jbrowse-plugin-msaview 2.6.5 → 2.6.6

package/dist/AddHighlightModel/MsaToGenomeHighlight.js

@@ -8,10 +8,15 @@ const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({ model, })
     const msaView = views
         .filter(isMsaView)
         .find(v => v.connectedViewId === model.id);
-    const highlights = msaView?.connectedHighlights;
-    // Suppress codon highlight while hovering the LGV — GenomeMouseoverHighlight
-    // handles the single-bp display in that case
-    return !hasHoverPosition(hovered) && highlights?.length ? (React.createElement(MsaToGenomeHighlightRenderer, { model: model, highlights: highlights })) : null;
+    // The persistent click selection always shows. The hover codon is suppressed
+    // while hovering the LGV — GenomeMouseoverHighlight handles the single-bp
+    // display in that case, so we don't stack a wider codon band on top of it.
+    const clickHighlight = msaView?.connectedClickHighlight;
+    const hoverHighlight = hasHoverPosition(hovered)
+        ? undefined
+        : msaView?.connectedHoverHighlight;
+    const highlights = [clickHighlight, hoverHighlight].filter((r) => r !== undefined);
+    return highlights.length ? (React.createElement(MsaToGenomeHighlightRenderer, { model: model, highlights: highlights })) : null;
 });
 // Inner component: handles the scroll-dependent rendering
 const MsaToGenomeHighlightRenderer = observer(function ({ model, highlights, }) {

package/dist/MsaViewPanel/model.d.ts

@@ -526,6 +526,19 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      */
     readonly connectedView: MaybeLGV;
 } & {
+    /**
+     * #getter
+     * Genome region under the current MSA hover column. Suppressed on the LGV
+     * while it's being hovered (GenomeMouseoverHighlight shows the crisp 1bp
+     * marker there instead of this wider codon band).
+     */
+    readonly connectedHoverHighlight: IRegion | undefined;
+    /**
+     * #getter
+     * Genome region under the persistent MSA click selection. Shown
+     * regardless of LGV hover, so hovering the genome doesn't hide it.
+     */
+    readonly connectedClickHighlight: IRegion | undefined;
     /**
      * #getter
      */

package/dist/MsaViewPanel/model.js

@@ -111,19 +111,34 @@ export default function stateModelFactory() {
         },
     }))
         .views(self => ({
+        /**
+         * #getter
+         * Genome region under the current MSA hover column. Suppressed on the LGV
+         * while it's being hovered (GenomeMouseoverHighlight shows the crisp 1bp
+         * marker there instead of this wider codon band).
+         */
+        get connectedHoverHighlight() {
+            const { mouseCol } = self;
+            return mouseCol === undefined
+                ? undefined
+                : msaCoordToGenomeCoord({ model: self, coord: mouseCol });
+        },
+        /**
+         * #getter
+         * Genome region under the persistent MSA click selection. Shown
+         * regardless of LGV hover, so hovering the genome doesn't hide it.
+         */
+        get connectedClickHighlight() {
+            const { mouseClickCol } = self;
+            return mouseClickCol === undefined
+                ? undefined
+                : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol });
+        },
         /**
          * #getter
          */
         get connectedHighlights() {
-            const { mouseCol, mouseClickCol } = self;
-            return [
-                mouseCol === undefined
-                    ? undefined
-                    : msaCoordToGenomeCoord({ model: self, coord: mouseCol }),
-                mouseClickCol === undefined
-                    ? undefined
-                    : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol }),
-            ].filter((r) => r !== undefined);
+            return [this.connectedHoverHighlight, this.connectedClickHighlight].filter((r) => r !== undefined);
         },
     }))
         .actions(self => ({

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

@@ -70,10 +70,10 @@ sp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR	142
 ${y}`}),C=await KQ({algorithm:o,sequence:[`>QUERY
 ${c}`,...p].join(`
 `),onProgress:x=>{e.setProgress(x)}}),I=JSON.stringify(d);return await qQ({proteinSequence:c,blastDatabase:r,blastProgram:n,msaAlgorithm:o,msa:C.msa,tree:C.tree,treeMetadata:I,rid:A,geneId:a?.get("parentId"),transcriptId:a?.id(),transcriptName:a?.get("name")??a?.get("id"),geneName:a?.get("gene_name")??a?.get("parentId")}),{...C,treeMetadata:I}}function t5(e,t){let r={},n=e.taxid?t.get(e.taxid):void 0;return n?.sciname&&(r["Scientific name"]=n.sciname),n?.commonName&&(r["Common name"]=n.commonName),e.accession&&(r.Accession=e.accession),e.id&&(r.ID=e.id),e.title&&(r.Description=e.title),r}ed();var nv=f(Rm());async function ov({location:e,name:t}){let r=i=>(0,nv.openLocation)({uri:i,locationType:"UriLocation"}),n=await r(`${e.uri}.idx`).readFile("utf8"),o=r5(n,t);if(o){let a=await new bi({filehandle:r(e.uri),gziFilehandle:r(`${e.uri}.gzi`)}).read(o.length,o.offset);return new TextDecoder().decode(a).trim()}}var rv=e=>e.replace(/\.\d+$/,"");function r5(e,t){let r=rv(t);for(let n of e.split(`
-`)){let[o,i,a]=n.split("	");if(o&&rv(o)===r)return{offset:Number(i),length:Number(a)}}}var iv=f(xe());function av({model:e}){let{hovered:t}=(0,iv.getSession)(e),{querySeqName:r,transcriptToMsaMap:n,connectedView:o,mafRegion:i}=e;if(!o?.initialized||!Kn(t))return;let{coord:a,refName:s}=t.hoverPosition;if(i)return s!==i.refName||!o.assemblyNames.includes(i.assemblyName)||a<i.start||a>=i.end?void 0:e.seqPosToVisibleCol(r,a-i.start);if(n){let c=n.g2p[a];if(c!==void 0)return e.seqPosToVisibleCol(r,c)}}Mi();var n5="jbrowse-msaview-domain-cache",fA="domains",o5=1;async function sv(){return an(n5,o5,{upgrade(e){e.objectStoreNames.contains(fA)||e.createObjectStore(fA,{keyPath:"accession"})}})}async function cv(e){let r=(await sv()).transaction(fA,"readonly"),n=await Promise.all(e.map(o=>r.store.get(o)));return await r.done,n}async function lv(e){let r=(await sv()).transaction(fA,"readwrite");for(let n of e)await r.store.put(n);await r.done}function Jn(e,t){return new RegExp(`<${t}>(.*?)</${t}>`,"s").exec(e)?.[1]}function i5(e){let t={},r=/<GBQualifier>([\s\S]*?)<\/GBQualifier>/g,n;for(;(n=r.exec(e))!==null;){let o=Jn(n[1],"GBQualifier_name"),i=Jn(n[1],"GBQualifier_value");o&&i!==void 0&&t[o]===void 0&&(t[o]=i)}return t}function a5(e){let t=[],r=[],n=/<GBInterval>([\s\S]*?)<\/GBInterval>/g,o;for(;(o=n.exec(e))!==null;){let i=o[1],a=Jn(i,"GBInterval_from"),s=Jn(i,"GBInterval_to"),c=Jn(i,"GBInterval_point");a&&s?(t.push(Number(a)),r.push(Number(s))):c&&(t.push(Number(c)),r.push(Number(c)))}return t.length>0?{start:Math.min(...t),end:Math.max(...r)}:void 0}var s5=2;function c5(e){let t=Jn(e,"GBFeature_key"),r=i5(e),n=r.db_xref,o=a5(e);if((t==="Region"||t==="Site")&&n?.startsWith("CDD:")&&o&&o.end-o.start+1>=s5){let i=n.replace("CDD:",""),a=t==="Region",s=r.note?.split(/[[(]/)[0]?.trim(),c=a?r.region_name??i:s||r.site_type||"site",l=a?i:`${i}:${c}`;return{signature:{entry:{name:c,description:r.note??c,accession:l}},locations:[o]}}}function l5(e){let t=new Map,r=/<GBSeq>([\s\S]*?)<\/GBSeq>/g,n;for(;(n=r.exec(e))!==null;){let o=n[1],i=[],a=/<GBFeature>([\s\S]*?)<\/GBFeature>/g,s;for(;(s=a.exec(o))!==null;){let c=c5(s[1]);c&&i.push(c)}for(let c of[Jn(o,"GBSeq_accession-version"),Jn(o,"GBSeq_primary-accession")])c&&t.set(c,i)}return t}async function Av(e){let t=[...new Set(e)].filter(Boolean),r=new Map,n=await cv(t),o=[];t.forEach((s,c)=>{let l=n[c];l?r.set(s,l.matches):o.push(s)});let i=[],a=100;for(let s=0;s<o.length;s+=a){let c=o.slice(s,s+a),l=await qr(uA({db:"protein",id:c.join(","),rettype:"gp",retmode:"xml"})),A=l5(l);for(let u of c){let m=A.get(u)??[];r.set(u,m),i.push({accession:u,matches:m})}}return i.length>0&&await lv(i),r}async function uv(e){let t=e.data.treeMetadata;if(!t)throw new Error("No sequence metadata available to look up domains");let r=JSON.parse(t),n=Object.entries(r).map(([a,s])=>({rowName:a,accession:s.Accession})).filter(a=>!!a.accession);if(n.length===0)throw new Error("No NCBI accessions found in alignment rows");e.setProgress(`Fetching protein domains from NCBI for ${n.length} sequences...`);let o=await Av(n.map(a=>a.accession)),i={};for(let{rowName:a,accession:s}of n){let c=o.get(s);c&&c.length>0&&(i[a]={matches:c,xref:[{id:a}]})}if(Object.keys(i).length===0)throw new Error("No CDD domain annotations found for these proteins");e.setDomains(i)}Mi();var A5="jbrowse-msaview-data",u5=1,Cs="msa-data";async function Km(){return an(A5,u5,{upgrade(e){e.objectStoreNames.contains(Cs)||e.createObjectStore(Cs,{keyPath:"id"}).createIndex("timestamp","timestamp",{unique:!1})}})}function fv(){return`msa-${Date.now()}-${Math.random().toString(36).slice(2,11)}`}async function dv(e,t){try{let r=await Km(),n={id:e,msa:t.msa,tree:t.tree,treeMetadata:t.treeMetadata,timestamp:Date.now()};return await r.put(Cs,n),!0}catch(r){return console.warn("Failed to store MSA data:",r),!1}}async function mv(e){try{let r=await(await Km()).get(Cs,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 pv(e=10080*60*1e3){try{let t=await Km(),r=Date.now()-e,i=await t.transaction(Cs,"readwrite").store.index("timestamp").openCursor(IDBKeyRange.upperBound(r)),a=0;for(;i;)await i.delete(),a++,i=await i.continue();return a}catch(t){return console.warn("Failed to cleanup old MSA data:",t),0}}function f5(e){let t=e;return t.type==="ProteinView"&&Array.isArray(t.structures)}function gv(e){return e.filter(f5)}function hv(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 Ev(e){let{dataStoreId:t,rows:r}=e;t&&r.length===0&&(async()=>{try{e.setLoadingStoredData(!0);let n=await mv(t);n&&(n.msa&&e.setMSA(n.msa),n.tree&&e.setTree(n.tree),n.treeMetadata&&e.setTreeMetadata(n.treeMetadata))}catch(n){console.error("Failed to load MSA data from IndexedDB:",n)}finally{e.setLoadingStoredData(!1)}})()}function xv(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 a=fv();await dv(a,{msa:o,tree:i,treeMetadata:e.data.treeMetadata})&&e.setDataStoreId(a)}catch(a){console.error("Failed to store MSA data to IndexedDB:",a)}finally{e.setIsStoringData(!1)}})())}}function Iv(e){e.blastParams&&(async()=>{try{e.setProgress("Submitting query"),e.setError(void 0);let t=await tv({self:e});e.setData(t),e.setBlastParams(void 0)}catch(t){e.setError(t),console.error(t)}finally{e.setProgress("")}})()}function yv(e){let{rows:t,domainsRequested:r,interProAnnotations:n}=e,o=e.data.treeMetadata?.includes('"Accession"')??!1;t.length>0&&o&&!n&&!r&&(e.setDomainsRequested(!0),(async()=>{try{await uv(e)}catch(i){console.error("[msaview-domains] auto-load failed:",i)}finally{e.setProgress("")}})())}function wv(e){let{init:t}=e;if(t){let{msaUrl:r,msaIndexedLocation:n,msaName:o,querySeqName:i}=t;(async()=>{try{if(e.setError(void 0),r){let a=Eg(r);a&&(e.setUniprotId(a),e.setQuerySeqName("query"))}if(i&&e.setQuerySeqName(i),r)e.setMSAFilehandle({uri:r,locationType:"UriLocation"});else if(n&&o){let a=await ov({location:n,name:o});if(a)e.setMSA(a);else throw new Error(`No alignment named ${o} in ${n.uri}`)}e.setInit(void 0)}catch(a){e.setError(a),console.error(a)}})()}}function bv(e){let t=!1;return()=>{let r=av({model:e});r!==void 0?(e.setMousePos(r),t=!0):t&&(e.setMousePos(void 0),t=!1)}}function Bv(e){let t=!1;return()=>{let{connectedViewId:r,transcriptToMsaMap:n,querySeqName:o}=e;if(!r||!n)return;let i=new Set;for(let s of gv((0,Cv.getSession)(e).views))for(let c of s.structures){if(c.connectedViewId!==r)continue;let l=c.hoverGenomeHighlights;if(!l||l.length===0)continue;let{g2p:A}=n;for(let u of l)for(let m=u.start;m<u.end;m++){let d=A[m];if(d!==void 0){let p=e.seqPosToGlobalCol(o,d);i.add(p)}}}let a=Array.from(i).map(s=>e.globalColToVisibleCol(s)).filter(s=>s!==void 0);a.length>0?(e.setHighlightedColumns(a),t=!0):t&&(e.setHighlightedColumns(e.highlightColumns?.length?e.highlightColumns:void 0),t=!1)}}function Sv(){pv().catch(e=>{console.error("Failed to cleanup old MSA data:",e)})}function dA({model:e,coord:t}){let{querySeqName:r,transcriptToMsaMap:n,mafRegion:o}=e,i=e.rows.find(s=>s[0]===r)?.[1];if(!i)return;let a=hv(i,t);if(a!==void 0){if(o){let s=o.start+a;return s<o.end?{refName:o.refName,start:s,end:s+1}:void 0}if(n){let{refName:s,p2g:c}=n,l=c[a],A=c[a+1];return l!==void 0&&A!==void 0?{refName:s,start:Math.min(l,A),end:Math.max(l,A)}:void 0}}}function Xm(){return At.types.compose(Qv.BaseViewModel,eA(),At.types.model("MsaView",{connectedViewId:At.types.maybe(At.types.string),connectedFeature:At.types.frozen(),blastParams:At.types.frozen(),querySeqName:"QUERY",uniprotId:At.types.maybe(At.types.string),zoomToBaseLevel:!1,init:At.types.frozen(),dataStoreId:At.types.maybe(At.types.string),mafRegion:At.types.frozen()})).volatile(()=>({rid:void 0,progress:"",error:void 0,loadingStoredData:!1,isStoringData:!1,domainsRequested:!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?yg(e.connectedFeature):void 0},get connectedView(){let{views:t}=(0,vv.getSession)(e);return t.find(r=>r.id===e.connectedViewId)}})).views(e=>({get connectedHighlights(){let{mouseCol:t,mouseClickCol:r}=e;return[t===void 0?void 0:dA({model:e,coord:t}),r===void 0?void 0:dA({model:e,coord:r})].filter(n=>n!==void 0)}})).actions(e=>({setZoomToBaseLevel(t){e.zoomToBaseLevel=t},setError(t){e.error=t},setProgress(t){e.progress=t},setRid(t){e.rid=t},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},setDomainsRequested(t){e.domainsRequested=t},handleMsaClick(t){let{connectedView:r,zoomToBaseLevel:n}=e,o=dA({model:e,coord:t});!o||!r||(n?r.navTo(o):r.centerAt(o.start,o.refName))}})).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)}}]}})).actions(e=>({afterCreate(){Sv();for(let t of[Ev,xv,Iv,wv,yv])(0,At.addDisposer)(e,(0,mA.autorun)(()=>{t(e)}));(0,At.addDisposer)(e,(0,mA.autorun)(bv(e))),(0,At.addDisposer)(e,(0,mA.autorun)(Bv(e)))}}))}function Yi(e){return e.type==="MsaView"}var d5=(0,ep.observer)(function({model:e}){let{hovered:t,views:r}=(0,Mv.getSession)(e);return r.some(o=>Yi(o)&&o.connectedViewId===e.id)&&Kn(t)?Zm.default.createElement(m5,{model:e,hovered:t}):null}),m5=(0,ep.observer)(function({model:e,hovered:t}){let{classes:r}=Ls(),{offsetPx:n}=e,{coord:o,refName:i}=t.hoverPosition,a=e.bpToPx({refName:i,coord:o-1}),s=e.bpToPx({refName:i,coord:o});if(a&&s){let c=Math.max(Math.abs(s.offsetPx-a.offsetPx),4),l=Math.min(a.offsetPx,s.offsetPx)-n;return Zm.default.createElement("div",{className:r.highlight,style:{left:l,width:c}})}return null}),_v=d5;var Es=f(M()),Tv=f(xe()),tp=f(H());var 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rp(e){e.addToExtensionPoint("LinearGenomeView-TracksContainerComponent",(t,{model:r})=>{let{views:n}=(0,Rv.getSession)(r);return n.some(i=>Yi(i)&&i.connectedViewId===r.id)?[...t,Lv.default.createElement(Nv,{key:"highlight_protein_viewer_msaview",model:r})]:t})}var qv=f(tu());var Fv=f(jo());function np(e){let t=e.getAdapterType("BgzipFastaAdapter");return(0,Fv.ConfigurationSchema)("BgzipFastaMsaAdapter",{msaRegex:{type:"string",defaultValue:"_"}},{baseConfiguration:t?.configSchema})}function op(e){return e.addAdapterType(()=>new qv.AdapterType({name:"BgzipFastaMsaAdapter",configSchema:np(e),adapterMetadata:{hiddenFromGUI:!0},getAdapterClass:()=>Promise.resolve().then(()=>(jv(),Hv)).then(t=>t.default)}))}var PA=f(xe());Y();var Jv=f(O(),1),Vv=(0,R.createSvgIcon)((0,Jv.jsx)("path",{d:"M19 13h-6v6h-2v-6H5v-2h6V5h2v6h6z"}),"Add");var Lt=f(M()),pM=f(Ne()),gM=f(xe()),ta=f(F());var oe=f(M()),bp=f(Ne()),S2=f(xe()),ir=f(F()),Q2=f(H()),v2=f(De());function Yv({session:e,newViewTitle:t,view:r,feature:n,msaFilehandle:o,treeFilehandle:i,querySeqName:a,data:s}){e.addView("MsaView",{type:"MsaView",displayName:t,connectedViewId:r.id,connectedFeature:n.toJSON(),msaFilehandle:o,treeFilehandle:i,querySeqName:a,data:s})}var ip=f(M()),Wv=f(F());function C5({children:e,...t}){return ip.default.createElement("div",null,ip.default.createElement(Wv.TextField,{...t},e))}var ut=C5;var ap=f(M()),zv=f(Ne()),$v=f(F()),Kv=f(De()),E5=(0,Kv.makeStyles)()({dialogContent:{width:"80em"}});function Cr({error:e,children:t}){let{classes:r}=E5();return ap.default.createElement($v.DialogContent,{className:r.dialogContent},e?ap.default.createElement(zv.ErrorMessage,{error:e}):null,t)}var gA=f(M()),Is=f(F());function dn({onSubmit:e,onCancel:t,submitDisabled:r,submitLabel:n="Submit",cancelLabel:o="Cancel"}){return gA.default.createElement(Is.DialogActions,null,gA.default.createElement(Is.Button,{color:"primary",variant:"contained",disabled:r,onClick:()=>{e()}},n),gA.default.createElement(Is.Button,{color:"secondary",variant:"contained",onClick:()=>{t()}},o))}var Er=f(M()),Wi=f(F()),e2=f(De());var Xv=f(M()),Zv=f(De());var x5=(0,Zv.makeStyles)()({textAreaFont:{fontFamily:"Courier New"}});function sp({value:e}){let{classes:t}=x5();return Xv.default.createElement(ut,{variant:"outlined",multiline:!0,minRows:5,maxRows:10,fullWidth:!0,value:e,slotProps:{input:{readOnly:!0,classes:{input:t.textAreaFont}}}})}var I5=(0,e2.makeStyles)()({flex:{display:"flex"},minWidth:{minWidth:300},centered:{alignContent:"center",marginLeft:20}});function xr({feature:e,options:t,selectedId:r,selectedTranscript:n,setSelectedId:o,proteinSequence:i,validIds:a}){let{classes:s}=I5(),[c,l]=(0,Er.useState)(!1);return Er.default.createElement(Er.default.Fragment,null,Er.default.createElement("div",{className:s.flex},Er.default.createElement(Wi.TextField,{variant:"outlined",label:`Choose isoform of ${Qo(e)}`,select:!0,className:s.minWidth,value:r,onChange:A=>{o(A.target.value)}},t.map(A=>{let u=a?a.some(p=>gs(A,p)):!0,{len:m,mod:d}=tA(A);return Er.default.createElement(Wi.MenuItem,{value:So(A),key:A.id(),disabled:!u},nA(A)," (",m," aa)"," ",d?" 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 /*! Bundled license information:
 
 react-is/cjs/react-is.production.min.js: