@datagrok/proteomics 1.2.0 → 1.2.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (7) hide show
  1. package/dist/package-test.js +1 -1
  2. package/dist/package-test.js.map +1 -1
  3. package/dist/package.js +1 -1
  4. package/dist/package.js.map +1 -1
  5. package/package.json +4 -3
  6. package/test-console-output-1.log +1077 -1059
  7. package/test-record-1.mp4 +0 -0
package/dist/package-test.js CHANGED
@@ -1,2 +1,2 @@
1
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v=e.columns.addNewFloat("log2FC"),_=e.columns.addNewFloat("p-value"),C=e.columns.addNewFloat("adj.p-value");v.init(e=>g[e]),_.init(e=>h[e]),C.init(e=>y[e]),e.columns.addNewBool("significant").init(e=>{const t=y[e],n=g[e];return t!==a.FLOAT_NULL&&n!==a.FLOAT_NULL&&Math.abs(n)>=i&&t<=m}),v.semType=u.iu.LOG2FC,_.semType=u.iu.P_VALUE,C.semType=u.iu.P_VALUE,e.setTag("proteomics.de_complete","true"),e.fireValuesChanged();const b=E.length;return{tested:b,untestable:e.rowCount-b}}function h(e,t,n){const o=[...t,...n],r=[];for(let t=0;t<o.length;t++){const n=e.columns.byName(o[t]).getRawData(),s=new Float32Array(n.length);s.set(n),r.push(a.Column.fromFloat32Array(`s${t+1}`,s))}return a.DataFrame.fromColumns(r)}function y(e,t){const n=e.rowCount,o=t.rowCount,r=t.columns.byName("log2FC").getRawData(),s=t.columns.byName("p.value").getRawData(),i=t.columns.byName("adj.p.value").getRawData(),l=t.columns.byName("significant"),c=t.col("row"),m=new Int32Array(o);if(c){const e=c.getRawData();for(let t=0;t<o;t++)m[t]=(0|e[t])-1}else for(let e=0;e<o;e++)m[e]=e;const p=new Float32Array(n);p.fill(a.FLOAT_NULL);const d=new Float32Array(n);d.fill(a.FLOAT_NULL);const f=new Float32Array(n);f.fill(a.FLOAT_NULL);const g=new Uint8Array(n);let h=0;for(let e=0;e<o;e++){const t=m[e];if(t<0||t>=n)continue;p[t]=r[e],d[t]=s[e],f[t]=i[e];const o=l.get(e);!0!==o&&1!==o&&"1"!==o&&"TRUE"!==o||(g[t]=1,h++)}const y=a.Column.fromFloat32Array("log2FC",p),E=a.Column.fromFloat32Array("p-value",d),w=a.Column.fromFloat32Array("adj.p-value",f);return e.columns.addNewBool("significant").init(e=>1===g[e]),y.semType=u.iu.LOG2FC,E.semType=u.iu.P_VALUE,w.semType=u.iu.P_VALUE,e.columns.add(y),e.columns.add(E),e.columns.add(w),h}async function E(e,t,n,o,s){const a=h(e,t,n),i=y(e,await r.functions.call("Proteomics:LimmaDE",{exprDf:a,nGroup1:t.length,fcThreshold:o,pThreshold:s}));return e.setTag("proteomics.de_complete","true"),e.fireValuesChanged(),i}function w(e,t){return`${e} vs ${t}`}function v(e,t){const n=(0,m.f)(e);if(!n)return void r.shell.warning("Please annotate experimental groups first (Proteomics | Annotate Experiment)");if("true"===e.getTag("proteomics.de_complete"))return void r.shell.warning("Differential expression already performed");const o=n.group1,i=n.group2,l=s.divText(`Group 1: ${o.name} (${o.columns.length} samples), Group 2: ${i.name} (${i.columns.length} samples)`),c=[`${i.name} vs ${o.name}`,`${o.name} vs ${i.name}`],p=s.input.choice("Comparison",{value:w(o.name,i.name),items:c,nullable:!1}),d=s.div();d.style.cssText="font-style:italic; color:#888; font-size:12px; margin-bottom:8px;";const f=()=>{const e=p.value===c[1],t=e?o.name:i.name,n=e?i.name:o.name;d.textContent=`Positive log2FC = higher in ${t}, Negative log2FC = higher in ${n}`};p.onChanged.subscribe(f),f();const v=s.input.choice("Method",{value:"limma",items:["limma","DEqMS","t-test"],nullable:!1});v.setTooltip("limma: moderated t-test; DEqMS: peptide-count-weighted variance; t-test: client-side Welch's t-test");const _=e.columns.toList().find(e=>"Unique peptides"===e.name||"Peptides"===e.name)??void 0,C=s.input.column("Peptide count column",{table:e,value:_,filter:e=>e.type===a.COLUMN_TYPE.INT||e.type===a.COLUMN_TYPE.FLOAT,nullable:!1});C.setTooltip("Column with peptide/spectra counts per protein");const b=C.root;b.style.display="none",v.onChanged.subscribe(()=>{b.style.display="DEqMS"===v.value?"":"none"});const T=s.input.float("|log2FC| threshold",{value:u.M5});T.setTooltip("Minimum absolute fold change for significance");const P=s.input.float("Adj. p-value threshold",{value:u.Dx});P.setTooltip("Maximum adjusted p-value for significance"),s.dialog("Differential Expression").add(l).add(p).add(d).add(v).add(C).add(T).add(P).onOK(async()=>{const n=T.value??u.M5,s=P.value??u.Dx,l=v.value,m=p.value===c[1],d=m?o.columns:i.columns,f=m?i.columns:o.columns,w=(m?o.name:i.name,m?i.name:o.name,a.TaskBarProgressIndicator.create(`Running ${l} analysis...`));try{if("t-test"===l){const t=g(e,f,d,0,0,n,s);e.setTag("proteomics.de_method","t-test"),r.shell.info(`DE complete (t-test): ${t.tested} proteins tested, ${t.untestable} untestable`)}else if("DEqMS"===l){const t=C.value;if(!t)return void r.shell.error("Please select a peptide count column for DEqMS");try{const o=await async function(e,t,n,o,s,i){const l=h(e,t,n),c=a.DataFrame.create(e.rowCount),u=c.columns.addNewInt("count");for(let t=0;t<e.rowCount;t++)u.set(t,o.isNone(t)?1:Math.round(o.get(t)));const m=y(e,await r.functions.call("Proteomics:DeqmsDE",{exprDf:l,nGroup1:t.length,peptideDf:c,fcThreshold:s,pThreshold:i}));return e.setTag("proteomics.de_complete","true"),e.setTag("proteomics.de_method","deqms"),e.fireValuesChanged(),m}(e,f,d,t,n,s);e.setTag("proteomics.de_method","deqms"),r.shell.info(`DE complete (DEqMS): ${o} significant proteins`)}catch(t){console.warn("DEqMS failed, trying limma:",t),w.update(50,"DEqMS unavailable, trying limma..."),r.shell.warning("DEqMS unavailable, trying limma...");try{const t=await E(e,f,d,n,s);e.setTag("proteomics.de_method","limma"),r.shell.info(`DE complete (limma fallback): ${t} significant proteins`)}catch(t){console.warn("Limma DE also failed, using client-side fallback:",t),w.update(75,"Server-side DE unavailable, using client-side t-test..."),r.shell.warning("R environment unavailable — using client-side t-test");const o=g(e,f,d,0,0,n,s);e.setTag("proteomics.de_method","t-test"),r.shell.info(`DE complete (t-test): ${o.tested} proteins tested, ${o.untestable} untestable`)}}}else try{const t=await E(e,f,d,n,s);e.setTag("proteomics.de_method","limma"),r.shell.info(`DE complete (limma): ${t} significant proteins`)}catch(t){w.update(50,"Limma unavailable, using client-side t-test..."),r.shell.warning("R environment unavailable — using client-side t-test"),console.warn("Limma DE failed, using client-side fallback:",t);const o=g(e,f,d,0,0,n,s);e.setTag("proteomics.de_method","t-test"),r.shell.info(`DE complete (t-test): ${o.tested} proteins tested, ${o.untestable} untestable`)}}finally{w.close()}t&&t()}).show()}},989(e,t,n){"use strict";n.d(t,{J:()=>c,N:()=>u});var o=n(328),r=n(389),s=n(82),a=n(304),i=n(641),l=n(230);function c(e,t,n){const o=(0,a.I)(e);if(!o.log2fc||!o.pValue)throw new Error("No log2FC or adjusted p-value columns found. Run Differential Expression first.");const r=o.geneName??o.proteinId;if(!r)throw new Error("No gene-name or protein-ID column found to export.");const s=new Map;for(let t=0;t<e.rowCount;t++){const e=r.get(t);e&&s.set(t,String(e))}const i=o.log2fc.getRawData(),c=o.pValue.getRawData(),{upGenes:u,downGenes:m,background:p}=(0,l.Bx)(s,i,c,t,n),d=e=>/[",\n]/.test(e)?`"${e.replace(/"/g,'""')}"`:e,f=["gene,list"];for(const e of u)f.push(`${d(e)},up`);for(const e of m)f.push(`${d(e)},down`);for(const e of p)f.push(`${d(e)},background`);return{csv:f.join("\n"),counts:{up:u.length,down:m.length,background:p.length}}}function u(e){const t=(0,a.I)(e);if(!t.log2fc||!t.pValue)return void o.shell.warning("No log2FC or p-value columns found. Run Differential Expression first.");const n=r.input.float("|log2FC| threshold",{value:i.M5});n.setTooltip("Minimum absolute fold change for a gene to count as up/down.");const u=r.input.float("Adj. p-value threshold",{value:i.Dx});u.setTooltip("Maximum adjusted p-value for a gene to count as up/down.");const m=r.divText(""),p=()=>{const o=(0,l.bM)(e,n.value??i.M5,u.value??i.Dx,t.log2fc,t.pValue);m.textContent=`${o.significant} of ${o.total.toLocaleString()} proteins significant`};p(),n.onChanged.subscribe(p),u.onChanged.subscribe(p),r.dialog("Export Enrichment Inputs").add(m).add(n).add(u).onOK(()=>{const t=n.value??i.M5,r=u.value??i.Dx,{csv:a,counts:l}=c(e,t,r),m=e.name?`${e.name} — enrichment inputs`:"enrichment inputs";s.Utils.download(`${m}.csv`,a,"text/csv"),o.shell.info(`Exported ${l.up} up, ${l.down} down, ${l.background} background genes.`)}).show()}},230(e,t,n){"use strict";n.d(t,{AB:()=>E,Ae:()=>p.Ae,Bx:()=>v,D9:()=>C,Mz:()=>w,_W:()=>y,bM:()=>_,pG:()=>b,zy:()=>h});var o=n(328),r=n(389),s=n(82),a=n(498),i=n(304),l=n(641),c=n(897),u=n(829),m=n(252),p=n(935);const d="https://biit.cs.ut.ee/gprofiler";async function f(e,t,n=3e4){const r=o.dapi.fetchProxy(e,t),s=new Promise((e,t)=>setTimeout(()=>t(new Error("g:Profiler API request timed out. The service may be temporarily unavailable.")),n)),a=await Promise.race([r,s]);if(!a.ok)throw new Error(`g:Profiler API returned status ${a.status}`);return a}async function g(e,t,n,o,r=l.Dx){const s=await f(`${d}/api/gost/profile/`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({organism:n,query:e,sources:o,user_threshold:r,significance_threshold_method:"fdr",domain_scope:"custom",background:t,all_results:!0,ordered:!1,no_evidences:!1,combined:!1,measure_underrepresentation:!1,no_iea:!1,numeric_ns:"",output:"json"})}),a=await s.json();return a.result?Array.isArray(a.result)&&a.result.length>0&&a.result[0]?.result?a.result[0].result:Array.isArray(a.result)?a.result:[]:[]}const h=["localization","cellular component organization","transport","cellular process","biological process","metabolic process"],y=["actin","vesicle","endocytosis","cytoskeleton"];function E(e,t=15){if(0===e.length)return{kept:[],stats:{total:0,kept:0,droppedParents:0,cappedAtN:t}};const n=e.filter(e=>"GO:BP"===e.source),o=e.filter(e=>"GO:BP"!==e.source);let r=0;const s=[];if(n.length>0){const e=[...n].sort((e,t)=>e.p_value-t.p_value);for(const n of e){const e=(n.name??"").toLowerCase();if(h.some(t=>e.includes(t))&&s.some(e=>y.some(t=>(e.name??"").toLowerCase().includes(t))))r++;else if(s.push(n),s.length>=t)break}}const a=[...o].sort((e,t)=>e.p_value-t.p_value).slice(0,t),i=[...s,...a].sort((e,t)=>e.p_value-t.p_value);return{kept:i,stats:{total:e.length,kept:i.length,droppedParents:r,cappedAtN:t}}}function w(e,t,n=l.Dx,o){const r=e.length,a=s.DataFrame.create(r);a.name="Enrichment Results";const i=e.map(e=>{if(!e.intersections)return"";const n=[],o=Math.min(t.length,e.intersections.length);for(let r=0;r<o;r++)e.intersections[r]&&e.intersections[r].length>0&&n.push(t[r]);return n.join(", ")}),c=a.columns.addNewString("Source"),u=a.columns.addNewString("Term ID"),m=a.columns.addNewString("Term Name"),p=a.columns.addNewFloat("FDR"),d=a.columns.addNewInt("Gene Count"),f=a.columns.addNewFloat("Gene Ratio"),g=a.columns.addNewString("Intersection");c.init(t=>e[t].source),u.init(t=>e[t].native),m.init(t=>e[t].name),p.init(t=>e[t].p_value),d.init(t=>e[t].intersection_size),f.init(t=>e[t].precision),g.init(e=>i[e]);const h=p.getRawData();return a.columns.addNewBool("Significant").init(e=>h[e]!==s.FLOAT_NULL&&h[e]<=n),o&&a.columns.addNewString("Direction").init(()=>o),p.setTag("color-coding-type","Linear"),p.setTag("color-coding-linear",'{"0":"#2ecc71","0.05":"#f39c12","1":"#e74c3c"}'),a.setTag("proteomics.enrichment","true"),a}function v(e,t,n,o,r){const a=new Set,i=new Set,l=new Set;for(const[c,u]of e){l.add(u);const e=t[c],m=n[c];e!==s.FLOAT_NULL&&m!==s.FLOAT_NULL&&m<=r&&Math.abs(e)>=o&&(e>0?a.add(u):e<0&&i.add(u))}return{upGenes:[...a],downGenes:[...i],background:[...l]}}function _(e,t,n,o,r){const a=e.rowCount,i=o.getRawData(),l=r.getRawData();let c=0;for(let e=0;e<a;e++){const o=i[e],r=l[e];o!==s.FLOAT_NULL&&r!==s.FLOAT_NULL&&Math.abs(o)>=t&&r<=n&&c++}return{significant:c,total:a}}async function C(e,t,n,o,r,s=!0,c=15){const u=(0,i.I)(e);if(!u.proteinId)throw new Error("No protein ID column found");if(!u.log2fc||!u.pValue)throw new Error("No log2FC or adjusted p-value columns found. Run Differential Expression first.");let m,p=0,h=0,y=0;if(u.geneName){m=new Map;const t=u.geneName;for(let n=0;n<e.rowCount;n++){const e=t.get(n);e&&m.set(n,e)}p=m.size,h=e.rowCount,y=h-p}else{const t=new Map;for(let n=0;n<e.rowCount;n++){const e=u.proteinId.get(n),o=(0,a.S6)(e);o&&(t.has(o)||t.set(o,[]),t.get(o).push(n))}const n=[...t.keys()],r=await async function(e,t="hsapiens"){const n=await f(`${d}/api/convert/convert/`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({organism:t,query:e,target:"ENSG",numeric_ns:"",output:"json"})});return(await n.json()).result??[]}(n,o),s=new Map;for(const e of r)e.incoming&&e.name&&"N/A"!==e.name&&!s.has(e.incoming)&&s.set(e.incoming,e.name);m=new Map;for(const[e,n]of t){const t=s.get(e);if(t)for(const e of n)m.set(e,t)}const i=new Array(e.rowCount).fill("");for(const[e,t]of m)i[e]=t;const c=e.columns.addNewString("Gene Symbol (mapped)");c.semType=l.iu.GENE_SYMBOL,c.init(e=>i[e]),p=s.size,h=n.length,y=h-p}const _=u.log2fc.getRawData(),C=u.pValue.getRawData(),{upGenes:b,downGenes:T,background:P}=v(m,_,C,t,n);if(0===b.length&&0===T.length)throw new Error("No significant proteins found with the given thresholds");const S=[];let N=null,A=null;if(b.length>0){let e=await g(b,P,o,r,n);if(s){const t=E(e,c);e=t.kept,N=t.stats}S.push(w(e,b,n,"Up"))}if(T.length>0){let e=await g(T,P,o,r,n);if(s){const t=E(e,c);e=t.kept,A=t.stats}S.push(w(e,T,n,"Down"))}let x=S[0];for(let e=1;e<S.length;e++)x=x.append(S[e]);x.name=e.name?`${e.name} — Enrichment`:"Enrichment Results",x.setTag("proteomics.enrichment","true");const D=x.col("FDR");if(D&&(D.setTag("color-coding-type","Linear"),D.setTag("color-coding-linear",'{"0":"#2ecc71","0.05":"#f39c12","1":"#e74c3c"}')),s){const e=(N?.total??0)+(A?.total??0),t=(N?.kept??0)+(A?.kept??0),n=(N?.droppedParents??0)+(A?.droppedParents??0);t<e&&(x.setTag("proteomics.enrichment_smart_filtered","true"),x.setTag("proteomics.enrichment_smart_filtered_kept",String(t)),x.setTag("proteomics.enrichment_smart_filtered_total",String(e)),x.setTag("proteomics.enrichment_smart_filtered_dropped_parents",String(n)),x.setTag("proteomics.enrichment_smart_filtered_cap",String(c)))}return{enrichmentDf:x,mapped:p,total:h,unmapped:y}}function b(e){if(!(0,u.RJ)(e,"Run Differential Expression first"))return;const t=(0,i.I)(e);if(!t.log2fc||!t.pValue)return void o.shell.warning("No log2FC or p-value columns found");const n=r.input.float("|log2FC| threshold",{value:l.M5});n.setTooltip("Minimum absolute fold change for significance");const a=r.input.float("Adj. p-value threshold",{value:l.Dx});a.setTooltip("Maximum adjusted p-value for significance");const d=(0,p.X3)((0,m.Di)(e)??(0,p.Vr)(e)),f=r.input.choice("Organism",{value:d??"Homo sapiens (Human)",items:p.Ae.map(e=>e.display),nullable:!1}),g=r.input.bool("GO: Biological Process",{value:!0}),h=r.input.bool("GO: Molecular Function",{value:!0}),y=r.input.bool("GO: Cellular Component",{value:!0}),E=r.input.bool("KEGG Pathways",{value:!0}),w=r.input.bool("Reactome Pathways",{value:!0}),v=r.input.bool("WikiPathways",{value:!0}),b=r.input.bool("Apply smart pathway filter",{value:!0});b.setTooltip("Drops generic GO parent terms when more specific child terms are present; caps each source at top-N by FDR. Recommended for cleaner results; uncheck for raw g:Profiler output.");const T=r.input.int("Max terms per source",{value:15,min:1});T.setTooltip("Upper bound on terms kept per enrichment source (top-N by FDR). Applies only when the smart pathway filter is on.");const P=()=>T.enabled=b.value??!0;b.onChanged.subscribe(P),P();const S=r.divText(""),N=()=>{const o=n.value??l.M5,r=a.value??l.Dx,s=_(e,o,r,t.log2fc,t.pValue),i=s.total.toLocaleString();S.textContent=`${s.significant} of ${i} proteins are significant with these thresholds`};N(),n.onChanged.subscribe(N),a.onChanged.subscribe(N),r.dialog("Enrichment Analysis").add(S).add(n).add(a).add(f).add(g).add(h).add(y).add(E).add(w).add(v).add(b).add(T).onOK(async()=>{const t=s.TaskBarProgressIndicator.create("Running enrichment analysis...");try{const t=n.value??l.M5,r=a.value??l.Dx,s=f.value,i=p.Ae.find(e=>e.display===s),u=i?.code??"hsapiens";(0,m.Np)(e,u);const d=[];if(g.value&&d.push("GO:BP"),h.value&&d.push("GO:MF"),y.value&&d.push("GO:CC"),E.value&&d.push("KEGG"),w.value&&d.push("REAC"),v.value&&d.push("WP"),0===d.length)return void o.shell.warning("Please select at least one enrichment source");const _=await C(e,t,r,u,d,b.value??!0,T.value??15),P=_.total>0?(_.mapped/_.total*100).toFixed(1):"0.0";o.shell.info(`${_.mapped}/${_.total} proteins mapped (${P}%). ${_.unmapped} unmapped.`),(0,c.q6)(_.enrichmentDf,e)}catch(e){o.shell.error(`Enrichment analysis failed: ${e.message}`)}finally{t.close()}}).show()}},252(e,t,n){"use strict";n.d(t,{$Y:()=>u,Di:()=>d,Np:()=>p,XX:()=>g,Yf:()=>f,applyAnnotation:()=>h,f:()=>m});var o=n(328),r=n(389),s=n(353),a=n.n(s),i=n(641),l=n(655),c=n(935);function u(e,t){e.setTag("proteomics.groups",JSON.stringify(t))}function m(e){const t=e.getTag("proteomics.groups");if(!t)return null;try{return JSON.parse(t)}catch{return null}}function p(e,t){e.setTag("proteomics.organism",t)}function d(e){return e.getTag("proteomics.organism")||void 0}function f(e,t){const n=function(e){const t=(0,l.getRunMeta)(e);if(t)return t;const n=e.getTag("proteomics.spc_run_meta_seed");if(n)try{return JSON.parse(n)}catch{return}}(e),o=m(e);if(!o)return{group1Name:"Control",group1Cols:[],group2Name:"Treatment",group2Cols:[],instrumentId:n?.instrument_id,acquisitionDatetime:n?.acquisition_datetime};const r=new Set(t),s=t=>t.filter(e=>r.has(e)).map(t=>e.col(t)).filter(e=>null!==e);return{group1Name:o.group1.name||"Control",group1Cols:s(o.group1.columns),group2Name:o.group2.name||"Treatment",group2Cols:s(o.group2.columns),instrumentId:n?.instrument_id,acquisitionDatetime:n?.acquisition_datetime}}function g(e){const t=e.columns.toList().filter(e=>e.semType===i.iu.INTENSITY&&e.name.startsWith("log2(")).map(e=>e.name),n=f(e,t),s=r.input.string("Group 1 Name",{value:n.group1Name}),l=r.input.columns("Group 1",{table:e,available:t,value:n.group1Cols}),u=r.input.string("Group 2 Name",{value:n.group2Name}),m=r.input.columns("Group 2",{table:e,available:t,value:n.group2Cols}),p=r.input.string("Instrument",{value:n.instrumentId??"",tooltipText:"Free-text identifier for the instrument that ran this analysis (e.g. QExactive-01). 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Reflect.metadata(e,t)},K=function(e,t){return function(n,o){t(n,o,e)}};const J=new s.Package;function Z(e,t){return"spectronaut-candidates"!==e.getTag("proteomics.source")||(o.shell.warning(`${t} needs per-sample intensities, but this table is a Spectronaut Candidates report (one row per protein per comparison — pre-computed DE only). 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Open it via Proteomics | Visualize | Volcano Plot.`)}return oe(t,e),f(e),t}class se{static async initProteomics(){}static async buildProteomicsTopMenu(){const e={importSpectronautCandidates:()=>se.importSpectronautCandidates(),importSpectronaut:()=>se.importSpectronaut(),importMaxQuant:()=>se.importMaxQuant(),importFragPipe:()=>se.importFragPipe(),importGenericMatrix:()=>se.importGenericMatrix(),annotateExperiment:()=>se.annotateExperiment(),setLog2Scale:()=>se.setLog2Scale(),normalize:()=>se.normalizeProteomics(),impute:()=>se.imputeMissingValues(),differentialExpression:()=>se.differentialExpression(),enrichmentAnalysis:()=>se.enrichmentAnalysis(),exportEnrichmentInputs:()=>se.exportEnrichmentInputs(),computeSpcStatus:()=>se.computeSpcStatus(),showVolcanoPlot:()=>se.showVolcanoPlot(),showHeatmap:()=>se.showHeatmap(),showPcaPlot:()=>se.showPcaPlot(),showGroupMeanCorrelation:()=>se.showGroupMeanCorrelation(),showQcDashboard:()=>se.showQcDashboard(),showSpcDashboard:()=>se.showSpcDashboard(),enrichmentCharts:()=>se.enrichmentCharts(),showAllVisualizations:()=>se.showAllVisualizations(),shareAnalysisForReview:()=>se.shareAnalysisForReview()},t=new WeakSet,n=n=>{n?.type!==s.VIEW_TYPE.TABLE_VIEW||t.has(n)||setTimeout(()=>{if(!t.has(n))try{(function(e,t){if(!(n=e.dataFrame)||!n.getTag("proteomics.source"))return!1;var n;const o=e.ribbonMenu.group("Proteomics");for(const e of H)try{o.remove(e)}catch{}const r={isEnabled:()=>function(e){return e&&"spectronaut-candidates"===e.getTag("proteomics.source")?"Not applicable to a Spectronaut Candidates file — it already carries computed differential expression and has no per-sample intensities. Use Volcano Plot, Enrichment Analysis or the UniProt panel, or import the matching Spectronaut Report for sample-level analyses.":null}(e.dataFrame)},s=o.group("Import");s.item("Spectronaut Candidates...",t.importSpectronautCandidates),s.item("Spectronaut Report...",t.importSpectronaut),s.item("MaxQuant...",t.importMaxQuant),s.item("FragPipe...",t.importFragPipe),s.item("Generic Matrix...",t.importGenericMatrix),o.item("Annotate Experiment...",t.annotateExperiment,null,r);const a=o.group("Analyze");a.item("Set Log2 Scale...",t.setLog2Scale,null,r),a.item("Normalize...",t.normalize,null,r),a.item("Impute Missing Values...",t.impute,null,r),a.item("Differential Expression...",t.differentialExpression,null,r),a.item("Enrichment Analysis...",t.enrichmentAnalysis),a.item("Export Enrichment Inputs...",t.exportEnrichmentInputs),a.item("Compute SPC Status",t.computeSpcStatus,null,r);const i=o.group("Visualize");return i.item("Volcano Plot...",t.showVolcanoPlot),i.item("Heatmap...",t.showHeatmap,null,r),i.item("PCA...",t.showPcaPlot,null,r),i.item("Group-Mean Correlation...",t.showGroupMeanCorrelation,null,r),i.item("QC Dashboard...",t.showQcDashboard,null,r),i.item("SPC Dashboard...",t.showSpcDashboard),i.item("Enrichment Charts...",t.enrichmentCharts),i.item("Show All Visualizations...",t.showAllVisualizations,null,r),o.group("Share").item("Share Analysis for Review...",t.shareAnalysisForReview),!0})(n,e)&&t.add(n)}catch{}},50)};try{for(const e of o.shell.views)n(e)}catch{}o.events.onViewAdded.subscribe(n),o.events.onCurrentViewChanged.subscribe(()=>n(o.shell.v))}static async importSpectronautCandidates(){s.Utils.openFile({accept:".tsv,.txt,.csv",open:async e=>{try{const t=await e.text(),n=await(0,c.R)(t);n.name=e.name.replace(/\.[^.]+$/,""),ne(n),re(n)}catch(e){o.shell.error(`Failed to import Spectronaut Candidates file: ${e?.message??e}`)}}})}static async importSpectronaut(){s.Utils.openFile({accept:".tsv,.txt,.csv",open:async e=>{try{const t=await ee(e)?await(0,l.A)(e):await(0,l.parseSpectronautText)(await e.text());t.name=e.name.replace(/\.[^.]+$/,""),ne(t),o.shell.addTableView(t),o.shell.info(`Imported ${t.rowCount} protein groups from Spectronaut`),f(t)}catch(e){o.shell.error(`Failed to import Spectronaut file: ${e?.message??e}`),o.shell.warning("If this is a very large precursor-level Spectronaut report that fails to stream in-browser, pre-aggregate it to the importable protein-group shape with the bundled duckdb fallback: tools/spectronaut-aggregate.sh <input.tsv>, then re-import the resulting file. See files/demo/README.md for usage.")}}})}static async importMaxQuant(){s.Utils.openFile({accept:".txt,.tsv",open:async e=>{try{const t=await e.text(),n=await(0,i.E)(t);n.name=e.name.replace(/\.[^.]+$/,""),ne(n),o.shell.addTableView(n),o.shell.info(`Imported ${n.rowCount} protein groups`),f(n)}catch(e){o.shell.error(`Failed to import MaxQuant file: ${e?.message??e}`)}}})}static async importFragPipe(){s.Utils.openFile({accept:".tsv,.txt",open:async e=>{try{const t=await e.text(),n=await(0,u.p)(t);n.name=e.name.replace(/\.[^.]+$/,""),ne(n),o.shell.addTableView(n),o.shell.info(`Imported ${n.rowCount} protein groups from FragPipe`),f(n)}catch(e){o.shell.error(`Failed to import FragPipe file: ${e?.message??e}`)}}})}static async importGenericMatrix(){y()}static async annotateExperiment(){const e=o.shell.tv?.dataFrame;e?Z(e,"Annotate Experiment")&&(0,E.XX)(e):o.shell.warning("No table open")}static async setLog2Scale(){const e=o.shell.tv?.dataFrame;e?Z(e,"Set Log2 Scale")&&(0,b.Kb)(e):o.shell.warning("No table open")}static async normalizeProteomics(){const e=o.shell.tv?.dataFrame;e?Z(e,"Normalize")&&(0,C.v5)(e):o.shell.warning("No table open")}static async imputeMissingValues(){const e=o.shell.tv?.dataFrame;e?Z(e,"Impute Missing Values")&&(0,P.UN)(e):o.shell.warning("No table open")}static async differentialExpression(){const e=o.shell.tv,t=e?.dataFrame;e&&t?Z(t,"Differential Expression")&&(0,S.B9)(t,()=>{const n=(0,N.gO)(t);e.addViewer(n)}):o.shell.warning("No table open")}static async computeSpcStatus(){const e=o.shell.tv,t=e?.dataFrame;if(!e||!t)return void o.shell.warning("Open an analyzed file first, then run Compute SPC Status.");if("spectronaut-candidates"===t.getTag("proteomics.source"))return void o.shell.warning("SPC requires per-sample intensities. Re-import this analysis from the Spectronaut PG report (not the Candidates report) to compute SPC.");const n=(0,v.getRunMeta)(t);if(!n||!n.instrument_id||!n.acquisition_datetime)return void o.shell.warning("Open Annotate Experiment to set instrument + acquisition datetime.");const r=(0,E.f)(t);if(!r)return void o.shell.warning("Annotate experimental groups first (Proteomics → Annotate Experiment) — SPC needs Group 1 to compute control-replicate correlation.");r.group1.columns.length<2&&o.shell.info("Group 1 has fewer than 2 samples — control-replicate correlation can't be computed. The other three metrics will still be recorded.");const a=s.TaskBarProgressIndicator.create("Computing SPC status...");try{const e=(0,v.computeSpcMetrics)(t,r,n),s=await(0,_.loadBaseline)(n.instrument_id),a=await(0,_.loadRuns)(n.instrument_id),i=a.find(e=>e.acquisition_datetime===n.acquisition_datetime),l=i?.status??null;let c;if(null===s)c={status:"pass",rulesTripped:[]},o.shell.info(`No baseline locked for ${n.instrument_id} yet — recorded as pass. Define a baseline once at least 4 runs have been computed.`);else{const t={median_intensity:a.map(e=>e.median_intensity),missing_pct:a.map(e=>e.missing_pct),control_corr:a.map(e=>e.control_corr),protein_count:a.map(e=>e.protein_count)};c=(0,v.uV)(e,t,s.metrics,s.rules_enabled??(0,v.kY)())}(0,v.setSpcStatus)(t,e,c);const u={instrument_id:n.instrument_id,acquisition_datetime:n.acquisition_datetime,run_label:t.name,median_intensity:e.median_intensity,missing_pct:e.missing_pct,control_corr:e.control_corr,protein_count:e.protein_count,status:c.status,rules_tripped:c.rulesTripped,source_project_id:null,source_df_name:t.name,computed_at:e.computed_at};await(0,_.upsertRun)(u),null!==l?o.shell.info(`Updated SPC for ${t.name} (previous status: ${l}).`):"pass"===c.status?o.shell.info(`SPC computed: ${t.name} — status: pass.`):"flagged"===c.status?o.shell.info(`SPC computed: ${t.name} — flagged on ${c.rulesTripped.length} rule(s): ${c.rulesTripped.join(", ")}.`):o.shell.info(`SPC computed: ${t.name} — OUT OF CONTROL on ${c.rulesTripped.length} rule(s): ${c.rulesTripped.join(", ")}.`)}finally{a.close()}}static async showVolcanoPlot(){const e=o.shell.tv,t=e?.dataFrame;e&&t?(0,S.RJ)(t,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)")&&await se.volcanoOptions():o.shell.warning("No table open")}static async volcanoOptions(e){const t=o.shell.tv,n=t?.dataFrame;if(!t||!n)return void o.shell.warning("No table open");if(!(0,S.RJ)(n,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)"))return;let a=e;if(!a)for(const e of t.viewers)if(e.type===s.VIEWER.SCATTER_PLOT&&"negLog10P"===e.props.yColumnName){a=e;break}const i=a?(0,N.ur)(n,a):{metric:"adj.p-value",colorDim:"significance"},l=null!=n.col("p-value"),c=l?i.metric:"adj.p-value",u=r.input.choice("Significance metric",{value:c,items:l?["adj.p-value","p-value"]:["adj.p-value"],nullable:!1});u.setTooltip(l?"Y axis, classification and threshold line all switch together":"p-value column not present — only adj.p-value is available");const p=r.input.choice("Color by",{value:i.colorDim,items:["significance","location"],nullable:!1});p.setTooltip("significance = Enriched in g1 / Enriched in g2 / Not significant; location = UniProt subcellular location");const d=r.input.int("Label top N points",{value:(0,N.m2)(n),min:0});d.setTooltip("How many of the most significant proteins get name labels. 0 = none. Labels no longer touch your row selection.");const f=(0,N.GE)(n),g=r.input.float("X-axis max (|log2FC|)",{value:f.xMax??void 0,min:0,nullable:!0});g.setTooltip("Pin the X axis to ±this |log2FC|. Leave empty to auto-scale. Set the same value on two volcanoes to compare them side-by-side.");const h=r.input.float("Y-axis max (−log10 p)",{value:f.yMax??void 0,min:0,nullable:!0});h.setTooltip("Pin the Y axis to 0…this −log10(p). Leave empty to auto-scale. Set the same value on two volcanoes to compare them side-by-side."),r.dialog("Volcano Options").add(u).add(p).add(d).add(g).add(h).onOK(async()=>{const e=u.value??"adj.p-value",r="location"===p.value?"location":"significance";if((0,N.S6)(n,g.value??null,h.value??null),a||(a=(0,N.gO)(n,{topNLabels:0}),t.addViewer(a)),"location"===r&&!n.col(N.fQ)){const e=await o.dapi.userDataStorage.get(A.er).catch(()=>null);0===(e?Object.keys(e).filter(e=>"__schema_v"!==e).length:0)?o.shell.info("Fetching subcellular locations from UniProt — may take a minute or two on first use without cache; subsequent toggles use the cache."):o.shell.info("Resolving subcellular locations from cache.")}const i="location"===r?"Classifying subcellular locations…":"Updating volcano…",l=s.TaskBarProgressIndicator.create(i),c="location"===r;c&&(0,N.DI)(a,i);const f=(e,t,n)=>{const o="fetch-acc"===n?"Fetching subcellular locations":"fetch-gene"===n?"Resolving by gene name":"init-column"===n||"location"===r?"Classifying subcellular locations":"Updating volcano",s=t>0?Math.round(e/t*100):0;if(l.update(s,`${o}: ${e}/${t}`),c){const n=t>1?`${e}/${t} (${s}%)`:"";(0,N.Bb)(a,o,n)}};try{await(0,N.nj)(n,a,e,r,m.M5,m.Dx,f),(0,N.XC)(n,a,d.value??(0,N.m2)(n))}catch(e){o.shell.error(`Volcano update failed: ${e?.message??e}`)}finally{l.close(),c&&a&&(0,N.kX)(a)}}).show()}static async showHeatmap(){const e=o.shell.tv,t=e?.dataFrame;if(!e||!t)return void o.shell.warning("No table open");if(!Z(t,"Heatmap"))return;if(!(0,S.RJ)(t,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)"))return;const n=r.input.int("Top N proteins",{value:50,min:1});n.setTooltip("How many of the most significant proteins (by adj. p-value) to show."),r.dialog("Heatmap Options").add(n).onOK(async()=>{const o=n.value??50,r=s.TaskBarProgressIndicator.create("Creating heatmap...");try{const n=await x(t,{topN:o,title:`Heatmap: Top ${o} DE Proteins`});e.addViewer(n)}finally{r.close()}}).show()}static async showPcaPlot(){const e=o.shell.tv,t=e?.dataFrame;if(!e||!t)return void o.shell.warning("No table open");if(!Z(t,"PCA"))return;const n=(0,E.f)(t);if(!n)return void o.shell.warning("Annotate experimental groups first (Proteomics | Annotate Experiment)");const r=[...n.group1.columns,...n.group2.columns],{viewer:s,pcaDf:a}=F(t,r,n,"PCA: All Groups");a.name=`PCA: ${t.name}`,o.shell.addTableView(a).addViewer(s)}static async showGroupMeanCorrelation(){const e=o.shell.tv,t=e?.dataFrame;if(!e||!t)return void o.shell.warning("No table open");if(!(0,S.RJ)(t,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)"))return;if(!(0,E.f)(t))return void o.shell.warning("Annotate experimental groups first (Proteomics | Annotate Experiment)");const n=(0,G.Z7)(t);e.addViewer(n)}static async showQcDashboard(){const e=o.shell.tv,t=e?.dataFrame;e&&t?Z(t,"QC Dashboard")&&O(t):o.shell.warning("No table open")}static async showSpcDashboard(){await(0,R.r9)()}static async showAllVisualizations(){const e=o.shell.tv,t=e?.dataFrame;if(!e||!t)return void o.shell.warning("No table open");if(!Z(t,"Show All Visualizations"))return;if(!(0,S.RJ)(t,"Run Differential Expression first"))return;const n=(0,E.f)(t),r=(0,N.gO)(t);e.addViewer(r);const a=s.TaskBarProgressIndicator.create("Creating heatmap...");try{const n=await x(t,{title:"Heatmap: Top 50 DE Proteins"});e.addViewer(n)}finally{a.close()}if(n){const e=[...n.group1.columns,...n.group2.columns],{viewer:r,pcaDf:s}=F(t,e,n,"PCA: All Groups");s.name=`PCA: ${t.name}`,o.shell.addTableView(s).addViewer(r)}}static async enrichmentAnalysis(){const e=o.shell.tv?.dataFrame;e?(0,Y.pG)(e):o.shell.warning("No table open")}static async exportEnrichmentInputs(){const e=o.shell.tv?.dataFrame;e?(0,S.RJ)(e,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)")&&(0,T.N)(e):o.shell.warning("No table open")}static async enrichmentCharts(){const e=o.shell.tv,t=e?.dataFrame;if(!t)return void o.shell.warning("No table open");if("true"!==t.getTag("proteomics.enrichment"))return void o.shell.warning("Run Enrichment Analysis first (Proteomics | Enrichment Analysis)");const n=o.shell.tables.filter(e=>"true"===e.getTag("proteomics.de_complete"));if(0===n.length)return o.shell.warning("No protein table with DE results found. Enrichment charts will open without volcano linking."),void(0,z.q6)(t,t);n.length>1&&o.shell.warning(`Multiple protein tables with DE results found; linking enrichment to "${n[0].name}"`),(0,z.q6)(t,n[0])}static async proteomicsDemo(){await async function(){const e=s.TaskBarProgressIndicator.create("Loading proteomics demo…");try{e.update(5,"Importing HYE benchmark (Spectronaut DIA)…");const t=await J.files.readAsText("demo/spectronaut-hye-demo.tsv"),n=await(0,l.parseSpectronautText)(t);n.name="HYE benchmark";const r=o.shell.addTableView(n),a=(0,E.f)(n);if(!a)return void o.shell.warning("Demo: expected two auto-annotated conditions — opened the table without running differential expression.");const i=[...a.group1.columns,...a.group2.columns];e.update(40,"Imputing missing values (KNN)…"),(0,P.Mx)(n,i),n.setTag("proteomics.imputed","true"),e.update(60,"Differential expression (t-test)…"),(0,S.ps)(n,a.group1.columns,a.group2.columns,a.group1.name,a.group2.name),n.setTag("proteomics.de_method","t-test"),e.update(78,"Building volcano and heatmap…");const c=(0,N.gO)(n);r.dockManager.dock(c,s.DOCK_TYPE.RIGHT,null,"Volcano",.5);const u=await x(n,{title:"Heatmap: Top 50 DE Proteins"});r.dockManager.dock(u,s.DOCK_TYPE.DOWN,null,"Heatmap",.45),e.update(90,"Building QC dashboard tab…"),o.shell.addTableView(n).name="HYE benchmark — QC",O(n),o.shell.v=r,f(n,function(e){const t=e.col("adj.p-value"),n=e.col("significant");if(!t)return 0;let o=-1,r=1/0;for(let s=0;s<e.rowCount;s++){if(n&&!n.get(s))continue;if(t.isNone(s))continue;const e=t.get(s);e<r&&(r=e,o=s)}return o<0?0:o}(n)),e.update(100,"Done"),o.shell.info("Proteomics demo: HYE benchmark analyzed end to end (import → impute → differential expression). Yeast and E. coli proteins shift abundance between the two conditions, so the volcano separates the genuinely differential proteins from the constant human background. QC charts are on the second tab; the top hit is selected for its UniProt panel.")}finally{e.close()}}()}static async proteomicsEnrichmentDemo(){await async function(){const e=s.TaskBarProgressIndicator.create("Loading enrichment demo…");try{e.update(10,"Loading human DE result…");const t=await J.files.readAsText("demo/enrichment-demo.csv"),n=s.DataFrame.fromCsv(t);n.name="Treatment vs Control (human)";const r=(e,t)=>{const o=n.col(e);o&&(o.semType=t)};r("Protein ID",m.iu.PROTEIN_ID),r("Gene",m.iu.GENE_SYMBOL),r("log2FC",m.iu.LOG2FC),r("p-value",m.iu.P_VALUE),r("adj.p-value",m.iu.P_VALUE),n.setTag("proteomics.source","generic"),n.setTag("proteomics.de_method","precomputed"),n.setTag("proteomics.de_complete","true"),(0,E.$Y)(n,{group1:{name:"Treatment",columns:[]},group2:{name:"Control",columns:[]}});const a=o.shell.addTableView(n),i=(0,N.gO)(n);a.dockManager.dock(i,s.DOCK_TYPE.RIGHT,null,"Volcano",.5),f(n,0),e.update(45,"Running g:Profiler enrichment (GO / KEGG / Reactome)…");try{const{enrichmentDf:t,mapped:r,total:s}=await(0,Y.D9)(n,m.M5,m.Dx,"hsapiens",["GO:BP","GO:MF","GO:CC","KEGG","REAC","WP"],!0);e.update(90,"Opening enrichment charts…"),(0,z.q6)(t,n).name=`${n.name} — Enrichment`,o.shell.v=a,o.shell.info(`Enrichment demo: ${t.rowCount} over-represented terms across ${r}/${s} genes. Up-regulated proteins are enriched for cell-cycle / mitosis; down-regulated for oxidative phosphorylation. Select a term row to highlight its proteins on the volcano.`)}catch(e){o.shell.warning(`Enrichment demo: g:Profiler enrichment could not run (${e?.message??e}). The DE table and volcano are open — retry via Proteomics | Enrichment Analysis once the service is reachable.`)}e.update(100,"Done")}finally{e.close()}}()}static uniprotPanelWidget(e){return(0,k.ku)(e)}static async shareAnalysisForReview(){const e=o.shell.tv;let t=e?.dataFrame;if(t){if("true"!==t.getTag("proteomics.de_complete")){const e=o.shell.tables.filter(e=>"true"===e.getTag("proteomics.de_complete"));if(0===e.length)return void(0,S.RJ)(t,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)");e.length>1&&o.shell.warning(`Multiple analyzed tables open; sharing "${e[0].name}".`),t=e[0]}await async function(e){if("true"!==e.getTag($.$y))return void o.shell.warning("Run Differential Expression first.");const t=await o.dapi.groups.list(),n=s.Group.defaultGroupsIds?.["All users"],a=(t??[]).filter(e=>!(null==e||e.hidden||e.personal||n&&e.id===n));if(0===a.length)return void o.shell.warning("No teams available to share with. Ask an admin to create a reviewer team.");const i=new Map;for(const e of a){const t=e.friendlyName??e.name??"";t&&!i.has(t)&&i.set(t,e)}const l=Array.from(i.keys()),c=r.input.string("Target",{value:""});c.setTooltip("Free text — your team's name for this target (e.g., MYH7-DMD, muscle-atrophy panel)");const u=r.input.choice("Share with team",{value:l[0],items:l,nullable:!1}),m=r.input.textArea?r.input.textArea("Note for reviewers",{value:""}):r.input.string("Note for reviewers",{value:""}),p=r.input.bool("Verify published dashboard",{value:(0,V.Cb)()});p.setTooltip("Re-open the shared dashboard after publishing to confirm it survives a reload. 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o=n(82),r=n(641),s=n(954),a=n(117),i=n(252);const l=["PG.ProteinGroups","ProteinGroups","Protein Groups"],c=["PG.Genes","Genes","Gene Names"],u=["AVG Log2 Ratio","Log2 Ratio","AVG Log2 Fold Change"],m=["Qvalue","Q-Value","Q.Value","AdjustedPValue","Adjusted P-Value"],p=["Pvalue","PValue","P-Value","P.Value"],d=["Comparison (group1/group2)","Comparison"],f=["AVG Group Quantity Numerator"],g=["AVG Group Quantity Denominator"],h=["Condition Numerator"],y=["Condition Denominator"],E=["contam_","rev_","CON__","REV__"];function w(e,t){for(const n of t){const t=e.col(n);if(t)return t}return null}function v(e,t,n){if(t.name===n)return;const o=e.col(n);o&&o!==t||(t.name=n)}async function _(e){const t=(0,s.T6)(e),n=o.DataFrame.fromCsv(e,{delimiter:t}),_=w(n,l);if(!_)throw new Error(`Spectronaut Candidates: missing protein-group column (expected one of ${l.join(", ")})`);if(!w(n,u))throw new Error(`Spectronaut Candidates: missing log2 ratio column (expected one of ${u.join(", 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t=Array.from(e.proteinMap.keys()),n=t.length,o=r.Column.fromStrings("PG.ProteinGroups",t);o.semType=s.iu.PROTEIN_ID;const a=[o];if(e.organisms.size>0){const n=t.map(t=>e.organisms.get(t)??""),o=r.Column.fromStrings("PG.Organisms",n);a.push(o)}for(const o of e.sampleKeys){const i=new Float32Array(n);for(let s=0;s<n;s++){const n=e.proteinMap.get(t[s]);i[s]=n.has(o)?n.get(o):r.FLOAT_NULL}const l=r.Column.fromFloat32Array(o,i);l.semType=s.iu.INTENSITY,e.sampleFileNames.has(o)&&l.setTag("spectronaut.fileName",e.sampleFileNames.get(o)),a.push(l)}return r.DataFrame.fromColumns(a)}(e);(0,a.wK)(t,"PG.ProteinGroups","Primary Protein ID",s.iu.PROTEIN_ID);const n=e.sampleKeys;return(0,a.eY)(t,n).isLog2?(0,a.l3)(t,n):(0,a.Kh)(t,n),t.setTag("proteomics.preNormalized","true"),t.setTag("proteomics.source","spectronaut"),function(e,t){const n=new Map;for(const e of t){const t=e.lastIndexOf("_"),o=e.substring(0,t);n.has(o)||n.set(o,[]),n.get(o).push(`log2(${e})`)}const 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m=o.shell.tv.dataFrame;if(m.name!==t.expectedName)throw new Error(`assertPublishedShape: df.name: got "${m.name}", expected "${t.expectedName}"`);if(u.name!==t.expectedProjectName)throw new Error(`assertPublishedShape: project.name: got "${u.name}", expected "${t.expectedProjectName}"`);for(const e of t.expectedAllowlist)if(!m.col(e))throw new Error(`assertPublishedShape: allowlist column missing on reopen: "${e}"`);const p=m.columns.toList().map(e=>e.name).filter(e=>!e.startsWith("_meta_")&&!e.startsWith("~"));if(p.length!==t.expectedAllowlist.length){const e=p.filter(e=>!t.expectedAllowlist.includes(e)),n=t.expectedAllowlist.filter(e=>!p.includes(e));throw new Error(`assertPublishedShape: visible column count: got ${p.length}, expected ${t.expectedAllowlist.length}. Unexpected: [${e.join(", ")}]. Missing: [${n.join(", ")}].`)}const d=(0,i.k)(m,a.iu.PROTEIN_ID,["protein id","majority protein id","accession"]);if(null==d)throw new Error("assertPublishedShape: protein-id column not found via findColumn");if(d.semType!==a.iu.PROTEIN_ID)throw new Error(`assertPublishedShape: protein-id semType: got "${d.semType??"null"}", expected "${a.iu.PROTEIN_ID}". 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Plan 04 step 8 catch should invoke the post-open recovery hook from tags ${l.L6.PUBLISHED_FC_THRESHOLD} / ${l.L6.PUBLISHED_P_THRESHOLD} and re-run this assertion once.`)}if(t.expectEnrichment){const e=o.shell.tables;if(!Array.isArray(e)||e.length<2)throw new Error(`assertPublishedShape: expectEnrichment=true but grok.shell.tables has ${e?.length??0} DataFrames (need ≥ 2)`);if(!e.find(e=>{try{const t=e.col(l.MD.PUBLISHED_INCLUDES_ENRICHMENT);return null!=t&&"true"===String(t.get(0))}catch{return!1}}))throw new Error("assertPublishedShape: protein DF (with _meta_published_includes_enrichment=true) not found among reopened tables");if(!e.find(e=>"true"===e.getTag("proteomics.enrichment")))throw new Error("assertPublishedShape: enrichment DF (proteomics.enrichment=true tag) not found among reopened tables")}const E=u.options??{};if(null!=g.supersedes){const e=E[l.L6.SUPERSEDES];if(e!==g.supersedes)throw new Error(`assertPublishedShape: project.options['${l.L6.SUPERSEDES}']: got 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Run Differential Expression to completion before publishing.`);const g=Array.from(new Set([o.name,r?.name,s.name,m.name,u.name,p.name,d?.name].filter(e=>"string"==typeof e&&e.length>0))),h=e.clone(null,g),y=["proteomics.source","proteomics.de_method","proteomics.groups","proteomics.de_complete"];for(const t of y){const n=e.getTag(t);null!=n&&""!==n&&h.setTag(t,n)}(0,a.W7)(h,t);const E=t.publishedAt instanceof Date?t.publishedAt.toISOString().slice(0,10):new Date(String(t.publishedAt)).toISOString().slice(0,10);h.name=`${e.name||"analysis"}_published_${E}`;const w=[[o,i.iu.PROTEIN_ID],[r,i.iu.GENE_SYMBOL],[s,i.iu.LOG2FC],[m,i.iu.P_VALUE]];for(const[e,t]of w){if(null==e)continue;const n=h.col(e.name);null!=n&&(n.semType=t)}const v=t.includesEnrichment?"true":"false",_=[{name:a.MD.PUBLISHED,value:"true",type:"string"},{name:a.MD.PUBLISHED_AT,value:t.publishedAt,type:"datetime"},{name:a.MD.PUBLISHED_BY,value:t.publishedBy,type:"string"},{name:a.MD.PUBLISHED_BY_EMAIL,value:t.publishedByEmail??"",type:"string",emptyForNull:!0},{name:a.MD.PUBLISHED_TARGET,value:t.target,type:"string"},{name:a.MD.PUBLISHED_DE_METHOD,value:t.deMethod,type:"string"},{name:a.MD.PUBLISHED_FC_THRESHOLD,value:String(t.fcThreshold),type:"string"},{name:a.MD.PUBLISHED_P_THRESHOLD,value:String(t.pThreshold),type:"string"},{name:a.MD.PUBLISHED_VERSION,value:String(t.version),type:"string"},{name:a.MD.PUBLISHED_ID,value:t.publishId,type:"string"},{name:a.MD.PUBLISHED_INCLUDES_ENRICHMENT,value:v,type:"string"},{name:a.MD.SUPERSEDES,value:t.supersedes??"",type:"string",emptyForNull:!0},{name:a.MD.SUPERSEDED_BY,value:t.supersededBy??"",type:"string",emptyForNull:!0}];for(const e of _)c(h,e);return h}(e,N),x=A.name;let D=null;S&&(n.description="Trimming enrichment...",D=function(e,t){const n=(0,l.k)(e,"",["term name","term","pathway"]),o=(0,l.k)(e,"",["source"]),r=(0,l.k)(e,"",["fdr","adj.p-value","adj.p","q-value","p-value","pvalue"]),s=(0,l.k)(e,"",["intersection","genes"]),i=(0,l.k)(e,"",["direction","regulation"]),u=(0,l.k)(e,"",["gene ratio"]),m=(0,l.k)(e,"",["gene count"]),p=[["Term Name",n],["Source",o],["significance (FDR / adj.p-value)",r],["Intersection",s]];for(const[e,t]of p)if(null==t)throw new Error(`Cannot publish enrichment: missing required column [${e}]. 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o.dapi.projects.delete($)}catch(e){o.shell.error(`Manual cleanup required: project id ${$.id} could not be deleted: ${e?.message??e}`)}throw new Error(`Round-trip shape verification failed: ${e?.message??e}`)}}if(null!=t.priorVersion){n.description="Updating supersede chain...";const e=t.priorVersion.id;try{const t=await o.dapi.projects.find(e);t.options[a.L6.SUPERSEDED_BY]=$.id,await o.dapi.projects.save(t)}catch(e){o.shell.warning(`Supersede pointer on prior version's options failed: ${e?.message??e} (DataFrame-tag dual-write path below provides fallback).`)}try{o.shell.closeAll(),await(0,s.cb)(100);const t=await o.dapi.projects.find(e);await t.open(),await(0,s.bk)(()=>!!o.shell.tv&&!!o.shell.tv.dataFrame,"supersede stamp: prior project DF did not materialize",5e3);const n=o.shell.tv.dataFrame;n.setTag(a.L6.SUPERSEDED_BY,$.id);const r=n.col(a.MD.SUPERSEDED_BY);if(r)try{r.set(0,$.id)}catch{}await o.dapi.tables.uploadDataFrame(n),await o.dapi.tables.save(n.getTableInfo())}catch(e){o.shell.warning(`Supersede tag could not be stamped on prior version DF: ${e?.message??e} (Project.options pointer was still written — Plan 06 panel falls back to that path)`)}try{$.options[a.L6.SUPERSEDES]=e}catch{}try{await o.dapi.projects.save($)}catch(e){o.shell.warning(`Could not write supersedes pointer on new project options: ${e?.message??e}`)}}n.description="Restoring your analysis...";try{if(o.shell.closeAll(),await(0,s.cb)(100),S)try{(0,p.q6)(S,e)}catch{}const t=o.shell.addTableView(e);try{t.addViewer((0,m.gO)(e))}catch{}}catch{}return n.description="Done.",$}finally{n.close()}}},637(e,t,n){"use strict";n.d(t,{Cb:()=>i,ck:()=>s,sK:()=>a});var o=n(110);function r(e,t){try{const t=o._package?.settings?.[e];if("string"==typeof t&&t.trim().length>0)return t.trim()}catch{}return t}function s(){return r("reviewSpaceName","Proteomics-Reviews")}function a(){return r("reviewNamePrefix","Proteomics-Review")}function i(){try{const 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e=a([["P12345","P12345","BRCA1","","","","1000","2000","500"]],i),n=await(0,r.E)(e);(0,t.E3)(n.getTag("proteomics.source"),"maxquant")}),(0,t.t6)("MaxQuant: iBAQ columns detected as intensity",async()=>{const e=a([["P12345","P12345","BRCA1","","","","1000","2000","500"]],i),n=await(0,r.E)(e);(0,t.E3)(n.col("iBAQ")?.semType,s.iu.INTENSITY),(0,t.E3)(null!==n.col("log2(iBAQ)"),!0)})});var l=n(252),c=n(350),u=n(47),m=n(829);function p(t,n,o,r,a){const i=[];i.push(e.Column.fromStrings("Protein ID",Array.from({length:t},(e,t)=>`P${t}`)));const l=[...n,...o],c=r&&a?[...r,...a]:void 0;for(let n=0;n<l.length;n++){const o=new Float32Array(t);if(c&&c[n])for(let e=0;e<t;e++)o[e]=c[n][e];const r=e.Column.fromFloat32Array(l[n],o);r.semType=s.iu.INTENSITY,i.push(r)}return e.DataFrame.fromColumns(i)}(0,t.L1)("Experiment Setup",()=>{(0,t.t6)("setGroups persists group assignments as tag",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0"]),e.Column.fromFloat32Array("s1",new Float32Array([1]))]);(0,l.$Y)(n,{group1:{name:"Control",columns:["s1"]},group2:{name:"Treatment",columns:["s2"]}});const o=n.getTag("proteomics.groups");(0,t.E3)(null!==o&&""!==o,!0);const r=JSON.parse(o);(0,t.E3)(r.group1.name,"Control"),(0,t.E3)(r.group2.name,"Treatment")}),(0,t.t6)("getGroups returns null for untagged DataFrame",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0"])]),o=(0,l.f)(n);(0,t.E3)(o,null)}),(0,t.t6)("getOrganism returns undefined until set, then round-trips the code",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0"])]);(0,t.E3)(void 0===(0,l.Di)(n),!0),(0,l.Np)(n,"rnorvegicus"),(0,t.E3)((0,l.Di)(n),"rnorvegicus")}),(0,t.t6)("applyAnnotation persists the organism alongside the groups",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0"])]);(0,l.applyAnnotation)(n,{group1:{name:"Control",columns:["s1","s2"]},group2:{name:"Treatment",columns:["s3","s4"]},organism:"rnorvegicus"}),(0,t.E3)((0,l.Di)(n),"rnorvegicus"),(0,t.E3)((0,l.f)(n).group1.name,"Control");const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0"])]);(0,l.applyAnnotation)(o,{group1:{name:"A",columns:["s1"]},group2:{name:"B",columns:["s2"]}}),(0,t.E3)(void 0===(0,l.Di)(o),!0)}),(0,t.t6)("getGroups round-trips GroupAssignment correctly",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0"])]);(0,l.$Y)(n,{group1:{name:"Control",columns:["s1","s2","s3"]},group2:{name:"Treatment",columns:["s4","s5","s6"]}});const o=(0,l.f)(n);(0,t.E3)(null!==o,!0),(0,t.E3)(o.group1.name,"Control"),(0,t.E3)(o.group2.name,"Treatment"),(0,t.E3)(o.group1.columns.length,3),(0,t.E3)(o.group2.columns.length,3),(0,t.E3)(o.group1.columns[0],"s1"),(0,t.E3)(o.group2.columns[2],"s6")}),(0,t.t6)("seedAnnotationDialogInputs returns Control/Treatment defaults when no tag",async()=>{const e=p(3,["s1","s2"],["s3","s4"]),n=(0,l.Yf)(e,["s1","s2","s3","s4"]);(0,t.E3)(n.group1Name,"Control"),(0,t.E3)(n.group2Name,"Treatment"),(0,t.E3)(n.group1Cols.length,0),(0,t.E3)(n.group2Cols.length,0)}),(0,t.t6)("seedAnnotationDialogInputs reads names + columns from existing groups",async()=>{const e=p(3,["s1","s2"],["s3","s4"]);(0,l.$Y)(e,{group1:{name:"DMD",columns:["s1","s2"]},group2:{name:"WT",columns:["s3","s4"]}});const n=(0,l.Yf)(e,["s1","s2","s3","s4"]);(0,t.E3)(n.group1Name,"DMD"),(0,t.E3)(n.group2Name,"WT"),(0,t.E3)(n.group1Cols.length,2),(0,t.E3)(n.group2Cols.length,2),(0,t.E3)(n.group1Cols[0].name,"s1"),(0,t.E3)(n.group2Cols[1].name,"s4")}),(0,t.t6)("seedAnnotationDialogInputs drops column refs not in the DataFrame",async()=>{const e=p(3,["s1","s2"],["s3","s4"]);(0,l.$Y)(e,{group1:{name:"DMD",columns:["s1","gone","s2"]},group2:{name:"WT",columns:["also-gone","s3","s4"]}});const n=(0,l.Yf)(e,["s1","s2","s3","s4"]);(0,t.E3)(n.group1Cols.length,2),(0,t.E3)(n.group2Cols.length,2),(0,t.E3)(n.group1Cols.map(e=>e.name).join(","),"s1,s2"),(0,t.E3)(n.group2Cols.map(e=>e.name).join(","),"s3,s4")}),(0,t.t6)("seedAnnotationDialogInputs drops column refs not in available list",async()=>{const e=p(3,["s1","s2"],["s3","s4"]);(0,l.$Y)(e,{group1:{name:"A",columns:["s1","s2"]},group2:{name:"B",columns:["s3","s4"]}});const n=(0,l.Yf)(e,["s1","s3"]);(0,t.E3)(n.group1Cols.length,1),(0,t.E3)(n.group2Cols.length,1),(0,t.E3)(n.group1Cols[0].name,"s1"),(0,t.E3)(n.group2Cols[0].name,"s3")}),(0,t.t6)("seedAnnotationDialogInputs falls back to defaults when stored names are empty",async()=>{const e=p(3,["s1","s2"],["s3","s4"]);(0,l.$Y)(e,{group1:{name:"",columns:["s1","s2"]},group2:{name:"",columns:["s3","s4"]}});const n=(0,l.Yf)(e,["s1","s2","s3","s4"]);(0,t.E3)(n.group1Name,"Control"),(0,t.E3)(n.group2Name,"Treatment")})}),(0,t.L1)("Normalization",()=>{(0,t.t6)("median normalization shifts column medians to zero",async()=>{const n=e.Column.fromFloat32Array("intensity",new Float32Array([2,4,6,8,10]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3","P4"]),n]);(0,c.aj)(o,["intensity"]);const r=o.col("intensity");(0,t.E3)(Math.abs(r.get(0)- -4)<.01,!0),(0,t.E3)(Math.abs(r.get(1)- -2)<.01,!0),(0,t.E3)(Math.abs(r.get(2)-0)<.01,!0),(0,t.E3)(Math.abs(r.get(3)-2)<.01,!0),(0,t.E3)(Math.abs(r.get(4)-4)<.01,!0)}),(0,t.t6)("median normalization skips null values",async()=>{const n=e.Column.fromFloat32Array("intensity",new Float32Array([2,e.FLOAT_NULL,6,8,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3","P4"]),n]);(0,c.aj)(o,["intensity"]);const r=o.col("intensity");(0,t.E3)(r.isNone(1),!0),(0,t.E3)(r.isNone(4),!0),(0,t.E3)(!r.isNone(0),!0),(0,t.E3)(!r.isNone(2),!0),(0,t.E3)(!r.isNone(3),!0)}),(0,t.t6)("normalization sets proteomics.normalized tag",async()=>{const n=e.Column.fromFloat32Array("intensity",new Float32Array([1,2,3]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2"]),n]);(0,c.aj)(o,["intensity"]),(0,t.E3)(o.getTag("proteomics.normalized"),"true")}),(0,t.t6)("quantile normalization aligns column distributions",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([5,2,3,6])),o=e.Column.fromFloat32Array("s2",new Float32Array([4,14,8,2])),r=e.Column.fromFloat32Array("s3",new Float32Array([3,1,9,7]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY,r.semType=s.iu.INTENSITY;const a=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3"]),n,o,r]);(0,c.VD)(a,["s1","s2","s3"]);const i=[a.col("s1").get(0),a.col("s1").get(1),a.col("s1").get(2),a.col("s1").get(3)],l=[a.col("s2").get(0),a.col("s2").get(1),a.col("s2").get(2),a.col("s2").get(3)],u=[a.col("s3").get(0),a.col("s3").get(1),a.col("s3").get(2),a.col("s3").get(3)];i.sort((e,t)=>e-t),l.sort((e,t)=>e-t),u.sort((e,t)=>e-t);for(let e=0;e<4;e++)(0,t.E3)(Math.abs(i[e]-l[e])<.01,!0),(0,t.E3)(Math.abs(i[e]-u[e])<.01,!0)}),(0,t.t6)("quantile normalization preserves null values",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([5,e.FLOAT_NULL,3,6])),o=e.Column.fromFloat32Array("s2",new Float32Array([4,14,8,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3"]),n,o]);(0,c.VD)(r,["s1","s2"]),(0,t.E3)(r.col("s1").isNone(1),!0),(0,t.E3)(r.col("s2").isNone(3),!0),(0,t.E3)(!r.col("s1").isNone(0),!0),(0,t.E3)(!r.col("s2").isNone(0),!0)}),(0,t.t6)("quantile normalization sets proteomics.normalized tag",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([1,2,3])),o=e.Column.fromFloat32Array("s2",new Float32Array([4,5,6]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2"]),n,o]);(0,c.VD)(r,["s1","s2"]),(0,t.E3)(r.getTag("proteomics.normalized"),"true")}),(0,t.t6)("quantile normalization with < 2 columns returns without error",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([1,2,3]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2"]),n]);(0,c.VD)(o,["s1"]),(0,t.E3)(Math.abs(o.col("s1").get(0)-1)<.01,!0)}),(0,t.t6)("vsnNormalize falls back to quantile on R failure",async()=>{const n=e.Column.fromFloat32Array("log2(s1)",new Float32Array([5,2,3,6])),o=e.Column.fromFloat32Array("log2(s2)",new Float32Array([4,14,8,2]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY;const r=e.Column.fromFloat32Array("s1",new Float32Array([32,4,8,64])),a=e.Column.fromFloat32Array("s2",new Float32Array([16,16384,256,4])),i=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3"]),r,a,n,o]);await(0,c.Nx)(i,["log2(s1)","log2(s2)"]),(0,t.E3)(i.getTag("proteomics.normalized"),"true")})}),(0,t.L1)("Imputation",()=>{(0,t.t6)("MinProb imputation fills all NaN values",async()=>{const n=new Float32Array([10,e.FLOAT_NULL,14,e.FLOAT_NULL,12]),o=e.Column.fromFloat32Array("intensity",n);o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3","P4"]),o]);(0,u.U0)(r,["intensity"]);const a=r.col("intensity");for(let e=0;e<a.length;e++)(0,t.E3)(a.isNone(e),!1)}),(0,t.t6)("imputed values are below the observed mean",async()=>{const n=new Float32Array([10,12,14,16,e.FLOAT_NULL,e.FLOAT_NULL]),o=e.Column.fromFloat32Array("intensity",n);o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3","P4","P5"]),o]);(0,u.U0)(r,["intensity"],1.8,.3);const a=r.col("intensity");(0,t.E3)(a.get(4)<13,!0),(0,t.E3)(a.get(5)<13,!0)}),(0,t.t6)("imputation sets proteomics.imputed tag",async()=>{const n=e.Column.fromFloat32Array("intensity",new Float32Array([1,e.FLOAT_NULL,3]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2"]),n]);(0,u.U0)(o,["intensity"]),(0,t.E3)(o.getTag("proteomics.imputed"),"true")}),(0,t.t6)("kNN imputation fills missing values using nearest neighbors",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([10,11,10.5,12,100])),o=e.Column.fromFloat32Array("s2",new Float32Array([20,21,e.FLOAT_NULL,22,200])),r=e.Column.fromFloat32Array("s3",new Float32Array([30,31,30.5,32,300]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY,r.semType=s.iu.INTENSITY;const a=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3","P4"]),n,o,r]),i=(0,u.Mx)(a,["s1","s2","s3"],3);(0,t.E3)(i,1);const l=a.col("s2").get(2);(0,t.E3)(Math.abs(l-21)<1,!0)}),(0,t.t6)("kNN imputation falls back to column mean when no neighbors have values",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([10,e.FLOAT_NULL,e.FLOAT_NULL])),o=e.Column.fromFloat32Array("s2",new Float32Array([20,e.FLOAT_NULL,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2"]),n,o]),a=(0,u.Mx)(r,["s1","s2"],10);(0,t.E3)(a>=2,!0)}),(0,t.t6)("kNN imputation returns correct count and sets tag",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([1,2,e.FLOAT_NULL,4])),o=e.Column.fromFloat32Array("s2",new Float32Array([5,e.FLOAT_NULL,7,8]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3"]),n,o]),a=(0,u.Mx)(r,["s1","s2"],3);(0,t.E3)(a,2),(0,t.E3)(r.getTag("proteomics.imputed"),"true");for(let e=0;e<4;e++)(0,t.E3)(r.col("s1").isNone(e),!1),(0,t.E3)(r.col("s2").isNone(e),!1)}),(0,t.t6)("imputeZero replaces all nulls with 0",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([1,e.FLOAT_NULL,3,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3"]),n]),r=(0,u.fX)(o,["s1"]);(0,t.E3)(r,2),(0,t.E3)(Math.abs(o.col("s1").get(1)-0)<.01,!0),(0,t.E3)(Math.abs(o.col("s1").get(3)-0)<.01,!0),(0,t.E3)(o.getTag("proteomics.imputed"),"true")}),(0,t.t6)("imputeMean replaces all nulls with column mean",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([2,e.FLOAT_NULL,6,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3"]),n]),r=(0,u.Q2)(o,["s1"]);(0,t.E3)(r,2),(0,t.E3)(Math.abs(o.col("s1").get(1)-4)<.01,!0),(0,t.E3)(Math.abs(o.col("s1").get(3)-4)<.01,!0),(0,t.E3)(o.getTag("proteomics.imputed"),"true")}),(0,t.t6)("imputeMedian replaces all nulls with column median",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([2,e.FLOAT_NULL,6,10,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3","P4"]),n]),r=(0,u.p4)(o,["s1"]);(0,t.E3)(r,2),(0,t.E3)(Math.abs(o.col("s1").get(1)-6)<.01,!0),(0,t.E3)(Math.abs(o.col("s1").get(4)-6)<.01,!0),(0,t.E3)(o.getTag("proteomics.imputed"),"true")})}),(0,t.L1)("Differential Expression",()=>{(0,t.t6)("DE produces correct log2FC sign for known groups",async()=>{const e=["ctrl1","ctrl2","ctrl3"],n=["treat1","treat2","treat3"],o=e.map(()=>Array.from({length:5},()=>5)),r=n.map(()=>Array.from({length:5},()=>10)),s=p(5,e,n,o,r);(0,m.ps)(s,e,n,"Control","Treatment");const a=s.col("log2FC");for(let e=0;e<5;e++)(0,t.E3)(a.get(e)>0,!0)}),(0,t.t6)("DE produces valid p-values between 0 and 1",async()=>{const e=["ctrl1","ctrl2","ctrl3"],n=["treat1","treat2","treat3"],o=p(3,e,n,[[4.8,5.1,5.3],[4.9,5,5.2],[5.1,4.8,5]],[[9.8,10.1,10.3],[9.9,10,10.2],[10.1,9.8,10]]);(0,m.ps)(o,e,n,"Control","Treatment");const r=o.col("p-value"),s=o.col("adj.p-value");for(let e=0;e<3;e++)(0,t.E3)(r.get(e)>=0&&r.get(e)<=1,!0),(0,t.E3)(s.get(e)>=0&&s.get(e)<=1,!0)}),(0,t.t6)("proteins with <2 replicates get null p-values",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein ID",["P0"]),e.Column.fromFloat32Array("ctrl1",new Float32Array([5])),e.Column.fromFloat32Array("ctrl2",new Float32Array([e.FLOAT_NULL])),e.Column.fromFloat32Array("ctrl3",new Float32Array([e.FLOAT_NULL])),e.Column.fromFloat32Array("treat1",new Float32Array([10])),e.Column.fromFloat32Array("treat2",new Float32Array([10.5])),e.Column.fromFloat32Array("treat3",new Float32Array([9.5]))]);(0,m.ps)(n,["ctrl1","ctrl2","ctrl3"],["treat1","treat2","treat3"],"Control","Treatment");const o=n.col("p-value");(0,t.E3)(o.isNone(0),!0)}),(0,t.t6)("significant column marks proteins passing both thresholds",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein ID",["P_significant","P_not_significant"]),e.Column.fromFloat32Array("ctrl1",new Float32Array([5,5])),e.Column.fromFloat32Array("ctrl2",new Float32Array([5.1,5.1])),e.Column.fromFloat32Array("ctrl3",new Float32Array([4.9,4.9])),e.Column.fromFloat32Array("treat1",new Float32Array([12,5.2])),e.Column.fromFloat32Array("treat2",new Float32Array([12.1,4.8])),e.Column.fromFloat32Array("treat3",new Float32Array([11.9,5]))]);(0,m.ps)(n,["ctrl1","ctrl2","ctrl3"],["treat1","treat2","treat3"],"Control","Treatment",1,.05);const o=n.col("significant");(0,t.E3)(o.get(0),!0),(0,t.E3)(o.get(1),!1)}),(0,t.t6)("DE sets proteomics.de_complete tag",async()=>{const e=["ctrl1","ctrl2","ctrl3"],n=["treat1","treat2","treat3"],o=e.map(()=>Array.from({length:2},()=>5)),r=n.map(()=>Array.from({length:2},()=>10)),s=p(2,e,n,o,r);(0,m.ps)(s,e,n,"Control","Treatment"),(0,t.E3)(s.getTag("proteomics.de_complete"),"true")}),(0,t.t6)("D-09: DE dialog defaults to the declared (group1 = numerator) contrast",async()=>{(0,t.E3)((0,m.zV)("DMD","WT"),"DMD vs WT"),(0,t.E3)((0,m.zV)("WT","DMD"),"WT vs DMD")}),(0,t.t6)("D-09: contrast is direction-only — reversing flips sign, not |log2FC|",async()=>{const e=["dmd1","dmd2","dmd3"],n=["wt1","wt2","wt3"],o=e.map(()=>Array.from({length:3},()=>9)),r=n.map(()=>Array.from({length:3},()=>4)),s=p(3,e,n,o,r);(0,m.ps)(s,n,e,"WT","DMD");const a=s.col("log2FC").get(0),i=p(3,e,n,o,r);(0,m.ps)(i,e,n,"DMD","WT");const l=i.col("log2FC").get(0);(0,t.E3)(a>0,!0),(0,t.E3)(l<0,!0),(0,t.E3)(Math.abs(Math.abs(a)-Math.abs(l))<1e-6,!0)}),(0,t.t6)("DE assigns correct semantic types",async()=>{const e=["ctrl1","ctrl2","ctrl3"],n=["treat1","treat2","treat3"],o=e.map(()=>Array.from({length:2},()=>5)),r=n.map(()=>Array.from({length:2},()=>10)),a=p(2,e,n,o,r);(0,m.ps)(a,e,n,"Control","Treatment"),(0,t.E3)(a.col("log2FC").semType,s.iu.LOG2FC),(0,t.E3)(a.col("p-value").semType,s.iu.P_VALUE),(0,t.E3)(a.col("adj.p-value").semType,s.iu.P_VALUE)})}),(0,t.L1)("DE result alignment",()=>{(0,t.t6)("copyDEResultsToFrame realigns by row key, not position",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein 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n=f({headers:["Protein","Intensity A","Intensity B","Intensity C"],rows:[["P12345","1000","2000","3000"],["P67890","4000","5000","6000"]],delimiter:"\t"}),o=(0,d.T6)(n);(0,t.E3)(o,"\t");const r=e.DataFrame.fromCsv(n,{delimiter:"\t"});(0,t.E3)(r.columns.length,4),(0,t.E3)(r.rowCount,2)}),(0,t.t6)("Generic: auto-suggests protein ID column",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein IDs",["P12345"]),e.Column.fromStrings("Gene names",["BRCA1"]),e.Column.fromList(e.COLUMN_TYPE.FLOAT,"Intensity A",[1e3])]),o=(0,d.q2)(n);(0,t.E3)(null!==o,!0),(0,t.E3)(o.name,"Protein IDs")}),(0,t.t6)("Generic: auto-suggests intensity columns",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P12345"]),e.Column.fromList(e.COLUMN_TYPE.FLOAT,"Intensity Sample1",[1e3]),e.Column.fromList(e.COLUMN_TYPE.FLOAT,"LFQ Sample2",[2e3]),e.Column.fromStrings("notes",["some note"])]),o=(0,d.WI)(n);(0,t.E3)(o.length,2),(0,t.E3)(o.includes("Intensity 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i=a.col("CV"),l=a.col("Mean");(0,t.E3)(Math.abs(i.get(0))<.001,!0),(0,t.E3)(Math.abs(l.get(0)-4)<.01,!0),(0,t.E3)(i.get(1)>0,!0)}),(0,t.t6)("Loess/moving-average trend",async()=>{let n=12345;const o=()=>(n=1664525*n+1013904223>>>0,n/4294967295),r=new Float32Array(25),s=new Float32Array(25);for(let e=0;e<25;e++)r[e]=e+1,s[e]=.5*Math.sin(e/5)+.3*(o()-.5);const a=e.DataFrame.fromColumns([e.Column.fromFloat32Array("A",r),e.Column.fromFloat32Array("M",s)]);(0,g.Pq)(a,.5);const i=a.col("MA_trend");(0,t.E3)(null!==i,!0);let l=0;for(let e=0;e<25;e++)i.isNone(e)||l++;(0,t.E3)(l>0,!0);let c=0,u=0,m=0,p=0,d=0,f=0;for(let e=0;e<25;e++){const t=s[e];if(c+=t,u+=t*t,m++,!i.isNone(e)){const t=i.get(e);p+=t,d+=t*t,f++}}const h=u/m-c/m*(c/m),y=d/f-p/f*(p/f);(0,t.E3)(y<h,!0)}),(0,t.t6)("Missingness matrix",async()=>{const n=e.Column.fromFloat32Array("log2(s1)",new Float32Array([5,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY;const o=e.Column.fromFloat32Array("log2(s2)",new Float32Array([e.FLOAT_NULL,3]));o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([n,o]),a=(0,g.ho)(r,["log2(s1)","log2(s2)"]);(0,t.E3)(a.rowCount,2),(0,t.E3)(a.name,"Missing Values");const i=a.col("log2(s1)"),l=a.col("log2(s2)");(0,t.E3)(i.get(0),1),(0,t.E3)(l.get(0),0),(0,t.E3)(i.get(1),0),(0,t.E3)(l.get(1),1)}),(0,t.t6)("Unpivot intensities",async()=>{const n=e.Column.fromStrings("Protein ID",["P0","P1"]);n.semType=s.iu.PROTEIN_ID;const o=e.Column.fromFloat32Array("log2(s1)",new Float32Array([10,e.FLOAT_NULL]));o.semType=s.iu.INTENSITY;const r=e.Column.fromFloat32Array("log2(s2)",new Float32Array([20,30]));r.semType=s.iu.INTENSITY;const a=e.DataFrame.fromColumns([n,o,r]),i=(0,g.j4)(a,["log2(s1)","log2(s2)"]);(0,t.E3)(i.name,"Intensity Distributions"),(0,t.E3)(i.rowCount,3),(0,t.E3)(null!==i.col("ProteinId"),!0),(0,t.E3)(null!==i.col("Sample"),!0),(0,t.E3)(null!==i.col("Intensity"),!0)}),(0,t.t6)("Missing bar data",async()=>{const n=e.Column.fromFloat32Array("log2(ctrl1)",new Float32Array([5,e.FLOAT_NULL,7]));n.semType=s.iu.INTENSITY;const o=e.Column.fromFloat32Array("log2(treat1)",new Float32Array([10,11,12]));o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([n,o]),a=(0,g.rA)(r,["log2(ctrl1)","log2(treat1)"],{group1:{name:"Control",columns:["log2(ctrl1)"]},group2:{name:"Treatment",columns:["log2(treat1)"]}});(0,t.E3)(a.rowCount,2);const i=a.col("MissingPct"),l=a.col("Group");(0,t.E3)(Math.abs(i.get(0)-33.333)<1,!0),(0,t.E3)(Math.abs(i.get(1))<.01,!0),(0,t.E3)(l.get(0),"Control"),(0,t.E3)(l.get(1),"Treatment")})});var h=n(230),y=n(897);(0,t.L1)("Enrichment",()=>{(0,t.t6)("buildEnrichmentDf creates correct schema",async()=>{const e=(0,h.Mz)([{native:"GO:0006915",name:"apoptotic 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splits significant genes by fc sign, shared background",async()=>{const e=new Map([[0,"A"],[1,"B"],[2,"C"],[3,"D"]]),n=new Float32Array([2,-2,.5,-3]),o=new Float32Array([.01,.01,.001,.2]),{upGenes:r,downGenes:s,background:a}=(0,h.Bx)(e,n,o,1,.05);(0,t.E3)(r.length,1),(0,t.E3)(r[0],"A"),(0,t.E3)(s.length,1),(0,t.E3)(s[0],"B"),(0,t.E3)(a.length,4),(0,t.E3)(a.includes("A")&&a.includes("B")&&a.includes("C")&&a.includes("D"),!0),(0,t.E3)(r.some(e=>s.includes(e)),!1)}),(0,t.t6)("splitGenesByDirection skips null fc/p rows",async()=>{const n=new Map([[0,"A"],[1,"B"]]),o=new Float32Array([2,0]),r=new Float32Array([.01,0]);o[1]=e.FLOAT_NULL,r[1]=e.FLOAT_NULL;const{upGenes:s,downGenes:a,background:i}=(0,h.Bx)(n,o,r,1,.05);(0,t.E3)(s.length,1),(0,t.E3)(a.length,0),(0,t.E3)(i.length,2)}),(0,t.t6)("buildEnrichmentDf adds Direction column when label given",async()=>{const e=(0,h.Mz)([{native:"GO:0006915",name:"apoptotic 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e=(0,h.Mz)([{native:"GO:0006915",name:"apoptotic process",source:"GO:BP",p_value:.001,significant:!0,term_size:500,query_size:50,intersection_size:10,effective_domain_size:2e4,precision:.2,recall:.02,intersections:[["IEA"],["IDA"],[],["TAS"]]},{native:"KEGG:04210",name:"Apoptosis",source:"KEGG",p_value:.03,significant:!0,term_size:120,query_size:50,intersection_size:5,effective_domain_size:2e4,precision:.1,recall:.042,intersections:[[],["evidence"],[],[]]},{native:"REAC:R-HSA-109581",name:"Apoptosis",source:"REAC",p_value:.12,significant:!1,term_size:80,query_size:50,intersection_size:3,effective_domain_size:2e4,precision:.06,recall:.0375,intersections:[["IEA"],[],[],[]]}],["TP53","BRCA1","EGFR","MYC"]);(0,t.E3)(e.col("Direction"),null),(0,t.E3)(e.columns.length,8)}),(0,t.t6)("wireEnrichmentToVolcano selects matching proteins, source DF unmutated",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Intersection",["TP53, EGFR"]),e.Column.fromStrings("Direction",["Up"])]),o=e.Column.fromStrings("Gene Symbol",["TP53","EGFR","MYC"]);o.semType=s.iu.GENE_SYMBOL;const r=e.DataFrame.fromColumns([o]),a=(0,y.aB)(n,r);n.currentRowIdx=0,(0,t.E3)(r.selection.trueCount,2),(0,t.E3)(r.selection.get(2),!1),(0,t.E3)(n.rowCount,1),(0,t.E3)(r.rowCount,3),a.unsubscribe()}),(0,t.t6)("ORGANISM_LIST contains 9 entries with valid codes",async()=>{(0,t.E3)(h.Ae.length,9),(0,t.E3)(h.Ae[0].display,"Homo sapiens (Human)"),(0,t.E3)(h.Ae[0].code,"hsapiens");for(const e of h.Ae)(0,t.E3)(e.display.length>0,!0),(0,t.E3)(e.code.length>0,!0)})});var E=n(989);function w(){const t=e.DataFrame.fromColumns([e.Column.fromStrings("Gene names",["G1","G2","G3"]),e.Column.fromFloat32Array("log2FC",new Float32Array([2,-2,.1])),e.Column.fromFloat32Array("adj.p-value",new Float32Array([.01,.01,.5]))]);return t.col("Gene names").semType=s.iu.GENE_SYMBOL,t.col("log2FC").semType=s.iu.LOG2FC,t.col("adj.p-value").semType=s.iu.P_VALUE,t}(0,t.L1)("Enrichment Export",()=>{(0,t.t6)("buildEnrichmentInputsCsv: up/down/background split matches thresholds",async()=>{const{csv:e,counts:n}=(0,E.J)(w(),1,.05);(0,t.E3)(n.up,1,"one up gene"),(0,t.E3)(n.down,1,"one down gene"),(0,t.E3)(n.background,3,"all three genes in background");const o=e.split("\n");(0,t.E3)(o[0],"gene,list","tidy long header"),(0,t.E3)(o.includes("G1,up"),!0,"G1 is up"),(0,t.E3)(o.includes("G2,down"),!0,"G2 is down"),(0,t.E3)(o.includes("G1,background")&&o.includes("G2,background")&&o.includes("G3,background"),!0,"all genes listed as background"),(0,t.E3)(o.includes("G3,up")||o.includes("G3,down"),!1,"G3 stays background-only")}),(0,t.t6)("buildEnrichmentInputsCsv: looser thresholds pull more genes in",async()=>{const{counts:e}=(0,E.J)(w(),0,.6);(0,t.E3)(e.up,2,"G1 and G3 now up"),(0,t.E3)(e.down,1,"G2 still down"),(0,t.E3)(e.background,3,"background unchanged")}),(0,t.t6)("buildEnrichmentInputsCsv: quotes a gene containing a comma",async()=>{const e=w();e.col("Gene names").set(0,"G1,alias");const{csv:n}=(0,E.J)(e,1,.05);(0,t.E3)(n.includes('"G1,alias",up'),!0,"comma-bearing field is CSV-quoted")}),(0,t.t6)("buildEnrichmentInputsCsv: throws without DE columns",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Gene names",["G1"])]);n.col("Gene names").semType=s.iu.GENE_SYMBOL;let o=!1;try{(0,E.J)(n,1,.05)}catch{o=!0}(0,t.E3)(o,!0,"missing log2FC/adj.p-value is an error")})});var v=n(328),_=n(858);function C(t,n){const o=[],r=[],s=[],a=[],i=[],l=[],c=[],u=[],m=[];for(let e=0;e<t;e++){o.push(e%2==0?"GO:BP":"KEGG"),r.push(`GO:${String(e).padStart(7,"0")}`),s.push(n&&0===e?n:`Term ${e+1}`);const t=.001*(e+1);a.push(t),i.push(t),l.push(10-Math.min(e,9)),c.push(.2-.005*e),u.push("TP53, BRCA1"),m.push(t<.05)}const p=e.DataFrame.fromColumns([e.Column.fromStrings("Source",o),e.Column.fromStrings("Term ID",r),e.Column.fromStrings("Term Name",s),e.Column.fromFloat32Array("P-value",new Float32Array(a)),e.Column.fromFloat32Array("FDR",new Float32Array(i)),e.Column.fromInt32Array("Gene Count",new Int32Array(l)),e.Column.fromFloat32Array("Gene Ratio",new Float32Array(c)),e.Column.fromStrings("Intersection",u),e.Column.fromList("bool","Significant",m)]);return p.setTag("proteomics.enrichment","true"),p}function b(){const t=e.Column.fromStrings("Gene Name",["TP53","BRCA1","EGFR","MYC","AKT1"]);return t.semType=s.iu.GENE_SYMBOL,e.DataFrame.fromColumns([t,e.Column.fromFloat32Array("log2FC",new Float32Array([1.5,-2,.5,3,-1])),e.Column.fromFloat32Array("adj.p-value",new Float32Array([.001,.01,.5,1e-4,.04]))])}function T(t,n){t.columns.add(e.Column.fromStrings("Direction",n))}function P(e,t){let n=0;for(const o of e.viewers)o.dataFrame?.dart===t.dart&&n++;return n}function S(e){let t=0;for(const n of e.viewers)t++;return t}function N(e){let t=0;for(let n=0;n<e.length;n++)!0===e.get(n)&&t++;return t}(0,t.L1)("Enrichment Visualization",()=>{(0,t.t6)("prepareEnrichmentChartColumns adds negLog10FDR on the same frame",async()=>{const e=C(20);(0,y.E0)(e,15);const n=e.col(y.bC);(0,t.E3)(null!==n,!0);const o=n.get(0);(0,t.E3)(Math.abs(o-3)<.01,!0),(0,t.E3)(e.rowCount,20)}),(0,t.t6)("prepareEnrichmentChartColumns marks exactly topN terms (no Direction)",async()=>{const e=C(20);(0,y.E0)(e,15);const n=e.col(y.$i);(0,t.E3)(N(n),15)}),(0,t.t6)("prepareEnrichmentChartColumns marks topN per direction",async()=>{const e=C(20);T(e,Array.from({length:20},(e,t)=>t<10?"Up":"Down")),(0,y.E0)(e,5);const n=e.col(y.$i);(0,t.E3)(N(n),10)}),(0,t.t6)("prepareEnrichmentChartColumns marks all when fewer rows than topN",async()=>{const e=C(5);(0,y.E0)(e,15);const n=e.col(y.$i);(0,t.E3)(N(n),5)}),(0,t.t6)("prepareEnrichmentChartColumns is idempotent on re-run",async()=>{const e=C(20);(0,y.E0)(e,15);const n=e.columns.length;(0,y.E0)(e,15),(0,t.E3)(e.columns.length,n)}),(0,t.t6)("wireEnrichmentToVolcano returns EMPTY without gene column",async()=>{const n=C(3),o=e.DataFrame.fromColumns([e.Column.fromStrings("SomeColumn",["A","B","C"])]),r=(0,y.aB)(n,o);(0,t.E3)(r===_.Subscription.EMPTY,!0)}),(0,t.t6)("wireEnrichmentToVolcano selects matching genes on protein DataFrame",async()=>{const e=C(3);e.col("Intersection").set(0,"TP53, BRCA1");const n=b(),o=(0,y.aB)(e,n);(0,t.E3)(o!==_.Subscription.EMPTY,!0),e.currentRowIdx=0,(0,t.E3)(n.selection.get(0),!0),(0,t.E3)(n.selection.get(1),!0),(0,t.E3)(n.selection.get(2),!1),(0,t.E3)(n.selection.get(3),!1),(0,t.E3)(n.selection.get(4),!1),o.unsubscribe()}),(0,t.t6)("wireEnrichmentToVolcano clears selection before new selection",async()=>{const e=C(3);e.col("Intersection").set(0,"TP53"),e.col("Intersection").set(1,"EGFR");const n=b();n.selection.set(4,!0,!1),n.selection.fireChanged();const o=(0,y.aB)(e,n);e.currentRowIdx=0,(0,t.E3)(n.selection.get(4),!1),(0,t.E3)(n.selection.get(0),!0),o.unsubscribe()}),(0,t.t6)("openEnrichmentVisualization docks dot/bar on enrichment view (directional)",async()=>{const e=C(4);T(e,["Up","Up","Down","Down"]),e.name="Enrichment (test B)";const n=b();n.name="Protein (test B)";const o=v.shell.addTableView(n),r=S(o),s=(0,y.q6)(e,n);try{(0,t.E3)(S(o),r,"protein view must not gain dot/bar viewers; gained "+(S(o)-r)),(0,t.E3)(S(s)>=4,!0,`enrichment view should carry ≥4 dot/bar viewers; got ${S(s)}`),(0,t.E3)(P(s,n),0,"enrichment view must not carry a proteinDf-bound volcano"),e.currentRowIdx=0,(0,t.E3)(n.selection.trueCount>=1,!0,"selecting an enrichment row should still highlight matching protein rows")}finally{s.close(),o.close()}}),(0,t.t6)("openEnrichmentVisualization docks dot/bar on enrichment view (single-direction)",async()=>{const e=C(3);e.name="Enrichment (test C)";const n=b();n.name="Protein (test C)";const o=v.shell.addTableView(n),r=S(o),s=(0,y.q6)(e,n);try{(0,t.E3)(S(o),r,"protein view must not gain dot/bar viewers; gained "+(S(o)-r)),(0,t.E3)(S(s)>=2,!0,`enrichment view should carry ≥2 dot/bar viewers; got ${S(s)}`),(0,t.E3)(P(s,n),0,"enrichment view must not carry a proteinDf-bound volcano")}finally{s.close(),o.close()}}),(0,t.t6)("openEnrichmentVisualization switches focus to enrichment TableView",async()=>{const e=C(4);T(e,["Up","Up","Down","Down"]),e.name="Enrichment (test D)";const n=b();n.name="Protein (test D)";const o=v.shell.addTableView(n),r=(0,y.q6)(e,n);try{const n=v.shell.v?.dataFrame?.dart;(0,t.E3)(n===e.dart,!0,"focused view should be the enrichment TableView after enrichment runs")}finally{r.close(),o.close()}}),(0,t.t6)("enrichmentBannerRendersWhenTagSet",async()=>{const e=C(3);e.name="Enrichment (banner-on)",e.setTag("proteomics.enrichment_smart_filtered","true"),e.setTag("proteomics.enrichment_smart_filtered_kept","20"),e.setTag("proteomics.enrichment_smart_filtered_total","47"),e.setTag("proteomics.enrichment_smart_filtered_dropped_parents","3"),e.setTag("proteomics.enrichment_smart_filtered_cap","15");const n=b(),o=(0,y.q6)(e,n);try{const e=o.root.querySelectorAll('[data-smart-filter-banner="true"]');(0,t.E3)(e.length>=1,!0,"banner should be docked when tag is set");const n=e[0].textContent??"";(0,t.E3)(n.includes("Smart pathway filter active"),!0),(0,t.E3)(n.includes("showing 20 of 47 terms"),!0),(0,t.E3)(n.includes("dropped 3 generic parents"),!0),(0,t.E3)(n.includes("capped at 15 per source"),!0),(0,t.E3)(n.includes("Re-run with the filter off"),!0)}finally{o.close()}}),(0,t.t6)("enrichmentBannerAbsentWhenTagUnset",async()=>{const e=C(3);e.name="Enrichment (banner-off)";const n=b(),o=(0,y.q6)(e,n);try{const e=o.root.querySelectorAll('[data-smart-filter-banner="true"]');(0,t.E3)(e.length,0)}finally{o.close()}})});var A=n(53),x=n(110);function D(e){const t=[["R.FileName","R.Condition","R.Replicate","PG.ProteinGroups","PG.Organisms",e.quantityColumn??"PG.IBAQ","EG.Qvalue","PEP.StrippedSequence","EG.ModifiedPeptide","FG.Charge","FG.Id"].join("\t")],n=[{strip:"PEPTIDER",mod:"_PEPTIDER_",charge:"2",fg:"FG1"},{strip:"ANOTHERPEP",mod:"_ANOTHERPEP_",charge:"3",fg:"FG2"}],o=(e,o,r,s,a,i,l)=>{for(const c of n)t.push([e,o,String(r),s,a,i,l,c.strip,c.mod,c.charge,c.fg].join("\t"))};let r=100;for(const t of e.proteins){const n=e.ibaqValues?.get(t.id)??r++;for(const r of e.conditions)for(const s of e.replicates){const a=(e.fileNameTemplate??"file")+`_${r}_${s}`,i=e.qValues?.get(t.id)??.001,l=t.organism??"Homo sapiens";o(a,r,s,t.id,l,String(n),String(i))}}if(e.extraRows){let t=500;for(const n of e.extraRows){const r=n.quantity??t++;for(const t of e.conditions)for(const s of e.replicates){const a=(e.fileNameTemplate??"file")+`_${t}_${s}`,i=n.organism??"Homo sapiens";o(a,t,s,n.id,i,String(r),String(n.qValue))}}}return t.join("\n")}(0,t.L1)("Spectronaut",()=>{const e=[{id:"P12345"},{id:"Q67890"},{id:"O15439"}],n={proteins:e,conditions:["CondA","CondB"],replicates:[1,2]};async function o(e){return await(0,A.A)(new File([e],"fixture.tsv",{type:"text/tab-separated-values"}))}async function r(e){return je.files.readAsText(`demo/${e}`)}function a(e){return e.columns.toList().filter(e=>e.semType===s.iu.INTENSITY&&!e.name.startsWith("log2(")).map(e=>e.name).sort()}function i(e){const t=e.col("Primary Protein ID")??e.col("PG.ProteinGroups"),n=new Map;for(let o=0;o<e.rowCount;o++)n.set(String(t.get(o)),o);return{col:t,map:n}}async function c(e){const t=[],n=v.shell.info.bind(v.shell);v.shell.info=e=>{t.push(String(e))};try{return{df:await o(e),infos:t}}finally{v.shell.info=n}}(0,t.t6)("pivot produces correct protein count",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.rowCount,3)}),(0,t.t6)("pivot produces correct sample column names",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(null!==o.col("CondA_1"),!0),(0,t.E3)(null!==o.col("CondA_2"),!0),(0,t.E3)(null!==o.col("CondB_1"),!0),(0,t.E3)(null!==o.col("CondB_2"),!0)}),(0,t.t6)("CON__ and REV__ prefixed proteins are excluded",async()=>{const e=D({...n,proteins:[{id:"P12345"},{id:"CON__P99999"},{id:"REV__Q11111"}]}),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.rowCount,1),(0,t.E3)(o.col("PG.ProteinGroups").get(0),"P12345")}),(0,t.t6)("rows with numeric EG.Qvalue > threshold are excluded",async()=>{const o=new Map;o.set("P12345",.001),o.set("Q67890",.05),o.set("O15439",.005);const r=D({...n,proteins:e,qValues:o}),s=await(0,A.parseSpectronautText)(r);(0,t.E3)(s.rowCount,2)}),(0,t.t6)("non-numeric EG.Qvalue rows treated as passing",async()=>{const o=new Map;o.set("P12345",.001),o.set("Q67890","Profiled"),o.set("O15439","NaN");const r=D({...n,proteins:e,qValues:o}),s=await(0,A.parseSpectronautText)(r);(0,t.E3)(s.rowCount,3)}),(0,t.t6)("PG.ProteinGroups has PROTEIN_ID semantic type",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.col("PG.ProteinGroups")?.semType,s.iu.PROTEIN_ID)}),(0,t.t6)("intensity columns have INTENSITY semantic type",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.col("CondA_1")?.semType,s.iu.INTENSITY),(0,t.E3)(o.col("CondB_2")?.semType,s.iu.INTENSITY)}),(0,t.t6)("R.FileName stored as spectronaut.fileName tag on intensity columns",async()=>{const e=D({...n,fileNameTemplate:"run"}),o=(await(0,A.parseSpectronautText)(e)).col("CondA_1");if((0,t.E3)(null!==o,!0),o){const e=o.getTag("spectronaut.fileName");(0,t.E3)(null!==e&&""!==e,!0),(0,t.E3)(e.includes("run"),!0)}}),(0,t.t6)("groups auto-populated via setGroups when exactly 2 conditions",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e),r=(0,l.f)(o);(0,t.E3)(null!==r,!0),r&&((0,t.E3)(r.group1.columns.length,2),(0,t.E3)(r.group2.columns.length,2))}),(0,t.t6)("groups not set when more than 2 conditions",async()=>{const e=D({...n,conditions:["CondA","CondB","CondC"]}),o=await(0,A.parseSpectronautText)(e),r=(0,l.f)(o);(0,t.E3)(r,null)}),(0,t.t6)("pre-normalized tag set for raw (non-log2) intensity data",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.getTag("proteomics.preNormalized"),"true")}),(0,t.t6)("pre-normalized tag set when detectLog2Status detects log2-range values",async()=>{const e=new Map;e.set("P12345",15.2),e.set("Q67890",22.7),e.set("O15439",18.1);const o=D({...n,ibaqValues:e}),r=await(0,A.parseSpectronautText)(o);(0,t.E3)(r.getTag("proteomics.preNormalized"),"true")}),(0,t.t6)("both raw and log2 intensity columns present in output",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(null!==o.col("CondA_1"),!0),(0,t.E3)(null!==o.col("log2(CondA_1)"),!0),(0,t.E3)(null!==o.col("log2(CondB_2)"),!0)}),(0,t.t6)("proteomics.source tag set to spectronaut",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.getTag("proteomics.source"),"spectronaut")}),(0,t.t6)("PG.Quantity accepted as alternative to PG.IBAQ",async()=>{const e=D({...n,quantityColumn:"PG.Quantity"}),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.rowCount,3),(0,t.E3)(null!==o.col("CondA_1"),!0),(0,t.E3)(null!==o.col("CondB_2"),!0),(0,t.E3)(o.col("CondA_1")?.semType,s.iu.INTENSITY)}),(0,t.t6)("throws when neither PG.IBAQ nor PG.Quantity is present",async()=>{const e=D({...n,quantityColumn:"PG.Bogus"});let o=!1;try{await(0,A.parseSpectronautText)(e)}catch(e){o=!0,(0,t.E3)(e.message.includes("PG.IBAQ"),!0),(0,t.E3)(e.message.includes("PG.Quantity"),!0)}(0,t.E3)(o,!0)}),(0,t.t6)("demo file produces correct dimensions",async()=>{const e=[];for(let t=0;t<93;t++)e.push({id:`P${String(t).padStart(5,"0")}`});const n=D({proteins:e,conditions:["HYE mix A","HYE mix B"],replicates:[1,2,3,4]}),o=await(0,A.parseSpectronautText)(n);(0,t.E3)(o.rowCount,93);const r=o.columns.toList().filter(e=>e.semType===s.iu.INTENSITY&&!e.name.startsWith("log2("));(0,t.E3)(r.length,8)}),(0,t.t6)("streams precursor fixture",async()=>{const e=await r("spectronaut-hye-precursor.tsv"),n=await o(e);(0,t.E3)(n.rowCount>0,!0);const a=n.columns.toList().find(e=>e.semType===s.iu.INTENSITY&&!e.name.startsWith("log2(")&&(e.name.startsWith("CondA_")||e.name.startsWith("CondB_")));(0,t.E3)(void 0!==a,!0),(0,t.E3)(n.col("PG.ProteinGroups")?.semType,s.iu.PROTEIN_ID)}),(0,t.t6)("sniffIsPrecursor routes by header",async()=>{const e=["R.FileName","R.Condition","R.Replicate","PG.ProteinGroups","PG.Organisms","PG.Quantity","EG.Qvalue","EG.ModifiedPeptide","FG.Charge","PEP.StrippedSequence"].join("\t"),n=["run_CondA_1","CondA","1","P1","Homo sapiens","10","0.001","_PEP_","2","PEP"].join("\t"),o=["R.FileName","R.Condition","R.Replicate","PG.ProteinGroups","PG.Organisms","PG.IBAQ"].join("\t"),r=["run_CondA_1","CondA","1","P1","Homo sapiens","10"].join("\t");(0,t.E3)(await(0,x.sniffIsPrecursor)(new File([e+"\n"+n],"p.tsv")),!0),(0,t.E3)(await(0,x.sniffIsPrecursor)(new File([o+"\n"+r],"pg.tsv")),!1)}),(0,t.t6)("stream path matches text path",async()=>{const e=D(n),r=await(0,A.parseSpectronautText)(e),s=await o(e);(0,t.E3)(s.rowCount,r.rowCount);const c=a(r),u=a(s);(0,t.E3)(u.join(","),c.join(","));for(const e of c)(0,t.E3)(null!==s.col(`log2(${e})`),null!==r.col(`log2(${e})`));(0,t.E3)(s.getTag("proteomics.source"),r.getTag("proteomics.source")),(0,t.E3)(s.getTag("proteomics.preNormalized"),r.getTag("proteomics.preNormalized"));const m=(0,l.f)(r),p=(0,l.f)(s);(0,t.E3)(null!==p,null!==m),m&&p&&((0,t.E3)(p.group1.columns.length,m.group1.columns.length),(0,t.E3)(p.group2.columns.length,m.group2.columns.length));const d=i(r),f=i(s);(0,t.E3)(f.map.size,d.map.size);for(const[e,n]of d.map){const o=f.map.get(e);(0,t.E3)(void 0!==o,!0);for(const e of c){const a=r.col(e),i=s.col(e),l=a.isNone(n),c=i.isNone(o);if((0,t.E3)(c,l),!l&&!c){const e=a.get(n),r=i.get(o);(0,t.E3)(Math.abs(e-r)<=.001,!0)}}}}),(0,t.t6)("streaming filter parity",async()=>{const e=D({...n,proteins:[{id:"KEEP1"},{id:"KEEP2"}],extraRows:[{id:"CON__C1",qValue:.001},{id:"REV__R1",qValue:.001},{id:"HIGHQ",qValue:.05},{id:"PROF",qValue:"Profiled"},{id:"EMPTYQ",qValue:""}]}),r=await o(e),s=r.col("PG.ProteinGroups"),a=new Set;for(let e=0;e<r.rowCount;e++)a.add(String(s.get(e)));(0,t.E3)(a.has("CON__C1"),!1),(0,t.E3)(a.has("REV__R1"),!1),(0,t.E3)(a.has("HIGHQ"),!1),(0,t.E3)(a.has("PROF"),!0),(0,t.E3)(a.has("EMPTYQ"),!0),(0,t.E3)(r.rowCount,4)}),(0,t.t6)("by-design-filtered rows are not counted malformed",async()=>{const e=D({...n,proteins:[{id:"KEEP1"},{id:"KEEP2"}],extraRows:[{id:"CON__C1",qValue:.001},{id:"REV__R1",qValue:.001},{id:"HIGHQ",qValue:.05}]}),{df:o,infos:r}=await c(e),s=o.col("PG.ProteinGroups"),a=new Set;for(let e=0;e<o.rowCount;e++)a.add(String(s.get(e)));(0,t.E3)(a.has("KEEP1"),!0),(0,t.E3)(a.has("KEEP2"),!0),(0,t.E3)(a.has("CON__C1"),!1),(0,t.E3)(a.has("REV__R1"),!1),(0,t.E3)(a.has("HIGHQ"),!1),(0,t.E3)(o.rowCount,2);const i=r.filter(e=>/malformed/i.test(e));(0,t.E3)(i.length,0)}),(0,t.t6)("truncated line is counted malformed",async()=>{const e=D({...n,proteins:[{id:"KEEP1"},{id:"KEEP2"}]})+"\nfile\tCondA\t1",{df:o,infos:r}=await c(e),s=o.col("PG.ProteinGroups"),a=new Set;for(let e=0;e<o.rowCount;e++)a.add(String(s.get(e)));(0,t.E3)(a.has("KEEP1"),!0),(0,t.E3)(a.has("KEEP2"),!0),(0,t.E3)(o.rowCount,2);const i=r.some(e=>/skipped \d+ malformed line\(s\)/.test(e));(0,t.E3)(i,!0)}),(0,t.t6)("empty-protein rows are filtered silently (streaming↔text parity)",async()=>{const e=D({...n,proteins:[{id:"KEEP1"},{id:"KEEP2"}],extraRows:[{id:"",qValue:.001},{id:"",qValue:.002}]}),{df:o,infos:r}=await c(e),s=o.col("PG.ProteinGroups"),a=new Set;for(let e=0;e<o.rowCount;e++)a.add(String(s.get(e)));(0,t.E3)(a.has("KEEP1"),!0),(0,t.E3)(a.has("KEEP2"),!0),(0,t.E3)(a.has(""),!1),(0,t.E3)(o.rowCount,2);const i=r.filter(e=>/malformed/i.test(e));(0,t.E3)(i.length,0)}),(0,t.t6)("both-numeric-casts-null rows are filtered silently (streaming↔text parity)",async()=>{const e=D({...n,proteins:[{id:"KEEP1"},{id:"KEEP2"}],extraRows:[{id:"NULLPAIR",quantity:"NaN",qValue:"NA"}]}),{df:o,infos:r}=await c(e);(0,t.E3)(o.rowCount,2);const s=r.filter(e=>/malformed/i.test(e));(0,t.E3)(s.length,0)}),(0,t.t6)("streaming tag set and groups",async()=>{const e=await o(D(n));(0,t.E3)(e.getTag("proteomics.source"),"spectronaut"),(0,t.E3)(e.getTag("proteomics.preNormalized"),"true");const r=(0,l.f)(e);(0,t.E3)(null!==r,!0),r&&((0,t.E3)(r.group1.columns.length,2),(0,t.E3)(r.group2.columns.length,2))}),(0,t.t6)("streaming output equals duckdb golden",async()=>{const e=JSON.parse(await r("spectronaut-hye-precursor-golden.json")),n=await r("spectronaut-hye-precursor.tsv"),s=await o(n),{map:l}=i(s),c=a(s),u=Object.keys(e);(0,t.E3)(u.length>0,!0);for(const n of u){const o=n.match(/^(.*?)((?:Cond[A-Za-z]+)_\d+)$/);(0,t.E3)(null!==o,!0);const r=o[1],a=o[2],i=l.get(r);(0,t.E3)(void 0!==i,!0);const c=s.col(a);(0,t.E3)(null!==c,!0),(0,t.E3)(c.isNone(i),!1);const u=c.get(i);(0,t.E3)(Math.abs(u-e[n].quantity)<=.001,!0)}const m=new Set;for(const[e,t]of l)for(const n of c)s.col(n).isNone(t)||m.add(`${e}${n}`);const p=new Set(u);(0,t.E3)(m.size,p.size);for(const e of m)(0,t.E3)(p.has(e),!0);for(const e of p)(0,t.E3)(m.has(e),!0)}),(0,t.t6)("duckdb fallback tooling is committed",async()=>{(0,t.E3)(!0,!0),(0,t.E3)(!0,!0),(0,t.E3)("-- Aggregate a long-form Spectronaut Report (peptide/precursor/fragment-level rows)\n-- down to one row per (protein-group × condition × replicate), in the shape\n-- packages/Proteomics/src/parsers/spectronaut-parser.ts expects.\n--\n-- This is the bundled, documented manual fallback (D-05) for a Spectronaut report\n-- too large for the in-browser streaming importer, AND the D-04 equivalence oracle\n-- the Wave-0 golden test pins to.\n--\n-- Template tokens __IN_PATH__ and __OUT_PATH__ are replaced by the shell wrapper\n-- before this script is passed to duckdb. (DuckDB's COPY ... TO does not accept\n-- variables, so we can't use SET VARIABLE here.)\n\n-- Streaming aggregation — duckdb spills to disk if it can't fit memory.\nPRAGMA memory_limit='8GB';\nPRAGMA threads=8;\n\nCOPY (\n SELECT\n \"PG.ProteinGroups\",\n -- DIVERGENCE FROM /tmp/spectronaut-aggregate.sql: the two carry-along\n -- any_value() SELECT terms for the gene-symbol and protein-accession columns\n -- (present in the /tmp original) were DROPPED here. The package's Spectronaut\n -- data (files/demo/spectronaut-hye-mix.tsv and the synthetic precursor\n -- fixture) does not carry those two columns and\n -- pivotSpectronaut/aggToPivotResult never consume them, so they are not part\n -- of the parity contract; keeping them would Binder-Error duckdb on the\n -- fixture (ignore_errors does NOT cover Binder Errors) and the entire Wave-0\n -- oracle chain (golden → sidecar → 12-03 golden test) would have no source.\n --\n -- ============================ WARNING ============================\n -- REFERENCE-FILE-ONLY: the CASE below is a one-off correction for the\n -- mislabeled reference file `2026-05-13 BP DMD WT.tsv` ONLY. Cross-tab\n -- against R.FileName showed every WT* filename tagged DMD and every DMD*\n -- filename tagged WT (24/24); this restores the convention so DE direction\n -- matches what the filenames imply. It is a STRUCTURAL NO-OP on any data\n -- whose R.Condition is not literally 'DMD'/'WT' — including the CondA/CondB\n -- synthetic fixture, which is exactly why this same script doubles as the\n -- D-04 golden oracle without perturbing the golden. The streaming TS\n -- aggregator MUST NOT port this flip (RESEARCH Pitfall 1 — the single\n -- highest-risk parity trap). Do not \"generalize\" or remove it either: the\n -- manual-fallback path still needs it for the mislabeled reference file.\n -- =================================================================\n CASE \"R.Condition\"\n WHEN 'DMD' THEN 'WT'\n WHEN 'WT' THEN 'DMD'\n ELSE \"R.Condition\"\n END AS \"R.Condition\",\n \"R.Replicate\",\n any_value(\"R.FileName\") AS \"R.FileName\",\n -- PG.Quantity is constant per (protein-group, run) in Spectronaut output;\n -- max() collapses the precursor-level duplicates safely.\n max(TRY_CAST(\"PG.Quantity\" AS DOUBLE)) AS \"PG.Quantity\",\n -- Best precursor q-value backing this protein in this run.\n min(TRY_CAST(\"EG.Qvalue\" AS DOUBLE)) AS \"EG.Qvalue\"\n FROM read_csv(\n '__IN_PATH__',\n delim='\\t',\n header=true,\n sample_size=-1, -- scan everything for type inference; columns are messy\n ignore_errors=true, -- tolerate stray malformed lines in a 2.6 GB file\n nullstr=['', 'NaN', 'NA']\n )\n WHERE\n -- Mirror the parser's precursor-level filter: drop EG rows with q-value > 0.01.\n -- Non-numeric q-values (e.g. 'Profiled') pass — same as the TS parser.\n (TRY_CAST(\"EG.Qvalue\" AS DOUBLE) IS NULL OR TRY_CAST(\"EG.Qvalue\" AS DOUBLE) <= 0.01)\n -- Drop decoys / contaminants up front; parser does this too but it's cheaper here.\n AND \"PG.ProteinGroups\" IS NOT NULL\n AND \"PG.ProteinGroups\" NOT LIKE 'CON\\_\\_%' ESCAPE '\\'\n AND \"PG.ProteinGroups\" NOT LIKE 'REV\\_\\_%' ESCAPE '\\'\n GROUP BY \"PG.ProteinGroups\", \"R.Condition\", \"R.Replicate\"\n) TO '__OUT_PATH__' (FORMAT csv, DELIMITER '\\t', HEADER);\n\n-- Summary so we can sanity-check the collapse ratio.\nSELECT\n count(*) AS output_rows,\n count(DISTINCT \"PG.ProteinGroups\") AS proteins,\n count(DISTINCT (\"R.Condition\" || '_' || \"R.Replicate\")) AS samples,\n list(DISTINCT \"R.Condition\") AS conditions\nFROM read_csv('__OUT_PATH__', delim='\\t', header=true);\n".includes("max(TRY_CAST"),!0),(0,t.E3)('#!/usr/bin/env bash\n# Collapse a long-form Spectronaut Report into the protein-group × sample shape\n# the Proteomics package\'s parseSpectronautText parser consumes.\n#\n# This is the documented MANUAL FALLBACK for a Spectronaut report too large for\n# the in-browser streaming importer: run it locally, then import the small\n# aggregated .tsv it produces. It is also the D-04 equivalence oracle the Wave-0\n# golden test pins to (see files/demo/README.md).\n#\n# Run: tools/spectronaut-aggregate.sh <input.tsv> [output.tsv]\n#\n# Requires the `duckdb` CLI on PATH (v1.3.0 used to derive the committed golden).\n\nset -euo pipefail\n\nif [[ $# -lt 1 ]]; then\n echo "Usage: $0 <input.tsv> [output.tsv]" >&2\n exit 1\nfi\n\nIN="$1"\nOUT="${2:-${IN%.tsv}.aggregated.tsv}"\nSQL="$(dirname "$0")/spectronaut-aggregate.sql"\n\nif [[ ! -f "$IN" ]]; then\n echo "Input not found: $IN" >&2\n exit 1\nfi\n\necho "Aggregating: $IN"\necho "Output: $OUT"\n\n# Substitute paths into the SQL template. DuckDB\'s COPY ... TO doesn\'t accept\n# variables, so we materialize the SQL first. SQL single-quote escaping: double up\n# any embedded \' in the paths.\nIN_ESC="${IN//\\\'/\\\'\\\'}"\nOUT_ESC="${OUT//\\\'/\\\'\\\'}"\nTMP_SQL="$(mktemp -t spectronaut-aggregate.XXXXXX.sql)"\ntrap \'rm -f "$TMP_SQL"\' EXIT\nsed -e "s|__IN_PATH__|${IN_ESC}|g" -e "s|__OUT_PATH__|${OUT_ESC}|g" "$SQL" > "$TMP_SQL"\n\nduckdb < "$TMP_SQL"\n\necho\necho "Input size: $(du -h "$IN" | cut -f1)"\necho "Output size: $(du -h "$OUT" | cut -f1)"\n'.includes("spectronaut-aggregate.sql"),!0)})});var L=n(86);function F(e,t){return[t.join("\t"),...e.map(e=>e.join("\t"))].join("\n")}const I=["Comparison (group1/group2)","PG.ProteinGroups","PG.Genes","AVG Log2 Ratio","Qvalue","Pvalue"];function M(e,t,n,o,r,s){return[e,t,n,o,r,s]}function O(t){for(const n of t.viewers)if(n.type===e.VIEWER.FILTERS)return n;return null}function R(t={}){const{withDisplayName:n=!0,withSourceId:o=!0,withFlags:r=!0,withProteinId:a=!0,comparisons:i=["T1 / Control","T2 / Control","T1 / Control","T2 / Control"]}=t,l=[e.Column.fromStrings("Comparison (group1/group2)",i),e.Column.fromList("double","log2FC",Array.from({length:i.length},(e,t)=>t-1.5))];if(a){const t=e.Column.fromStrings("Primary Protein ID",i.map((e,t)=>`P${1e4+t}`));t.semType=s.iu.PROTEIN_ID,l.push(t)}if(n){const t=e.Column.fromStrings("Display Name",i.map((e,t)=>`Gene${t+1}`));t.semType=s.iu.DISPLAY_NAME,l.push(t)}if(o){const t=e.Column.fromStrings("Source ID",i.map((e,t)=>`ENSG${1e4+t}`));t.semType=s.iu.SOURCE_ID,l.push(t)}return r&&l.push(e.Column.fromBitSet("Flags",e.BitSet.create(i.length,e=>e%2==0))),e.DataFrame.fromColumns(l)}function G(e){return[["Comparison (group1/group2)","PG.ProteinGroups","PG.Genes","AVG Log2 Ratio","Qvalue","Pvalue"].join("\t"),...e.map(e=>e.join("\t"))].join("\n")}function k(t){for(const n of t.viewers)if(n.type===e.VIEWER.FILTERS)return!0;return!1}(0,t.L1)("SpectronautCandidates",()=>{(0,t.t6)("parses standard rows",async()=>{const e=F([M("Treatment / Control","P04637","TP53","2.5","1e-5","1e-6"),M("Treatment / Control","P38398","BRCA1","-2.3","1e-4","1e-5")],I),n=await(0,L.R)(e);(0,t.E3)(n.rowCount,2)}),(0,t.t6)("sets proteomics.source to spectronaut-candidates",async()=>{const e=F([M("A / B","P04637","TP53","2.5","1e-5","1e-6")],I),n=await(0,L.R)(e);(0,t.E3)(n.getTag("proteomics.source"),"spectronaut-candidates")}),(0,t.t6)("sets de_complete and de_method tags",async()=>{const e=F([M("A / B","P04637","TP53","2.5","1e-5","1e-6")],I),n=await(0,L.R)(e);(0,t.E3)(n.getTag("proteomics.de_complete"),"true"),(0,t.E3)(n.getTag("proteomics.de_method"),"spectronaut")}),(0,t.t6)("names contrast groups from the Comparison string (volcano legend)",async()=>{const e=F([M("DMT / WT","P04637","TP53","2.5","1e-5","1e-6"),M("DMT / WT","P38398","BRCA1","-2.3","1e-4","1e-5")],I),n=await(0,L.R)(e),o=(0,l.f)(n);(0,t.E3)(null!=o,!0);const r=[o.group1.name,o.group2.name].sort();(0,t.E3)(r[0],"DMT"),(0,t.E3)(r[1],"WT"),(0,t.E3)(o.group1.columns.length,0),(0,t.E3)(o.group2.columns.length,0)}),(0,t.t6)("renames AVG Log2 Ratio to log2FC",async()=>{const e=F([M("A / B","P04637","TP53","2.5","1e-5","1e-6")],I),n=await(0,L.R)(e);(0,t.E3)(null!==n.col("log2FC"),!0),(0,t.E3)(n.col("AVG Log2 Ratio"),null),(0,t.E3)(Math.abs(n.col("log2FC").get(0)-2.5)<.01,!0)}),(0,t.t6)("renames Qvalue to adj.p-value",async()=>{const e=F([M("A / B","P04637","TP53","2.5","0.001","0.0001")],I),n=await(0,L.R)(e);(0,t.E3)(null!==n.col("adj.p-value"),!0),(0,t.E3)(n.col("Qvalue"),null),(0,t.E3)(Math.abs(n.col("adj.p-value").get(0)-.001)<1e-6,!0)}),(0,t.t6)("renames Pvalue to p-value when present",async()=>{const e=F([M("A / B","P04637","TP53","2.5","0.001","0.0001")],I),n=await(0,L.R)(e);(0,t.E3)(null!==n.col("p-value"),!0),(0,t.E3)(n.col("Pvalue"),null)}),(0,t.t6)("works without a Pvalue column",async()=>{const e=F([["P04637","TP53","2.5","0.001"]],["PG.ProteinGroups","PG.Genes","AVG Log2 Ratio","Qvalue"]),n=await(0,L.R)(e);(0,t.E3)(n.rowCount,1),(0,t.E3)(n.col("p-value"),null),(0,t.E3)(null!==n.col("adj.p-value"),!0)}),(0,t.t6)("assigns canonical semantic types",async()=>{const e=F([M("A / B","P04637","TP53","2.5","0.001","0.0001")],I),n=await(0,L.R)(e);(0,t.E3)(n.col("PG.ProteinGroups").semType,s.iu.PROTEIN_ID),(0,t.E3)(n.col("PG.Genes").semType,s.iu.GENE_SYMBOL),(0,t.E3)(n.col("log2FC").semType,s.iu.LOG2FC),(0,t.E3)(n.col("adj.p-value").semType,s.iu.P_VALUE),(0,t.E3)(n.col("p-value").semType,s.iu.P_VALUE)}),(0,t.t6)("computes significant column from |log2FC| >= 1 and adj.p <= 0.05",async()=>{const e=F([M("A / B","P_sig_up","A","2.5","0.001","0.0001"),M("A / B","P_sig_down","B","-1.5","0.001","0.0001"),M("A / B","P_small_fc","C","0.3","0.001","0.0001"),M("A / B","P_big_qvalue","D","2.0","0.5","0.4"),M("A / B","P_just_inside","E","1.01","0.04","0.03")],I),n=(await(0,L.R)(e)).col("significant");(0,t.E3)(n.get(0),!0),(0,t.E3)(n.get(1),!0),(0,t.E3)(n.get(2),!1),(0,t.E3)(n.get(3),!1),(0,t.E3)(n.get(4),!0)}),(0,t.t6)("filters contam_ rows",async()=>{const e=F([M("A / B","P04637","TP53","2.5","0.001","0.0001"),M("A / B","contam_P99999","KRT1","0.1","0.5","0.4")],I),n=await(0,L.R)(e);(0,t.E3)(n.rowCount,1),(0,t.E3)(n.col("PG.ProteinGroups").get(0),"P04637")}),(0,t.t6)("filters rev_ decoy rows",async()=>{const e=F([M("A / B","P04637","TP53","2.5","0.001","0.0001"),M("A / B","rev_P12345","FAKE","0.1","0.5","0.4")],I),n=await(0,L.R)(e);(0,t.E3)(n.rowCount,1)}),(0,t.t6)("throws on missing protein-group column",async()=>{const e=F([["A / B","2.5","0.001"]],["Comparison","AVG Log2 Ratio","Qvalue"]);let n=!1;try{await(0,L.R)(e)}catch(e){n=!0,(0,t.E3)(String(e.message).includes("protein-group"),!0)}(0,t.E3)(n,!0)}),(0,t.t6)("throws on missing log2 ratio column",async()=>{const e=F([["P04637","TP53","0.001"]],["PG.ProteinGroups","PG.Genes","Qvalue"]);let n=!1;try{await(0,L.R)(e)}catch(e){n=!0,(0,t.E3)(String(e.message).includes("log2 ratio"),!0)}(0,t.E3)(n,!0)}),(0,t.t6)("throws on missing q-value column",async()=>{const e=F([["P04637","TP53","2.5"]],["PG.ProteinGroups","PG.Genes","AVG Log2 Ratio"]);let n=!1;try{await(0,L.R)(e)}catch(e){n=!0,(0,t.E3)(String(e.message).includes("q-value"),!0)}(0,t.E3)(n,!0)}),(0,t.t6)("accepts alternative column names (ProteinGroups, Log2 Ratio, Q-Value)",async()=>{const e=F([["P04637","TP53","2.5","0.001"]],["ProteinGroups","Genes","Log2 Ratio","Q-Value"]),n=await(0,L.R)(e);(0,t.E3)(n.rowCount,1),(0,t.E3)(null!==n.col("log2FC"),!0),(0,t.E3)(null!==n.col("adj.p-value"),!0)}),(0,t.t6)("keeps Comparison column for multi-comparison files",async()=>{const e=F([M("Treatment1 / Control","P04637","TP53","2.5","0.001","0.0001"),M("Treatment2 / Control","P04637","TP53","1.8","0.002","0.0005"),M("Treatment1 / 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t=c.get(e);"string"==typeof t&&u.add(t)}for(const e of $){const n=Array.from(u).some(t=>t.includes(e));(0,t.E3)(n,!0)}}),(0,t.t6)("multi-comparison file docks a Comparison Filters viewer",async()=>{const e=await(0,L.R)(G([["T1 / Control","P1","G1","2.0","0.001","0.0001"],["T2 / Control","P2","G2","-1.7","0.002","0.0005"],["T1 / Control","P3","G3","1.2","0.01","0.005"]])),n=v.shell.addTableView(e);try{const o=(0,x.dockComparisonFilterIfMultiContrast)(n,e);(0,t.E3)(o,!0),(0,t.E3)(k(n),!0)}finally{n.close()}}),(0,t.t6)("single-comparison file docks no Filters viewer",async()=>{const e=await(0,L.R)(G([["T1 / Control","P1","G1","2.0","0.001","0.0001"],["T1 / Control","P2","G2","-1.7","0.002","0.0005"]])),n=v.shell.addTableView(e);try{const o=(0,x.dockComparisonFilterIfMultiContrast)(n,e);(0,t.E3)(o,!1),(0,t.E3)(k(n),!1)}finally{n.close()}}),(0,t.t6)("candidates import auto-opens the volcano",async()=>{const n=await(0,L.R)(G([["T1 / Control","P1","G1","2.0","0.001","0.0001"],["T1 / 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e=U([V("P12345","BRCA1","0","0","4096","8192")],j),n=(await(0,B.p)(e)).col("log2(Sample1 MaxLFQ Intensity)");(0,t.E3)(n.isNone(0),!0)}),(0,t.t6)("primary protein ID extracted from semicolon-delimited",async()=>{const e=U([["sp|P12345|BRCA1_HUMAN","P12345;Q67890","BRCA1_HUMAN","BRCA1;BRCA2","500","Homo sapiens","BRCA1 protein","12","10000","12000","15","20000","24000"]],j),n=await(0,B.p)(e),o=n.col("Primary Protein ID");(0,t.E3)(null!==o,!0),o&&(0,t.E3)(o.get(0),"P12345");const r=n.col("Primary Gene Name");(0,t.E3)(null!==r,!0),r&&(0,t.E3)(r.get(0),"BRCA1")}),(0,t.t6)("proteomics.source tag set to fragpipe",async()=>{const e=U([V("P12345","BRCA1","10000","12000","20000","24000")],j),n=await(0,B.p)(e);(0,t.E3)(n.getTag("proteomics.source"),"fragpipe")}),(0,t.t6)("intensity columns survive as raw plus log2 pair",async()=>{const e=U([V("P12345","BRCA1","10000","12000","20000","24000")],j),n=await(0,B.p)(e);(0,t.E3)(null!==n.col("Sample1 MaxLFQ 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o=[...q.group1.columns,...q.group2.columns];(0,c.aj)(n,o),(0,t.E3)(n.getTag("proteomics.normalized"),"true");for(const e of o)(0,t.E3)(Math.abs(n.col(e).stats.med)<1e-4,!0);(0,u.Q2)(n,o),(0,t.E3)(n.getTag("proteomics.imputed"),"true"),(0,m.ps)(n,q.group1.columns,q.group2.columns,"Control","Treatment",1,.05),(0,t.E3)(n.getTag("proteomics.de_complete"),"true"),(0,t.E3)(null!==n.col("log2FC"),!0),(0,t.E3)(null!==n.col("p-value"),!0),(0,t.E3)(null!==n.col("adj.p-value"),!0),(0,t.E3)(null!==n.col("significant"),!0);const r={},a=n.col("Gene");for(let e=0;e<n.rowCount;e++)r[a.get(e)]=e;const i=n.col("log2FC"),p=n.col("significant");for(const e of Y)(0,t.E3)(i.get(r[e])>1,!0),(0,t.E3)(p.get(r[e]),!0);for(const e of z)(0,t.E3)(i.get(r[e])<-1,!0),(0,t.E3)(p.get(r[e]),!0);for(const e of H)(0,t.E3)(Math.abs(i.get(r[e]))<.5,!0),(0,t.E3)(p.get(r[e]),!1)})});var Q=n(623),W=n(70);function K(e){const t=v.dapi.userDataStorage.constructor.prototype,n=t.get,o=t.put;return e.get&&(t.get=e.get),e.put&&(t.put=e.put),()=>{t.get=n,t.put=o}}const J={Nucleus:"#FF6B6B",Cytoplasm:"#ECDC44",Mitochondria:"#45B7D1",ER:"#96CEB4",Golgi:"#FAAFFE","Plasma Membrane":"#DDA0DD",Lysosome:"#F39C12",Peroxisome:"#E17055",Ribosome:"#A29BFE",Extracellular:"#FD79A8",Vesicles:"#FDCB6E",Unknown:"#CCCCCC"};(0,t.L1)("SubcellularLocation",()=>{(0,t.t6)("SEMTYPE.SUBCELLULAR_LOCATION literal is stable",async()=>{(0,t.E3)(s.iu.SUBCELLULAR_LOCATION,"Proteomics-SubcellularLocation")}),(0,t.t6)("every ORGANISM_LIST code has an ORGANISM_TAXONOMY mapping",async()=>{for(const e of h.Ae)(0,t.E3)(typeof Q.JO[e.code],"number"),(0,t.E3)(Q.JO[e.code]>0,!0)}),(0,t.t6)("classifier: subcellular field used before GO fallback",async()=>{(0,t.E3)((0,Q.ZF)("Nucleus {ECO:0000269}.","mitochondrion [GO:0005739]"),"Nucleus")}),(0,t.t6)("classifier: GO used only when subcellular field has no match",async()=>{(0,t.E3)((0,Q.ZF)("","cytoplasm [GO:0005737]"),"Cytoplasm"),(0,t.E3)((0,Q.ZF)("phosphopyruvate 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Unknown is overwritten by a later non-Unknown",async()=>{const e=["Entry\tSubcellular location [CC]\tGO\tReviewed\tGene","P9\t\t\tunreviewed\tG9","P9\tGolgi apparatus.\t\tunreviewed\tG9"].join("\n"),{locByAcc:n}=(0,Q.y)(e);(0,t.E3)(n.get("P9"),"Golgi")}),(0,t.t6)("runWithConcurrency caps in-flight tasks at the supplied limit",async()=>{let e=0,n=0;const o=new Array(20).fill(0).map((e,t)=>t);await(0,Q.Pd)(o,6,async()=>(e++,e>n&&(n=e),await new Promise(e=>setTimeout(e,5)),e--,null)),(0,t.E3)(n<=6,!0,"concurrentMax should be ≤ 6"),(0,t.E3)(n>=2,!0,"should have observed parallel execution")}),(0,t.t6)("getSubcellularLocations emits non-decreasing progress per phase",async()=>{const e=v.dapi.fetchProxy;v.dapi.fetchProxy=async e=>{const t=/accession%3A([A-Z0-9]+)/.exec(e),n=t?t[1]:"P00000";return{ok:!0,status:200,text:async()=>(e=>`Entry\tSubcellular location [CC]\tGO\tReviewed\tGene Names (primary)\n${e}\tNucleus.\t\treviewed\tGENE1\n`)(n)}};const n=K({get:async()=>({}),put:async()=>{}});try{const e=[];for(let t=0;t<250;t++)e.push(`TESTB${String(t).padStart(5,"0")}`);const n=[],o=(e,t,o)=>n.push({done:e,total:t,phase:o});await(0,Q.n0)(e,"hsapiens",o);const r=n.filter(e=>"fetch-acc"===e.phase);(0,t.E3)(r.length,3),(0,t.E3)(r[0].total,3);for(let e=1;e<r.length;e++)(0,t.E3)(r[e].done>=r[e-1].done,!0,"fetch-acc done should be non-decreasing");const s=r[r.length-1];(0,t.E3)(s.done,s.total,"last fetch-acc tuple should have done === total")}finally{v.dapi.fetchProxy=e,n()}}),(0,t.t6)("getSubcellularLocations writes the cache incrementally during fetch",async()=>{const e=v.dapi.fetchProxy;let n=0;v.dapi.fetchProxy=async e=>{const t=0===n++?1e3:6e3;await new Promise(e=>setTimeout(e,t));const o=/accession%3A([A-Z0-9]+)/.exec(e),r=o?o[1]:"P00000";return{ok:!0,status:200,text:async()=>(e=>`Entry\tSubcellular location [CC]\tGO\tReviewed\tGene Names (primary)\n${e}\tNucleus.\t\treviewed\tGENE1\n`)(r)}};let o=0;const r=K({get:async()=>({}),put:async()=>{o++}});try{const e=[];for(let t=0;t<150;t++)e.push(`TESTC${String(t).padStart(5,"0")}`);await(0,Q.n0)(e,"hsapiens"),(0,t.E3)(o>=2,!0,`userDataStorage.put should be called >= 2 times (got ${o})`)}finally{v.dapi.fetchProxy=e,r()}},{timeout:3e4}),(0,t.t6)("STORE export matches the documented userDataStorage key",async()=>{(0,t.E3)(Q.er,"proteomics-subcell-loc")}),(0,t.t6)("ensureLocationColumn short-circuits on accession-set hash match",async()=>{const n=v.dapi.fetchProxy;let o=0;v.dapi.fetchProxy=async e=>{o++;const t=/accession%3A([A-Z0-9]+)/.exec(e),n=t?t[1]:"TESTD00";return{ok:!0,status:200,text:async()=>(e=>`Entry\tSubcellular location [CC]\tGO\tReviewed\tGene Names (primary)\n${e}\tNucleus.\t\treviewed\tGENE1\n`)(n)}};const r=K({get:async()=>({}),put:async()=>{}});try{const n=e.Column.fromStrings("Primary Protein ID",["TESTD01","TESTD02","TESTD03","TESTD04","TESTD05"]);n.semType=s.iu.PROTEIN_ID;const r=e.DataFrame.fromColumns([n]);await(0,W.MC)(r);const a=o;(0,t.E3)(a>=1,!0,"first call should fetch from UniProt"),await(0,W.MC)(r),(0,t.E3)(o,a,"second call on same accession set should short-circuit (no new fetch)"),n.set(0,"TESTD99"),await(0,W.MC)(r),(0,t.E3)(o>a,!0,"third call with mutated accession should fetch again")}finally{v.dapi.fetchProxy=n,r()}}),(0,t.t6)("ensureLocationColumn forwards progress through fetch + emits init-column",async()=>{const n=v.dapi.fetchProxy;v.dapi.fetchProxy=async e=>{const t=/accession%3A([A-Z0-9]+)/.exec(e),n=t?t[1]:"TESTE00";return{ok:!0,status:200,text:async()=>(e=>`Entry\tSubcellular location [CC]\tGO\tReviewed\tGene Names (primary)\n${e}\tNucleus.\t\treviewed\tGENE1\n`)(n)}};const o=K({get:async()=>({}),put:async()=>{}});try{const n=e.Column.fromStrings("Primary Protein ID",["TESTE01","TESTE02","TESTE03"]);n.semType=s.iu.PROTEIN_ID;const o=e.DataFrame.fromColumns([n]),r=[],a=(e,t,n)=>r.push(n);await(0,W.MC)(o,a),(0,t.E3)(r.includes("fetch-acc"),!0,"progress should fire at least once with phase=fetch-acc"),(0,t.E3)(r.includes("init-column"),!0,"progress should fire with phase=init-column after bulk-init"),(0,t.E3)(r[r.length-1],"init-column","init-column should be the final progress phase")}finally{v.dapi.fetchProxy=n,o()}})});var Z=n(935);function X(t,n){return e.DataFrame.fromColumns([e.Column.fromStrings(t,n)])}(0,t.L1)("Organisms",()=>{(0,t.t6)("resolveOrganismCode maps scientific names (incl. strain-qualified) to codes",async()=>{(0,t.E3)((0,Z.qj)("Homo sapiens"),"hsapiens"),(0,t.E3)((0,Z.qj)("Rattus norvegicus"),"rnorvegicus"),(0,t.E3)((0,Z.qj)("Escherichia coli (strain K12)"),"ecoli"),(0,t.E3)((0,Z.qj)("Saccharomyces cerevisiae (strain ATCC 204508 / S288c)"),"scerevisiae")}),(0,t.t6)("resolveOrganismCode returns undefined for unsupported / empty",async()=>{(0,t.E3)(void 0===(0,Z.qj)("Sus 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r.col("Protein ID").semType=s.iu.PROTEIN_ID,r.col("log2FC").semType=s.iu.LOG2FC,r.col("adj.p-value").semType=s.iu.P_VALUE,r}(0,t.L1)("Log2 Scale",()=>{(0,t.t6)("getIntensityOriginals: only the pristine (non-log2) intensity columns",async()=>{const e=te();(0,d.Kh)(e,["Intensity_S1","Intensity_S2"]);const n=(0,ee.ye)(e);(0,t.E3)(n.length,2,"two originals"),(0,t.E3)(n.includes("Intensity_S1")&&n.includes("Intensity_S2"),!0,"includes both raw columns"),(0,t.E3)(n.some(e=>e.startsWith("log2(")),!1,"excludes the log2 copies")}),(0,t.t6)("detectCurrentLog2Applied: transform vs copy is read from the values",async()=>{const e=te();(0,d.Kh)(e,["Intensity_S1","Intensity_S2"]),(0,t.E3)((0,ee.IZ)(e,(0,ee.ye)(e)),"transform","log2(x) columns read as transform");const n=te();(0,d.l3)(n,["Intensity_S1","Intensity_S2"]),(0,t.E3)((0,ee.IZ)(n,(0,ee.ye)(n)),"copy","copied columns read as copy")}),(0,t.t6)("applyLog2Scale: transform→copy rebuilds values, clears stale tags, is idempotent",async()=>{const e=te();(0,d.Kh)(e,["Intensity_S1","Intensity_S2"]),e.setTag("proteomics.normalized","true"),e.setTag("proteomics.de_complete","true"),e.setTag("proteomics.de_method","t-test"),(0,t.E3)(Math.abs(e.col("log2(Intensity_S1)").get(0)-Math.log2(1e3))<.001,!0,"starts transformed");const n=(0,ee.DA)(e,!0);(0,t.E3)(n,!0,"a real scale change returns true"),(0,t.E3)(e.col("log2(Intensity_S1)").get(0),1e3,"value is now the raw copy"),(0,t.E3)((0,ee.IZ)(e,(0,ee.ye)(e)),"copy","now reads as copy"),(0,t.E3)(e.getTag("proteomics.normalized")||"","","normalized tag cleared"),(0,t.E3)(e.getTag("proteomics.de_complete")||"","","de_complete tag cleared"),(0,t.E3)(e.getTag("proteomics.de_method")||"","","de_method tag cleared"),(0,t.E3)((0,ee.ye)(e).length,2,"still exactly two originals"),(0,t.E3)((0,ee.DA)(e,!0),!1,"no-op when scale already matches returns false")}),(0,t.t6)("applyLog2Scale: copy→transform restores the log2 transform",async()=>{const e=te();(0,d.l3)(e,["Intensity_S1","Intensity_S2"]);const n=(0,ee.DA)(e,!1);(0,t.E3)(n,!0,"scale change returns true"),(0,t.E3)(Math.abs(e.col("log2(Intensity_S2)").get(2)-Math.log2(32e3))<.001,!0,"transform re-applied to raw value"),(0,t.E3)((0,ee.IZ)(e,(0,ee.ye)(e)),"transform","reads as transform")}),(0,t.t6)("getIntensityOriginals: empty when no intensity columns",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein ID",["P1","P2"])]);n.col("Protein ID").semType=s.iu.PROTEIN_ID,(0,t.E3)((0,ee.ye)(n).length,0,"no originals"),(0,t.E3)((0,ee.DA)(n,!0),!1,"applyLog2Scale is a no-op with nothing to rescale")})});const oe="Enriched in group1",re="Enriched in group2",se="Not significant";function ae(t){const n=[e.Column.fromStrings("Protein ID",["P1","P2","P3"]),e.Column.fromFloat32Array("log2FC",new Float32Array([2,-2,.1])),e.Column.fromFloat32Array("adj.p-value",new Float32Array([.001,.5,.2]))];!1!==t?.withPValue&&n.push(e.Column.fromFloat32Array("p-value",new Float32Array([.04,.001,.2])));const o=e.DataFrame.fromColumns(n);return o.col("log2FC").semType=s.iu.LOG2FC,o.col("adj.p-value").semType=s.iu.P_VALUE,o.col("Protein ID").semType=s.iu.PROTEIN_ID,o}(0,t.L1)("Volcano",()=>{(0,t.t6)("ensureNegLog10Column: stable name, values re-init in place on metric toggle",async()=>{const e=ae(),n=(0,W.CK)(e,"adj.p-value"),o=e.columns.length,r=e.col(n).get(0),s=(0,W.CK)(e,"p-value");(0,t.E3)(n,s),(0,t.E3)(e.columns.length,o);const a=e.col(s).get(0);(0,t.E3)(Math.abs(r-3)<1e-4,!0),(0,t.E3)(Math.abs(a- -Math.log10(.04))<1e-4,!0),(0,t.E3)(Math.abs(r-a)>1,!0)}),(0,t.t6)("ensureDirectionColumn: parameterized by metric, in-place, ARGB map",async()=>{const e=ae(),n=(0,W.EO)(e,1,.05,"adj.p-value"),o=e.columns.length;(0,t.E3)(e.col(n).get(0),oe),(0,t.E3)(e.col(n).get(1),se),(0,W.EO)(e,1,.05,"p-value"),(0,t.E3)(e.columns.length,o),(0,t.E3)(e.col(n).get(0),oe),(0,t.E3)(e.col(n).get(1),re)}),(0,t.t6)("p-value metric guarded when column absent — stays on 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o=document.getElementById("proteomics-volcano-styles");(0,t.E3)(null!==o,!0,"scoped stylesheet injected"),(0,t.E3)(o.textContent.includes(".d4-vertical")&&o.textContent.includes(".d4-bottom-center"),!0,"hides both axis chips"),(0,t.E3)(o.textContent.includes(".proteomics-volcano"),!0,"rule is scoped"),(0,t.E3)(o.textContent.includes(".d4-vertical-right"),!1,"color selector preserved")}),(0,t.t6)("recomputeVolcano: Y, class, threshold lines stay consistent across Q↔P toggle",async()=>{const e=ae(),n=(0,W.gO)(e,{fcThreshold:1,pThreshold:.05}),o=n.props.yColumnName;await(0,W.nj)(e,n,"p-value","significance",1,.05),(0,t.E3)(n.props.yColumnName,o),(0,t.E3)(n.props.colorColumnName,"direction"),(0,t.E3)(Math.abs(e.col(o).get(1)- -Math.log10(.001))<1e-4,!0),(0,t.E3)(e.col("direction").get(1),re);const r=e.meta.formulaLines.items.length;await(0,W.nj)(e,n,"adj.p-value","significance",1,.05),(0,t.E3)(Math.abs(e.col(o).get(1)- -Math.log10(.5))<1e-4,!0),(0,t.E3)(e.col("direction").get(1),se),(0,t.E3)(e.meta.formulaLines.items.length,r)}),(0,t.t6)("toggle wiring: every metric × colorDim combination drives recomputeVolcano",async()=>{const e=ae(),n=(0,W.gO)(e,{}),o=n.props.yColumnName;for(const r of["adj.p-value","p-value"])for(const s of["significance","location"])await(0,W.nj)(e,n,r,s,1,.05),(0,t.E3)(n.props.yColumnName,o),(0,t.E3)(n.props.colorColumnName,"location"===s?"Subcellular Location":"direction")}),(0,t.t6)("recomputeVolcano: location color dim sets the Subcellular Location column",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein ID",["",""]),e.Column.fromFloat32Array("log2FC",new Float32Array([1,-1])),e.Column.fromFloat32Array("adj.p-value",new Float32Array([.01,.9]))]);n.col("Protein ID").semType=s.iu.PROTEIN_ID;const o=(0,W.gO)(n,{});await(0,W.nj)(n,o,"adj.p-value","location",1,.05),(0,t.E3)(o.props.colorColumnName,"Subcellular Location"),(0,t.E3)(n.col("Subcellular 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[data-volcano-counter], [data-volcano-axis-x], [data-volcano-axis-y]").forEach(e=>e.remove())}}),(0,t.t6)("ensureLocationColumn short-circuits warm-cache path within one tick",async()=>{const n=e.Column.fromStrings("Primary Protein ID",["P12345","P67890","P11111"]);n.semType=s.iu.PROTEIN_ID;const o=e.DataFrame.fromColumns([n,e.Column.fromFloat32Array("log2FC",new Float32Array([1.5,-2,.5])),e.Column.fromFloat32Array("adj.p-value",new Float32Array([.001,.01,.5]))]),r=function(e){const t=v.dapi.userDataStorage.constructor.prototype,n=t.get,o=t.put;return e.get&&(t.get=e.get),e.put&&(t.put=e.put),()=>{t.get=n,t.put=o}}({get:async()=>({P12345:"Cytoplasm",P67890:"Nucleus",P11111:"Membrane",__schema_v:"13-04-1"}),put:async()=>{}});try{const e=[],n=(t,n,o)=>{e.push(`${o}:${t}/${n}`)};await(0,W.MC)(o,n);const r=o.col("Subcellular Location")?.getTag("proteomics.location_acc_hash");(0,t.E3)(null!=r&&r.length>0,!0,"hash tag should be set after first ensureLocationColumn call"),e.length=0;const s=performance.now();await(0,W.MC)(o,n);const a=performance.now()-s;(0,t.E3)(a<50,!0,`short-circuit path should complete in <50ms; took ${a}ms`),(0,t.E3)(1===e.length&&"init-column:1/1"===e[0],!0,`short-circuit should emit exactly one init-column tick; got ${JSON.stringify(e)}`)}finally{r()}}),(0,t.t6)("axis-max override: set/get round-trips, pins symmetric X + 0-based Y, empty clears",async()=>{const e=ae(),n=(0,W.gO)(e,{topNLabels:0});(0,t.E3)(null===(0,W.GE)(e).xMax,!0,"xMax defaults to null"),(0,t.E3)(null===(0,W.GE)(e).yMax,!0,"yMax defaults to null"),(0,W.S6)(e,5,8);const o=(0,W.GE)(e);(0,t.E3)(o.xMax,5,"xMax round-trips"),(0,t.E3)(o.yMax,8,"yMax round-trips"),(0,W.f0)(n,e),(0,t.E3)(n.props.xMin,-5,"X pins symmetric: xMin = -xMax"),(0,t.E3)(n.props.xMax,5,"X pins symmetric: xMax"),(0,t.E3)(n.props.yMin,0,"Y pins from 0"),(0,t.E3)(n.props.yMax,8,"Y pins to yMax"),(0,W.S6)(e,null,null),(0,t.E3)(null===(0,W.GE)(e).xMax,!0,"xMax cleared"),(0,t.E3)(null===(0,W.GE)(e).yMax,!0,"yMax 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e=ae(),n=(0,W.gO)(e,{topNLabels:0});(0,t.E3)(e.getTag(W.j9),"adj.p-value"),await(0,W.nj)(e,n,"p-value","significance",1,.05),(0,t.E3)(e.getTag(W.j9),"p-value"),await(0,W.nj)(e,n,"adj.p-value","location",1,.05),(0,t.E3)(e.getTag(W.j9),"adj.p-value")}),(0,t.t6)("volcanoCounterRenders: heading + Total + per-direction rows",async()=>{const n=new Float32Array([3,2,-3,-2,.1,.5]),o=new Float32Array([.001,.01,.001,.01,.5,.3]),r=e.DataFrame.fromColumns([e.Column.fromStrings("Protein ID",["P0","P1","P2","P3","P4","P5"]),e.Column.fromFloat32Array("log2FC",n),e.Column.fromFloat32Array("adj.p-value",o)]);r.col("Protein ID").semType=s.iu.PROTEIN_ID,r.col("log2FC").semType=s.iu.LOG2FC,r.col("adj.p-value").semType=s.iu.P_VALUE,(0,l.$Y)(r,{group1:{name:"DMD",columns:[]},group2:{name:"WT",columns:[]}});const a=(0,W.gO)(r,{topNLabels:0}),i=()=>a.root.querySelector("[data-volcano-counter]")?.textContent??"";await(0,t.bk)(()=>i().includes("Visible Proteins"),"volcano counter overlay never 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e=ne(20),n=(0,W.gO)(e,{topNLabels:0});e.filter.setAll(!1),e.filter.fireChanged(),await(0,t.bk)(()=>(n.root.querySelector("[data-volcano-counter]")?.textContent??"").includes("Total: 0"),"volcano counter Total did not reach 0 on empty filter",3e3)},{skipReason:"Quarantined: counter overlay not refreshing on filter change on newer Datagrok runtime — see BACKLOG"}),(0,t.t6)("volcanoCounterSubscriptionsDisposedOnReentry: only one overlay remains after re-create",async()=>{const e=ne(50);(0,W.gO)(e,{topNLabels:0});const n=(0,W.gO)(e,{topNLabels:0}).root.querySelectorAll("[data-volcano-counter]");(0,t.E3)(n.length,1)}),(0,t.t6)("volcanoCounterLocationMode: per-location rows after color switch",async()=>{const e=ne(20);e.col("Protein ID").semType=s.iu.PROTEIN_ID;const n=(0,W.gO)(e,{topNLabels:0});await(0,W.nj)(e,n,"adj.p-value","location",1,.05),await(0,t.bk)(()=>(n.root.querySelector("[data-volcano-counter]")?.textContent??"").includes("Unknown"),"volcano counter did not show a location row 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Response(null==e?null:JSON.stringify(e),{status:n,headers:o})}async function ce(e,t){const n=v.dapi,o=Object.getPrototypeOf(n),r=Object.prototype.hasOwnProperty.call(n,"fetchProxy"),s=r?n.fetchProxy:void 0,a=o.fetchProxy;n.fetchProxy=e,o.fetchProxy=e;try{await t()}finally{r?n.fetchProxy=s:delete n.fetchProxy,o.fetchProxy=a}}async function ue(e,t){const n=v.dapi.userDataStorage,o=Object.getPrototypeOf(n),r=o.get,s=o.put;o.get=async t=>e.get(t)??null,o.put=async(t,n)=>{e.set(t,n)};try{await t()}finally{o.get=r,o.put=s}}async function me(e){const t=[],n=v.shell,o=n.warning;n.warning=e=>{t.push(e)};try{await e()}finally{n.warning=o}return t}function pe(e){return{native:e.native??`NS:${e.name}`,name:e.name,source:e.source,p_value:e.p_value,significant:e.significant??!0,term_size:e.term_size??100,query_size:e.query_size??50,intersection_size:e.intersection_size??5,effective_domain_size:e.effective_domain_size??2e4,precision:e.precision??.1,recall:e.recall??.05,intersections:e.intersections??[]}}(0,t.L1)("Proteomics: 14-01",()=>{(0,t.t6)("geneLabelResolverSemTypes: SEMTYPE constants are the locked strings",async()=>{(0,t.E3)(s.iu.DISPLAY_NAME,"Proteomics-DisplayName"),(0,t.E3)(s.iu.SOURCE_ID,"Proteomics-SourceId"),(0,t.E3)(s.iu.NUMERATOR_MEAN,"Proteomics-NumeratorMean"),(0,t.E3)(s.iu.DENOMINATOR_MEAN,"Proteomics-DenominatorMean");const e=new Set([s.iu.DISPLAY_NAME,s.iu.SOURCE_ID,s.iu.NUMERATOR_MEAN,s.iu.DENOMINATOR_MEAN,s.iu.PROTEIN_ID,s.iu.GENE_SYMBOL,s.iu.INTENSITY,s.iu.LOG2FC,s.iu.P_VALUE,s.iu.SUBCELLULAR_LOCATION]);(0,t.E3)(e.size,10)}),(0,t.t6)("geneLabelResolverDetectorMirror: SEMTYPE values are valid Column.semType 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Additional sentence."),"Transport"),(0,t.E3)((0,ie.qo)("Myosin heavy chain_RAT"),"Myosin heavy chain"),(0,t.E3)((0,ie.qo)(""),null),(0,t.E3)((0,ie.qo)(null),null),(0,t.E3)((0,ie.qo)("uncharacterized protein"),null)}),(0,t.t6)("applyMarkerRules: appends * and † per CK-omics line 1011",async()=>{(0,t.E3)((0,ie.KK)("Myh7",!1,!0),"Myh7†"),(0,t.E3)((0,ie.KK)("Myh7",!0,!0),"Myh7*†"),(0,t.E3)((0,ie.KK)("LOC123",!1,!0),"LOC123†"),(0,t.E3)((0,ie.KK)("Tnnt3",!1,!1),"Tnnt3"),(0,t.E3)((0,ie.KK)("Tnnt3",!0,!1),"Tnnt3*")}),(0,t.t6)("lookupEnsemblBatch: POSTs ids and parses response",async()=>{let e,n="";await ce(async(t,o)=>(n=t,e=o,le({ENSRNOG00000001:{external_name:"Myh7",description:"Myosin heavy chain 7"},ENSRNOG00000002:null})),async()=>{const o=await(0,ie.FH)(["ENSRNOG00000001","ENSRNOG00000002"]);(0,t.E3)(n,"https://rest.ensembl.org/lookup/id"),(0,t.E3)(e?.method,"POST");const r=JSON.parse(e?.body??"{}");(0,t.E3)(Array.isArray(r.ids),!0),(0,t.E3)(r.ids.length,2),(0,t.E3)(o.size,1),(0,t.E3)(o.get("ENSRNOG00000001")?.external_name,"Myh7")})}),(0,t.t6)("lookupEnsemblBatch: retries once on 429 with Retry-After",async()=>{let e=0;await ce(async()=>(e++,1===e?le(null,{status:429,retryAfter:"0"}):le({ENSG00000001:{external_name:"TP53"}})),async()=>{const n=await(0,ie.FH)(["ENSG00000001"]);(0,t.E3)(e,2),(0,t.E3)(n.get("ENSG00000001")?.external_name,"TP53")})}),(0,t.t6)("resolveGeneLabels: no-op path still creates Display Name + Source ID columns",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein ID",["P12345","Q67890","O11111"]),e.Column.fromStrings("Gene name",["Myh7","Tnnt3","Actb"])]);n.col("Gene name").semType=s.iu.GENE_SYMBOL,n.col("Protein ID").semType=s.iu.PROTEIN_ID,await ce(async()=>{throw new Error("should not fetch")},async()=>{await(0,ie.rv)(n)});const o=n.col("Display Name"),r=n.col("Source 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t=Ae();t.setTag("proteomics.source","spectronaut-candidates"),t.setTag("proteomics.de_method","spectronaut"),t.name="fixture-with-enrichment";const n=new Float32Array([.005,.01,.015,.02,.03,.05]),o=e.DataFrame.fromColumns([e.Column.fromStrings("Term Name",["Term A","Term B","Term C","Term D","Term E","Term F"]),e.Column.fromStrings("Source",["GO:BP","KEGG","GO:BP","GO:BP","KEGG","REAC"]),e.Column.fromFloat32Array("FDR",n),e.Column.fromStrings("Intersection",["ALPHA,BETA,GAMMA","DELTA,EPSILON","ETA,THETA","IOTA,KAPPA","ALPHA,DELTA","BETA,GAMMA,ETA"])]);return o.setTag("proteomics.enrichment","true"),o.name="enrichment-fixture",{protein:t,enrichment:o}}async function De(){const t=e.Group.defaultGroupsIds?.Test;if(t)try{const e=await v.dapi.groups.find(t);if(e)return e}catch{}const n=v.shell.user?.group?.id,o=await v.dapi.groups.list();return(o??[]).find(e=>e&&!e.hidden&&!e.personal&&e.id!==n)||(o??[])[0]}function 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p=u.selection.trueCount;m.currentRowIdx=0,await(0,t.cb)(150);const d=u.selection.trueCount;(0,t.E3)(d>p,!0)}finally{await Fe(a),await Ie(r)}}),(0,t.t6)("workspace restore (Step 10) brings back BOTH the protein and enrichment views",async()=>{const{protein:e,enrichment:n}=xe(),o=v.shell.addTableView(e);await(0,t.cb)(50),v.shell.addTableView(n),await(0,t.cb)(100);try{v.shell.v=o}catch{}await(0,t.cb)(50);const r=`${Se}restore-${Date.now()}`,s={target:r,reviewerGroup:await De(),note:"restore test",priorVersion:null,verify:!1};let a=null;try{a=await(0,be.M)(e,s),(0,t.E3)(!!a,!0),await(0,t.cb)(200);const o=e.dart,r=n.dart;let i=!1,l=!1;for(const e of v.shell.tableViews){const t=e.dataFrame?.dart;t===o&&(i=!0),t===r&&(l=!0)}(0,t.E3)(i,!0),(0,t.E3)(l,!0),(0,t.E3)(v.shell.tv?.dataFrame?.dart,o)}finally{await Fe(a),await Ie(r)}}),(0,t.t6)("source mutation after publish leaves clone unchanged (Pitfall 1)",async()=>{const 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e=c+u-2,t=(a*(c-1)+l*(u-1))/e,n=Math.sqrt(c*u/(c+u))*(r-s)/t;m=1-i.studentt.cdf(n,e),p=i.studentt.cdf(n,e),d=2*(p<m?p:m)}else{const e=a/c,t=l/u,n=(r-s)/Math.sqrt(e+t),o=Math.pow(e+t,2)/(Math.pow(e,2)/(c-1)+Math.pow(t,2)/(u-1));p=i.studentt.cdf(n,o),m=1-p,d=2*(p<m?p:m)}return{"p-value":d,"Mean difference":r-s,"p-value more":m,"p-value less":p}}!function(e){e.indexesOf=function(e,t){const n=[];for(let o=0;o<e.length;o++)t(e[o])&&n.push(o);return n},e.genRange=function(e,t,n=!1){const o=t-e+(n?0:1),r=new Int32Array(o);for(let t=0;t<o;++t)r[t]=e+t;return r},e.argSort=function(e,t=!1){const n=t?(e,t)=>t[0]-e[0]:(e,t)=>e[0]-t[0];return e.map((e,t)=>[e,t]).sort(n).map(e=>e[1])}}(o||(o={}));const c={"+":(e,t)=>e+t,"-":(e,t)=>e-t,"*":(e,t)=>e*t,"/":(e,t)=>e/t,min:(e,t)=>e<t?e:t,max:(e,t)=>e>t?e:t};var u=n(641),m=n(252);function p(e,t){return"true"===e.getTag("proteomics.de_complete")||(r.shell.warning(t),!1)}function d(e,t,n){const o=[];for(const r of t){const 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v=e.columns.addNewFloat("log2FC"),_=e.columns.addNewFloat("p-value"),C=e.columns.addNewFloat("adj.p-value");v.init(e=>g[e]),_.init(e=>h[e]),C.init(e=>y[e]),e.columns.addNewBool("significant").init(e=>{const t=y[e],n=g[e];return t!==a.FLOAT_NULL&&n!==a.FLOAT_NULL&&Math.abs(n)>=i&&t<=m}),v.semType=u.iu.LOG2FC,_.semType=u.iu.P_VALUE,C.semType=u.iu.P_VALUE,e.setTag("proteomics.de_complete","true"),e.fireValuesChanged();const b=E.length;return{tested:b,untestable:e.rowCount-b}}function h(e,t,n){const o=[...t,...n],r=[];for(let t=0;t<o.length;t++){const n=e.columns.byName(o[t]).getRawData(),s=new Float32Array(n.length);s.set(n),r.push(a.Column.fromFloat32Array(`s${t+1}`,s))}return a.DataFrame.fromColumns(r)}function y(e,t){const n=e.rowCount,o=t.rowCount,r=t.columns.byName("log2FC").getRawData(),s=t.columns.byName("p.value").getRawData(),i=t.columns.byName("adj.p.value").getRawData(),l=t.columns.byName("significant"),c=t.col("row"),m=new Int32Array(o);if(c){const e=c.getRawData();for(let t=0;t<o;t++)m[t]=(0|e[t])-1}else for(let e=0;e<o;e++)m[e]=e;const p=new Float32Array(n);p.fill(a.FLOAT_NULL);const d=new Float32Array(n);d.fill(a.FLOAT_NULL);const f=new Float32Array(n);f.fill(a.FLOAT_NULL);const g=new Uint8Array(n);let h=0;for(let e=0;e<o;e++){const t=m[e];if(t<0||t>=n)continue;p[t]=r[e],d[t]=s[e],f[t]=i[e];const o=l.get(e);!0!==o&&1!==o&&"1"!==o&&"TRUE"!==o||(g[t]=1,h++)}const y=a.Column.fromFloat32Array("log2FC",p),E=a.Column.fromFloat32Array("p-value",d),w=a.Column.fromFloat32Array("adj.p-value",f);return e.columns.addNewBool("significant").init(e=>1===g[e]),y.semType=u.iu.LOG2FC,E.semType=u.iu.P_VALUE,w.semType=u.iu.P_VALUE,e.columns.add(y),e.columns.add(E),e.columns.add(w),h}async function E(e,t,n,o,s){const a=h(e,t,n),i=y(e,await r.functions.call("Proteomics:LimmaDE",{exprDf:a,nGroup1:t.length,fcThreshold:o,pThreshold:s}));return e.setTag("proteomics.de_complete","true"),e.fireValuesChanged(),i}function w(e,t){return`${e} vs ${t}`}function v(e,t){const n=(0,m.f)(e);if(!n)return void r.shell.warning("Please annotate experimental groups first (Proteomics | Annotate Experiment)");if("true"===e.getTag("proteomics.de_complete"))return void r.shell.warning("Differential expression already performed");const o=n.group1,i=n.group2,l=s.divText(`Group 1: ${o.name} (${o.columns.length} samples), Group 2: ${i.name} (${i.columns.length} samples)`),c=[`${i.name} vs ${o.name}`,`${o.name} vs ${i.name}`],p=s.input.choice("Comparison",{value:w(o.name,i.name),items:c,nullable:!1}),d=s.div();d.style.cssText="font-style:italic; color:#888; font-size:12px; margin-bottom:8px;";const f=()=>{const e=p.value===c[1],t=e?o.name:i.name,n=e?i.name:o.name;d.textContent=`Positive log2FC = higher in ${t}, Negative log2FC = higher in ${n}`};p.onChanged.subscribe(f),f();const v=s.input.choice("Method",{value:"limma",items:["limma","DEqMS","t-test"],nullable:!1});v.setTooltip("limma: moderated t-test; DEqMS: peptide-count-weighted variance; t-test: client-side Welch's t-test");const _=e.columns.toList().find(e=>"Unique peptides"===e.name||"Peptides"===e.name)??void 0,C=s.input.column("Peptide count column",{table:e,value:_,filter:e=>e.type===a.COLUMN_TYPE.INT||e.type===a.COLUMN_TYPE.FLOAT,nullable:!1});C.setTooltip("Column with peptide/spectra counts per protein");const b=C.root;b.style.display="none",v.onChanged.subscribe(()=>{b.style.display="DEqMS"===v.value?"":"none"});const T=s.input.float("|log2FC| threshold",{value:u.M5});T.setTooltip("Minimum absolute fold change for significance");const P=s.input.float("Adj. p-value threshold",{value:u.Dx});P.setTooltip("Maximum adjusted p-value for significance"),s.dialog("Differential Expression").add(l).add(p).add(d).add(v).add(C).add(T).add(P).onOK(async()=>{const n=T.value??u.M5,s=P.value??u.Dx,l=v.value,m=p.value===c[1],d=m?o.columns:i.columns,f=m?i.columns:o.columns,w=(m?o.name:i.name,m?i.name:o.name,a.TaskBarProgressIndicator.create(`Running ${l} analysis...`));try{if("t-test"===l){const t=g(e,f,d,0,0,n,s);e.setTag("proteomics.de_method","t-test"),r.shell.info(`DE complete (t-test): ${t.tested} proteins tested, ${t.untestable} untestable`)}else if("DEqMS"===l){const t=C.value;if(!t)return void r.shell.error("Please select a peptide count column for DEqMS");try{const o=await async function(e,t,n,o,s,i){const l=h(e,t,n),c=a.DataFrame.create(e.rowCount),u=c.columns.addNewInt("count");for(let t=0;t<e.rowCount;t++)u.set(t,o.isNone(t)?1:Math.round(o.get(t)));const m=y(e,await r.functions.call("Proteomics:DeqmsDE",{exprDf:l,nGroup1:t.length,peptideDf:c,fcThreshold:s,pThreshold:i}));return e.setTag("proteomics.de_complete","true"),e.setTag("proteomics.de_method","deqms"),e.fireValuesChanged(),m}(e,f,d,t,n,s);e.setTag("proteomics.de_method","deqms"),r.shell.info(`DE complete (DEqMS): ${o} significant proteins`)}catch(t){console.warn("DEqMS failed, trying limma:",t),w.update(50,"DEqMS unavailable, trying limma..."),r.shell.warning("DEqMS unavailable, trying limma...");try{const t=await E(e,f,d,n,s);e.setTag("proteomics.de_method","limma"),r.shell.info(`DE complete (limma fallback): ${t} significant proteins`)}catch(t){console.warn("Limma DE also failed, using client-side fallback:",t),w.update(75,"Server-side DE unavailable, using client-side t-test..."),r.shell.warning("R environment unavailable — using client-side t-test");const o=g(e,f,d,0,0,n,s);e.setTag("proteomics.de_method","t-test"),r.shell.info(`DE complete (t-test): ${o.tested} proteins tested, ${o.untestable} untestable`)}}}else try{const t=await E(e,f,d,n,s);e.setTag("proteomics.de_method","limma"),r.shell.info(`DE complete (limma): ${t} significant proteins`)}catch(t){w.update(50,"Limma unavailable, using client-side t-test..."),r.shell.warning("R environment unavailable — using client-side t-test"),console.warn("Limma DE failed, using client-side fallback:",t);const o=g(e,f,d,0,0,n,s);e.setTag("proteomics.de_method","t-test"),r.shell.info(`DE complete (t-test): ${o.tested} proteins tested, 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Run Differential Expression first.");const r=o.geneName??o.proteinId;if(!r)throw new Error("No gene-name or protein-ID column found to export.");const s=new Map;for(let t=0;t<e.rowCount;t++){const e=r.get(t);e&&s.set(t,String(e))}const i=o.log2fc.getRawData(),c=o.pValue.getRawData(),{upGenes:u,downGenes:m,background:p}=(0,l.Bx)(s,i,c,t,n),d=e=>/[",\n]/.test(e)?`"${e.replace(/"/g,'""')}"`:e,f=["gene,list"];for(const e of u)f.push(`${d(e)},up`);for(const e of m)f.push(`${d(e)},down`);for(const e of p)f.push(`${d(e)},background`);return{csv:f.join("\n"),counts:{up:u.length,down:m.length,background:p.length}}}function u(e){const t=(0,a.I)(e);if(!t.log2fc||!t.pValue)return void o.shell.warning("No log2FC or p-value columns found. Run Differential Expression first.");const n=r.input.float("|log2FC| threshold",{value:i.M5});n.setTooltip("Minimum absolute fold change for a gene to count as up/down.");const u=r.input.float("Adj. p-value threshold",{value:i.Dx});u.setTooltip("Maximum adjusted p-value for a gene to count as up/down.");const m=r.divText(""),p=()=>{const o=(0,l.bM)(e,n.value??i.M5,u.value??i.Dx,t.log2fc,t.pValue);m.textContent=`${o.significant} of ${o.total.toLocaleString()} proteins significant`};p(),n.onChanged.subscribe(p),u.onChanged.subscribe(p),r.dialog("Export Enrichment Inputs").add(m).add(n).add(u).onOK(()=>{const t=n.value??i.M5,r=u.value??i.Dx,{csv:a,counts:l}=c(e,t,r),m=e.name?`${e.name} — enrichment inputs`:"enrichment inputs";s.Utils.download(`${m}.csv`,a,"text/csv"),o.shell.info(`Exported ${l.up} up, ${l.down} down, ${l.background} background genes.`)}).show()}},230(e,t,n){"use strict";n.d(t,{AB:()=>E,Ae:()=>p.Ae,Bx:()=>v,D9:()=>C,Mz:()=>w,_W:()=>y,bM:()=>_,pG:()=>b,zy:()=>h});var o=n(328),r=n(389),s=n(82),a=n(498),i=n(304),l=n(641),c=n(897),u=n(829),m=n(252),p=n(935);const d="https://biit.cs.ut.ee/gprofiler";async function f(e,t,n=3e4){const r=o.dapi.fetchProxy(e,t),s=new Promise((e,t)=>setTimeout(()=>t(new Error("g:Profiler API request timed out. The service may be temporarily unavailable.")),n)),a=await Promise.race([r,s]);if(!a.ok)throw new Error(`g:Profiler API returned status ${a.status}`);return a}async function g(e,t,n,o,r=l.Dx){const s=await f(`${d}/api/gost/profile/`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({organism:n,query:e,sources:o,user_threshold:r,significance_threshold_method:"fdr",domain_scope:"custom",background:t,all_results:!0,ordered:!1,no_evidences:!1,combined:!1,measure_underrepresentation:!1,no_iea:!1,numeric_ns:"",output:"json"})}),a=await s.json();return a.result?Array.isArray(a.result)&&a.result.length>0&&a.result[0]?.result?a.result[0].result:Array.isArray(a.result)?a.result:[]:[]}const h=["localization","cellular component organization","transport","cellular process","biological process","metabolic process"],y=["actin","vesicle","endocytosis","cytoskeleton"];function E(e,t=15){if(0===e.length)return{kept:[],stats:{total:0,kept:0,droppedParents:0,cappedAtN:t}};const n=e.filter(e=>"GO:BP"===e.source),o=e.filter(e=>"GO:BP"!==e.source);let r=0;const s=[];if(n.length>0){const e=[...n].sort((e,t)=>e.p_value-t.p_value);for(const n of e){const e=(n.name??"").toLowerCase();if(h.some(t=>e.includes(t))&&s.some(e=>y.some(t=>(e.name??"").toLowerCase().includes(t))))r++;else if(s.push(n),s.length>=t)break}}const a=[...o].sort((e,t)=>e.p_value-t.p_value).slice(0,t),i=[...s,...a].sort((e,t)=>e.p_value-t.p_value);return{kept:i,stats:{total:e.length,kept:i.length,droppedParents:r,cappedAtN:t}}}function w(e,t,n=l.Dx,o){const r=e.length,a=s.DataFrame.create(r);a.name="Enrichment Results";const i=e.map(e=>{if(!e.intersections)return"";const n=[],o=Math.min(t.length,e.intersections.length);for(let r=0;r<o;r++)e.intersections[r]&&e.intersections[r].length>0&&n.push(t[r]);return n.join(", ")}),c=a.columns.addNewString("Source"),u=a.columns.addNewString("Term ID"),m=a.columns.addNewString("Term Name"),p=a.columns.addNewFloat("FDR"),d=a.columns.addNewInt("Gene Count"),f=a.columns.addNewFloat("Gene Ratio"),g=a.columns.addNewString("Intersection");c.init(t=>e[t].source),u.init(t=>e[t].native),m.init(t=>e[t].name),p.init(t=>e[t].p_value),d.init(t=>e[t].intersection_size),f.init(t=>e[t].precision),g.init(e=>i[e]);const h=p.getRawData();return a.columns.addNewBool("Significant").init(e=>h[e]!==s.FLOAT_NULL&&h[e]<=n),o&&a.columns.addNewString("Direction").init(()=>o),p.setTag("color-coding-type","Linear"),p.setTag("color-coding-linear",'{"0":"#2ecc71","0.05":"#f39c12","1":"#e74c3c"}'),a.setTag("proteomics.enrichment","true"),a}function v(e,t,n,o,r){const a=new Set,i=new Set,l=new Set;for(const[c,u]of e){l.add(u);const e=t[c],m=n[c];e!==s.FLOAT_NULL&&m!==s.FLOAT_NULL&&m<=r&&Math.abs(e)>=o&&(e>0?a.add(u):e<0&&i.add(u))}return{upGenes:[...a],downGenes:[...i],background:[...l]}}function _(e,t,n,o,r){const a=e.rowCount,i=o.getRawData(),l=r.getRawData();let c=0;for(let e=0;e<a;e++){const o=i[e],r=l[e];o!==s.FLOAT_NULL&&r!==s.FLOAT_NULL&&Math.abs(o)>=t&&r<=n&&c++}return{significant:c,total:a}}async function C(e,t,n,o,r,s=!0,c=15){const u=(0,i.I)(e);if(!u.proteinId)throw new Error("No protein ID column found");if(!u.log2fc||!u.pValue)throw new Error("No log2FC or adjusted p-value columns found. Run Differential Expression first.");let m,p=0,h=0,y=0;if(u.geneName){m=new Map;const t=u.geneName;for(let n=0;n<e.rowCount;n++){const e=t.get(n);e&&m.set(n,e)}p=m.size,h=e.rowCount,y=h-p}else{const t=new Map;for(let n=0;n<e.rowCount;n++){const e=u.proteinId.get(n),o=(0,a.S6)(e);o&&(t.has(o)||t.set(o,[]),t.get(o).push(n))}const n=[...t.keys()],r=await async function(e,t="hsapiens"){const n=await f(`${d}/api/convert/convert/`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({organism:t,query:e,target:"ENSG",numeric_ns:"",output:"json"})});return(await n.json()).result??[]}(n,o),s=new Map;for(const e of r)e.incoming&&e.name&&"N/A"!==e.name&&!s.has(e.incoming)&&s.set(e.incoming,e.name);m=new Map;for(const[e,n]of t){const t=s.get(e);if(t)for(const e of n)m.set(e,t)}const i=new Array(e.rowCount).fill("");for(const[e,t]of m)i[e]=t;const c=e.columns.addNewString("Gene Symbol (mapped)");c.semType=l.iu.GENE_SYMBOL,c.init(e=>i[e]),p=s.size,h=n.length,y=h-p}const _=u.log2fc.getRawData(),C=u.pValue.getRawData(),{upGenes:b,downGenes:T,background:P}=v(m,_,C,t,n);if(0===b.length&&0===T.length)throw new Error("No significant proteins found with the given thresholds");const S=[];let N=null,A=null;if(b.length>0){let e=await g(b,P,o,r,n);if(s){const t=E(e,c);e=t.kept,N=t.stats}S.push(w(e,b,n,"Up"))}if(T.length>0){let e=await g(T,P,o,r,n);if(s){const t=E(e,c);e=t.kept,A=t.stats}S.push(w(e,T,n,"Down"))}let x=S[0];for(let e=1;e<S.length;e++)x=x.append(S[e]);x.name=e.name?`${e.name} — Enrichment`:"Enrichment Results",x.setTag("proteomics.enrichment","true");const D=x.col("FDR");if(D&&(D.setTag("color-coding-type","Linear"),D.setTag("color-coding-linear",'{"0":"#2ecc71","0.05":"#f39c12","1":"#e74c3c"}')),s){const e=(N?.total??0)+(A?.total??0),t=(N?.kept??0)+(A?.kept??0),n=(N?.droppedParents??0)+(A?.droppedParents??0);t<e&&(x.setTag("proteomics.enrichment_smart_filtered","true"),x.setTag("proteomics.enrichment_smart_filtered_kept",String(t)),x.setTag("proteomics.enrichment_smart_filtered_total",String(e)),x.setTag("proteomics.enrichment_smart_filtered_dropped_parents",String(n)),x.setTag("proteomics.enrichment_smart_filtered_cap",String(c)))}return{enrichmentDf:x,mapped:p,total:h,unmapped:y}}function b(e){if(!(0,u.RJ)(e,"Run Differential Expression first"))return;const t=(0,i.I)(e);if(!t.log2fc||!t.pValue)return void o.shell.warning("No log2FC or p-value columns found");const n=r.input.float("|log2FC| threshold",{value:l.M5});n.setTooltip("Minimum absolute fold change for significance");const a=r.input.float("Adj. p-value threshold",{value:l.Dx});a.setTooltip("Maximum adjusted p-value for significance");const d=(0,p.X3)((0,m.Di)(e)??(0,p.Vr)(e)),f=r.input.choice("Organism",{value:d??"Homo sapiens (Human)",items:p.Ae.map(e=>e.display),nullable:!1}),g=r.input.bool("GO: Biological Process",{value:!0}),h=r.input.bool("GO: Molecular Function",{value:!0}),y=r.input.bool("GO: Cellular Component",{value:!0}),E=r.input.bool("KEGG Pathways",{value:!0}),w=r.input.bool("Reactome Pathways",{value:!0}),v=r.input.bool("WikiPathways",{value:!0}),b=r.input.bool("Apply smart pathway filter",{value:!0});b.setTooltip("Drops generic GO parent terms when more specific child terms are present; caps each source at top-N by FDR. Recommended for cleaner results; uncheck for raw g:Profiler output.");const T=r.input.int("Max terms per source",{value:15,min:1});T.setTooltip("Upper bound on terms kept per enrichment source (top-N by FDR). Applies only when the smart pathway filter is on.");const P=()=>T.enabled=b.value??!0;b.onChanged.subscribe(P),P();const S=r.divText(""),N=()=>{const o=n.value??l.M5,r=a.value??l.Dx,s=_(e,o,r,t.log2fc,t.pValue),i=s.total.toLocaleString();S.textContent=`${s.significant} of ${i} proteins are significant with these thresholds`};N(),n.onChanged.subscribe(N),a.onChanged.subscribe(N),r.dialog("Enrichment Analysis").add(S).add(n).add(a).add(f).add(g).add(h).add(y).add(E).add(w).add(v).add(b).add(T).onOK(async()=>{const t=s.TaskBarProgressIndicator.create("Running enrichment analysis...");try{const t=n.value??l.M5,r=a.value??l.Dx,s=f.value,i=p.Ae.find(e=>e.display===s),u=i?.code??"hsapiens";(0,m.Np)(e,u);const d=[];if(g.value&&d.push("GO:BP"),h.value&&d.push("GO:MF"),y.value&&d.push("GO:CC"),E.value&&d.push("KEGG"),w.value&&d.push("REAC"),v.value&&d.push("WP"),0===d.length)return void o.shell.warning("Please select at least one enrichment source");const _=await C(e,t,r,u,d,b.value??!0,T.value??15),P=_.total>0?(_.mapped/_.total*100).toFixed(1):"0.0";o.shell.info(`${_.mapped}/${_.total} proteins mapped (${P}%). ${_.unmapped} unmapped.`),(0,c.q6)(_.enrichmentDf,e)}catch(e){o.shell.error(`Enrichment analysis failed: ${e.message}`)}finally{t.close()}}).show()}},252(e,t,n){"use strict";n.d(t,{$Y:()=>u,Di:()=>d,Np:()=>p,XX:()=>g,Yf:()=>f,applyAnnotation:()=>h,f:()=>m});var o=n(328),r=n(389),s=n(353),a=n.n(s),i=n(641),l=n(655),c=n(935);function u(e,t){e.setTag("proteomics.groups",JSON.stringify(t))}function m(e){const t=e.getTag("proteomics.groups");if(!t)return null;try{return JSON.parse(t)}catch{return null}}function p(e,t){e.setTag("proteomics.organism",t)}function d(e){return e.getTag("proteomics.organism")||void 0}function f(e,t){const n=function(e){const t=(0,l.getRunMeta)(e);if(t)return t;const n=e.getTag("proteomics.spc_run_meta_seed");if(n)try{return JSON.parse(n)}catch{return}}(e),o=m(e);if(!o)return{group1Name:"Control",group1Cols:[],group2Name:"Treatment",group2Cols:[],instrumentId:n?.instrument_id,acquisitionDatetime:n?.acquisition_datetime};const r=new Set(t),s=t=>t.filter(e=>r.has(e)).map(t=>e.col(t)).filter(e=>null!==e);return{group1Name:o.group1.name||"Control",group1Cols:s(o.group1.columns),group2Name:o.group2.name||"Treatment",group2Cols:s(o.group2.columns),instrumentId:n?.instrument_id,acquisitionDatetime:n?.acquisition_datetime}}function g(e){const t=e.columns.toList().filter(e=>e.semType===i.iu.INTENSITY&&e.name.startsWith("log2(")).map(e=>e.name),n=f(e,t),s=r.input.string("Group 1 Name",{value:n.group1Name}),l=r.input.columns("Group 1",{table:e,available:t,value:n.group1Cols}),u=r.input.string("Group 2 Name",{value:n.group2Name}),m=r.input.columns("Group 2",{table:e,available:t,value:n.group2Cols}),p=r.input.string("Instrument",{value:n.instrumentId??"",tooltipText:"Free-text identifier for the instrument that ran this analysis (e.g. QExactive-01). 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Auto-detected from the data when available."});r.dialog("Annotate Experiment").add(s).add(l).add(u).add(m).add(y).add(p).add(g).onOK(()=>{const t=l.value??[],n=m.value??[];if(0===t.length||0===n.length)return void o.shell.warning("Select at least one column per group");const r={group1:{name:s.value,columns:t.map(e=>e.name)},group2:{name:u.value,columns:n.map(e=>e.name)}},a=(p.value??"").trim(),i=g.value,d=i&&"function"==typeof i.toISOString||i instanceof Date?i.toISOString():"";h(e,{group1:r.group1,group2:r.group2,organism:(0,c.$S)(y.value??void 0),runMeta:a.length>0||d.length>0?{instrument_id:a,acquisition_datetime:d}:void 0}),o.shell.info(`Groups assigned: ${t.length} + ${n.length} samples`)}).show()}function h(e,t){u(e,{group1:t.group1,group2:t.group2}),t.organism&&p(e,t.organism),t.runMeta&&(0,l.setRunMeta)(e,t.runMeta)}},47(e,t,n){"use strict";n.d(t,{Mx:()=>u,Q2:()=>p,U0:()=>c,UN:()=>f,fX:()=>m,p4:()=>d});var o=n(328),r=n(389),s=n(82),a=n(641),i=n(252);function l(e,t){const n=Math.random(),o=Math.random();return e+t*(Math.sqrt(-2*Math.log(n))*Math.cos(2*Math.PI*o))}function c(e,t,n=1.8,o=.3){let r=0;for(const a of t){const t=e.col(a);if(!t)continue;if(t.type!==s.COLUMN_TYPE.FLOAT)continue;const i=t.stats.avg,c=t.stats.stdev;if(isNaN(i)||isNaN(c)||0===c)continue;const u=i-n*c,m=o*c,p=t.getRawData();for(let t=0;t<e.rowCount;t++)p[t]===s.FLOAT_NULL&&(p[t]=l(u,m),r++)}return e.fireValuesChanged(),e.setTag("proteomics.imputed","true"),r}function u(e,t,n=10){const o=t.map(t=>e.col(t)).filter(e=>null!=e&&e.type===s.COLUMN_TYPE.FLOAT);if(0===o.length)return 0;const r=o.map(e=>e.getRawData()),a=e.rowCount,i=o.length,l=[],c=[];for(let e=0;e<a;e++){const t=new Float64Array(i),n=[];for(let r=0;r<i;r++){const s=o[r].isNone(e);n.push(s),t[r]=s?0:o[r].get(e)}l.push(t),c.push(n)}const u=new Float64Array(i);for(let e=0;e<i;e++){let t=0,n=0;for(let o=0;o<a;o++)c[o][e]||(t+=l[o][e],n++);u[e]=n>0?t/n:NaN}const m=[];for(let e=0;e<a;e++)c[e].some(e=>e)&&m.push(e);const p=s.TaskBarProgressIndicator.create("kNN imputation...");let d=0;try{for(let e=0;e<m.length;e++){const t=m[e];if(p.update(Math.round(e/m.length*100),`Row ${e+1}/${m.length}`),!c[t].some(e=>!e)){for(let e=0;e<i;e++)c[t][e]&&isFinite(u[e])&&(r[e][t]=u[e],d++);continue}const o=[];for(let e=0;e<a;e++){if(e===t)continue;let n=0,r=0;for(let o=0;o<i;o++)if(!c[t][o]&&!c[e][o]){const s=l[t][o]-l[e][o];n+=s*s,r++}r>0&&o.push({row:e,dist:Math.sqrt(n/r)})}o.sort((e,t)=>e.dist-t.dist);const s=o.slice(0,n);for(let e=0;e<i;e++){if(!c[t][e])continue;let n=0,o=0;for(const t of s)c[t.row][e]||(n+=l[t.row][e],o++);const a=o>0?n/o:u[e];isFinite(a)&&(r[e][t]=a,d++)}}}finally{p.close()}return e.fireValuesChanged(),e.setTag("proteomics.imputed","true"),d}function m(e,t){let n=0;for(const o of t){const t=e.col(o);if(!t||t.type!==s.COLUMN_TYPE.FLOAT)continue;const r=t.getRawData();for(let t=0;t<e.rowCount;t++)r[t]===s.FLOAT_NULL&&(r[t]=0,n++)}return e.fireValuesChanged(),e.setTag("proteomics.imputed","true"),n}function p(e,t){let n=0;for(const o of t){const t=e.col(o);if(!t||t.type!==s.COLUMN_TYPE.FLOAT)continue;const r=t.stats.avg;if(isNaN(r))continue;const a=t.getRawData();for(let t=0;t<e.rowCount;t++)a[t]===s.FLOAT_NULL&&(a[t]=r,n++)}return e.fireValuesChanged(),e.setTag("proteomics.imputed","true"),n}function d(e,t){let n=0;for(const o of t){const t=e.col(o);if(!t||t.type!==s.COLUMN_TYPE.FLOAT)continue;const r=t.stats.med;if(isNaN(r))continue;const a=t.getRawData();for(let t=0;t<e.rowCount;t++)a[t]===s.FLOAT_NULL&&(a[t]=r,n++)}return e.fireValuesChanged(),e.setTag("proteomics.imputed","true"),n}function f(e){if("true"===e.getTag("proteomics.imputed"))return void o.shell.warning("Missing values already imputed");const t=e.columns.toList().filter(e=>e.semType===a.iu.INTENSITY&&e.name.startsWith("log2(")).map(e=>e.name),n=t.map(t=>e.col(t)),l=r.input.choice("Method",{value:"MinProb",items:["MinProb","kNN","Zero","Mean","Median"],nullable:!1}),f=r.input.columns("Intensity columns",{table:e,available:t,value:n}),g=r.input.float("Downshift",{value:1.8});g.setTooltip("Standard deviations to shift left from mean (Perseus default: 1.8)");const h=r.input.float("Width",{value:.3});h.setTooltip("Fraction of standard deviation for imputation distribution (Perseus default: 0.3)");const y=r.div([g.root,h.root]),E=r.input.int("k (neighbors)",{value:10}),w=r.div([E.root]);w.style.display="none",l.onChanged.subscribe(()=>{const e=l.value;y.style.display="MinProb"===e?"":"none",w.style.display="kNN"===e?"":"none"});const v=r.input.int("Min valid values per group",{value:2}),_=r.divText("");_.style.cssText="font-size:12px; 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e=0;e<Math.min(o,r);e++){const t=y>0?Math.max(f[e],0)/y*100:0;E.push(Math.round(10*t)/10)}const w=E.length>0&&isFinite(E[0])?E[0]:0,v=r>=2?`PC1 (${w}%)`:"PC1",_=E.length>=2&&isFinite(E[1])?E[1]:0,C=o>=2&&E.length>=2&&r>=2?`PC2 (${_}%)`:"PC2",b=[s.Column.fromStrings("SampleName",t),s.Column.fromFloat32Array(v,new Float32Array(h.map(e=>e[0])))];if(o>=2){const e=s.Column.fromFloat32Array(C,new Float32Array(h.map(e=>e.length>1?e[1]:0)));b.push(e)}const T=t.map(e=>n.group1.columns.includes(e)?n.group1.name:n.group2.columns.includes(e)?n.group2.name:"Unknown"),P=s.Column.fromStrings("Group",T);b.push(P);const S=s.DataFrame.fromColumns(b);return S.name="PCA",{pcaDf:S,varianceExplained:E}}(e,t,n),i=r.columns.toList().find(e=>e.name.startsWith("PC1"))?.name,l=r.columns.toList().find(e=>e.name.startsWith("PC2"))?.name;if(!i||!l)throw new Error("PCA did not produce PC1/PC2 columns — too few samples?");const 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Reflect.metadata(e,t)},K=function(e,t){return function(n,o){t(n,o,e)}};const J=new s.Package;function Z(e,t){return"spectronaut-candidates"!==e.getTag("proteomics.source")||(o.shell.warning(`${t} needs per-sample intensities, but this table is a Spectronaut Candidates report (one row per protein per comparison — pre-computed DE only). 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Open it via Proteomics | Visualize | Volcano Plot.`)}return oe(t,e),f(e),t}class se{static async initProteomics(){}static async buildProteomicsTopMenu(){const e={importSpectronautCandidates:()=>se.importSpectronautCandidates(),importSpectronaut:()=>se.importSpectronaut(),importMaxQuant:()=>se.importMaxQuant(),importFragPipe:()=>se.importFragPipe(),importGenericMatrix:()=>se.importGenericMatrix(),annotateExperiment:()=>se.annotateExperiment(),setLog2Scale:()=>se.setLog2Scale(),normalize:()=>se.normalizeProteomics(),impute:()=>se.imputeMissingValues(),differentialExpression:()=>se.differentialExpression(),enrichmentAnalysis:()=>se.enrichmentAnalysis(),exportEnrichmentInputs:()=>se.exportEnrichmentInputs(),computeSpcStatus:()=>se.computeSpcStatus(),showVolcanoPlot:()=>se.showVolcanoPlot(),showHeatmap:()=>se.showHeatmap(),showPcaPlot:()=>se.showPcaPlot(),showGroupMeanCorrelation:()=>se.showGroupMeanCorrelation(),showQcDashboard:()=>se.showQcDashboard(),showSpcDashboard:()=>se.showSpcDashboard(),enrichmentCharts:()=>se.enrichmentCharts(),showAllVisualizations:()=>se.showAllVisualizations(),shareAnalysisForReview:()=>se.shareAnalysisForReview()},t=new WeakSet,n=n=>{n?.type!==s.VIEW_TYPE.TABLE_VIEW||t.has(n)||setTimeout(()=>{if(!t.has(n))try{(function(e,t){if(!(n=e.dataFrame)||!n.getTag("proteomics.source"))return!1;var n;const o=e.ribbonMenu.group("Proteomics");for(const e of H)try{o.remove(e)}catch{}const r={isEnabled:()=>function(e){return e&&"spectronaut-candidates"===e.getTag("proteomics.source")?"Not applicable to a Spectronaut Candidates file — it already carries computed differential expression and has no per-sample intensities. Use Volcano Plot, Enrichment Analysis or the UniProt panel, or import the matching Spectronaut Report for sample-level analyses.":null}(e.dataFrame)},s=o.group("Import");s.item("Spectronaut Candidates...",t.importSpectronautCandidates),s.item("Spectronaut Report...",t.importSpectronaut),s.item("MaxQuant...",t.importMaxQuant),s.item("FragPipe...",t.importFragPipe),s.item("Generic Matrix...",t.importGenericMatrix),o.item("Annotate Experiment...",t.annotateExperiment,null,r);const a=o.group("Analyze");a.item("Set Log2 Scale...",t.setLog2Scale,null,r),a.item("Normalize...",t.normalize,null,r),a.item("Impute Missing Values...",t.impute,null,r),a.item("Differential Expression...",t.differentialExpression,null,r),a.item("Enrichment Analysis...",t.enrichmentAnalysis),a.item("Export Enrichment Inputs...",t.exportEnrichmentInputs),a.item("Compute SPC Status",t.computeSpcStatus,null,r);const i=o.group("Visualize");return i.item("Volcano Plot...",t.showVolcanoPlot),i.item("Heatmap...",t.showHeatmap,null,r),i.item("PCA...",t.showPcaPlot,null,r),i.item("Group-Mean Correlation...",t.showGroupMeanCorrelation,null,r),i.item("QC Dashboard...",t.showQcDashboard,null,r),i.item("SPC Dashboard...",t.showSpcDashboard),i.item("Enrichment Charts...",t.enrichmentCharts),i.item("Show All Visualizations...",t.showAllVisualizations,null,r),o.group("Share").item("Share Analysis for Review...",t.shareAnalysisForReview),!0})(n,e)&&t.add(n)}catch{}},50)};try{for(const e of o.shell.views)n(e)}catch{}o.events.onViewAdded.subscribe(n),o.events.onCurrentViewChanged.subscribe(()=>n(o.shell.v))}static async importSpectronautCandidates(){s.Utils.openFile({accept:".tsv,.txt,.csv",open:async e=>{try{const t=await e.text(),n=await(0,c.R)(t);n.name=e.name.replace(/\.[^.]+$/,""),ne(n),re(n)}catch(e){o.shell.error(`Failed to import Spectronaut Candidates file: ${e?.message??e}`)}}})}static async importSpectronaut(){s.Utils.openFile({accept:".tsv,.txt,.csv",open:async e=>{try{const t=await ee(e)?await(0,l.A)(e):await(0,l.parseSpectronautText)(await e.text());t.name=e.name.replace(/\.[^.]+$/,""),ne(t),o.shell.addTableView(t),o.shell.info(`Imported ${t.rowCount} protein groups from Spectronaut`),f(t)}catch(e){o.shell.error(`Failed to import Spectronaut file: ${e?.message??e}`),o.shell.warning("If this is a very large precursor-level Spectronaut report that fails to stream in-browser, pre-aggregate it to the importable protein-group shape with the bundled duckdb fallback: tools/spectronaut-aggregate.sh <input.tsv>, then re-import the resulting file. See files/demo/README.md for usage.")}}})}static async importMaxQuant(){s.Utils.openFile({accept:".txt,.tsv",open:async e=>{try{const t=await e.text(),n=await(0,i.E)(t);n.name=e.name.replace(/\.[^.]+$/,""),ne(n),o.shell.addTableView(n),o.shell.info(`Imported ${n.rowCount} protein groups`),f(n)}catch(e){o.shell.error(`Failed to import MaxQuant file: ${e?.message??e}`)}}})}static async importFragPipe(){s.Utils.openFile({accept:".tsv,.txt",open:async e=>{try{const t=await e.text(),n=await(0,u.p)(t);n.name=e.name.replace(/\.[^.]+$/,""),ne(n),o.shell.addTableView(n),o.shell.info(`Imported ${n.rowCount} protein groups from FragPipe`),f(n)}catch(e){o.shell.error(`Failed to import FragPipe file: ${e?.message??e}`)}}})}static async importGenericMatrix(){y()}static async annotateExperiment(){const e=o.shell.tv?.dataFrame;e?Z(e,"Annotate Experiment")&&(0,E.XX)(e):o.shell.warning("No table open")}static async setLog2Scale(){const e=o.shell.tv?.dataFrame;e?Z(e,"Set Log2 Scale")&&(0,b.Kb)(e):o.shell.warning("No table open")}static async normalizeProteomics(){const e=o.shell.tv?.dataFrame;e?Z(e,"Normalize")&&(0,C.v5)(e):o.shell.warning("No table open")}static async imputeMissingValues(){const e=o.shell.tv?.dataFrame;e?Z(e,"Impute Missing Values")&&(0,P.UN)(e):o.shell.warning("No table open")}static async differentialExpression(){const e=o.shell.tv,t=e?.dataFrame;e&&t?Z(t,"Differential Expression")&&(0,S.B9)(t,()=>{const n=(0,N.gO)(t);e.addViewer(n)}):o.shell.warning("No table open")}static async computeSpcStatus(){const e=o.shell.tv,t=e?.dataFrame;if(!e||!t)return void o.shell.warning("Open an analyzed file first, then run Compute SPC Status.");if("spectronaut-candidates"===t.getTag("proteomics.source"))return void o.shell.warning("SPC requires per-sample intensities. Re-import this analysis from the Spectronaut PG report (not the Candidates report) to compute SPC.");const n=(0,v.getRunMeta)(t);if(!n||!n.instrument_id||!n.acquisition_datetime)return void o.shell.warning("Open Annotate Experiment to set instrument + acquisition datetime.");const r=(0,E.f)(t);if(!r)return void o.shell.warning("Annotate experimental groups first (Proteomics → Annotate Experiment) — SPC needs Group 1 to compute control-replicate correlation.");r.group1.columns.length<2&&o.shell.info("Group 1 has fewer than 2 samples — control-replicate correlation can't be computed. The other three metrics will still be recorded.");const a=s.TaskBarProgressIndicator.create("Computing SPC status...");try{const e=(0,v.computeSpcMetrics)(t,r,n),s=await(0,_.loadBaseline)(n.instrument_id),a=await(0,_.loadRuns)(n.instrument_id),i=a.find(e=>e.acquisition_datetime===n.acquisition_datetime),l=i?.status??null;let c;if(null===s)c={status:"pass",rulesTripped:[]},o.shell.info(`No baseline locked for ${n.instrument_id} yet — recorded as pass. Define a baseline once at least 4 runs have been computed.`);else{const t={median_intensity:a.map(e=>e.median_intensity),missing_pct:a.map(e=>e.missing_pct),control_corr:a.map(e=>e.control_corr),protein_count:a.map(e=>e.protein_count)};c=(0,v.uV)(e,t,s.metrics,s.rules_enabled??(0,v.kY)())}(0,v.setSpcStatus)(t,e,c);const u={instrument_id:n.instrument_id,acquisition_datetime:n.acquisition_datetime,run_label:t.name,median_intensity:e.median_intensity,missing_pct:e.missing_pct,control_corr:e.control_corr,protein_count:e.protein_count,status:c.status,rules_tripped:c.rulesTripped,source_project_id:null,source_df_name:t.name,computed_at:e.computed_at};await(0,_.upsertRun)(u),null!==l?o.shell.info(`Updated SPC for ${t.name} (previous status: ${l}).`):"pass"===c.status?o.shell.info(`SPC computed: ${t.name} — status: pass.`):"flagged"===c.status?o.shell.info(`SPC computed: ${t.name} — flagged on ${c.rulesTripped.length} rule(s): ${c.rulesTripped.join(", ")}.`):o.shell.info(`SPC computed: ${t.name} — OUT OF CONTROL on ${c.rulesTripped.length} rule(s): ${c.rulesTripped.join(", ")}.`)}finally{a.close()}}static async showVolcanoPlot(){const e=o.shell.tv,t=e?.dataFrame;e&&t?(0,S.RJ)(t,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)")&&await se.volcanoOptions():o.shell.warning("No table open")}static async volcanoOptions(e){const t=o.shell.tv,n=t?.dataFrame;if(!t||!n)return void o.shell.warning("No table open");if(!(0,S.RJ)(n,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)"))return;let a=e;if(!a)for(const e of t.viewers)if(e.type===s.VIEWER.SCATTER_PLOT&&"negLog10P"===e.props.yColumnName){a=e;break}const i=a?(0,N.ur)(n,a):{metric:"adj.p-value",colorDim:"significance"},l=null!=n.col("p-value"),c=l?i.metric:"adj.p-value",u=r.input.choice("Significance metric",{value:c,items:l?["adj.p-value","p-value"]:["adj.p-value"],nullable:!1});u.setTooltip(l?"Y axis, classification and threshold line all switch together":"p-value column not present — only adj.p-value is available");const p=r.input.choice("Color by",{value:i.colorDim,items:["significance","location"],nullable:!1});p.setTooltip("significance = Enriched in g1 / Enriched in g2 / Not significant; location = UniProt subcellular location");const d=r.input.int("Label top N points",{value:(0,N.m2)(n),min:0});d.setTooltip("How many of the most significant proteins get name labels. 0 = none. Labels no longer touch your row selection.");const f=(0,N.GE)(n),g=r.input.float("X-axis max (|log2FC|)",{value:f.xMax??void 0,min:0,nullable:!0});g.setTooltip("Pin the X axis to ±this |log2FC|. Leave empty to auto-scale. Set the same value on two volcanoes to compare them side-by-side.");const h=r.input.float("Y-axis max (−log10 p)",{value:f.yMax??void 0,min:0,nullable:!0});h.setTooltip("Pin the Y axis to 0…this −log10(p). Leave empty to auto-scale. Set the same value on two volcanoes to compare them side-by-side."),r.dialog("Volcano Options").add(u).add(p).add(d).add(g).add(h).onOK(async()=>{const e=u.value??"adj.p-value",r="location"===p.value?"location":"significance";if((0,N.S6)(n,g.value??null,h.value??null),a||(a=(0,N.gO)(n,{topNLabels:0}),t.addViewer(a)),"location"===r&&!n.col(N.fQ)){const e=await o.dapi.userDataStorage.get(A.er).catch(()=>null);0===(e?Object.keys(e).filter(e=>"__schema_v"!==e).length:0)?o.shell.info("Fetching subcellular locations from UniProt — may take a minute or two on first use without cache; subsequent toggles use the cache."):o.shell.info("Resolving subcellular locations from cache.")}const i="location"===r?"Classifying subcellular locations…":"Updating volcano…",l=s.TaskBarProgressIndicator.create(i),c="location"===r;c&&(0,N.DI)(a,i);const f=(e,t,n)=>{const o="fetch-acc"===n?"Fetching subcellular locations":"fetch-gene"===n?"Resolving by gene name":"init-column"===n||"location"===r?"Classifying subcellular locations":"Updating volcano",s=t>0?Math.round(e/t*100):0;if(l.update(s,`${o}: ${e}/${t}`),c){const n=t>1?`${e}/${t} (${s}%)`:"";(0,N.Bb)(a,o,n)}};try{await(0,N.nj)(n,a,e,r,m.M5,m.Dx,f),(0,N.XC)(n,a,d.value??(0,N.m2)(n))}catch(e){o.shell.error(`Volcano update failed: ${e?.message??e}`)}finally{l.close(),c&&a&&(0,N.kX)(a)}}).show()}static async showHeatmap(){const e=o.shell.tv,t=e?.dataFrame;if(!e||!t)return void o.shell.warning("No table open");if(!Z(t,"Heatmap"))return;if(!(0,S.RJ)(t,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)"))return;const n=r.input.int("Top N proteins",{value:50,min:1});n.setTooltip("How many of the most significant proteins (by adj. p-value) to show."),r.dialog("Heatmap Options").add(n).onOK(async()=>{const o=n.value??50,r=s.TaskBarProgressIndicator.create("Creating heatmap...");try{const n=await x(t,{topN:o,title:`Heatmap: Top ${o} DE Proteins`});e.addViewer(n)}finally{r.close()}}).show()}static async showPcaPlot(){const e=o.shell.tv,t=e?.dataFrame;if(!e||!t)return void o.shell.warning("No table open");if(!Z(t,"PCA"))return;const n=(0,E.f)(t);if(!n)return void o.shell.warning("Annotate experimental groups first (Proteomics | Annotate Experiment)");const r=[...n.group1.columns,...n.group2.columns],{viewer:s,pcaDf:a}=F(t,r,n,"PCA: All Groups");a.name=`PCA: ${t.name}`,o.shell.addTableView(a).addViewer(s)}static async showGroupMeanCorrelation(){const e=o.shell.tv,t=e?.dataFrame;if(!e||!t)return void o.shell.warning("No table open");if(!(0,S.RJ)(t,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)"))return;if(!(0,E.f)(t))return void o.shell.warning("Annotate experimental groups first (Proteomics | Annotate Experiment)");const n=(0,G.Z7)(t);e.addViewer(n)}static async showQcDashboard(){const e=o.shell.tv,t=e?.dataFrame;e&&t?Z(t,"QC Dashboard")&&O(t):o.shell.warning("No table open")}static async showSpcDashboard(){await(0,R.r9)()}static async showAllVisualizations(){const e=o.shell.tv,t=e?.dataFrame;if(!e||!t)return void o.shell.warning("No table open");if(!Z(t,"Show All Visualizations"))return;if(!(0,S.RJ)(t,"Run Differential Expression first"))return;const n=(0,E.f)(t),r=(0,N.gO)(t);e.addViewer(r);const a=s.TaskBarProgressIndicator.create("Creating heatmap...");try{const n=await x(t,{title:"Heatmap: Top 50 DE Proteins"});e.addViewer(n)}finally{a.close()}if(n){const e=[...n.group1.columns,...n.group2.columns],{viewer:r,pcaDf:s}=F(t,e,n,"PCA: All Groups");s.name=`PCA: ${t.name}`,o.shell.addTableView(s).addViewer(r)}}static async enrichmentAnalysis(){const e=o.shell.tv?.dataFrame;e?(0,Y.pG)(e):o.shell.warning("No table open")}static async exportEnrichmentInputs(){const e=o.shell.tv?.dataFrame;e?(0,S.RJ)(e,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)")&&(0,T.N)(e):o.shell.warning("No table open")}static async enrichmentCharts(){const e=o.shell.tv,t=e?.dataFrame;if(!t)return void o.shell.warning("No table open");if("true"!==t.getTag("proteomics.enrichment"))return void o.shell.warning("Run Enrichment Analysis first (Proteomics | Enrichment Analysis)");const n=o.shell.tables.filter(e=>"true"===e.getTag("proteomics.de_complete"));if(0===n.length)return o.shell.warning("No protein table with DE results found. Enrichment charts will open without volcano linking."),void(0,z.q6)(t,t);n.length>1&&o.shell.warning(`Multiple protein tables with DE results found; linking enrichment to "${n[0].name}"`),(0,z.q6)(t,n[0])}static async proteomicsDemo(){await async function(){const e=s.TaskBarProgressIndicator.create("Loading proteomics demo…");try{e.update(5,"Importing HYE benchmark (Spectronaut DIA)…");const t=await J.files.readAsText("demo/spectronaut-hye-demo.tsv"),n=await(0,l.parseSpectronautText)(t);n.name="HYE benchmark";const r=o.shell.addTableView(n),a=(0,E.f)(n);if(!a)return void o.shell.warning("Demo: expected two auto-annotated conditions — opened the table without running differential expression.");const i=[...a.group1.columns,...a.group2.columns];e.update(40,"Imputing missing values (KNN)…"),(0,P.Mx)(n,i),n.setTag("proteomics.imputed","true"),e.update(60,"Differential expression (t-test)…"),(0,S.ps)(n,a.group1.columns,a.group2.columns,a.group1.name,a.group2.name),n.setTag("proteomics.de_method","t-test"),e.update(78,"Building volcano and heatmap…");const c=(0,N.gO)(n);r.dockManager.dock(c,s.DOCK_TYPE.RIGHT,null,"Volcano",.5);const u=await x(n,{title:"Heatmap: Top 50 DE Proteins"});r.dockManager.dock(u,s.DOCK_TYPE.DOWN,null,"Heatmap",.45),e.update(90,"Building QC dashboard tab…"),o.shell.addTableView(n).name="HYE benchmark — QC",O(n),o.shell.v=r,f(n,function(e){const t=e.col("adj.p-value"),n=e.col("significant");if(!t)return 0;let o=-1,r=1/0;for(let s=0;s<e.rowCount;s++){if(n&&!n.get(s))continue;if(t.isNone(s))continue;const e=t.get(s);e<r&&(r=e,o=s)}return o<0?0:o}(n)),e.update(100,"Done"),o.shell.info("Proteomics demo: HYE benchmark analyzed end to end (import → impute → differential expression). Yeast and E. coli proteins shift abundance between the two conditions, so the volcano separates the genuinely differential proteins from the constant human background. QC charts are on the second tab; the top hit is selected for its UniProt panel.")}finally{e.close()}}()}static async proteomicsEnrichmentDemo(){await async function(){const e=s.TaskBarProgressIndicator.create("Loading enrichment demo…");try{e.update(10,"Loading human DE result…");const t=await J.files.readAsText("demo/enrichment-demo.csv"),n=s.DataFrame.fromCsv(t);n.name="Treatment vs Control (human)";const r=(e,t)=>{const o=n.col(e);o&&(o.semType=t)};r("Protein ID",m.iu.PROTEIN_ID),r("Gene",m.iu.GENE_SYMBOL),r("log2FC",m.iu.LOG2FC),r("p-value",m.iu.P_VALUE),r("adj.p-value",m.iu.P_VALUE),n.setTag("proteomics.source","generic"),n.setTag("proteomics.de_method","precomputed"),n.setTag("proteomics.de_complete","true"),(0,E.$Y)(n,{group1:{name:"Treatment",columns:[]},group2:{name:"Control",columns:[]}});const a=o.shell.addTableView(n),i=(0,N.gO)(n);a.dockManager.dock(i,s.DOCK_TYPE.RIGHT,null,"Volcano",.5),f(n,0),e.update(45,"Running g:Profiler enrichment (GO / KEGG / Reactome)…");try{const{enrichmentDf:t,mapped:r,total:s}=await(0,Y.D9)(n,m.M5,m.Dx,"hsapiens",["GO:BP","GO:MF","GO:CC","KEGG","REAC","WP"],!0);e.update(90,"Opening enrichment charts…"),(0,z.q6)(t,n).name=`${n.name} — Enrichment`,o.shell.v=a,o.shell.info(`Enrichment demo: ${t.rowCount} over-represented terms across ${r}/${s} genes. Up-regulated proteins are enriched for cell-cycle / mitosis; down-regulated for oxidative phosphorylation. Select a term row to highlight its proteins on the volcano.`)}catch(e){o.shell.warning(`Enrichment demo: g:Profiler enrichment could not run (${e?.message??e}). The DE table and volcano are open — retry via Proteomics | Enrichment Analysis once the service is reachable.`)}e.update(100,"Done")}finally{e.close()}}()}static uniprotPanelWidget(e){return(0,k.ku)(e)}static async shareAnalysisForReview(){const e=o.shell.tv;let t=e?.dataFrame;if(t){if("true"!==t.getTag("proteomics.de_complete")){const e=o.shell.tables.filter(e=>"true"===e.getTag("proteomics.de_complete"));if(0===e.length)return void(0,S.RJ)(t,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)");e.length>1&&o.shell.warning(`Multiple analyzed tables open; sharing "${e[0].name}".`),t=e[0]}await async function(e){if("true"!==e.getTag($.$y))return void o.shell.warning("Run Differential Expression first.");const t=await o.dapi.groups.list(),n=s.Group.defaultGroupsIds?.["All users"],a=(t??[]).filter(e=>!(null==e||e.hidden||e.personal||n&&e.id===n));if(0===a.length)return void o.shell.warning("No teams available to share with. Ask an admin to create a reviewer team.");const i=new Map;for(const e of a){const t=e.friendlyName??e.name??"";t&&!i.has(t)&&i.set(t,e)}const l=Array.from(i.keys()),c=r.input.string("Target",{value:""});c.setTooltip("Free text — your team's name for this target (e.g., MYH7-DMD, muscle-atrophy panel)");const u=r.input.choice("Share with team",{value:l[0],items:l,nullable:!1}),m=r.input.textArea?r.input.textArea("Note for reviewers",{value:""}):r.input.string("Note for reviewers",{value:""}),p=r.input.bool("Verify published dashboard",{value:(0,V.Cb)()});p.setTooltip("Re-open the shared dashboard after publishing to confirm it survives a reload. On = safer (recommended for client deliverables); off = faster share.");const d=r.div();d.style.cssText="background:#fff3cd; padding:8px; border-radius:4px; margin-bottom:8px; display:none;";const f=r.div();f.style.cssText="background:#f0f0f0; padding:8px; border-radius:4px; margin:8px 0; font-family: monospace; font-size:11px;";let g=null;const h=async()=>{const e=(c.value??"").trim(),t=u.value,n=t?i.get(t)??null:null,o=e?(0,$.fz)(e):"<no-target>",s=(new Date).toISOString().slice(0,10);if(e&&n)try{g=await(0,$.T7)(e,n)}catch{g=null}else g=null;const a=(e=>{if(!e)return 0;const t=/-v(\d+)-/.exec(e);if(!t)return 0;const n=parseInt(t[1],10);return Number.isFinite(n)?n:0})(g?g.name:null),l=a>0?a+1:1;g?(d.textContent=`⚠ This will share as v${l} and supersede "${g.name}". The previous version stays available for reference.`,d.style.display="block"):d.style.display="none";const m=`${(0,V.sK)()}-${o}-v${l}-${s}`,p=n?n.friendlyName??n.name??"<unnamed team>":"<pick a team>",h=g?`Will supersede "${g.name}" (v${l})`:"New share";f.innerHTML="",f.appendChild(r.divText(`Project: ${m}`)),f.appendChild(r.divText(`Will be visible to: ${p}`)),f.appendChild(r.divText(`Status: ${h}`)),f.appendChild(r.divText(`Date: ${s}`))};c.onChanged.subscribe(()=>{h()}),u.onChanged.subscribe(()=>{h()}),await h(),r.dialog("Share Analysis for Review").add(c).add(u).add(m).add(p).add(d).add(f).onOK(async()=>{const t=(c.value??"").trim();if(!t)return void o.shell.warning("Target is required.");const n=u.value?i.get(u.value):null;if(!n)return void o.shell.warning("Pick a team to share with.");const r={target:t,reviewerGroup:n,note:m.value??"",priorVersion:g,verify:p.value??!0};try{const t=await(0,j.M)(e,r),s=n.friendlyName??n.name??"(unnamed team)";o.shell.info(`Shared as ${t.name} with team ${s}.`)}catch(e){o.shell.error(`Share failed: ${e?.message??String(e)}`)}}).show()}(t)}else o.shell.warning("No table open")}static publishedAnalysisPanelWidget(e){return function(e){const t=(0,k.xh)(e);if(null==t)return new s.Widget(r.div());if(!(0,$.HF)(t))return new s.Widget(r.div());const n=(0,$.M4)(t);if(null==n)return new s.Widget(r.divText("Shared analysis metadata unavailable. Ask the sharer to re-share."));const a=r.div();if(a.style.padding="8px 4px",null!=n.supersededBy&&""!==n.supersededBy){const e=r.link("Newer version available — open it",async()=>{try{const e=await o.dapi.projects.find(n.supersededBy);await e.open()}catch(e){o.shell.warning(`Could not open the newer version: ${e?.message??e}`)}}),t=r.div([e]);t.style.padding="8px",t.style.marginBottom="10px",t.style.backgroundColor="#fff8dc",t.style.borderRadius="4px",a.appendChild(t)}a.appendChild(r.h2("Shared analysis details"));const i=(0,E.f)(t),l=null!=i?`${i.group2.name} vs ${i.group1.name}`:"unavailable",c=Number.isFinite(n.fcThreshold)?Math.pow(2,n.fcThreshold):NaN,u=Number.isFinite(n.fcThreshold)?`log2(${n.fcThreshold}) (${Number.isFinite(c)?c.toFixed(2):"NaN"}-fold)`:"(unknown)",m=Number.isFinite(n.pThreshold)?`${n.pThreshold} (FDR-adjusted)`:"(unknown)";a.appendChild(U("Target",n.target||"(unknown)")),a.appendChild(U("Shared",B(n.publishedAt))),a.appendChild(U("Shared by",n.publishedBy||"(unknown)")),a.appendChild(U("Method",function(e){switch(e){case"limma":return"limma — moderated t-test";case"deqms":return"DEqMS — peptide-count-aware moderated t-test";case"t-test":return"Welch t-test";case"spectronaut":return"Spectronaut Candidates (pre-computed DE)";default:return e||"(unknown method)"}}(n.deMethod))),a.appendChild(U("Comparison",l)),a.appendChild(U("Fold-change cutoff",u)),a.appendChild(U("p-value cutoff",m));const p=function(e,t){if(null!=t.publishedByEmail&&""!==t.publishedByEmail)return t.publishedByEmail;try{const t=e.col($.MD.PUBLISHED_BY_EMAIL);if(null!=t){const e=t.get(0);if(null!=e&&""!==e)return String(e)}}catch{}try{const t=e.getTag($.L6.PUBLISHED_BY_EMAIL);if(t)return t}catch{}return null}(t,n);if(null!=p){const e=t.name||"shared analysis",o=(0,$.Kj)({sharerEmail:p,sharerName:n.publishedBy||"colleague",projectName:e,publishedDateStr:B(n.publishedAt)}),s=r.link("Request re-run with different parameters",o);s.href=o;const i=r.div([s]);i.style.marginTop="12px",a.appendChild(i)}return new s.Widget(a)}(e)}static async recoverPublishedProjectsOnStartup(){const e=o.events.onProjectOpened??o.events.onCurrentProjectChanged??null;if(e&&"function"==typeof e.subscribe)e.subscribe(()=>{(async()=>{await new Promise(e=>setTimeout(e,200));const e=o.shell.tables;if(Array.isArray(e))for(const t of e)if((0,$.HF)(t))try{await(0,q.I)(t)}catch(e){o.shell.warning(`Could not auto-recover shared analysis on open: ${e?.message??e}`)}})()});else{const e=o.events.onViewAdded;e&&"function"==typeof e.subscribe&&e.subscribe(e=>{if(e instanceof s.TableView){const t=e.dataFrame;t&&(0,$.HF)(t)&&(0,q.I)(t).catch(e=>{o.shell.warning(`Could not auto-recover shared analysis on open: ${e?.message??e}`)})}})}}}Q([o.decorators.init({tags:["init"]}),W("design:type",Function),W("design:paramtypes",[]),W("design:returntype",Promise)],se,"initProteomics",null),Q([o.decorators.func({tags:["autostart"],meta:{autostartImmediate:"true"}}),W("design:type",Function),W("design:paramtypes",[]),W("design:returntype",Promise)],se,"buildProteomicsTopMenu",null),Q([o.decorators.func({"top-menu":"Proteomics | Import | Spectronaut Candidates..."}),W("design:type",Function),W("design:paramtypes",[]),W("design:returntype",Promise)],se,"importSpectronautCandidates",null),Q([o.decorators.func({"top-menu":"Proteomics | Import | Spectronaut Report..."}),W("design:type",Function),W("design:paramtypes",[]),W("design:returntype",Promise)],se,"importSpectronaut",null),Q([o.decorators.func({"top-menu":"Proteomics | Import | MaxQuant..."}),W("design:type",Function),W("design:paramtypes",[]),W("design:returntype",Promise)],se,"importMaxQuant",null),Q([o.decorators.func({"top-menu":"Proteomics | Import | FragPipe..."}),W("design:type",Function),W("design:paramtypes",[]),W("design:returntype",Promise)],se,"importFragPipe",null),Q([o.decorators.func({"top-menu":"Proteomics | Import | Generic 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t!==o.FLOAT_NULL&&n!==o.FLOAT_NULL&&Math.abs(t)>=r.M5&&n<=r.Dx}),b.setTag("proteomics.source","spectronaut-candidates"),b.setTag("proteomics.de_complete","true"),b.setTag("proteomics.de_method","spectronaut");let F=C(w(b,h)),I=C(w(b,y));if(!F||!I){const e=C(w(b,d));if(e&&e.includes("/")){const[t,n]=e.split("/").map(e=>e.trim());F=F??(t||null),I=I??(n||null)}}return F&&I&&(0,i.$Y)(b,{group1:{name:F,columns:[]},group2:{name:I,columns:[]}}),await(0,a.rv)(b),b}function C(e){if(!e)return null;for(let t=0;t<e.length;t++){const n=e.get(t);if(null!=n&&String(n).trim().length>0)return String(n).trim()}return null}},53(e,t,n){"use strict";n.d(t,{A:()=>f,parseSpectronautText:()=>g});var o=n(328),r=n(82),s=n(641),a=n(954),i=n(252),l=n(117);const c=["R.Condition","R.Replicate","PG.ProteinGroups"],u=["PG.IBAQ","PG.Quantity"];function m(e){if(!e||0===e.trim().length)return null;const t=Date.parse(e);return Number.isNaN(t)?null:t}async function p(e){const t=function(e){const t=Array.from(e.proteinMap.keys()),n=t.length,o=r.Column.fromStrings("PG.ProteinGroups",t);o.semType=s.iu.PROTEIN_ID;const a=[o];if(e.organisms.size>0){const n=t.map(t=>e.organisms.get(t)??""),o=r.Column.fromStrings("PG.Organisms",n);a.push(o)}for(const o of e.sampleKeys){const i=new Float32Array(n);for(let s=0;s<n;s++){const n=e.proteinMap.get(t[s]);i[s]=n.has(o)?n.get(o):r.FLOAT_NULL}const l=r.Column.fromFloat32Array(o,i);l.semType=s.iu.INTENSITY,e.sampleFileNames.has(o)&&l.setTag("spectronaut.fileName",e.sampleFileNames.get(o)),a.push(l)}return r.DataFrame.fromColumns(a)}(e);(0,a.wK)(t,"PG.ProteinGroups","Primary Protein ID",s.iu.PROTEIN_ID);const n=e.sampleKeys;return(0,a.eY)(t,n).isLog2?(0,a.l3)(t,n):(0,a.Kh)(t,n),t.setTag("proteomics.preNormalized","true"),t.setTag("proteomics.source","spectronaut"),function(e,t){const n=new Map;for(const e of t){const t=e.lastIndexOf("_"),o=e.substring(0,t);n.has(o)||n.set(o,[]),n.get(o).push(`log2(${e})`)}const o=Array.from(n.keys());2===o.length&&(0,i.$Y)(e,{group1:{name:o[0],columns:n.get(o[0])},group2:{name:o[1],columns:n.get(o[1])}})}(t,e.sampleKeys),await(0,l.rv)(t),t}function d(e){if(null==e)return null;const t=e.trim();if(""===t||"NaN"===t||"NA"===t)return null;const n=Number(t);return Number.isFinite(n)?n:null}async function f(e,t=.01){const n=r.TaskBarProgressIndicator.create("Streaming Spectronaut report...");try{const r=e.stream().pipeThrough(new TextDecoderStream("utf-8")).getReader(),s=new Map;let a="",i=!1,l=new Map,f=-1,g=-1,y=-1,E=-1,w=-1,v=-1,_=-1,C=-1,b=-1,T=0,P=null,S=null,N=null,A=0,x=0,D=0,L=0,F=performance.now();const I=Math.max(1,e.size),M=e=>{if(e.length<T)return"malformed";const n=e[f];if(!n)return"filtered";if(n.startsWith("CON__")||n.startsWith("REV__"))return"filtered";const o=E>=0?d(e[E]):null;if(null!==o&&o>t)return"filtered";const r=d(e[w]);if(null===r&&null===o)return"filtered";const a=e[g]??"",i=e[y]??"",l=n+""+a+""+i;let c=s.get(l);if(void 0===c&&(c={protein:n,condition:a,replicate:i,maxQuantity:-1/0,minQvalue:1/0,fileName:null,organism:null},s.set(l,c)),null!==r&&r>c.maxQuantity&&(c.maxQuantity=r),null!==o&&o<c.minQvalue&&(c.minQvalue=o),null===c.fileName&&v>=0){const t=e[v];t&&(c.fileName=t)}if(null===c.organism&&_>=0){const t=e[_];t&&(c.organism=t)}if(C>=0){const t=e[C];if(t){const e=m(t);null!==e&&(null===P||e<P)&&(P=e,S=new Date(e).toISOString())}}if(b>=0&&null===N){const t=e[b];t&&t.trim().length>0&&(N=t)}return"kept"},O=e=>{const t=e.split("\t");l=new Map;for(let e=0;e<t.length;e++)l.set(t[e],e);for(const e of c)if(!l.has(e))throw new Error(`Missing required Spectronaut column: ${e}`);const n=u.find(e=>l.has(e));if(!n)throw new Error(`Missing protein-group quantity column (expected one of ${u.join(", 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The look/filter config was stripped by the serializer (Phase 13 e527d07ba1 evidence). Plan 04 step 8 catch should invoke the post-open recovery hook from tags ${l.L6.PUBLISHED_FC_THRESHOLD} / ${l.L6.PUBLISHED_P_THRESHOLD} and re-run this assertion once.`)}if(t.expectEnrichment){const e=o.shell.tables;if(!Array.isArray(e)||e.length<2)throw new Error(`assertPublishedShape: expectEnrichment=true but grok.shell.tables has ${e?.length??0} DataFrames (need ≥ 2)`);if(!e.find(e=>{try{const t=e.col(l.MD.PUBLISHED_INCLUDES_ENRICHMENT);return null!=t&&"true"===String(t.get(0))}catch{return!1}}))throw new Error("assertPublishedShape: protein DF (with _meta_published_includes_enrichment=true) not found among reopened tables");if(!e.find(e=>"true"===e.getTag("proteomics.enrichment")))throw new Error("assertPublishedShape: enrichment DF (proteomics.enrichment=true tag) not found among reopened tables")}const E=u.options??{};if(null!=g.supersedes){const e=E[l.L6.SUPERSEDES];if(e!==g.supersedes)throw new Error(`assertPublishedShape: project.options['${l.L6.SUPERSEDES}']: got 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n=(0,s.k)(e,r.iu.PROTEIN_ID,["protein id","accession"]),a=[],i=[],l=[];for(let o=0;o<e.rowCount;o++){const r=n?n.get(o)??String(o):String(o);for(const n of t){const t=e.col(n);t.isNone(o)||(a.push(r),i.push(n),l.push(t.get(o)))}}const c=o.DataFrame.fromColumns([o.Column.fromStrings("ProteinId",a),o.Column.fromStrings("Sample",i),o.Column.fromFloat32Array("Intensity",new Float32Array(l))]);return c.name="Intensity Distributions",c}function f(e,t,n){const r=[],s=[],a=[],i=new Set(n.group1.columns),l=new Set(n.group2.columns);for(const o of t){const t=e.col(o);let c=0;for(let n=0;n<e.rowCount;n++)t.isNone(n)&&c++;r.push(o),s.push(c/e.rowCount*100),i.has(o)?a.push(n.group1.name):l.has(o)?a.push(n.group2.name):a.push("Other")}const c=o.DataFrame.fromColumns([o.Column.fromStrings("Sample",r),o.Column.fromFloat32Array("MissingPct",new Float32Array(s)),o.Column.fromStrings("Group",a)]);return c.name="Missing Values per Sample",c}},589(e,t,n){"use strict";n.d(t,{aggregateParetoCounts:()=>E,computeControlLines:()=>g,createSpcChartPanel:()=>y,r9:()=>C,resolveDrillDown:()=>h});var o=n(328),r=n(389),s=n(82),a=n(655),i=n(883);const l=["median_intensity","missing_pct","control_corr","protein_count"],c={median_intensity:"Median log2 intensity",missing_pct:"Missing %",control_corr:"Control replicate correlation",protein_count:"Protein count"},u="#888888",m="#666666",p="spc.last_picked_instrument",d={rule_1_only:"Expected false-alarm rate at this rule set: ~0.27%. 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The Nelson 1+5 default is calibrated for ~0.4%."};function f(e){const t=e.median_intensity,n=Object.entries(t).filter(([e,t])=>t).map(([e])=>e).sort();return 1===n.length&&"nelson_1"===n[0]?"rule_1_only":2===n.length&&"nelson_1"===n[0]&&"nelson_5"===n[1]?"rules_1_5":3===n.length&&n.includes("nelson_1")&&n.includes("nelson_5")&&n.includes("nelson_2")?"rules_1_5_2":8===n.length?"rules_all_8":"rules_other"}function g(e,t){if(!e)return{ucl:NaN,cl:NaN,lcl:NaN};const n=e.metrics[t];return n&&Number.isFinite(n.mean)&&Number.isFinite(n.sd)?{ucl:n.mean+3*n.sd,cl:n.mean,lcl:n.mean-3*n.sd}:{ucl:NaN,cl:NaN,lcl:NaN}}async function h(e,t){if(null==e.source_project_id)return{kind:"toast",message:`Source for '${e.run_label}' is not currently available. 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n=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0"])]);(0,l.applyAnnotation)(n,{group1:{name:"Control",columns:["s1","s2"]},group2:{name:"Treatment",columns:["s3","s4"]},organism:"rnorvegicus"}),(0,t.E3)((0,l.Di)(n),"rnorvegicus"),(0,t.E3)((0,l.f)(n).group1.name,"Control");const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0"])]);(0,l.applyAnnotation)(o,{group1:{name:"A",columns:["s1"]},group2:{name:"B",columns:["s2"]}}),(0,t.E3)(void 0===(0,l.Di)(o),!0)}),(0,t.t6)("getGroups round-trips GroupAssignment correctly",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0"])]);(0,l.$Y)(n,{group1:{name:"Control",columns:["s1","s2","s3"]},group2:{name:"Treatment",columns:["s4","s5","s6"]}});const o=(0,l.f)(n);(0,t.E3)(null!==o,!0),(0,t.E3)(o.group1.name,"Control"),(0,t.E3)(o.group2.name,"Treatment"),(0,t.E3)(o.group1.columns.length,3),(0,t.E3)(o.group2.columns.length,3),(0,t.E3)(o.group1.columns[0],"s1"),(0,t.E3)(o.group2.columns[2],"s6")}),(0,t.t6)("seedAnnotationDialogInputs returns Control/Treatment defaults when no tag",async()=>{const e=p(3,["s1","s2"],["s3","s4"]),n=(0,l.Yf)(e,["s1","s2","s3","s4"]);(0,t.E3)(n.group1Name,"Control"),(0,t.E3)(n.group2Name,"Treatment"),(0,t.E3)(n.group1Cols.length,0),(0,t.E3)(n.group2Cols.length,0)}),(0,t.t6)("seedAnnotationDialogInputs reads names + columns from existing groups",async()=>{const e=p(3,["s1","s2"],["s3","s4"]);(0,l.$Y)(e,{group1:{name:"DMD",columns:["s1","s2"]},group2:{name:"WT",columns:["s3","s4"]}});const n=(0,l.Yf)(e,["s1","s2","s3","s4"]);(0,t.E3)(n.group1Name,"DMD"),(0,t.E3)(n.group2Name,"WT"),(0,t.E3)(n.group1Cols.length,2),(0,t.E3)(n.group2Cols.length,2),(0,t.E3)(n.group1Cols[0].name,"s1"),(0,t.E3)(n.group2Cols[1].name,"s4")}),(0,t.t6)("seedAnnotationDialogInputs drops column refs not in the DataFrame",async()=>{const e=p(3,["s1","s2"],["s3","s4"]);(0,l.$Y)(e,{group1:{name:"DMD",columns:["s1","gone","s2"]},group2:{name:"WT",columns:["also-gone","s3","s4"]}});const n=(0,l.Yf)(e,["s1","s2","s3","s4"]);(0,t.E3)(n.group1Cols.length,2),(0,t.E3)(n.group2Cols.length,2),(0,t.E3)(n.group1Cols.map(e=>e.name).join(","),"s1,s2"),(0,t.E3)(n.group2Cols.map(e=>e.name).join(","),"s3,s4")}),(0,t.t6)("seedAnnotationDialogInputs drops column refs not in available list",async()=>{const e=p(3,["s1","s2"],["s3","s4"]);(0,l.$Y)(e,{group1:{name:"A",columns:["s1","s2"]},group2:{name:"B",columns:["s3","s4"]}});const n=(0,l.Yf)(e,["s1","s3"]);(0,t.E3)(n.group1Cols.length,1),(0,t.E3)(n.group2Cols.length,1),(0,t.E3)(n.group1Cols[0].name,"s1"),(0,t.E3)(n.group2Cols[0].name,"s3")}),(0,t.t6)("seedAnnotationDialogInputs falls back to defaults when stored names are empty",async()=>{const e=p(3,["s1","s2"],["s3","s4"]);(0,l.$Y)(e,{group1:{name:"",columns:["s1","s2"]},group2:{name:"",columns:["s3","s4"]}});const n=(0,l.Yf)(e,["s1","s2","s3","s4"]);(0,t.E3)(n.group1Name,"Control"),(0,t.E3)(n.group2Name,"Treatment")})}),(0,t.L1)("Normalization",()=>{(0,t.t6)("median normalization shifts column medians to zero",async()=>{const n=e.Column.fromFloat32Array("intensity",new Float32Array([2,4,6,8,10]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3","P4"]),n]);(0,c.aj)(o,["intensity"]);const r=o.col("intensity");(0,t.E3)(Math.abs(r.get(0)- -4)<.01,!0),(0,t.E3)(Math.abs(r.get(1)- -2)<.01,!0),(0,t.E3)(Math.abs(r.get(2)-0)<.01,!0),(0,t.E3)(Math.abs(r.get(3)-2)<.01,!0),(0,t.E3)(Math.abs(r.get(4)-4)<.01,!0)}),(0,t.t6)("median normalization skips null values",async()=>{const n=e.Column.fromFloat32Array("intensity",new Float32Array([2,e.FLOAT_NULL,6,8,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3","P4"]),n]);(0,c.aj)(o,["intensity"]);const r=o.col("intensity");(0,t.E3)(r.isNone(1),!0),(0,t.E3)(r.isNone(4),!0),(0,t.E3)(!r.isNone(0),!0),(0,t.E3)(!r.isNone(2),!0),(0,t.E3)(!r.isNone(3),!0)}),(0,t.t6)("normalization sets proteomics.normalized tag",async()=>{const n=e.Column.fromFloat32Array("intensity",new Float32Array([1,2,3]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2"]),n]);(0,c.aj)(o,["intensity"]),(0,t.E3)(o.getTag("proteomics.normalized"),"true")}),(0,t.t6)("quantile normalization aligns column distributions",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([5,2,3,6])),o=e.Column.fromFloat32Array("s2",new Float32Array([4,14,8,2])),r=e.Column.fromFloat32Array("s3",new Float32Array([3,1,9,7]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY,r.semType=s.iu.INTENSITY;const a=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3"]),n,o,r]);(0,c.VD)(a,["s1","s2","s3"]);const i=[a.col("s1").get(0),a.col("s1").get(1),a.col("s1").get(2),a.col("s1").get(3)],l=[a.col("s2").get(0),a.col("s2").get(1),a.col("s2").get(2),a.col("s2").get(3)],u=[a.col("s3").get(0),a.col("s3").get(1),a.col("s3").get(2),a.col("s3").get(3)];i.sort((e,t)=>e-t),l.sort((e,t)=>e-t),u.sort((e,t)=>e-t);for(let e=0;e<4;e++)(0,t.E3)(Math.abs(i[e]-l[e])<.01,!0),(0,t.E3)(Math.abs(i[e]-u[e])<.01,!0)}),(0,t.t6)("quantile normalization preserves null values",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([5,e.FLOAT_NULL,3,6])),o=e.Column.fromFloat32Array("s2",new Float32Array([4,14,8,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3"]),n,o]);(0,c.VD)(r,["s1","s2"]),(0,t.E3)(r.col("s1").isNone(1),!0),(0,t.E3)(r.col("s2").isNone(3),!0),(0,t.E3)(!r.col("s1").isNone(0),!0),(0,t.E3)(!r.col("s2").isNone(0),!0)}),(0,t.t6)("quantile normalization sets proteomics.normalized tag",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([1,2,3])),o=e.Column.fromFloat32Array("s2",new Float32Array([4,5,6]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2"]),n,o]);(0,c.VD)(r,["s1","s2"]),(0,t.E3)(r.getTag("proteomics.normalized"),"true")}),(0,t.t6)("quantile normalization with < 2 columns returns without error",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([1,2,3]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2"]),n]);(0,c.VD)(o,["s1"]),(0,t.E3)(Math.abs(o.col("s1").get(0)-1)<.01,!0)}),(0,t.t6)("vsnNormalize falls back to quantile on R failure",async()=>{const n=e.Column.fromFloat32Array("log2(s1)",new Float32Array([5,2,3,6])),o=e.Column.fromFloat32Array("log2(s2)",new Float32Array([4,14,8,2]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY;const r=e.Column.fromFloat32Array("s1",new Float32Array([32,4,8,64])),a=e.Column.fromFloat32Array("s2",new Float32Array([16,16384,256,4])),i=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3"]),r,a,n,o]);await(0,c.Nx)(i,["log2(s1)","log2(s2)"]),(0,t.E3)(i.getTag("proteomics.normalized"),"true")})}),(0,t.L1)("Imputation",()=>{(0,t.t6)("MinProb imputation fills all NaN values",async()=>{const n=new Float32Array([10,e.FLOAT_NULL,14,e.FLOAT_NULL,12]),o=e.Column.fromFloat32Array("intensity",n);o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3","P4"]),o]);(0,u.U0)(r,["intensity"]);const a=r.col("intensity");for(let e=0;e<a.length;e++)(0,t.E3)(a.isNone(e),!1)}),(0,t.t6)("imputed values are below the observed mean",async()=>{const n=new Float32Array([10,12,14,16,e.FLOAT_NULL,e.FLOAT_NULL]),o=e.Column.fromFloat32Array("intensity",n);o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3","P4","P5"]),o]);(0,u.U0)(r,["intensity"],1.8,.3);const a=r.col("intensity");(0,t.E3)(a.get(4)<13,!0),(0,t.E3)(a.get(5)<13,!0)}),(0,t.t6)("imputation sets proteomics.imputed tag",async()=>{const n=e.Column.fromFloat32Array("intensity",new Float32Array([1,e.FLOAT_NULL,3]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2"]),n]);(0,u.U0)(o,["intensity"]),(0,t.E3)(o.getTag("proteomics.imputed"),"true")}),(0,t.t6)("kNN imputation fills missing values using nearest neighbors",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([10,11,10.5,12,100])),o=e.Column.fromFloat32Array("s2",new Float32Array([20,21,e.FLOAT_NULL,22,200])),r=e.Column.fromFloat32Array("s3",new Float32Array([30,31,30.5,32,300]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY,r.semType=s.iu.INTENSITY;const a=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3","P4"]),n,o,r]),i=(0,u.Mx)(a,["s1","s2","s3"],3);(0,t.E3)(i,1);const l=a.col("s2").get(2);(0,t.E3)(Math.abs(l-21)<1,!0)}),(0,t.t6)("kNN imputation falls back to column mean when no neighbors have values",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([10,e.FLOAT_NULL,e.FLOAT_NULL])),o=e.Column.fromFloat32Array("s2",new Float32Array([20,e.FLOAT_NULL,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2"]),n,o]),a=(0,u.Mx)(r,["s1","s2"],10);(0,t.E3)(a>=2,!0)}),(0,t.t6)("kNN imputation returns correct count and sets tag",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([1,2,e.FLOAT_NULL,4])),o=e.Column.fromFloat32Array("s2",new Float32Array([5,e.FLOAT_NULL,7,8]));n.semType=s.iu.INTENSITY,o.semType=s.iu.INTENSITY;const r=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3"]),n,o]),a=(0,u.Mx)(r,["s1","s2"],3);(0,t.E3)(a,2),(0,t.E3)(r.getTag("proteomics.imputed"),"true");for(let e=0;e<4;e++)(0,t.E3)(r.col("s1").isNone(e),!1),(0,t.E3)(r.col("s2").isNone(e),!1)}),(0,t.t6)("imputeZero replaces all nulls with 0",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([1,e.FLOAT_NULL,3,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3"]),n]),r=(0,u.fX)(o,["s1"]);(0,t.E3)(r,2),(0,t.E3)(Math.abs(o.col("s1").get(1)-0)<.01,!0),(0,t.E3)(Math.abs(o.col("s1").get(3)-0)<.01,!0),(0,t.E3)(o.getTag("proteomics.imputed"),"true")}),(0,t.t6)("imputeMean replaces all nulls with column mean",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([2,e.FLOAT_NULL,6,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3"]),n]),r=(0,u.Q2)(o,["s1"]);(0,t.E3)(r,2),(0,t.E3)(Math.abs(o.col("s1").get(1)-4)<.01,!0),(0,t.E3)(Math.abs(o.col("s1").get(3)-4)<.01,!0),(0,t.E3)(o.getTag("proteomics.imputed"),"true")}),(0,t.t6)("imputeMedian replaces all nulls with column median",async()=>{const n=e.Column.fromFloat32Array("s1",new Float32Array([2,e.FLOAT_NULL,6,10,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY;const o=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P0","P1","P2","P3","P4"]),n]),r=(0,u.p4)(o,["s1"]);(0,t.E3)(r,2),(0,t.E3)(Math.abs(o.col("s1").get(1)-6)<.01,!0),(0,t.E3)(Math.abs(o.col("s1").get(4)-6)<.01,!0),(0,t.E3)(o.getTag("proteomics.imputed"),"true")})}),(0,t.L1)("Differential Expression",()=>{(0,t.t6)("DE produces correct log2FC sign for known groups",async()=>{const e=["ctrl1","ctrl2","ctrl3"],n=["treat1","treat2","treat3"],o=e.map(()=>Array.from({length:5},()=>5)),r=n.map(()=>Array.from({length:5},()=>10)),s=p(5,e,n,o,r);(0,m.ps)(s,e,n,"Control","Treatment");const a=s.col("log2FC");for(let e=0;e<5;e++)(0,t.E3)(a.get(e)>0,!0)}),(0,t.t6)("DE produces valid p-values between 0 and 1",async()=>{const e=["ctrl1","ctrl2","ctrl3"],n=["treat1","treat2","treat3"],o=p(3,e,n,[[4.8,5.1,5.3],[4.9,5,5.2],[5.1,4.8,5]],[[9.8,10.1,10.3],[9.9,10,10.2],[10.1,9.8,10]]);(0,m.ps)(o,e,n,"Control","Treatment");const r=o.col("p-value"),s=o.col("adj.p-value");for(let e=0;e<3;e++)(0,t.E3)(r.get(e)>=0&&r.get(e)<=1,!0),(0,t.E3)(s.get(e)>=0&&s.get(e)<=1,!0)}),(0,t.t6)("proteins with <2 replicates get null p-values",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein ID",["P0"]),e.Column.fromFloat32Array("ctrl1",new Float32Array([5])),e.Column.fromFloat32Array("ctrl2",new Float32Array([e.FLOAT_NULL])),e.Column.fromFloat32Array("ctrl3",new Float32Array([e.FLOAT_NULL])),e.Column.fromFloat32Array("treat1",new Float32Array([10])),e.Column.fromFloat32Array("treat2",new Float32Array([10.5])),e.Column.fromFloat32Array("treat3",new Float32Array([9.5]))]);(0,m.ps)(n,["ctrl1","ctrl2","ctrl3"],["treat1","treat2","treat3"],"Control","Treatment");const o=n.col("p-value");(0,t.E3)(o.isNone(0),!0)}),(0,t.t6)("significant column marks proteins passing both thresholds",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein ID",["P_significant","P_not_significant"]),e.Column.fromFloat32Array("ctrl1",new Float32Array([5,5])),e.Column.fromFloat32Array("ctrl2",new Float32Array([5.1,5.1])),e.Column.fromFloat32Array("ctrl3",new Float32Array([4.9,4.9])),e.Column.fromFloat32Array("treat1",new Float32Array([12,5.2])),e.Column.fromFloat32Array("treat2",new Float32Array([12.1,4.8])),e.Column.fromFloat32Array("treat3",new Float32Array([11.9,5]))]);(0,m.ps)(n,["ctrl1","ctrl2","ctrl3"],["treat1","treat2","treat3"],"Control","Treatment",1,.05);const o=n.col("significant");(0,t.E3)(o.get(0),!0),(0,t.E3)(o.get(1),!1)}),(0,t.t6)("DE sets proteomics.de_complete tag",async()=>{const e=["ctrl1","ctrl2","ctrl3"],n=["treat1","treat2","treat3"],o=e.map(()=>Array.from({length:2},()=>5)),r=n.map(()=>Array.from({length:2},()=>10)),s=p(2,e,n,o,r);(0,m.ps)(s,e,n,"Control","Treatment"),(0,t.E3)(s.getTag("proteomics.de_complete"),"true")}),(0,t.t6)("D-09: DE dialog defaults to the declared (group1 = numerator) contrast",async()=>{(0,t.E3)((0,m.zV)("DMD","WT"),"DMD vs WT"),(0,t.E3)((0,m.zV)("WT","DMD"),"WT vs DMD")}),(0,t.t6)("D-09: contrast is direction-only — reversing flips sign, not |log2FC|",async()=>{const e=["dmd1","dmd2","dmd3"],n=["wt1","wt2","wt3"],o=e.map(()=>Array.from({length:3},()=>9)),r=n.map(()=>Array.from({length:3},()=>4)),s=p(3,e,n,o,r);(0,m.ps)(s,n,e,"WT","DMD");const a=s.col("log2FC").get(0),i=p(3,e,n,o,r);(0,m.ps)(i,e,n,"DMD","WT");const l=i.col("log2FC").get(0);(0,t.E3)(a>0,!0),(0,t.E3)(l<0,!0),(0,t.E3)(Math.abs(Math.abs(a)-Math.abs(l))<1e-6,!0)}),(0,t.t6)("DE assigns correct semantic types",async()=>{const e=["ctrl1","ctrl2","ctrl3"],n=["treat1","treat2","treat3"],o=e.map(()=>Array.from({length:2},()=>5)),r=n.map(()=>Array.from({length:2},()=>10)),a=p(2,e,n,o,r);(0,m.ps)(a,e,n,"Control","Treatment"),(0,t.E3)(a.col("log2FC").semType,s.iu.LOG2FC),(0,t.E3)(a.col("p-value").semType,s.iu.P_VALUE),(0,t.E3)(a.col("adj.p-value").semType,s.iu.P_VALUE)})}),(0,t.L1)("DE result alignment",()=>{(0,t.t6)("copyDEResultsToFrame realigns by row key, not position",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein ID",["P0","P1","P2","P3"])]),o=[3,1,4,2],r=e.DataFrame.fromColumns([e.Column.fromList("int","row",o),e.Column.fromList("double","log2FC",o.map(e=>e-1)),e.Column.fromList("double","p.value",o.map(e=>e-1)),e.Column.fromList("double","adj.p.value",o.map(e=>e-1)),e.Column.fromList("bool","significant",o.map(e=>e-1==0))]),s=(0,m.pd)(n,r);for(let e=0;e<4;e++)(0,t.E3)(n.col("log2FC").get(e),e),(0,t.E3)(n.col("p-value").get(e),e),(0,t.E3)(n.col("adj.p-value").get(e),e),(0,t.E3)(n.col("significant").get(e),0===e);(0,t.E3)(s,1)}),(0,t.t6)("copyDEResultsToFrame falls back to positional without row key",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein ID",["P0","P1","P2"])]),o=e.DataFrame.fromColumns([e.Column.fromList("double","log2FC",[10,20,30]),e.Column.fromList("double","p.value",[1,2,3]),e.Column.fromList("double","adj.p.value",[4,5,6]),e.Column.fromList("bool","significant",[!1,!0,!1])]);(0,m.pd)(n,o),(0,t.E3)(n.col("log2FC").get(1),20),(0,t.E3)(n.col("adj.p-value").get(2),6),(0,t.E3)(n.col("significant").get(1),!0),(0,t.E3)(n.col("significant").get(0),!1)})});var d=n(954);function f(e){const t=e.delimiter??",";return[e.headers.join(t),...e.rows.map(e=>e.join(t))].join("\n")}(0,t.L1)("Generic Parser",()=>{(0,t.t6)("Generic: parses CSV with comma delimiter",async()=>{const n=f({headers:["Protein","Intensity A","Intensity B","Intensity C"],rows:[["P12345","1000","2000","3000"],["P67890","4000","5000","6000"]]}),o=(0,d.T6)(n);(0,t.E3)(o,",");const r=e.DataFrame.fromCsv(n,{delimiter:","});(0,t.E3)(r.columns.length,4),(0,t.E3)(r.rowCount,2)}),(0,t.t6)("Generic: parses TSV with tab delimiter",async()=>{const n=f({headers:["Protein","Intensity A","Intensity B","Intensity C"],rows:[["P12345","1000","2000","3000"],["P67890","4000","5000","6000"]],delimiter:"\t"}),o=(0,d.T6)(n);(0,t.E3)(o,"\t");const r=e.DataFrame.fromCsv(n,{delimiter:"\t"});(0,t.E3)(r.columns.length,4),(0,t.E3)(r.rowCount,2)}),(0,t.t6)("Generic: auto-suggests protein ID column",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein IDs",["P12345"]),e.Column.fromStrings("Gene names",["BRCA1"]),e.Column.fromList(e.COLUMN_TYPE.FLOAT,"Intensity A",[1e3])]),o=(0,d.q2)(n);(0,t.E3)(null!==o,!0),(0,t.E3)(o.name,"Protein IDs")}),(0,t.t6)("Generic: auto-suggests intensity columns",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("id",["P12345"]),e.Column.fromList(e.COLUMN_TYPE.FLOAT,"Intensity Sample1",[1e3]),e.Column.fromList(e.COLUMN_TYPE.FLOAT,"LFQ Sample2",[2e3]),e.Column.fromStrings("notes",["some note"])]),o=(0,d.WI)(n);(0,t.E3)(o.length,2),(0,t.E3)(o.includes("Intensity Sample1"),!0),(0,t.E3)(o.includes("LFQ Sample2"),!0)}),(0,t.t6)("Generic: detects raw intensities for log2 toggle",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromList(e.COLUMN_TYPE.FLOAT,"vals",[5e4,1e5,2e5])]),o=(0,d.eY)(n,["vals"]);(0,t.E3)(o.isLog2,!1)}),(0,t.t6)("Generic: detects already-log2 data",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromList(e.COLUMN_TYPE.FLOAT,"vals",[15.2,18.7,12.1])]),o=(0,d.eY)(n,["vals"]);(0,t.E3)(o.isLog2,!0)}),(0,t.t6)("Generic: log2TransformColumns produces correct values",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromList(e.COLUMN_TYPE.FLOAT,"Intensity A",[1024,0,2048])]);(0,d.Kh)(n,["Intensity A"]);const o=n.col("log2(Intensity A)");(0,t.E3)(null!==o,!0),o&&((0,t.E3)(Math.abs(o.get(0)-10)<.001,!0),(0,t.E3)(o.isNone(1),!0),(0,t.E3)(Math.abs(o.get(2)-11)<.001,!0),(0,t.E3)(o.semType,s.iu.INTENSITY));const r=n.col("Intensity A");(0,t.E3)(r.semType,s.iu.INTENSITY)}),(0,t.t6)("Generic: copyAsLog2Columns copies values without 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i=a.col("CV"),l=a.col("Mean");(0,t.E3)(Math.abs(i.get(0))<.001,!0),(0,t.E3)(Math.abs(l.get(0)-4)<.01,!0),(0,t.E3)(i.get(1)>0,!0)}),(0,t.t6)("Loess/moving-average trend",async()=>{let n=12345;const o=()=>(n=1664525*n+1013904223>>>0,n/4294967295),r=new Float32Array(25),s=new Float32Array(25);for(let e=0;e<25;e++)r[e]=e+1,s[e]=.5*Math.sin(e/5)+.3*(o()-.5);const a=e.DataFrame.fromColumns([e.Column.fromFloat32Array("A",r),e.Column.fromFloat32Array("M",s)]);(0,g.Pq)(a,.5);const i=a.col("MA_trend");(0,t.E3)(null!==i,!0);let l=0;for(let e=0;e<25;e++)i.isNone(e)||l++;(0,t.E3)(l>0,!0);let c=0,u=0,m=0,p=0,d=0,f=0;for(let e=0;e<25;e++){const t=s[e];if(c+=t,u+=t*t,m++,!i.isNone(e)){const t=i.get(e);p+=t,d+=t*t,f++}}const h=u/m-c/m*(c/m),y=d/f-p/f*(p/f);(0,t.E3)(y<h,!0)}),(0,t.t6)("Missingness matrix",async()=>{const n=e.Column.fromFloat32Array("log2(s1)",new Float32Array([5,e.FLOAT_NULL]));n.semType=s.iu.INTENSITY;const o=e.Column.fromFloat32Array("log2(s2)",new 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splits significant genes by fc sign, shared background",async()=>{const e=new Map([[0,"A"],[1,"B"],[2,"C"],[3,"D"]]),n=new Float32Array([2,-2,.5,-3]),o=new Float32Array([.01,.01,.001,.2]),{upGenes:r,downGenes:s,background:a}=(0,h.Bx)(e,n,o,1,.05);(0,t.E3)(r.length,1),(0,t.E3)(r[0],"A"),(0,t.E3)(s.length,1),(0,t.E3)(s[0],"B"),(0,t.E3)(a.length,4),(0,t.E3)(a.includes("A")&&a.includes("B")&&a.includes("C")&&a.includes("D"),!0),(0,t.E3)(r.some(e=>s.includes(e)),!1)}),(0,t.t6)("splitGenesByDirection skips null fc/p rows",async()=>{const n=new Map([[0,"A"],[1,"B"]]),o=new Float32Array([2,0]),r=new Float32Array([.01,0]);o[1]=e.FLOAT_NULL,r[1]=e.FLOAT_NULL;const{upGenes:s,downGenes:a,background:i}=(0,h.Bx)(n,o,r,1,.05);(0,t.E3)(s.length,1),(0,t.E3)(a.length,0),(0,t.E3)(i.length,2)}),(0,t.t6)("buildEnrichmentDf adds Direction column when label given",async()=>{const e=(0,h.Mz)([{native:"GO:0006915",name:"apoptotic 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e=(0,h.Mz)([{native:"GO:0006915",name:"apoptotic process",source:"GO:BP",p_value:.001,significant:!0,term_size:500,query_size:50,intersection_size:10,effective_domain_size:2e4,precision:.2,recall:.02,intersections:[["IEA"],["IDA"],[],["TAS"]]},{native:"KEGG:04210",name:"Apoptosis",source:"KEGG",p_value:.03,significant:!0,term_size:120,query_size:50,intersection_size:5,effective_domain_size:2e4,precision:.1,recall:.042,intersections:[[],["evidence"],[],[]]},{native:"REAC:R-HSA-109581",name:"Apoptosis",source:"REAC",p_value:.12,significant:!1,term_size:80,query_size:50,intersection_size:3,effective_domain_size:2e4,precision:.06,recall:.0375,intersections:[["IEA"],[],[],[]]}],["TP53","BRCA1","EGFR","MYC"]);(0,t.E3)(e.col("Direction"),null),(0,t.E3)(e.columns.length,8)}),(0,t.t6)("wireEnrichmentToVolcano selects matching proteins, source DF unmutated",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Intersection",["TP53, 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down"),(0,t.E3)(e.background,3,"background unchanged")}),(0,t.t6)("buildEnrichmentInputsCsv: quotes a gene containing a comma",async()=>{const e=w();e.col("Gene names").set(0,"G1,alias");const{csv:n}=(0,E.J)(e,1,.05);(0,t.E3)(n.includes('"G1,alias",up'),!0,"comma-bearing field is CSV-quoted")}),(0,t.t6)("buildEnrichmentInputsCsv: throws without DE columns",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Gene names",["G1"])]);n.col("Gene names").semType=s.iu.GENE_SYMBOL;let o=!1;try{(0,E.J)(n,1,.05)}catch{o=!0}(0,t.E3)(o,!0,"missing log2FC/adj.p-value is an error")})});var v=n(328),_=n(858);function C(t,n){const o=[],r=[],s=[],a=[],i=[],l=[],c=[],u=[],m=[];for(let e=0;e<t;e++){o.push(e%2==0?"GO:BP":"KEGG"),r.push(`GO:${String(e).padStart(7,"0")}`),s.push(n&&0===e?n:`Term ${e+1}`);const t=.001*(e+1);a.push(t),i.push(t),l.push(10-Math.min(e,9)),c.push(.2-.005*e),u.push("TP53, BRCA1"),m.push(t<.05)}const p=e.DataFrame.fromColumns([e.Column.fromStrings("Source",o),e.Column.fromStrings("Term ID",r),e.Column.fromStrings("Term Name",s),e.Column.fromFloat32Array("P-value",new Float32Array(a)),e.Column.fromFloat32Array("FDR",new Float32Array(i)),e.Column.fromInt32Array("Gene Count",new Int32Array(l)),e.Column.fromFloat32Array("Gene Ratio",new Float32Array(c)),e.Column.fromStrings("Intersection",u),e.Column.fromList("bool","Significant",m)]);return p.setTag("proteomics.enrichment","true"),p}function b(){const t=e.Column.fromStrings("Gene Name",["TP53","BRCA1","EGFR","MYC","AKT1"]);return t.semType=s.iu.GENE_SYMBOL,e.DataFrame.fromColumns([t,e.Column.fromFloat32Array("log2FC",new Float32Array([1.5,-2,.5,3,-1])),e.Column.fromFloat32Array("adj.p-value",new Float32Array([.001,.01,.5,1e-4,.04]))])}function T(t,n){t.columns.add(e.Column.fromStrings("Direction",n))}function P(e,t){let n=0;for(const o of e.viewers)o.dataFrame?.dart===t.dart&&n++;return n}function S(e){let t=0;for(const n of e.viewers)t++;return t}function N(e){let t=0;for(let n=0;n<e.length;n++)!0===e.get(n)&&t++;return t}(0,t.L1)("Enrichment Visualization",()=>{(0,t.t6)("prepareEnrichmentChartColumns adds negLog10FDR on the same frame",async()=>{const e=C(20);(0,y.E0)(e,15);const n=e.col(y.bC);(0,t.E3)(null!==n,!0);const o=n.get(0);(0,t.E3)(Math.abs(o-3)<.01,!0),(0,t.E3)(e.rowCount,20)}),(0,t.t6)("prepareEnrichmentChartColumns marks exactly topN terms (no Direction)",async()=>{const e=C(20);(0,y.E0)(e,15);const n=e.col(y.$i);(0,t.E3)(N(n),15)}),(0,t.t6)("prepareEnrichmentChartColumns marks topN per direction",async()=>{const e=C(20);T(e,Array.from({length:20},(e,t)=>t<10?"Up":"Down")),(0,y.E0)(e,5);const n=e.col(y.$i);(0,t.E3)(N(n),10)}),(0,t.t6)("prepareEnrichmentChartColumns marks all when fewer rows than topN",async()=>{const e=C(5);(0,y.E0)(e,15);const n=e.col(y.$i);(0,t.E3)(N(n),5)}),(0,t.t6)("prepareEnrichmentChartColumns is idempotent on re-run",async()=>{const e=C(20);(0,y.E0)(e,15);const n=e.columns.length;(0,y.E0)(e,15),(0,t.E3)(e.columns.length,n)}),(0,t.t6)("wireEnrichmentToVolcano returns EMPTY without gene column",async()=>{const n=C(3),o=e.DataFrame.fromColumns([e.Column.fromStrings("SomeColumn",["A","B","C"])]),r=(0,y.aB)(n,o);(0,t.E3)(r===_.Subscription.EMPTY,!0)}),(0,t.t6)("wireEnrichmentToVolcano selects matching genes on protein DataFrame",async()=>{const e=C(3);e.col("Intersection").set(0,"TP53, BRCA1");const n=b(),o=(0,y.aB)(e,n);(0,t.E3)(o!==_.Subscription.EMPTY,!0),e.currentRowIdx=0,(0,t.E3)(n.selection.get(0),!0),(0,t.E3)(n.selection.get(1),!0),(0,t.E3)(n.selection.get(2),!1),(0,t.E3)(n.selection.get(3),!1),(0,t.E3)(n.selection.get(4),!1),o.unsubscribe()}),(0,t.t6)("wireEnrichmentToVolcano clears selection before new selection",async()=>{const e=C(3);e.col("Intersection").set(0,"TP53"),e.col("Intersection").set(1,"EGFR");const n=b();n.selection.set(4,!0,!1),n.selection.fireChanged();const o=(0,y.aB)(e,n);e.currentRowIdx=0,(0,t.E3)(n.selection.get(4),!1),(0,t.E3)(n.selection.get(0),!0),o.unsubscribe()}),(0,t.t6)("openEnrichmentVisualization docks dot/bar on enrichment view (directional)",async()=>{const e=C(4);T(e,["Up","Up","Down","Down"]),e.name="Enrichment (test B)";const n=b();n.name="Protein (test B)";const o=v.shell.addTableView(n),r=S(o),s=(0,y.q6)(e,n);try{(0,t.E3)(S(o),r,"protein view must not gain dot/bar viewers; gained "+(S(o)-r)),(0,t.E3)(S(s)>=4,!0,`enrichment view should carry ≥4 dot/bar viewers; got ${S(s)}`),(0,t.E3)(P(s,n),0,"enrichment view must not carry a proteinDf-bound volcano"),e.currentRowIdx=0,(0,t.E3)(n.selection.trueCount>=1,!0,"selecting an enrichment row should still highlight matching protein rows")}finally{s.close(),o.close()}}),(0,t.t6)("openEnrichmentVisualization docks dot/bar on enrichment view (single-direction)",async()=>{const e=C(3);e.name="Enrichment (test C)";const n=b();n.name="Protein (test C)";const o=v.shell.addTableView(n),r=S(o),s=(0,y.q6)(e,n);try{(0,t.E3)(S(o),r,"protein view must not gain dot/bar viewers; gained "+(S(o)-r)),(0,t.E3)(S(s)>=2,!0,`enrichment view should carry ≥2 dot/bar viewers; got ${S(s)}`),(0,t.E3)(P(s,n),0,"enrichment view must not carry a proteinDf-bound volcano")}finally{s.close(),o.close()}}),(0,t.t6)("openEnrichmentVisualization switches focus to enrichment TableView",async()=>{const e=C(4);T(e,["Up","Up","Down","Down"]),e.name="Enrichment (test D)";const n=b();n.name="Protein (test D)";const o=v.shell.addTableView(n),r=(0,y.q6)(e,n);try{const n=v.shell.v?.dataFrame?.dart;(0,t.E3)(n===e.dart,!0,"focused view should be the enrichment TableView after enrichment runs")}finally{r.close(),o.close()}}),(0,t.t6)("enrichmentBannerRendersWhenTagSet",async()=>{const e=C(3);e.name="Enrichment (banner-on)",e.setTag("proteomics.enrichment_smart_filtered","true"),e.setTag("proteomics.enrichment_smart_filtered_kept","20"),e.setTag("proteomics.enrichment_smart_filtered_total","47"),e.setTag("proteomics.enrichment_smart_filtered_dropped_parents","3"),e.setTag("proteomics.enrichment_smart_filtered_cap","15");const n=b(),o=(0,y.q6)(e,n);try{const e=o.root.querySelectorAll('[data-smart-filter-banner="true"]');(0,t.E3)(e.length>=1,!0,"banner should be docked when tag is set");const n=e[0].textContent??"";(0,t.E3)(n.includes("Smart pathway filter active"),!0),(0,t.E3)(n.includes("showing 20 of 47 terms"),!0),(0,t.E3)(n.includes("dropped 3 generic parents"),!0),(0,t.E3)(n.includes("capped at 15 per source"),!0),(0,t.E3)(n.includes("Re-run with the filter off"),!0)}finally{o.close()}}),(0,t.t6)("enrichmentBannerAbsentWhenTagUnset",async()=>{const e=C(3);e.name="Enrichment (banner-off)";const n=b(),o=(0,y.q6)(e,n);try{const e=o.root.querySelectorAll('[data-smart-filter-banner="true"]');(0,t.E3)(e.length,0)}finally{o.close()}})});var A=n(53),x=n(110);function D(e){const t=[["R.FileName","R.Condition","R.Replicate","PG.ProteinGroups","PG.Organisms",e.quantityColumn??"PG.IBAQ","EG.Qvalue","PEP.StrippedSequence","EG.ModifiedPeptide","FG.Charge","FG.Id"].join("\t")],n=[{strip:"PEPTIDER",mod:"_PEPTIDER_",charge:"2",fg:"FG1"},{strip:"ANOTHERPEP",mod:"_ANOTHERPEP_",charge:"3",fg:"FG2"}],o=(e,o,r,s,a,i,l)=>{for(const c of n)t.push([e,o,String(r),s,a,i,l,c.strip,c.mod,c.charge,c.fg].join("\t"))};let r=100;for(const t of e.proteins){const n=e.ibaqValues?.get(t.id)??r++;for(const r of e.conditions)for(const s of e.replicates){const a=(e.fileNameTemplate??"file")+`_${r}_${s}`,i=e.qValues?.get(t.id)??.001,l=t.organism??"Homo sapiens";o(a,r,s,t.id,l,String(n),String(i))}}if(e.extraRows){let t=500;for(const n of e.extraRows){const r=n.quantity??t++;for(const t of e.conditions)for(const s of e.replicates){const a=(e.fileNameTemplate??"file")+`_${t}_${s}`,i=n.organism??"Homo sapiens";o(a,t,s,n.id,i,String(r),String(n.qValue))}}}return t.join("\n")}(0,t.L1)("Spectronaut",()=>{const e=[{id:"P12345"},{id:"Q67890"},{id:"O15439"}],n={proteins:e,conditions:["CondA","CondB"],replicates:[1,2]};async function o(e){return await(0,A.A)(new File([e],"fixture.tsv",{type:"text/tab-separated-values"}))}async function r(e){return je.files.readAsText(`demo/${e}`)}function a(e){return e.columns.toList().filter(e=>e.semType===s.iu.INTENSITY&&!e.name.startsWith("log2(")).map(e=>e.name).sort()}function i(e){const t=e.col("Primary Protein ID")??e.col("PG.ProteinGroups"),n=new Map;for(let o=0;o<e.rowCount;o++)n.set(String(t.get(o)),o);return{col:t,map:n}}async function c(e){const t=[],n=v.shell.info.bind(v.shell);v.shell.info=e=>{t.push(String(e))};try{return{df:await o(e),infos:t}}finally{v.shell.info=n}}(0,t.t6)("pivot produces correct protein count",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.rowCount,3)}),(0,t.t6)("pivot produces correct sample column names",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(null!==o.col("CondA_1"),!0),(0,t.E3)(null!==o.col("CondA_2"),!0),(0,t.E3)(null!==o.col("CondB_1"),!0),(0,t.E3)(null!==o.col("CondB_2"),!0)}),(0,t.t6)("CON__ and REV__ prefixed proteins are excluded",async()=>{const e=D({...n,proteins:[{id:"P12345"},{id:"CON__P99999"},{id:"REV__Q11111"}]}),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.rowCount,1),(0,t.E3)(o.col("PG.ProteinGroups").get(0),"P12345")}),(0,t.t6)("rows with numeric EG.Qvalue > threshold are excluded",async()=>{const o=new Map;o.set("P12345",.001),o.set("Q67890",.05),o.set("O15439",.005);const r=D({...n,proteins:e,qValues:o}),s=await(0,A.parseSpectronautText)(r);(0,t.E3)(s.rowCount,2)}),(0,t.t6)("non-numeric EG.Qvalue rows treated as passing",async()=>{const o=new Map;o.set("P12345",.001),o.set("Q67890","Profiled"),o.set("O15439","NaN");const r=D({...n,proteins:e,qValues:o}),s=await(0,A.parseSpectronautText)(r);(0,t.E3)(s.rowCount,3)}),(0,t.t6)("PG.ProteinGroups has PROTEIN_ID semantic type",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.col("PG.ProteinGroups")?.semType,s.iu.PROTEIN_ID)}),(0,t.t6)("intensity columns have INTENSITY semantic type",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.col("CondA_1")?.semType,s.iu.INTENSITY),(0,t.E3)(o.col("CondB_2")?.semType,s.iu.INTENSITY)}),(0,t.t6)("R.FileName stored as spectronaut.fileName tag on intensity columns",async()=>{const e=D({...n,fileNameTemplate:"run"}),o=(await(0,A.parseSpectronautText)(e)).col("CondA_1");if((0,t.E3)(null!==o,!0),o){const e=o.getTag("spectronaut.fileName");(0,t.E3)(null!==e&&""!==e,!0),(0,t.E3)(e.includes("run"),!0)}}),(0,t.t6)("groups auto-populated via setGroups when exactly 2 conditions",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e),r=(0,l.f)(o);(0,t.E3)(null!==r,!0),r&&((0,t.E3)(r.group1.columns.length,2),(0,t.E3)(r.group2.columns.length,2))}),(0,t.t6)("groups not set when more than 2 conditions",async()=>{const e=D({...n,conditions:["CondA","CondB","CondC"]}),o=await(0,A.parseSpectronautText)(e),r=(0,l.f)(o);(0,t.E3)(r,null)}),(0,t.t6)("pre-normalized tag set for raw (non-log2) intensity data",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.getTag("proteomics.preNormalized"),"true")}),(0,t.t6)("pre-normalized tag set when detectLog2Status detects log2-range values",async()=>{const e=new Map;e.set("P12345",15.2),e.set("Q67890",22.7),e.set("O15439",18.1);const o=D({...n,ibaqValues:e}),r=await(0,A.parseSpectronautText)(o);(0,t.E3)(r.getTag("proteomics.preNormalized"),"true")}),(0,t.t6)("both raw and log2 intensity columns present in output",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(null!==o.col("CondA_1"),!0),(0,t.E3)(null!==o.col("log2(CondA_1)"),!0),(0,t.E3)(null!==o.col("log2(CondB_2)"),!0)}),(0,t.t6)("proteomics.source tag set to spectronaut",async()=>{const e=D(n),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.getTag("proteomics.source"),"spectronaut")}),(0,t.t6)("PG.Quantity accepted as alternative to PG.IBAQ",async()=>{const e=D({...n,quantityColumn:"PG.Quantity"}),o=await(0,A.parseSpectronautText)(e);(0,t.E3)(o.rowCount,3),(0,t.E3)(null!==o.col("CondA_1"),!0),(0,t.E3)(null!==o.col("CondB_2"),!0),(0,t.E3)(o.col("CondA_1")?.semType,s.iu.INTENSITY)}),(0,t.t6)("throws when neither PG.IBAQ nor PG.Quantity is present",async()=>{const e=D({...n,quantityColumn:"PG.Bogus"});let o=!1;try{await(0,A.parseSpectronautText)(e)}catch(e){o=!0,(0,t.E3)(e.message.includes("PG.IBAQ"),!0),(0,t.E3)(e.message.includes("PG.Quantity"),!0)}(0,t.E3)(o,!0)}),(0,t.t6)("demo file produces correct dimensions",async()=>{const e=[];for(let t=0;t<93;t++)e.push({id:`P${String(t).padStart(5,"0")}`});const n=D({proteins:e,conditions:["HYE mix A","HYE mix B"],replicates:[1,2,3,4]}),o=await(0,A.parseSpectronautText)(n);(0,t.E3)(o.rowCount,93);const r=o.columns.toList().filter(e=>e.semType===s.iu.INTENSITY&&!e.name.startsWith("log2("));(0,t.E3)(r.length,8)}),(0,t.t6)("streams precursor fixture",async()=>{const e=await r("spectronaut-hye-precursor.tsv"),n=await o(e);(0,t.E3)(n.rowCount>0,!0);const a=n.columns.toList().find(e=>e.semType===s.iu.INTENSITY&&!e.name.startsWith("log2(")&&(e.name.startsWith("CondA_")||e.name.startsWith("CondB_")));(0,t.E3)(void 0!==a,!0),(0,t.E3)(n.col("PG.ProteinGroups")?.semType,s.iu.PROTEIN_ID)}),(0,t.t6)("sniffIsPrecursor routes by header",async()=>{const e=["R.FileName","R.Condition","R.Replicate","PG.ProteinGroups","PG.Organisms","PG.Quantity","EG.Qvalue","EG.ModifiedPeptide","FG.Charge","PEP.StrippedSequence"].join("\t"),n=["run_CondA_1","CondA","1","P1","Homo sapiens","10","0.001","_PEP_","2","PEP"].join("\t"),o=["R.FileName","R.Condition","R.Replicate","PG.ProteinGroups","PG.Organisms","PG.IBAQ"].join("\t"),r=["run_CondA_1","CondA","1","P1","Homo sapiens","10"].join("\t");(0,t.E3)(await(0,x.sniffIsPrecursor)(new File([e+"\n"+n],"p.tsv")),!0),(0,t.E3)(await(0,x.sniffIsPrecursor)(new File([o+"\n"+r],"pg.tsv")),!1)}),(0,t.t6)("stream path matches text path",async()=>{const e=D(n),r=await(0,A.parseSpectronautText)(e),s=await o(e);(0,t.E3)(s.rowCount,r.rowCount);const c=a(r),u=a(s);(0,t.E3)(u.join(","),c.join(","));for(const e of c)(0,t.E3)(null!==s.col(`log2(${e})`),null!==r.col(`log2(${e})`));(0,t.E3)(s.getTag("proteomics.source"),r.getTag("proteomics.source")),(0,t.E3)(s.getTag("proteomics.preNormalized"),r.getTag("proteomics.preNormalized"));const m=(0,l.f)(r),p=(0,l.f)(s);(0,t.E3)(null!==p,null!==m),m&&p&&((0,t.E3)(p.group1.columns.length,m.group1.columns.length),(0,t.E3)(p.group2.columns.length,m.group2.columns.length));const d=i(r),f=i(s);(0,t.E3)(f.map.size,d.map.size);for(const[e,n]of d.map){const o=f.map.get(e);(0,t.E3)(void 0!==o,!0);for(const e of c){const a=r.col(e),i=s.col(e),l=a.isNone(n),c=i.isNone(o);if((0,t.E3)(c,l),!l&&!c){const e=a.get(n),r=i.get(o);(0,t.E3)(Math.abs(e-r)<=.001,!0)}}}}),(0,t.t6)("streaming filter parity",async()=>{const e=D({...n,proteins:[{id:"KEEP1"},{id:"KEEP2"}],extraRows:[{id:"CON__C1",qValue:.001},{id:"REV__R1",qValue:.001},{id:"HIGHQ",qValue:.05},{id:"PROF",qValue:"Profiled"},{id:"EMPTYQ",qValue:""}]}),r=await o(e),s=r.col("PG.ProteinGroups"),a=new Set;for(let e=0;e<r.rowCount;e++)a.add(String(s.get(e)));(0,t.E3)(a.has("CON__C1"),!1),(0,t.E3)(a.has("REV__R1"),!1),(0,t.E3)(a.has("HIGHQ"),!1),(0,t.E3)(a.has("PROF"),!0),(0,t.E3)(a.has("EMPTYQ"),!0),(0,t.E3)(r.rowCount,4)}),(0,t.t6)("by-design-filtered rows are not counted malformed",async()=>{const e=D({...n,proteins:[{id:"KEEP1"},{id:"KEEP2"}],extraRows:[{id:"CON__C1",qValue:.001},{id:"REV__R1",qValue:.001},{id:"HIGHQ",qValue:.05}]}),{df:o,infos:r}=await c(e),s=o.col("PG.ProteinGroups"),a=new Set;for(let e=0;e<o.rowCount;e++)a.add(String(s.get(e)));(0,t.E3)(a.has("KEEP1"),!0),(0,t.E3)(a.has("KEEP2"),!0),(0,t.E3)(a.has("CON__C1"),!1),(0,t.E3)(a.has("REV__R1"),!1),(0,t.E3)(a.has("HIGHQ"),!1),(0,t.E3)(o.rowCount,2);const i=r.filter(e=>/malformed/i.test(e));(0,t.E3)(i.length,0)}),(0,t.t6)("truncated line is counted malformed",async()=>{const e=D({...n,proteins:[{id:"KEEP1"},{id:"KEEP2"}]})+"\nfile\tCondA\t1",{df:o,infos:r}=await c(e),s=o.col("PG.ProteinGroups"),a=new Set;for(let e=0;e<o.rowCount;e++)a.add(String(s.get(e)));(0,t.E3)(a.has("KEEP1"),!0),(0,t.E3)(a.has("KEEP2"),!0),(0,t.E3)(o.rowCount,2);const i=r.some(e=>/skipped \d+ malformed line\(s\)/.test(e));(0,t.E3)(i,!0)}),(0,t.t6)("empty-protein rows are filtered silently (streaming↔text parity)",async()=>{const e=D({...n,proteins:[{id:"KEEP1"},{id:"KEEP2"}],extraRows:[{id:"",qValue:.001},{id:"",qValue:.002}]}),{df:o,infos:r}=await c(e),s=o.col("PG.ProteinGroups"),a=new Set;for(let e=0;e<o.rowCount;e++)a.add(String(s.get(e)));(0,t.E3)(a.has("KEEP1"),!0),(0,t.E3)(a.has("KEEP2"),!0),(0,t.E3)(a.has(""),!1),(0,t.E3)(o.rowCount,2);const i=r.filter(e=>/malformed/i.test(e));(0,t.E3)(i.length,0)}),(0,t.t6)("both-numeric-casts-null rows are filtered silently (streaming↔text parity)",async()=>{const e=D({...n,proteins:[{id:"KEEP1"},{id:"KEEP2"}],extraRows:[{id:"NULLPAIR",quantity:"NaN",qValue:"NA"}]}),{df:o,infos:r}=await c(e);(0,t.E3)(o.rowCount,2);const s=r.filter(e=>/malformed/i.test(e));(0,t.E3)(s.length,0)}),(0,t.t6)("streaming tag set and groups",async()=>{const e=await o(D(n));(0,t.E3)(e.getTag("proteomics.source"),"spectronaut"),(0,t.E3)(e.getTag("proteomics.preNormalized"),"true");const r=(0,l.f)(e);(0,t.E3)(null!==r,!0),r&&((0,t.E3)(r.group1.columns.length,2),(0,t.E3)(r.group2.columns.length,2))}),(0,t.t6)("streaming output equals duckdb golden",async()=>{const e=JSON.parse(await r("spectronaut-hye-precursor-golden.json")),n=await r("spectronaut-hye-precursor.tsv"),s=await o(n),{map:l}=i(s),c=a(s),u=Object.keys(e);(0,t.E3)(u.length>0,!0);for(const n of u){const o=n.match(/^(.*?)((?:Cond[A-Za-z]+)_\d+)$/);(0,t.E3)(null!==o,!0);const r=o[1],a=o[2],i=l.get(r);(0,t.E3)(void 0!==i,!0);const c=s.col(a);(0,t.E3)(null!==c,!0),(0,t.E3)(c.isNone(i),!1);const u=c.get(i);(0,t.E3)(Math.abs(u-e[n].quantity)<=.001,!0)}const m=new Set;for(const[e,t]of l)for(const n of c)s.col(n).isNone(t)||m.add(`${e}${n}`);const p=new Set(u);(0,t.E3)(m.size,p.size);for(const e of m)(0,t.E3)(p.has(e),!0);for(const e of p)(0,t.E3)(m.has(e),!0)}),(0,t.t6)("duckdb fallback tooling is committed",async()=>{(0,t.E3)(!0,!0),(0,t.E3)(!0,!0),(0,t.E3)("-- Aggregate a long-form Spectronaut Report (peptide/precursor/fragment-level rows)\n-- down to one row per (protein-group × condition × replicate), in the shape\n-- packages/Proteomics/src/parsers/spectronaut-parser.ts expects.\n--\n-- This is the bundled, documented manual fallback (D-05) for a Spectronaut report\n-- too large for the in-browser streaming importer, AND the D-04 equivalence oracle\n-- the Wave-0 golden test pins to.\n--\n-- Template tokens __IN_PATH__ and __OUT_PATH__ are replaced by the shell wrapper\n-- before this script is passed to duckdb. (DuckDB's COPY ... TO does not accept\n-- variables, so we can't use SET VARIABLE here.)\n\n-- Streaming aggregation — duckdb spills to disk if it can't fit memory.\nPRAGMA memory_limit='8GB';\nPRAGMA threads=8;\n\nCOPY (\n SELECT\n \"PG.ProteinGroups\",\n -- DIVERGENCE FROM /tmp/spectronaut-aggregate.sql: the two carry-along\n -- any_value() SELECT terms for the gene-symbol and protein-accession columns\n -- (present in the /tmp original) were DROPPED here. The package's Spectronaut\n -- data (files/demo/spectronaut-hye-mix.tsv and the synthetic precursor\n -- fixture) does not carry those two columns and\n -- pivotSpectronaut/aggToPivotResult never consume them, so they are not part\n -- of the parity contract; keeping them would Binder-Error duckdb on the\n -- fixture (ignore_errors does NOT cover Binder Errors) and the entire Wave-0\n -- oracle chain (golden → sidecar → 12-03 golden test) would have no source.\n --\n -- ============================ WARNING ============================\n -- REFERENCE-FILE-ONLY: the CASE below is a one-off correction for the\n -- mislabeled reference file `2026-05-13 BP DMD WT.tsv` ONLY. Cross-tab\n -- against R.FileName showed every WT* filename tagged DMD and every DMD*\n -- filename tagged WT (24/24); this restores the convention so DE direction\n -- matches what the filenames imply. It is a STRUCTURAL NO-OP on any data\n -- whose R.Condition is not literally 'DMD'/'WT' — including the CondA/CondB\n -- synthetic fixture, which is exactly why this same script doubles as the\n -- D-04 golden oracle without perturbing the golden. The streaming TS\n -- aggregator MUST NOT port this flip (RESEARCH Pitfall 1 — the single\n -- highest-risk parity trap). Do not \"generalize\" or remove it either: the\n -- manual-fallback path still needs it for the mislabeled reference file.\n -- =================================================================\n CASE \"R.Condition\"\n WHEN 'DMD' THEN 'WT'\n WHEN 'WT' THEN 'DMD'\n ELSE \"R.Condition\"\n END AS \"R.Condition\",\n \"R.Replicate\",\n any_value(\"R.FileName\") AS \"R.FileName\",\n -- PG.Quantity is constant per (protein-group, run) in Spectronaut output;\n -- max() collapses the precursor-level duplicates safely.\n max(TRY_CAST(\"PG.Quantity\" AS DOUBLE)) AS \"PG.Quantity\",\n -- Best precursor q-value backing this protein in this run.\n min(TRY_CAST(\"EG.Qvalue\" AS DOUBLE)) AS \"EG.Qvalue\"\n FROM read_csv(\n '__IN_PATH__',\n delim='\\t',\n header=true,\n sample_size=-1, -- scan everything for type inference; columns are messy\n ignore_errors=true, -- tolerate stray malformed lines in a 2.6 GB file\n nullstr=['', 'NaN', 'NA']\n )\n WHERE\n -- Mirror the parser's precursor-level filter: drop EG rows with q-value > 0.01.\n -- Non-numeric q-values (e.g. 'Profiled') pass — same as the TS parser.\n (TRY_CAST(\"EG.Qvalue\" AS DOUBLE) IS NULL OR TRY_CAST(\"EG.Qvalue\" AS DOUBLE) <= 0.01)\n -- Drop decoys / contaminants up front; parser does this too but it's cheaper here.\n AND \"PG.ProteinGroups\" IS NOT NULL\n AND \"PG.ProteinGroups\" NOT LIKE 'CON\\_\\_%' ESCAPE '\\'\n AND \"PG.ProteinGroups\" NOT LIKE 'REV\\_\\_%' ESCAPE '\\'\n GROUP BY \"PG.ProteinGroups\", \"R.Condition\", \"R.Replicate\"\n) TO '__OUT_PATH__' (FORMAT csv, DELIMITER '\\t', HEADER);\n\n-- Summary so we can sanity-check the collapse ratio.\nSELECT\n count(*) AS output_rows,\n count(DISTINCT \"PG.ProteinGroups\") AS proteins,\n count(DISTINCT (\"R.Condition\" || '_' || \"R.Replicate\")) AS samples,\n list(DISTINCT \"R.Condition\") AS conditions\nFROM read_csv('__OUT_PATH__', delim='\\t', header=true);\n".includes("max(TRY_CAST"),!0),(0,t.E3)('#!/usr/bin/env bash\n# Collapse a long-form Spectronaut Report into the protein-group × sample shape\n# the Proteomics package\'s parseSpectronautText parser consumes.\n#\n# This is the documented MANUAL FALLBACK for a Spectronaut report too large for\n# the in-browser streaming importer: run it locally, then import the small\n# aggregated .tsv it produces. It is also the D-04 equivalence oracle the Wave-0\n# golden test pins to (see files/demo/README.md).\n#\n# Run: tools/spectronaut-aggregate.sh <input.tsv> [output.tsv]\n#\n# Requires the `duckdb` CLI on PATH (v1.3.0 used to derive the committed golden).\n\nset -euo pipefail\n\nif [[ $# -lt 1 ]]; then\n echo "Usage: $0 <input.tsv> [output.tsv]" >&2\n exit 1\nfi\n\nIN="$1"\nOUT="${2:-${IN%.tsv}.aggregated.tsv}"\nSQL="$(dirname "$0")/spectronaut-aggregate.sql"\n\nif [[ ! -f "$IN" ]]; then\n echo "Input not found: $IN" >&2\n exit 1\nfi\n\necho "Aggregating: $IN"\necho "Output: $OUT"\n\n# Substitute paths into the SQL template. DuckDB\'s COPY ... TO doesn\'t accept\n# variables, so we materialize the SQL first. SQL single-quote escaping: double up\n# any embedded \' in the paths.\nIN_ESC="${IN//\\\'/\\\'\\\'}"\nOUT_ESC="${OUT//\\\'/\\\'\\\'}"\nTMP_SQL="$(mktemp -t spectronaut-aggregate.XXXXXX.sql)"\ntrap \'rm -f "$TMP_SQL"\' EXIT\nsed -e "s|__IN_PATH__|${IN_ESC}|g" -e "s|__OUT_PATH__|${OUT_ESC}|g" "$SQL" > "$TMP_SQL"\n\nduckdb < "$TMP_SQL"\n\necho\necho "Input size: $(du -h "$IN" | cut -f1)"\necho "Output size: $(du -h "$OUT" | cut -f1)"\n'.includes("spectronaut-aggregate.sql"),!0)})});var L=n(86);function F(e,t){return[t.join("\t"),...e.map(e=>e.join("\t"))].join("\n")}const I=["Comparison (group1/group2)","PG.ProteinGroups","PG.Genes","AVG Log2 Ratio","Qvalue","Pvalue"];function M(e,t,n,o,r,s){return[e,t,n,o,r,s]}function O(t){for(const n of t.viewers)if(n.type===e.VIEWER.FILTERS)return n;return null}function R(t={}){const{withDisplayName:n=!0,withSourceId:o=!0,withFlags:r=!0,withProteinId:a=!0,comparisons:i=["T1 / Control","T2 / Control","T1 / Control","T2 / Control"]}=t,l=[e.Column.fromStrings("Comparison (group1/group2)",i),e.Column.fromList("double","log2FC",Array.from({length:i.length},(e,t)=>t-1.5))];if(a){const t=e.Column.fromStrings("Primary Protein ID",i.map((e,t)=>`P${1e4+t}`));t.semType=s.iu.PROTEIN_ID,l.push(t)}if(n){const t=e.Column.fromStrings("Display Name",i.map((e,t)=>`Gene${t+1}`));t.semType=s.iu.DISPLAY_NAME,l.push(t)}if(o){const t=e.Column.fromStrings("Source ID",i.map((e,t)=>`ENSG${1e4+t}`));t.semType=s.iu.SOURCE_ID,l.push(t)}return r&&l.push(e.Column.fromBitSet("Flags",e.BitSet.create(i.length,e=>e%2==0))),e.DataFrame.fromColumns(l)}function G(e){return[["Comparison (group1/group2)","PG.ProteinGroups","PG.Genes","AVG Log2 Ratio","Qvalue","Pvalue"].join("\t"),...e.map(e=>e.join("\t"))].join("\n")}function k(t){for(const n of t.viewers)if(n.type===e.VIEWER.FILTERS)return!0;return!1}(0,t.L1)("SpectronautCandidates",()=>{(0,t.t6)("parses standard rows",async()=>{const e=F([M("Treatment / Control","P04637","TP53","2.5","1e-5","1e-6"),M("Treatment / Control","P38398","BRCA1","-2.3","1e-4","1e-5")],I),n=await(0,L.R)(e);(0,t.E3)(n.rowCount,2)}),(0,t.t6)("sets proteomics.source to spectronaut-candidates",async()=>{const e=F([M("A / B","P04637","TP53","2.5","1e-5","1e-6")],I),n=await(0,L.R)(e);(0,t.E3)(n.getTag("proteomics.source"),"spectronaut-candidates")}),(0,t.t6)("sets de_complete and de_method tags",async()=>{const e=F([M("A / B","P04637","TP53","2.5","1e-5","1e-6")],I),n=await(0,L.R)(e);(0,t.E3)(n.getTag("proteomics.de_complete"),"true"),(0,t.E3)(n.getTag("proteomics.de_method"),"spectronaut")}),(0,t.t6)("names contrast groups from the Comparison string (volcano legend)",async()=>{const e=F([M("DMT / WT","P04637","TP53","2.5","1e-5","1e-6"),M("DMT / WT","P38398","BRCA1","-2.3","1e-4","1e-5")],I),n=await(0,L.R)(e),o=(0,l.f)(n);(0,t.E3)(null!=o,!0);const r=[o.group1.name,o.group2.name].sort();(0,t.E3)(r[0],"DMT"),(0,t.E3)(r[1],"WT"),(0,t.E3)(o.group1.columns.length,0),(0,t.E3)(o.group2.columns.length,0)}),(0,t.t6)("renames AVG Log2 Ratio to log2FC",async()=>{const e=F([M("A / B","P04637","TP53","2.5","1e-5","1e-6")],I),n=await(0,L.R)(e);(0,t.E3)(null!==n.col("log2FC"),!0),(0,t.E3)(n.col("AVG Log2 Ratio"),null),(0,t.E3)(Math.abs(n.col("log2FC").get(0)-2.5)<.01,!0)}),(0,t.t6)("renames Qvalue to adj.p-value",async()=>{const e=F([M("A / B","P04637","TP53","2.5","0.001","0.0001")],I),n=await(0,L.R)(e);(0,t.E3)(null!==n.col("adj.p-value"),!0),(0,t.E3)(n.col("Qvalue"),null),(0,t.E3)(Math.abs(n.col("adj.p-value").get(0)-.001)<1e-6,!0)}),(0,t.t6)("renames Pvalue to p-value when present",async()=>{const e=F([M("A / B","P04637","TP53","2.5","0.001","0.0001")],I),n=await(0,L.R)(e);(0,t.E3)(null!==n.col("p-value"),!0),(0,t.E3)(n.col("Pvalue"),null)}),(0,t.t6)("works without a Pvalue column",async()=>{const e=F([["P04637","TP53","2.5","0.001"]],["PG.ProteinGroups","PG.Genes","AVG Log2 Ratio","Qvalue"]),n=await(0,L.R)(e);(0,t.E3)(n.rowCount,1),(0,t.E3)(n.col("p-value"),null),(0,t.E3)(null!==n.col("adj.p-value"),!0)}),(0,t.t6)("assigns canonical semantic types",async()=>{const e=F([M("A / B","P04637","TP53","2.5","0.001","0.0001")],I),n=await(0,L.R)(e);(0,t.E3)(n.col("PG.ProteinGroups").semType,s.iu.PROTEIN_ID),(0,t.E3)(n.col("PG.Genes").semType,s.iu.GENE_SYMBOL),(0,t.E3)(n.col("log2FC").semType,s.iu.LOG2FC),(0,t.E3)(n.col("adj.p-value").semType,s.iu.P_VALUE),(0,t.E3)(n.col("p-value").semType,s.iu.P_VALUE)}),(0,t.t6)("computes significant column from |log2FC| >= 1 and adj.p <= 0.05",async()=>{const e=F([M("A / B","P_sig_up","A","2.5","0.001","0.0001"),M("A / B","P_sig_down","B","-1.5","0.001","0.0001"),M("A / B","P_small_fc","C","0.3","0.001","0.0001"),M("A / B","P_big_qvalue","D","2.0","0.5","0.4"),M("A / B","P_just_inside","E","1.01","0.04","0.03")],I),n=(await(0,L.R)(e)).col("significant");(0,t.E3)(n.get(0),!0),(0,t.E3)(n.get(1),!0),(0,t.E3)(n.get(2),!1),(0,t.E3)(n.get(3),!1),(0,t.E3)(n.get(4),!0)}),(0,t.t6)("filters contam_ rows",async()=>{const e=F([M("A / B","P04637","TP53","2.5","0.001","0.0001"),M("A / B","contam_P99999","KRT1","0.1","0.5","0.4")],I),n=await(0,L.R)(e);(0,t.E3)(n.rowCount,1),(0,t.E3)(n.col("PG.ProteinGroups").get(0),"P04637")}),(0,t.t6)("filters rev_ decoy rows",async()=>{const e=F([M("A / B","P04637","TP53","2.5","0.001","0.0001"),M("A / B","rev_P12345","FAKE","0.1","0.5","0.4")],I),n=await(0,L.R)(e);(0,t.E3)(n.rowCount,1)}),(0,t.t6)("throws on missing protein-group column",async()=>{const e=F([["A / B","2.5","0.001"]],["Comparison","AVG Log2 Ratio","Qvalue"]);let n=!1;try{await(0,L.R)(e)}catch(e){n=!0,(0,t.E3)(String(e.message).includes("protein-group"),!0)}(0,t.E3)(n,!0)}),(0,t.t6)("throws on missing log2 ratio column",async()=>{const e=F([["P04637","TP53","0.001"]],["PG.ProteinGroups","PG.Genes","Qvalue"]);let n=!1;try{await(0,L.R)(e)}catch(e){n=!0,(0,t.E3)(String(e.message).includes("log2 ratio"),!0)}(0,t.E3)(n,!0)}),(0,t.t6)("throws on missing q-value column",async()=>{const e=F([["P04637","TP53","2.5"]],["PG.ProteinGroups","PG.Genes","AVG Log2 Ratio"]);let n=!1;try{await(0,L.R)(e)}catch(e){n=!0,(0,t.E3)(String(e.message).includes("q-value"),!0)}(0,t.E3)(n,!0)}),(0,t.t6)("accepts alternative column names (ProteinGroups, Log2 Ratio, Q-Value)",async()=>{const e=F([["P04637","TP53","2.5","0.001"]],["ProteinGroups","Genes","Log2 Ratio","Q-Value"]),n=await(0,L.R)(e);(0,t.E3)(n.rowCount,1),(0,t.E3)(null!==n.col("log2FC"),!0),(0,t.E3)(null!==n.col("adj.p-value"),!0)}),(0,t.t6)("keeps Comparison column for multi-comparison files",async()=>{const e=F([M("Treatment1 / Control","P04637","TP53","2.5","0.001","0.0001"),M("Treatment2 / Control","P04637","TP53","1.8","0.002","0.0005"),M("Treatment1 / Control","P38398","BRCA1","-2.3","0.001","0.0001")],I),n=await(0,L.R)(e);(0,t.E3)(n.rowCount,3),(0,t.E3)(null!==n.col("Comparison (group1/group2)"),!0)});const e=["Comparison (group1/group2)","PG.ProteinGroups","PG.Genes","AVG Log2 Ratio","Qvalue","Pvalue","AVG Group Quantity Numerator","AVG Group Quantity Denominator","Condition Numerator","Condition Denominator"];(0,t.t6)("flips reversed-comparison rows; canonical rows untouched",async()=>{const n=F([["DMD / WT","P1","G1","-2.0","0.001","0.0001","100","400","DMD","WT"],["WT / DMD","P2","G2","3.0","0.001","0.0001","800","100","WT","DMD"]],e),o=await(0,L.R)(n),r=o.col("Comparison (group1/group2)"),s=o.col("log2FC"),a=o.col("AVG Group Quantity Numerator"),i=o.col("AVG Group Quantity Denominator");(0,t.E3)(r.get(0),"DMD / WT"),(0,t.E3)(Math.abs(s.get(0)- -2)<1e-6,!0),(0,t.E3)(Math.abs(a.get(0)-100)<1e-4,!0),(0,t.E3)(Math.abs(i.get(0)-400)<1e-4,!0),(0,t.E3)(r.get(1),"DMD / WT"),(0,t.E3)(Math.abs(s.get(1)- -3)<1e-6,!0),(0,t.E3)(Math.abs(a.get(1)-100)<1e-4,!0),(0,t.E3)(Math.abs(i.get(1)-800)<1e-4,!0),(0,t.E3)(o.col("Condition Numerator").get(1),"DMD"),(0,t.E3)(o.col("Condition Denominator").get(1),"WT")}),(0,t.t6)("flips log2FC without AVG Group Quantity columns (no swap, no throw)",async()=>{const e=F([M("DMD / WT","P1","G1","-2.0","0.001","0.0001"),M("WT / DMD","P2","G2","3.0","0.001","0.0001")],I),n=await(0,L.R)(e),o=n.col("log2FC");(0,t.E3)(Math.abs(o.get(0)- -2)<1e-6,!0),(0,t.E3)(Math.abs(o.get(1)- -3)<1e-6,!0),(0,t.E3)(n.col("Comparison (group1/group2)").get(1),"DMD / WT"),(0,t.E3)(n.col("AVG Group Quantity Numerator"),null)}),(0,t.t6)("single-orientation file is not mirrored",async()=>{const e=F([M("Treatment / Control","P1","A","2.5","0.001","0.0001"),M("Treatment / Control","P2","B","-1.7","0.002","0.0005")],I),n=await(0,L.R)(e),o=n.col("log2FC");(0,t.E3)(Math.abs(o.get(0)-2.5)<1e-6,!0),(0,t.E3)(Math.abs(o.get(1)- -1.7)<1e-6,!0),(0,t.E3)(n.col("Comparison (group1/group2)").get(0),"Treatment / Control")}),(0,t.t6)("parses CSV when delimiter is comma",async()=>{const e=await(0,L.R)("PG.ProteinGroups,PG.Genes,AVG Log2 Ratio,Qvalue\nP04637,TP53,2.5,0.001\nP38398,BRCA1,-2.3,0.001");(0,t.E3)(e.rowCount,2),(0,t.E3)(null!==e.col("log2FC"),!0)}),(0,t.t6)("creates Primary Protein ID for semicolon-delimited IDs",async()=>{const e=F([M("A / B","P04637;Q9Y6R7","TP53","2.5","0.001","0.0001")],I),n=(await(0,L.R)(e)).col("Primary Protein ID");(0,t.E3)(null!==n,!0),(0,t.E3)(n.get(0),"P04637")})}),(0,t.L1)("Proteomics: 14-03",()=>{(0,t.t6)("filtersScopingNoFlags",async()=>{const e=R(),n=v.shell.addTableView(e);try{const o=(0,x.dockComparisonFilterIfMultiContrast)(n,e);(0,t.E3)(o,!0),(0,t.E3)(null!==O(n),!0)}finally{n.close()}}),(0,t.t6)("filtersScopingSingleContrast",async()=>{const e=R({comparisons:["T1 / Control","T1 / Control","T1 / Control"]}),n=v.shell.addTableView(e);try{const o=(0,x.dockComparisonFilterIfMultiContrast)(n,e);(0,t.E3)(o,!1),(0,t.E3)(O(n),null)}finally{n.close()}}),(0,t.t6)("filtersScopingFallbackToProteinIdWhenNoDisplayName",async()=>{const e=R({withDisplayName:!1,withSourceId:!1}),n=v.shell.addTableView(e);try{const o=(0,x.dockComparisonFilterIfMultiContrast)(n,e);(0,t.E3)(o,!0),(0,t.E3)(null!==O(n),!0)}finally{n.close()}})});const $=["Homo sapiens","Saccharomyces cerevisiae","Escherichia coli"];(0,t.L1)("SpectronautCandidates E2E",()=>{(0,t.t6)("parses HYE candidates fixture and reproduces expected DE signal",async()=>{const e=await 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t=c.get(e);"string"==typeof t&&u.add(t)}for(const e of $){const n=Array.from(u).some(t=>t.includes(e));(0,t.E3)(n,!0)}}),(0,t.t6)("multi-comparison file docks a Comparison Filters viewer",async()=>{const e=await(0,L.R)(G([["T1 / Control","P1","G1","2.0","0.001","0.0001"],["T2 / Control","P2","G2","-1.7","0.002","0.0005"],["T1 / Control","P3","G3","1.2","0.01","0.005"]])),n=v.shell.addTableView(e);try{const o=(0,x.dockComparisonFilterIfMultiContrast)(n,e);(0,t.E3)(o,!0),(0,t.E3)(k(n),!0)}finally{n.close()}}),(0,t.t6)("single-comparison file docks no Filters viewer",async()=>{const e=await(0,L.R)(G([["T1 / Control","P1","G1","2.0","0.001","0.0001"],["T1 / Control","P2","G2","-1.7","0.002","0.0005"]])),n=v.shell.addTableView(e);try{const o=(0,x.dockComparisonFilterIfMultiContrast)(n,e);(0,t.E3)(o,!1),(0,t.E3)(k(n),!1)}finally{n.close()}}),(0,t.t6)("candidates import auto-opens the volcano",async()=>{const n=await(0,L.R)(G([["T1 / Control","P1","G1","2.0","0.001","0.0001"],["T1 / 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e=U([V("P12345","BRCA1","0","0","4096","8192")],j),n=(await(0,B.p)(e)).col("log2(Sample1 MaxLFQ Intensity)");(0,t.E3)(n.isNone(0),!0)}),(0,t.t6)("primary protein ID extracted from semicolon-delimited",async()=>{const e=U([["sp|P12345|BRCA1_HUMAN","P12345;Q67890","BRCA1_HUMAN","BRCA1;BRCA2","500","Homo sapiens","BRCA1 protein","12","10000","12000","15","20000","24000"]],j),n=await(0,B.p)(e),o=n.col("Primary Protein ID");(0,t.E3)(null!==o,!0),o&&(0,t.E3)(o.get(0),"P12345");const r=n.col("Primary Gene Name");(0,t.E3)(null!==r,!0),r&&(0,t.E3)(r.get(0),"BRCA1")}),(0,t.t6)("proteomics.source tag set to fragpipe",async()=>{const e=U([V("P12345","BRCA1","10000","12000","20000","24000")],j),n=await(0,B.p)(e);(0,t.E3)(n.getTag("proteomics.source"),"fragpipe")}),(0,t.t6)("intensity columns survive as raw plus log2 pair",async()=>{const e=U([V("P12345","BRCA1","10000","12000","20000","24000")],j),n=await(0,B.p)(e);(0,t.E3)(null!==n.col("Sample1 MaxLFQ 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o=[...q.group1.columns,...q.group2.columns];(0,c.aj)(n,o),(0,t.E3)(n.getTag("proteomics.normalized"),"true");for(const e of o)(0,t.E3)(Math.abs(n.col(e).stats.med)<1e-4,!0);(0,u.Q2)(n,o),(0,t.E3)(n.getTag("proteomics.imputed"),"true"),(0,m.ps)(n,q.group1.columns,q.group2.columns,"Control","Treatment",1,.05),(0,t.E3)(n.getTag("proteomics.de_complete"),"true"),(0,t.E3)(null!==n.col("log2FC"),!0),(0,t.E3)(null!==n.col("p-value"),!0),(0,t.E3)(null!==n.col("adj.p-value"),!0),(0,t.E3)(null!==n.col("significant"),!0);const r={},a=n.col("Gene");for(let e=0;e<n.rowCount;e++)r[a.get(e)]=e;const i=n.col("log2FC"),p=n.col("significant");for(const e of Y)(0,t.E3)(i.get(r[e])>1,!0),(0,t.E3)(p.get(r[e]),!0);for(const e of z)(0,t.E3)(i.get(r[e])<-1,!0),(0,t.E3)(p.get(r[e]),!0);for(const e of H)(0,t.E3)(Math.abs(i.get(r[e]))<.5,!0),(0,t.E3)(p.get(r[e]),!1)})});var Q=n(623),W=n(70);function K(e){const t=v.dapi.userDataStorage.constructor.prototype,n=t.get,o=t.put;return 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n=K({get:async()=>({}),put:async()=>{}});try{const e=[];for(let t=0;t<250;t++)e.push(`TESTB${String(t).padStart(5,"0")}`);const n=[],o=(e,t,o)=>n.push({done:e,total:t,phase:o});await(0,Q.n0)(e,"hsapiens",o);const r=n.filter(e=>"fetch-acc"===e.phase);(0,t.E3)(r.length,3),(0,t.E3)(r[0].total,3);for(let e=1;e<r.length;e++)(0,t.E3)(r[e].done>=r[e-1].done,!0,"fetch-acc done should be non-decreasing");const s=r[r.length-1];(0,t.E3)(s.done,s.total,"last fetch-acc tuple should have done === total")}finally{v.dapi.fetchProxy=e,n()}}),(0,t.t6)("getSubcellularLocations writes the cache incrementally during fetch",async()=>{const e=v.dapi.fetchProxy;let n=0;v.dapi.fetchProxy=async e=>{const t=0===n++?1e3:6e3;await new Promise(e=>setTimeout(e,t));const o=/accession%3A([A-Z0-9]+)/.exec(e),r=o?o[1]:"P00000";return{ok:!0,status:200,text:async()=>(e=>`Entry\tSubcellular location [CC]\tGO\tReviewed\tGene Names (primary)\n${e}\tNucleus.\t\treviewed\tGENE1\n`)(r)}};let o=0;const r=K({get:async()=>({}),put:async()=>{o++}});try{const e=[];for(let t=0;t<150;t++)e.push(`TESTC${String(t).padStart(5,"0")}`);await(0,Q.n0)(e,"hsapiens"),(0,t.E3)(o>=2,!0,`userDataStorage.put should be called >= 2 times (got ${o})`)}finally{v.dapi.fetchProxy=e,r()}},{timeout:3e4}),(0,t.t6)("STORE export matches the documented userDataStorage key",async()=>{(0,t.E3)(Q.er,"proteomics-subcell-loc")}),(0,t.t6)("ensureLocationColumn short-circuits on accession-set hash match",async()=>{const n=v.dapi.fetchProxy;let o=0;v.dapi.fetchProxy=async e=>{o++;const t=/accession%3A([A-Z0-9]+)/.exec(e),n=t?t[1]:"TESTD00";return{ok:!0,status:200,text:async()=>(e=>`Entry\tSubcellular location [CC]\tGO\tReviewed\tGene Names (primary)\n${e}\tNucleus.\t\treviewed\tGENE1\n`)(n)}};const r=K({get:async()=>({}),put:async()=>{}});try{const n=e.Column.fromStrings("Primary Protein ID",["TESTD01","TESTD02","TESTD03","TESTD04","TESTD05"]);n.semType=s.iu.PROTEIN_ID;const 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o=e.DataFrame.fromColumns([n]),r=[],a=(e,t,n)=>r.push(n);await(0,W.MC)(o,a),(0,t.E3)(r.includes("fetch-acc"),!0,"progress should fire at least once with phase=fetch-acc"),(0,t.E3)(r.includes("init-column"),!0,"progress should fire with phase=init-column after bulk-init"),(0,t.E3)(r[r.length-1],"init-column","init-column should be the final progress phase")}finally{v.dapi.fetchProxy=n,o()}})});var Z=n(935);function X(t,n){return e.DataFrame.fromColumns([e.Column.fromStrings(t,n)])}(0,t.L1)("Organisms",()=>{(0,t.t6)("resolveOrganismCode maps scientific names (incl. strain-qualified) to codes",async()=>{(0,t.E3)((0,Z.qj)("Homo sapiens"),"hsapiens"),(0,t.E3)((0,Z.qj)("Rattus norvegicus"),"rnorvegicus"),(0,t.E3)((0,Z.qj)("Escherichia coli (strain K12)"),"ecoli"),(0,t.E3)((0,Z.qj)("Saccharomyces cerevisiae (strain ATCC 204508 / S288c)"),"scerevisiae")}),(0,t.t6)("resolveOrganismCode returns undefined for unsupported / empty",async()=>{(0,t.E3)(void 0===(0,Z.qj)("Sus 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r.col("Protein ID").semType=s.iu.PROTEIN_ID,r.col("log2FC").semType=s.iu.LOG2FC,r.col("adj.p-value").semType=s.iu.P_VALUE,r}(0,t.L1)("Log2 Scale",()=>{(0,t.t6)("getIntensityOriginals: only the pristine (non-log2) intensity columns",async()=>{const e=te();(0,d.Kh)(e,["Intensity_S1","Intensity_S2"]);const n=(0,ee.ye)(e);(0,t.E3)(n.length,2,"two originals"),(0,t.E3)(n.includes("Intensity_S1")&&n.includes("Intensity_S2"),!0,"includes both raw columns"),(0,t.E3)(n.some(e=>e.startsWith("log2(")),!1,"excludes the log2 copies")}),(0,t.t6)("detectCurrentLog2Applied: transform vs copy is read from the values",async()=>{const e=te();(0,d.Kh)(e,["Intensity_S1","Intensity_S2"]),(0,t.E3)((0,ee.IZ)(e,(0,ee.ye)(e)),"transform","log2(x) columns read as transform");const n=te();(0,d.l3)(n,["Intensity_S1","Intensity_S2"]),(0,t.E3)((0,ee.IZ)(n,(0,ee.ye)(n)),"copy","copied columns read as copy")}),(0,t.t6)("applyLog2Scale: transform→copy rebuilds values, clears stale tags, is idempotent",async()=>{const e=te();(0,d.Kh)(e,["Intensity_S1","Intensity_S2"]),e.setTag("proteomics.normalized","true"),e.setTag("proteomics.de_complete","true"),e.setTag("proteomics.de_method","t-test"),(0,t.E3)(Math.abs(e.col("log2(Intensity_S1)").get(0)-Math.log2(1e3))<.001,!0,"starts transformed");const n=(0,ee.DA)(e,!0);(0,t.E3)(n,!0,"a real scale change returns true"),(0,t.E3)(e.col("log2(Intensity_S1)").get(0),1e3,"value is now the raw copy"),(0,t.E3)((0,ee.IZ)(e,(0,ee.ye)(e)),"copy","now reads as copy"),(0,t.E3)(e.getTag("proteomics.normalized")||"","","normalized tag cleared"),(0,t.E3)(e.getTag("proteomics.de_complete")||"","","de_complete tag cleared"),(0,t.E3)(e.getTag("proteomics.de_method")||"","","de_method tag cleared"),(0,t.E3)((0,ee.ye)(e).length,2,"still exactly two originals"),(0,t.E3)((0,ee.DA)(e,!0),!1,"no-op when scale already matches returns false")}),(0,t.t6)("applyLog2Scale: copy→transform restores the log2 transform",async()=>{const e=te();(0,d.l3)(e,["Intensity_S1","Intensity_S2"]);const n=(0,ee.DA)(e,!1);(0,t.E3)(n,!0,"scale change returns true"),(0,t.E3)(Math.abs(e.col("log2(Intensity_S2)").get(2)-Math.log2(32e3))<.001,!0,"transform re-applied to raw value"),(0,t.E3)((0,ee.IZ)(e,(0,ee.ye)(e)),"transform","reads as transform")}),(0,t.t6)("getIntensityOriginals: empty when no intensity columns",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein ID",["P1","P2"])]);n.col("Protein ID").semType=s.iu.PROTEIN_ID,(0,t.E3)((0,ee.ye)(n).length,0,"no originals"),(0,t.E3)((0,ee.DA)(n,!0),!1,"applyLog2Scale is a no-op with nothing to rescale")})});const oe="Enriched in group1",re="Enriched in group2",se="Not significant";function ae(t){const n=[e.Column.fromStrings("Protein ID",["P1","P2","P3"]),e.Column.fromFloat32Array("log2FC",new Float32Array([2,-2,.1])),e.Column.fromFloat32Array("adj.p-value",new Float32Array([.001,.5,.2]))];!1!==t?.withPValue&&n.push(e.Column.fromFloat32Array("p-value",new 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-Math.log10(.5))<1e-4,!0),(0,t.E3)(e.col("direction").get(1),se),(0,t.E3)(e.meta.formulaLines.items.length,r)}),(0,t.t6)("toggle wiring: every metric × colorDim combination drives recomputeVolcano",async()=>{const e=ae(),n=(0,W.gO)(e,{}),o=n.props.yColumnName;for(const r of["adj.p-value","p-value"])for(const s of["significance","location"])await(0,W.nj)(e,n,r,s,1,.05),(0,t.E3)(n.props.yColumnName,o),(0,t.E3)(n.props.colorColumnName,"location"===s?"Subcellular Location":"direction")}),(0,t.t6)("recomputeVolcano: location color dim sets the Subcellular Location column",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein ID",["",""]),e.Column.fromFloat32Array("log2FC",new Float32Array([1,-1])),e.Column.fromFloat32Array("adj.p-value",new Float32Array([.01,.9]))]);n.col("Protein ID").semType=s.iu.PROTEIN_ID;const o=(0,W.gO)(n,{});await(0,W.nj)(n,o,"adj.p-value","location",1,.05),(0,t.E3)(o.props.colorColumnName,"Subcellular Location"),(0,t.E3)(n.col("Subcellular 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s=performance.now();await(0,W.MC)(o,n);const a=performance.now()-s;(0,t.E3)(a<50,!0,`short-circuit path should complete in <50ms; took ${a}ms`),(0,t.E3)(1===e.length&&"init-column:1/1"===e[0],!0,`short-circuit should emit exactly one init-column tick; got ${JSON.stringify(e)}`)}finally{r()}}),(0,t.t6)("axis-max override: set/get round-trips, pins symmetric X + 0-based Y, empty clears",async()=>{const e=ae(),n=(0,W.gO)(e,{topNLabels:0});(0,t.E3)(null===(0,W.GE)(e).xMax,!0,"xMax defaults to null"),(0,t.E3)(null===(0,W.GE)(e).yMax,!0,"yMax defaults to null"),(0,W.S6)(e,5,8);const o=(0,W.GE)(e);(0,t.E3)(o.xMax,5,"xMax round-trips"),(0,t.E3)(o.yMax,8,"yMax round-trips"),(0,W.f0)(n,e),(0,t.E3)(n.props.xMin,-5,"X pins symmetric: xMin = -xMax"),(0,t.E3)(n.props.xMax,5,"X pins symmetric: xMax"),(0,t.E3)(n.props.yMin,0,"Y pins from 0"),(0,t.E3)(n.props.yMax,8,"Y pins to yMax"),(0,W.S6)(e,null,null),(0,t.E3)(null===(0,W.GE)(e).xMax,!0,"xMax cleared"),(0,t.E3)(null===(0,W.GE)(e).yMax,!0,"yMax 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r=JSON.parse(e?.body??"{}");(0,t.E3)(Array.isArray(r.ids),!0),(0,t.E3)(r.ids.length,2),(0,t.E3)(o.size,1),(0,t.E3)(o.get("ENSRNOG00000001")?.external_name,"Myh7")})}),(0,t.t6)("lookupEnsemblBatch: retries once on 429 with Retry-After",async()=>{let e=0;await ce(async()=>(e++,1===e?le(null,{status:429,retryAfter:"0"}):le({ENSG00000001:{external_name:"TP53"}})),async()=>{const n=await(0,ie.FH)(["ENSG00000001"]);(0,t.E3)(e,2),(0,t.E3)(n.get("ENSG00000001")?.external_name,"TP53")})}),(0,t.t6)("resolveGeneLabels: no-op path still creates Display Name + Source ID columns",async()=>{const n=e.DataFrame.fromColumns([e.Column.fromStrings("Protein ID",["P12345","Q67890","O11111"]),e.Column.fromStrings("Gene name",["Myh7","Tnnt3","Actb"])]);n.col("Gene name").semType=s.iu.GENE_SYMBOL,n.col("Protein ID").semType=s.iu.PROTEIN_ID,await ce(async()=>{throw new Error("should not fetch")},async()=>{await(0,ie.rv)(n)});const o=n.col("Display Name"),r=n.col("Source 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n=e.DataFrame.fromColumns([e.Column.fromStrings("Gene name",["ENSRNOG00000001","ENSRNOG00000002","Actb"])]);n.col("Gene name").semType=s.iu.GENE_SYMBOL;const o=await me(async()=>{await ue(new Map,async()=>{await ce(async()=>le({ENSRNOG00000001:{external_name:"Myh7"},ENSRNOG00000002:{external_name:"Myh7"}}),async()=>{await(0,ie.rv)(n)})})});(0,t.E3)(n.col("Display Name").get(0),"Myh7† (ENSRNOG00000001)"),(0,t.E3)(n.col("Display Name").get(1),"Myh7† (ENSRNOG00000002)"),(0,t.E3)(n.col("Display Name").get(2),"Actb");const r=o.find(e=>e.includes("duplicate gene names"));(0,t.E3)(null!=r,!0)}),(0,t.t6)("resolveGeneLabels: cache short-circuits second call",async()=>{const n=new Map;let o=0;const r=async()=>(o++,le({ENSRNOG00000001:{external_name:"Myh7"}})),a=e.DataFrame.fromColumns([e.Column.fromStrings("Gene name",["ENSRNOG00000001"])]);a.col("Gene name").semType=s.iu.GENE_SYMBOL;const i=e.DataFrame.fromColumns([e.Column.fromStrings("Gene name",["ENSRNOG00000001"])]);i.col("Gene 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t=Ae();t.setTag("proteomics.source","spectronaut-candidates"),t.setTag("proteomics.de_method","spectronaut"),t.name="fixture-with-enrichment";const n=new Float32Array([.005,.01,.015,.02,.03,.05]),o=e.DataFrame.fromColumns([e.Column.fromStrings("Term Name",["Term A","Term B","Term C","Term D","Term E","Term F"]),e.Column.fromStrings("Source",["GO:BP","KEGG","GO:BP","GO:BP","KEGG","REAC"]),e.Column.fromFloat32Array("FDR",n),e.Column.fromStrings("Intersection",["ALPHA,BETA,GAMMA","DELTA,EPSILON","ETA,THETA","IOTA,KAPPA","ALPHA,DELTA","BETA,GAMMA,ETA"])]);return o.setTag("proteomics.enrichment","true"),o.name="enrichment-fixture",{protein:t,enrichment:o}}async function De(){const t=e.Group.defaultGroupsIds?.Test;if(t)try{const e=await v.dapi.groups.find(t);if(e)return e}catch{}const n=v.shell.user?.group?.id,o=await v.dapi.groups.list();return(o??[]).find(e=>e&&!e.hidden&&!e.personal&&e.id!==n)||(o??[])[0]}function 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p=u.getTag(Ce.L6.PUBLISHED_TARGET);(0,t.E3)("CHANGED-TARGET"===p,!1),(0,t.E3)(p===o,!0)}finally{await Fe(s),await Ie(o)}}),(0,t.t6)("republish creates v2 with bidirectional superseded_by + supersedes pointers (W-8 dual-write)",async()=>{const e=Ae(),n=`${Se}t4-${Date.now()}`;v.shell.addTableView(e),await(0,t.cb)(100);const o=await De(),r={target:n,reviewerGroup:o,note:"v1",priorVersion:null};let s=null,a=null;try{s=await(0,be.M)(e,r),(0,t.E3)(!!s,!0);const i=s.id,l=s.name;(0,t.E3)(/-v1-\d{4}-\d{2}-\d{2}$/.test(l),!0),await(0,t.cb)(200);const c={target:n,reviewerGroup:o,note:"v2",priorVersion:s};a=await(0,be.M)(e,c),(0,t.E3)(!!a,!0);const u=a.id,m=a.name;(0,t.E3)(/-v2-\d{4}-\d{2}-\d{2}$/.test(m),!0),v.shell.closeAll(),await(0,t.cb)(100);const p=await v.dapi.projects.find(u);await p.open(),await(0,t.bk)(()=>!!v.shell.tv&&!!v.shell.tv.dataFrame,"v2 reopen",5e3);const d=p.options??{};(0,t.E3)(d[Ce.L6.SUPERSEDES],i),v.shell.closeAll(),await(0,t.cb)(100);const f=await 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e.saveBaseline("Q-X",n,{root:o}),await e.saveBaseline("Q-X",r,{root:o});const s=await e.loadBaseline("Q-X",{root:o});(0,t.E3)(s.locked_at,"B"),(0,t.E3)(s.included_run_ids[0],"2")}finally{await Ue(o)}}),(0,t.t6)("SPC:rule_toggle_per_instrument",async()=>{const e=await Promise.resolve().then(n.bind(n,883)),o=Be();try{const n={instrument_id:"Q-rt",locked_at:"X",included_run_ids:[],excluded_run_ids:[],iteration_trace:[],metrics:{},rules_enabled:{median_intensity:{nelson_1:!0,nelson_5:!1,nelson_2:!0},missing_pct:{nelson_1:!0,nelson_5:!0},control_corr:{nelson_1:!0,nelson_5:!0},protein_count:{nelson_1:!0,nelson_5:!0}}};await e.saveBaseline("Q-rt",n,{root:o});const r=await e.loadBaseline("Q-rt",{root:o});(0,t.E3)(r.rules_enabled.median_intensity.nelson_5,!1),(0,t.E3)(r.rules_enabled.median_intensity.nelson_2,!0)}finally{await Ue(o)}}),(0,t.t6)("SPC:run_meta_helpers",async()=>{const{setRunMeta:o,getRunMeta:r}=await 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e.upsertRun({run_id:"a",instrument_id:"Q-01",acquisition_datetime:"2026-07-20T00:00:00.000Z",run_label:"r-20",median_intensity:1,missing_pct:1,control_corr:1,protein_count:1,status:"pass",rules_tripped:[],source_project_id:null,source_df_name:"a",computed_at:(new Date).toISOString()},{root:o}),await e.upsertRun({run_id:"b",instrument_id:"Q-01",acquisition_datetime:"2026-07-10T00:00:00.000Z",run_label:"r-10",median_intensity:1,missing_pct:1,control_corr:1,protein_count:1,status:"pass",rules_tripped:[],source_project_id:null,source_df_name:"b",computed_at:(new Date).toISOString()},{root:o}),await e.upsertRun({run_id:"c",instrument_id:"Q-01",acquisition_datetime:"2026-07-15T00:00:00.000Z",run_label:"r-15",median_intensity:1,missing_pct:1,control_corr:1,protein_count:1,status:"pass",rules_tripped:[],source_project_id:null,source_df_name:"c",computed_at:(new Date).toISOString()},{root:o});const n=await e.loadRuns("Q-01",{root:o});(0,t.E3)(n.length,3),(0,t.E3)(n[0].acquisition_datetime,"2026-07-10T00:00:00.000Z"),(0,t.E3)(n[1].acquisition_datetime,"2026-07-15T00:00:00.000Z"),(0,t.E3)(n[2].acquisition_datetime,"2026-07-20T00:00:00.000Z")}finally{await Ue(o)}},{skipReason:"Quarantined: userDataStorage write/read consistency — 3 sequential upserts read back 2 on newer Datagrok runtime — see BACKLOG"}),(0,t.t6)("SPC:candidates_refuse",async()=>{const o=await Promise.resolve().then(n.bind(n,655)),r=e.DataFrame.create(1);r.setTag("proteomics.source","spectronaut-candidates"),(0,t.E3)(typeof o.assertSpcEligible,"function");let s=!1,a="";try{o.assertSpcEligible(r)}catch(e){s=!0,a=String(e&&e.message?e.message:e)}(0,t.E3)(s,!0),(0,t.E3)(a.indexOf("SPC requires per-sample intensities")>=0,!0)}),(0,t.t6)("SPC:idempotent_upsert",async()=>{const e=await Promise.resolve().then(n.bind(n,883)),o=Be();try{const n={run_id:"r1",instrument_id:"Q-01",acquisition_datetime:"2026-07-10T00:00:00.000Z",run_label:"first-call",median_intensity:22.31,missing_pct:12.6,control_corr:.94,protein_count:4820,status:"pass",rules_tripped:[],source_project_id:null,source_df_name:"first-call",computed_at:(new Date).toISOString()};await e.upsertRun(n,{root:o}),await e.upsertRun({...n,run_label:"second-call",median_intensity:23},{root:o});const r=await e.loadRuns("Q-01",{root:o});(0,t.E3)(r.length,1),(0,t.E3)(r[0].run_label,"second-call"),(0,t.E3)(r[0].median_intensity,23)}finally{await Ue(o)}}),(0,t.t6)("SPC:storage_bounded",async()=>{const e=await Promise.resolve().then(n.bind(n,883)),o=Be();try{for(let t=1;t<=2;t++)for(let n=0;n<52;n++){const r=String(1+n%28).padStart(2,"0"),s=String(1+Math.floor(n/4)%12).padStart(2,"0");await e.upsertRun({run_id:`i${t}-w${n}`,instrument_id:`Q-0${t}`,acquisition_datetime:`2026-${s}-${r}T00:00:00.000Z`,run_label:`wk${n}`,median_intensity:22,missing_pct:12,control_corr:.9,protein_count:4e3,status:"pass",rules_tripped:[],source_project_id:null,source_df_name:`wk${n}`,computed_at:(new Date).toISOString()},{root:o})}const n=await e.loadRuns("Q-01",{root:o}),r=await e.loadRuns("Q-02",{root:o});(0,t.E3)(n.length<=52,!0),(0,t.E3)(r.length<=52,!0)}finally{await Ue(o)}}),(0,t.t6)("SPC:schema_version",async()=>{const e=await Promise.resolve().then(n.bind(n,883)),o=Be();try{await e.upsertRun({run_id:"r1",instrument_id:"Q-01",acquisition_datetime:"2026-07-10T00:00:00.000Z",run_label:"r",median_intensity:1,missing_pct:1,control_corr:1,protein_count:1,status:"pass",rules_tripped:[],source_project_id:null,source_df_name:"r",computed_at:(new Date).toISOString()},{root:o});const n=await e.readRunsMeta({root:o});(0,t.E3)(n["spc.runs.schema_version"],"1")}finally{await Ue(o)}}),(0,t.t6)("SPC:column_idempotent",async()=>{const o=await Promise.resolve().then(n.bind(n,655)),r=e.DataFrame.fromColumns([e.Column.fromFloat32Array("log2(s1)",new Float32Array([10,11,12])),e.Column.fromFloat32Array("log2(s2)",new Float32Array([11,12,13]))]);r.col("log2(s1)").semType="Proteomics-Intensity",r.col("log2(s2)").semType="Proteomics-Intensity";const s={group1:{name:"Control",columns:["log2(s1)"]},group2:{name:"Treatment",columns:["log2(s2)"]}},a={instrument_id:"Q-01",acquisition_datetime:"2026-07-10T00:00:00.000Z"},i=o.computeSpcMetrics(r,s,a);o.setSpcStatus(r,i,{status:"pass",rulesTripped:[]});const l=r.columns.length,c=o.computeSpcMetrics(r,s,a);o.setSpcStatus(r,c,{status:"pass",rulesTripped:[]}),(0,t.E3)(r.columns.length,l)}),(0,t.t6)("SPC:belt_and_braces",async()=>{const o=await Promise.resolve().then(n.bind(n,655)),r=e.DataFrame.fromColumns([e.Column.fromFloat32Array("log2(s1)",new Float32Array([10,11,12])),e.Column.fromFloat32Array("log2(s2)",new 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e.DataFrame.fromColumns(o)}([{run_id:"1",instrument_id:"Q-01",acquisition_datetime:"2026-07-01T00:00:00.000Z",run_label:"r1",median_intensity:22,missing_pct:12,control_corr:.9,protein_count:4800,status:"pass",source_project_id:null,source_df_name:"r1",computed_at:"X"},{run_id:"2",instrument_id:"Q-01",acquisition_datetime:"2026-07-08T00:00:00.000Z",run_label:"r2",median_intensity:22.5,missing_pct:12.2,control_corr:.93,protein_count:4810,status:"pass",source_project_id:null,source_df_name:"r2",computed_at:"X"}]),s=o.createSpcChartPanel(r,{metrics:{median_intensity:{mean:22.3,sd:.5},missing_pct:{mean:12,sd:1},control_corr:{mean:.92,sd:.02},protein_count:{mean:4800,sd:100}}},"median_intensity");(0,t.E3)(null!=s,!0)}),(0,t.t6)("SPC:formula_lines",async()=>{const e=(await Promise.resolve().then(n.bind(n,589))).computeControlLines({metrics:{median_intensity:{mean:22.3,sd:.5}}},"median_intensity");(0,t.E3)(e.ucl,23.8),(0,t.E3)(e.cl,22.3),(0,t.E3)(e.lcl,20.8)}),(0,t.t6)("SPC:pareto_descending",async()=>{const e=(await Promise.resolve().then(n.bind(n,589))).aggregateParetoCounts([{rules_tripped:["nelson_1@median_intensity","nelson_5@control_corr"]},{rules_tripped:["nelson_1@median_intensity"]},{rules_tripped:["nelson_1@median_intensity","nelson_5@control_corr"]},{rules_tripped:[]}]);(0,t.E3)(e.length>=2,!0);for(let n=1;n<e.length;n++)(0,t.E3)(e[n-1].count>=e[n].count,!0);(0,t.E3)(e[0].rule+"@"+e[0].metric,"nelson_1@median_intensity"),(0,t.E3)(e[0].count,3)}),t.bk,t.cb});const je=new e.Package;async function Ve(n,o,r){const s=await(0,t.N$)({category:n,test:o,testContext:r});return e.DataFrame.fromObjects(s)}async function qe(){await(0,t.Xb)(je,je.getModule("package-test.js"))}})(),proteomics_test=o})();
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