icn3d 3.28.0 → 3.28.2

package/icn3d.js

@@ -40790,7 +40790,7 @@ class AddTrack {
 
     async showMsaTracks(chainid, seqFirst, trackTitleArray, trackSeqArray, startpos, type, acc2exons) { let ic = this.icn3d; ic.icn3dui;
         //ic.startposGiSeq = undefined;
-        for(let i = 0, il = ic.giSeq[chainid].length; i < il; ++i) {
+        for(let i = 0, il = ic.chainsSeq[chainid].length; i < il; ++i) {
             //let pos =(i >= ic.matchedPos[chainid] && i - ic.matchedPos[chainid] < ic.chainsSeq, [chainid].length) ? ic.chainsSeq[chainid][i - ic.matchedPos[chainid]].resi : ic.baseResi[chainid] + 1 + i;
             let pos = ic.ParserUtilsCls.getResi(chainid, i);
 
@@ -40925,11 +40925,11 @@ class AddTrack {
             let exonArray = (acc2exons) ? acc2exons[trackTitleArray[j]] : undefined;
             this.showNewTrack(chainid, title, text, undefined, undefined, type, undefined, bMsa, fromArray, toArray, seqStartLen, exonArray);
         }
-
+/*
         // set color for the master seq
         if(trackSeqArray.length > 0) {
-            if(ic.queryresi2score === undefined) ic.queryresi2score = {};
-            if(ic.queryresi2score[chainid] === undefined) ic.queryresi2score[chainid] = {};
+            if(ic.queryresi2score === undefined) ic.queryresi2score = {}
+            if(ic.queryresi2score[chainid] === undefined) ic.queryresi2score[chainid] = {}
 
             let nSeq = trackSeqArray.length;
             for(let resi in resi2cntSameRes) {
@@ -40960,6 +40960,7 @@ class AddTrack {
 
             //me.htmlCls.clickMenuCls.setLogCmd('color align custom | ' + chainid + ' | range ' + start + '_' + end + ' | ' + resiScoreStr, true);
         }
+        */
     }
 
     processAccList(acclist) { let ic = this.icn3d; ic.icn3dui;
@@ -40994,6 +40995,8 @@ class AddTrack {
     }
 
     async addExonTracks(chainid, geneid, startpos, type) { let ic = this.icn3d, me = ic.icn3dui;
+        let thisClass = this;
+
         let seqFirst, trackTitleArray = [], trackSeqArray = [];
 
         // get acclist from geneid
@@ -41102,12 +41105,14 @@ class AddTrack {
             ++j;
         }
 
-        await this.showMsaTracks(chainid, seqFirst, trackTitleArray, trackSeqArray, startpos, type, acc2exons);
+        await thisClass.showMsaTracks(chainid, seqFirst, trackTitleArray, trackSeqArray, startpos, type, acc2exons);
 
         me.htmlCls.clickMenuCls.setLogCmd("add exon track | chainid " + chainid + " | geneid " + geneid + " | startpos " + startpos + " | type " + type, true);
     }
 
     async addMsaTracks(chainid, startpos, type, fastaList) { let ic = this.icn3d, me = ic.icn3dui;
+        let thisClass = this;
+
         let seqFirst, trackTitleArray = [], trackSeqArray = [];
 
         let fastaArray = fastaList.split('>');
@@ -41132,8 +41137,8 @@ class AddTrack {
             trackSeqArray.push(seq);
         }
 
-        await this.showMsaTracks(chainid, seqFirst, trackTitleArray, trackSeqArray, startpos, type);
-
+        await thisClass.showMsaTracks(chainid, seqFirst, trackTitleArray, trackSeqArray, startpos, type);
+        
         me.htmlCls.clickMenuCls.setLogCmd("add msa track | chainid " + chainid + " | startpos " + startpos + " | type " + type + " | fastaList " + fastaList , true);
     }
 }
@@ -41982,8 +41987,8 @@ class ShowAnno {
                 // get Gene info from uniprot
                 url = "https://rest.uniprot.org/uniprotkb/search?format=json&fields=xref_geneid,gene_names&query=" + structure;
                 let geneData = await me.getAjaxPromise(url, 'json');
-                let geneId = (geneData.results[0] && geneData.results[0].uniProtKBCrossReferences[0]) ? geneData.results[0].uniProtKBCrossReferences[0].id : undefined;
-                let geneSymbol = (geneData.results[0] && geneData.results[0].genes[0] && geneData.results[0].genes[0].geneName) ? geneData.results[0].genes[0].geneName.value : undefined;
+                let geneId = (geneData.results[0] && geneData.results[0].uniProtKBCrossReferences && geneData.results[0].uniProtKBCrossReferences[0]) ? geneData.results[0].uniProtKBCrossReferences[0].id : undefined;
+                let geneSymbol = (geneData.results[0] && geneData.results[0].genes && geneData.results[0].genes[0] && geneData.results[0].genes[0].geneName) ? geneData.results[0].genes[0].geneName.value : undefined;
                 ic.chainsGene[chnid] = {geneId: geneId, geneSymbol: geneSymbol};
             }
         }