Merge pull request #104 in STRUC/icn3d from release252b to master

* commit 'b9d7a86c7718dccb8ac199f20c8187d4a4a3b864':
  The style Lines was fixed by replacing THREE.Line with THREE.LineSegments
  The style Lines was fixed by replacing THREE.Line with THREE.LineSegments
  The style Lines was fixed by replacing THREE.Line with THREE.LineSegments

README.md

@@ -42,7 +42,7 @@ See the [help page](https://www.ncbi.nlm.nih.gov/Structure/icn3d/docs/icn3d_help
 
 iCn3D can be embedded in a web page by including the URL in HTML iframe, e.g. <iframe src="https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1tup&showanno=1&show2d=1&showsets=1&width=800&height=450&showmenu=1&showcommand=1&rotate=right" width="900" height="600" style="border:none"></iframe>. This method always shows the most recent version of iCn3D.
 
-To embed iCn3D with JavaScript libraries, the following libraries need to be included: jQuery, jQuery UI, Three.js, and iCn3D library. An html div tag to hold the 3D viewer is added: "<div id='icn3dwrap'></div>". The iCn3D widget is initialized with the custom defined parameter "cfg": "var icn3dui = new iCn3DUI(cfg); icn3dui.show3DStructure();". Multiple iCn3D widgets can be embedded in a single page. 
+To embed iCn3D with JavaScript libraries, the following libraries need to be included: jQuery, jQuery UI, Three.js, and iCn3D library. An html div tag to hold the 3D viewer is added. The iCn3D widget is initialized with the custom defined parameter "cfg": "var icn3dui = new iCn3DUI(cfg); icn3dui.show3DStructure();". Multiple iCn3D widgets can be embedded in a single page. 
 
 Users can choose to show the most recent version of iCn3D, or a locked version of iCn3D. To show the most recent version, use the library files without the version postfix as shown in the [iCn3D Web API page] (https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#HowToUse). To show a locked version, use the library files with the version postfix as shown in the source code of [iCn3D page] (https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1tup). If the input is provided as an MMDB ID, both library files and backend cgis are versioned so that the 3D display will be stable. 
 

src/icn3dui/highlight/hl_update_simple.js

@@ -0,0 +1,99 @@
+/**
+ * @author Jiyao Wang <wangjiy@ncbi.nlm.nih.gov> / https://github.com/ncbi/icn3d
+ */
+
+iCn3DUI.prototype.removeHlAll = function() { var me = this;
+       me.removeHlObjects();
+};
+
+iCn3DUI.prototype.removeHlObjects = function() { var me = this;
+       me.icn3d.removeHlObjects();
+};
+
+iCn3DUI.prototype.updateHlAll = function(commandnameArray, bSetMenu, bUnion) { var me = this;
+       me.updateHlObjects();
+};
+
+iCn3DUI.prototype.updateHlObjects = function() { var me = this;
+       me.icn3d.removeHlObjects();
+       me.icn3d.addHlObjects();
+};
+
+iCn3DUI.prototype.toggleHighlight = function() { var me = this;
+    //me.setLogCmd("toggle highlight", true);
+
+    if(me.icn3d.prevHighlightObjects.length > 0 || me.icn3d.prevHighlightObjects_ghost.length > 0) { // remove
+        me.clearHighlight();
+    }
+    else { // add
+        me.showHighlight();
+    }
+
+    me.setLogCmd("toggle highlight", true);
+};
+
+iCn3DUI.prototype.clearHighlight = function() { var me = this;
+    me.icn3d.labels['picking']=[];
+    me.icn3d.draw();
+
+    me.icn3d.removeHlObjects();
+    me.icn3d.render();
+};
+
+iCn3DUI.prototype.showHighlight = function() { var me = this;
+    me.icn3d.addHlObjects();
+    me.updateHlAll();
+    //me.bSelectResidue = true;
+};
+
+iCn3DUI.prototype.selectAChain = function (chainid, commandname, bAlign, bUnion) { var me = this;
+    var commandname = commandname.replace(/\s/g, '');
+    var command = 'select chain ' + chainid;
+
+    //var residueHash = {}, chainHash = {};
+
+    if(bUnion === undefined || !bUnion) {
+        me.icn3d.hAtoms = {};
+        me.menuHlHash = {};
+    }
+    else {
+        me.icn3d.hAtoms = me.icn3d.unionHash(me.icn3d.hAtoms, me.icn3d.chains[chainid]);
+
+        if(me.menuHlHash === undefined) me.menuHlHash = {};
+    }
+
+    me.menuHlHash[chainid] = 1;
+
+    //chainHash[chainid] = 1;
+
+    var chnsSeq = (bAlign) ? me.icn3d.alnChainsSeq[chainid] : me.icn3d.chainsSeq[chainid];
+
+    var oriResidueHash = {};
+    for(var i = 0, il = chnsSeq.length; i < il; ++i) { // get residue number
+        var resObj = chnsSeq[i];
+        var residueid = chainid + "_" + resObj.resi;
+
+        var value = resObj.name;
+
+        if(value !== '' && value !== '-') {
+          oriResidueHash[residueid] = 1;
+          for(var j in me.icn3d.residues[residueid]) {
+            me.icn3d.hAtoms[j] = 1;
+          }
+        }
+    }
+
+    if((me.icn3d.defNames2Atoms === undefined || !me.icn3d.defNames2Atoms.hasOwnProperty(chainid)) && (me.icn3d.defNames2Residues === undefined || !me.icn3d.defNames2Residues.hasOwnProperty(chainid)) ) {
+        me.addCustomSelection(Object.keys(oriResidueHash), commandname, commandname, command, true);
+    }
+
+    if(bAlign) {
+        me.updateHlAll(undefined, undefined, bUnion);
+    }
+    else {
+        me.updateHlAll(Object.keys(me.menuHlHash), undefined, bUnion);
+    }
+
+//        me.icn3d.addHlObjects();
+//        me.updateHl2D(Object.keys(chainHash));
+};