t.id)??s[0],o=a=>{this.chosenMap.set(t.id,a),this.chosenRun.delete(t.id),this.drawn=null,this.refresh()},r=a=>{const l=s.indexOf(i);o(s[(l+a+s.length)%s.length])};this.mapsEl.classList.remove("hidden"),this.mapsEl.replaceChildren(et("chevron-left","The previous map",()=>r(-1),{class:"btn-quiet"}),...e.map(a=>I(a.target.label,()=>o(a.target.map),{class:`btn btn-quiet analysis-map${a.target.map===i?" is-on":""}`,title:`The result measured on ${a.target.label}`})),I("all maps",()=>o(kt),{class:`btn btn-quiet analysis-map${i===kt?" is-on":""}`,title:"Every map’s curves on one axis and every map’s tables as one — the comparison the deck was opened for"}),et("chevron-right","The next map",()=>r(1),{class:"btn-quiet"}))}syncRuns(t,e,s){if(e.length<2){this.runsEl.classList.add("hidden"),this.runsEl.replaceChildren();return}const i=l=>{this.chosenRun.set(t.id,Math.max(0,Math.min(e.length-1,l))),this.drawn=null,this.refresh()},o=I("older",()=>i(s+1),{class:"btn btn-quiet",title:"The run before this one, with the figures it produced"});o.disabled=s>=e.length-1;const r=I("newer",()=>i(s-1),{class:"btn btn-quiet",title:"Back towards the most recent run"});r.disabled=s<=0;const a=I("latest",()=>i(0),{class:"btn btn-quiet",title:"The most recent run of this task"});a.disabled=s===0,this.runsEl.classList.remove("hidden"),this.runsEl.replaceChildren(ie("rotate-cw",{size:13,class:"analysis-runs-mark"}),o,p("span",{class:"analysis-run-at",text:s===0?`latest of ${e.length} runs`:`run ${e.length-s} of ${e.length} · ${be(e[s])}`,title:Ka(e[s],e[0],t)}),r,a)}syncCombined(t){this.drawn=null,this.combined=!0,this.clearFigures(),this.setStatus(""),this.notesEl.classList.add("hidden"),this.recordEl.classList.remove("hidden"),this.recordNote.textContent=`${t.length} maps, together`;const{outputs:e,perMapOnly:s}=Io(t.map(a=>({label:a.target.label,result:a.result})),a=>a.kind==="curve"?a:a.kind==="profile"?Ei(a):null),i=t.map(a=>({label:a.target.label,provenance:a.target.uri===""||a.target.uri===a.result.provenance.framing.uri?a.result.provenance:{...a.result.provenance,framing:{...a.result.provenance.framing,uri:a.target.uri}}}));this.across=i;const o=i[0];o!==void 0&&this.paintCli(o.provenance);const r=e.map(a=>this.combinedBlock(a,i));s.length>0&&r.push(p("p",{class:"analysis-elsewhere",text:`${s.join(", ")} ${s.length===1?"is":"are"} one picture per map rather than one across them — a pileup averaged over four libraries would be a fifth thing nobody asked for. They are on the tabs above.`})),r.length===0&&r.push(p("p",{class:"analysis-elsewhere",text:"Nothing this task produces can be drawn across maps. Its tabs are above."})),this.outputsEl.replaceChildren(...r),this.paintWidth()}combinedBlock(t,e){const s=sn({output:t,task:`${this.current?.id??"task"}:combined`,uri:xt(this.context()),extras:[I("TSV",()=>this.saveCombinedTsv(t,e),{class:"btn",title:"The numbers of every map as one table, with each map’s provenance above them — the file, the framing and the settings every row was measured with."})],onPng:i=>void this.savePngPlain(i,t.label),onPdf:i=>void this.savePdfPlain(i,t.label),onCopy:i=>this.copyPng(i,t.label)});return this.figures.push(s),s.el}saveCombinedTsv(t,e){const s=j(new Date),i=new Blob([...po(t,e)],{type:"text/tab-separated-values"});it(i,Mt(this.current?.id??"task",t,s))}syncFraming(t){const e=this.options.framing();if(this.current!==null&&!st(this.current)){const s=gn(this.current);this.framingEl.className="analysis-framing",this.framingEl.textContent=t===null?`reads ${s}, not the map`:`from ${s}, not the map`,this.framingEl.title="",this.recomputeButton.classList.add("hidden");return}if(t!==null){const s=t.provenance,i=e!==null&&!Ga(s,e);this.framingEl.className=i?"analysis-framing is-stale":"analysis-framing",this.framingEl.textContent=i?`from ${s.framing.label} — the view has moved since`:`from ${s.framing.label}`,this.framingEl.title=s.framing.label,this.recomputeButton.classList.toggle("hidden",!i);return}this.framingEl.className="analysis-framing",this.framingEl.textContent=e===null?"no contact map in this view":`will run on ${e.label}`,this.framingEl.title=e?.label??"",this.recomputeButton.classList.add("hidden")}syncOutputs(t){if(t===this.drawn&&!this.combined)return;if(this.combined=!1,this.across=null,this.drawn=t,this.clearFigures(),this.setStatus(""),t===null){this.outputsEl.replaceChildren(),this.notesEl.replaceChildren(),this.notesEl.classList.add("hidden"),this.recordEl.classList.add("hidden");return}const e=t.provenance;this.recordEl.classList.remove("hidden"),this.recordNote.textContent=`computed in ${In(t.ms)} at ${be(t)}`,this.recordNote.title=e.createdAt,this.paintCli(e),this.notesEl.replaceChildren(...t.notes.map(s=>p("li",{text:s}))),this.notesEl.classList.toggle("hidden",t.notes.length===0),this.outputsEl.replaceChildren(...t.outputs.length===0?[p("p",{class:"analysis-elsewhere",text:t.notes.length===0?"This run produced no output, and said nothing about why. That is a bug — please report it.":"No output was produced. The reason is above."})]:this.outputBlocks(t.outputs,e))}outputBlocks(t,e){const s=[];let i=null;const o=()=>{i!==null&&(s.push(this.elsewhere(i.where,i.items,e)),i=null)};for(const r of t){const a=this.elsewhereOf(r);a===null?(o(),s.push(this.block(r,e))):i!==null&&i.where===a?i.items.push(r):(o(),i={where:a,items:[r]})}return o(),s}elsewhereOf(t){return t.kind==="intervals"?t.entryKind==="structure"?"structure":this.options.hasLanes()?"overlay":"loose":t.kind==="profile"&&this.options.hasLanes()?"lane":null}block(t,e){const s=sn({output:t,task:this.current?.id??"task",uri:xt(this.context()),extras:[...t.kind==="profile"?this.profileButtons(t,e):[],this.tsvButton(t,e)],onPng:i=>void this.savePng(i,t,e),onPdf:i=>void this.savePdf(i,t,e),onCopy:i=>this.copyPng(i,t.label)});return this.figures.push(s),s.el}profileButtons(t,e){const s=i=>{this.options.writeProfile(t,e,i).catch(o=>{this.setStatus(o instanceof Error?o.message:String(o))})};return[I("bigWig",()=>s("bigwig"),{class:"btn",title:"Written here, byte for byte — no bedGraphToBigWig step. What IGV, deepTools and pyBigWig open."}),I("bedGraph",()=>s("bedgraph"),{class:"btn",title:"One line per bin that has a value; bins with none are omitted, never written as 0."})]}elsewhere(t,e,s){const i=e.length>1,o=t==="lane"?i?`${z.int(e.length)} tracks added to the Tracks card in the Annotations panel, marked *.`:"Added to the Tracks card in the Annotations panel, marked *.":t==="structure"?"Added to the Structures card in the Annotations panel, and shown in the deck’s structure cell (add one from the deck’s bar if none is open).":t==="overlay"&&this.context()?.hasMap===!1?i?`${z.int(e.length)} sets added to the Tracks card in the Annotations panel as 1D tracks, marked *.`:"Added to the Tracks card in the Annotations panel as a 1D track, marked *.":t==="overlay"?i?`${z.int(e.length)} sets added to the Tracks card in the Annotations panel, marked *.`:"Added to the Tracks card in the Annotations panel, marked *.":"This file carries no annotation layer, so there is no overlay to draw these on. Take them as a BED, which this app reads back on any file that has one.";return p("div",{class:"analysis-elsewhere"},p("span",{text:o}),...e.map(r=>p("div",{class:"plot-icon-row"},p("span",{class:"analysis-elsewhere-name",text:r.label,title:r.label}),...r.kind==="intervals"?[this.bedButton(r,s)]:[],...r.kind==="intervals"&&r.entryKind==="structure"?[this.pdbButton(r,s)]:[],this.tsvButton(r,s))).flatMap((r,a)=>{const l=e[a];if(l.kind!=="intervals"||l.entryKind==="structure")return[r];const c=p("div",{class:"analysis-surfaces"});return this.surfaceSlots.push({slot:c,output:l}),this.fillSurface(c,l),[r,c]}))}fillSurfaces(){this.surfaceSlots=this.surfaceSlots.filter(({slot:t})=>t.isConnected);for(const{slot:t,output:e}of this.surfaceSlots)t.contains(document.activeElement)||this.fillSurface(t,e)}fillSurface(t,e){const s=this.options.surfaces?.(e)??null;t.replaceChildren(...s===null?[]:[s])}bedButton(t,e){const s=t.entryKind==="structure",i=s?"bed3d":t.payload.kind==="pairs"?"BEDPE":"BED";return I(i,()=>this.saveIntervals(t,e),{class:"btn",title:s?"The model as a bed3d — chrom, start, end, x, y, z — which this app and g3dtools read back":`The called intervals as a ${i} — what bedtools reads, and what this app reads back`})}saveIntervals(t,e){const s=j(new Date),i={label:t.label,file:e.framing.label,created:e.createdAt},o=t.payload,r=t.entryKind==="structure"&&o.kind==="features",a=r&&o.kind==="features"?On(o.data,i):re(o,i),l=r?"bed3d":o.kind==="pairs"?"bedpe":"bed";it(new Blob([a],{type:"text/plain"}),Bt(t,e,s,l))}pdbButton(t,e){const s=t.payload,i=s.kind==="features"?ki(s.data):"This output holds no model.",o=I("PDB",()=>this.savePdb(t,e),{class:"btn",title:i??"The model as a PDB — an atom per bead, a chain per sequence, bonds along the fibre — which PyMOL and ChimeraX open and this app reads back"});return o.disabled=i!==null,o}savePdb(t,e){const s=t.payload;if(s.kind!=="features")return;const i=xi(s.data,{label:t.label,file:e.framing.label,created:e.createdAt});it(new Blob([i],{type:"text/plain"}),Bt(t,e,j(new Date),"pdb"))}tsvButton(t,e){return I("TSV",()=>this.saveTsv(t,e),{class:"btn",title:"The numbers as a table, with the provenance above them — what makes a figure checkable by the person reading it."})}saveTsv(t,e){const s=j(new Date),i=new Blob([...ae(t,e)],{type:"text/tab-separated-values"});it(i,Mt(e.task,t,s))}copyPng(t,e){let s;try{s=se(t)}catch(i){this.setStatus(i instanceof Error?i.message:String(i));return}Si(Zt(s)).then(()=>{this.setStatus(""),$i(`Copied ${e} · ${s.width} × ${s.height} px`)},i=>this.setStatus(`${e} could not be copied: ${i instanceof Error?i.message:String(i)}`))}async savePngPlain(t,e){const s=await gt(`${bn(e)}-${j(new Date)}.png`,"image/png");if(s!==null)try{await s.write(await Zt(se(t))),this.setStatus("")}catch(i){this.setStatus(i instanceof Error?i.message:String(i))}}async savePdfPlain(t,e){const s=new Date,i=await gt(`${bn(e)}-${j(s)}.pdf`,"application/pdf");if(i!==null)try{const o=ye(t.el),r=new Oe(o.width,o.height);t.draw(r.ctx,o);const a=await r.toBlob({title:e,created:s});await i.write(a),this.setStatus("")}catch(o){this.setStatus(o instanceof Error?o.message:String(o))}}async savePng(t,e,s){const i=await gt(Bt(e,s,j(new Date),"png"),"image/png");if(i!==null)try{await i.write(await Zt(se(t))),this.setStatus("")}catch(o){this.setStatus(o instanceof Error?o.message:String(o))}}async savePdf(t,e,s){const i=new Date,o=await gt(Bt(e,s,j(i),"pdf"),"application/pdf");if(o!==null)try{const r=ye(t.el),a=new Oe(r.width,r.height);t.draw(a.ctx,r);const l=await a.toBlob({title:e.label,created:i});await o.write(l),this.setStatus("")}catch(r){this.setStatus(r instanceof Error?r.message:String(r))}}paintCli(t){const e=$t(t.task)===void 0;this.cliButton.disabled=e,this.cliButton.title=e?`This build does not have the task ${t.task}, so it cannot write its flags.`:"The same run as a chromosomix command line — the file, the window, the balancing and every parameter — for the other two hundred files."}shownProvenances(){return this.drawn!==null?[{label:null,provenance:this.drawn.provenance}]:(this.across??[]).map(t=>({label:t.label,provenance:t.provenance}))}copyCliCommand(){const t=this.shownProvenances(),e=t[0];if(e===void 0)return;const s=$t(e.provenance.task);if(s===void 0)return;const o=t.map(({label:a,provenance:l})=>{const c=qn({task:s,provenance:l,context:this.options.context(s)}).text;return a===null?c:`# ${a}
 ${c}`}).join(`
 
 `),r=t.length>1?0:o.split(`
-`).filter(a=>a.startsWith("#")).length;Fe(o).then(()=>{this.setStatus(t.length>1?`${t.length} CLI commands copied, one per map.`:r===0?"CLI command copied.":`CLI command copied, with ${r} note${r===1?"":"s"} on what a shell cannot be told.`)},a=>{this.setStatus(a instanceof Error?a.message:String(a))})}copyProvenance(){const t=this.shownProvenances();if(t.length===0)return;const e=(this.drawn===null?Hn(t.map(({label:s,provenance:i})=>({label:s??"",provenance:i}))):ht(t[0].provenance)).join(`
-`);Fe(e).then(()=>{this.setStatus("Provenance copied.")},s=>{this.setStatus(s instanceof Error?s.message:String(s))})}}function Ss(n){return Number.isInteger(n)?String(n):String(Number(n.toPrecision(7)))}function $s(n){return n!==void 0&&Number.isFinite(n)}function Za(n,t,e){const s=ht(e),{values:i,extent:o,binsize:r}=n,a=new Gn(s);for(const l of t)for(let c=0;c<l.bins;c++){const u=l.startBin+c;if(u<o[0]||u>=o[1])continue;const d=i[u-o[0]];if(!$s(d))continue;const f=c*r,m=Math.min(l.length,f+r);m>f&&a.push(`${l.name}	${f}	${m}	${Ss(d)}`)}return a.flush(),s.push(""),s.join(`
-`)}function Xa(n,t,e){const s=ht(e),i=new Map;for(const o of n){const r=i.get(o.contig);r===void 0?i.set(o.contig,[o]):r.push(o)}for(const o of t){const r=i.get(o.name);if(r===void 0)continue;const a=[];for(const l of r)for(let c=0;c<l.starts.length;c+=1){const u=l.values[c];if(!$s(u))continue;const d=Math.max(0,l.starts[c]),f=Math.min(o.length,l.ends[c]);f>d&&a.push([d,f,u])}a.sort((l,c)=>l[0]-c[0]);for(const[l,c,u]of a)s.push(`${o.name}	${l}	${c}	${Ss(u)}`)}return s.push(""),s.join(`
-`)}class tl{constructor(t){this.host=t;const e={context:a=>this.host.context(a),source:a=>this.host.source(a),block:()=>this.host.block(),payload:a=>this.host.store()?.byId(a)?.payload,label:a=>this.host.store()?.byId(a)?.label,vector:a=>this.binVector(a),annotations:()=>this.host.annotations(),contigLengths:a=>{const l={};for(const c of this.host.contigs(a))l[c.name]=c.length;return l},...this.host.targetMap===void 0?{}:{targetMap:()=>this.host.targetMap?.()??J},allTargets:()=>this.host.allTargets?.()??[],...this.host.allTargetsReady===void 0?{}:{allTargetsReady:()=>this.host.allTargetsReady?.()??Promise.resolve([])},...this.host.targetCount===void 0?{}:{targetCount:()=>this.host.targetCount?.()??0},finished:(a,l,c)=>this.adopt(a,l,c)};this.runner=new To(e),this.panel=new pa({runner:this.runner,context:()=>this.host.context(),blocked:()=>this.host.blocked?.()??null,onOpen:a=>this.show(a),active:()=>this.open?.id??null}),this.panelEl=this.panel.el,this.drawer=new Ua({runner:this.runner,context:a=>this.host.context(a),blocked:()=>this.host.blocked?.()??null,framing:()=>this.host.framing(),onClose:()=>this.show(null),hasLanes:()=>this.laneable(),surfaces:a=>{const l=this.host.store();if(l===null)return null;for(const[c,u]of this.intervals){if(u.output!==a)continue;const d=l.byId(c);if(d!==void 0){const f=Pe.find(m=>m.id===u.task);return Ci(l,d,{map:this.host.context(f)?.hasMap??!0})}}return null},writeProfile:(a,l,c)=>this.writeProfile(a,l,c,this.gridFor(a.binsize))}),this.drawerEl=this.drawer.el;const s=t.store(),i=this.runner.subscribe(()=>{this.panel.refresh(),this.drawer.refresh()});let o=s===null?"":wn(s);const r=s===null?()=>{}:s.subscribe(()=>{const a=wn(s);a!==o&&(o=a,this.drawer.fillSurfaces());const l=vn(s);l!==this.entries&&(this.entries=l,this.refresh())});s!==null&&(this.entries=vn(s)),this.unsubscribe=()=>{i(),r()},this.adoptCarried(t.carried?.()??[])}panelEl;drawerEl;runner;panel;drawer;profiles=new Map;intervals=new Map;open=null;entries="";unsubscribe;get hasTasks(){const t=this.host.context();return t!==null&&An(t).length>0}get isDrawerOpen(){return this.drawer.isOpen}get openTask(){return this.drawer.task?.id??null}runsOf(t){return this.runner.runsOf(t)}isRunning(t){const e=this.runner.stateOf(t).status;return e==="running"||e==="queued"}show(t){this.open=t,this.drawer.show(t),this.panel.refresh(),this.host.changed()}refresh(){this.panel.refresh(),this.drawer.refresh()}relayout(){this.drawer.relayout()}destroy(){this.unsubscribe(),this.panel.destroy(),this.drawer.destroy(),this.runner.destroy(),this.profiles.clear()}adopt(t,e,s){const i=s.map,o=e.provenance.framing.uri,r=this.host.context(t),a=this.host.memoryKey?.(o)??o;if(ie(a,t.id,Ai(t,e.provenance.params,Fn(a,t.id),r?.uri===o?r:null)),t.id==="cellqc"){const h=e.outputs.find(y=>y.kind==="table"&&y.id==="cellqc");h!==void 0&&this.host.cellMeasurements?.(e.provenance.framing.uri,h)}if(t.id==="oriter"){const h=Ni(e.outputs);Object.keys(h).length>0&&this.host.originsFound?.(e.provenance.framing.uri,h)}const l=this.host.store(),c=e.outputs.filter(h=>h.kind==="profile"),u=e.outputs.filter(h=>h.kind==="intervals");if(c.length===0&&u.length===0)return;if(l!==null&&!this.laneable()){for(const h of u)this.adoptIntervals(t,e,h,l,s,null,!1);for(const h of c)this.profiles.set(vt(h.id),{output:h,provenance:e.provenance,task:t.id,grid:this.gridFor(h.binsize,t)});this.drawer.refresh(),this.host.changed();return}if(l===null){for(const h of u)this.intervals.set(`analysis:${t.id}:${h.id}`,{output:h,provenance:e.provenance,task:t.id});for(const h of c)this.profiles.set(vt(h.id),{output:h,provenance:e.provenance,task:t.id,grid:this.gridFor(h.binsize,t)});this.drawer.refresh();return}const f=[...c.map(h=>vt(h.id,i)),...u.map(h=>kn(t.id,h.id,i))].map(h=>l.byId(h)?.style.colour).find(h=>h!==void 0)??l.nextColour();for(const h of c){const y={kind:"computed",name:h.label,task:t.id,recipe:{taskVersion:e.provenance.taskVersion,params:e.provenance.params,framing:e.provenance.framing},framing:e.provenance.framing.label},g=Li(h,y,h.colour??f,s),w=l.byId(g.id)?.revision??0;if(h.group!==void 0&&h.groupMode!==void 0){const S=this.host.groups?.()??null,A=Ii(h.group,s);S!==null&&!S.knowsMode(A)&&S.setMode(A,h.groupMode)}l.begin({card:"synthetic",kind:"track",id:g.id,label:g.label,source:y,placement:g.placement,style:g.style}),this.placeOnTarget(l,g.id,g.placement,i);const b=this.gridFor(h.binsize,t);this.profiles.set(g.id,{output:h,provenance:e.provenance,task:t.id,grid:b}),this.register(g.id,h,b),l.update(g.id,{status:"ready",...g.fileExtent===void 0?{}:{fileExtent:g.fileExtent},revision:w+1})}let m=c.length===0?null:vt(c[c.length-1].id,i);for(const h of u){const y=h.lane?.under,g=this.adoptIntervals(t,e,h,l,s,y===void 0?m:"output"in y?vt(y.output,i):y.entry,!0,f);y===void 0&&g!==null&&(m=g)}u.length>0&&this.drawer.fillSurfaces(),this.host.changed()}adoptIntervals(t,e,s,i,o,r,a=!0,l){const c=o.map,u={kind:"computed",name:s.label,task:t.id,recipe:{taskVersion:e.provenance.taskVersion,params:e.provenance.params,framing:e.provenance.framing},framing:e.provenance.framing.label},d=s.entryKind==="structure",f=kn(t.id,s.id,c),m=c===J?s.label:`${s.label} · ${o.label}`,h={output:s,provenance:e.provenance,task:t.id};if(!d){const b=Oi(i,{id:f,label:m,source:u,payload:s.payload,summary:yn(s),colour:i.byId(f)?.style.colour??l??i.nextColour(),map:c,display:a?s.display??(s.payload.kind==="pairs"?"overlay":"lane"):"overlay",look:s.look??"corner",overlay:this.host.context(t)?.hasMap??!0,under:r});return this.intervals.set(b,h),b}const y=ja(i,f),g=y===f?1:Number(y.slice(f.length+1)),w=i.nextColour();return i.begin({card:"structure",kind:"structure",id:y,label:g>1?`${m} (${g})`:m,source:u,placement:Pi(),style:Fi("structure",w)}),i.update(y,{status:"ready",payload:s.payload,summary:s.payload.kind==="features"?Bi(s.payload.data):yn(s)}),this.intervals.set(y,h),null}carry(){const t=this.host.store();if(t===null)return[];const e=[];for(const s of t.entries){if(s.source.kind!=="computed")continue;const i=this.profiles.get(s.id),o=this.intervals.get(s.id);e.push({entry:s,...i===void 0?{}:{profile:i},...o===void 0?{}:{intervals:o}})}return e}placeOnTarget(t,e,s,i){i!==J&&(t.placeOn(e,i,s),t.unplaceFrom(e,J))}adoptCarried(t){const e=this.host.store();if(!(e===null||t.length===0)){for(const{entry:s,profile:i,intervals:o}of t){const r=s.source;r.kind==="computed"&&(e.begin({card:s.card,kind:s.kind,id:s.id,label:s.label,source:r,placement:s.placement,style:s.style,visible:s.visible,...s.partner===void 0?{}:{partner:s.partner}}),i!==void 0&&(this.profiles.set(s.id,i),this.register(s.id,i.output,i.grid)),o!==void 0&&this.intervals.set(s.id,o),e.update(s.id,{status:s.status,...s.summary===void 0?{}:{summary:s.summary},...s.payload===void 0?{}:{payload:s.payload},...s.fileExtent===void 0?{}:{fileExtent:s.fileExtent}}))}this.host.changed()}}grid(t){return this.host.contigs(t).map(e=>({name:e.name,startBin:e.startBin,bins:e.bins,length:e.length}))}gridFor(t,e){return this.host.context(e)?.binsize===t?this.grid(e):qi(this.host.contigs(e),t)}gridBins(){let t=0;for(const e of this.host.contigs())t=Math.max(t,e.startBin+e.bins);return t}async binVector(t){const e=this.host.annotations(),s=this.host.context();if(e===null||s===null)return;const i=this.host.contigs();if(i.length===0)return;const o=s.binsize,r=this.gridBins();if(!(o>0)||r===0)return;const a=i.filter(m=>m.length>0).map(m=>({contig:m.name,start:0,end:m.length}));let l;try{l=await e.request({kind:"sample",entry:t,regions:a,basesPerPixel:o})}catch{return}const c=new Map(i.map(m=>[m.name,m.startBin])),u=new Float32Array(r).fill(Number.NaN),d=new Float64Array(r),f=new Float64Array(r);for(const m of l.regions){const h=c.get(m.contig);if(h!==void 0)for(let y=0;y<m.values.length;y++){const g=m.values[y];if(!Number.isFinite(g))continue;const w=m.starts[y],b=m.ends[y];if(!(b>w))continue;const S=Math.floor(w/o),A=Math.floor((b-1)/o);for(let v=S;v<=A;v++){const k=h+v;if(k<0||k>=u.length)continue;const M=Math.min(b,(v+1)*o)-Math.max(w,v*o);M>0&&(f[k]+=g*M,d[k]+=M)}}}for(let m=0;m<u.length;m++)d[m]>0&&(u[m]=f[m]/d[m]);return u}laneable(){return this.host.store()!==null&&this.host.annotations()!==null}register(t,e,s){const i=this.host.annotations();if(i===null)return;const o={binsize:e.binsize,firstBin:e.extent[0],values:e.values.slice(),contigs:s};i.request({kind:"register",entry:t,vector:o}).catch(()=>{})}recompute(t){const e=t.source;if(e.kind!=="computed")return;const s=Pe.find(i=>i.id===e.task);s!==void 0&&this.show(s)}createdAt(t){return this.intervals.get(t)?.provenance.createdAt}async exportEntry(t,e){const s=j(new Date),i=Rt(t.label);if(e==="anchors"){const a=Be(t);if(a?.kind!=="pairs")return;const l=this.intervals.get(t.id),c=oe({kind:"features",data:zi(a.data)},{label:`${t.label} anchors`,...l===void 0?{}:{file:l.provenance.framing.label,created:l.provenance.createdAt}});st(new Blob([c],{type:"text/plain"}),`${i}-anchors-${s}.bed`);return}if(e==="bed"){const a=Be(t);if(a===void 0)return;const l=this.intervals.get(t.id),c={label:t.label,...l===void 0?{}:{file:l.provenance.framing.label,created:l.provenance.createdAt}},u=t.kind==="structure"&&a.kind==="features",d=u?On(a.data,c):oe(a,c),f=u?"bed3d":a.kind==="pairs"?"bedpe":"bed";st(new Blob([d],{type:"text/plain"}),`${i}-${s}.${f}`);return}const o=this.intervals.get(t.id);if(o!==void 0&&e==="tsv"){st(new Blob([re(o.output,o.provenance)],{type:"text/tab-separated-values"}),$t(i,o.output,s));return}if(t.source.kind==="derived"){await this.exportDerived(t,e,i,s);return}const r=this.profiles.get(t.id);if(r!==void 0){if(e==="tsv"){st(new Blob([re(r.output,r.provenance)],{type:"text/tab-separated-values"}),$t(i,r.output,s));return}await this.writeProfile(r.output,r.provenance,e,r.grid,i)}}async exportDerived(t,e,s,i){const o=t.derivedFrom,r=this.host.context();if(o===void 0||r===null||e==="bed")return;const a=await pt(`${s}-${i}.${e==="tsv"?"tsv":e==="bedgraph"?"bedGraph":"bw"}`,e==="tsv"?"text/tab-separated-values":e==="bedgraph"?"text/plain":"application/octet-stream");if(a===null)return;const[l,c]=await Promise.all([this.exactSamples(o.a),this.exactSamples(o.b)]),u=Ri(l,c,o.op,"drop");if(u===null)return;const d=u.regions.map(y=>({contig:y.contig,starts:y.starts,ends:y.ends,values:y.values})),f=Qa(t,o.op,r),m=this.host.contigs();if(e==="tsv"){await a.write(new Blob([mo(t.label,Pn[o.op],d,m,f)],{type:"text/tab-separated-values"}));return}if(e==="bedgraph"){await a.write(new Blob([Xa(d,m,f)],{type:"text/plain"}));return}const h=await qe({contigs:m.map(y=>({name:y.name,length:y.length})),spans:d});await a.write(h)}async exactSamples(t){const e=this.host.annotations();if(e===null)return null;const s=this.host.contigs().filter(i=>i.length>0);if(s.length===0)return null;try{return await e.request({kind:"sample",entry:t,regions:s.map(i=>({contig:i.name,start:0,end:i.length})),basesPerPixel:1,exact:!0})}catch{return null}}async writeProfile(t,e,s,i,o=Rt(t.label)){const r=j(new Date),a=await pt(`${o}-${r}.${s==="bedgraph"?"bedGraph":"bw"}`,s==="bedgraph"?"text/plain":"application/octet-stream");if(a===null)return;if(s==="bedgraph"){await a.write(new Blob([Za(t,i,e)],{type:"text/plain"}));return}const l=await qe({contigs:i.map(c=>({name:c.name,length:c.length})),values:t.values,firstBin:t.extent[0],binsize:t.binsize});await a.write(l)}}function ja(n,t){if(n.byId(t)===void 0)return t;for(let e=2;e<1e3;e++){const s=`${t}#${e}`;if(n.byId(s)===void 0)return s}return`${t}#${Date.now()}`}function yn(n){const t=n.payload,e=t.data.length,s=n.noun??(t.kind==="pairs"?{one:"pair",many:"pairs"}:{one:"interval",many:"intervals"});return`${z.int(e)} ${e===1?s.one:s.many}`}function Qa(n,t,e){const s=`${e.binsize.toLocaleString()} bp bins`;return{task:`track ${Pn[t]}`,taskVersion:1,params:{operation:t,of:n.label},framing:{uri:e.uri,label:e.hasMap?`two loaded tracks, read onto this file’s ${s}`:`two loaded tracks, read onto the assembly’s ${s}`,binsize:e.binsize,binsPerCell:1,rows:[0,e.nBins],cols:[0,e.nBins],balance:!1,value:"",normalise:null,level:"bin"},app:xn,createdAt:new Date().toISOString()}}function vn(n){return n.entries.map(t=>`${t.id}:${t.kind}:${t.status}:${t.label}`).join("|")}function wn(n){return n.entries.filter(_i).map(t=>`${t.id}:${t.card}:${t.style.shape}`).join("|")}function kn(n,t,e){return e===J?`analysis:${n}:${t}`:`analysis:${e}:${n}:${t}`}export{tl as AnalysisWorkspace,vn as entrySignature,ja as freshId};
+`).filter(a=>a.startsWith("#")).length;Fe(o).then(()=>{this.setStatus(t.length>1?`${t.length} CLI commands copied, one per map.`:r===0?"CLI command copied.":`CLI command copied, with ${r} note${r===1?"":"s"} on what a shell cannot be told.`)},a=>{this.setStatus(a instanceof Error?a.message:String(a))})}copyProvenance(){const t=this.shownProvenances();if(t.length===0)return;const e=(this.drawn===null?Hn(t.map(({label:s,provenance:i})=>({label:s??"",provenance:i}))):ft(t[0].provenance)).join(`
+`);Fe(e).then(()=>{this.setStatus("Provenance copied.")},s=>{this.setStatus(s instanceof Error?s.message:String(s))})}}function Ss(n){return Number.isInteger(n)?String(n):String(Number(n.toPrecision(7)))}function $s(n){return n!==void 0&&Number.isFinite(n)}function*Za(n,t,e){yield*tt(ft(e));const{values:s,extent:i,binsize:o}=n,r=new Gn;for(const l of t)for(let c=0;c<l.bins;c++){const u=l.startBin+c;if(u<i[0]||u>=i[1])continue;const d=s[u-i[0]];if(!$s(d))continue;const f=c*o,m=Math.min(l.length,f+o);if(!(m>f))continue;const h=r.push(`${l.name}	${f}	${m}	${Ss(d)}`);h!==void 0&&(yield h)}const a=r.flush();a!==void 0&&(yield a)}function Xa(n,t,e){const s=ft(e),i=new Map;for(const o of n){const r=i.get(o.contig);r===void 0?i.set(o.contig,[o]):r.push(o)}for(const o of t){const r=i.get(o.name);if(r===void 0)continue;const a=[];for(const l of r)for(let c=0;c<l.starts.length;c+=1){const u=l.values[c];if(!$s(u))continue;const d=Math.max(0,l.starts[c]),f=Math.min(o.length,l.ends[c]);f>d&&a.push([d,f,u])}a.sort((l,c)=>l[0]-c[0]);for(const[l,c,u]of a)s.push(`${o.name}	${l}	${c}	${Ss(u)}`)}return tt(s)}class tl{constructor(t){this.host=t;const e={context:a=>this.host.context(a),source:a=>this.host.source(a),block:()=>this.host.block(),payload:a=>this.host.store()?.byId(a)?.payload,label:a=>this.host.store()?.byId(a)?.label,vector:a=>this.binVector(a),annotations:()=>this.host.annotations(),contigLengths:a=>{const l={};for(const c of this.host.contigs(a))l[c.name]=c.length;return l},...this.host.targetMap===void 0?{}:{targetMap:()=>this.host.targetMap?.()??J},allTargets:()=>this.host.allTargets?.()??[],...this.host.allTargetsReady===void 0?{}:{allTargetsReady:()=>this.host.allTargetsReady?.()??Promise.resolve([])},...this.host.targetCount===void 0?{}:{targetCount:()=>this.host.targetCount?.()??0},finished:(a,l,c)=>this.adopt(a,l,c)};this.runner=new To(e),this.panel=new pa({runner:this.runner,context:()=>this.host.context(),blocked:()=>this.host.blocked?.()??null,onOpen:a=>this.show(a),active:()=>this.open?.id??null}),this.panelEl=this.panel.el,this.drawer=new Ua({runner:this.runner,context:a=>this.host.context(a),blocked:()=>this.host.blocked?.()??null,framing:()=>this.host.framing(),onClose:()=>this.show(null),hasLanes:()=>this.laneable(),surfaces:a=>{const l=this.host.store();if(l===null)return null;for(const[c,u]of this.intervals){if(u.output!==a)continue;const d=l.byId(c);if(d!==void 0){const f=Pe.find(m=>m.id===u.task);return Ci(l,d,{map:this.host.context(f)?.hasMap??!0})}}return null},writeProfile:(a,l,c)=>this.writeProfile(a,l,c,this.gridFor(a.binsize))}),this.drawerEl=this.drawer.el;const s=t.store(),i=this.runner.subscribe(()=>{this.panel.refresh(),this.drawer.refresh()});let o=s===null?"":wn(s);const r=s===null?()=>{}:s.subscribe(()=>{const a=wn(s);a!==o&&(o=a,this.drawer.fillSurfaces());const l=vn(s);l!==this.entries&&(this.entries=l,this.refresh())});s!==null&&(this.entries=vn(s)),this.unsubscribe=()=>{i(),r()},this.adoptCarried(t.carried?.()??[])}panelEl;drawerEl;runner;panel;drawer;profiles=new Map;intervals=new Map;open=null;entries="";unsubscribe;get hasTasks(){const t=this.host.context();return t!==null&&An(t).length>0}get isDrawerOpen(){return this.drawer.isOpen}get openTask(){return this.drawer.task?.id??null}runsOf(t){return this.runner.runsOf(t)}isRunning(t){const e=this.runner.stateOf(t).status;return e==="running"||e==="queued"}show(t){this.open=t,this.drawer.show(t),this.panel.refresh(),this.host.changed()}refresh(){this.panel.refresh(),this.drawer.refresh()}relayout(){this.drawer.relayout()}destroy(){this.unsubscribe(),this.panel.destroy(),this.drawer.destroy(),this.runner.destroy(),this.profiles.clear()}adopt(t,e,s){const i=s.map,o=e.provenance.framing.uri,r=this.host.context(t),a=this.host.memoryKey?.(o)??o;if(oe(a,t.id,Ai(t,e.provenance.params,Fn(a,t.id),r?.uri===o?r:null)),t.id==="cellqc"){const h=e.outputs.find(y=>y.kind==="table"&&y.id==="cellqc");h!==void 0&&this.host.cellMeasurements?.(e.provenance.framing.uri,h)}if(t.id==="oriter"){const h=Ni(e.outputs);Object.keys(h).length>0&&this.host.originsFound?.(e.provenance.framing.uri,h)}const l=this.host.store(),c=e.outputs.filter(h=>h.kind==="profile"),u=e.outputs.filter(h=>h.kind==="intervals");if(c.length===0&&u.length===0)return;if(l!==null&&!this.laneable()){for(const h of u)this.adoptIntervals(t,e,h,l,s,null,!1);for(const h of c)this.profiles.set(wt(h.id),{output:h,provenance:e.provenance,task:t.id,grid:this.gridFor(h.binsize,t)});this.drawer.refresh(),this.host.changed();return}if(l===null){for(const h of u)this.intervals.set(`analysis:${t.id}:${h.id}`,{output:h,provenance:e.provenance,task:t.id});for(const h of c)this.profiles.set(wt(h.id),{output:h,provenance:e.provenance,task:t.id,grid:this.gridFor(h.binsize,t)});this.drawer.refresh();return}const f=[...c.map(h=>wt(h.id,i)),...u.map(h=>kn(t.id,h.id,i))].map(h=>l.byId(h)?.style.colour).find(h=>h!==void 0)??l.nextColour();for(const h of c){const y={kind:"computed",name:h.label,task:t.id,recipe:{taskVersion:e.provenance.taskVersion,params:e.provenance.params,framing:e.provenance.framing},framing:e.provenance.framing.label},g=Li(h,y,h.colour??f,s),w=l.byId(g.id)?.revision??0;if(h.group!==void 0&&h.groupMode!==void 0){const S=this.host.groups?.()??null,A=Ii(h.group,s);S!==null&&!S.knowsMode(A)&&S.setMode(A,h.groupMode)}l.begin({card:"synthetic",kind:"track",id:g.id,label:g.label,source:y,placement:g.placement,style:g.style}),this.placeOnTarget(l,g.id,g.placement,i);const b=this.gridFor(h.binsize,t);this.profiles.set(g.id,{output:h,provenance:e.provenance,task:t.id,grid:b}),this.register(g.id,h,b),l.update(g.id,{status:"ready",...g.fileExtent===void 0?{}:{fileExtent:g.fileExtent},revision:w+1})}let m=c.length===0?null:wt(c[c.length-1].id,i);for(const h of u){const y=h.lane?.under,g=this.adoptIntervals(t,e,h,l,s,y===void 0?m:"output"in y?wt(y.output,i):y.entry,!0,f);y===void 0&&g!==null&&(m=g)}u.length>0&&this.drawer.fillSurfaces(),this.host.changed()}adoptIntervals(t,e,s,i,o,r,a=!0,l){const c=o.map,u={kind:"computed",name:s.label,task:t.id,recipe:{taskVersion:e.provenance.taskVersion,params:e.provenance.params,framing:e.provenance.framing},framing:e.provenance.framing.label},d=s.entryKind==="structure",f=kn(t.id,s.id,c),m=c===J?s.label:`${s.label} · ${o.label}`,h={output:s,provenance:e.provenance,task:t.id};if(!d){const b=Oi(i,{id:f,label:m,source:u,payload:s.payload,summary:yn(s),colour:i.byId(f)?.style.colour??l??i.nextColour(),map:c,display:a?s.display??(s.payload.kind==="pairs"?"overlay":"lane"):"overlay",look:s.look??"corner",overlay:this.host.context(t)?.hasMap??!0,under:r});return this.intervals.set(b,h),b}const y=ja(i,f),g=y===f?1:Number(y.slice(f.length+1)),w=i.nextColour();return i.begin({card:"structure",kind:"structure",id:y,label:g>1?`${m} (${g})`:m,source:u,placement:Pi(),style:Fi("structure",w)}),i.update(y,{status:"ready",payload:s.payload,summary:s.payload.kind==="features"?Bi(s.payload.data):yn(s)}),this.intervals.set(y,h),null}carry(){const t=this.host.store();if(t===null)return[];const e=[];for(const s of t.entries){if(s.source.kind!=="computed")continue;const i=this.profiles.get(s.id),o=this.intervals.get(s.id);e.push({entry:s,...i===void 0?{}:{profile:i},...o===void 0?{}:{intervals:o}})}return e}placeOnTarget(t,e,s,i){i!==J&&(t.placeOn(e,i,s),t.unplaceFrom(e,J))}adoptCarried(t){const e=this.host.store();if(!(e===null||t.length===0)){for(const{entry:s,profile:i,intervals:o}of t){const r=s.source;r.kind==="computed"&&(e.begin({card:s.card,kind:s.kind,id:s.id,label:s.label,source:r,placement:s.placement,style:s.style,visible:s.visible,...s.partner===void 0?{}:{partner:s.partner}}),i!==void 0&&(this.profiles.set(s.id,i),this.register(s.id,i.output,i.grid)),o!==void 0&&this.intervals.set(s.id,o),e.update(s.id,{status:s.status,...s.summary===void 0?{}:{summary:s.summary},...s.payload===void 0?{}:{payload:s.payload},...s.fileExtent===void 0?{}:{fileExtent:s.fileExtent}}))}this.host.changed()}}grid(t){return this.host.contigs(t).map(e=>({name:e.name,startBin:e.startBin,bins:e.bins,length:e.length}))}gridFor(t,e){return this.host.context(e)?.binsize===t?this.grid(e):qi(this.host.contigs(e),t)}gridBins(){let t=0;for(const e of this.host.contigs())t=Math.max(t,e.startBin+e.bins);return t}async binVector(t){const e=this.host.annotations(),s=this.host.context();if(e===null||s===null)return;const i=this.host.contigs();if(i.length===0)return;const o=s.binsize,r=this.gridBins();if(!(o>0)||r===0)return;const a=i.filter(m=>m.length>0).map(m=>({contig:m.name,start:0,end:m.length}));let l;try{l=await e.request({kind:"sample",entry:t,regions:a,basesPerPixel:o})}catch{return}const c=new Map(i.map(m=>[m.name,m.startBin])),u=new Float32Array(r).fill(Number.NaN),d=new Float64Array(r),f=new Float64Array(r);for(const m of l.regions){const h=c.get(m.contig);if(h!==void 0)for(let y=0;y<m.values.length;y++){const g=m.values[y];if(!Number.isFinite(g))continue;const w=m.starts[y],b=m.ends[y];if(!(b>w))continue;const S=Math.floor(w/o),A=Math.floor((b-1)/o);for(let v=S;v<=A;v++){const k=h+v;if(k<0||k>=u.length)continue;const M=Math.min(b,(v+1)*o)-Math.max(w,v*o);M>0&&(f[k]+=g*M,d[k]+=M)}}}for(let m=0;m<u.length;m++)d[m]>0&&(u[m]=f[m]/d[m]);return u}laneable(){return this.host.store()!==null&&this.host.annotations()!==null}register(t,e,s){const i=this.host.annotations();if(i===null)return;const o={binsize:e.binsize,firstBin:e.extent[0],values:e.values.slice(),contigs:s};i.request({kind:"register",entry:t,vector:o}).catch(()=>{})}recompute(t){const e=t.source;if(e.kind!=="computed")return;const s=Pe.find(i=>i.id===e.task);s!==void 0&&this.show(s)}createdAt(t){return this.intervals.get(t)?.provenance.createdAt}async exportEntry(t,e){const s=j(new Date),i=_t(t.label);if(e==="anchors"){const a=Be(t);if(a?.kind!=="pairs")return;const l=this.intervals.get(t.id),c=re({kind:"features",data:zi(a.data)},{label:`${t.label} anchors`,...l===void 0?{}:{file:l.provenance.framing.label,created:l.provenance.createdAt}});it(new Blob([c],{type:"text/plain"}),`${i}-anchors-${s}.bed`);return}if(e==="bed"){const a=Be(t);if(a===void 0)return;const l=this.intervals.get(t.id),c={label:t.label,...l===void 0?{}:{file:l.provenance.framing.label,created:l.provenance.createdAt}},u=t.kind==="structure"&&a.kind==="features",d=u?On(a.data,c):re(a,c),f=u?"bed3d":a.kind==="pairs"?"bedpe":"bed";it(new Blob([d],{type:"text/plain"}),`${i}-${s}.${f}`);return}const o=this.intervals.get(t.id);if(o!==void 0&&e==="tsv"){it(new Blob([...ae(o.output,o.provenance)],{type:"text/tab-separated-values"}),Mt(i,o.output,s));return}if(t.source.kind==="derived"){await this.exportDerived(t,e,i,s);return}const r=this.profiles.get(t.id);if(r!==void 0){if(e==="tsv"){it(new Blob([...ae(r.output,r.provenance)],{type:"text/tab-separated-values"}),Mt(i,r.output,s));return}await this.writeProfile(r.output,r.provenance,e,r.grid,i)}}async exportDerived(t,e,s,i){const o=t.derivedFrom,r=this.host.context();if(o===void 0||r===null||e==="bed")return;const a=await gt(`${s}-${i}.${e==="tsv"?"tsv":e==="bedgraph"?"bedGraph":"bw"}`,e==="tsv"?"text/tab-separated-values":e==="bedgraph"?"text/plain":"application/octet-stream");if(a===null)return;const[l,c]=await Promise.all([this.exactSamples(o.a),this.exactSamples(o.b)]),u=Ri(l,c,o.op,"drop");if(u===null)return;const d=u.regions.map(y=>({contig:y.contig,starts:y.starts,ends:y.ends,values:y.values})),f=Qa(t,o.op,r),m=this.host.contigs();if(e==="tsv"){await a.write(new Blob([...mo(t.label,Pn[o.op],d,m,f)],{type:"text/tab-separated-values"}));return}if(e==="bedgraph"){await a.write(new Blob([...Xa(d,m,f)],{type:"text/plain"}));return}const h=await qe({contigs:m.map(y=>({name:y.name,length:y.length})),spans:d});await a.write(h)}async exactSamples(t){const e=this.host.annotations();if(e===null)return null;const s=this.host.contigs().filter(i=>i.length>0);if(s.length===0)return null;try{return await e.request({kind:"sample",entry:t,regions:s.map(i=>({contig:i.name,start:0,end:i.length})),basesPerPixel:1,exact:!0})}catch{return null}}async writeProfile(t,e,s,i,o=_t(t.label)){const r=j(new Date),a=await gt(`${o}-${r}.${s==="bedgraph"?"bedGraph":"bw"}`,s==="bedgraph"?"text/plain":"application/octet-stream");if(a===null)return;if(s==="bedgraph"){await a.write(new Blob([...Za(t,i,e)],{type:"text/plain"}));return}const l=await qe({contigs:i.map(c=>({name:c.name,length:c.length})),values:t.values,firstBin:t.extent[0],binsize:t.binsize});await a.write(l)}}function ja(n,t){if(n.byId(t)===void 0)return t;for(let e=2;e<1e3;e++){const s=`${t}#${e}`;if(n.byId(s)===void 0)return s}return`${t}#${Date.now()}`}function yn(n){const t=n.payload,e=t.data.length,s=n.noun??(t.kind==="pairs"?{one:"pair",many:"pairs"}:{one:"interval",many:"intervals"});return`${z.int(e)} ${e===1?s.one:s.many}`}function Qa(n,t,e){const s=`${e.binsize.toLocaleString()} bp bins`;return{task:`track ${Pn[t]}`,taskVersion:1,params:{operation:t,of:n.label},framing:{uri:e.uri,label:e.hasMap?`two loaded tracks, read onto this file’s ${s}`:`two loaded tracks, read onto the assembly’s ${s}`,binsize:e.binsize,binsPerCell:1,rows:[0,e.nBins],cols:[0,e.nBins],balance:!1,value:"",normalise:null,level:"bin"},app:xn,createdAt:new Date().toISOString()}}function vn(n){return n.entries.map(t=>`${t.id}:${t.kind}:${t.status}:${t.label}`).join("|")}function wn(n){return n.entries.filter(_i).map(t=>`${t.id}:${t.card}:${t.style.shape}`).join("|")}function kn(n,t,e){return e===J?`analysis:${n}:${t}`:`analysis:${e}:${n}:${t}`}export{tl as AnalysisWorkspace,vn as entrySignature,ja as freshId};