@datagrok/proteomics 1.0.1 → 1.2.1

package/dist/package.js

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t=0;t<r;t++)f[t]=(0|e[t])-1}else for(let e=0;e<r;e++)f[e]=e;const p=new Float32Array(n);p.fill(a.FLOAT_NULL);const d=new Float32Array(n);d.fill(a.FLOAT_NULL);const m=new Float32Array(n);m.fill(a.FLOAT_NULL);const h=new Uint8Array(n);let g=0;for(let e=0;e<r;e++){const t=f[e];if(t<0||t>=n)continue;p[t]=o[e],d[t]=i[e],m[t]=s[e];const r=l.get(e);!0!==r&&1!==r&&"1"!==r&&"TRUE"!==r||(h[t]=1,g++)}const y=a.Column.fromFloat32Array("log2FC",p),w=a.Column.fromFloat32Array("p-value",d),v=a.Column.fromFloat32Array("adj.p-value",m);return e.columns.addNewBool("significant").init(e=>1===h[e]),y.semType=u.iu.LOG2FC,w.semType=u.iu.P_VALUE,v.semType=u.iu.P_VALUE,e.columns.add(y),e.columns.add(w),e.columns.add(v),g}async function w(e,t,n,r,i){const a=g(e,t,n),s=y(e,await o.functions.call("Proteomics:LimmaDE",{exprDf:a,nGroup1:t.length,fcThreshold:r,pThreshold:i}));return e.setTag("proteomics.de_complete","true"),e.fireValuesChanged(),s}function v(e,t){const n=(0,f.f)(e);if(!n)return void 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t=h(e,m,d,0,0,n,i);e.setTag("proteomics.de_method","t-test"),o.shell.info(`DE complete (t-test): ${t.tested} proteins tested, ${t.untestable} untestable`)}else if("DEqMS"===l){const t=N.value;if(!t)return void o.shell.error("Please select a peptide count column for DEqMS");try{const r=await async function(e,t,n,r,i,s){const l=g(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,r.isNone(t)?1:Math.round(r.get(t)));const f=y(e,await o.functions.call("Proteomics:DeqmsDE",{exprDf:l,nGroup1:t.length,peptideDf:c,fcThreshold:i,pThreshold:s}));return e.setTag("proteomics.de_complete","true"),e.setTag("proteomics.de_method","deqms"),e.fireValuesChanged(),f}(e,m,d,t,n,i);e.setTag("proteomics.de_method","deqms"),o.shell.info(`DE complete (DEqMS): ${r} significant proteins`)}catch(t){console.warn("DEqMS failed, trying limma:",t),v.update(50,"DEqMS unavailable, trying limma..."),o.shell.warning("DEqMS unavailable, trying limma...");try{const t=await w(e,m,d,n,i);e.setTag("proteomics.de_method","limma"),o.shell.info(`DE complete (limma fallback): ${t} significant proteins`)}catch(t){console.warn("Limma DE also failed, using client-side fallback:",t),v.update(75,"Server-side DE unavailable, using client-side t-test..."),o.shell.warning("R environment unavailable — using client-side t-test");const r=h(e,m,d,0,0,n,i);e.setTag("proteomics.de_method","t-test"),o.shell.info(`DE complete (t-test): ${r.tested} proteins tested, ${r.untestable} untestable`)}}}else try{const t=await w(e,m,d,n,i);e.setTag("proteomics.de_method","limma"),o.shell.info(`DE complete (limma): ${t} significant proteins`)}catch(t){v.update(50,"Limma unavailable, using client-side t-test..."),o.shell.warning("R environment unavailable — using client-side t-test"),console.warn("Limma DE failed, using client-side fallback:",t);const r=h(e,m,d,0,0,n,i);e.setTag("proteomics.de_method","t-test"),o.shell.info(`DE complete (t-test): ${r.tested} proteins tested, 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Run Differential Expression first.");const o=r.geneName??r.proteinId;if(!o)throw new Error("No gene-name or protein-ID column found to export.");const i=new Map;for(let t=0;t<e.rowCount;t++){const e=o.get(t);e&&i.set(t,String(e))}const s=r.log2fc.getRawData(),c=r.pValue.getRawData(),{upGenes:u,downGenes:f,background:p}=(0,l.Bx)(i,s,c,t,n),d=e=>/[",\n]/.test(e)?`"${e.replace(/"/g,'""')}"`:e,m=["gene,list"];for(const e of u)m.push(`${d(e)},up`);for(const e of f)m.push(`${d(e)},down`);for(const e of p)m.push(`${d(e)},background`);return{csv:m.join("\n"),counts:{up:u.length,down:f.length,background:p.length}}}(e,t,o),p=e.name?`${e.name} — enrichment inputs`:"enrichment inputs";i.Utils.download(`${p}.csv`,u,"text/csv"),r.shell.info(`Exported ${f.up} up, ${f.down} down, ${f.background} background genes.`)}).show()}},230(e,t,n){"use strict";n.d(t,{Bx:()=>b,D9:()=>x,bM:()=>_,pG:()=>N});var r=n(328),o=n(389),i=n(82),a=n(498),s=n(304),l=n(641),c=n(897),u=n(829),f=n(252),p=n(935);const d="https://biit.cs.ut.ee/gprofiler";async function m(e,t,n=3e4){const o=r.dapi.fetchProxy(e,t),i=new Promise((e,t)=>setTimeout(()=>t(new Error("g:Profiler API request timed out. 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Run Differential Expression first.");let f,p=0,g=0,y=0;if(u.geneName){f=new Map;const t=u.geneName;for(let n=0;n<e.rowCount;n++){const e=t.get(n);e&&f.set(n,e)}p=f.size,g=e.rowCount,y=g-p}else{const t=new Map;for(let n=0;n<e.rowCount;n++){const e=u.proteinId.get(n),r=(0,a.S6)(e);r&&(t.has(r)||t.set(r,[]),t.get(r).push(n))}const n=[...t.keys()],o=await async function(e,t="hsapiens"){const n=await m(`${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,r),i=new Map;for(const e of o)e.incoming&&e.name&&"N/A"!==e.name&&!i.has(e.incoming)&&i.set(e.incoming,e.name);f=new Map;for(const[e,n]of t){const t=i.get(e);if(t)for(const e of n)f.set(e,t)}const s=new Array(e.rowCount).fill("");for(const[e,t]of f)s[e]=t;const c=e.columns.addNewString("Gene Symbol (mapped)");c.semType=l.iu.GENE_SYMBOL,c.init(e=>s[e]),p=i.size,g=n.length,y=g-p}const _=u.log2fc.getRawData(),x=u.pValue.getRawData(),{upGenes:N,downGenes:C,background:S}=b(f,_,x,t,n);if(0===N.length&&0===C.length)throw new Error("No significant proteins found with the given thresholds");const T=[];let E=null,P=null;if(N.length>0){let e=await h(N,S,r,o,n);if(i){const t=w(e,c);e=t.kept,E=t.stats}T.push(v(e,N,n,"Up"))}if(C.length>0){let e=await h(C,S,r,o,n);if(i){const t=w(e,c);e=t.kept,P=t.stats}T.push(v(e,C,n,"Down"))}let D=T[0];for(let e=1;e<T.length;e++)D=D.append(T[e]);D.name=e.name?`${e.name} — Enrichment`:"Enrichment Results",D.setTag("proteomics.enrichment","true");const L=D.col("FDR");if(L&&(L.setTag("color-coding-type","Linear"),L.setTag("color-coding-linear",'{"0":"#2ecc71","0.05":"#f39c12","1":"#e74c3c"}')),i){const e=(E?.total??0)+(P?.total??0),t=(E?.kept??0)+(P?.kept??0),n=(E?.droppedParents??0)+(P?.droppedParents??0);t<e&&(D.setTag("proteomics.enrichment_smart_filtered","true"),D.setTag("proteomics.enrichment_smart_filtered_kept",String(t)),D.setTag("proteomics.enrichment_smart_filtered_total",String(e)),D.setTag("proteomics.enrichment_smart_filtered_dropped_parents",String(n)),D.setTag("proteomics.enrichment_smart_filtered_cap",String(c)))}return{enrichmentDf:D,mapped:p,total:g,unmapped:y}}function N(e){if(!(0,u.RJ)(e,"Run Differential Expression first"))return;const t=(0,s.I)(e);if(!t.log2fc||!t.pValue)return void r.shell.warning("No log2FC or p-value columns found");const n=o.input.float("|log2FC| threshold",{value:l.M5});n.setTooltip("Minimum absolute fold change for significance");const a=o.input.float("Adj. p-value threshold",{value:l.Dx});a.setTooltip("Maximum adjusted p-value for significance");const d=(0,p.X3)((0,f.Di)(e)??(0,p.Vr)(e)),m=o.input.choice("Organism",{value:d??"Homo sapiens (Human)",items:p.Ae.map(e=>e.display),nullable:!1}),h=o.input.bool("GO: Biological Process",{value:!0}),g=o.input.bool("GO: Molecular Function",{value:!0}),y=o.input.bool("GO: Cellular Component",{value:!0}),w=o.input.bool("KEGG Pathways",{value:!0}),v=o.input.bool("Reactome Pathways",{value:!0}),b=o.input.bool("WikiPathways",{value:!0}),N=o.input.bool("Apply smart pathway filter",{value:!0});N.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 C=o.input.int("Max terms per source",{value:15,min:1});C.setTooltip("Upper bound on terms kept per enrichment source (top-N by FDR). Applies only when the smart pathway filter is on.");const S=()=>C.enabled=N.value??!0;N.onChanged.subscribe(S),S();const T=o.divText(""),E=()=>{const r=n.value??l.M5,o=a.value??l.Dx,i=_(e,r,o,t.log2fc,t.pValue),s=i.total.toLocaleString();T.textContent=`${i.significant} of ${s} proteins are significant with these thresholds`};E(),n.onChanged.subscribe(E),a.onChanged.subscribe(E),o.dialog("Enrichment Analysis").add(T).add(n).add(a).add(m).add(h).add(g).add(y).add(w).add(v).add(b).add(N).add(C).onOK(async()=>{const t=i.TaskBarProgressIndicator.create("Running enrichment analysis...");try{const t=n.value??l.M5,o=a.value??l.Dx,i=m.value,s=p.Ae.find(e=>e.display===i),u=s?.code??"hsapiens";(0,f.Np)(e,u);const d=[];if(h.value&&d.push("GO:BP"),g.value&&d.push("GO:MF"),y.value&&d.push("GO:CC"),w.value&&d.push("KEGG"),v.value&&d.push("REAC"),b.value&&d.push("WP"),0===d.length)return void r.shell.warning("Please select at least one enrichment source");const _=await x(e,t,o,u,d,N.value??!0,C.value??15),S=_.total>0?(_.mapped/_.total*100).toFixed(1):"0.0";r.shell.info(`${_.mapped}/${_.total} proteins mapped (${S}%). ${_.unmapped} unmapped.`),(0,c.q6)(_.enrichmentDf,e)}catch(e){r.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:()=>m,f:()=>f});var r=n(328),o=n(389),i=n(353),a=n.n(i),s=n(641),l=n(655),c=n(935);function u(e,t){e.setTag("proteomics.groups",JSON.stringify(t))}function f(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 m(e){const t=e.columns.toList().filter(e=>e.semType===s.iu.INTENSITY&&e.name.startsWith("log2(")).map(e=>e.name),n=function(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),r=f(e);if(!r)return{group1Name:"Control",group1Cols:[],group2Name:"Treatment",group2Cols:[],instrumentId:n?.instrument_id,acquisitionDatetime:n?.acquisition_datetime};const o=new Set(t),i=t=>t.filter(e=>o.has(e)).map(t=>e.col(t)).filter(e=>null!==e);return{group1Name:r.group1.name||"Control",group1Cols:i(r.group1.columns),group2Name:r.group2.name||"Treatment",group2Cols:i(r.group2.columns),instrumentId:n?.instrument_id,acquisitionDatetime:n?.acquisition_datetime}}(e,t),i=o.input.string("Group 1 Name",{value:n.group1Name}),m=o.input.columns("Group 1",{table:e,available:t,value:n.group1Cols}),h=o.input.string("Group 2 Name",{value:n.group2Name}),g=o.input.columns("Group 2",{table:e,available:t,value:n.group2Cols}),y=o.input.string("Instrument",{value:n.instrumentId??"",tooltipText:"Free-text identifier for the instrument that ran this analysis (e.g. QExactive-01). Used to group runs in the SPC dashboard."}),w=o.input.date("Acquisition datetime",{value:n.acquisitionDatetime?a()(n.acquisitionDatetime):null,tooltipText:"When the samples were acquired on the instrument. Used to order runs on the SPC trend chart — not the file-import time."}),v=o.input.choice("Organism",{value:(0,c.X3)(d(e)??(0,c.Vr)(e))??"Homo sapiens (Human)",items:c.Ae.map(e=>e.display),nullable:!1,tooltipText:"Species for enrichment (g:Profiler) and UniProt subcellular-location lookup. Auto-detected from the data when available."});o.dialog("Annotate Experiment").add(i).add(m).add(h).add(g).add(v).add(y).add(w).onOK(()=>{const t=m.value??[],n=g.value??[];if(0===t.length||0===n.length)return void r.shell.warning("Select at least one column per group");const o={group1:{name:i.value,columns:t.map(e=>e.name)},group2:{name:h.value,columns:n.map(e=>e.name)}},a=(y.value??"").trim(),s=w.value,f=s&&"function"==typeof s.toISOString||s instanceof Date?s.toISOString():"";!function(e,t){u(e,{group1:t.group1,group2:t.group2}),t.organism&&p(e,t.organism),t.runMeta&&(0,l.setRunMeta)(e,t.runMeta)}(e,{group1:o.group1,group2:o.group2,organism:(0,c.$S)(v.value??void 0),runMeta:a.length>0||f.length>0?{instrument_id:a,acquisition_datetime:f}:void 0}),r.shell.info(`Groups assigned: ${t.length} + ${n.length} samples`)}).show()}},47(e,t,n){"use strict";n.d(t,{Mx:()=>c,UN:()=>u});var r=n(328),o=n(389),i=n(82),a=n(641),s=n(252);function l(e,t){const n=Math.random(),r=Math.random();return e+t*(Math.sqrt(-2*Math.log(n))*Math.cos(2*Math.PI*r))}function c(e,t,n=10){const r=t.map(t=>e.col(t)).filter(e=>null!=e&&e.type===i.COLUMN_TYPE.FLOAT);if(0===r.length)return 0;const o=r.map(e=>e.getRawData()),a=e.rowCount,s=r.length,l=[],c=[];for(let e=0;e<a;e++){const t=new Float64Array(s),n=[];for(let o=0;o<s;o++){const i=r[o].isNone(e);n.push(i),t[o]=i?0:r[o].get(e)}l.push(t),c.push(n)}const u=new Float64Array(s);for(let e=0;e<s;e++){let t=0,n=0;for(let r=0;r<a;r++)c[r][e]||(t+=l[r][e],n++);u[e]=n>0?t/n:NaN}const f=[];for(let e=0;e<a;e++)c[e].some(e=>e)&&f.push(e);const p=i.TaskBarProgressIndicator.create("kNN imputation...");let d=0;try{for(let e=0;e<f.length;e++){const t=f[e];if(p.update(Math.round(e/f.length*100),`Row ${e+1}/${f.length}`),!c[t].some(e=>!e)){for(let e=0;e<s;e++)c[t][e]&&isFinite(u[e])&&(o[e][t]=u[e],d++);continue}const r=[];for(let e=0;e<a;e++){if(e===t)continue;let n=0,o=0;for(let r=0;r<s;r++)if(!c[t][r]&&!c[e][r]){const i=l[t][r]-l[e][r];n+=i*i,o++}o>0&&r.push({row:e,dist:Math.sqrt(n/o)})}r.sort((e,t)=>e.dist-t.dist);const i=r.slice(0,n);for(let e=0;e<s;e++){if(!c[t][e])continue;let n=0,r=0;for(const t of i)c[t.row][e]||(n+=l[t.row][e],r++);const a=r>0?n/r:u[e];isFinite(a)&&(o[e][t]=a,d++)}}}finally{p.close()}return e.fireValuesChanged(),e.setTag("proteomics.imputed","true"),d}function u(e){if("true"===e.getTag("proteomics.imputed"))return void r.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)),u=o.input.choice("Method",{value:"MinProb",items:["MinProb","kNN","Zero","Mean","Median"],nullable:!1}),f=o.input.columns("Intensity columns",{table:e,available:t,value:n}),p=o.input.float("Downshift",{value:1.8});p.setTooltip("Standard deviations to shift left from mean (Perseus default: 1.8)");const d=o.input.float("Width",{value:.3});d.setTooltip("Fraction of standard deviation for imputation distribution (Perseus default: 0.3)");const m=o.div([p.root,d.root]),h=o.input.int("k (neighbors)",{value:10}),g=o.div([h.root]);g.style.display="none",u.onChanged.subscribe(()=>{const e=u.value;m.style.display="MinProb"===e?"":"none",g.style.display="kNN"===e?"":"none"});const y=o.input.int("Min valid values per group",{value:2}),w=o.divText("");w.style.cssText="font-size:12px; color:#888; margin-bottom:8px;";const v=()=>{const t=y.value??0,n=(0,s.f)(e);if(0===t||!n)return void(w.textContent=`Will keep all ${e.rowCount} proteins`);const r=n.group1.columns.map(t=>e.col(t)).filter(e=>null!=e),o=n.group2.columns.map(t=>e.col(t)).filter(e=>null!=e);let i=0;for(let n=0;n<e.rowCount;n++){let e=0;for(const t of r)t.isNone(n)||e++;let a=0;for(const e of o)e.isNone(n)||a++;(e>=t||a>=t)&&i++}const a=e.rowCount-i;w.textContent=`Will keep ${i}/${e.rowCount} proteins (${a} removed)`};y.onChanged.subscribe(v),v(),o.dialog("Impute Missing Values").add(u).add(f).add(m).add(g).add(y).add(w).onOK(()=>{const t=f.value.map(e=>e.name),n=u.value,o=y.value??0,a=(0,s.f)(e);if(o>0&&a){const t=a.group1.columns.map(t=>e.col(t)).filter(e=>null!=e),n=a.group2.columns.map(t=>e.col(t)).filter(e=>null!=e),s=i.BitSet.create(e.rowCount);for(let r=0;r<e.rowCount;r++){let e=0;for(const n of t)n.isNone(r)||e++;let i=0;for(const e of n)e.isNone(r)||i++;e<o&&i<o&&s.set(r,!0)}const l=s.trueCount;l>0&&(e.rows.removeWhere(e=>s.get(e.idx)),r.shell.info(`Filtered: removed ${l} proteins below threshold`))}let m=0;try{switch(n){case"MinProb":m=function(e,t,n=1.8,r=.3){let o=0;for(const a of t){const t=e.col(a);if(!t)continue;if(t.type!==i.COLUMN_TYPE.FLOAT)continue;const s=t.stats.avg,c=t.stats.stdev;if(isNaN(s)||isNaN(c)||0===c)continue;const u=s-n*c,f=r*c,p=t.getRawData();for(let t=0;t<e.rowCount;t++)p[t]===i.FLOAT_NULL&&(p[t]=l(u,f),o++)}return e.fireValuesChanged(),e.setTag("proteomics.imputed","true"),o}(e,t,p.value,d.value);break;case"kNN":m=c(e,t,h.value);break;case"Zero":m=function(e,t){let n=0;for(const r of t){const t=e.col(r);if(!t||t.type!==i.COLUMN_TYPE.FLOAT)continue;const o=t.getRawData();for(let t=0;t<e.rowCount;t++)o[t]===i.FLOAT_NULL&&(o[t]=0,n++)}return e.fireValuesChanged(),e.setTag("proteomics.imputed","true"),n}(e,t);break;case"Mean":m=function(e,t){let n=0;for(const r of t){const t=e.col(r);if(!t||t.type!==i.COLUMN_TYPE.FLOAT)continue;const o=t.stats.avg;if(isNaN(o))continue;const a=t.getRawData();for(let t=0;t<e.rowCount;t++)a[t]===i.FLOAT_NULL&&(a[t]=o,n++)}return e.fireValuesChanged(),e.setTag("proteomics.imputed","true"),n}(e,t);break;case"Median":m=function(e,t){let n=0;for(const r of t){const t=e.col(r);if(!t||t.type!==i.COLUMN_TYPE.FLOAT)continue;const o=t.stats.med;if(isNaN(o))continue;const a=t.getRawData();for(let t=0;t<e.rowCount;t++)a[t]===i.FLOAT_NULL&&(a[t]=o,n++)}return e.fireValuesChanged(),e.setTag("proteomics.imputed","true"),n}(e,t)}}catch(e){return void r.shell.error(`Imputation failed: ${e?.message??e}. 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r=n(328),o=n(389),i=n(82),a=n(713),s=n(312),l=n(53),c=n(86),u=n(119),f=n(641),p=n(304);const d=["primary protein id","pg.proteingroups","protein id","uniprot","accession"];function m(e,t=0){if(0===e.rowCount||t<0||t>=e.rowCount)return;const n=(0,p.k)(e,f.iu.PROTEIN_ID,d);n&&(e.currentCell=e.cell(t,n.name),r.shell.windows.showContextPanel=!0,async function(){const e=["Proteomics","UniProt"];for(let t=0;t<12;t++){await new Promise(e=>setTimeout(e,250));try{const t=document.querySelector('[d4-title="semantic meta.Proteomics-ProteinId"]');if(!t)continue;let n=!0;for(const r of e){const e=Array.from(t.querySelectorAll(".d4-accordion-pane-header")).find(e=>e.textContent?.trim()===r);e?e.classList.contains("expanded")||(e.click(),n=!1):n=!1}if(n)return}catch{}}}())}var h=n(954),g=n(117);function y(){i.Utils.openFile({accept:".csv,.tsv,.txt",open:e=>{const t=new FileReader;t.onload=()=>{try{const n=t.result,a=(0,h.T6)(n);!function(e,t){const 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e=0;e<Math.min(r,o);e++){const t=y>0?Math.max(m[e],0)/y*100:0;w.push(Math.round(10*t)/10)}const v=w.length>0&&isFinite(w[0])?w[0]:0,b=o>=2?`PC1 (${v}%)`:"PC1",_=w.length>=2&&isFinite(w[1])?w[1]:0,x=r>=2&&w.length>=2&&o>=2?`PC2 (${_}%)`:"PC2",N=[i.Column.fromStrings("SampleName",t),i.Column.fromFloat32Array(b,new Float32Array(g.map(e=>e[0])))];if(r>=2){const e=i.Column.fromFloat32Array(x,new Float32Array(g.map(e=>e.length>1?e[1]:0)));N.push(e)}const C=t.map(e=>n.group1.columns.includes(e)?n.group1.name:n.group2.columns.includes(e)?n.group2.name:"Unknown"),S=i.Column.fromStrings("Group",C);N.push(S);const T=i.DataFrame.fromColumns(N);return T.name="PCA",{pcaDf:T,varianceExplained:w}}(e,t,n),s=o.columns.toList().find(e=>e.name.startsWith("PC1"))?.name,l=o.columns.toList().find(e=>e.name.startsWith("PC2"))?.name;if(!s||!l)throw new Error("PCA did not produce PC1/PC2 columns — too few samples?");const c=o.plot.scatter({x:s,y:l,color:"Group"});c.props.labelColumnNames=["SampleName"],c.props.displayLabels="Always";try{const e=o.col(s),t=o.col(l),r=o.col("Group"),i=[n.group1.name,n.group2.name];for(let n=0;n<i.length;n++){const a=i[n],u=[],f=[];for(let n=0;n<o.rowCount;n++)r.get(n)===a&&(u.push(e.get(n)),f.push(t.get(n)));const p=A(u,f);if(p){const e=L[n%L.length],t={type:"area",area:p,fillColor:e,opacity:.15,outlineColor:e,outlineWidth:1,x:s,y:l};c.meta.annotationRegions?.add(t)}}}catch(e){console.warn("PCA: could not add confidence ellipses:",e?.message??e)}return r&&c.setOptions({title:r}),{viewer:c,pcaDf:o}}var I=n(715);const O=["M","A","MA_trend","CV_group1","meanInt_group1","CV_group2","meanInt_group2"];function F(e){const t=i.TaskBarProgressIndicator.create("Creating QC dashboard...");try{const t=(0,w.f)(e);if(!t)return void r.shell.warning("Annotate experimental groups first (Proteomics | Annotate Experiment)");for(const t of O)e.columns.contains(t)&&e.columns.remove(t);const 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function re(){await Oe.normalizeProteomics()}async function oe(){await Oe.imputeMissingValues()}async function ie(){await Oe.differentialExpression()}async function ae(){await Oe.computeSpcStatus()}async function se(){await Oe.showVolcanoPlot()}async function le(){await Oe.showHeatmap()}async function ce(){await Oe.showPcaPlot()}async function ue(){await Oe.showGroupMeanCorrelation()}async function fe(){await Oe.showQcDashboard()}async function pe(){await Oe.showSpcDashboard()}async function de(){await Oe.showAllVisualizations()}async function me(){await Oe.enrichmentAnalysis()}async function he(){await Oe.exportEnrichmentInputs()}async function ge(){await Oe.enrichmentCharts()}async function ye(){await Oe.proteomicsDemo()}async function we(){await Oe.proteomicsEnrichmentDemo()}function ve(e){return Oe.uniprotPanelWidget(e)}async function be(){await Oe.shareAnalysisForReview()}function _e(e){return Oe.publishedAnalysisPanelWidget(e)}async function xe(){await Oe.recoverPublishedProjectsOnStartup()}var Ne=function(e,t,n,r){var o,i=arguments.length,a=i<3?t:null===r?r=Object.getOwnPropertyDescriptor(t,n):r;if("object"==typeof Reflect&&"function"==typeof Reflect.decorate)a=Reflect.decorate(e,t,n,r);else for(var s=e.length-1;s>=0;s--)(o=e[s])&&(a=(i<3?o(a):i>3?o(t,n,a):o(t,n))||a);return i>3&&a&&Object.defineProperty(t,n,a),a},Ce=function(e,t){if("object"==typeof Reflect&&"function"==typeof Reflect.metadata)return Reflect.metadata(e,t)},Se=function(e,t){return function(n,r){t(n,r,e)}};const Te=new i.Package;function Ee(e,t){return"spectronaut-candidates"!==e.getTag("proteomics.source")||(r.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 Me(t,e),m(e),t}class Oe{static async initProteomics(){}static async buildProteomicsTopMenu(){const e={importSpectronautCandidates:()=>Oe.importSpectronautCandidates(),importSpectronaut:()=>Oe.importSpectronaut(),importMaxQuant:()=>Oe.importMaxQuant(),importFragPipe:()=>Oe.importFragPipe(),importGenericMatrix:()=>Oe.importGenericMatrix(),annotateExperiment:()=>Oe.annotateExperiment(),setLog2Scale:()=>Oe.setLog2Scale(),normalize:()=>Oe.normalizeProteomics(),impute:()=>Oe.imputeMissingValues(),differentialExpression:()=>Oe.differentialExpression(),enrichmentAnalysis:()=>Oe.enrichmentAnalysis(),exportEnrichmentInputs:()=>Oe.exportEnrichmentInputs(),computeSpcStatus:()=>Oe.computeSpcStatus(),showVolcanoPlot:()=>Oe.showVolcanoPlot(),showHeatmap:()=>Oe.showHeatmap(),showPcaPlot:()=>Oe.showPcaPlot(),showGroupMeanCorrelation:()=>Oe.showGroupMeanCorrelation(),showQcDashboard:()=>Oe.showQcDashboard(),showSpcDashboard:()=>Oe.showSpcDashboard(),enrichmentCharts:()=>Oe.enrichmentCharts(),showAllVisualizations:()=>Oe.showAllVisualizations(),shareAnalysisForReview:()=>Oe.shareAnalysisForReview()},t=new WeakSet,n=n=>{n?.type!==i.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 r=e.ribbonMenu.group("Proteomics");for(const e of z)try{r.remove(e)}catch{}const o={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)},i=r.group("Import");i.item("Spectronaut Candidates...",t.importSpectronautCandidates),i.item("Spectronaut Report...",t.importSpectronaut),i.item("MaxQuant...",t.importMaxQuant),i.item("FragPipe...",t.importFragPipe),i.item("Generic Matrix...",t.importGenericMatrix),r.item("Annotate Experiment...",t.annotateExperiment,null,o);const a=r.group("Analyze");a.item("Set Log2 Scale...",t.setLog2Scale,null,o),a.item("Normalize...",t.normalize,null,o),a.item("Impute Missing Values...",t.impute,null,o),a.item("Differential Expression...",t.differentialExpression,null,o),a.item("Enrichment Analysis...",t.enrichmentAnalysis),a.item("Export Enrichment Inputs...",t.exportEnrichmentInputs),a.item("Compute SPC Status",t.computeSpcStatus,null,o);const s=r.group("Visualize");return s.item("Volcano Plot...",t.showVolcanoPlot),s.item("Heatmap...",t.showHeatmap,null,o),s.item("PCA...",t.showPcaPlot,null,o),s.item("Group-Mean Correlation...",t.showGroupMeanCorrelation,null,o),s.item("QC Dashboard...",t.showQcDashboard,null,o),s.item("SPC Dashboard...",t.showSpcDashboard),s.item("Enrichment Charts...",t.enrichmentCharts),s.item("Show All Visualizations...",t.showAllVisualizations,null,o),r.group("Share").item("Share Analysis for Review...",t.shareAnalysisForReview),!0})(n,e)&&t.add(n)}catch{}},50)};try{for(const e of r.shell.views)n(e)}catch{}r.events.onViewAdded.subscribe(n),r.events.onCurrentViewChanged.subscribe(()=>n(r.shell.v))}static async importSpectronautCandidates(){i.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(/\.[^.]+$/,""),Ae(n),Ie(n)}catch(e){r.shell.error(`Failed to import Spectronaut Candidates file: ${e?.message??e}`)}}})}static async importSpectronaut(){i.Utils.openFile({accept:".tsv,.txt,.csv",open:async e=>{try{const t=await De(e)?await(0,l.A)(e):await(0,l.parseSpectronautText)(await e.text());t.name=e.name.replace(/\.[^.]+$/,""),Ae(t),r.shell.addTableView(t),r.shell.info(`Imported ${t.rowCount} protein groups from Spectronaut`),m(t)}catch(e){r.shell.error(`Failed to import Spectronaut file: ${e?.message??e}`),r.shell.warning("If this is a very large precursor-level Spectronaut report that fails to stream in-browser, pre-aggregate it to the importable protein-group shape with the bundled duckdb fallback: tools/spectronaut-aggregate.sh <input.tsv>, then re-import the resulting file. See files/demo/README.md for usage.")}}})}static async importMaxQuant(){i.Utils.openFile({accept:".txt,.tsv",open:async e=>{try{const t=await e.text(),n=await(0,s.E)(t);n.name=e.name.replace(/\.[^.]+$/,""),Ae(n),r.shell.addTableView(n),r.shell.info(`Imported ${n.rowCount} protein groups`),m(n)}catch(e){r.shell.error(`Failed to import MaxQuant file: ${e?.message??e}`)}}})}static async importFragPipe(){i.Utils.openFile({accept:".tsv,.txt",open:async e=>{try{const t=await e.text(),n=await(0,u.p)(t);n.name=e.name.replace(/\.[^.]+$/,""),Ae(n),r.shell.addTableView(n),r.shell.info(`Imported ${n.rowCount} protein groups from FragPipe`),m(n)}catch(e){r.shell.error(`Failed to import FragPipe file: ${e?.message??e}`)}}})}static async importGenericMatrix(){y()}static async annotateExperiment(){const e=r.shell.tv?.dataFrame;e?Ee(e,"Annotate Experiment")&&(0,w.XX)(e):r.shell.warning("No table open")}static async setLog2Scale(){const e=r.shell.tv?.dataFrame;e?Ee(e,"Set Log2 Scale")&&(0,N.Kb)(e):r.shell.warning("No table open")}static async normalizeProteomics(){const e=r.shell.tv?.dataFrame;e?Ee(e,"Normalize")&&(0,x.v5)(e):r.shell.warning("No table open")}static async imputeMissingValues(){const e=r.shell.tv?.dataFrame;e?Ee(e,"Impute Missing Values")&&(0,S.UN)(e):r.shell.warning("No table open")}static async differentialExpression(){const e=r.shell.tv,t=e?.dataFrame;e&&t?Ee(t,"Differential Expression")&&(0,T.B9)(t,()=>{const n=(0,E.gO)(t);e.addViewer(n)}):r.shell.warning("No table open")}static async computeSpcStatus(){const e=r.shell.tv,t=e?.dataFrame;if(!e||!t)return void r.shell.warning("Open an analyzed file first, then run Compute SPC Status.");if("spectronaut-candidates"===t.getTag("proteomics.source"))return void r.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,b.getRunMeta)(t);if(!n||!n.instrument_id||!n.acquisition_datetime)return void r.shell.warning("Open Annotate Experiment to set instrument + acquisition datetime.");const o=(0,w.f)(t);if(!o)return void r.shell.warning("Annotate experimental groups first (Proteomics → Annotate Experiment) — SPC needs Group 1 to compute control-replicate correlation.");o.group1.columns.length<2&&r.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=i.TaskBarProgressIndicator.create("Computing SPC status...");try{const e=(0,b.computeSpcMetrics)(t,o,n),i=await(0,_.loadBaseline)(n.instrument_id),a=await(0,_.loadRuns)(n.instrument_id),s=a.find(e=>e.acquisition_datetime===n.acquisition_datetime),l=s?.status??null;let c;if(null===i)c={status:"pass",rulesTripped:[]},r.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,b.uV)(e,t,i.metrics,i.rules_enabled??(0,b.kY)())}(0,b.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?r.shell.info(`Updated SPC for ${t.name} (previous status: ${l}).`):"pass"===c.status?r.shell.info(`SPC computed: ${t.name} — status: pass.`):"flagged"===c.status?r.shell.info(`SPC computed: ${t.name} — flagged on ${c.rulesTripped.length} rule(s): ${c.rulesTripped.join(", ")}.`):r.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=r.shell.tv,t=e?.dataFrame;e&&t?(0,T.RJ)(t,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)")&&await Oe.volcanoOptions():r.shell.warning("No table open")}static async volcanoOptions(e){const t=r.shell.tv,n=t?.dataFrame;if(!t||!n)return void r.shell.warning("No table open");if(!(0,T.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===i.VIEWER.SCATTER_PLOT&&"negLog10P"===e.props.yColumnName){a=e;break}const s=a?(0,E.ur)(n,a):{metric:"adj.p-value",colorDim:"significance"},l=null!=n.col("p-value"),c=l?s.metric:"adj.p-value",u=o.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=o.input.choice("Color by",{value:s.colorDim,items:["significance","location"],nullable:!1});p.setTooltip("significance = Enriched in g1 / Enriched in g2 / Not significant; location = UniProt subcellular location");const d=o.input.int("Label top N points",{value:(0,E.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 m=(0,E.GE)(n),h=o.input.float("X-axis max (|log2FC|)",{value:m.xMax??void 0,min:0,nullable:!0});h.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 g=o.input.float("Y-axis max (−log10 p)",{value:m.yMax??void 0,min:0,nullable:!0});g.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."),o.dialog("Volcano Options").add(u).add(p).add(d).add(h).add(g).onOK(async()=>{const e=u.value??"adj.p-value",o="location"===p.value?"location":"significance";if((0,E.S6)(n,h.value??null,g.value??null),a||(a=(0,E.gO)(n,{topNLabels:0}),t.addViewer(a)),"location"===o&&!n.col(E.fQ)){const e=await r.dapi.userDataStorage.get(P.er).catch(()=>null);0===(e?Object.keys(e).filter(e=>"__schema_v"!==e).length:0)?r.shell.info("Fetching subcellular locations from UniProt — may take a minute or two on first use without cache; subsequent toggles use the cache."):r.shell.info("Resolving subcellular locations from cache.")}const s="location"===o?"Classifying subcellular locations…":"Updating volcano…",l=i.TaskBarProgressIndicator.create(s),c="location"===o;c&&(0,E.DI)(a,s);const m=(e,t,n)=>{const r="fetch-acc"===n?"Fetching subcellular locations":"fetch-gene"===n?"Resolving by gene name":"init-column"===n||"location"===o?"Classifying subcellular locations":"Updating volcano",i=t>0?Math.round(e/t*100):0;if(l.update(i,`${r}: ${e}/${t}`),c){const n=t>1?`${e}/${t} (${i}%)`:"";(0,E.Bb)(a,r,n)}};try{await(0,E.nj)(n,a,e,o,f.M5,f.Dx,m),(0,E.XC)(n,a,d.value??(0,E.m2)(n))}catch(e){r.shell.error(`Volcano update failed: ${e?.message??e}`)}finally{l.close(),c&&a&&(0,E.kX)(a)}}).show()}static async showHeatmap(){const e=r.shell.tv,t=e?.dataFrame;if(!e||!t)return void r.shell.warning("No table open");if(!Ee(t,"Heatmap"))return;if(!(0,T.RJ)(t,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)"))return;const n=o.input.int("Top N proteins",{value:50,min:1});n.setTooltip("How many of the most significant proteins (by adj. p-value) to show."),o.dialog("Heatmap Options").add(n).onOK(async()=>{const r=n.value??50,o=i.TaskBarProgressIndicator.create("Creating heatmap...");try{const n=await D(t,{topN:r,title:`Heatmap: Top ${r} DE Proteins`});e.addViewer(n)}finally{o.close()}}).show()}static async showPcaPlot(){const e=r.shell.tv,t=e?.dataFrame;if(!e||!t)return void r.shell.warning("No table open");if(!Ee(t,"PCA"))return;const n=(0,w.f)(t);if(!n)return void r.shell.warning("Annotate experimental groups first (Proteomics | Annotate Experiment)");const o=[...n.group1.columns,...n.group2.columns],{viewer:i,pcaDf:a}=M(t,o,n,"PCA: All Groups");a.name=`PCA: ${t.name}`,r.shell.addTableView(a).addViewer(i)}static async showGroupMeanCorrelation(){const e=r.shell.tv,t=e?.dataFrame;if(!e||!t)return void r.shell.warning("No table open");if(!(0,T.RJ)(t,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)"))return;if(!(0,w.f)(t))return void r.shell.warning("Annotate experimental groups first (Proteomics | Annotate Experiment)");const n=(0,R.Z7)(t);e.addViewer(n)}static async showQcDashboard(){const e=r.shell.tv,t=e?.dataFrame;e&&t?Ee(t,"QC Dashboard")&&F(t):r.shell.warning("No table open")}static async showSpcDashboard(){await(0,$.r9)()}static async showAllVisualizations(){const e=r.shell.tv,t=e?.dataFrame;if(!e||!t)return void r.shell.warning("No table open");if(!Ee(t,"Show All Visualizations"))return;if(!(0,T.RJ)(t,"Run Differential Expression first"))return;const n=(0,w.f)(t),o=(0,E.gO)(t);e.addViewer(o);const a=i.TaskBarProgressIndicator.create("Creating heatmap...");try{const n=await D(t,{title:"Heatmap: Top 50 DE Proteins"});e.addViewer(n)}finally{a.close()}if(n){const e=[...n.group1.columns,...n.group2.columns],{viewer:o,pcaDf:i}=M(t,e,n,"PCA: All Groups");i.name=`PCA: ${t.name}`,r.shell.addTableView(i).addViewer(o)}}static async enrichmentAnalysis(){const e=r.shell.tv?.dataFrame;e?(0,q.pG)(e):r.shell.warning("No table open")}static async exportEnrichmentInputs(){const e=r.shell.tv?.dataFrame;e?(0,T.RJ)(e,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)")&&(0,C.N)(e):r.shell.warning("No table open")}static async enrichmentCharts(){const e=r.shell.tv,t=e?.dataFrame;if(!t)return void r.shell.warning("No table open");if("true"!==t.getTag("proteomics.enrichment"))return void r.shell.warning("Run Enrichment Analysis first (Proteomics | Enrichment Analysis)");const n=r.shell.tables.filter(e=>"true"===e.getTag("proteomics.de_complete"));if(0===n.length)return r.shell.warning("No protein table with DE results found. Enrichment charts will open without volcano linking."),void(0,Y.q6)(t,t);n.length>1&&r.shell.warning(`Multiple protein tables with DE results found; linking enrichment to "${n[0].name}"`),(0,Y.q6)(t,n[0])}static async proteomicsDemo(){await async function(){const e=i.TaskBarProgressIndicator.create("Loading proteomics demo…");try{e.update(5,"Importing HYE benchmark (Spectronaut DIA)…");const t=await Te.files.readAsText("demo/spectronaut-hye-demo.tsv"),n=await(0,l.parseSpectronautText)(t);n.name="HYE benchmark";const o=r.shell.addTableView(n),a=(0,w.f)(n);if(!a)return void r.shell.warning("Demo: expected two auto-annotated conditions — opened the table without running differential expression.");const s=[...a.group1.columns,...a.group2.columns];e.update(40,"Imputing missing values (KNN)…"),(0,S.Mx)(n,s),n.setTag("proteomics.imputed","true"),e.update(60,"Differential expression (t-test)…"),(0,T.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,E.gO)(n);o.dockManager.dock(c,i.DOCK_TYPE.RIGHT,null,"Volcano",.5);const u=await D(n,{title:"Heatmap: Top 50 DE Proteins"});o.dockManager.dock(u,i.DOCK_TYPE.DOWN,null,"Heatmap",.45),e.update(90,"Building QC dashboard tab…"),r.shell.addTableView(n).name="HYE benchmark — QC",F(n),r.shell.v=o,m(n,function(e){const t=e.col("adj.p-value"),n=e.col("significant");if(!t)return 0;let r=-1,o=1/0;for(let i=0;i<e.rowCount;i++){if(n&&!n.get(i))continue;if(t.isNone(i))continue;const e=t.get(i);e<o&&(o=e,r=i)}return r<0?0:r}(n)),e.update(100,"Done"),r.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=i.TaskBarProgressIndicator.create("Loading enrichment demo…");try{e.update(10,"Loading human DE result…");const t=await Te.files.readAsText("demo/enrichment-demo.csv"),n=i.DataFrame.fromCsv(t);n.name="Treatment vs Control (human)";const o=(e,t)=>{const r=n.col(e);r&&(r.semType=t)};o("Protein ID",f.iu.PROTEIN_ID),o("Gene",f.iu.GENE_SYMBOL),o("log2FC",f.iu.LOG2FC),o("p-value",f.iu.P_VALUE),o("adj.p-value",f.iu.P_VALUE),n.setTag("proteomics.source","generic"),n.setTag("proteomics.de_method","precomputed"),n.setTag("proteomics.de_complete","true"),(0,w.$Y)(n,{group1:{name:"Treatment",columns:[]},group2:{name:"Control",columns:[]}});const a=r.shell.addTableView(n),s=(0,E.gO)(n);a.dockManager.dock(s,i.DOCK_TYPE.RIGHT,null,"Volcano",.5),m(n,0),e.update(45,"Running g:Profiler enrichment (GO / KEGG / Reactome)…");try{const{enrichmentDf:t,mapped:o,total:i}=await(0,q.D9)(n,f.M5,f.Dx,"hsapiens",["GO:BP","GO:MF","GO:CC","KEGG","REAC","WP"],!0);e.update(90,"Opening enrichment charts…"),(0,Y.q6)(t,n).name=`${n.name} — Enrichment`,r.shell.v=a,r.shell.info(`Enrichment demo: ${t.rowCount} over-represented terms across ${o}/${i} 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){r.shell.warning(`Enrichment demo: g:Profiler enrichment could not run (${e?.message??e}). The DE table and volcano are open — retry via Proteomics | Enrichment Analysis once the service is reachable.`)}e.update(100,"Done")}finally{e.close()}}()}static uniprotPanelWidget(e){return(0,k.ku)(e)}static async shareAnalysisForReview(){const e=r.shell.tv;let t=e?.dataFrame;if(t){if("true"!==t.getTag("proteomics.de_complete")){const e=r.shell.tables.filter(e=>"true"===e.getTag("proteomics.de_complete"));if(0===e.length)return void(0,T.RJ)(t,"Run Differential Expression first (Proteomics | Analyze | Differential Expression)");e.length>1&&r.shell.warning(`Multiple analyzed tables open; sharing "${e[0].name}".`),t=e[0]}await async function(e){if("true"!==e.getTag(U.$y))return void r.shell.warning("Run Differential Expression first.");const t=await r.dapi.groups.list(),n=i.Group.defaultGroupsIds?.["All users"],a=(t??[]).filter(e=>!(null==e||e.hidden||e.personal||n&&e.id===n));if(0===a.length)return void r.shell.warning("No teams available to share with. Ask an admin to create a reviewer team.");const s=new Map;for(const e of a){const t=e.friendlyName??e.name??"";t&&!s.has(t)&&s.set(t,e)}const l=Array.from(s.keys()),c=o.input.string("Target",{value:""});c.setTooltip("Free text — your team's name for this target (e.g., MYH7-DMD, muscle-atrophy panel)");const u=o.input.choice("Share with team",{value:l[0],items:l,nullable:!1}),f=o.input.textArea?o.input.textArea("Note for reviewers",{value:""}):o.input.string("Note for reviewers",{value:""}),p=o.input.bool("Verify published dashboard",{value:(0,H.Cb)()});p.setTooltip("Re-open the shared dashboard after publishing to confirm it survives a reload. On = safer (recommended for client deliverables); off = faster share.");const d=o.div();d.style.cssText="background:#fff3cd; padding:8px; border-radius:4px; margin-bottom:8px; display:none;";const m=o.div();m.style.cssText="background:#f0f0f0; padding:8px; border-radius:4px; margin:8px 0; font-family: monospace; font-size:11px;";let h=null;const g=async()=>{const e=(c.value??"").trim(),t=u.value,n=t?s.get(t)??null:null,r=e?(0,U.fz)(e):"<no-target>",i=(new Date).toISOString().slice(0,10);if(e&&n)try{h=await(0,U.T7)(e,n)}catch{h=null}else h=null;const a=(e=>{if(!e)return 0;const t=/-v(\d+)-/.exec(e);if(!t)return 0;const n=parseInt(t[1],10);return Number.isFinite(n)?n:0})(h?h.name:null),l=a>0?a+1:1;h?(d.textContent=`⚠ This will share as v${l} and supersede "${h.name}". 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Ask the sharer to re-share."));const a=o.div();if(a.style.padding="8px 4px",null!=n.supersededBy&&""!==n.supersededBy){const e=o.link("Newer version available — open it",async()=>{try{const e=await r.dapi.projects.find(n.supersededBy);await e.open()}catch(e){r.shell.warning(`Could not open the newer version: ${e?.message??e}`)}}),t=o.div([e]);t.style.padding="8px",t.style.marginBottom="10px",t.style.backgroundColor="#fff8dc",t.style.borderRadius="4px",a.appendChild(t)}a.appendChild(o.h2("Shared analysis details"));const s=(0,w.f)(t),l=null!=s?`${s.group2.name} vs ${s.group1.name}`:"unavailable",c=Number.isFinite(n.fcThreshold)?Math.pow(2,n.fcThreshold):NaN,u=Number.isFinite(n.fcThreshold)?`log2(${n.fcThreshold}) (${Number.isFinite(c)?c.toFixed(2):"NaN"}-fold)`:"(unknown)",f=Number.isFinite(n.pThreshold)?`${n.pThreshold} (FDR-adjusted)`:"(unknown)";a.appendChild(V("Target",n.target||"(unknown)")),a.appendChild(V("Shared",B(n.publishedAt))),a.appendChild(V("Shared by",n.publishedBy||"(unknown)")),a.appendChild(V("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(V("Comparison",l)),a.appendChild(V("Fold-change cutoff",u)),a.appendChild(V("p-value cutoff",f));const p=function(e,t){if(null!=t.publishedByEmail&&""!==t.publishedByEmail)return t.publishedByEmail;try{const t=e.col(U.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(U.L6.PUBLISHED_BY_EMAIL);if(t)return t}catch{}return null}(t,n);if(null!=p){const e=t.name||"shared analysis",r=(0,U.Kj)({sharerEmail:p,sharerName:n.publishedBy||"colleague",projectName:e,publishedDateStr:B(n.publishedAt)}),i=o.link("Request re-run with different parameters",r);i.href=r;const s=o.div([i]);s.style.marginTop="12px",a.appendChild(s)}return new i.Widget(a)}(e)}static async recoverPublishedProjectsOnStartup(){const e=r.events.onProjectOpened??r.events.onCurrentProjectChanged??null;if(e&&"function"==typeof e.subscribe)e.subscribe(()=>{(async()=>{await new Promise(e=>setTimeout(e,200));const e=r.shell.tables;if(Array.isArray(e))for(const t of e)if((0,U.HF)(t))try{await(0,j.I)(t)}catch(e){r.shell.warning(`Could not auto-recover shared analysis on open: ${e?.message??e}`)}})()});else{const e=r.events.onViewAdded;e&&"function"==typeof e.subscribe&&e.subscribe(e=>{if(e instanceof i.TableView){const t=e.dataFrame;t&&(0,U.HF)(t)&&(0,j.I)(t).catch(e=>{r.shell.warning(`Could not auto-recover shared analysis on open: 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t!==r.FLOAT_NULL&&n!==r.FLOAT_NULL&&Math.abs(t)>=o.M5&&n<=o.Dx}),N.setTag("proteomics.source","spectronaut-candidates"),N.setTag("proteomics.de_complete","true"),N.setTag("proteomics.de_method","spectronaut");let M=x(v(N,g)),I=x(v(N,y));if(!M||!I){const e=x(v(N,d));if(e&&e.includes("/")){const[t,n]=e.split("/").map(e=>e.trim());M=M??(t||null),I=I??(n||null)}}return M&&I&&(0,s.$Y)(N,{group1:{name:M,columns:[]},group2:{name:I,columns:[]}}),await(0,a.rv)(N),N}function x(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:()=>m,parseSpectronautText:()=>h});var r=n(328),o=n(82),i=n(641),a=n(954),s=n(252),l=n(117);const c=["R.Condition","R.Replicate","PG.ProteinGroups"],u=["PG.IBAQ","PG.Quantity"];function f(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,r=o.Column.fromStrings("PG.ProteinGroups",t);r.semType=i.iu.PROTEIN_ID;const a=[r];if(e.organisms.size>0){const n=t.map(t=>e.organisms.get(t)??""),r=o.Column.fromStrings("PG.Organisms",n);a.push(r)}for(const r of e.sampleKeys){const s=new Float32Array(n);for(let i=0;i<n;i++){const n=e.proteinMap.get(t[i]);s[i]=n.has(r)?n.get(r):o.FLOAT_NULL}const l=o.Column.fromFloat32Array(r,s);l.semType=i.iu.INTENSITY,e.sampleFileNames.has(r)&&l.setTag("spectronaut.fileName",e.sampleFileNames.get(r)),a.push(l)}return o.DataFrame.fromColumns(a)}(e);(0,a.wK)(t,"PG.ProteinGroups","Primary Protein ID",i.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("_"),r=e.substring(0,t);n.has(r)||n.set(r,[]),n.get(r).push(`log2(${e})`)}const r=Array.from(n.keys());2===r.length&&(0,s.$Y)(e,{group1:{name:r[0],columns:n.get(r[0])},group2:{name:r[1],columns:n.get(r[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 m(e,t=.01){const n=o.TaskBarProgressIndicator.create("Streaming Spectronaut report...");try{const o=e.stream().pipeThrough(new TextDecoderStream("utf-8")).getReader(),i=new Map;let a="",s=!1,l=new Map,m=-1,h=-1,y=-1,w=-1,v=-1,b=-1,_=-1,x=-1,N=-1,C=0,S=null,T=null,E=null,P=0,D=0,L=0,A=0,M=performance.now();const I=Math.max(1,e.size),O=e=>{if(e.length<C)return"malformed";const n=e[m];if(!n)return"filtered";if(n.startsWith("CON__")||n.startsWith("REV__"))return"filtered";const r=w>=0?d(e[w]):null;if(null!==r&&r>t)return"filtered";const o=d(e[v]);if(null===o&&null===r)return"filtered";const a=e[h]??"",s=e[y]??"",l=n+""+a+""+s;let c=i.get(l);if(void 0===c&&(c={protein:n,condition:a,replicate:s,maxQuantity:-1/0,minQvalue:1/0,fileName:null,organism:null},i.set(l,c)),null!==o&&o>c.maxQuantity&&(c.maxQuantity=o),null!==r&&r<c.minQvalue&&(c.minQvalue=r),null===c.fileName&&b>=0){const t=e[b];t&&(c.fileName=t)}if(null===c.organism&&_>=0){const t=e[_];t&&(c.organism=t)}if(x>=0){const t=e[x];if(t){const e=f(t);null!==e&&(null===S||e<S)&&(S=e,T=new Date(e).toISOString())}}if(N>=0&&null===E){const t=e[N];t&&t.trim().length>0&&(E=t)}return"kept"},F=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 ${u.join(", ")})`);m=l.get("PG.ProteinGroups"),h=l.get("R.Condition"),y=l.get("R.Replicate"),v=l.get(n),w=l.has("EG.Qvalue")?l.get("EG.Qvalue"):-1,b=l.has("R.FileName")?l.get("R.FileName"):-1,_=l.has("PG.Organisms")?l.get("PG.Organisms"):-1,x=l.has("R.RunDate")?l.get("R.RunDate"):-1,N=l.has("R.InstrumentMethod")?l.get("R.InstrumentMethod"):-1,C=Math.max(m,h,y,v,w,b,_,x,N)+1,s=!0};for(;;){const{value:e,done:t}=await o.read();if(t)break;let r;for(P+=e.length,a+=e;(r=a.indexOf("\n"))>=0;){let e=a.slice(0,r);if(a=a.slice(r+1),e.endsWith("\r")&&(e=e.slice(0,-1)),s){if(0!==e.length)switch(O(e.split("\t"))){case"kept":D++;break;case"malformed":L++;break;case"filtered":A++}}else{if(0===e.length)continue;F(e)}}if(performance.now()-M>=16){const e=Math.min(99,P/I*100),t=L>0?`${D} rows (${L} malformed skipped)`:`${D} rows`;n.update(e,t),await new Promise(e=>setTimeout(e,0)),M=performance.now()}}if(a.length>0){let e=a;if(e.endsWith("\r")&&(e=e.slice(0,-1)),e.length>0)if(s)switch(O(e.split("\t"))){case"kept":D++;break;case"malformed":L++;break;case"filtered":A++}else F(e)}if(!s)throw new Error("Missing required Spectronaut column: R.Condition");L>0&&r.shell.info(`Spectronaut import: skipped ${L} malformed line(s)`);const $=function(e){const t=new Map,n=new Set,r=new Map,o=new Map;for(const i of e.values()){if(!Number.isFinite(i.maxQuantity))continue;const e=`${i.condition}_${i.replicate}`;n.add(e),t.has(i.protein)||t.set(i.protein,new Map),t.get(i.protein).set(e,i.maxQuantity),null===i.fileName||r.has(e)||r.set(e,i.fileName),null===i.organism||o.has(i.protein)||o.set(i.protein,i.organism)}return{proteinMap:t,sampleKeys:Array.from(n).sort(),sampleFileNames:r,organisms:o}}(i);$.earliestRunDate=T,$.firstInstrumentMethod=E;const R=await p($);return g(R,$),R}finally{n.close()}}async function h(e,t=.01){const n=o.DataFrame.fromCsv(e,{delimiter:"\t"});for(const e of c)if(!n.col(e))throw new Error(`Missing required Spectronaut column: ${e}`);const r=u.find(e=>null!==n.col(e));if(!r)throw new Error(`Missing protein-group quantity column (expected one of ${u.join(", ")})`);const i=function(e,t,n){const r=e.col("R.Condition"),o=e.col("R.Replicate"),i=e.col("PG.ProteinGroups"),a=e.col(t),s=e.col("EG.Qvalue"),l=e.col("R.FileName"),c=e.col("PG.Organisms"),u=e.col("R.RunDate"),p=e.col("R.InstrumentMethod"),d=new Map,m=new Set,h=new Map,g=new Map;let y=null,w=null,v=null;for(let t=0;t<e.rowCount;t++){if(s)if(s.isNone(t));else{const e=s.get(t),r=Number(e);if(!isNaN(r)&&r>n)continue}const e=i.get(t);if(!e)continue;if(e.startsWith("CON__")||e.startsWith("REV__"))continue;const b=`${String(r.get(t))}_${String(o.get(t))}`;if(m.add(b),d.has(e)||d.set(e,new Map),d.get(e).has(b)||a.isNone(t)||d.get(e).set(b,Number(a.get(t))),!l||h.has(b)||l.isNone(t)||h.set(b,l.get(t)),!c||g.has(e)||c.isNone(t)||g.set(e,c.get(t)),u&&!u.isNone(t)){const e=f(String(u.get(t)));null!==e&&(null===y||e<y)&&(y=e,w=new Date(e).toISOString())}if(p&&null===v&&!p.isNone(t)){const e=String(p.get(t));e.trim().length>0&&(v=e)}}return{proteinMap:d,sampleKeys:Array.from(m).sort(),sampleFileNames:h,organisms:g,earliestRunDate:w,firstInstrumentMethod:v}}(n,r,t),a=await p(i);return g(a,i),a}function g(e,t){const n=null!=t.earliestRunDate,r=null!=t.firstInstrumentMethod;(n||r)&&e.setTag("proteomics.spc_run_meta_seed",JSON.stringify({instrument_id:t.firstInstrumentMethod??"",acquisition_datetime:t.earliestRunDate??""}))}},691(e,t,n){"use strict";n.d(t,{F:()=>u,Y:()=>c});var r=n(328),o=n(82),i=n(749),a=n(641),s=n(304),l=n(771);const c="FORMULA_LINE_MISSING:";async function u(e,t){const n=e.id;r.shell.closeAll(),await(0,i.cb)(100);const u=await r.dapi.projects.find(n);await u.open(),await(0,i.bk)(()=>!!r.shell.tv&&!!r.shell.tv.dataFrame,"assertPublishedShape: TableView never materialized after project.open()",5e3);const f=r.shell.tv.dataFrame;if(f.name!==t.expectedName)throw new Error(`assertPublishedShape: df.name: got "${f.name}", expected "${t.expectedName}"`);if(u.name!==t.expectedProjectName)throw new Error(`assertPublishedShape: project.name: got "${u.name}", expected "${t.expectedProjectName}"`);for(const e of t.expectedAllowlist)if(!f.col(e))throw new Error(`assertPublishedShape: allowlist column missing on reopen: "${e}"`);const p=f.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: [${n.join(", ")}].`)}const d=(0,s.k)(f,a.iu.PROTEIN_ID,["protein id","majority protein id","accession"]);if(null==d)throw new Error("assertPublishedShape: protein-id column not found via findColumn");if(d.semType!==a.iu.PROTEIN_ID)throw new Error(`assertPublishedShape: protein-id semType: got "${d.semType??"null"}", expected "${a.iu.PROTEIN_ID}". Detectors may not have re-fired on reopen — re-assign in trim-dataframe.ts Step E.`);const m=(0,l.M4)(f);if(null==m)throw new Error("assertPublishedShape: getPublishedMetadata returned null — published flag not set or all critical fields unreadable");const h=t.expectedMeta,g=(e,t)=>!(Math.abs(e-t)>1e-9);if(m.target!==h.target)throw new Error(`assertPublishedShape: meta.target: got "${m.target}", expected "${h.target}"`);if(m.deMethod!==h.deMethod)throw new Error(`assertPublishedShape: meta.deMethod: got "${m.deMethod}", expected "${h.deMethod}"`);if(!g(m.fcThreshold,h.fcThreshold))throw new Error(`assertPublishedShape: meta.fcThreshold: got ${m.fcThreshold}, expected ${h.fcThreshold}`);if(!g(m.pThreshold,h.pThreshold))throw new Error(`assertPublishedShape: meta.pThreshold: got ${m.pThreshold}, expected ${h.pThreshold}`);if(m.version!==h.version)throw new Error(`assertPublishedShape: meta.version: got ${m.version}, expected ${h.version}`);if(m.publishId!==h.publishId)throw new Error(`assertPublishedShape: meta.publishId: got "${m.publishId}", expected "${h.publishId}"`);if(m.includesEnrichment!==h.includesEnrichment)throw new Error(`assertPublishedShape: meta.includesEnrichment: got ${m.includesEnrichment}, expected ${h.includesEnrichment}`);if(m.publishedBy!==h.publishedBy)throw new Error(`assertPublishedShape: meta.publishedBy: got "${m.publishedBy}", expected "${h.publishedBy}"`);for(const e of Object.keys(l.MD)){const t=l.MD[e];if(!f.col(t))throw new Error(`assertPublishedShape: metadata column missing: "${t}"`)}let y=null;if(t.expectVolcano)try{await(0,i.bk)(()=>{const e=r.shell.tv;if(!e)return!1;for(const t of e.viewers)if(t.type===o.VIEWER.SCATTER_PLOT)return y=t,!0;return!1},"assertPublishedShape: volcano scatter plot not present on reopen — consider post-open recomputeVolcano in publish-project.ts",5e3)}catch(e){throw new Error(`assertPublishedShape: volcano viewer assertion failed: ${e?.message??e}`)}if(t.expectVolcano&&t.expectFormulaLines&&null!=y){const e=String(h.fcThreshold),t=String(h.pThreshold),n=String(-Math.log10(h.pThreshold)),r=[];try{const e=f.meta?.formulaLines?.items??[];Array.isArray(e)&&r.push(...e)}catch{}try{const e=y.getOptions?.(),t=e?.look?.formulaLines,n="string"==typeof t?JSON.parse(t):t;Array.isArray(n)&&r.push(...n)}catch{}try{const e=y?.props?.formulaLines,t="string"==typeof e?JSON.parse(e):e;Array.isArray(t)&&r.push(...t)}catch{}const o=r.map(e=>"string"==typeof e?.formula?e.formula:"").filter(e=>e.length>0),i=o.some(t=>t.includes(e)||t.includes(`-${e}`)),a=o.some(e=>e.includes(n)||e.includes(t));if(!i||!a)throw new Error(`${c} volcano reopened without formula lines for FC=${h.fcThreshold} and/or p=${h.pThreshold}. 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=r.shell.tables;if(!Array.isArray(e)||e.length<2)throw new Error(`assertPublishedShape: expectEnrichment=true but grok.shell.tables has ${e?.length??0} DataFrames (need ≥ 2)`);if(!e.find(e=>{try{const t=e.col(l.MD.PUBLISHED_INCLUDES_ENRICHMENT);return null!=t&&"true"===String(t.get(0))}catch{return!1}}))throw new Error("assertPublishedShape: protein DF (with _meta_published_includes_enrichment=true) not found among reopened tables");if(!e.find(e=>"true"===e.getTag("proteomics.enrichment")))throw new Error("assertPublishedShape: enrichment DF (proteomics.enrichment=true tag) not found among reopened tables")}const w=u.options??{};if(null!=h.supersedes){const e=w[l.L6.SUPERSEDES];if(e!==h.supersedes)throw new Error(`assertPublishedShape: project.options['${l.L6.SUPERSEDES}']: got "${e??"null"}", expected "${h.supersedes}"`)}if(null!=h.supersededBy){const e=w[l.L6.SUPERSEDED_BY];if(e!==h.supersededBy)throw new Error(`assertPublishedShape: project.options['${l.L6.SUPERSEDED_BY}']: got "${e??"null"}", expected "${h.supersededBy}"`)}}},649(e,t,n){"use strict";n.d(t,{I:()=>c});var r=n(328),o=n(82),i=n(771),a=n(807),s=n(897);const l="proteomics.enrichment_wired";async function c(e){if(!(0,i.HF)(e))return;const t=function(e){try{const t=r.shell.tableViews;if(Array.isArray(t)){const n=t.find(t=>t?.dataFrame===e);if(n)return n}}catch{}try{const t=r.shell.tv;if(t&&t.dataFrame===e)return t}catch{}return null}(e);if(t){const n=Array.from(t.viewers).find(e=>e.type===o.VIEWER.SCATTER_PLOT);if(n){const t=e.getTag(i.L6.PUBLISHED_FC_THRESHOLD),r=e.getTag(i.L6.PUBLISHED_P_THRESHOLD);if(t&&r){const o=parseFloat(t),i=parseFloat(r);if(Number.isFinite(o)&&Number.isFinite(i)&&!function(e,t){try{const t=e.meta?.formulaLines?.items??[];if(Array.isArray(t)&&t.length>0)return!0}catch{}try{const e=t.getOptions?.(),n=e?.look?.formulaLines;if("string"==typeof n&&""!==n&&"[]"!==n)return!0;if(Array.isArray(n)&&n.length>0)return!0}catch{}return!1}(e,n))try{(0,a.u)(n,o,i)}catch{}}}}const n=function(e){try{const t=r.shell.tables;return Array.isArray(t)?t.find(t=>t!==e&&"true"===t?.getTag?.("proteomics.enrichment")&&"true"===t?.getTag?.(i.L6.PUBLISHED))??null:null}catch{return null}}(e);if(n&&"true"!==n.getTag(l))try{(0,s.aB)(n,e),n.setTag(l,"true")}catch{}}},807(e,t,n){"use strict";n.d(t,{u:()=>m,M:()=>h});var r=n(328),o=n(82),i=n(749),a=n(771),s=n(641),l=n(304);function c(e,t){let n,r;switch(e.columns.contains(t.name)&&e.columns.remove(t.name),t.type){case"datetime":n=e.columns.addNewDateTime(t.name);break;case"float":n=e.columns.addNewFloat(t.name);break;case"int":n=e.columns.addNewInt(t.name);break;default:n=e.columns.addNewString(t.name)}if(null==t.value){if(!t.emptyForNull)return;r="string"===t.type?"":0}else r=t.value instanceof Date?t.value:"boolean"==typeof t.value?t.value?"true":"false":"string"===t.type?String(t.value):t.value;n.init(()=>r),n.setTag(".hidden","true")}var u=n(691),f=n(70),p=n(897),d=n(637);function m(e,t,n){const r=e.dataFrame;if(!r)return;let o=null;try{const t=e.getOptions?.();o=t?.look?.yColumnName??null}catch{}if(!o)try{o=e.props?.yColumnName??null}catch{}if(!o)return;const i=`\${${o}}`,a="${log2FC}",s=-Math.log10(n),l=r.meta,c=l?.formulaLines;if(c){try{const e=Array.isArray(c.items)?c.items:[];c.items=e.filter(e=>{const t=e?.formula??"";return!("string"==typeof t&&(t.startsWith(i)||t.startsWith(a)))})}catch{}try{c.addLine({formula:`${i} = ${s}`,color:"#888888",width:1,visible:!0}),c.addLine({formula:`${a} = ${t}`,color:"#888888",width:1,visible:!0}),c.addLine({formula:`${a} = ${-t}`,color:"#888888",width:1,visible:!0})}catch{}try{e.props.showViewerFormulaLines=!0}catch{}}}async function h(e,t){const n=o.TaskBarProgressIndicator.create("Publishing snapshot...");try{n.description="Preparing metadata...";const h=r.shell.user?.friendlyName??"",g=r.shell.user?.email??null,y=e.getTag("proteomics.de_method")??"t-test";let w=s.M5,v=s.Dx;try{const e=t;"number"==typeof e.fcThreshold&&Number.isFinite(e.fcThreshold)&&(w=e.fcThreshold),"number"==typeof e.pThreshold&&Number.isFinite(e.pThreshold)&&(v=e.pThreshold)}catch{}const b=(0,a.fz)(t.target),_=function(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}(t.priorVersion?.name),x=_>0?_+1:1,N=function(){try{const 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