X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Fjavascript%2Fjalview.js;h=1c1f1c2cc49107d372441c859122bf24a9e3a83c;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=66c5a3ee9b87df2741d0cb7ab4f4ce4cc56d970a;hpb=9e3e20c98eae9498a68bb0a770359564797a12ef;p=jalview.git

diff --git a/examples/javascript/jalview.js b/examples/javascript/jalview.js
index 66c5a3e..1c1f1c2 100644
--- a/examples/javascript/jalview.js
+++ b/examples/javascript/jalview.js
@@ -1,309 +1,380 @@
-// default console to report messages
-var _console = document.getElementById("stdout");
-var _jvapps = new Array();
-// jvjmols is a list associating a jmol id to { modelstofiles }
-var _jvjmols = new Hashtable();
-// array of model names used to lookup index in Jmol
-var _modeltofiles = new Array();
-// counter for jmol structures
-var mnum = 1;
-
-function setConsole(console) {
-	_console = console;
-}
-
-function getDestinationFrms(source, frames) {
-	var frms = new Array();
-	var frid = "";
-	for (frm in frames) {
-		try {
-			frid = (source!=null) && (("" + source.getSequenceSetId()) == ("" + frames[frm].currentAlignFrame
-					.getSequenceSetId()));
-		} catch (q) {
-		};
-		
-		if (!frames[frm].equals(source) && !frid
-				&& !frames[frm].currentAlignFrame.equals(source)) {
-			frms[frms.length] = frames[frm];
-		}
-	}
-	return frms;
-}
-
-function mouseover(list1, list2, list3, list4) {
-	// list1 = new Object(list1);
-	var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
-	var msg = "Mouse over :\n" + "AlignFrame obj: " + list1 + " Seq : "
-			+ list[1] + "\nPos: " + list[2] + "(" + list[3] + ")\n";
-
-	var flist = getDestinationFrms(list1, _jvapps);
-	if (_console) {
-		_console.value = msg + "\n";
-	}
-
-	for (follower in flist) {
-		if (_console) {
-			_console.value += "Sending to " + flist[follower] + "\n";
-		}
-		flist[follower].highlight(list[1], list[2], "true");
-	}
-	return true;
-}
-
-function sellist(list1, list2, list3, list4) {
-	// list1 = new Object(list1);
-	var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
-	var msg = "Selection:\n" + "AlignFrame obj: " + list[0] + " id : "
-			+ list[1] + "\nSeqs " + list[2] + "\nColumns " + list[3] + "\n";
-	var flist = getDestinationFrms(list1, _jvapps);
-	if (_console) {
-		_console.value = msg + "\n";
-	}
-	
-	for (follower in flist) {
-		if (_console) {
-			_console.value += "Sending to " + flist[follower] + "\n";
-		}
-		flist[follower].selectIn(flist[follower].getDefaultTargetFrame(),
-				list[2], list[3])
-	}
-	return true;
-}
-
-function viewlist(list1, list2, list3, list4) {
-	// list1 = new Object(list1);
-	var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
-	var msg = "Viewport extent change::\n" + "AlignFrame obj: " + list[0]
-			+ " id : " + list[1] + "\nRow from " + list[2] + " and to "
-			+ list[3] + "\nVisible columns: " + list[4] + "\n";
-	var flist = getDestinationFrms(list1, _jvapps);
-	if (_console) {
-		_console.value = msg + "\n";
-	}
-
-	for (follower in flist) {
-		if (_console) {
-			_console.value += "Sending to " + flist[follower] + "\n";
-		}
-		flist[follower].scrollToViewIn(flist[follower].getDefaultTargetFrame(),
-				list[2], "-1");
-	}
-	return true;
-}
-
-// register a jalview applet and add some handlers to it
-// jmolView is a reference to a jmol applet that is displaying the PDB files listed (in order) in the modeltofiles Array
-function linkJvJmol(applet, jmolView, modeltofiles) {
-	var i = _jvapps.length;
-	while (i--) {
-		if (_jvapps[i].equals(applet)) {
-			throw ("Ignoring additional linkJvJmol call for "
-					+ applet.getName() + ".");
-		}
-	}
-	_jvapps[_jvapps.length] = applet;
-	applet.setMouseoverListener("mouseover");
-	applet.setSelectionListener("sellist");
-	// viewListener not fully implemented in 2.7
-	// try { applet.setViewListener("viewlist"); } catch (err) {};
-	if (jmolView)
-	{
-		var sep = applet.getSeparator();
-		var oldjm=jmolView;
-		// recover full id of Jmol applet
-		jmolView=_jmolGetApplet(jmolView).id;
-		var jmbinding=_jvjmols.get(jmolView);
-		if (!jmbinding)
-		{	
-			jmbinding=new Object();
-			jmbinding._modelstofiles=new Array();
-			jmbinding._fullmpath=new Array();
-			jmbinding._filetonum=new Hashtable();
-			jmbinding._jmol=jmolView;
-			jmbinding._jmhandle=oldjm;
-			_jvjmols.put(jmolView,jmbinding);
-		}
-		
-		jmbinding._modelstofiles=jmbinding._modelstofiles.concat(jmbinding._modelstofiles,modeltofiles);
-		jmbinding._jmol=jmolView;
-		// now update structureListener list
-		mtf="";
-		var dbase = document.baseURI.substring(0,document.baseURI.lastIndexOf("/")+1);
-		for (m in jmbinding._modelstofiles)
-		{ if (m>0) { mtf+=sep; }
-		mtf+=jmbinding._modelstofiles[m];
-		if (jmbinding._modelstofiles[m].indexOf("//")==-1)
-			{ jmbinding._fullmpath[m] = dbase+((jmbinding._modelstofiles[m].indexOf("/")==0) ? jmbinding._modelstofiles[m].substring(1) : jmbinding._modelstofiles[m]); }
-		  jmbinding._filetonum.put(jmbinding._modelstofiles[m], m+1); 
-		  jmbinding._filetonum.put(jmbinding._fullmpath[m], m+1);
-		  
-		  }
-		applet.setStructureListener("_structure", mtf);
-	}
-}
-
-/*function _addJmolModel(jmolid, modelname) {
-	modelname=""+modelname;
-	var jminf = _jvjmols[jmolid];
-	if (!jminf) {
-		jminf = new Object();
-		jminf._modelstofiles = new Array(); //new Hashtable();
-		jminf._jmol = jmolid;
-		jminf._modellist=new Array();
-		_jvjmols[jmolid] = jminf;
-	}
-	var obj = new Object();
-	jminf._modeltofiles[modelname] = obj; // .put(modelname, obj);
-	obj.id = modelname;
-	obj.mnum = jminf._modeltofiles.length;
-	jminf._modellist+=modelname;
-}*/
-
-
-
-// jmol Jalview Methods
-
-function _structure(list1, list2, list3, list4) {
-	var follower;
-	// if (_console) { if (!_console.value) { _console.value="";} }
-	if (list1 == "mouseover") {
-		var list = new Array(("" + list1), ("" + list2), ("" + list3),
-				("" + list4));
-		// 1 is pdb file, 2 is residue number, 3 is chain
-		// list1 = new Object(list1);
-		var base = list[1].indexOf(document.baseURI
-				.substring(0, document.baseURI.lastIndexOf('/'))
-				); // .indexOf(_path);
-		if (base==0) { base = document.baseURI.lastIndexOf('/'); }
-		var sid = list[1]; // .substring(base);
-		base = list[1].substring(0, base);
-		if (_console) {
-			_console.value += "Model is " + list[1] + ", Structure id is : "
-					+ sid + "\n";
-		}
-		;
-		var siddat;
-		for ( var jmolappi in _jvjmols.values()) {
-			var jmolapp=_jvjmols.values()[jmolappi];
-			var msg = "";
-			if (siddat = jmolapp._filetonum.get(sid)) {
-				// we don't putin chain number because there isn't one ?
-				// skip select 0 bit
-				var ch = ""+list[3];
-				if ((""+list[2]).trim().length==1)
-					{
-					ch+=":"+list[2];
-					}
-				msg = "select (" + ch + " /" + siddat + ") ;";
-			}
-			if (msg) {
-				if (_console) {
-					_console.value += "Sending '" + msg + "' to jmol." + "\n";
-				}
-			}
-			jmolScriptWait(msg, "" + jmolapp._jmhandle);
-			// only do highlight for one jmol ?
-			// return 1;
-		}
-	}
-	if (list1 == "colourstruct") {
-		if (_console) {
-			_console.value += 'colourStruct("' + list1 + '","' + list2
-			+ '") [' + list4 + ']' + "\n";
-		}
-		setTimeout('colourStruct("'+list4+'","' + list1 + '","' + list2 + '")', 1);
-		return 1;
-	}
-	return 1;
-}
-// last colour message
-var _lastMsg = "";
-// indicator - if _colourStruct==0 then no colouring is going on
-var _colourStruct = 0;
-
-function colourStruct(involves, msg, handle) {
-	if (_colourStruct == 0) {
-		_colourStruct = 1;
-		for (ap in _jvapps) {
-			var _msg = "";
-			do {
-				if (_msg.match(/\S/)) {
-					_lastMsg += _msg;
-				}
-				_msg = "" + _jvapps[ap].getJsMessage(msg, handle);
-			} while (_msg.match(/\S/));
-		}
-		// locate the jmol that should get the message
-		for (var jmol in _jvjmols.values())
-			{
-			var jml=_jvjmols.values()[jmol];
-			if (jml._filetonum.get(involves))
-				{
-					colourStructs(jml._jmhandle);
-				}
-			}
-		_colourStruct = 0;
-	} else {
-		// setTimeout('colourStruct("'+msg+'","'+handle+'")',3);
-	}
-}
-
-function colourStructs(jmolapp) {
-	dbg(0, "Colouring the structures\n");
-	jmolScriptWait("set selectionhalos false;" + _lastMsg
-			+ "; select 0; set selectionhalos true;", jmolapp);
-	_lastMsg = "";
-}
-var _jmolhovermsg="";
-function _jmolhover(jmid, atomlabel, atomidx) {
-	var msg=""+jmid+" "+atomlabel+" "+atomidx;
-	if (_jmolhovermsg==msg)
-		{
-		return;
-		}
-	_jmolhovermsg=msg;
-	modeltofiles = _jvjmols.get(jmid)._modelstofiles;
-	// atomlabel=(""+atomlabel).match(/\[(.+)\](\d+):(.)\.(\S+)\s*\/(\d+)\..+/);
-	// relaxed third parameter - may be null or a model number for multi model
-	// views
-	atomlabel = ("" + atomlabel)
-			.match(/\[(.+)\](\d+):(.)\.([^\/]+)(\/\d+\.|).+/);
-	atomidx = "" + atomidx;
-	if (atomlabel[5]) {
-		atomlabel[5] = atomlabel[5].match(/\/(.+)\./)[1];
-		atomlabel[5] = parseInt(atomlabel[5])-1;
-	} else {
-		// default - first model
-		atomlabel[5] = 0;
-	}
-	// use atomlabel[5] to look up model filename so we can highlight associated positions in any jalviews
-	for (ap in _jvapps) {
-		_jvapps[ap].mouseOverStructure(atomlabel[2], atomlabel[3],
-				document.baseURI
-						.substring(0, document.baseURI.lastIndexOf('/'))
-						+ "/" + 
-						modeltofiles[atomlabel[5]]);
-		msg = _jmolhovermsg;
-	}
-}
-function _jmolpick(jmid, atomlabel, atomidx) {
-	atomlabel = "" + atomlabel;
-	atomidx = "" + atomidx;
-	// label is atom id, atom number, and xyz coordinates in the form:
-	// C6 #6 -0.30683374 -1.6836332 -0.716934
-	// atom index, starting with 0.
-
-}
-function _jmolMessagecallback(jmid, statmess) {
-	// if (statmess.indexOf("Script Terminated")==0)
-	{
-		var thisTime = new Date();
-		if (_console) {
-			_console.value += "Last script execution took : "
-					+ (thisTime.valueOf() - _lastTime.valueOf()) / 1000.0
-					+ " seconds.";
-		}
-		_lastTime = thisTime;
-
-	}
-}
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+
+
+
+
+
+
+
+
+// default console to report messages
+var _console = document.getElementById("stdout");
+var _jvapps = new Array();
+// jvjmols is a list associating a jmol id to { modelstofiles }
+var _jvjmols = new Hashtable();
+// array of model names used to lookup index in Jmol
+var _modeltofiles = new Array();
+// counter for jmol structures
+var mnum = 1;
+
+function getDocumentBase() {
+	var dburi = document.baseURI;
+	// IE does not support document.baseURI
+	// logic from patch to TYPO3:
+	// http://forge.typo3.org/projects/typo3cms-core/repository/revisions/f61358afad28adb6dcaeb270ba480e998dfb0b79/diff/typo3/sysext/rtehtmlarea/htmlarea/htmlarea.js
+	if (!dburi) {
+		var baseTags = document.getElementsByTagName('base');
+		if (baseTags.length > 0) {
+			dburi = baseTags[0].href;
+		} else {
+			dburi = document.URL;
+		}
+	}
+	return dburi.substring(0, dburi.lastIndexOf("/") + 1);
+}
+function setConsole(console) {
+	_console = console;
+}
+
+function getDestinationFrms(source, frames) {
+	var frms = new Array();
+	var frid = "";
+	for (frm in frames) {
+		try {
+			frid = (source!=null) && (("" + source.getSequenceSetId()) == ("" + frames[frm].currentAlignFrame
+					.getSequenceSetId()));
+		} catch (q) {
+		};
+		
+		if (!frames[frm].equals(source) && !frid
+				&& !frames[frm].currentAlignFrame.equals(source)) {
+			frms[frms.length] = frames[frm];
+		}
+	}
+	return frms;
+}
+
+function mouseover(list1, list2, list3, list4) {
+	// list1 = new Object(list1);
+	var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
+	var msg = "Mouse over :\n" + "AlignFrame obj: " + list1 + " Seq : "
+			+ list[1] + "\nPos: " + list[2] + "(" + list[3] + ")\n";
+
+	var flist = getDestinationFrms(list1, _jvapps);
+	if (_console) {
+		_console.value = msg + "\n";
+	}
+
+	for (follower in flist) {
+		if (_console) {
+			_console.value += "Sending to " + flist[follower] + "\n";
+		}
+		flist[follower].highlight(list[1], list[2], "true");
+	}
+	return true;
+}
+
+function sellist(list1, list2, list3, list4) {
+	// list1 = new Object(list1);
+	var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
+	var msg = "Selection:\n" + "AlignFrame obj: " + list[0] + " id : "
+			+ list[1] + "\nSeqs " + list[2] + "\nColumns " + list[3] + "\n";
+	var flist = getDestinationFrms(list1, _jvapps);
+	if (_console) {
+		_console.value = msg + "\n";
+	}
+	
+	for (follower in flist) {
+		if (_console) {
+			_console.value += "Sending to " + flist[follower] + "\n";
+		}
+		flist[follower].selectIn(flist[follower].getDefaultTargetFrame(),
+				list[2], list[3])
+	}
+	return true;
+}
+
+function viewlist(list1, list2, list3, list4) {
+	// list1 = new Object(list1);
+	var list = new Array(("" + list1), ("" + list2), ("" + list3), ("" + list4));
+	var msg = "Viewport extent change::\n" + "AlignFrame obj: " + list[0]
+			+ " id : " + list[1] + "\nRow from " + list[2] + " and to "
+			+ list[3] + "\nVisible columns: " + list[4] + "\n";
+	var flist = getDestinationFrms(list1, _jvapps);
+	if (_console) {
+		_console.value = msg + "\n";
+	}
+
+	for (follower in flist) {
+		if (_console) {
+			_console.value += "Sending to " + flist[follower] + "\n";
+		}
+		flist[follower].scrollToViewIn(flist[follower].getDefaultTargetFrame(),
+				list[2], "-1");
+	}
+	return true;
+}
+
+// register a jalview applet and add some handlers to it
+// jmolView is a reference to a jmol applet that is displaying the PDB files listed (in order) in the modeltofiles Array
+function linkJvJmol(applet, jmolView, modeltofiles) {
+	var i = _jvapps.length;
+	while (i--) {
+		if (_jvapps[i].equals(applet)) {
+			throw ("Ignoring additional linkJvJmol call for "
+					+ applet.getName() + ".");
+		}
+	}
+	_jvapps[_jvapps.length] = applet;
+	applet.setMouseoverListener("mouseover");
+	applet.setSelectionListener("sellist");
+	// viewListener not fully implemented in 2.7
+	// try { applet.setViewListener("viewlist"); } catch (err) {};
+	if (jmolView)
+	{
+		var sep = applet.getSeparator();
+		var oldjm=jmolView;
+		// recover full id of Jmol applet
+		jmolView=jmolFindTarget(jmolView)._id; // Jmol 14.2.14
+		var jmbinding=_jvjmols.get(jmolView);
+		if (!jmbinding)
+		{	
+			jmbinding=new Object();
+			jmbinding._modelstofiles=new Array();
+			jmbinding._fullmpath=new Array();
+			jmbinding._filetonum=new Hashtable();
+			jmbinding._jmol=jmolView;
+			jmbinding._jmhandle=oldjm;
+			_jvjmols.put(jmolView,jmbinding);
+		}
+		
+		jmbinding._modelstofiles=jmbinding._modelstofiles.concat(jmbinding._modelstofiles,modeltofiles);
+		jmbinding._jmol=jmolView;
+		// now update structureListener list
+		mtf="";
+		var dbase = getDocumentBase();
+		for (m in jmbinding._modelstofiles)
+		{ if (m>0) { mtf+=sep; }
+		mtf+=jmbinding._modelstofiles[m];
+		if (jmbinding._modelstofiles[m].indexOf("//")==-1)
+			{ jmbinding._fullmpath[m] = dbase+((jmbinding._modelstofiles[m].indexOf("/")==0) ? jmbinding._modelstofiles[m].substring(1) : jmbinding._modelstofiles[m]); }
+		  jmbinding._filetonum.put(jmbinding._modelstofiles[m], m+1); 
+		  jmbinding._filetonum.put(jmbinding._fullmpath[m], m+1);
+		  
+		  }
+		applet.setStructureListener("_structure", mtf);
+	}
+}
+
+/*function _addJmolModel(jmolid, modelname) {
+	modelname=""+modelname;
+	var jminf = _jvjmols[jmolid];
+	if (!jminf) {
+		jminf = new Object();
+		jminf._modelstofiles = new Array(); //new Hashtable();
+		jminf._jmol = jmolid;
+		jminf._modellist=new Array();
+		_jvjmols[jmolid] = jminf;
+	}
+	var obj = new Object();
+	jminf._modeltofiles[modelname] = obj; // .put(modelname, obj);
+	obj.id = modelname;
+	obj.mnum = jminf._modeltofiles.length;
+	jminf._modellist+=modelname;
+}*/
+
+
+
+// jmol Jalview Methods
+
+function _structure(list1, list2, list3, list4) {
+	var follower;
+	// if (_console) { if (!_console.value) { _console.value="";} }
+	if (list1 == "mouseover") {
+		var list = new Array(("" + list1), ("" + list2), ("" + list3),
+				("" + list4));
+		// 1 is pdb file, 2 is residue number, 3 is chain
+		// list1 = new Object(list1);
+		var base = list[1].indexOf(getDocumentBase()); // .indexOf(_path);
+		if (base==0) { base = getDocumentBase(); }
+		var sid = list[1]; // .substring(base);
+		base = list[1].substring(0, base);
+		if (_console) {
+			_console.value += "Model is " + list[1] + ", Structure id is : "
+					+ sid + "\n";
+		}
+		;
+		var siddat;
+		for ( var jmolappi in _jvjmols.values()) {
+			var jmolapp=_jvjmols.values()[jmolappi];
+			var msg = "";
+			if (siddat = jmolapp._filetonum.get(sid)) {
+				// we don't putin chain number because there isn't one ?
+				// skip select 0 bit
+				var ch = ""+list[3];
+				if ((""+list[2]).trim().length==1)
+					{
+					ch+=":"+list[2];
+					}
+				msg = "select (" + ch + " /" + siddat + ") ;";
+			}
+			if (msg) {
+				if (_console) {
+					_console.value += "Sending '" + msg + "' to jmol." + "\n";
+				}
+			}
+			jmolScriptWait(msg, "" + jmolapp._jmhandle);
+			// only do highlight for one jmol ?
+			// return 1;
+		}
+	}
+	if (list1 == "colourstruct") {
+		if (_console) {
+			_console.value += 'colourStruct("' + list1 + '","' + list2
+			+ '") [' + list4 + ']' + "\n";
+		}
+		setTimeout('colourStruct("'+list4+'","' + list1 + '","' + list2 + '")', 1);
+		return 1;
+	}
+	return 1;
+}
+// last colour message
+var _lastMsg = "";
+// indicator - if _colourStruct==0 then no colouring is going on
+var _colourStruct = 0;
+
+function colourStruct(involves, msg, handle) {
+	if (_colourStruct == 0) {
+		_colourStruct = 1;
+		for (ap in _jvapps) {
+			var _msg = "";
+			do {
+				if (_msg.match(/\S/)) {
+					_lastMsg += _msg;
+				}
+				_msg = "" + _jvapps[ap].getJsMessage(msg, handle);
+			} while (_msg.match(/\S/));
+		}
+		// locate the jmol that should get the message
+		for (var jmol in _jvjmols.values())
+			{
+			var jml=_jvjmols.values()[jmol];
+			if (jml._filetonum.get(involves))
+				{
+					colourStructs(jml._jmhandle);
+				}
+			}
+		_colourStruct = 0;
+	} else {
+		// setTimeout('colourStruct("'+msg+'","'+handle+'")',3);
+	}
+}
+
+function colourStructs(jmolapp) {
+	dbg(0, "Colouring the structures\n");
+	jmolScriptWait("set selectionhalos false;" + _lastMsg
+			+ "; select 0; set selectionhalos true;", jmolapp);
+	_lastMsg = "";
+}
+var _jmolhovermsg="";
+function _jmolhover(jmid, atomlabel, atomidx) {
+	var msg=""+jmid+" "+atomlabel+" "+atomidx;
+	if (_jmolhovermsg==msg)
+		{
+		return;
+		}
+	_jmolhovermsg=msg;
+	modeltofiles = _jvjmols.get(jmid)._modelstofiles;
+	// atomlabel=(""+atomlabel).match(/\[(.+)\](\d+):(.)\.(\S+)\s*\/(\d+)\..+/);
+	// relaxed third parameter - may be null or a model number for multi model
+	// views
+	atomlabel = ("" + atomlabel)
+			.match(/\[(.+)\](\d+):(.)\.([^\/]+)(\/\d+\.|).+/);
+	atomidx = "" + atomidx;
+	if (atomlabel[5]) {
+		atomlabel[5] = atomlabel[5].match(/\/(.+)\./)[1];
+		atomlabel[5] = parseInt(atomlabel[5])-1;
+	} else {
+		// default - first model
+		atomlabel[5] = 0;
+	}
+	// use atomlabel[5] to look up model filename so we can highlight associated positions in any jalviews
+	for (ap in _jvapps) {
+		pdb = getDocumentBase() + modeltofiles[atomlabel[5]];
+		_jvapps[ap].mouseOverStructure(atomlabel[2], atomlabel[3], pdb);
+		msg = _jmolhovermsg;
+	}
+}
+function _jmolpick(jmid, atomlabel, atomidx) {
+	atomlabel = "" + atomlabel;
+	atomidx = "" + atomidx;
+	// label is atom id, atom number, and xyz coordinates in the form:
+	// C6 #6 -0.30683374 -1.6836332 -0.716934
+	// atom index, starting with 0.
+
+}
+function _jmolMessagecallback(jmid, statmess) {
+	// if (statmess.indexOf("Script Terminated")==0)
+	{
+		var thisTime = new Date();
+		if (_console) {
+			_console.value += "Last script execution took : "
+					+ (thisTime.valueOf() - _lastTime.valueOf()) / 1000.0
+					+ " seconds.";
+		}
+		_lastTime = thisTime;
+
+	}
+}
+
+
+  function lJvApp() {
+    setTimeout(function() {
+       //alert("in lJvApp");
+       var jvapp = document.getElementById("jvapp");
+       var jvfollower = document.getElementById("jvfollower");
+       //console.log(">>>>>>>> lJvApp" + jvapp);
+       linkJvJmol(jvapp);
+    }, 200);
+    setConsole(document.getElementById("stdout"));
+  };
+
+  function lJvFollow() {
+    setTimeout(function() {
+       //alert("in lJvFollow");
+       var jvapp = document.getElementById("jvapp");
+       var jvfollower = document.getElementById("jvfollower");
+       console.log(">>>>>>> lJvFollow" + jvfollower);
+       linkJvJmol(jvfollower);
+    }, 200);
+  };
+
+  function lJvA() {
+    setTimeout(function() {
+      //alert("lJvA");
+      jvfollower = document.getElementById("jvA");
+      setConsole(document.getElementById("stdout"));  
+      //sep = jvfollower.getSeparator();
+      //jvapp.setSeparator(""+jvapp.getSeparator());
+      linkJvJmol(jvfollower, "jmolView", modeltofiles);
+    }, 100);
+  };
+