jbrowse-plugin-msaview 2.4.1 → 2.4.2

package/dist/jbrowse-plugin-msaview.umd.production.min.js

@@ -71,7 +71,7 @@ ${F.get("seq")}`).join(`
 `)}}),r()}catch(Q){l(Q)}}},"Submit"),Je.default.createElement($r.Button,{color:"secondary",variant:"contained",onClick:()=>{r()}},"Cancel")))}),Lh=$2;var WA=f(B());function Ni({children:e,value:t,index:r,...n}){return WA.default.createElement("div",{role:"tabpanel",hidden:t!==r,...n},t===r?WA.default.createElement("div",null,e):null)}function zA({handleClose:e,feature:t,model:r}){let n=(0,Rh.getSession)(r),i=!!va(n.jbrowse)?.length,[s,a]=(0,vt.useState)("ncbi_blast");return vt.default.createElement(Fh.Dialog,{maxWidth:"xl",title:"Launch MSA view",open:!0,onClose:e},vt.default.createElement(ko.Tabs,{value:s,onChange:(l,A)=>{a(A)}},vt.default.createElement(ko.Tab,{label:"NCBI BLAST query",value:"ncbi_blast"}),i?vt.default.createElement(ko.Tab,{label:"Pre-loaded MSA datasets",value:"preloaded_msa"}):null,vt.default.createElement(ko.Tab,{label:"Manual upload",value:"manual_msa"})),vt.default.createElement(Ni,{value:s,index:"ncbi_blast"},vt.default.createElement(MA,{handleClose:e,feature:t,model:r})),i?vt.default.createElement(Ni,{value:s,index:"preloaded_msa"},vt.default.createElement(Lh,{model:r,feature:t,handleClose:e})):null,vt.default.createElement(Ni,{value:s,index:"manual_msa"},vt.default.createElement(Wg,{model:r,feature:t,handleClose:e})))}function K2(e){return e.name==="LinearBasicDisplay"}function X2(e){return e.views(t=>{let r=t.contextMenuItems;return{contextMenuItems(){let n=t.contextMenuFeature,o=(0,Ta.getContainingTrack)(t),i=n?.get("type"),s=n&&["gene","mRNA","transcript"].includes(i);return[...r(),...s?[{label:"Launch MSA view",icon:lg,onClick:()=>{(0,Ta.getSession)(o).queueDialog(a=>[zA,{model:o,handleClose:a,feature:n}])}}]:[]]}}})}function $A(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(K2(t)&&(t.stateModel=X2(t.stateModel)),t))}function KA(e){e.addToExtensionPoint("LaunchView-MsaView",({session:t,data:r,msaFileLocation:n,treeFileLocation:o,connectedViewId:i,connectedFeature:s,displayName:a,colorSchemeName:c,colWidth:l,rowHeight:A,treeAreaWidth:u,treeWidth:d,drawNodeBubbles:m,labelsAlignRight:p,showBranchLen:C,querySeqName:x})=>{if(!r&&!n)throw new Error("No MSA data or file location provided when launching MSA view");t.addView("MsaView",{type:"MsaView",displayName:a,connectedViewId:i,connectedFeature:s,colorSchemeName:c,colWidth:l,rowHeight:A,treeAreaWidth:u,treeWidth:d,drawNodeBubbles:m,labelsAlignRight:p,showBranchLen:C,init:{msaData:r?.msa,treeData:r?.tree,msaUrl:n?.uri,treeUrl:o?.uri,querySeqName:x}})})}var PQ=f(B()),OQ=f(Oh());var xQ=f(B()),yQ=f(_l()),xi=f(ie()),xe=f(Nt());function*Z2(e,t){if(t!==-1)for(let r=e.start;r<e.end;r++)yield r;else for(let r=e.end-1;r>=e.start;r--)yield r}function Gh(e){let t=e.strand,r=e.refName;if(t!==-1&&t!==1)throw new Error(`Invalid strand value: ${t}. Expected 1 or -1.`);if(!r)throw new Error("refName is required");let n=e.subfeatures?.filter(c=>c.type==="CDS")??[],o=new Set,i=n.filter(c=>{if(c.start>=c.end)return!1;let l=`${c.start}-${c.end}`;return o.has(l)?!1:(o.add(l),!0)}).sort((c,l)=>t*(c.start-l.start)),s={},a={};if(i.length!==0){let l=(3-(i[0]?.phase??0))%3,A=-1;for(let u of i)for(let d of Z2(u,t)){let m=Math.floor(l++/3);s[d]=m,m!==A&&(a[m]=d,A=m)}}return{g2p:s,p2g:a,refName:r,strand:t}}var wQ=f(zr());Nd();var Rd=f(ie());function HS(e,t){let r=e.sciname.replaceAll(" ","_");if(e.taxid&&t?.has(e.taxid)){let n=t.get(e.taxid);n.commonName&&(r=n.commonName.split(" ").map(o=>o.charAt(0).toUpperCase()+o.slice(1).toLowerCase()).join("_"))}return`${e.accession}-${r}`}function US(e){return e.replaceAll("-","")}async function qS(e,t){let r=await fetch(e,t);if(!r.ok)throw new Error(`HTTP ${r.status} fetching ${e} ${await r.text()}`);return r}async function Mn(e,t){return(await qS(e,t)).text()}async function jS(e,t){return(await qS(e,t)).json()}function ul(e){return new Promise(t=>setTimeout(t,e))}var fl="https://www.ebi.ac.uk/Tools/services/rest",Lk={clustalo:{params:{email:"colin.diesh@gmail.com"},msaResult:"aln-clustal_num",treeResult:"phylotree"},muscle:{params:{email:"colin.diesh@gmail.com",format:"clw",tree:"tree1"},msaResult:"fa",treeResult:"phylotree"},kalign:{params:{email:"colin.diesh@gmail.com",stype:"protein"},msaResult:"fa",treeResult:"phylotree"},mafft:{params:{email:"colin.diesh@gmail.com",stype:"protein"},msaResult:"fa",treeResult:"phylotree"}};async function Fk({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let o=0;o<10;o++)await ul(1e3),e(`Re-checking MSA status in... ${10-o}`);let n=await Mn(`${fl}/${r}/status/${t}`);if(n==="FINISHED")break;if(n.includes("FAILURE"))throw new Error(`Failed to run: jobId ${t}`)}}async function JS({algorithm:e,sequence:t,onProgress:r}){let n=Lk[e];r(`Launching ${e} MSA...`);let o=await Mn(`${fl}/${e}/run`,{method:"POST",body:new URLSearchParams({...n.params,sequence:t})});return await Fk({jobId:o,algorithm:e,onProgress:r}),{msa:await Mn(`${fl}/${e}/result/${o}/${n.msaResult}`),tree:await Mn(`${fl}/${e}/result/${o}/${n.treeResult}`)}}async function Ld({rid:e,baseUrl:t,onProgress:r}){r(`Checking BLAST status for RID: ${e}...`),await Pk({rid:e,onProgress:r,baseUrl:t});let n=await jS(`${t}?CMD=Get&RID=${e}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);return{rid:e,hits:n.BlastOutput2[0]?.report.results.search.hits??[]}}async function VS({query:e,blastDatabase:t,blastProgram:r,baseUrl:n,onProgress:o,onRid:i}){o("Submitting to NCBI BLAST...");let{rid:s}=await Rk({query:e,blastDatabase:t,blastProgram:r,baseUrl:n});return i(s),Ld({rid:s,baseUrl:n,onProgress:o})}async function Rk({query:e,blastProgram:t,blastDatabase:r,baseUrl:n}){let o=await Mn(n,{method:"POST",body:new URLSearchParams({CMD:"Put",PROGRAM:t==="quick-blastp"?"blastp":t,DATABASE:r,QUERY:e,...r==="nr_cluster_seq"?{CLUSTERED_DB:"on",DB_TYPE:"Experimental Databases"}:{},...t==="quick-blastp"?{BLAST_PROGRAMS:"kmerBlastp"}:{}})}),i=/^ {4}RID = (.*$)/m.exec(o)?.[1],s=/^ {4}RTOE = (.*$)/m.exec(o)?.[1];if(!i)throw new Error("Failed to get RID from BLAST request");return{rid:i,rtoe:s}}async function Pk({rid:e,onProgress:t,baseUrl:r}){for(;;){for(let c=0;c<20;c++)await ul(1e3),t(`Re-checking BLAST status in... ${20-c}`);let o=await Mn(`${r}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${e}`),s=/\s+Status=(\S+)/m.exec(o)?.[1],a=/\s+ThereAreHits=yes/m.test(o);if(s!=="WAITING"){if(s==="FAILED")throw new Error(`BLAST ${e} failed`);if(s==="READY"){if(a)return!0;throw new Error("No hits found")}throw new Error(`BLAST ${e} returned unexpected status: ${s??"unknown"}`)}}}_i();var Ok="jbrowse-msaview-taxonomy-cache",xs="common-names",Gk=2;async function YS(){return Rn(Ok,Gk,{upgrade(e){e.objectStoreNames.contains(xs)&&e.deleteObjectStore(xs),e.createObjectStore(xs,{keyPath:"taxid"})}})}async function Hk(e){let r=(await YS()).transaction(xs,"readonly"),n=await Promise.all(e.map(o=>r.store.get(o)));return await r.done,n}async function Uk(e){let r=(await YS()).transaction(xs,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function WS(e){let t=new Map,r=[],n=await Hk(e);for(let s=0;s<e.length;s++){let a=e[s],c=n[s];c?t.set(a,{sciname:c.sciname,commonName:c.commonName}):r.push(a)}if(r.length===0)return t;let o=100,i=[];for(let s=0;s<r.length;s+=o){let a=r.slice(s,s+o),c=a.join(",");try{let A=await(await fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${c}&retmode=xml`)).text(),u=new Map,d=/<Taxon>\s*<TaxId>(\d+)<\/TaxId>/g,m;for(;(m=d.exec(A))!==null;){let p=Number(m[1]),C=m.index,x=1,I=C+m[0].length;for(;x>0&&I<A.length;){let v=A.indexOf("<Taxon>",I),M=A.indexOf("</Taxon>",I);if(M===-1)break;v!==-1&&v<M?(x++,I=v+7):(x--,I=M+8)}let h=A.slice(C,I),y=u.get(p),w=h.includes("<LineageEx>"),S=y?.includes("<LineageEx>");(!y||w&&!S)&&u.set(p,h)}for(let p of a){let C=u.get(p);if(C){let x=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(C),I=/<CommonName>(.*?)<\/CommonName>/.exec(C),h=/<ScientificName>(.*?)<\/ScientificName>/.exec(C),y=x?.[1]??I?.[1],w=h?.[1]??"";t.set(p,{sciname:w,commonName:y}),i.push({taxid:p,sciname:w,commonName:y})}}}catch(l){console.error("Failed to fetch taxonomy data:",l)}}return i.length>0&&await Uk(i),t}async function zS({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s,rid:a}=e.blastParams,c=Vs(i),l,A;if(a){e.setRid(a);let I=await Ld({rid:a,baseUrl:t,onProgress:h=>{e.setProgress(h)}});l=I.hits,A=I.rid}else{let I=await VS({query:c,blastDatabase:r,blastProgram:n,baseUrl:t,onProgress:h=>{e.setProgress(h)},onRid:h=>{e.setRid(h)}});l=I.hits,A=I.rid}e.setProgress("Fetching species taxonomy info...");let u=l.map(I=>I.description[0]?.taxid).filter(I=>I!==void 0),d=await WS(u),m={},p=l.map(I=>{let h=I.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"},y=HS(h,d),w=US(I.hsps[0]?.hseq??"");return m[y]=qk(h,d),`>${y}
 ${w}`}),C=await JS({algorithm:o,sequence:[`>QUERY
 ${c}`,...p].join(`
-`),onProgress:I=>{e.setProgress(I)}}),x=JSON.stringify(m);return await ap({proteinSequence:c,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:C.msa,tree:C.tree,treeMetadata:x,rid:A,geneId:s?.get("parentId"),transcriptId:s?.id(),transcriptName:s?.get("name")??s?.get("id"),geneName:s?.get("gene_name")??s?.get("parentId")}),{...C,treeMetadata:x}}function qk(e,t){let r={},n=e.taxid?t.get(e.taxid):void 0;return n?.sciname&&(r["Scientific name"]=n.sciname),n?.commonName&&(r["Common name"]=n.commonName),e.accession&&(r.Accession=e.accession),e.id&&(r.ID=e.id),e.title&&(r.Description=e.title),r}ys();function ws({model:e,coord:t}){let{querySeqName:r,transcriptToMsaMap:n,mafRegion:o}=e,s=e.rows.find(c=>c[0]===r)?.[1];if(!s)return;let a=dl(s,t);if(a!==void 0){if(o){let c=o.start+a;return c>=o.end?void 0:{refName:o.refName,start:c,end:c+1}}if(n){let{refName:c,p2g:l}=n,A=l[a],u=l[a+1];return A!==void 0&&u!==void 0?{refName:c,start:Math.min(A,u),end:Math.max(A,u)}:void 0}}}_i();var Jk="jbrowse-msaview-data",Vk=1,bs="msa-data";async function Fd(){return Rn(Jk,Vk,{upgrade(e){e.objectStoreNames.contains(bs)||e.createObjectStore(bs,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function KS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function XS(e,t){try{let r=await Fd(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(bs,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function ZS(e){try{let r=await(await Fd()).get(bs,e);return r?{msa:r.msa,tree:r.tree,treeMetadata:r.treeMetadata}:void 0}catch(t){console.warn("Failed to retrieve MSA data:",t);return}}async function eQ(e=10080*60*1e3){try{let t=await Fd(),r=Date.now()-e,i=await t.transaction(bs,"readwrite").store.index("timestamp").openCursor(IDBKeyRange.upperBound(r)),s=0;for(;i;)await i.delete(),s++,i=await i.continue();return s}catch(t){return console.warn("Failed to cleanup old MSA data:",t),0}}ys();function tQ(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await ZS(t);n&&(n.msa&&e.setMSA(n.msa),n.tree&&e.setTree(n.tree))}catch(n){console.error("Failed to load MSA data from IndexedDB:",n)}finally{e.setLoadingStoredData(!1)}})()}function rQ(e){let{rows:t,dataStoreId:r,isStoringData:n}=e;if(t.length>0&&!r&&!n){if(e.msaFilehandle||e.treeFilehandle)return;let o=e.data.msa,i=e.data.tree;(o||i)&&(e.setIsStoringData(!0),(async()=>{try{let s=KS();await XS(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to IndexedDB:",s)}finally{e.setIsStoringData(!1)}})())}}function nQ(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await zS({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})()}function oQ(e){let{init:t}=e;t&&(async()=>{try{e.setError(void 0);let{msaData:r,msaUrl:n,treeData:o,treeUrl:i,querySeqName:s}=t;if(n){let a=xm(n);a&&(e.setUniprotId(a),e.setQuerySeqName("query"))}if(s&&e.setQuerySeqName(s),r)e.setMSA(r);else if(n){let a=await fetch(n);if(!a.ok)throw new Error(`Failed to fetch MSA: ${a.status}`);let c=await a.text();e.setMSA(c)}if(o)e.setTree(o);else if(i){let a=await fetch(i);if(!a.ok)throw new Error(`Failed to fetch tree: ${a.status}`);let c=await a.text();e.setTree(c)}e.setInit(void 0)}catch(r){e.setError(r),console.error(r)}})()}function iQ(e){let{mouseCol:t,mouseClickCol:r}=e,n=t===void 0?void 0:ws({model:e,coord:t}),o=r===void 0?void 0:ws({model:e,coord:r});e.setConnectedHighlights([n,o].filter(i=>!!i))}function sQ(e){let{mouseCol:t,connectedProteinViews:r}=e;if(r.length!==0)for(let n of r){let o=n.proteinView.structures[n.structureIdx];if(!o)continue;if(t===void 0){o.clearHighlightFromExternal?.();continue}let i=e.getSequenceByRowName(n.msaRowName);if(!i)continue;let s=dl(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function aQ(e){let{connectedViewId:t,uniprotId:r,rows:n,connectedStructures:o}=e;if(!(!r||n.length===0))for(let i of vn((0,Rd.getSession)(e).views))for(let s=0;s<i.structures.length;s++){let a=i.structures[s];if(!(!a||a.connectedViewId!==t||a.uniprotId!==r||o.some(l=>l.proteinViewId===i.id&&l.structureIdx===s))&&a.structureSequences?.[0])try{e.connectToStructure(i.id,s)}catch(l){console.error("Failed to auto-connect to ProteinView:",l)}}}function cQ(e){let{connectedViewId:t,transcriptToMsaMap:r,querySeqName:n}=e;if(!t||!r)return;let o=new Set;for(let s of vn((0,Rd.getSession)(e).views))for(let a of s.structures){if(a.connectedViewId!==t)continue;let c=a.hoverGenomeHighlights;if(!c||c.length===0)continue;let{g2p:l}=r;for(let A of c)for(let u=A.start;u<A.end;u++){let d=l[u];if(d!==void 0){let m=e.seqPosToGlobalCol(n,d);o.add(m)}}}let i=Array.from(o).map(s=>e.globalColToVisibleCol(s)).filter(s=>s!==void 0);e.setHighlightedColumns(i.length>0?i:void 0)}function lQ(){eQ().catch(e=>{console.error("Failed to cleanup old MSA data:",e)})}var AQ=f(ie());function uQ({model:e}){let{hovered:t}=(0,AQ.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!Im(t))return;let{coord:s,refName:a}=t.hoverPosition;if(i){if(a!==i.refName||!o.assemblyNames.includes(i.assemblyName)||s<i.start||s>=i.end)return;let l=s-i.start;return e.seqPosToVisibleCol(r,l)}if(n){let{g2p:c}=n,l=c[s];if(l!==void 0)return e.seqPosToVisibleCol(r,l)}}var 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dQ(e,t){return fQ[e.toUpperCase()]?.[t.toUpperCase()]??-4}var Wk=-10,zk=-.5;function $k(e,t,r=Wk,n=zk){let o=e.length,i=t.length,s=[],a=[],c=[];for(let h=0;h<=o;h++){s[h]=[],a[h]=[],c[h]=[];for(let y=0;y<=i;y++)s[h][y]=-1/0,a[h][y]=-1/0,c[h][y]=-1/0}s[0][0]=0;for(let h=1;h<=o;h++)a[h][0]=r+(h-1)*n;for(let h=1;h<=i;h++)c[0][h]=r+(h-1)*n;for(let h=1;h<=o;h++)for(let y=1;y<=i;y++){let w=dQ(e[h-1],t[y-1]);s[h][y]=Math.max(s[h-1][y-1],a[h-1][y-1],c[h-1][y-1])+w,a[h][y]=Math.max(s[h-1][y]+r,a[h-1][y]+n),c[h][y]=Math.max(s[h][y-1]+r,c[h][y-1]+n)}let l="",A="",u=o,d=i,m=s[o][i],p=a[o][i],C=c[o][i],x=Math.max(m,p,C),I=x===m?"M":x===p?"Ix":"Iy";for(;u>0||d>0;)if(I==="M"&&u>0&&d>0){l=e[u-1]+l,A=t[d-1]+A;let h=dQ(e[u-1],t[d-1]),y=s[u-1][d-1],w=a[u-1][d-1],S=s[u][d];S===y+h?I="M":S===w+h?I="Ix":I="Iy",u--,d--}else if(I==="Ix"&&u>0){l=e[u-1]+l,A="-"+A;let h=a[u][d],y=s[u-1][d]+r;I=h===y?"M":"Ix",u--}else if(d>0){l="-"+l,A=t[d-1]+A;let h=c[u][d],y=s[u][d-1]+r;I=h===y?"M":"Iy",d--}else break;return{alignedSeq1:l,alignedSeq2:A,score:x}}function Kk(e,t){let r="";for(let n=0;n<e.length;n++){let o=e[n],i=t[n];o==="-"||i==="-"?r+=" ":o.toUpperCase()===i.toUpperCase()?r+="|":r+=" "}return r}function mQ(e,t){let{alignedSeq1:r,alignedSeq2:n}=$k(e,t);return{consensus:Kk(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function gQ(e){let t=e.alns[0].seq,r=e.alns[1].seq;if(t.length!==r.length)throw new Error("Aligned sequences must have same length");let n=0,o=0,i=new Map,s=new Map;for(let a=0;a<t.length;a++){let c=t[a],l=r[a];c!=="-"&&l!=="-"?(i.set(n,o),s.set(o,n),n++,o++):c==="-"?o++:n++}return{seq1ToSeq2:i,seq2ToSeq1:s}}ys();var tN=(0,xQ.lazy)(()=>Promise.resolve().then(()=>(IQ(),EQ)));function Pd(){return xe.types.compose(yQ.BaseViewModel,Al(),xe.types.model("MsaView",{connectedViewId:xe.types.maybe(xe.types.string),connectedFeature:xe.types.frozen(),connectedHighlights:xe.types.array(xe.types.model({refName:xe.types.string,start:xe.types.number,end:xe.types.number})),blastParams:xe.types.frozen(),querySeqName:"QUERY",uniprotId:xe.types.maybe(xe.types.string),zoomToBaseLevel:!1,init:xe.types.frozen(),connectedStructures:xe.types.array(xe.types.frozen()),dataStoreId:xe.types.maybe(xe.types.string),mafRegion:xe.types.frozen()})).volatile(()=>({rid:void 0,progress:"",error:void 0,loadingStoredData:!1,isStoringData:!1})).views(e=>({getRowByName(t){return e.rows.find(r=>r[0]===t)},getSequenceByRowName(t){return e.rows.find(r=>r[0]===t)?.[1]}})).views(e=>({get transcriptToMsaMap(){return e.connectedFeature?Gh(e.connectedFeature):void 0},get connectedView(){let{views:t}=(0,xi.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let t=vn((0,xi.getSession)(e).views),r=[];for(let n of e.connectedStructures){let o=t.find(i=>i.id===n.proteinViewId);o&&r.push({...n,proteinView:o})}return r}})).views(e=>({get structureHoverCol(){for(let t of e.connectedProteinViews){let n=t.proteinView.structures[t.structureIdx]?.hoverPosition?.structureSeqPos;if(n!==void 0){let o=t.structureToMsa[n];if(o!==void 0){let i=e.getSequenceByRowName(t.msaRowName);if(i){let s=$S(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:uQ({model:e})}})).actions(e=>({setZoomToBaseLevel(t){e.zoomToBaseLevel=t},setError(t){e.error=t},setProgress(t){e.progress=t},setRid(t){e.rid=t},setConnectedHighlights(t){e.connectedHighlights=(0,xe.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,xe.cast)([])},setBlastParams(t){e.blastParams=t},setInit(t){e.init=t},setQuerySeqName(t){e.querySeqName=t},setUniprotId(t){e.uniprotId=t},setDataStoreId(t){e.dataStoreId=t},setMafRegion(t){e.mafRegion=t},setLoadingStoredData(t){e.loadingStoredData=t},setIsStoringData(t){e.isStoringData=t},handleMsaClick(t){let{connectedView:r,zoomToBaseLevel:n}=e,{assemblyManager:o}=(0,xi.getSession)(e),i=ws({model:e,coord:t});if(!(!i||!r))if(n)r.navTo(i);else{let s=Ls({assemblyManager:o,assemblyNames:r.assemblyNames,refName:i.refName});r.centerAt(i.start,s)}},connectToStructure(t,r,n){let o=n??e.querySeqName,i=e.getSequenceByRowName(o);if(!i)throw new Error(`MSA row "${o}" not found`);let s=i.replaceAll("-",""),a=vn((0,xi.getSession)(e).views).find(p=>p.id===t);if(!a)throw new Error(`ProteinView "${t}" not found`);let c=a.structures[r];if(!c)throw new Error(`Structure at index ${r} not found`);let l=c.structureSequences?.[0];if(!l)throw new Error("Structure sequence not available");let A=mQ(s,l),{seq1ToSeq2:u,seq2ToSeq1:d}=gQ(A),m={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:Object.fromEntries(u),structureToMsa:Object.fromEntries(d)};e.connectedStructures.push(m)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,xi.getSession)(e).queueDialog(t=>[tN,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){lQ();for(let t of[tQ,rQ,nQ,oQ,iQ,sQ,aQ,cQ])(0,xe.addDisposer)(e,(0,wQ.autorun)(()=>{t(e)}))}}))}var lN=(0,PQ.lazy)(()=>Promise.resolve().then(()=>(RQ(),FQ)));function Ud(e){e.addViewType(()=>new OQ.default({name:"MsaView",stateModel:Pd(),ReactComponent:lN}))}var GQ="2.4.1";var hl=class extends HQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=GQ;this.rootConfigurationSchema=r=>({msa:(0,qd.ConfigurationSchema)("MSA",{datasets:jd.types.maybe(jd.types.array((0,qd.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Ud(r),$A(r),KA(r),Tl(r),zl(r)}configure(r){(0,UQ.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:dm,onClick:n=>{n.addView("MsaView",{})}})}};return t1(AN);})();
+`),onProgress:I=>{e.setProgress(I)}}),x=JSON.stringify(m);return await ap({proteinSequence:c,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:C.msa,tree:C.tree,treeMetadata:x,rid:A,geneId:s?.get("parentId"),transcriptId:s?.id(),transcriptName:s?.get("name")??s?.get("id"),geneName:s?.get("gene_name")??s?.get("parentId")}),{...C,treeMetadata:x}}function qk(e,t){let r={},n=e.taxid?t.get(e.taxid):void 0;return n?.sciname&&(r["Scientific name"]=n.sciname),n?.commonName&&(r["Common name"]=n.commonName),e.accession&&(r.Accession=e.accession),e.id&&(r.ID=e.id),e.title&&(r.Description=e.title),r}ys();function ws({model:e,coord:t}){let{querySeqName:r,transcriptToMsaMap:n,mafRegion:o}=e,s=e.rows.find(c=>c[0]===r)?.[1];if(!s)return;let a=dl(s,t);if(a!==void 0){if(o){let c=o.start+a;return c>=o.end?void 0:{refName:o.refName,start:c,end:c+1}}if(n){let{refName:c,p2g:l}=n,A=l[a],u=l[a+1];return A!==void 0&&u!==void 0?{refName:c,start:Math.min(A,u),end:Math.max(A,u)}:void 0}}}_i();var Jk="jbrowse-msaview-data",Vk=1,bs="msa-data";async function Fd(){return Rn(Jk,Vk,{upgrade(e){e.objectStoreNames.contains(bs)||e.createObjectStore(bs,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function KS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function XS(e,t){try{let r=await Fd(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(bs,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function ZS(e){try{let r=await(await Fd()).get(bs,e);return r?{msa:r.msa,tree:r.tree,treeMetadata:r.treeMetadata}:void 0}catch(t){console.warn("Failed to retrieve MSA data:",t);return}}async function eQ(e=10080*60*1e3){try{let t=await Fd(),r=Date.now()-e,i=await t.transaction(bs,"readwrite").store.index("timestamp").openCursor(IDBKeyRange.upperBound(r)),s=0;for(;i;)await i.delete(),s++,i=await i.continue();return s}catch(t){return console.warn("Failed to cleanup old MSA data:",t),0}}ys();function tQ(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await ZS(t);n&&(n.msa&&e.setMSA(n.msa),n.tree&&e.setTree(n.tree))}catch(n){console.error("Failed to load MSA data from IndexedDB:",n)}finally{e.setLoadingStoredData(!1)}})()}function rQ(e){let{rows:t,dataStoreId:r,isStoringData:n}=e;if(t.length>0&&!r&&!n){if(e.msaFilehandle||e.treeFilehandle)return;let o=e.data.msa,i=e.data.tree;(o||i)&&(e.setIsStoringData(!0),(async()=>{try{let s=KS();await XS(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to IndexedDB:",s)}finally{e.setIsStoringData(!1)}})())}}function nQ(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await zS({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})()}function oQ(e){let{init:t}=e;t&&(async()=>{try{e.setError(void 0);let{msaData:r,msaUrl:n,treeData:o,treeUrl:i,querySeqName:s}=t;if(n){let a=xm(n);a&&(e.setUniprotId(a),e.setQuerySeqName("query"))}if(s&&e.setQuerySeqName(s),r)e.setMSA(r);else if(n){let a=await fetch(n);if(!a.ok)throw new Error(`Failed to fetch MSA: ${a.status}`);let c=await a.text();e.setMSA(c)}if(o)e.setTree(o);else if(i){let a=await fetch(i);if(!a.ok)throw new Error(`Failed to fetch tree: ${a.status}`);let c=await a.text();e.setTree(c)}e.setInit(void 0)}catch(r){e.setError(r),console.error(r)}})()}function iQ(e){let{mouseCol:t,mouseClickCol:r}=e,n=t===void 0?void 0:ws({model:e,coord:t}),o=r===void 0?void 0:ws({model:e,coord:r});e.setConnectedHighlights([n,o].filter(i=>!!i))}function sQ(e){let{mouseCol:t,connectedProteinViews:r}=e;if(r.length!==0)for(let n of r){let o=n.proteinView.structures[n.structureIdx];if(!o)continue;if(t===void 0){o.clearHighlightFromExternal?.();continue}let i=e.getSequenceByRowName(n.msaRowName);if(!i)continue;let s=dl(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function aQ(e){let{connectedViewId:t,uniprotId:r,rows:n,connectedStructures:o}=e;if(!(!r||n.length===0))for(let i of vn((0,Rd.getSession)(e).views))for(let s=0;s<i.structures.length;s++){let a=i.structures[s];if(!(!a||a.connectedViewId!==t||a.uniprotId!==r||o.some(l=>l.proteinViewId===i.id&&l.structureIdx===s))&&a.structureSequences?.[0])try{e.connectToStructure(i.id,s)}catch(l){console.error("Failed to auto-connect to ProteinView:",l)}}}function cQ(e){let{connectedViewId:t,transcriptToMsaMap:r,querySeqName:n}=e;if(!t||!r)return;let o=new Set;for(let s of vn((0,Rd.getSession)(e).views))for(let a of s.structures){if(a.connectedViewId!==t)continue;let c=a.hoverGenomeHighlights;if(!c||c.length===0)continue;let{g2p:l}=r;for(let A of c)for(let u=A.start;u<A.end;u++){let d=l[u];if(d!==void 0){let m=e.seqPosToGlobalCol(n,d);o.add(m)}}}let i=Array.from(o).map(s=>e.globalColToVisibleCol(s)).filter(s=>s!==void 0);e.setHighlightedColumns(i.length>0?i:void 0)}function lQ(){eQ().catch(e=>{console.error("Failed to cleanup old MSA data:",e)})}var AQ=f(ie());function uQ({model:e}){let{hovered:t}=(0,AQ.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!Im(t))return;let{coord:s,refName:a}=t.hoverPosition;if(i){if(a!==i.refName||!o.assemblyNames.includes(i.assemblyName)||s<i.start||s>=i.end)return;let l=s-i.start;return e.seqPosToVisibleCol(r,l)}if(n){let{g2p:c}=n,l=c[s];if(l!==void 0)return e.seqPosToVisibleCol(r,l)}}var 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dQ(e,t){return fQ[e.toUpperCase()]?.[t.toUpperCase()]??-4}var Wk=-10,zk=-.5;function $k(e,t,r=Wk,n=zk){let o=e.length,i=t.length,s=[],a=[],c=[];for(let h=0;h<=o;h++){s[h]=[],a[h]=[],c[h]=[];for(let y=0;y<=i;y++)s[h][y]=-1/0,a[h][y]=-1/0,c[h][y]=-1/0}s[0][0]=0;for(let h=1;h<=o;h++)a[h][0]=r+(h-1)*n;for(let h=1;h<=i;h++)c[0][h]=r+(h-1)*n;for(let h=1;h<=o;h++)for(let y=1;y<=i;y++){let w=dQ(e[h-1],t[y-1]);s[h][y]=Math.max(s[h-1][y-1],a[h-1][y-1],c[h-1][y-1])+w,a[h][y]=Math.max(s[h-1][y]+r,a[h-1][y]+n),c[h][y]=Math.max(s[h][y-1]+r,c[h][y-1]+n)}let l="",A="",u=o,d=i,m=s[o][i],p=a[o][i],C=c[o][i],x=Math.max(m,p,C),I=x===m?"M":x===p?"Ix":"Iy";for(;u>0||d>0;)if(I==="M"&&u>0&&d>0){l=e[u-1]+l,A=t[d-1]+A;let h=dQ(e[u-1],t[d-1]),y=s[u-1][d-1],w=a[u-1][d-1],S=s[u][d];S===y+h?I="M":S===w+h?I="Ix":I="Iy",u--,d--}else if(I==="Ix"&&u>0){l=e[u-1]+l,A="-"+A;let h=a[u][d],y=s[u-1][d]+r;I=h===y?"M":"Ix",u--}else if(d>0){l="-"+l,A=t[d-1]+A;let h=c[u][d],y=s[u][d-1]+r;I=h===y?"M":"Iy",d--}else break;return{alignedSeq1:l,alignedSeq2:A,score:x}}function Kk(e,t){let r="";for(let n=0;n<e.length;n++){let o=e[n],i=t[n];o==="-"||i==="-"?r+=" ":o.toUpperCase()===i.toUpperCase()?r+="|":r+=" "}return r}function mQ(e,t){let{alignedSeq1:r,alignedSeq2:n}=$k(e,t);return{consensus:Kk(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function gQ(e){let t=e.alns[0].seq,r=e.alns[1].seq;if(t.length!==r.length)throw new Error("Aligned sequences must have same length");let n=0,o=0,i=new Map,s=new Map;for(let a=0;a<t.length;a++){let c=t[a],l=r[a];c!=="-"&&l!=="-"?(i.set(n,o),s.set(o,n),n++,o++):c==="-"?o++:n++}return{seq1ToSeq2:i,seq2ToSeq1:s}}ys();var tN=(0,xQ.lazy)(()=>Promise.resolve().then(()=>(IQ(),EQ)));function Pd(){return xe.types.compose(yQ.BaseViewModel,Al(),xe.types.model("MsaView",{connectedViewId:xe.types.maybe(xe.types.string),connectedFeature:xe.types.frozen(),connectedHighlights:xe.types.array(xe.types.model({refName:xe.types.string,start:xe.types.number,end:xe.types.number})),blastParams:xe.types.frozen(),querySeqName:"QUERY",uniprotId:xe.types.maybe(xe.types.string),zoomToBaseLevel:!1,init:xe.types.frozen(),connectedStructures:xe.types.array(xe.types.frozen()),dataStoreId:xe.types.maybe(xe.types.string),mafRegion:xe.types.frozen()})).volatile(()=>({rid:void 0,progress:"",error:void 0,loadingStoredData:!1,isStoringData:!1})).views(e=>({getRowByName(t){return e.rows.find(r=>r[0]===t)},getSequenceByRowName(t){return e.rows.find(r=>r[0]===t)?.[1]}})).views(e=>({get transcriptToMsaMap(){return e.connectedFeature?Gh(e.connectedFeature):void 0},get connectedView(){let{views:t}=(0,xi.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let t=vn((0,xi.getSession)(e).views),r=[];for(let n of e.connectedStructures){let o=t.find(i=>i.id===n.proteinViewId);o&&r.push({...n,proteinView:o})}return r}})).views(e=>({get structureHoverCol(){for(let t of e.connectedProteinViews){let n=t.proteinView.structures[t.structureIdx]?.hoverPosition?.structureSeqPos;if(n!==void 0){let o=t.structureToMsa[n];if(o!==void 0){let i=e.getSequenceByRowName(t.msaRowName);if(i){let s=$S(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:uQ({model:e})}})).actions(e=>({setZoomToBaseLevel(t){e.zoomToBaseLevel=t},setError(t){e.error=t},setProgress(t){e.progress=t},setRid(t){e.rid=t},setConnectedHighlights(t){e.connectedHighlights=(0,xe.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,xe.cast)([])},setBlastParams(t){e.blastParams=t},setInit(t){e.init=t},setQuerySeqName(t){e.querySeqName=t},setUniprotId(t){e.uniprotId=t},setDataStoreId(t){e.dataStoreId=t},setMafRegion(t){e.mafRegion=t},setLoadingStoredData(t){e.loadingStoredData=t},setIsStoringData(t){e.isStoringData=t},handleMsaClick(t){let{connectedView:r,zoomToBaseLevel:n}=e,{assemblyManager:o}=(0,xi.getSession)(e),i=ws({model:e,coord:t});if(!(!i||!r))if(n)r.navTo(i);else{let s=Ls({assemblyManager:o,assemblyNames:r.assemblyNames,refName:i.refName});r.centerAt(i.start,s)}},connectToStructure(t,r,n){let o=n??e.querySeqName,i=e.getSequenceByRowName(o);if(!i)throw new Error(`MSA row "${o}" not found`);let s=i.replaceAll("-",""),a=vn((0,xi.getSession)(e).views).find(p=>p.id===t);if(!a)throw new Error(`ProteinView "${t}" not found`);let c=a.structures[r];if(!c)throw new Error(`Structure at index ${r} not found`);let l=c.structureSequences?.[0];if(!l)throw new Error("Structure sequence not available");let A=mQ(s,l),{seq1ToSeq2:u,seq2ToSeq1:d}=gQ(A),m={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:Object.fromEntries(u),structureToMsa:Object.fromEntries(d)};e.connectedStructures.push(m)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,xi.getSession)(e).queueDialog(t=>[tN,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){lQ();for(let t of[tQ,rQ,nQ,oQ,iQ,sQ,aQ,cQ])(0,xe.addDisposer)(e,(0,wQ.autorun)(()=>{t(e)}))}}))}var lN=(0,PQ.lazy)(()=>Promise.resolve().then(()=>(RQ(),FQ)));function Ud(e){e.addViewType(()=>new OQ.default({name:"MsaView",stateModel:Pd(),ReactComponent:lN}))}var GQ="2.4.2";var hl=class extends HQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=GQ;this.rootConfigurationSchema=r=>({msa:(0,qd.ConfigurationSchema)("MSA",{datasets:jd.types.maybe(jd.types.array((0,qd.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Ud(r),$A(r),KA(r),Tl(r),zl(r)}configure(r){(0,UQ.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:dm,onClick:n=>{n.addView("MsaView",{})}})}};return t1(AN);})();
 /*! Bundled license information:
 
 use-sync-external-store/cjs/use-sync-external-store-shim.production.js: