icn3d 3.25.6 → 3.25.8

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;
@@ -41923,9 +41923,9 @@ class ShowSeq {
         let index = 1, bStart = false;
         
         // 1. get the range of each strand excluding loops
-        let strandArray = [], strandHash = {}, strandCnt = 0, resCnt = 0, resCntBfAnchor = 0;
+        let strandArray = [], strandHash = {}, strandCnt = 0, resCnt = 0, resCntBfAnchor = 0, resCntAtAnchor = 0;
         if(!bCustom && !kabat_or_imgt) {
-            for(let i = 0, il = giSeq.length; i < il; ++i, ++resCnt, ++resCntBfAnchor) {
+            for(let i = 0, il = giSeq.length; i < il; ++i, ++resCnt, ++resCntBfAnchor, ++resCntAtAnchor) {
                 let currResi = ic.ParserUtilsCls.getResi(chnid, i);
                 let residueid = chnid + '_' + currResi;
                 refnumLabel = ic.resid2refnum[residueid];
@@ -41976,6 +41976,8 @@ class ShowSeq {
                                 if(lastTwo == 50) {
                                     strandArray[strandCnt].anchorRefnum = refnum;
                                     strandArray[strandCnt].resCntBfAnchor = resCntBfAnchor;
+
+                                    resCntAtAnchor = 0;
                                 }
 
                                 strandArray[strandCnt].strandPostfix = strandPostfix; // a in A1250a
@@ -41990,12 +41992,22 @@ class ShowSeq {
                             }
                             else {
                                 if(strandHash[currStrand + postfix]) {
-                                    strandArray[strandCnt - 1].endResi = currResi;
-                                    strandArray[strandCnt - 1].endRefnum = refnum; // 1250a
-
                                     if(lastTwo == 50) {
                                         strandArray[strandCnt - 1].anchorRefnum = refnum;
                                         strandArray[strandCnt - 1].resCntBfAnchor = resCntBfAnchor;
+
+                                        // update
+                                        strandArray[strandCnt - 1].startRefnum = strandArray[strandCnt - 1].anchorRefnum - strandArray[strandCnt - 1].resCntBfAnchor;
+
+                                        resCntAtAnchor = 0;
+                                    }
+
+                                    strandArray[strandCnt - 1].endResi = currResi;
+                                    strandArray[strandCnt - 1].endRefnum = refnum; // 1250a
+                                    strandArray[strandCnt - 1].resCntAtAnchor = resCntAtAnchor;
+
+                                    if(strandArray[strandCnt - 1].anchorRefnum) {
+                                        strandArray[strandCnt - 1].endRefnum = strandArray[strandCnt - 1].anchorRefnum + strandArray[strandCnt - 1].resCntAtAnchor;
                                     }
 
                                     resCnt = 0;
@@ -42018,12 +42030,12 @@ class ShowSeq {
                     strandArray.splice(i, 1);
                 }
             }
-
+            
             // 3. assign refnumLabel for each resid
             strandCnt = 0;
             let loopCnt = 0;
 
-            let bNterminal = true, refnumLabelNoPostfix, prevStrandCnt = 0, currRefnum;
+            let bNterminal = true, bCterminal = true, refnumLabelNoPostfix, prevStrandCnt = 0, currRefnum;
             bStart = false;
             let refnumInStrand = 0;
             if(strandArray.length > 0) {
@@ -42098,6 +42110,7 @@ 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
 
                             if(strandArray[strandCnt].anchorRefnum) { // use anchor to name refnum
                                 if(currResi == strandArray[strandCnt].startResi) {
@@ -42124,14 +42137,28 @@ class ShowSeq {
                         else if(parseInt(currResi) > parseInt(strandArray[strandCnt].endResi)) {     
                             ic.residIgLoop[residueid] = 1;    
 
-                            // C-terminal
-                            if(!ic.resid2refnum[residueid]) {
-                                break;
+                            if(!bCterminal) {
+                                refnumLabelNoPostfix = undefined;
+                                refnumLabel = undefined;
                             }
                             else {
-                                currRefnum = strandArray[strandCnt].endRefnum + loopCnt;
-                                refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
-                                refnumLabel = refnumLabelNoPostfix  + strandArray[strandCnt].strandPostfix; 
+                                // C-terminal
+                                if(!ic.resid2refnum[residueid]) {
+                                    //break;
+
+                                    bCterminal = false;
+                                    //bNterminal = true; // The next will be N-terminal
+
+                                    refnumLabelNoPostfix = undefined;
+                                    refnumLabel = undefined;
+                                }
+                                else {
+                                    bCterminal = true;
+
+                                    currRefnum = strandArray[strandCnt].endRefnum + loopCnt;
+                                    refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
+                                    refnumLabel = refnumLabelNoPostfix  + strandArray[strandCnt].strandPostfix; 
+                                }
                             }
                         }
                     }
@@ -62320,7 +62347,7 @@ if(!me.bNode) {
                     prevStrand = (refnumLabel) ? refnumLabel.replace(new RegExp(refnum,'g'), '') : undefined;
 
                     ic.resid2refnum[resid] = refnumLabel;
-console.log(resid + " " + refnumLabel);
+
                     // final reference numbers will be assign in ic.showSeqCls.showRefNum()
 
                     // if(!ic.refnum2residArray.hasOwnProperty(refnum)) {
@@ -70430,7 +70457,7 @@ 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;