icn3d 3.28.2 → 3.28.4

package/icn3d.js

@@ -11612,10 +11612,10 @@ class SetDialog {
 
         html += "<b>Position of the first residue in Sequences & Annotations window</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "fasta_startpos2' value='1' size=2> <br><br>";
 
-        html += "Color Sequence by: <select id='" + me.pre + "colorseqby2'>";
-        html += me.htmlCls.optionStr + "'identity' selected>Identity</option>";
-        html += me.htmlCls.optionStr + "'conservation'>Conservation</option>";
-        html += "</select> <br><br>";
+        // html += "Color Sequence by: <select id='" + me.pre + "colorseqby2'>";
+        // html += me.htmlCls.optionStr + "'identity' selected>Identity</option>";
+        // html += me.htmlCls.optionStr + "'conservation'>Conservation</option>";
+        // html += "</select> <br><br>";
 
         html += me.htmlCls.buttonStr + "addtrack_button2c'>Show Isoforms & Exons</button>";
         html += "</div>";
@@ -30574,7 +30574,6 @@ class ApplySymd {
                 }
                 else { // bSymd, subset, and one chain
                     if(Object.keys(ic.hAtoms).length == 0) {
-                        //ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
                         ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
                     }
 
@@ -35560,6 +35559,9 @@ class SetOption {
         else if(colorType == 'ig protodomain') {
             colorLabel = 'Ig Protodomain';
         }
+        else if(colorType == 'exon') {
+            colorLabel = 'Exon';
+        }
 
         let html = "Color by <b>" + colorLabel + "</b><br><br>";
  
@@ -35652,6 +35654,17 @@ class SetOption {
         else if (colorType == 'confidence') {
             html += me.htmlCls.clickMenuCls.setLegendHtml(true);
         }
+        else if (colorType == 'exon') {
+            ic.startColor = 'red';
+            ic.midColor = 'white';
+            ic.endColor = 'blue';
+
+            ic.startValue = 'Start';
+            ic.midValue = 'Middle';
+            ic.endValue = 'End';
+
+            html += me.htmlCls.clickMenuCls.setLegendHtml();
+        }
         else {
             html = '';
         }
@@ -35660,6 +35673,9 @@ class SetOption {
             $("#" + me.pre + "dl_legend_html").html(html);
             me.htmlCls.dialogCls.openDlg('dl_legend', 'Color Legend');
         }
+        else {
+            $("#" + me.pre + "dl_legend").dialog("close");
+        }
 
         // if(bClose) {
         //     if(window.dialog && window.dialog.hasClass('ui-dialog-content')) window.dialog.dialog( "close" );
@@ -39456,8 +39472,10 @@ class AddTrack {
             let startpos = $("#" + ic.pre + "fasta_startpos2").val();
             if(!startpos) startpos = 1;
 
-            let colorseqby = $("#" + ic.pre + "colorseqby2").val();
-            let type =(colorseqby == 'identity') ? 'identity' : 'custom';
+            //let colorseqby = $("#" + ic.pre + "colorseqby2").val();
+            //let type =(colorseqby == 'identity') ? 'identity' : 'custom';
+
+            let type = 'identity';
     
             await thisClass.addExonTracks(chainid, geneid, startpos, type);
         });
@@ -39813,6 +39831,13 @@ class AddTrack {
               let tmpStrExon = 'style="background-color:' + pos2exonColor[cnt] + '"';
               htmlExon += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" title="' + c + pos + ', Exon ' + (pos2exonIndex[cnt] + 1) + ': ' + pos2genome[cnt] + '" class="icn3d-residue" ' + tmpStrExon + '>&nbsp;</span>';
 
+              // set atom color
+              for(let serial in ic.residues[chnid + '_' + pos]) {
+                let atom = ic.atoms[serial];
+                atom.color = me.parasCls.thr(pos2exonColor[cnt]);
+                ic.atomPrevColors[serial] = atom.color;
+              }
+
               htmlTmp2 += ic.showSeqCls.insertGapOverview(chnid, i);
 
             //   let emptyWidth =(me.cfg.blast_rep_id == chnid) ? Math.round(ic.seqAnnWidth * i /(ic.maxAnnoLength + ic.nTotalGap) - prevEmptyWidth - prevLineWidth) : Math.round(ic.seqAnnWidth * i / ic.maxAnnoLength - prevEmptyWidth - prevLineWidth);
@@ -40925,6 +40950,14 @@ class AddTrack {
             let exonArray = (acc2exons) ? acc2exons[trackTitleArray[j]] : undefined;
             this.showNewTrack(chainid, title, text, undefined, undefined, type, undefined, bMsa, fromArray, toArray, seqStartLen, exonArray);
         }
+
+        // update exon color
+        ic.opts['color'] = 'exon';
+        ic.legendTableCls.showColorLegend(ic.opts['color']);
+
+        ic.hlUpdateCls.updateHlAll();
+        ic.drawCls.draw();
+
 /*
         // set color for the master seq
         if(trackSeqArray.length > 0) {
@@ -41961,23 +41994,26 @@ class ShowAnno {
             let structure = chnid.substr(0, chnid.indexOf('_'));
             // UniProt or NCBI protein accession
             if(structure.length > 5) {
-                let refseqid, url;
+                let url;
                 if(ic.uniprot2acc && ic.uniprot2acc[structure]) {
-                    refseqid = ic.uniprot2acc[structure];
+                    ic.uniprot2acc[structure];
                 }
                 else {
-                    try {
-                        if(!ic.uniprot2acc) ic.uniprot2acc = {};
-                        url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?uniprot2refseq=" + structure;
-                        let result = await me.getAjaxPromise(url, 'jsonp');
-                        refseqid = (result && result.refseq) ? result.refseq : structure;
+                    ic.uniprot2acc = {};
 
-                        ic.uniprot2acc[structure] = refseqid;
-                    }
-                    catch {
-                        console.log("Problem in getting protein accession from UniProt ID...");
-                        refseqid = structure;
-                    }
+                    // try {
+                    //     if(!ic.uniprot2acc) ic.uniprot2acc = {};
+                    // the following query is slow due to the missing index in DB
+                    //     url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?uniprot2refseq=" + structure;
+                    //     let result = await me.getAjaxPromise(url, 'jsonp');
+                    //     refseqid = (result && result.refseq) ? result.refseq : structure;
+
+                    //     ic.uniprot2acc[structure] = refseqid;
+                    // }
+                    // catch {
+                    //     console.log("Problem in getting protein accession from UniProt ID...")
+                    //     refseqid = structure;
+                    // }
                 }
 
                 // get Gene info from protein name
@@ -49685,16 +49721,16 @@ class ChainalignParser {
             // try {
                 let data = await me.getAjaxPromise(url, 'jsonp');
 
-                let mmdbid = data.mmdbid;
-                ic.selectedPdbid = mmdbid;
-                
-                if(!mmdbid) {
+                if(!data || !data.mmdbid) {
                   if(!ic.bCommandLoad) ic.init(); // remove all previously loaded data
                   await thisClass.downloadChainalignmentPart2(data1, data2, undefined, chainidArray);
 
                   /// if(ic.deferredOpm !== undefined) ic.deferredOpm.resolve();
                 }
                 else {
+                    let mmdbid = data.mmdbid;
+                    ic.selectedPdbid = mmdbid;
+
                     let url2 = "https://opm-assets.storage.googleapis.com/pdb/" + mmdbid.toLowerCase()+ ".pdb";
 
                     // try {
@@ -60892,9 +60928,9 @@ class DefinedSets {
        this.setHAtomsFromSets(orArray, 'or');
 
        if(Object.keys(ic.hAtoms).length == 0) {
-           //ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
            ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
        }
+
        this.setHAtomsFromSets(andArray, 'and');
 
        this.setHAtomsFromSets(notArray, 'not');
@@ -62749,7 +62785,6 @@ class Selection {
         //ic.dAtoms = {};
 
         if(Object.keys(ic.hAtoms).length == 0) {
-            //this.selectAll_base();
             ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
         }
 
@@ -62790,9 +62825,12 @@ class Selection {
     }
 
     hideSelection() { let ic = this.icn3d, me = ic.icn3dui;
-        ic.dAtoms = me.hashUtilsCls.exclHash(ic.dAtoms, ic.hAtoms);
+        ic.hAtoms = me.hashUtilsCls.exclHash(ic.dAtoms, ic.hAtoms);
+        if(Object.keys(ic.hAtoms).length == 0) {
+            ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
+        }
 
-        ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
+        ic.dAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
 
         let centerAtomsResults = ic.applyCenterCls.centerAtoms(me.hashUtilsCls.hash2Atoms(ic.dAtoms, ic.atoms));
         ic.maxD = centerAtomsResults.maxD;