WebSVN – wimsdev – Blame – /trunk/wims/public_html/java/jmol/Jmol.js

Rev	Author	Line No.	Line
1365	bpr	1	/* Jmol 11.7 script library Jmol.js 15:32 06.12.2008 Bob Hanson
		2
		3	checkbox heirarchy -- see http://chemapps.stolaf.edu/jmol/docs/examples-11/check.htm
		4
		5	based on:
		6	*
		7	* Copyright (C) 2004-2005 Miguel, Jmol Development, www.jmol.org
		8	*
		9	* Contact: hansonr@stolaf.edu
		10	*
		11	* This library is free software; you can redistribute it and/or
		12	* modify it under the terms of the GNU Lesser General Public
		13	* License as published by the Free Software Foundation; either
		14	* version 2.1 of the License, or (at your option) any later version.
		15	*
		16	* This library is distributed in the hope that it will be useful,
		17	* but WITHOUT ANY WARRANTY; without even the implied warranty of
		18	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
		19	* Lesser General Public License for more details.
		20	*
		21	* You should have received a copy of the GNU Lesser General Public
		22	* License along with this library; if not, write to the Free Software
		23	* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
		24	* 02111-1307 USA.
		25	*/
		26
		27	// for documentation see www.jmol.org/jslibrary
		28
		29	try{if(typeof(_jmol)!="undefined")exit()
		30
		31	// place "?NOAPPLET" on your command line to check applet control action with a textarea
		32	// place "?JMOLJAR=xxxxx" to use a specific jar file
		33
		34	// bob hanson -- jmolResize(w,h) -- resizes absolutely or by percent (w or h 0.5 means 50%)
		35	// bob hanson -- jmolEvaluate -- evaluates molecular math 8:37 AM 2/23/2007
		36	// bob hanson -- jmolScriptMessage -- returns all "scriptStatus" messages 8:37 AM 2/23/2007
		37	// bob hanson -- jmolScriptEcho -- returns all "scriptEcho" messages 8:37 AM 2/23/2007
		38	// bob hanson -- jmolScriptWait -- 11:31 AM 5/2/2006
		39	// bob hanson -- remove trailing separatorHTML in radio groups -- 12:18 PM 5/6/2006
		40	// bob hanson -- adds support for dynamic DOM script nodes 7:04 AM 5/19/2006
		41	// bob hanson -- adds try/catch for wiki - multiple code passes 7:05 AM 5/19/2006
		42	// bob hanson -- auto-initiates to defaultdir/defaultjar -- change as desired.
		43	// bob hanson -- adding save/restore orientation w/ and w/o delay 11:49 AM 5/25/2006
		44	// bob hanson -- adding AjaxJS service 11:16 AM 6/3/2006
		45	// bob hanson -- fix for iframes not available for finding applet
		46	// bob hanson -- added applet fake ?NOAPPLET URL flag
		47	// bob hanson -- added jmolSetCallback(calbackName, funcName) 3:32 PM 6/13/2006
		48	// used PRIOR to jmolApplet() or jmolAppletInline()
		49	// added 4th array element in jmolRadioGroup -- title
		50	// added <span> and id around link, checkbox, radio, menu
		51	// fixing AJAX loads for MSIE/Opera-Mozilla incompatibility
		52	// -- renamed Jmol-11.js from Jmol-new.js; JmolApplet.jar from JmolAppletProto.jar
		53	// renamed Jmol.js for Jmol 11 distribution
		54	// -- modified jmolRestoreOrientation() to be immediate, no 1-second delay
		55	// bob hanson -- jmolScriptWait always returns a string -- 11:23 AM 9/16/2006
		56	// bh -- jmolCommandInput()
		57	// bh -- jmolSetTranslation(TF) -- forces translation even if there might be message callback issues
		58	// bh -- minor fixes suggested by Angel
		59	// bh -- adds jmolSetSyncId() and jmolGetSyncId()
		60	// bh 3/2008 -- adds jmolAppendInlineScript() and jmolAppendInlineArray()
		61	// bh 3/2008 -- fixes IE7 bug in relation to jmolLoadInlineArray()
		62	// bh 6/2008 -- adds jmolSetAppletWindow()
		63	// Angel H. 6/2008 -- added html <label> tags to checkboxes and radio buttons [in jmolCheckbox() and _jmolRadio() functions]
		64	// bh 7/2008 -- code fix "for(i..." not "for(var i..."
		65	// bh 12/2008 -- jmolLoadInline, jmolLoadInlineArray, jmolLoadInlineScript, jmolAppendInlineScript, jmolAppendInlineArray all return error message or null (Jmol 11.7.16)
		66	// bh 12/2008 -- jmolScriptWaitOutput() -- waits for script to complete and delivers output normally sent to console
		67
		68	var defaultdir = "."
		69	var defaultjar = "JmolApplet.jar"
		70
		71
		72	// Note added 12:41 PM 9/21/2008 by Bob Hanson, hansonr@stolaf.edu:
		73
		74	// JMOLJAR=xxxxx.jar on the URL for this page will override
		75	// the JAR file specified in the jmolInitialize() call.
		76
		77	// The idea is that it can be very useful to test a web page with different JAR files
		78	// Or for an expert user to substitute a signed applet for an unsigned one
		79	// so as to use a broader range of models or to create JPEG files, for example.
		80
		81	// If the JAR file is not in the current directory (has any sort of "/" in its name)
		82	// then the user is presented with a warning and asked whether it is OK to change Jar files.
		83	// The default action, if the user just presses "OK" is to NOT allow the change.
		84	// The user must type the word "yes" in the prompt box for the change to be approved.
		85
		86	// If you don't want people to be able to switch in their own JAR file on your page,
		87	// simply set this next line to read "var allowJMOLJAR = false".
		88
		89
		90	var allowJMOLJAR = true
		91
		92
		93	var undefined; // for IE 5 ... wherein undefined is undefined
		94
		95	////////////////////////////////////////////////////////////////
		96	// Basic Scripting infrastruture
		97	////////////////////////////////////////////////////////////////
		98
		99	function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {
		100	if (_jmol.initialized)
		101	return;
		102	_jmol.initialized = true;
		103	if(allowJMOLJAR && document.location.search.indexOf("JMOLJAR=")>=0) {
		104	var f = document.location.search.split("JMOLJAR=")[1].split("&")[0];
		105	if (f.indexOf("/") >= 0) {
		106	alert ("This web page URL is requesting that the applet used be " + f + ". This is a possible security risk, particularly if the applet is signed, because signed applets can read and write files on your local machine or network.")
		107	var ok = prompt("Do you want to use applet " + f + "? ","yes or no")
		108	if (ok == "yes") {
		109	codebaseDirectory = f.substring(0, f.lastIndexOf("/"));
		110	fileNameOrUseSignedApplet = f.substring(f.lastIndexOf("/") + 1);
		111	} else {
		112	_jmolGetJarFilename(fileNameOrUseSignedApplet);
		113	alert("The web page URL was ignored. Continuing using " + _jmol.archivePath + ' in directory "' + codebaseDirectory + '"');
		114	}
		115	} else {
		116	fileNameOrUseSignedApplet = f;
		117	}
		118	}
		119	_jmolSetCodebase(codebaseDirectory);
		120	_jmolGetJarFilename(fileNameOrUseSignedApplet);
		121	_jmolOnloadResetForms();
		122	}
		123
		124	function jmolSetTranslation(TF) {
		125	_jmol.params.doTranslate = ''+TF;
		126	}
		127
		128	function _jmolGetJarFilename(fileNameOrFlag) {
		129	_jmol.archivePath =
		130	(typeof(fileNameOrFlag) == "string" ? fileNameOrFlag : (fileNameOrFlag ? "JmolAppletSigned" : "JmolApplet") + "0.jar");
		131	}
		132
		133	function jmolSetDocument(doc) {
		134	_jmol.currentDocument = doc;
		135	}
		136
		137	function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {
		138	_jmolInitCheck();
		139	_jmol.params.boxbgcolor = boxbgcolor;
		140	if (boxfgcolor)
		141	_jmol.params.boxfgcolor = boxfgcolor
		142	else if (boxbgcolor == "white" \|\| boxbgcolor == "#FFFFFF")
		143	_jmol.params.boxfgcolor = "black";
		144	else
		145	_jmol.params.boxfgcolor = "white";
		146	if (progresscolor)
		147	_jmol.params.progresscolor = progresscolor;
		148	if (_jmol.debugAlert)
		149	alert(" boxbgcolor=" + _jmol.params.boxbgcolor +
		150	" boxfgcolor=" + _jmol.params.boxfgcolor +
		151	" progresscolor=" + _jmol.params.progresscolor);
		152	}
		153
		154	function jmolSetAppletWindow(w) {
		155	_jmol.appletWindow = w;
		156	}
		157
		158	function jmolApplet(size, script, nameSuffix) {
		159	_jmolInitCheck();
		160	return _jmolApplet(size, null, script, nameSuffix);
		161	}
		162
		163	////////////////////////////////////////////////////////////////
		164	// Basic controls
		165	////////////////////////////////////////////////////////////////
		166
		167	function jmolButton(script, label, id, title) {
		168	_jmolInitCheck();
		169	if (id == undefined \|\| id == null)
		170	id = "jmolButton" + _jmol.buttonCount;
		171	if (label == undefined \|\| label == null)
		172	label = script.substring(0, 32);
		173	++_jmol.buttonCount;
		174	var scriptIndex = _jmolAddScript(script);
		175	var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input type='button' name='" + id + "' id='" + id +
		176	"' value='" + label +
		177	"' onClick='_jmolClick(" + scriptIndex + _jmol.targetText +
		178	")' onMouseover='_jmolMouseOver(" + scriptIndex +
		179	");return true' onMouseout='_jmolMouseOut()' " +
		180	_jmol.buttonCssText + "/></span>";
		181	if (_jmol.debugAlert)
		182	alert(t);
		183	return _jmolDocumentWrite(t);
		184	}
		185
		186	function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked,
		187	labelHtml, isChecked, id, title) {
		188	_jmolInitCheck();
		189	if (id == undefined \|\| id == null)
		190	id = "jmolCheckbox" + _jmol.checkboxCount;
		191	++_jmol.checkboxCount;
		192	if (scriptWhenChecked == undefined \|\| scriptWhenChecked == null \|\|
		193	scriptWhenUnchecked == undefined \|\| scriptWhenUnchecked == null) {
		194	alert("jmolCheckbox requires two scripts");
		195	return;
		196	}
		197	if (labelHtml == undefined \|\| labelHtml == null) {
		198	alert("jmolCheckbox requires a label");
		199	return;
		200	}
		201	var indexChecked = _jmolAddScript(scriptWhenChecked);
		202	var indexUnchecked = _jmolAddScript(scriptWhenUnchecked);
		203	var eospan = "</span>"
		204	var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input type='checkbox' name='" + id + "' id='" + id +
		205	"' onClick='_jmolCbClick(this," +
		206	indexChecked + "," + indexUnchecked + _jmol.targetText +
		207	")' onMouseover='_jmolCbOver(this," + indexChecked + "," +
		208	indexUnchecked +
		209	");return true' onMouseout='_jmolMouseOut()' " +
		210	(isChecked ? "checked " : "") + _jmol.checkboxCssText + "/>"
		211	if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
		212	t += eospan
		213	eospan = "";
		214	}
		215	t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan;
		216	if (_jmol.debugAlert)
		217	alert(t);
		218	return _jmolDocumentWrite(t);
		219	}
		220
		221	function jmolStartNewRadioGroup() {
		222	++_jmol.radioGroupCount;
		223	}
		224
		225	function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) {
		226	/*
		227
		228	array: [radio1,radio2,radio3...]
		229	where radioN = ["script","label",isSelected,"id","title"]
		230
		231	*/
		232
		233	_jmolInitCheck();
		234	var type = typeof arrayOfRadioButtons;
		235	if (type != "object" \|\| type == null \|\| ! arrayOfRadioButtons.length) {
		236	alert("invalid arrayOfRadioButtons");
		237	return;
		238	}
		239	if (separatorHtml == undefined \|\| separatorHtml == null)
		240	separatorHtml = "  ";
		241	var len = arrayOfRadioButtons.length;
		242	jmolStartNewRadioGroup();
		243	if (!groupName)
		244	groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1);
		245	var t = "<span id='"+(id ? id : groupName)+"'>";
		246	for (var i = 0; i < len; ++i) {
		247	if (i == len - 1)
		248	separatorHtml = "";
		249	var radio = arrayOfRadioButtons[i];
		250	type = typeof radio;
		251	if (type == "object") {
		252	t += _jmolRadio(radio[0], radio[1], radio[2], separatorHtml, groupName, (radio.length > 3 ? radio[3]: (id ? id : groupName)+"_"+i), (radio.length > 4 ? radio[4] : 0), title);
		253	} else {
		254	t += _jmolRadio(radio, null, null, separatorHtml, groupName, (id ? id : groupName)+"_"+i, title);
		255	}
		256	}
		257	t+="</span>"
		258	if (_jmol.debugAlert)
		259	alert(t);
		260	return _jmolDocumentWrite(t);
		261	}
		262
		263
		264	function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
		265	_jmolInitCheck();
		266	if (_jmol.radioGroupCount == 0)
		267	++_jmol.radioGroupCount;
		268	var t = _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, (id ? id : groupName + "_" + _jmol.radioCount), title ? title : 0);
		269	if (_jmol.debugAlert)
		270	alert(t);
		271	return _jmolDocumentWrite(t);
		272	}
		273
		274	function jmolLink(script, label, id, title) {
		275	_jmolInitCheck();
		276	if (id == undefined \|\| id == null)
		277	id = "jmolLink" + _jmol.linkCount;
		278	if (label == undefined \|\| label == null)
		279	label = script.substring(0, 32);
		280	++_jmol.linkCount;
		281	var scriptIndex = _jmolAddScript(script);
		282	var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><a name='" + id + "' id='" + id +
		283	"' href='javascript:_jmolClick(" + scriptIndex + _jmol.targetText + ");' onMouseover='_jmolMouseOver(" + scriptIndex +
		284	");return true;' onMouseout='_jmolMouseOut()' " +
		285	_jmol.linkCssText + ">" + label + "</a></span>";
		286	if (_jmol.debugAlert)
		287	alert(t);
		288	return _jmolDocumentWrite(t);
		289	}
		290
		291	function jmolCommandInput(label, size, id, title) {
		292	_jmolInitCheck();
		293	if (id == undefined \|\| id == null)
		294	id = "jmolCmd" + _jmol.cmdCount;
		295	if (label == undefined \|\| label == null)
		296	label = "Execute";
		297	if (size == undefined \|\| isNaN(size))
		298	size = 60;
		299	++_jmol.cmdCount;
		300	var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input name='" + id + "' id='" + id +
		301	"' size='"+size+"'><input type=button value = '"+label+"' onClick='jmolScript(document.getElementById(\""+id+"\").value" + _jmol.targetText + ")'/></span>";
		302	if (_jmol.debugAlert)
		303	alert(t);
		304	return _jmolDocumentWrite(t);
		305	}
		306
		307	function jmolMenu(arrayOfMenuItems, size, id, title) {
		308	_jmolInitCheck();
		309	if (id == undefined \|\| id == null)
		310	id = "jmolMenu" + _jmol.menuCount;
		311	++_jmol.menuCount;
		312	var type = typeof arrayOfMenuItems;
		313	if (type != null && type == "object" && arrayOfMenuItems.length) {
		314	var len = arrayOfMenuItems.length;
		315	if (typeof size != "number" \|\| size == 1)
		316	size = null;
		317	else if (size < 0)
		318	size = len;
		319	var sizeText = size ? " size='" + size + "' " : "";
		320	var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><select name='" + id + "' id='" + id +
		321	"' onChange='_jmolMenuSelected(this" + _jmol.targetText + ")'" +
		322	sizeText + _jmol.menuCssText + ">";
		323	for (var i = 0; i < len; ++i) {
		324	var menuItem = arrayOfMenuItems[i];
		325	type = typeof menuItem;
		326	var script, text;
		327	var isSelected = undefined;
		328	if (type == "object" && menuItem != null) {
		329	script = menuItem[0];
		330	text = menuItem[1];
		331	isSelected = menuItem[2];
		332	} else {
		333	script = text = menuItem;
		334	}
		335	if (text == undefined \|\| text == null)
		336	text = script;
		337	if (script=="#optgroup") {
		338	t += "<optgroup label='" + text + "'>";
		339	} else if (script=="#optgroupEnd") {
		340	t += "</optgroup>";
		341	} else {
		342	var scriptIndex = _jmolAddScript(script);
		343	var selectedText = isSelected ? "' selected>" : "'>";
		344	t += "<option value='" + scriptIndex + selectedText + text + "</option>";
		345	}
		346	}
		347	t += "</select></span>";
		348	if (_jmol.debugAlert)
		349	alert(t);
		350	return _jmolDocumentWrite(t);
		351	}
		352	}
		353
		354	function jmolHtml(html) {
		355	return _jmolDocumentWrite(html);
		356	}
		357
		358	function jmolBr() {
		359	return _jmolDocumentWrite("<br />");
		360	}
		361
		362	////////////////////////////////////////////////////////////////
		363	// advanced scripting functions
		364	////////////////////////////////////////////////////////////////
		365
		366	function jmolDebugAlert(enableAlerts) {
		367	_jmol.debugAlert = (enableAlerts == undefined \|\| enableAlerts)
		368	}
		369
		370	function jmolAppletInline(size, inlineModel, script, nameSuffix) {
		371	_jmolInitCheck();
		372	return _jmolApplet(size, _jmolSterilizeInline(inlineModel),
		373	script, nameSuffix);
		374	}
		375
		376	function jmolSetTarget(targetSuffix) {
		377	_jmol.targetSuffix = targetSuffix;
		378	_jmol.targetText = targetSuffix ? ",\"" + targetSuffix + "\"" : "";
		379	}
		380
		381	function jmolScript(script, targetSuffix) {
		382	if (script) {
		383	_jmolCheckBrowser();
		384	if (targetSuffix == "all") {
		385	with (_jmol) {
		386	for (var i = 0; i < appletSuffixes.length; ++i) {
		387	var applet = _jmolGetApplet(appletSuffixes[i]);
		388	if (applet) applet.script(script);
		389	}
		390	}
		391	} else {
		392	var applet=_jmolGetApplet(targetSuffix);
		393	if (applet) applet.script(script);
		394	}
		395	}
		396	}
		397
		398	function jmolLoadInline(model, targetSuffix) {
		399	if (!model)return "ERROR: NO MODEL"
		400	var applet=_jmolGetApplet(targetSuffix);
		401	if (!applet)return "ERROR: NO APPLET"
		402	if (typeof(model) == "string")
		403	return applet.loadInlineString(model, "", false);
		404	else
		405	return applet.loadInlineArray(model, "", false);
		406	}
		407
		408
		409	function jmolLoadInlineScript(model, script, targetSuffix) {
		410	if (!model)return "ERROR: NO MODEL"
		411	var applet=_jmolGetApplet(targetSuffix);
		412	if (!applet)return "ERROR: NO APPLET"
		413	return applet.loadInlineString(model, script, false);
		414	}
		415
		416
		417	function jmolLoadInlineArray(ModelArray, script, targetSuffix) {
		418	if (!model)return "ERROR: NO MODEL"
		419	if (!script)script=""
		420	var applet=_jmolGetApplet(targetSuffix);
		421	if (!applet)return "ERROR: NO APPLET"
		422	try {
		423	return applet.loadInlineArray(ModelArray, script, false);
		424	} catch (err) {
		425	//IE 7 bug
		426	return applet.loadInlineString(ModelArray.join("\n"), script, false);
		427	}
		428	}
		429
		430	function jmolAppendInlineArray(ModelArray, script, targetSuffix) {
		431	if (!model)return "ERROR: NO MODEL"
		432	if (!script)script=""
		433	var applet=_jmolGetApplet(targetSuffix);
		434	if (!applet)return "ERROR: NO APPLET"
		435	try {
		436	return applet.loadInlineArray(ModelArray, script, true);
		437	} catch (err) {
		438	//IE 7 bug
		439	return applet.loadInlineString(ModelArray.join("\n"), script, true);
		440	}
		441	}
		442
		443	function jmolAppendInlineScript(model, script, targetSuffix) {
		444	if (!model)return "ERROR: NO MODEL"
		445	var applet=_jmolGetApplet(targetSuffix);
		446	if (!applet)return "ERROR: NO APPLET"
		447	return applet.loadInlineString(model, script, true);
		448	}
		449
		450	function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {
		451	if (typeof action == "string") {
		452	action = action.toLowerCase();
		453	if (action != "alert" && action != "redirect" && action != "popup")
		454	action = null;
		455	}
		456	if (typeof action != "string")
		457	alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
		458	"action must be 'alert', 'redirect', or 'popup'");
		459	else {
		460	if (typeof urlOrMessage != "string")
		461	alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
		462	"urlOrMessage must be a string");
		463	else {
		464	_jmol.checkBrowserAction = action;
		465	_jmol.checkBrowserUrlOrMessage = urlOrMessage;
		466	}
		467	}
		468	if (typeof nowOrLater == "string" && nowOrLater.toLowerCase() == "now")
		469	_jmolCheckBrowser();
		470	}
		471
		472	////////////////////////////////////////////////////////////////
		473	// Cascading Style Sheet Class support
		474	////////////////////////////////////////////////////////////////
		475
		476	function jmolSetAppletCssClass(appletCssClass) {
		477	if (_jmol.hasGetElementById) {
		478	_jmol.appletCssClass = appletCssClass;
		479	_jmol.appletCssText = appletCssClass ? "class='" + appletCssClass + "' " : "";
		480	}
		481	}
		482
		483	function jmolSetButtonCssClass(buttonCssClass) {
		484	if (_jmol.hasGetElementById) {
		485	_jmol.buttonCssClass = buttonCssClass;
		486	_jmol.buttonCssText = buttonCssClass ? "class='" + buttonCssClass + "' " : "";
		487	}
		488	}
		489
		490	function jmolSetCheckboxCssClass(checkboxCssClass) {
		491	if (_jmol.hasGetElementById) {
		492	_jmol.checkboxCssClass = checkboxCssClass;
		493	_jmol.checkboxCssText = checkboxCssClass ? "class='" + checkboxCssClass + "' " : "";
		494	}
		495	}
		496
		497	function jmolSetRadioCssClass(radioCssClass) {
		498	if (_jmol.hasGetElementById) {
		499	_jmol.radioCssClass = radioCssClass;
		500	_jmol.radioCssText = radioCssClass ? "class='" + radioCssClass + "' " : "";
		501	}
		502	}
		503
		504	function jmolSetLinkCssClass(linkCssClass) {
		505	if (_jmol.hasGetElementById) {
		506	_jmol.linkCssClass = linkCssClass;
		507	_jmol.linkCssText = linkCssClass ? "class='" + linkCssClass + "' " : "";
		508	}
		509	}
		510
		511	function jmolSetMenuCssClass(menuCssClass) {
		512	if (_jmol.hasGetElementById) {
		513	_jmol.menuCssClass = menuCssClass;
		514	_jmol.menuCssText = menuCssClass ? "class='" + menuCssClass + "' " : "";
		515	}
		516	}
		517
		518	////////////////////////////////////////////////////////////////
		519	// functions for INTERNAL USE ONLY which are subject to change
		520	// use at your own risk ... you have been WARNED!
		521	////////////////////////////////////////////////////////////////
		522	var _jmol = {
		523	currentDocument: document,
		524
		525	debugAlert: false,
		526
		527	codebase: "",
		528	modelbase: ".",
		529
		530	appletCount: 0,
		531	appletSuffixes: [],
		532	appletWindow: null,
		533
		534	buttonCount: 0,
		535	checkboxCount: 0,
		536	linkCount: 0,
		537	cmdCount: 0,
		538	menuCount: 0,
		539	radioCount: 0,
		540	radioGroupCount: 0,
		541
		542	appletCssClass: null,
		543	appletCssText: "",
		544	buttonCssClass: null,
		545	buttonCssText: "",
		546	checkboxCssClass: null,
		547	checkboxCssText: "",
		548	radioCssClass: null,
		549	radioCssText: "",
		550	linkCssClass: null,
		551	linkCssText: "",
		552	menuCssClass: null,
		553	menuCssText: "",
		554
		555	targetSuffix: 0,
		556	targetText: "",
		557	scripts: [""],
		558	params: {
		559	syncId: ("" + Math.random()).substring(3),
		560	progressbar: "true",
		561	progresscolor: "blue",
		562	boxbgcolor: "black",
		563	boxfgcolor: "white",
		564	boxmessage: "Downloading JmolApplet ..."
		565	},
		566	ua: navigator.userAgent.toLowerCase(),
		567	uaVersion: parseFloat(navigator.appVersion),
		568
		569	os: "unknown",
		570	browser: "unknown",
		571	browserVersion: 0,
		572	hasGetElementById: !!document.getElementById,
		573	isJavaEnabled: navigator.javaEnabled(),
		574	isNetscape47Win: false,
		575	isIEWin: false,
		576	useIEObject: false,
		577	useHtml4Object: false,
		578
		579	windowsClassId: "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93",
		580	windowsCabUrl:
		581	"http://java.sun.com/update/1.5.0/jinstall-1_5_0_05-windows-i586.cab",
		582
		583	isBrowserCompliant: false,
		584	isJavaCompliant: false,
		585	isFullyCompliant: false,
		586
		587	initialized: false,
		588	initChecked: false,
		589
		590	browserChecked: false,
		591	checkBrowserAction: "alert",
		592	checkBrowserUrlOrMessage: null,
		593
		594	archivePath: null, // JmolApplet0.jar OR JmolAppletSigned0.jar
		595
		596	previousOnloadHandler: null,
		597	ready: {}
		598	}
		599
		600	with (_jmol) {
		601	function _jmolTestUA(candidate) {
		602	var ua = _jmol.ua;
		603	var index = ua.indexOf(candidate);
		604	if (index < 0)
		605	return false;
		606	_jmol.browser = candidate;
		607	_jmol.browserVersion = parseFloat(ua.substring(index+candidate.length+1));
		608	return true;
		609	}
		610
		611	function _jmolTestOS(candidate) {
		612	if (_jmol.ua.indexOf(candidate) < 0)
		613	return false;
		614	_jmol.os = candidate;
		615	return true;
		616	}
		617
		618	_jmolTestUA("konqueror") \|\|
		619	_jmolTestUA("safari") \|\|
		620	_jmolTestUA("omniweb") \|\|
		621	_jmolTestUA("opera") \|\|
		622	_jmolTestUA("webtv") \|\|
		623	_jmolTestUA("icab") \|\|
		624	_jmolTestUA("msie") \|\|
		625	(_jmol.ua.indexOf("compatible") < 0 && _jmolTestUA("mozilla"));
		626
		627	_jmolTestOS("linux") \|\|
		628	_jmolTestOS("unix") \|\|
		629	_jmolTestOS("mac") \|\|
		630	_jmolTestOS("win");
		631
		632	isNetscape47Win = (os == "win" && browser == "mozilla" &&
		633	browserVersion >= 4.78 && browserVersion <= 4.8);
		634
		635	if (os == "win") {
		636	isBrowserCompliant = hasGetElementById;
		637	} else if (os == "mac") { // mac is the problem child :-(
		638	if (browser == "mozilla" && browserVersion >= 5) {
		639	// miguel 2004 11 17
		640	// checking the plugins array does not work because
		641	// Netscape 7.2 OS X still has Java 1.3.1 listed even though
		642	// javaplugin.sf.net is installed to upgrade to 1.4.2
		643	eval("try {var v = java.lang.System.getProperty('java.version');" +
		644	" _jmol.isBrowserCompliant = v >= '1.4.2';" +
		645	" } catch (e) { }");
		646	} else if (browser == "opera" && browserVersion <= 7.54) {
		647	isBrowserCompliant = false;
		648	} else {
		649	isBrowserCompliant = hasGetElementById &&
		650	!((browser == "msie") \|\|
		651	(browser == "safari" && browserVersion < 125.12));
		652	}
		653	} else if (os == "linux" \|\| os == "unix") {
		654	if (browser == "konqueror" && browserVersion <= 3.3)
		655	isBrowserCompliant = false;
		656	else
		657	isBrowserCompliant = hasGetElementById;
		658	} else { // other OS
		659	isBrowserCompliant = hasGetElementById;
		660	}
		661
		662	// possibly more checks in the future for this
		663	isJavaCompliant = isJavaEnabled;
		664
		665	isFullyCompliant = isBrowserCompliant && isJavaCompliant;
		666
		667	// IE5.5 works just fine ... but let's push them to Sun Java
		668	isIEWin = (os == "win" && browser == "msie" && browserVersion >= 5.5);
		669	useIEObject = isIEWin;
		670	useHtml4Object =
		671	(os != "mac" && browser == "mozilla" && browserVersion >= 5) \|\|
		672	(os == "win" && browser == "opera" && browserVersion >= 8) \|\|
		673	(os == "mac" && browser == "safari" && browserVersion >= 412.2);
		674
		675	doTranslate = true;
		676	haveSetTranslate = false;
		677	}
		678
		679
		680	function jmolSetCallback(callbackName,funcName) {
		681	_jmol.params[callbackName] = funcName
		682	}
		683
		684	function jmolSetSyncId(n) {
		685	return _jmol.params["syncId"] = n
		686	}
		687
		688	function jmolGetSyncId() {
		689	return _jmol.params["syncId"]
		690	}
		691
		692	function jmolSetLogLevel(n) {
		693	_jmol.params.logLevel = ''+n;
		694	}
		695
		696	/* AngelH, mar2007:
		697	By (re)setting these variables in the webpage before calling jmolApplet(),
		698	a custom message can be provided (e.g. localized for user's language) when no Java is installed.
		699	*/
		700	if (noJavaMsg==undefined) var noJavaMsg =
		701	"You do not have Java applets enabled in your web browser, or your browser is blocking this applet.<br />\n" +
		702	"Check the warning message from your browser and/or enable Java applets in<br />\n" +
		703	"your web browser preferences, or install the Java Runtime Environment from <a href='http://www.java.com'>www.java.com</a><br />";
		704	if (noJavaMsg2==undefined) var noJavaMsg2 =
		705	"You do not have the<br />\n" +
		706	"Java Runtime Environment<br />\n" +
		707	"installed for applet support.<br />\n" +
		708	"Visit <a href='http://www.java.com'>www.java.com</a>";
		709	function _jmolApplet(size, inlineModel, script, nameSuffix) {
		710	/* AngelH, mar2007
		711	Fixed percent / pixel business, to avoid browser errors:
		712	put "px" where needed, avoid where not.
		713	*/
		714	with (_jmol) {
		715	if (! nameSuffix)
		716	nameSuffix = appletCount;
		717	appletSuffixes.push(nameSuffix);
		718	++appletCount;
		719	if (! script)
		720	script = "select *";
		721	var sz = _jmolGetAppletSize(size);
		722	var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' ";
		723	var tHeader, tFooter;
		724	if (!codebase)
		725	jmolInitialize(".");
		726	if (useIEObject \|\| useHtml4Object) {
		727	params.name = 'jmolApplet' + nameSuffix;
		728	params.archive = archivePath;
		729	params.mayscript = 'true';
		730	params.codebase = codebase;
		731	}
		732	if (useIEObject) { // use MSFT IE6 object tag with .cab file reference
		733	winCodebase = (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : "");
		734	params.code = 'JmolApplet';
		735	tHeader =
		736	"<object name='jmolApplet" + nameSuffix +
		737	"' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
		738	" classid='" + windowsClassId + "'\n" + winCodebase + widthAndHeight + ">\n";
		739	tFooter = "</object>";
		740	} else if (useHtml4Object) { // use HTML4 object tag
		741	tHeader =
		742	"<object name='jmolApplet" + nameSuffix +
		743	"' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
		744	" classid='java:JmolApplet'\n" +
		745	" type='application/x-java-applet'\n" +
		746	widthAndHeight + ">\n";
		747	tFooter = "</object>";
		748	} else { // use applet tag
		749	tHeader =
		750	"<applet name='jmolApplet" + nameSuffix +
		751	"' id='jmolApplet" + nameSuffix +
		752	"' " + appletCssText +
		753	" code='JmolApplet'" +
		754	" archive='" + archivePath + "' codebase='" + codebase + "'\n" +
		755	widthAndHeight +
		756	" mayscript='true'>\n";
		757	tFooter = "</applet>";
		758	}
		759	var visitJava;
		760	if (isIEWin \|\| useHtml4Object) {
		761	var szX = "width:" + sz[0]
		762	if ( szX.indexOf("%")==-1 ) szX+="px"
		763	var szY = "height:" + sz[1]
		764	if ( szY.indexOf("%")==-1 ) szY+="px"
		765	visitJava =
		766	"<p style='background-color:yellow; color:black; " +
		767	szX + ";" + szY + ";" +
		768	// why doesn't this vertical-align work?
		769	"text-align:center;vertical-align:middle;'>\n" +
		770	noJavaMsg +
		771	"</p>";
		772	} else {
		773	visitJava =
		774	"<table bgcolor='yellow'><tr>" +
		775	"<td align='center' valign='middle' " + widthAndHeight + "><font color='black'>\n" +
		776	noJavaMsg2 +
		777	"</font></td></tr></table>";
		778	}
		779	params.loadInline = (inlineModel ? inlineModel : "");
		780	params.script = (script ? _jmolSterilizeScript(script) : "");
		781	var t = tHeader + _jmolParams() + visitJava + tFooter;
		782	jmolSetTarget(nameSuffix);
		783	ready["jmolApplet" + nameSuffix] = false;
		784	if (_jmol.debugAlert)
		785	alert(t);
		786	return _jmolDocumentWrite(t);
		787	}
		788	}
		789
		790	function _jmolParams() {
		791	var t = "";
		792	for (i in _jmol.params)
		793	if(_jmol.params[i]!="")
		794	t+=" <param name='"+i+"' value='"+_jmol.params[i]+"' />\n";
		795	return t
		796	}
		797
		798	function _jmolInitCheck() {
		799	if (_jmol.initChecked)
		800	return;
		801	_jmol.initChecked = true;
		802	jmolInitialize(defaultdir, defaultjar)
		803	}
		804
		805	function _jmolCheckBrowser() {
		806	with (_jmol) {
		807	if (browserChecked)
		808	return;
		809	browserChecked = true;
		810
		811	if (isFullyCompliant)
		812	return true;
		813
		814	if (checkBrowserAction == "redirect")
		815	location.href = checkBrowserUrlOrMessage;
		816	else if (checkBrowserAction == "popup")
		817	_jmolPopup(checkBrowserUrlOrMessage);
		818	else {
		819	var msg = checkBrowserUrlOrMessage;
		820	if (msg == null)
		821	msg = "Your web browser is not fully compatible with Jmol\n\n" +
		822	"browser: " + browser +
		823	" version: " + browserVersion +
		824	" os: " + os +
		825	"\n\n" + ua;
		826	alert(msg);
		827	}
		828	}
		829	return false;
		830	}
		831
		832	function _jmolDocumentWrite(text) {
		833	if (_jmol.currentDocument)
		834	_jmol.currentDocument.write(text);
		835	return text;
		836	}
		837
		838	function _jmolPopup(url) {
		839	var popup = window.open(url, "JmolPopup",
		840	"left=150,top=150,height=400,width=600," +
		841	"directories=yes,location=yes,menubar=yes," +
		842	"toolbar=yes," +
		843	"resizable=yes,scrollbars=yes,status=yes");
		844	if (popup.focus)
		845	poup.focus();
		846	}
		847
		848	function _jmolReadyCallback(name) {
		849	if (_jmol.debugAlert)
		850	alert(name + " is ready");
		851	_jmol.ready["" + name] = true;
		852	}
		853
		854	function _jmolSterilizeScript(script) {
		855	var inlineScript = script.replace(/'/g, "'");
		856	if (_jmol.debugAlert)
		857	alert("script:\n" + inlineScript);
		858	return inlineScript;
		859	}
		860
		861	function _jmolSterilizeInline(model) {
		862	var inlineModel =
		863	model.replace(/\r\|\n\|\r\n/g, "\|").replace(/'/g, "'");
		864	if (_jmol.debugAlert)
		865	alert("inline model:\n" + inlineModel);
		866	return inlineModel;
		867	}
		868
		869	/* AngelH, mar2007:
		870	By (re)setting this variable in the webpage before calling jmolApplet(), limits for applet size can be overriden.
		871	*/
		872
		873	/* hansonr, jun2007:
		874	2048 standard for GeoWall (http://geowall.geo.lsa.umich.edu/home.html)
		875	*/
		876
		877	if (allowedJmolSize==undefined) var allowedJmolSize = [1, 2048, 300] // min, max, default (pixels)
		878	function _jmolGetAppletSize(size) {
		879	/* AngelH, mar2007
		880	Accepts single number or 2-value array, each one can be either:
		881	percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.)
		882	Size is now returned as string or number, no "px".
		883	*/
		884	var width, height;
		885	if ( (typeof size) == "object" && size != null ) {
		886	width = size[0]; height = size[1];
		887	} else {
		888	width = height = size;
		889	}
		890	// if percent, leave it as it is:
		891	if ( width.toString().charAt(width.toString().length-1) != "%" ) {
		892	width = parseFloat(width); // convert to nr., or strip text, or make zero
		893	if ( width <= 1 && width > 0 ) { width = (width*100)+"%" } // decimal: convert to percent and quit
		894	else if ( width >= allowedJmolSize[0] && width <= allowedJmolSize[1] ) { width = parseInt(width) } // accept only that range (pixels)
		895	else { width = allowedJmolSize[2] } // default size 300 pixels
		896	}
		897	if ( height.toString().charAt(height.toString().length-1) != "%" ) {
		898	height = parseFloat(height);
		899	if ( height <= 1 && height > 0 ) { height = (height*100)+"%" }
		900	else if ( height >= allowedJmolSize[0] && height <= allowedJmolSize[1] ) { height = parseInt(height) }
		901	else { height = allowedJmolSize[2] }
		902	}
		903	return [width, height];
		904	}
		905
		906	function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
		907	++_jmol.radioCount;
		908	if (groupName == undefined \|\| groupName == null)
		909	groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1);
		910	if (!script)
		911	return "";
		912	if (labelHtml == undefined \|\| labelHtml == null)
		913	labelHtml = script.substring(0, 32);
		914	if (! separatorHtml)
		915	separatorHtml = "";
		916	var scriptIndex = _jmolAddScript(script);
		917	var eospan = "</span>"
		918	var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input name='"
		919	+ groupName + "' id='"+id+"' type='radio' onClick='_jmolClick(" +
		920	scriptIndex + _jmol.targetText + ");return true;' onMouseover='_jmolMouseOver(" +
		921	scriptIndex + ");return true;' onMouseout='_jmolMouseOut()' " +
		922	(isChecked ? "checked " : "") + _jmol.radioCssText + "/>"
		923	if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
		924	t += eospan
		925	eospan = "";
		926	}
		927	t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan + separatorHtml;
		928
		929	return t;
		930	}
		931
		932	function _jmolFindApplet(target) {
		933	// first look for the target in the current window
		934	var applet = _jmolFindAppletInWindow(_jmol.appletWindow != null ? _jmol.appletWindow : window, target);
		935	// THEN look for the target in child frames
		936	if (applet == undefined)
		937	applet = _jmolSearchFrames(window, target);
		938	// FINALLY look for the target in sibling frames
		939	if (applet == undefined)
		940	applet = _jmolSearchFrames(top, target); // look starting in top frame
		941	return applet;
		942	}
		943
		944	function _jmolGetApplet(targetSuffix){
		945	var target = "jmolApplet" + (targetSuffix ? targetSuffix : "0");
		946	var applet = _jmolFindApplet(target);
		947	if (applet) return applet
		948	if(!_jmol.alerted)alert("could not find applet " + target);
		949	_jmol.alerted = true;
		950	return null
		951	}
		952
		953	function _jmolSearchFrames(win, target) {
		954	var applet;
		955	var frames = win.frames;
		956	if (frames && frames.length) { // look in all the frames below this window
		957	try{
		958	for (var i = 0; i < frames.length; ++i) {
		959	applet = _jmolSearchFrames(frames[i], target);
		960	if (applet)
		961	return applet;
		962	}
		963	}catch(e) {
		964	if (_jmol.debugAlert)
		965	alert("Jmol.js _jmolSearchFrames cannot access " + win.name + ".frame[" + i + "] consider using jmolSetAppletWindow()")
		966	}
		967	}
		968	return applet = _jmolFindAppletInWindow(win, target)
		969	}
		970
		971	function _jmolFindAppletInWindow(win, target) {
		972	var doc = win.document;
		973	// getElementById fails on MacOSX Safari & Mozilla
		974	if (_jmol.useHtml4Object \|\| _jmol.useIEObject)
		975	return doc.getElementById(target);
		976	else if (doc.applets)
		977	return doc.applets[target];
		978	else
		979	return doc[target];
		980	}
		981
		982	function _jmolAddScript(script) {
		983	if (! script)
		984	return 0;
		985	var index = _jmol.scripts.length;
		986	_jmol.scripts[index] = script;
		987	return index;
		988	}
		989
		990	function _jmolClick(scriptIndex, targetSuffix, elementClicked) {
		991	_jmol.element = elementClicked;
		992	jmolScript(_jmol.scripts[scriptIndex], targetSuffix);
		993	}
		994
		995	function _jmolMenuSelected(menuObject, targetSuffix) {
		996	var scriptIndex = menuObject.value;
		997	if (scriptIndex != undefined) {
		998	jmolScript(_jmol.scripts[scriptIndex], targetSuffix);
		999	return;
		1000	}
		1001	var len = menuObject.length;
		1002	if (typeof len == "number") {
		1003	for (var i = 0; i < len; ++i) {
		1004	if (menuObject[i].selected) {
		1005	_jmolClick(menuObject[i].value, targetSuffix);
		1006	return;
		1007	}
		1008	}
		1009	}
		1010	alert("?Que? menu selected bug #8734");
		1011	}
		1012
		1013
		1014	_jmol.checkboxMasters = {};
		1015	_jmol.checkboxItems = {};
		1016
		1017	function jmolSetCheckboxGroup(chkMaster,chkBox) {
		1018	var id = chkMaster;
		1019	if(typeof(id)=="number")id = "jmolCheckbox" + id;
		1020	chkMaster = document.getElementById(id);
		1021	if (!chkMaster)alert("jmolSetCheckboxGroup: master checkbox not found: " + id);
		1022	var m = _jmol.checkboxMasters[id] = {};
		1023	m.chkMaster = chkMaster;
		1024	m.chkGroup = {};
		1025	for (var i = 1; i < arguments.length; i++){
		1026	var id = arguments[i];
		1027	if(typeof(id)=="number")id = "jmolCheckbox" + id;
		1028	checkboxItem = document.getElementById(id);
		1029	if (!checkboxItem)alert("jmolSetCheckboxGroup: group checkbox not found: " + id);
		1030	m.chkGroup[id] = checkboxItem;
		1031	_jmol.checkboxItems[id] = m;
		1032	}
		1033	}
		1034
		1035	function _jmolNotifyMaster(m){
		1036	//called when a group item is checked
		1037	var allOn = true;
		1038	var allOff = true;
		1039	for (var chkBox in m.chkGroup){
		1040	if(m.chkGroup[chkBox].checked)
		1041	allOff = false;
		1042	else
		1043	allOn = false;
		1044	}
		1045	if (allOn)m.chkMaster.checked = true;
		1046	if (allOff)m.chkMaster.checked = false;
		1047	if ((allOn \|\| allOff) && _jmol.checkboxItems[m.chkMaster.id])
		1048	_jmolNotifyMaster(_jmol.checkboxItems[m.chkMaster.id])
		1049	}
		1050
		1051	function _jmolNotifyGroup(m, isOn){
		1052	//called when a master item is checked
		1053	for (var chkBox in m.chkGroup){
		1054	var item = m.chkGroup[chkBox]
		1055	item.checked = isOn;
		1056	if (_jmol.checkboxMasters[item.id])
		1057	_jmolNotifyGroup(_jmol.checkboxMasters[item.id], isOn)
		1058	}
		1059	}
		1060
		1061	function _jmolCbClick(ckbox, whenChecked, whenUnchecked, targetSuffix) {
		1062	_jmol.control = ckbox
		1063	_jmolClick(ckbox.checked ? whenChecked : whenUnchecked, targetSuffix);
		1064	if(_jmol.checkboxMasters[ckbox.id])
		1065	_jmolNotifyGroup(_jmol.checkboxMasters[ckbox.id], ckbox.checked)
		1066	if(_jmol.checkboxItems[ckbox.id])
		1067	_jmolNotifyMaster(_jmol.checkboxItems[ckbox.id])
		1068	}
		1069
		1070	function _jmolCbOver(ckbox, whenChecked, whenUnchecked) {
		1071	window.status = _jmol.scripts[ckbox.checked ? whenUnchecked : whenChecked];
		1072	}
		1073
		1074	function _jmolMouseOver(scriptIndex) {
		1075	window.status = _jmol.scripts[scriptIndex];
		1076	}
		1077
		1078	function _jmolMouseOut() {
		1079	window.status = " ";
		1080	return true;
		1081	}
		1082
		1083	function _jmolSetCodebase(codebase) {
		1084	_jmol.codebase = codebase ? codebase : ".";
		1085	if (_jmol.debugAlert)
		1086	alert("jmolCodebase=" + _jmol.codebase);
		1087	}
		1088
		1089	function _jmolOnloadResetForms() {
		1090	// must be evaluated ONLY once
		1091	_jmol.previousOnloadHandler = window.onload;
		1092	window.onload =
		1093	function() {
		1094	with (_jmol) {
		1095	if (buttonCount+checkboxCount+menuCount+radioCount+radioGroupCount > 0) {
		1096	var forms = document.forms;
		1097	for (var i = forms.length; --i >= 0; )
		1098	forms[i].reset();
		1099	}
		1100	if (previousOnloadHandler)
		1101	previousOnloadHandler();
		1102	}
		1103	}
		1104	}
		1105
		1106	////////////////////////////////////
		1107	/////extensions for getProperty/////
		1108	////////////////////////////////////
		1109
		1110
		1111	function _jmolEvalJSON(s,key){
		1112	s=s+""
		1113	if(!s)return []
		1114	if(s.charAt(0)!="{"){
		1115	if(s.indexOf(" \| ")>=0)s=s.replace(/\ \\|\ /g, "\n")
		1116	return s
		1117	}
		1118	var A = eval("("+s+")")
		1119	if(!A)return
		1120	if(key && A[key])A=A[key]
		1121	return A
		1122	}
		1123
		1124	function _jmolEnumerateObject(A,key){
		1125	var sout=""
		1126	if(typeof(A) == "string" && A!="null"){
		1127	sout+="\n"+key+"=\""+A+"\""
		1128	}else if(!isNaN(A)\|\|A==null){
		1129	sout+="\n"+key+"="+(A+""==""?"null":A)
		1130	}else if(A.length){
		1131	sout+=key+"=[]"
		1132	for(var i=0;i<A.length;i++){
		1133	sout+="\n"
		1134	if(typeof(A[i]) == "object"\|\|typeof(A[i]) == "array"){
		1135	sout+=_jmolEnumerateObject(A[i],key+"["+i+"]")
		1136	}else{
		1137	sout+=key+"["+i+"]="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])
		1138	}
		1139	}
		1140	}else{
		1141	if(key != ""){
		1142	sout+=key+"={}"
		1143	key+="."
		1144	}
		1145
		1146	for(var i in A){
		1147	sout+="\n"
		1148	if(typeof(A[i]) == "object"\|\|typeof(A[i]) == "array"){
		1149	sout+=_jmolEnumerateObject(A[i],key+i)
		1150	}else{
		1151	sout+=key+i+"="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])
		1152	}
		1153	}
		1154	}
		1155	return sout
		1156	}
		1157
		1158
		1159	function _jmolSortKey0(a,b){
		1160	return (a[0]<b[0]?1:a[0]>b[0]?-1:0)
		1161	}
		1162
		1163	function _jmolSortMessages(A){
		1164	if(!A \|\| typeof(A)!="object")return []
		1165	var B = []
		1166	for(var i=A.length-1;i>=0;i--)for(var j=0;j<A[i].length;j++)B[B.length]=A[i][j]
		1167	if(B.length == 0) return
		1168	B=B.sort(_jmolSortKey0)
		1169	return B
		1170	}
		1171
		1172	/////////additional extensions //////////
		1173
		1174
		1175	function _jmolDomScriptLoad(URL){
		1176	//open(URL) //to debug
		1177	_jmol.servercall=URL
		1178	var node = document.getElementById("_jmolScriptNode")
		1179	if (node && _jmol.browser!="msie"){
		1180	document.getElementsByTagName("HEAD")[0].removeChild(node)
		1181	node=null
		1182	}
		1183	if (node) {
		1184	node.setAttribute("src",URL)
		1185	} else {
		1186	node=document.createElement("script")
		1187	node.setAttribute("id","_jmolScriptNode")
		1188	node.setAttribute("type","text/javascript")
		1189	node.setAttribute("src",URL)
		1190	document.getElementsByTagName("HEAD")[0].appendChild(node)
		1191	}
		1192	}
		1193
		1194
		1195	function _jmolExtractPostData(url){
		1196	S=url.split("&POST:")
		1197	var s=""
		1198	for(var i=1;i<S.length;i++){
		1199	KV=S[i].split("=")
		1200	s+="&POSTKEY"+i+"="+KV[0]
		1201	s+="&POSTVALUE"+i+"="+KV[1]
		1202	}
		1203	return "&url="+escape(S[0])+s
		1204	}
		1205
		1206	function _jmolLoadModel(targetSuffix,remoteURL,array,isError,errorMessage){
		1207	//called by server, but in client
		1208	//overload this function to customize return
		1209	_jmol.remoteURL=remoteURL
		1210	if(isError)alert(errorMessage)
		1211	jmolLoadInlineScript(array.join("\n"),_jmol.optionalscript,targetSuffix)
		1212	}
		1213
		1214	//////////user property/status functions/////////
		1215
		1216	function jmolGetStatus(strStatus,targetSuffix){
		1217	return _jmolSortMessages(jmolGetPropertyAsArray("jmolStatus",strStatus,targetSuffix))
		1218	}
		1219
		1220	function jmolGetPropertyAsArray(sKey,sValue,targetSuffix) {
		1221	return _jmolEvalJSON(jmolGetPropertyAsJSON(sKey,sValue,targetSuffix),sKey)
		1222	}
		1223
		1224	function jmolGetPropertyAsString(sKey,sValue,targetSuffix) {
		1225	var applet = _jmolGetApplet(targetSuffix);
		1226	if(!sValue)sValue=""
		1227	return (applet ? applet.getPropertyAsString(sKey,sValue) + "" : "")
		1228	}
		1229
		1230	function jmolGetPropertyAsJSON(sKey,sValue,targetSuffix) {
		1231	if(!sValue)sValue = ""
		1232	var applet = _jmolGetApplet(targetSuffix);
		1233	try {
		1234	return (applet ? applet.getPropertyAsJSON(sKey,sValue) + "" : "")
		1235	} catch(e) {
		1236	return ""
		1237	}
		1238	}
		1239
		1240	function jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix) {
		1241	if(!sValue)sValue = ""
		1242	var applet = _jmolGetApplet(targetSuffix);
		1243	return (applet ? applet.getProperty(sKey,sValue) : null)
		1244	}
		1245
		1246
		1247	function jmolDecodeJSON(s) {
		1248	return _jmolEnumerateObject(_jmolEvalJSON(s),"")
		1249	}
		1250
		1251
		1252	///////// synchronous scripting ////////
		1253
		1254	function jmolScriptWait(script, targetSuffix) {
		1255	if(!targetSuffix)targetSuffix="0"
		1256	var Ret=jmolScriptWaitAsArray(script, targetSuffix)
		1257	var s = ""
		1258	for(var i=Ret.length;--i>=0;)
		1259	for(var j=0;j< Ret[i].length;j++)
		1260	s+=Ret[i][j]+"\n"
		1261	return s
		1262	}
		1263
		1264	function jmolScriptWaitOutput(script, targetSuffix) {
		1265	if(!targetSuffix)targetSuffix="0"
		1266	var ret = ""
		1267	try{
		1268	if (script) {
		1269	_jmolCheckBrowser();
		1270	var applet=_jmolGetApplet(targetSuffix);
		1271	if (applet) ret += applet.scriptWaitOutput(script);
		1272	}
		1273	}catch(e){
		1274	}
		1275	return ret;
		1276	}
		1277
		1278	function jmolEvaluate(molecularMath, targetSuffix) {
		1279
		1280	//carries out molecular math on a model
		1281
		1282	if(!targetSuffix)targetSuffix="0"
		1283	var result = "" + jmolGetPropertyAsJavaObject("evaluate", molecularMath, targetSuffix);
		1284	var s = result.replace(/\-*\d+/,"")
		1285	if (s == "" && !isNaN(parseInt(result)))return parseInt(result);
		1286	var s = result.replace(/\-\d\.\d*/,"")
		1287	if (s == "" && !isNaN(parseFloat(result)))return parseFloat(result);
		1288	return result;
		1289	}
		1290
		1291	function jmolScriptEcho(script, targetSuffix) {
		1292	// returns a newline-separated list of all echos from a script
		1293	if(!targetSuffix)targetSuffix="0"
		1294	var Ret=jmolScriptWaitAsArray(script, targetSuffix)
		1295	var s = ""
		1296	for(var i=Ret.length;--i>=0;)
		1297	for(var j=Ret[i].length;--j>=0;)
		1298	if (Ret[i][j][1] == "scriptEcho")s+=Ret[i][j][3]+"\n"
		1299	return s.replace(/ \\| /g, "\n")
		1300	}
		1301
		1302
		1303	function jmolScriptMessage(script, targetSuffix) {
		1304	// returns a newline-separated list of all messages from a script, ending with "script completed\n"
		1305	if(!targetSuffix)targetSuffix="0"
		1306	var Ret=jmolScriptWaitAsArray(script, targetSuffix)
		1307	var s = ""
		1308	for(var i=Ret.length;--i>=0;)
		1309	for(var j=Ret[i].length;--j>=0;)
		1310	if (Ret[i][j][1] == "scriptStatus")s+=Ret[i][j][3]+"\n"
		1311	return s.replace(/ \\| /g, "\n")
		1312	}
		1313
		1314
		1315	function jmolScriptWaitAsArray(script, targetSuffix) {
		1316	var ret = ""
		1317	try{
		1318	jmolGetStatus("scriptEcho,scriptMessage,scriptStatus,scriptError",targetSuffix)
		1319	if (script) {
		1320	_jmolCheckBrowser();
		1321	var applet=_jmolGetApplet(targetSuffix);
		1322	if (applet) ret += applet.scriptWait(script);
		1323	ret = _jmolEvalJSON(ret,"jmolStatus")
		1324	if(typeof ret == "object")
		1325	return ret
		1326	}
		1327	}catch(e){
		1328	}
		1329	return [[ret]]
		1330	}
		1331
		1332
		1333
		1334	//////////// save/restore orientation /////////////
		1335
		1336	function jmolSaveOrientation(id, targetSuffix) {
		1337	if(!targetSuffix)targetSuffix="0"
		1338	return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo
		1339	}
		1340
		1341	function jmolRestoreOrientation(id, targetSuffix) {
		1342	if(!targetSuffix)targetSuffix="0"
		1343	var s=_jmol["savedOrientation"+id]
		1344	if (!s \|\| s == "")return
		1345	s=s.replace(/1\.0/,"0")
		1346	return jmolScriptWait(s,targetSuffix)
		1347	}
		1348
		1349	function jmolRestoreOrientationDelayed(id, delay, targetSuffix) {
		1350	if(arguments.length < 2)delay=1;
		1351	if(!targetSuffix)targetSuffix="0"
		1352	var s=_jmol["savedOrientation"+id]
		1353	if (!s \|\| s == "")return
		1354	s=s.replace(/1\.0/,delay)
		1355	return jmolScriptWait(s,targetSuffix)
		1356	}
		1357
		1358	//////////// add parameter /////////////
		1359	/*
		1360	* for adding callbacks or other parameters. Use:
		1361
		1362	jmolSetDocument(0)
		1363	var s= jmolApplet(....)
		1364	s = jmolAppletAddParam(s,"messageCallback", "myFunctionName")
		1365	document.write(s)
		1366	jmolSetDocument(document) // if you want to then write buttons and such normally
		1367
		1368	*/
		1369
		1370	function jmolAppletAddParam(appletCode,name,value){
		1371	if(value == "")return appletCode
		1372	return appletCode.replace(/\<param/,"\n<param name='"+name+"' value='"+value+"' />\n<param")
		1373	}
		1374
		1375	///////////////auto load Research Consortium for Structural Biology (RCSB) data ///////////
		1376
		1377	function jmolLoadAjax_STOLAF_RCSB(fileformat,pdbid,optionalscript,targetSuffix){
		1378
		1379	if(!_jmol.thismodel)_jmol.thismodel = "1crn"
		1380	if(!_jmol.serverURL)_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm"
		1381	if(!_jmol.RCSBserver)_jmol.RCSBserver="http://www.rcsb.org"
		1382	if(!_jmol.defaultURL_RCSB)_jmol.defaultURL_RCSB=_jmol.RCSBserver+"/pdb/files/1CRN.CIF"
		1383	if(!fileformat)fileformat="PDB"
		1384	if(!pdbid)pdbid=prompt("Enter a 4-digit PDB ID:",_jmol.thismodel)
		1385	if(!pdbid \|\| pdbid.length != 4)return ""
		1386	if(!targetSuffix)targetSuffix="0"
		1387	if(!optionalscript)optionalscript=""
		1388	var url=_jmol.defaultURL_RCSB.replace(/1CRN/g,pdbid.toUpperCase())
		1389	if(fileformat!="CIF")url=url.replace(/CIF/,fileformat)
		1390	_jmol.optionalscript=optionalscript
		1391	_jmol.thismodel=pdbid
		1392	_jmol.thistargetsuffix=targetSuffix
		1393	_jmol.thisurl=url
		1394	_jmol.modelArray = []
		1395	url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
		1396	_jmolDomScriptLoad(url)
		1397	return url
		1398	}
		1399
		1400	/////////////// St. Olaf College AJAX server -- ANY URL ///////////
		1401
		1402	function jmolLoadAjax_STOLAF_ANY(url, userid, optionalscript,targetSuffix){
		1403	_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm"
		1404	if(!_jmol.thisurlANY)_jmol.thisurlANY = "http://www.stolaf.edu/depts/chemistry/mo/struc/data/ycp3-1.mol"
		1405	if(!url)url=prompt("Enter any (uncompressed file) URL:", _jmol.thisurlANY)
		1406	if(!userid)userid="0"
		1407	if(!targetSuffix)targetSuffix="0"
		1408	if(!optionalscript)optionalscript=""
		1409	_jmol.optionalscript=optionalscript
		1410	_jmol.thistargetsuffix=targetSuffix
		1411	_jmol.modelArray = []
		1412	_jmol.thisurl = url
		1413	url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
		1414	_jmolDomScriptLoad(url)
		1415	}
		1416
		1417
		1418	/////////////// Mineralogical Society of America (MSA) data /////////
		1419
		1420	function jmolLoadAjax_MSA(key,value,optionalscript,targetSuffix){
		1421
		1422	if(!_jmol.thiskeyMSA)_jmol.thiskeyMSA = "mineral"
		1423	if(!_jmol.thismodelMSA)_jmol.thismodelMSA = "quartz"
		1424	if(!_jmol.ajaxURL_MSA)_jmol.ajaxURL_MSA="http://rruff.geo.arizona.edu/AMS/result.php?mineral=quartz&viewing=ajaxjs"
		1425	if(!key)key=prompt("Enter a field:", _jmol.thiskeyMSA)
		1426	if(!key)return ""
		1427	if(!value)value=prompt("Enter a "+key+":", _jmol.thismodelMSA)
		1428	if(!value)return ""
		1429	if(!targetSuffix)targetSuffix="0"
		1430	if(!optionalscript)optionalscript=""
		1431	if(optionalscript == 1)optionalscript='load "" {1 1 1}'
		1432	var url=_jmol.ajaxURL_MSA.replace(/mineral/g,key).replace(/quartz/g,value)
		1433	_jmol.optionalscript=optionalscript
		1434	_jmol.thiskeyMSA=key
		1435	_jmol.thismodelMSA=value
		1436	_jmol.thistargetsuffix=targetSuffix
		1437	_jmol.thisurl=url
		1438	_jmol.modelArray = []
		1439	loadModel=_jmolLoadModel
		1440	_jmolDomScriptLoad(url)
		1441	return url
		1442	}
		1443
		1444
		1445
		1446	function jmolLoadAjaxJS(url, userid, optionalscript,targetSuffix){
		1447	if(!userid)userid="0"
		1448	if(!targetSuffix)targetSuffix="0"
		1449	if(!optionalscript)optionalscript=""
		1450	_jmol.optionalscript=optionalscript
		1451	_jmol.thismodel=userid
		1452	_jmol.thistargetsuffix=targetSuffix
		1453	_jmol.modelArray = []
		1454	_jmol.thisurl = url
		1455	url+="&returnFunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix
		1456	_jmolDomScriptLoad(url)
		1457	}
		1458
		1459
		1460	//// in case Jmol library has already been loaded:
		1461
		1462	}catch(e){}
		1463
		1464	///////////////moving atoms //////////////
		1465
		1466	// HIGHLY experimental!!
		1467
		1468	function jmolSetAtomCoord(i,x,y,z,targetSuffix){
		1469	_jmolCheckBrowser();
		1470	var applet=_jmolGetApplet(targetSuffix);
		1471	if (applet) applet.getProperty('jmolViewer').setAtomCoord(i,x,y,z)
		1472	}
		1473
		1474	function jmolSetAtomCoordRelative(i,x,y,z,targetSuffix){
		1475	_jmolCheckBrowser();
		1476	var applet=_jmolGetApplet(targetSuffix);
		1477	if (applet) applet.getProperty('jmolViewer').setAtomCoordRelative(i,x,y,z)
		1478	}
		1479
		1480
		1481	///////////////applet fake for testing buttons/////////////
		1482
		1483
		1484	if(document.location.search.indexOf("NOAPPLET")>=0){
		1485	jmolApplet = function(w){
		1486	var s="<table style='background-color:black' width="+w+"><tr height="+w+">"
		1487	+"<td align=center valign=center style='background-color:white'>"
		1488	+"Applet would be here"
		1489	+"<p><textarea id=fakeApplet rows=5 cols=50></textarea>"
		1490	+"</td></tr></table>"
		1491	return _jmolDocumentWrite(s)
		1492	}
		1493
		1494	_jmolFindApplet = function(){return jmolApplet0}
		1495
		1496	jmolApplet0 = {
		1497	script: function(script){document.getElementById("fakeApplet").value="\njmolScript:\n"+script}
		1498	,scriptWait: function(script){document.getElementById("fakeApplet").value="\njmolScriptWait:\n"+script}
		1499	,loadInline: function(data,script){document.getElementById("fakeApplet").value="\njmolLoadInline data:\n"+data+"\n\nscript:\n"+script}
		1500	}
		1501	}
		1502
		1503
		1504	///////////////////////////////////////////
		1505
		1506	//new 9:49 AM 3/6/2007:
		1507
		1508	//both w and h are optional.
		1509	//if either is between 0 and 1, then it is taken as percent/100.
		1510	//if either is greater than 1, then it is taken as a size.
		1511	function jmolResize(w,h) {
		1512	_jmol.alerted = true;
		1513	var percentW = (!w ? 100 : w <= 1 && w > 0 ? w * 100 : 0)
		1514	var percentH = (!h ? percentW : h <= 1 && h > 0 ? h * 100 : 0)
		1515	if (_jmol.browser=="msie") {
		1516	var width=document.body.clientWidth;
		1517	var height=document.body.clientHeight;
		1518	} else {
		1519	var netscapeScrollWidth=15;
		1520	var width=window.innerWidth - netscapeScrollWidth;
		1521	var height=window.innerHeight-netscapeScrollWidth;
		1522	}
		1523	var applet = _jmolGetApplet(0);
		1524	if(!applet)return;
		1525	applet.style.width = (percentW ? width * percentW/100 : w)+"px"
		1526	applet.style.height = (percentH ? height * percentH/100 : h)+"px"
		1527	title=width + " " + height + " " + (new Date())
		1528	}
		1529

Subversion Repositories wimsdev

(root)/trunk/wims/public_html/java/jmol/Jmol.js – Rev 1365