icn3d 3.25.10 → 3.25.11

package/icn3d.js

@@ -32289,7 +32289,7 @@ class Alternate {
         ic.impostorCls.clearImpostors();
 
         // show membranes
-        if(ic.bOpm) {
+        if(ic.bOpm && !me.cfg.chainalign) {
             //if(window.dialog && window.dialog.hasClass('ui-dialog-content')) window.dialog.dialog( "close" );
             
             let html = me.utilsCls.getMemDesc();
@@ -41362,6 +41362,10 @@ class ShowAnno {
         }
     }
     getColorhexFromBlosum62(resA, resB) { let ic = this.icn3d, me = ic.icn3dui;
+        let color = '333333';
+
+        if(!resA || !resB) return color;
+        
         resA = resA.toUpperCase();
         resB = resB.toUpperCase();
 
@@ -41371,7 +41375,7 @@ class ShowAnno {
         if(matrixValue === undefined) return '333333';
         // range and color: blue for -4 ~ 0, red for 0 ~ 11
         // max value 221 to avoid white
-        let color = '333333';
+        
         if(matrixValue > 0) {
             let c = 221 - parseInt(matrixValue / 11.0 * 221);
             let cStr =(c < 10) ? '0' + c.toString(16) : c.toString(16);
@@ -42029,7 +42033,9 @@ 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].loopResCnt + strandArray[i].endRefnum - strandArray[i].startRefnum + 1;
+                        // strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + strandArray[i].endRefnum - strandArray[i].startRefnum + 1;
+
+                        strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + parseInt(strandArray[i].endResi) - parseInt(strandArray[i].startResi) + 1;
                     }
 
                     strandArray.splice(i, 1);
@@ -51858,7 +51864,7 @@ class ParserUtils {
               if(rmsd) {
                   me.htmlCls.clickMenuCls.setLogCmd("realignment RMSD: " + rmsd.toPrecision(4), false);
                   let html = "<br><b>Realignment RMSD</b>: " + rmsd.toPrecision(4) + " &#8491;<br><br>";
-                  if(ic.bAfMem) {
+                  if(ic.bAfMem && !me.cfg.chainalign) {
                     //if(window.dialog && window.dialog.hasClass('ui-dialog-content')) window.dialog.dialog( "close" );
                     html += me.utilsCls.getMemDesc();
                   }
@@ -62547,18 +62553,35 @@ class Scap {
         }
     }
 
-    adjust2DWidth(id) { let ic = this.icn3d, me = ic.icn3dui;
-        let halfWidth = 125;
+    adjust2DWidth(id) { let ic = this.icn3d; ic.icn3dui;
         id = ic.pre + id;
-
+/*
         let height =($("#" + ic.pre + 'dl_selectannotations').hasClass("ui-dialog-content")) ? $("#" + ic.pre + 'dl_selectannotations').dialog( "option", "height") : me.htmlCls.HEIGHT;
         let width =($("#" + ic.pre + 'dl_selectannotations').hasClass("ui-dialog-content")) ? halfWidth * 2 : me.htmlCls.WIDTH * 0.5;
 
         $("#" + id).dialog( "option", "width", width );
         $("#" + id).dialog( "option", "height", height);
-        let position = { my: "left-" + halfWidth + " top+" + me.htmlCls.MENU_HEIGHT, at: "right top", of: "#" + ic.pre + "viewer", collision: "none" };
+        let position = { my: "left-" + halfWidth + " top+" + me.htmlCls.MENU_HEIGHT, at: "right top", of: "#" + ic.pre + "viewer", collision: "none" }
 
-         $("#" + id).dialog( "option", "position", position );
+        $("#" + id).dialog( "option", "position", position );
+*/
+
+        let width, height, top;
+        
+        if($("#" + ic.pre + 'dl_selectannotations').hasClass("ui-dialog-content")) {
+          width = $("#" + ic.pre + 'dl_selectannotations').dialog( "option", "width");
+          height = $("#" + ic.pre + 'dl_selectannotations').dialog( "option", "height") * 0.5;
+          top = height;
+
+          $("#" + ic.pre + "dl_selectannotations").dialog( "option", "height", height);
+
+          $("#" + id).dialog( "option", "width", width );
+          $("#" + id).dialog( "option", "height", height);
+          
+          let position = { my: "left top", at: "right top+" + top, of: "#" + ic.pre + "viewer", collision: "none" };
+  
+          $("#" + id).dialog( "option", "position", position );
+        }
     }
 
     async retrieveScap(snp, bInteraction, bPdb) { let ic = this.icn3d, me = ic.icn3dui;