jbrowse-plugin-msaview 5.2.0 → 5.3.0

package/dist/chunks/chunk-ZCT7RD24.js

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-import{j as m,p as l,q as h}from"./chunk-F726IWCW.js";import{d as p}from"./chunk-QQ5LZUIO.js";var g="ncbiblast";function f(e){return(e.hits??[]).map(t=>{let n=Number.parseInt(t.hit_uni_ox??"",10);return{accession:t.hit_acc??"unknown",id:t.hit_id??t.hit_acc??"unknown",sciname:t.hit_uni_os??t.hit_os??"unknown",taxid:Number.isNaN(n)?void 0:n,title:t.hit_uni_de??t.hit_desc,sequence:(t.hit_hsps?.[0]?.hsp_hseq??"").replaceAll("-","")}})}function E(e){return`https://www.ebi.ac.uk/jdispatcher/sss/${g}/summary?jobId=${e}`}async function w({query:e,blastDatabase:t,maxHits:n,onProgress:r,onRid:s,signal:i}){let a=String(h(n??l)),o=await m({tool:g,label:"BLAST",params:{program:"blastp",stype:"protein",database:t,sequence:e,alignments:a,scores:a},onProgress:r,onRid:s,signal:i});return{rid:o.jobId,hits:f(JSON.parse(await o.result("json")))}}var R=({database:e,...t})=>w({blastDatabase:e,...t});var u="hmmer3_phmmer";function O(e){return`https://www.ebi.ac.uk/jdispatcher/sss/${u}/summary?jobId=${e}`}function H(e){return e.startsWith(`${u}-`)}function x({rf:e,query:t}){let n=0,r=Array.from(e,s=>s==="x"?t[n++]??"-":"-").join("");if(n!==t.length)throw new Error(`phmmer alignment has ${n} match columns for a query of ${t.length} residues, so the query row cannot be placed`);return r}function _(e){let t=(e??"").replace("[subseq from] ","");if(t.includes("^|^")){let s=t.split("^|^"),i=s[6];return{id:s[0]||void 0,sciname:s[5]||"unknown",taxid:i&&/^\d+$/.test(i)?Number.parseInt(i,10):void 0,title:s[2]||void 0}}let n=/OS=(.*?)\s+(?:OX|GN|PE|SV)=/.exec(t)?.[1],r=/OX=(\d+)/.exec(t)?.[1];return{id:void 0,sciname:n??"unknown",taxid:r?Number.parseInt(r,10):void 0,title:t.split(" OS=")[0]||void 0}}function S(e){let t=e.lastIndexOf("/"),n=t===-1?void 0:/^\d+-\d+$/.exec(e.slice(t+1))?.[0],r=n===void 0?e:e.slice(0,t),s=r.split("|");return s.length===3?{accession:s[1],id:s[2],range:n}:{accession:r,id:r,range:n}}function y({stockholm:e,query:t}){let{gc:n,gs:r,seqdata:s,seqname:i}=new p(e,0).getMSA(),a=n.RF;if(!a)throw new Error("phmmer alignment has no #=GC RF line");return{queryRow:x({rf:a,query:t}),rows:i.map(o=>{let{id:d,...b}=_(r.DE?.[o]?.[0]),c=S(o);return{...c,id:c.id===c.accession&&d?d:c.id,...b,aligned:(s[o]??"").replaceAll(".","-").toUpperCase()}})}}async function B({query:e,database:t,maxHits:n,onProgress:r,onRid:s,signal:i}){let a=await m({tool:u,label:"phmmer",params:{database:t,sequence:e,alignView:"true",...n?{nhits:String(n)}:{}},onProgress:r,onRid:s,signal:i});return{rid:a.jobId,...y({stockholm:await a.result("sto"),query:e})}}function q(e){return e.map(({aligned:t,...n})=>({...n,sequence:t}))}var I=async({database:e,...t})=>{let{rows:n,queryRow:r,rid:s}=await B({database:e,...t});return{rid:s,queryRow:r,hits:q(n)}};export{E as a,R as b,O as c,H as d,I as e};
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package/dist/chunks/dist-R73J3CC3.js

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-import{a as c,b as d,c as e,d as f,e as g,f as h,g as i,h as j,i as k,j as l}from"./chunk-NMYD2GWF.js";import"./chunk-F3EC6OCO.js";import"./chunk-FCWXYIFC.js";import"./chunk-YUKJI2AH.js";import"./chunk-QQ5LZUIO.js";import"./chunk-IBBQUV2I.js";import{M as a,Ua as b}from"./chunk-QUWPHTZQ.js";import"./chunk-73KAPCJ2.js";import"./chunk-GIHMPOCO.js";import"./chunk-CVLB4VFP.js";import"./chunk-DNFD5II2.js";import"./chunk-BX4Z274Q.js";import"./chunk-J6KYLXRD.js";import"./chunk-FY3BTKY4.js";export{d as CHAR_WIDTH_RATIO,h as MSAModelF,g as MSAView,i as MSAViewer,k as defineMsaElement,f as expandSpec,c as installHeadlessRenderEnv,a as maxNeighborJoiningRows,j as mount,b as renderToSvg,e as residueLabel,l as useMsaSvgFigure};
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package/dist/chunks/renderToSvg-VDXAB7TT.js

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-import{Ua as a}from"./chunk-QUWPHTZQ.js";import"./chunk-73KAPCJ2.js";import"./chunk-BX4Z274Q.js";import"./chunk-J6KYLXRD.js";import"./chunk-FY3BTKY4.js";export{a as renderToSvg};
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