jbrowse-plugin-mafviewer 1.4.2 → 1.4.3

package/dist/LinearMafRenderer/components/LinearMafRendering.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { RenderedBase } from '../rendering';
 import { Sample } from '../../LinearMafDisplay/types';
+import { RenderedBase } from '../rendering';
 type SerializedRBush = any;
 declare const LinearMafRendering: (props: {
     width: number;

package/dist/LinearMafRenderer/components/LinearMafRendering.js.map

@@ -1 +1 @@
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+{"version":3,"file":"LinearMafRendering.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/components/LinearMafRendering.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAE9C,OAAO,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAA;AACpD,OAAO,QAAQ,MAAM,UAAU,CAAA;AAC/B,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAOrC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,KAO7C;IACC,MAAM,EAAE,KAAK,EAAE,YAAY,EAAE,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAChE,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAA;IAEjE,SAAS,oBAAoB,CAAC,YAAoB,EAAE,YAAoB;QACtE,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;YAChB,MAAM,CAAC,GAAG,GAAG,CAAC,OAAO,CAAC,qBAAqB,EAAE,CAAA;YAC7C,OAAO,GAAG,YAAY,GAAG,CAAC,CAAC,IAAI,CAAA;YAC/B,OAAO,GAAG,YAAY,GAAG,CAAC,CAAC,GAAG,CAAA;QAChC,CAAC;QAED,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,EAAE,OAAO,GAAG,CAAC,EAAE,OAAO,GAAG,CAAC,CAAC,CAAA;QACnE,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC;YACb,MAAM,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,WAAW,CAAC,CAAA;YAClD,MAAM,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAE,CAAE,CAAA;YACzD,MAAM,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAA;YAC7B,OAAO;gBACL,GAAG,CAAC;gBACJ,QAAQ,EAAE,CAAC,EAAE,KAAK,IAAI,CAAC,EAAE,EAAE,IAAI,SAAS;aACzC,CAAA;QACH,CAAC;aAAM,CAAC;YACN,OAAO,SAAS,CAAA;QAClB,CAAC;IACH,CAAC;IACD,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,CAAC,CAAC,EAAE,CACf,YAAY,CAAC,cAAc,EAAE,CAC3B,oBAAoB,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,OAAO,CAAC,CAC3C,EAEH,YAAY,EAAE,GAAG,EAAE;YACjB,YAAY,CAAC,cAAc,EAAE,CAAC,SAAS,CAAC,CAAA;QAC1C,CAAC,EACD,UAAU,EAAE,GAAG,EAAE;YACf,YAAY,CAAC,cAAc,EAAE,CAAC,SAAS,CAAC,CAAA;QAC1C,CAAC,EACD,KAAK,EAAE;YACL,QAAQ,EAAE,SAAS;YACnB,QAAQ,EAAE,UAAU;YACpB,MAAM;SACP;QAED,oBAAC,iBAAiB,OACZ,KAAK,EACT,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,IAAI,EAAE,CAAC;aACR,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}

package/dist/LinearMafRenderer/makeImageData.js

@@ -40,9 +40,14 @@ export function makeImageData({ ctx, renderArgs, }) {
     for (const feature of features.values()) {
         processFeatureInsertions(feature, region, bpPerPx, sampleToRowMap, renderingContext);
     }
-    const flatbush = new Flatbush(renderingContext.spatialIndex.length);
-    for (let i = 0, l = renderingContext.spatialIndexCoords.length; i < l; i += 4) {
-        flatbush.add(renderingContext.spatialIndexCoords[i], renderingContext.spatialIndexCoords[i + 1], renderingContext.spatialIndexCoords[i + 2], renderingContext.spatialIndexCoords[i + 3]);
+    const flatbush = new Flatbush(renderingContext.spatialIndex.length || 1);
+    if (renderingContext.spatialIndex.length === 0) {
+        flatbush.add(0, 0, 1, 1);
+    }
+    else {
+        for (let i = 0, l = renderingContext.spatialIndexCoords.length; i < l; i += 4) {
+            flatbush.add(renderingContext.spatialIndexCoords[i], renderingContext.spatialIndexCoords[i + 1], renderingContext.spatialIndexCoords[i + 2], renderingContext.spatialIndexCoords[i + 3]);
+        }
     }
     flatbush.finish();
     return {

package/dist/LinearMafRenderer/makeImageData.js.map

@@ -1 +1 @@
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package/dist/jbrowse-plugin-mafviewer.umd.production.min.js

@@ -5,7 +5,7 @@ In order to be iterable, non-array objects must have a [Symbol.iterator]() metho
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B0({ctx:e,renderArgs:t}){let{regions:r,bpPerPx:n,rowHeight:i,showAllLetters:o,theme:a,mismatchRendering:u,samples:l,rowProportion:s,features:c,showAsUpperCase:f}=t,d=r[0],p=(d.end-d.start)/n,m=i*s,h=(0,D0.createJBrowseTheme)(a),v=Qp(h),y=M0(h),w=new Map(l.map((T,C)=>[T.id,C])),_=1/n,x=m/2,S=(i-m)/2;e.font=R0;let E={ctx:e,scale:_,canvasWidth:p,rowHeight:i,h:m,hp2:x,offset:S,colorForBase:v,contrastForBase:y,showAllLetters:o,mismatchRendering:u,showAsUpperCase:f,spatialIndex:[],spatialIndexCoords:[],lastInsertedX:-1/0};for(let T of c.values())L0(T,d,n,w,E);for(let T of c.values())N0(T,d,n,w,E);let R=new ai(E.spatialIndex.length||1);if(E.spatialIndex.length===0)R.add(0,0,1,1);else for(let T=0,C=E.spatialIndexCoords.length;T<C;T+=4)R.add(E.spatialIndexCoords[T],E.spatialIndexCoords[T+1],E.spatialIndexCoords[T+2],E.spatialIndexCoords[T+3]);return R.finish(),{flatbush:R.data,items:E.spatialIndex,samples:l}}var qa=class extends 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nh({model:e}){let{classes:t}=wk(),[r,n]=(0,ve.useState)(""),[i,o]=(0,ve.useState)(),[a,u]=(0,ve.useState)(),[l,s]=(0,ve.useState)(),[c,f]=(0,ve.useState)(),[d,p]=(0,ve.useState)("MAF track"),[m,h]=(0,ve.useState)("BigMafAdapter"),[v,y]=(0,ve.useState)("TBI"),w=(0,$0.getRoot)(e);return ve.default.createElement(De.Paper,{className:t.paper},ve.default.createElement(De.Paper,null,c?ve.default.createElement(qr.ErrorMessage,{error:c}):null,ve.default.createElement(De.FormControl,null,ve.default.createElement(De.FormLabel,null,"File type"),ve.default.createElement(De.RadioGroup,{value:m,onChange:_=>{h(_.target.value)}},["BigMafAdapter","MafTabixAdapter"].map(_=>ve.default.createElement(De.FormControlLabel,{key:_,value:_,control:ve.default.createElement(De.Radio,null),checked:m===_,label:_})))),m==="BigMafAdapter"?ve.default.createElement(qr.FileSelector,{location:i,name:"Path to 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rP=L(ub()),nP=L(vb());function tP({regions:e,showAllLetters:t,samples:r,features:n}){let i=e[0],o=new Map(r.map((l,s)=>[l.id,s])),a=i.end-i.start,u=r.map(()=>"-".repeat(a));for(let l of n.values()){let s=l.get("start"),c=l.get("alignments"),f=l.get("seq");for(let[d,p]of Object.entries(c)){let h=p.seq,v=o.get(d);if(v!==void 0){for(let y=0,w=0,_=h.length;y<_;y++)if(f[y]!=="-"){if(h[y]==="-"){let x=s+w-i.start;x>=0&&x<a&&(u[v]=u[v].slice(0,x)+"-"+u[v].slice(x+1))}w++}if(!t){for(let y=0,w=0,_=h.length;y<_;y++)if(f[y]!=="-"){let x=h[y],S=s+w-i.start;S>=0&&S<a&&f[y]===x&&x!=="-"&&x!==" "&&(u[v]=u[v].slice(0,S)+"."+u[v].slice(S+1)),w++}}for(let y=0,w=0,_=h.length;y<_;y++){let x=h[y];if(f[y]!=="-"){if(x!=="-"){let S=s+w-i.start;S>=0&&S<a&&(f[y]!==x&&x!==" "||t)&&(u[v]=u[v].slice(0,S)+x+u[v].slice(S+1))}w++}}}}}return u}var Vu=class extends nP.default{name="MafGetSequences";async execute(t,r){let n=await this.deserializeArguments(t,r),{samples:i,regions:o,adapterConfig:a,sessionId:u,showAllLetters:l}=n,s=(await(0,rP.getAdapter)(this.pluginManager,u,a)).dataAdapter,c=await Gn(s.getFeatures(o[0],n).pipe($n()));return tP({features:new Map(c.map(f=>[f.id(),f])),samples:i,regions:o,showAllLetters:l})}};function gb(e){e.addRpcMethod(()=>new Vu(e))}var cP=L(Gr());var iP=L(Nd()),da=L(ct()),oP=L(Dd()),aP=L(Bd()),uP=L(ht());var Gu=class extends iP.BaseFeatureDataAdapter{setupP;async setupPre(){if(!this.getSubAdapter)throw new Error("no getSubAdapter available");return{adapter:(await this.getSubAdapter({...(0,uP.getSnapshot)(this.config),type:"BedTabixAdapter"})).dataAdapter}}async setupPre2(){return this.setupP||(this.setupP=this.setupPre().catch(t=>{throw this.setupP=void 0,t})),this.setupP}async setup(t){let{statusCallback:r=()=>{}}=t||{};return(0,da.updateStatus)("Downloading index",r,()=>this.setupPre2())}async getRefNames(t){let{adapter:r}=await this.setup(t);return r.getRefNames()}async getHeader(t){let{adapter:r}=await this.setup(t);return r.getHeader()}getFeatures(t,r){let{statusCallback:n=()=>{}}=r||{};return(0,aP.ObservableCreate)(async i=>{let{adapter:o}=await this.setup(r),a=await(0,da.updateStatus)("Downloading alignments",n,()=>Gn(o.getFeatures(t).pipe($n())));await(0,da.updateStatus)("Processing alignments",n,()=>{let u="",l=this.getConf("refAssemblyName");for(let s of a){let c=s.get("field5").split(","),f={},d=c.length;for(let p=0;p<d;p++){let h=c[p].split(":"),[v,y,w,_,x,S]=h;if(!v||!S)continue;let E,R,T=v.indexOf(".");if(T===-1)E=v,R="";else{let C=v.indexOf(".",T+1);if(C===-1)E=v.slice(0,Math.max(0,T)),R=v.slice(Math.max(0,T+1));else{let M=v.slice(T+1,C);M.length>0&&!Number.isNaN(+M)?(E=v.slice(0,Math.max(0,C)),R=v.slice(Math.max(0,C+1))):(E=v.slice(0,Math.max(0,T)),R=v.slice(Math.max(0,T+1)))}}E&&(u||(u=E),f[E]={chr:R,start:+y,srcSize:+w,strand:_==="-"?-1:1,unknown:+x,seq:S})}i.next(new da.SimpleFeature({id:s.id(),data:{start:s.get("start"),end:s.get("end"),refName:s.get("refName"),name:s.get("name"),score:s.get("score"),alignments:f,seq:f[l||t.assemblyName]?.seq||f[u]?.seq}}))}}),i.complete()})}async getSamples(t){let r=this.getConf("nhLocation"),n=r.uri==="/path/to/my.nh"?void 0:await(0,oP.openLocation)(r).readFile("utf8");return{samples:zi(this.getConf("samples")),tree:n?ba(n):void 0}}freeResources(){}};var yb=L(Kn());var kK=(0,yb.ConfigurationSchema)("MafTabixAdapter",{samples:{type:"frozen",description:"string[] or {id:string,label:string,color?:string}[]",defaultValue:[]},bedGzLocation:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bed.gz.tbi",locationType:"UriLocation"}},refAssemblyName:{type:"string",defaultValue:""},index:(0,yb.ConfigurationSchema)("Index",{location:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bed.gz.tbi"}},indexType:{type:"string",defaultValue:"TBI"}}),nhLocation:{type:"fileLocation",description:"newick 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 /*! Bundled license information:
 
 tabbable/dist/index.esm.js: