jbrowse-plugin-msaview 2.3.2 → 2.3.3

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

@@ -73,7 +73,7 @@ ${J.get("seq")}`).join(`
 `)}}),r()}catch(T){l(T)}}},"Submit"),Ue.default.createElement(Kr.Button,{color:"secondary",variant:"contained",onClick:r},"Cancel")))}),Th=PM;var HA=f(B());function Lo({children:e,value:t,index:r,...n}){return HA.default.createElement("div",{role:"tabpanel",hidden:t!==r,...n},t===r&&HA.default.createElement("div",null,e))}function UA({handleClose:e,feature:t,model:r}){let n=(0,kh.getSession)(r),{jbrowse:o}=n,i=(0,_h.readConfObject)(o,["msa","datasets"]),s=i&&i.length>0,[a,c]=(0,rt.useState)("ncbi_blast");return rt.default.createElement(Dh.Dialog,{maxWidth:"xl",title:"Launch MSA view",open:!0,onClose:e},rt.default.createElement(Jn.Tabs,{value:a,onChange:(A,u)=>{c(u)}},rt.default.createElement(Jn.Tab,{label:"NCBI BLAST query",value:"ncbi_blast"}),s?rt.default.createElement(Jn.Tab,{label:"Pre-loaded MSA datasets",value:"preloaded_msa"}):null,rt.default.createElement(Jn.Tab,{label:"Ensembl GeneTree",value:"ensembl_genetree"}),rt.default.createElement(Jn.Tab,{label:"Manual upload",value:"manual_msa"})),rt.default.createElement(Lo,{value:a,index:"ncbi_blast"},rt.default.createElement(yA,{handleClose:e,feature:t,model:r})),s?rt.default.createElement(Lo,{value:a,index:"preloaded_msa"},rt.default.createElement(Th,{model:r,feature:t,handleClose:e})):null,rt.default.createElement(Lo,{value:a,index:"ensembl_genetree"},rt.default.createElement(Yg,{model:r,feature:t,handleClose:e})),rt.default.createElement(Lo,{value:a,index:"manual_msa"},rt.default.createElement(zg,{model:r,feature:t,handleClose:e})))}function OM(e){return e.name==="LinearBasicDisplay"}function GM(e){return e.views(t=>{let r=t.contextMenuItems;return{contextMenuItems(){let n=t.contextMenuFeature,o=(0,va.getContainingTrack)(t),i=n?.get("type"),s=n&&["gene","mRNA","transcript"].includes(i);return[...r(),...s?[{label:"Launch MSA view",icon:ng,onClick:()=>{(0,va.getSession)(o).queueDialog(a=>[UA,{model:o,handleClose:a,feature:n}])}}]:[]]}}})}function qA(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(OM(t)&&(t.stateModel=GM(t.stateModel)),t))}function YA(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:g,showBranchLen:h,querySeqName:I})=>{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:g,showBranchLen:h,init:{msaData:r?.msa,treeData:r?.tree,msaUrl:n?.uri,treeUrl:o?.uri,querySeqName:I}})})}var QQ=f(B()),MQ=f(Lh());var dQ=f(B()),mQ=f(Bl()),Ii=f(ne()),Ie=f(Dt());function*JM(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 Fh(e){let t=e.strand,r=e.refName;if(t!==-1&&t!==1)throw new Error(`Invalid strand value: ${t}. Expected 1 or -1.`);if(!r)throw new Error("refName is required");let n=e.subfeatures?.filter(u=>u.type==="CDS")??[],o=new Set,i=n.filter(u=>{if(u.start>=u.end)return!1;let d=`${u.start}-${u.end}`;return o.has(d)?!1:(o.add(d),!0)}).sort((u,d)=>t*(u.start-d.start)),s={},a={};if(i.length===0)return{g2p:s,p2g:a,refName:r,strand:t};let l=(3-(i[0]?.phase??0))%3,A=-1;for(let u of i)for(let d of JM(u,t)){let m=Math.floor(l++/3);s[d]=m,m!==A&&(a[m]=d,A=m)}return{g2p:s,p2g:a,refName:r,strand:t}}var gQ=f($r());vd();var kd=f(ne());function kS(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 NS(e){return e.replaceAll("-","")}var Al="https://www.ebi.ac.uk/Tools/services/rest",Ik={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 xk({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let o=0;o<10;o++)await Zs(1e3),e(`Re-checking MSA status in... ${10-o}`);let n=await fr(`${Al}/${r}/status/${t}`);if(n==="FINISHED")break;if(n.includes("FAILURE"))throw new Error(`Failed to run: jobId ${t}`)}}async function LS({algorithm:e,sequence:t,onProgress:r}){let n=Ik[e];if(!n)throw new Error(`unknown algorithm: ${e}`);r(`Launching ${e} MSA...`);let o=await fr(`${Al}/${e}/run`,{method:"POST",body:new URLSearchParams({...n.params,sequence:t})});return await xk({jobId:o,algorithm:e,onProgress:r}),{msa:await fr(`${Al}/${e}/result/${o}/${n.msaResult}`),tree:await fr(`${Al}/${e}/result/${o}/${n.treeResult}`)}}async function Td({rid:e,baseUrl:t,onProgress:r}){r(`Checking BLAST status for RID: ${e}...`),await wk({rid:e,onProgress:r,baseUrl:t});let n=await bo(`${t}?CMD=Get&RID=${e}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);return{rid:e,hits:n.BlastOutput2[0]?.report.results.search.hits??[]}}async function FS({query:e,blastDatabase:t,blastProgram:r,baseUrl:n,onProgress:o,onRid:i}){o("Submitting to NCBI BLAST...");let{rid:s}=await yk({query:e,blastDatabase:t,blastProgram:r,baseUrl:n});return i(s),Td({rid:s,baseUrl:n,onProgress:o})}async function yk({query:e,blastProgram:t,blastDatabase:r,baseUrl:n}){let o=await fr(n,{method:"POST",body:new URLSearchParams({CMD:"Put",PROGRAM:t==="quick-blastp"?"blastp":t,DATABASE:r,QUERY:e,...r==="nr_clustered_seq"?{CLUSTERED_DB:"on",DB_TYPE:"Experimental Databases"}:{},...t==="quick-blastp"?{BLAST_PROGRAMS:"kmerBlastp"}:{}})}),i=/^ {4}RID = (.*$)/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 wk({rid:e,onProgress:t,baseUrl:r}){for(;;){for(let l=0;l<20;l++)await Zs(1e3),t(`Re-checking BLAST status in... ${20-l}`);let o=await fr(`${r}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${e}`),i=/\s+Status=WAITING/m.test(o),s=/\s+Status=FAILED/m.test(o),a=/\s+Status=READY/m.test(o),c=/\s+ThereAreHits=yes/m.test(o);if(!i){if(s)throw new Error(`BLAST ${e} failed`);if(a){if(c)return!0;throw new Error("No hits found")}}}}Di();var Bk="jbrowse-msaview-taxonomy-cache",Is="common-names",bk=2;async function RS(){return Rn(Bk,bk,{upgrade(e){e.objectStoreNames.contains(Is)&&e.deleteObjectStore(Is),e.createObjectStore(Is,{keyPath:"taxid"})}})}async function Sk(e){return(await RS()).get(Is,e)}async function Qk(e){let r=(await RS()).transaction(Is,"readwrite");for(let n of e)await r.store.put(n);await r.done}async function PS(e){let t=new Map,r=[];for(let i of e){let s=await Sk(i);s?t.set(i,{sciname:s.sciname,commonName:s.commonName}):r.push(i)}if(r.length===0)return t;let n=100,o=[];for(let i=0;i<r.length;i+=n){let s=r.slice(i,i+n),a=s.join(",");try{let l=await(await fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${a}&retmode=xml`)).text(),A=new Map,u=/<Taxon>\s*<TaxId>(\d+)<\/TaxId>/g,d;for(;(d=u.exec(l))!==null;){let m=Number(d[1]),g=d.index,h=1,I=g+d[0].length;for(;h>0&&I<l.length;){let S=l.indexOf("<Taxon>",I),v=l.indexOf("</Taxon>",I);if(v===-1)break;S!==-1&&S<v?(h++,I=S+7):(h--,I=v+8)}let C=l.slice(g,I),x=A.get(m),y=C.includes("<LineageEx>"),b=x?.includes("<LineageEx>");(!x||y&&!b)&&A.set(m,C)}for(let m of s){let g=A.get(m);if(g){let h=/<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(g),I=/<CommonName>(.*?)<\/CommonName>/.exec(g),C=/<ScientificName>(.*?)<\/ScientificName>/.exec(g),x=h?.[1]??I?.[1],y=C?.[1]??"";t.set(m,{sciname:y,commonName:x}),o.push({taxid:m,sciname:y,commonName:x})}else o.push({taxid:m,sciname:"",commonName:void 0})}}catch(c){console.error("Failed to fetch taxonomy data:",c)}}return o.length>0&&await Qk(o),t}async function OS({self:e}){let{baseUrl:t,blastDatabase:r,blastProgram:n,msaAlgorithm:o,proteinSequence:i,selectedTranscript:s,rid:a}=e.blastParams,c=ra(i),l,A;if(a){e.setRid(a);let C=await Td({rid:a,baseUrl:t,onProgress:x=>{e.setProgress(x)}});l=C.hits,A=C.rid}else{let C=await FS({query:c,blastDatabase:r,blastProgram:n,baseUrl:t,onProgress:x=>{e.setProgress(x)},onRid:x=>{e.setRid(x)}});l=C.hits,A=C.rid}e.setProgress("Fetching species taxonomy info...");let u=l.map(C=>C.description[0]?.taxid).filter(C=>C!==void 0),d=await PS(u),m={},g=l.map(C=>{let x=C.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"},y=kS(x,d),b=NS(C.hsps[0]?.hseq??"");return m[y]=Mk(x,d),`>${y}
 ${b}`}),h=await LS({algorithm:o,sequence:[`>QUERY
 ${c}`,...g].join(`
-`),onProgress:C=>{e.setProgress(C)}}),I=JSON.stringify(m);return await cp({proteinSequence:c,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:h.msa,tree:h.tree,treeMetadata:I,rid:A,geneId:s?.get("parentId"),transcriptId:s?.id(),transcriptName:s?.get("name")??s?.get("id"),geneName:s?.get("gene_name")??s?.get("parentId")}),{...h,treeMetadata:I}}function Mk(e,t){let r={},n=e.taxid?t.get(e.taxid):void 0;return n?.sciname&&(r["Scientific name"]=n.sciname),n?.commonName&&(r["Common name"]=n.commonName),e.accession&&(r.Accession=e.accession),e.id&&(r.ID=e.id),e.title&&(r.Description=e.title),r}function ul(e,t){if(t<0||t>=e.length)return;let r=0;for(let n=0;n<t;n++)e[n]!=="-"&&r++;if(e[t]!=="-")return r}function GS(e,t){let r=0;for(let n=0;n<e.length;n++)if(e[n]!=="-"){if(r===t)return n;r++}}function _d(e){return Object.fromEntries(e)}function xs({model:e,coord:t}){let{querySeqName:r,transcriptToMsaMap:n,mafRegion:o}=e,s=e.rows.find(c=>c[0]===r)?.[1];if(!s)return;let a=ul(s,t);if(a!==void 0){if(o){let c=o.start+a;return c>=o.end?void 0:{refName:o.refName,start:c,end:c+1}}if(n){let{refName:c,p2g:l}=n,A=l[a],u=l[a+1];return A!==void 0&&u!==void 0?{refName:c,start:Math.min(A,u),end:Math.max(A,u)}:void 0}}}Di();var vk="jbrowse-msaview-data",Tk=1,ys="msa-data";async function Dd(){return Rn(vk,Tk,{upgrade(e){e.objectStoreNames.contains(ys)||e.createObjectStore(ys,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function JS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function HS(e,t){try{let r=await Dd(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(ys,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function US(e){try{let r=await(await Dd()).get(ys,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 qS(e=10080*60*1e3){try{let t=await Dd(),r=Date.now()-e,i=await t.transaction(ys,"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}}function YS(e){return typeof e=="object"&&e!==null&&"hoverFeature"in e&&"hoverPosition"in e}function jS(e){return/AF-([A-Z0-9]+)-F\d+/.exec(e)?.[1]}function VS(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await US(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 WS(e){let{rows:t,dataStoreId:r}=e;if(t.length>0&&!r){if(!!(e.msaFilehandle??e.treeFilehandle))return;let o=e.data.msa,i=e.data.tree;(o||i)&&(async()=>{try{let s=JS();await HS(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to IndexedDB:",s)}})()}}function zS(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await OS({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})()}function $S(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=jS(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 KS(e){let{mouseCol:t,mouseClickCol:r}=e,n=t===void 0?void 0:xs({model:e,coord:t}),o=r===void 0?void 0:xs({model:e,coord:r});e.setConnectedHighlights([n,o].filter(i=>!!i))}function XS(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=ul(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function ZS(e){let{views:t}=(0,kd.getSession)(e),{connectedViewId:r,uniprotId:n,rows:o,connectedStructures:i}=e;if(!(!n||o.length===0))for(let s of t){let a=s;if(!(a.type!=="ProteinView"||!a.structures))for(let c=0;c<a.structures.length;c++){let l=a.structures[c];if(!(l.connectedViewId!==r||l.uniprotId!==n||i.some(u=>u.proteinViewId===a.id&&u.structureIdx===c))&&l.structureSequences?.[0])try{e.connectToStructure(a.id,c)}catch(u){console.error("Failed to auto-connect to ProteinView:",u)}}}}function eQ(e){let{views:t}=(0,kd.getSession)(e),{connectedViewId:r,transcriptToMsaMap:n,querySeqName:o}=e;if(!r||!n)return;let i=[];for(let a of t){let c=a;if(!(c.type!=="ProteinView"||!c.structures))for(let l of c.structures){if(l.connectedViewId!==r)continue;let A=l.hoverGenomeHighlights;if(!A||A.length===0)continue;let{g2p:u}=n;for(let d of A)for(let m=d.start;m<d.end;m++){let g=u[m];if(g!==void 0){let h=e.seqPosToGlobalCol(o,g);i.includes(h)||i.push(h)}}}}let s=i.map(a=>e.globalColToVisibleCol(a)).filter(a=>a!==void 0);e.setHighlightedColumns(s.length>0?s:void 0)}function tQ(){qS().catch(e=>{console.error("Failed to cleanup old MSA data:",e)})}var rQ=f(ne());function nQ({model:e}){let{hovered:t}=(0,rQ.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!YS(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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iQ(e,t){let r=e.toUpperCase(),n=t.toUpperCase();return oQ[r]?.[n]??-4}var Dk=-10,kk=-.5;function Nk(e,t,r=Dk,n=kk){let o=e.length,i=t.length,s=[],a=[],c=[];for(let I=0;I<=o;I++){s[I]=[],a[I]=[],c[I]=[];for(let C=0;C<=i;C++)s[I][C]=-1/0,a[I][C]=-1/0,c[I][C]=-1/0}s[0][0]=0;for(let I=1;I<=o;I++)a[I][0]=r+(I-1)*n;for(let I=1;I<=i;I++)c[0][I]=r+(I-1)*n;for(let I=1;I<=o;I++)for(let C=1;C<=i;C++){let x=iQ(e[I-1],t[C-1]);s[I][C]=Math.max(s[I-1][C-1],a[I-1][C-1],c[I-1][C-1])+x,a[I][C]=Math.max(s[I-1][C]+r,a[I-1][C]+n),c[I][C]=Math.max(s[I][C-1]+r,c[I][C-1]+n)}let l="",A="",u=o,d=i,m=[s[o][i],a[o][i],c[o][i]],g=Math.max(...m),h=g===s[o][i]?"M":g===a[o][i]?"Ix":"Iy";for(;u>0||d>0;)if(h==="M"&&u>0&&d>0){l=e[u-1]+l,A=t[d-1]+A;let I=iQ(e[u-1],t[d-1]),C=s[u-1][d-1],x=a[u-1][d-1];s[u][d]===C+I?h="M":s[u][d]===x+I?h="Ix":h="Iy",u--,d--}else if(h==="Ix"&&u>0)l=e[u-1]+l,A="-"+A,h=a[u][d]===s[u-1][d]+r?"M":"Ix",u--;else if(d>0)l="-"+l,A=t[d-1]+A,h=c[u][d]===s[u][d-1]+r?"M":"Iy",d--;else break;return{alignedSeq1:l,alignedSeq2:A,score:g}}function Lk(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 sQ(e,t){let{alignedSeq1:r,alignedSeq2:n}=Nk(e,t);return{consensus:Lk(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function aQ(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}}var Pk=(0,dQ.lazy)(()=>Promise.resolve().then(()=>(fQ(),uQ)));function Nd(){return Ie.types.compose(mQ.BaseViewModel,ll(),Ie.types.model("MsaView",{connectedViewId:Ie.types.maybe(Ie.types.string),connectedFeature:Ie.types.frozen(),connectedHighlights:Ie.types.array(Ie.types.model({refName:Ie.types.string,start:Ie.types.number,end:Ie.types.number})),blastParams:Ie.types.frozen(),querySeqName:"QUERY",uniprotId:Ie.types.maybe(Ie.types.string),zoomToBaseLevel:!1,init:Ie.types.frozen(),connectedStructures:Ie.types.array(Ie.types.frozen()),dataStoreId:Ie.types.maybe(Ie.types.string),mafRegion:Ie.types.frozen()})).volatile(()=>({rid:void 0,progress:"",error:void 0,loadingStoredData:!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?Fh(e.connectedFeature):void 0},get processing(){return!!e.progress},get connectedView(){let{views:t}=(0,Ii.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let{views:t}=(0,Ii.getSession)(e);return e.connectedStructures.map(r=>{let n=t.find(o=>o.id===r.proteinViewId);return n?{...r,proteinView:n}:void 0}).filter(r=>!!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=GS(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:nQ({model:e})},get clickCol2(){}})).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,Ie.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,Ie.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},handleMsaClick(t){let{connectedView:r,zoomToBaseLevel:n}=e,{assemblyManager:o}=(0,Ii.getSession)(e),i=xs({model:e,coord:t});if(!(!i||!r))if(n)r.navTo(i);else{let s=o.get(r.assemblyNames[0])?.getCanonicalRefName(i.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("-",""),{views:a}=(0,Ii.getSession)(e),c=a.find(h=>h.id===t);if(!c)throw new Error(`ProteinView "${t}" not found`);let l=c.structures?.[r];if(!l)throw new Error(`Structure at index ${r} not found`);let A=l.structureSequences?.[0];if(!A)throw new Error("Structure sequence not available");let u=sQ(s,A),{seq1ToSeq2:d,seq2ToSeq1:m}=aQ(u),g={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:_d(d),structureToMsa:_d(m)};e.connectedStructures.push(g)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,Ii.getSession)(e).queueDialog(t=>[Pk,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){tQ();for(let t of[VS,WS,zS,$S,KS,XS,ZS,eQ])(0,Ie.addDisposer)(e,(0,gQ.autorun)(()=>{t(e)}))}}))}var Yk=(0,QQ.lazy)(()=>Promise.resolve().then(()=>(SQ(),bQ)));function Pd(e){e.addViewType(()=>new MQ.default({name:"MsaView",stateModel:Nd(),ReactComponent:Yk}))}var vQ="2.2.11";var dl=class extends TQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=vQ;this.rootConfigurationSchema=r=>({msa:(0,Od.ConfigurationSchema)("MSA",{datasets:Gd.types.maybe(Gd.types.array((0,Od.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Pd(r),qA(r),YA(r),wl(r),Hl(r)}configure(r){(0,_Q.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:lm,onClick:n=>{n.addView("MsaView",{})}})}};return qQ(jk);})();
+`),onProgress:C=>{e.setProgress(C)}}),I=JSON.stringify(m);return await cp({proteinSequence:c,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:h.msa,tree:h.tree,treeMetadata:I,rid:A,geneId:s?.get("parentId"),transcriptId:s?.id(),transcriptName:s?.get("name")??s?.get("id"),geneName:s?.get("gene_name")??s?.get("parentId")}),{...h,treeMetadata:I}}function Mk(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}function ul(e,t){if(t<0||t>=e.length)return;let r=0;for(let n=0;n<t;n++)e[n]!=="-"&&r++;if(e[t]!=="-")return r}function GS(e,t){let r=0;for(let n=0;n<e.length;n++)if(e[n]!=="-"){if(r===t)return n;r++}}function _d(e){return Object.fromEntries(e)}function xs({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=ul(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}}}Di();var vk="jbrowse-msaview-data",Tk=1,ys="msa-data";async function Dd(){return Rn(vk,Tk,{upgrade(e){e.objectStoreNames.contains(ys)||e.createObjectStore(ys,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function JS(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function HS(e,t){try{let r=await Dd(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(ys,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function US(e){try{let r=await(await Dd()).get(ys,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 qS(e=10080*60*1e3){try{let t=await Dd(),r=Date.now()-e,i=await t.transaction(ys,"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}}function YS(e){return typeof e=="object"&&e!==null&&"hoverFeature"in e&&"hoverPosition"in e}function jS(e){return/AF-([A-Z0-9]+)-F\d+/.exec(e)?.[1]}function VS(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await US(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 WS(e){let{rows:t,dataStoreId:r}=e;if(t.length>0&&!r){if(!!(e.msaFilehandle??e.treeFilehandle))return;let o=e.data.msa,i=e.data.tree;(o||i)&&(async()=>{try{let s=JS();await HS(s,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(s)}catch(s){console.error("Failed to store MSA data to IndexedDB:",s)}})()}}function zS(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await OS({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})()}function $S(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=jS(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 KS(e){let{mouseCol:t,mouseClickCol:r}=e,n=t===void 0?void 0:xs({model:e,coord:t}),o=r===void 0?void 0:xs({model:e,coord:r});e.setConnectedHighlights([n,o].filter(i=>!!i))}function XS(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=ul(i,t);if(s===void 0){o.clearHighlightFromExternal?.();continue}let a=n.msaToStructure[s];a===void 0?o.clearHighlightFromExternal?.():o.highlightFromExternal?.(a)}}function ZS(e){let{views:t}=(0,kd.getSession)(e),{connectedViewId:r,uniprotId:n,rows:o,connectedStructures:i}=e;if(!(!n||o.length===0))for(let s of t){let a=s;if(!(a.type!=="ProteinView"||!a.structures))for(let c=0;c<a.structures.length;c++){let l=a.structures[c];if(!(l.connectedViewId!==r||l.uniprotId!==n||i.some(u=>u.proteinViewId===a.id&&u.structureIdx===c))&&l.structureSequences?.[0])try{e.connectToStructure(a.id,c)}catch(u){console.error("Failed to auto-connect to 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iQ(e,t){let r=e.toUpperCase(),n=t.toUpperCase();return oQ[r]?.[n]??-4}var Dk=-10,kk=-.5;function Nk(e,t,r=Dk,n=kk){let o=e.length,i=t.length,s=[],a=[],c=[];for(let I=0;I<=o;I++){s[I]=[],a[I]=[],c[I]=[];for(let C=0;C<=i;C++)s[I][C]=-1/0,a[I][C]=-1/0,c[I][C]=-1/0}s[0][0]=0;for(let I=1;I<=o;I++)a[I][0]=r+(I-1)*n;for(let I=1;I<=i;I++)c[0][I]=r+(I-1)*n;for(let I=1;I<=o;I++)for(let C=1;C<=i;C++){let x=iQ(e[I-1],t[C-1]);s[I][C]=Math.max(s[I-1][C-1],a[I-1][C-1],c[I-1][C-1])+x,a[I][C]=Math.max(s[I-1][C]+r,a[I-1][C]+n),c[I][C]=Math.max(s[I][C-1]+r,c[I][C-1]+n)}let l="",A="",u=o,d=i,m=[s[o][i],a[o][i],c[o][i]],g=Math.max(...m),h=g===s[o][i]?"M":g===a[o][i]?"Ix":"Iy";for(;u>0||d>0;)if(h==="M"&&u>0&&d>0){l=e[u-1]+l,A=t[d-1]+A;let I=iQ(e[u-1],t[d-1]),C=s[u-1][d-1],x=a[u-1][d-1];s[u][d]===C+I?h="M":s[u][d]===x+I?h="Ix":h="Iy",u--,d--}else if(h==="Ix"&&u>0)l=e[u-1]+l,A="-"+A,h=a[u][d]===s[u-1][d]+r?"M":"Ix",u--;else if(d>0)l="-"+l,A=t[d-1]+A,h=c[u][d]===s[u][d-1]+r?"M":"Iy",d--;else break;return{alignedSeq1:l,alignedSeq2:A,score:g}}function Lk(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 sQ(e,t){let{alignedSeq1:r,alignedSeq2:n}=Nk(e,t);return{consensus:Lk(r,n),alns:[{id:"msa",seq:r},{id:"structure",seq:n}]}}function aQ(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}}var Pk=(0,dQ.lazy)(()=>Promise.resolve().then(()=>(fQ(),uQ)));function Nd(){return Ie.types.compose(mQ.BaseViewModel,ll(),Ie.types.model("MsaView",{connectedViewId:Ie.types.maybe(Ie.types.string),connectedFeature:Ie.types.frozen(),connectedHighlights:Ie.types.array(Ie.types.model({refName:Ie.types.string,start:Ie.types.number,end:Ie.types.number})),blastParams:Ie.types.frozen(),querySeqName:"QUERY",uniprotId:Ie.types.maybe(Ie.types.string),zoomToBaseLevel:!1,init:Ie.types.frozen(),connectedStructures:Ie.types.array(Ie.types.frozen()),dataStoreId:Ie.types.maybe(Ie.types.string),mafRegion:Ie.types.frozen()})).volatile(()=>({rid:void 0,progress:"",error:void 0,loadingStoredData:!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?Fh(e.connectedFeature):void 0},get processing(){return!!e.progress},get connectedView(){let{views:t}=(0,Ii.getSession)(e);return t.find(r=>r.id===e.connectedViewId)},get connectedProteinViews(){let{views:t}=(0,Ii.getSession)(e);return e.connectedStructures.map(r=>{let n=t.find(o=>o.id===r.proteinViewId);return n?{...r,proteinView:n}:void 0}).filter(r=>!!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=GS(i,o);if(s!==void 0)return e.globalColToVisibleCol(s)}}}}}})).views(e=>({get mouseCol2(){let t=e.structureHoverCol;return t!==void 0?t:nQ({model:e})},get clickCol2(){}})).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,Ie.cast)(t)},addToConnectedHighlights(t){e.connectedHighlights.push(t)},clearConnectedHighlights(){e.connectedHighlights=(0,Ie.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},handleMsaClick(t){let{connectedView:r,zoomToBaseLevel:n}=e,{assemblyManager:o}=(0,Ii.getSession)(e),i=xs({model:e,coord:t});if(!(!i||!r))if(n)r.navTo(i);else{let s=o.get(r.assemblyNames[0])?.getCanonicalRefName(i.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("-",""),{views:a}=(0,Ii.getSession)(e),c=a.find(h=>h.id===t);if(!c)throw new Error(`ProteinView "${t}" not found`);let l=c.structures?.[r];if(!l)throw new Error(`Structure at index ${r} not found`);let A=l.structureSequences?.[0];if(!A)throw new Error("Structure sequence not available");let u=sQ(s,A),{seq1ToSeq2:d,seq2ToSeq1:m}=aQ(u),g={proteinViewId:t,structureIdx:r,msaRowName:o,msaToStructure:_d(d),structureToMsa:_d(m)};e.connectedStructures.push(g)},disconnectFromStructure(t,r){let n=e.connectedStructures.findIndex(o=>o.proteinViewId===t&&o.structureIdx===r);n!==-1&&e.connectedStructures.splice(n,1)},disconnectAllStructures(){e.connectedStructures.clear()}})).actions(e=>{let t=e.setMouseClickPos.bind(e);return{setMouseClickPos(r,n){t(r,n),r!==void 0&&e.handleMsaClick(r)}}}).views(e=>({extraViewMenuItems(){return[{label:"Zoom to base level on click?",checked:e.zoomToBaseLevel,type:"checkbox",onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Connect to protein structure...",onClick:()=>{(0,Ii.getSession)(e).queueDialog(t=>[Pk,{model:e,handleClose:t}])}},...e.connectedStructures.length>0?[{label:"Disconnect from protein structures",onClick:()=>{e.disconnectAllStructures()}}]:[]]}})).actions(e=>({afterCreate(){tQ();for(let t of[VS,WS,zS,$S,KS,XS,ZS,eQ])(0,Ie.addDisposer)(e,(0,gQ.autorun)(()=>{t(e)}))}}))}var Yk=(0,QQ.lazy)(()=>Promise.resolve().then(()=>(SQ(),bQ)));function Pd(e){e.addViewType(()=>new MQ.default({name:"MsaView",stateModel:Nd(),ReactComponent:Yk}))}var vQ="2.3.3";var dl=class extends TQ.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=vQ;this.rootConfigurationSchema=r=>({msa:(0,Od.ConfigurationSchema)("MSA",{datasets:Gd.types.maybe(Gd.types.array((0,Od.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Pd(r),qA(r),YA(r),wl(r),Hl(r)}configure(r){(0,_Q.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:lm,onClick:n=>{n.addView("MsaView",{})}})}};return qQ(jk);})();
 /*! Bundled license information:
 
 use-sync-external-store/cjs/use-sync-external-store-shim.production.js: