icn3d 3.25.2 → 3.25.4

package/icn3d.js

@@ -15291,7 +15291,7 @@ class SetHtml {
        let matchedStrState = "Start of state file======\n";
        let posState = imageStr.indexOf(matchedStrState);
        if(pos == -1 && posState == -1) {
-           var aaa = 1; //alert('Please load a PNG image saved by clicking "Save Datas > PNG Image" in the Data menu...');
+           var aaa = 1; //alert('Please load a PNG image saved by clicking the menu "File > Save File > iCn3D PNG Image"...');
        }
        else if(pos != -1) {
            let url = imageStr.substr(pos + matchedStr.length);
@@ -41922,10 +41922,10 @@ class ShowSeq {
         // sometimes one chain may have several Ig domains,set an index for each IgDomain
         let index = 1, bStart = false;
         
-        // get the range of each strand excluding loops
-        let strandArray = [], strandHash = {}, strandCnt = 0, resCnt = 0;
+        // 1. get the range of each strand excluding loops
+        let strandArray = [], strandHash = {}, strandCnt = 0, resCnt = 0, resCntBfAnchor = 0;
         if(!bCustom && !kabat_or_imgt) {
-            for(let i = 0, il = giSeq.length; i < il; ++i, ++resCnt) {
+            for(let i = 0, il = giSeq.length; i < il; ++i, ++resCnt, ++resCntBfAnchor) {
                 let currResi = ic.ParserUtilsCls.getResi(chnid, i);
                 let residueid = chnid + '_' + currResi;
                 refnumLabel = ic.resid2refnum[residueid];
@@ -41954,6 +41954,8 @@ class ShowSeq {
 
                     if(currStrand && currStrand != ' ') {
                         if(refnum3c.substr(0,1) != '9') {
+                            let lastTwo = parseInt(refnum.toString().substr(refnum.toString().length - 2, 2));
+                            
                             if(currStrand != prevStrand) { // reset currCnt
                                 if(strandHash[currStrand + postfix]) {
                                     ++index;
@@ -41965,10 +41967,17 @@ class ShowSeq {
                                 strandArray[strandCnt] = {};    
                                 strandArray[strandCnt].startResi = currResi;
                                 strandArray[strandCnt].startRefnum = refnum; // 1250 in A1250a
+
+                                resCntBfAnchor = 0;
                                 
                                 strandArray[strandCnt].endResi = currResi;
                                 strandArray[strandCnt].endRefnum = refnum; // 1250a
 
+                                if(lastTwo == 50) {
+                                    strandArray[strandCnt].anchorRefnum = refnum;
+                                    strandArray[strandCnt].resCntBfAnchor = resCntBfAnchor;
+                                }
+
                                 strandArray[strandCnt].strandPostfix = strandPostfix; // a in A1250a
                                 strandArray[strandCnt].strand = currStrand; // A in A1250a
 
@@ -41984,6 +41993,11 @@ class ShowSeq {
                                     strandArray[strandCnt - 1].endResi = currResi;
                                     strandArray[strandCnt - 1].endRefnum = refnum; // 1250a
 
+                                    if(lastTwo == 50) {
+                                        strandArray[strandCnt - 1].anchorRefnum = refnum;
+                                        strandArray[strandCnt - 1].resCntBfAnchor = resCntBfAnchor;
+                                    }
+
                                     resCnt = 0;
                                 }
                             }
@@ -41994,13 +42008,22 @@ class ShowSeq {
                 prevStrand = currStrand;
             }
 
+            // 2. remove strands with less than 3 residues
+            for(let il = strandArray.length, i = il - 1; i >= 0; --i) {
+                if(strandArray[i].endRefnum - strandArray[i].startRefnum < 3 - 1) { // remove the strand
+                    strandArray.splice(i, 1);
+                }
+            }
+
+            // 3. assign refnumLabel for each resid
             strandCnt = 0;
             let loopCnt = 0;
 
             let bNterminal = true, refnumLabelNoPostfix, prevStrandCnt = 0, currRefnum;
             bStart = false;
+            let refnumInStrand = 0;
             if(strandArray.length > 0) {
-                for(let i = 0, il = giSeq.length; i < il; ++i, ++loopCnt) {
+                for(let i = 0, il = giSeq.length; i < il; ++i, ++loopCnt, ++refnumInStrand) {
                     let currResi = ic.ParserUtilsCls.getResi(chnid, i);
                     let residueid = chnid + '_' + currResi;
                     refnumLabel = ic.resid2refnum[residueid];
@@ -42072,6 +42095,15 @@ class ShowSeq {
                         else if(parseInt(currResi) >= parseInt(strandArray[strandCnt].startResi) && parseInt(currResi) <= parseInt(strandArray[strandCnt].endResi)) {
                             bNterminal = false;
 
+                            if(strandArray[strandCnt].anchorRefnum) { // use anchor to name refnum
+                                if(currResi == strandArray[strandCnt].startResi) {
+                                    refnumInStrand = strandArray[strandCnt].anchorRefnum - strandArray[strandCnt].resCntBfAnchor;
+                                }
+
+                                refnumLabelNoPostfix = strandArray[strandCnt].strand + refnumInStrand;
+                                refnumLabel = refnumLabelNoPostfix  + strandArray[strandCnt].strandPostfix; 
+                            }
+
                             if(currResi == strandArray[strandCnt].endResi) {
                                 ++strandCnt; // next strand
                                 loopCnt = 0;
@@ -44096,7 +44128,11 @@ class GetGraph {
         let fontsize = '6px'; // '6';
         //let html = (bAfMap) ? "<g>" : "<g class='icn3d-node' resid='" + resid + "' >";
         let html = "<g class='icn3d-node' resid='" + resid + "' >";
-        html += "<title>" + node.id + "</title>";
+        let title = node.id;
+        if(ic.resid2refnum[resid]) {
+            title += '=>' + ic.resid2refnum[resid];
+        }
+        html += "<title>" + title + "</title>";
         if(bVertical) {
             html += "<circle cx='" + y + "' cy='" + x + "' r='" + r + "' fill='" + color + "' stroke-width='" + strokewidth + "' stroke='" + strokecolor + "' resid='" + resid + "' />";
             html += "<text x='" +(y - 20).toString() + "' y='" +(x + 2).toString() + "' fill='" + textcolor + "' stroke='none' style='font-size:" + fontsize + "; text-anchor:middle' >" + nodeName + "</text>";
@@ -50276,7 +50312,7 @@ class RealignParser {
 
     async realignOnStructAlign() { let ic = this.icn3d, me = ic.icn3dui;
         // each 3D domain should have at least 3 secondary structures
-        let minSseCnt = 3;
+        let minSseCnt = (me.cfg.aligntool != 'tmalign') ? 3 : 0;
         let struct2domain = {};
         for(let struct in ic.structures) {
             struct2domain[struct] = {};
@@ -66315,7 +66351,7 @@ class SaveFile {
             if(me.utilsCls.isIE()) {
                 blob = ic.renderer.domElement.msToBlob();
 
-                if(bAddURL && typeof(blob) == 'Blob') {
+                if(bAddURL) {
                     let reader = new FileReader();
                     reader.onload = function(e) {
                         let arrayBuffer = e.target.result; // or = reader.result;
@@ -66341,7 +66377,7 @@ class SaveFile {
             }
             else {
                 ic.renderer.domElement.toBlob(function(data) {
-                    if(bAddURL && typeof(blob) == 'data') {
+                    if(bAddURL) {
                         let reader = new FileReader();
                         reader.onload = function(e) {
                             let arrayBuffer = e.target.result; // or = reader.result;