icn3d 3.25.7 → 3.25.9

package/icn3d.js

@@ -38626,12 +38626,12 @@ class Domain3d {
 
 		if (nsse <= 3)
 			// too small, can't split or trim
-			return {subdomains: subdomains, substruct: substruct};
+			return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi};
 
 		if (nsse > this.MAX_SSE) {
 			// we have a problem...
 
-			return {subdomains: subdomains, substruct: substruct};
+			return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi};
 		}
 
 		let seqLen = residueArray.length; // + resiOffset;
@@ -38903,7 +38903,7 @@ class Domain3d {
 				let k = prts[i] - 1;
 
 				if ((k < 0) || (k >= substruct.length)) {
-					return {subdomains: subdomains, substruct: substruct};
+					return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi};
 				}
 
 				//SSE_Rec sserec = substruct[k];
@@ -39020,7 +39020,7 @@ class Domain3d {
 			}
 		}
 				
-		return {subdomains: subdomains, substruct: substruct, pos2resi:pos2resi };
+		return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi };
 	} // end c2b_NewSplitChain
 
 	getDomainJsonForAlign(atoms) { let ic = this.icn3d, me = ic.icn3dui;
@@ -42024,18 +42024,18 @@ class ShowSeq {
             for(let il = strandArray.length, i = il - 1; i >= 0; --i) {
                 if(strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
                     if(i != il - 1) { // modify 
-                        strandArray[i + 1].loopResCnt += strandArray[i].endRefnum - strandArray[i].startRefnum + 1;
+                        strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + strandArray[i].endRefnum - strandArray[i].startRefnum + 1;
                     }
 
                     strandArray.splice(i, 1);
                 }
             }
-            
+
             // 3. assign refnumLabel for each resid
             strandCnt = 0;
             let loopCnt = 0;
 
-            let bNterminal = true, bCterminal = true, refnumLabelNoPostfix, prevStrandCnt = 0, currRefnum;
+            let bBeforeAstrand = true, bAfterGstrand = true, refnumLabelNoPostfix, prevStrandCnt = 0, currRefnum;
             bStart = false;
             let refnumInStrand = 0;
             if(strandArray.length > 0) {
@@ -42054,7 +42054,7 @@ class ShowSeq {
                         let firstChar = refnumLabel.substr(0,1);
                         if(!bStart && (firstChar == ' ' || firstChar == 'A' || firstChar == 'B')) { // start of a new IG domain
                             bStart = true;
-                            bNterminal = true;
+                            bBeforeAstrand = true;
                             loopCnt = 0;
                         }
                     }
@@ -42069,29 +42069,48 @@ class ShowSeq {
                         if(parseInt(currResi) < parseInt(strandArray[strandCnt].startResi)) {
                             ic.residIgLoop[residueid] = 1;
 
-                            if(bNterminal) { // make it continuous to the 1st strand
+                            if(bBeforeAstrand) { // make it continuous to the 1st strand
                                 if(bStart) {
                                     currRefnum = strandArray[strandCnt].startRefnum - strandArray[strandCnt].loopResCnt + loopCnt;
                                     refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
                                     refnumLabel = refnumLabelNoPostfix  + strandArray[strandCnt].strandPostfix;
-                                }                            
+                                }    
+                                else {
+                                    //loopCnt = 0;
+                                    refnumLabelNoPostfix = undefined;
+                                    refnumLabel = undefined;
+                                }                        
                             }
                             else {
-                                //currStrand = strandArray[prevStrandCnt].strand;
-
                                 if(prevStrandCnt >= 0 && strandArray[prevStrandCnt].strand.substr(0, 1) == 'G') {
-                                    if(bStart && ic.resid2refnum[residueid]) {
-                                        currRefnum = strandArray[prevStrandCnt].endRefnum + loopCnt;
-                                        refnumLabelNoPostfix = strandArray[prevStrandCnt].strand + currRefnum;
-                                        refnumLabel = refnumLabelNoPostfix  + strandArray[prevStrandCnt].strandPostfix; 
+                                    if(!bAfterGstrand) {
+                                        //loopCnt = 0;
+                                        refnumLabelNoPostfix = undefined;
+                                        refnumLabel = undefined;
                                     }
                                     else {
-                                        bStart = false;
-                                        bNterminal = true;
-                                        loopCnt = 0;
+                                        if(bStart && ic.resid2refnum[residueid]) {
+                                            bAfterGstrand = true;
+
+                                            currRefnum = strandArray[prevStrandCnt].endRefnum + loopCnt;
+                                            refnumLabelNoPostfix = strandArray[prevStrandCnt].strand + currRefnum;
+                                            refnumLabel = refnumLabelNoPostfix  + strandArray[prevStrandCnt].strandPostfix; 
+                                        }
+                                        else {
+                                            bStart = false;
+                                            bBeforeAstrand = true;
+                                            //loopCnt = 0;
+
+                                            bAfterGstrand = false;
+        
+                                            refnumLabelNoPostfix = undefined;
+                                            refnumLabel = undefined;
+                                        }
                                     }
                                 }
                                 else {
+                                    bAfterGstrand = true; // reset
+
                                     let len = strandArray[strandCnt].loopResCnt;
                                     let halfLen = parseInt(len / 2.0 + 0.5);
                         
@@ -42109,8 +42128,7 @@ class ShowSeq {
                             }
                         }
                         else if(parseInt(currResi) >= parseInt(strandArray[strandCnt].startResi) && parseInt(currResi) <= parseInt(strandArray[strandCnt].endResi)) {
-                            bNterminal = false;
-                            //bCterminal = true; // The next will be C-terminal
+                            bBeforeAstrand = false;
 
                             if(strandArray[strandCnt].anchorRefnum) { // use anchor to name refnum
                                 if(currResi == strandArray[strandCnt].startResi) {
@@ -42137,23 +42155,20 @@ class ShowSeq {
                         else if(parseInt(currResi) > parseInt(strandArray[strandCnt].endResi)) {     
                             ic.residIgLoop[residueid] = 1;    
 
-                            if(!bCterminal) {
+                            if(!bAfterGstrand) {
                                 refnumLabelNoPostfix = undefined;
                                 refnumLabel = undefined;
                             }
                             else {
                                 // C-terminal
                                 if(!ic.resid2refnum[residueid]) {
-                                    //break;
-
-                                    bCterminal = false;
-                                    //bNterminal = true; // The next will be N-terminal
+                                    bAfterGstrand = false;
 
                                     refnumLabelNoPostfix = undefined;
                                     refnumLabel = undefined;
                                 }
                                 else {
-                                    bCterminal = true;
+                                    bAfterGstrand = true;
 
                                     currRefnum = strandArray[strandCnt].endRefnum + loopCnt;
                                     refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
@@ -42289,7 +42304,8 @@ class ShowSeq {
         let color = this.getRefnumColor(currStrand, true);
         let colorStr = (!bLoop) ? 'style="color:' + color + '; text-decoration: underline overline;"' : 'style="color:' + color + '"';
 
-        let lastTwo = parseInt(refnum.substr(refnum.length - 2, 2));
+        let lastTwoStr = refnum.substr(refnum.length - 2, 2);
+        let lastTwo = parseInt(lastTwoStr);
         parseInt(refnum.substr(refnum.length - 3, 3));
 
         let html = '';
@@ -42302,7 +42318,7 @@ class ShowSeq {
         }
         else if(refnumLabel && lastTwo % 2 == 0 && lastTwo != 52 && !bHidelabel) { // don't show label for the first, middle, and last loop residues
             // e.g., 2152a
-            let lastTwoStr = isNaN(refnumStr) ? lastTwo + refnumStr.substr(refnumStr.length - 1, 1) : lastTwo;
+            lastTwoStr = isNaN(refnumStr) ? lastTwoStr + refnumStr.substr(refnumStr.length - 1, 1) : lastTwoStr;
             html += '<span ' + colorStr + ' title="' + refnumLabel + '">' + lastTwoStr + '</span>';
         }
         else {
@@ -70457,7 +70473,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.25.0';
+    this.REVISION = '3.25.1';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;