/* Jmol 12.0 script library Jmol.js 9:48 PM 1/31/2011 Bob Hanson
checkbox heirarchy -- see http://chemapps.stolaf.edu/jmol/docs/examples-11/check.htm
based on:
*
* Copyright (C) 2004-2005 Miguel, Jmol Development, www.jmol.org
*
* Contact: hansonr@stolaf.edu
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library 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
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
* 02111-1307 USA.
*/
// for documentation see www.jmol.org/jslibrary
try{if(typeof(_jmol)!="undefined")exit()
// place "?NOAPPLET" on your command line to check applet control action with a textarea
// place "?JMOLJAR=xxxxx" to use a specific jar file
// bob hanson -- jmolResize(w,h) -- resizes absolutely or by percent (w or h 0.5 means 50%)
// angel herraez -- update of jmolResize(w,h,targetSuffix) so it is not tied to first applet
// bob hanson -- jmolEvaluate -- evaluates molecular math 8:37 AM 2/23/2007
// bob hanson -- jmolScriptMessage -- returns all "scriptStatus" messages 8:37 AM 2/23/2007
// bob hanson -- jmolScriptEcho -- returns all "scriptEcho" messages 8:37 AM 2/23/2007
// bob hanson -- jmolScriptWait -- 11:31 AM 5/2/2006
// bob hanson -- remove trailing separatorHTML in radio groups -- 12:18 PM 5/6/2006
// bob hanson -- adds support for dynamic DOM script nodes 7:04 AM 5/19/2006
// bob hanson -- adds try/catch for wiki - multiple code passes 7:05 AM 5/19/2006
// bob hanson -- auto-initiates to defaultdir/defaultjar -- change as desired.
// bob hanson -- adding save/restore orientation w/ and w/o delay 11:49 AM 5/25/2006
// bob hanson -- adding AjaxJS service 11:16 AM 6/3/2006
// bob hanson -- fix for iframes not available for finding applet
// bob hanson -- added applet fake ?NOAPPLET URL flag
// bob hanson -- added jmolSetCallback(calbackName, funcName) 3:32 PM 6/13/2006
// used PRIOR to jmolApplet() or jmolAppletInline()
// added 4th array element in jmolRadioGroup -- title
// added and id around link, checkbox, radio, menu
// fixing AJAX loads for MSIE/Opera-Mozilla incompatibility
// -- renamed Jmol-11.js from Jmol-new.js; JmolApplet.jar from JmolAppletProto.jar
// renamed Jmol.js for Jmol 11 distribution
// -- modified jmolRestoreOrientation() to be immediate, no 1-second delay
// bob hanson -- jmolScriptWait always returns a string -- 11:23 AM 9/16/2006
// bh -- jmolCommandInput()
// bh -- jmolSetTranslation(TF) -- forces translation even if there might be message callback issues
// bh -- minor fixes suggested by Angel
// bh -- adds jmolSetSyncId() and jmolGetSyncId()
// bh 3/2008 -- adds jmolAppendInlineScript() and jmolAppendInlineArray()
// bh 3/2008 -- fixes IE7 bug in relation to jmolLoadInlineArray()
// bh 6/2008 -- adds jmolSetAppletWindow()
// Angel H. 6/2008 -- added html tags to checkboxes and radio buttons [in jmolCheckbox() and _jmolRadio() functions]
// bh 7/2008 -- code fix "for(i..." not "for(var i..."
// bh 12/2008 -- jmolLoadInline, jmolLoadInlineArray, jmolLoadInlineScript, jmolAppendInlineScript, jmolAppendInlineArray all return error message or null (Jmol 11.7.16)
// bh 12/2008 -- jmolScriptWaitOutput() -- waits for script to complete and delivers output normally sent to console
// bh 5/2009 -- Support for XHTML using jmolSetXHTML(id)
// ah & bh 6/2009 -- New jmolResizeApplet() more flexible, similar to jmolApplet() size syntax
// bh 11/2009 -- care in accessing top.document
// bh 12/2009 -- added jmolSetParameter(name, value)
// bh 12/2009 -- added PARAMS=name:value;name:value;name:value... for command line
// bh 12/2009 -- overhaul of target checking
// bh 1/2010 -- all _xxxx() methods ALWAYS have complete argument list
// bh 1/2010 -- adds option to run a JavaScript function from any Jmol control.
// This is accomplished by passing an array rather than a script:
// jmolHref([myfunc,"my param 1", "my param 2"], "testing")
// function myfunc(jmolControlObject, [myfunc,"my param 1", "my param 2"], target){...}
// and allows much more flexibility with responding to controls
// bh 4/2010 -- added jmolSetMemoryMb(nMb)
// ah 1/2011 -- wider detection of browsers; more browsers now use the object tag instead of the applet tag;
// fix of object tag (removed classid) accounts for change of behavior in Chrome
var defaultdir = "."
var defaultjar = "JmolApplet.jar"
// Note added 12:41 PM 9/21/2008 by Bob Hanson, hansonr@stolaf.edu:
// JMOLJAR=xxxxx.jar on the URL for this page will override
// the JAR file specified in the jmolInitialize() call.
// The idea is that it can be very useful to test a web page with different JAR files
// Or for an expert user to substitute a signed applet for an unsigned one
// so as to use a broader range of models or to create JPEG files, for example.
// If the JAR file is not in the current directory (has any sort of "/" in its name)
// then the user is presented with a warning and asked whether it is OK to change Jar files.
// The default action, if the user just presses "OK" is to NOT allow the change.
// The user must type the word "yes" in the prompt box for the change to be approved.
// If you don't want people to be able to switch in their own JAR file on your page,
// simply set this next line to read "var allowJMOLJAR = false".
var undefined; // for IE 5 ... wherein undefined is undefined
////////////////////////////////////////////////////////////////
// Basic Scripting infrastruture
////////////////////////////////////////////////////////////////
function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {
if (_jmol.initialized)
return;
_jmol.initialized = true;
if(_jmol.jmoljar) {
var f = _jmol.jmoljar;
if (f.indexOf("/") >= 0) {
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.")
var ok = prompt("Do you want to use applet " + f + "? ","yes or no")
if (ok == "yes") {
codebaseDirectory = f.substring(0, f.lastIndexOf("/"));
fileNameOrUseSignedApplet = f.substring(f.lastIndexOf("/") + 1);
} else {
_jmolGetJarFilename(fileNameOrUseSignedApplet);
alert("The web page URL was ignored. Continuing using " + _jmol.archivePath + ' in directory "' + codebaseDirectory + '"');
}
} else {
fileNameOrUseSignedApplet = f;
}
}
_jmolSetCodebase(codebaseDirectory);
_jmolGetJarFilename(fileNameOrUseSignedApplet);
_jmolOnloadResetForms();
}
function jmolSetTranslation(TF) {
_jmol.params.doTranslate = ''+TF;
}
function jmolToSigned(){
_jmolGetJarFilename(true);
}
function _jmolGetJarFilename(fileNameOrFlag) {
_jmol.archivePath =
(typeof(fileNameOrFlag) == "string" ? fileNameOrFlag : (fileNameOrFlag ? "JmolAppletSigned" : "JmolApplet") + "0.jar");
}
function jmolSetDocument(doc) {
_jmol.currentDocument = doc;
}
function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {
_jmolInitCheck();
_jmol.params.boxbgcolor = boxbgcolor;
if (boxfgcolor)
_jmol.params.boxfgcolor = boxfgcolor
else if (boxbgcolor == "white" || boxbgcolor == "#FFFFFF")
_jmol.params.boxfgcolor = "black";
else
_jmol.params.boxfgcolor = "white";
if (progresscolor)
_jmol.params.progresscolor = progresscolor;
if (_jmol.debugAlert)
alert(" boxbgcolor=" + _jmol.params.boxbgcolor +
" boxfgcolor=" + _jmol.params.boxfgcolor +
" progresscolor=" + _jmol.params.progresscolor);
}
function jmolSetAppletWindow(w) {
_jmol.appletWindow = w;
}
function jmolApplet(size, script, nameSuffix) {
_jmolInitCheck();
return _jmolApplet(size, null, script, nameSuffix);
}
////////////////////////////////////////////////////////////////
// Basic controls
////////////////////////////////////////////////////////////////
// undefined means it wasn't there; null means it was explicitly listed as null (so as to skip it)
function jmolButton(script, label, id, title) {
_jmolInitCheck();
id != undefined && id != null || (id = "jmolButton" + _jmol.buttonCount);
label != undefined && label != null || (label = script.substring(0, 32));
++_jmol.buttonCount;
var scriptIndex = _jmolAddScript(script);
var t = " ";
if (_jmol.debugAlert)
alert(t);
return _jmolDocumentWrite(t);
}
function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked,
labelHtml, isChecked, id, title) {
_jmolInitCheck();
id != undefined && id != null || (id = "jmolCheckbox" + _jmol.checkboxCount);
++_jmol.checkboxCount;
if (scriptWhenChecked == undefined || scriptWhenChecked == null ||
scriptWhenUnchecked == undefined || scriptWhenUnchecked == null) {
alert("jmolCheckbox requires two scripts");
return;
}
if (labelHtml == undefined || labelHtml == null) {
alert("jmolCheckbox requires a label");
return;
}
var indexChecked = _jmolAddScript(scriptWhenChecked);
var indexUnchecked = _jmolAddScript(scriptWhenUnchecked);
var eospan = " "
var t = " "
if (labelHtml.toLowerCase().indexOf("
")>=0) {
t += eospan
eospan = "";
}
t += "" + labelHtml + " " +eospan;
if (_jmol.debugAlert)
alert(t);
return _jmolDocumentWrite(t);
}
function jmolStartNewRadioGroup() {
++_jmol.radioGroupCount;
}
function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) {
/*
array: [radio1,radio2,radio3...]
where radioN = ["script","label",isSelected,"id","title"]
*/
_jmolInitCheck();
var type = typeof arrayOfRadioButtons;
if (type != "object" || type == null || ! arrayOfRadioButtons.length) {
alert("invalid arrayOfRadioButtons");
return;
}
separatorHtml != undefined && separatorHtml != null || (separatorHtml = " ");
var len = arrayOfRadioButtons.length;
jmolStartNewRadioGroup();
groupName || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));
var t = "";
for (var i = 0; i < len; ++i) {
if (i == len - 1)
separatorHtml = "";
var radio = arrayOfRadioButtons[i];
type = typeof radio;
if (type == "object") {
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);
} else {
t += _jmolRadio(radio, null, null, separatorHtml, groupName, (id ? id : groupName)+"_"+i, title);
}
}
t+=" "
if (_jmol.debugAlert)
alert(t);
return _jmolDocumentWrite(t);
}
function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
_jmolInitCheck();
if (_jmol.radioGroupCount == 0)
++_jmol.radioGroupCount;
var t = _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, (id ? id : groupName + "_" + _jmol.radioCount), title ? title : 0);
if (_jmol.debugAlert)
alert(t);
return _jmolDocumentWrite(t);
}
function jmolLink(script, label, id, title) {
_jmolInitCheck();
id != undefined && id != null || (id = "jmolLink" + _jmol.linkCount);
label != undefined && label != null || (label = script.substring(0, 32));
++_jmol.linkCount;
var scriptIndex = _jmolAddScript(script);
var t = "" + label + " ";
if (_jmol.debugAlert)
alert(t);
return _jmolDocumentWrite(t);
}
function jmolCommandInput(label, size, id, title) {
_jmolInitCheck();
id != undefined && id != null || (id = "jmolCmd" + _jmol.cmdCount);
label != undefined && label != null || (label = "Execute");
size != undefined && !isNaN(size) || (size = 60);
++_jmol.cmdCount;
var t = " ";
if (_jmol.debugAlert)
alert(t);
return _jmolDocumentWrite(t);
}
function _jmolCommandKeyPress(e, id, target) {
var keycode = (window.event ? window.event.keyCode : e ? e.which : 0);
if (keycode == 13) {
var inputBox = document.getElementById(id)
_jmolScriptExecute(inputBox, inputBox.value, target)
}
}
function _jmolScriptExecute(element,script,target) {
if (typeof(script) == "object")
script[0](element, script, target)
else
jmolScript(script, target)
}
function jmolMenu(arrayOfMenuItems, size, id, title) {
_jmolInitCheck();
id != undefined && id != null || (id = "jmolMenu" + _jmol.menuCount);
++_jmol.menuCount;
var type = typeof arrayOfMenuItems;
if (type != null && type == "object" && arrayOfMenuItems.length) {
var len = arrayOfMenuItems.length;
if (typeof size != "number" || size == 1)
size = null;
else if (size < 0)
size = len;
var sizeText = size ? " size='" + size + "' " : "";
var t = "";
for (var i = 0; i < len; ++i) {
var menuItem = arrayOfMenuItems[i];
type = typeof menuItem;
var script, text;
var isSelected = undefined;
if (type == "object" && menuItem != null) {
script = menuItem[0];
text = menuItem[1];
isSelected = menuItem[2];
} else {
script = text = menuItem;
}
text != undefined && text != null || (text = script);
if (script=="#optgroup") {
t += "";
} else if (script=="#optgroupEnd") {
t += " ";
} else {
var scriptIndex = _jmolAddScript(script);
var selectedText = isSelected ? "' selected='true'>" : "'>";
t += "= 5.5);
useHtml4Object =
(browser == "mozilla" && browserVersion >= 5) ||
(browser == "opera" && browserVersion >= 8) ||
(browser == "webkit" && browserVersion >= 412.2);
try {
if (top.location.search.indexOf("JMOLJAR=")>=0)
jmoljar = top.location.search.split("JMOLJAR=")[1].split("&")[0];
} catch(e) {
// can't access top.location
}
try {
useNoApplet = (top.location.search.indexOf("NOAPPLET")>=0);
} catch(e) {
// can't access top.document
}
}
function jmolSetMemoryMb(nMb) {
_jmol.java_arguments = "-Xmx" + Math.round(nMb) + "m"
}
function jmolSetParameter(name,value) {
_jmol.params[name] = value
}
function jmolSetCallback(callbackName,funcName) {
_jmol.params[callbackName] = funcName
}
try {
// note this is done FIRST, so it cannot override a setting done by the developer
if (top.location.search.indexOf("PARAMS=")>=0) {
var pars = unescape(top.location.search.split("PARAMS=")[1].split("&")[0]).split(";");
for (var i = 0; i < pars.length; i++) {
var p = pars[i].split(":");
jmolSetParameter(p[0],p[1]);
}
}
} catch(e) {
// can't access top.location
}
function jmolSetSyncId(n) {
return _jmol.params["syncId"] = n
}
function jmolGetSyncId() {
return _jmol.params["syncId"]
}
function jmolSetLogLevel(n) {
_jmol.params.logLevel = ''+n;
}
/* AngelH, mar2007:
By (re)setting these variables in the webpage before calling jmolApplet(),
a custom message can be provided (e.g. localized for user's language) when no Java is installed.
*/
if (noJavaMsg==undefined) var noJavaMsg =
"You do not have Java applets enabled in your web browser, or your browser is blocking this applet. \n" +
"Check the warning message from your browser and/or enable Java applets in \n" +
"your web browser preferences, or install the Java Runtime Environment from www.java.com ";
if (noJavaMsg2==undefined) var noJavaMsg2 =
"You do not have the \n" +
"Java Runtime Environment \n" +
"installed for applet support. \n" +
"Visit www.java.com ";
function _jmolApplet(size, inlineModel, script, nameSuffix) {
/* AngelH, mar2007
Fixed percent / pixel business, to avoid browser errors:
put "px" where needed, avoid where not.
Bob Hanson, 1/2010
Fixed inline escape changing returns to |
*/
with (_jmol) {
nameSuffix == undefined && (nameSuffix = appletCount);
appletSuffixes.push(nameSuffix);
++appletCount;
script || (script = "select *");
var sz = _jmolGetAppletSize(size);
var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' ";
var tHeader, tFooter;
codebase || jmolInitialize(".");
if (useIEObject || useHtml4Object) {
params.archive = archivePath;
params.mayscript = 'true';
params.codebase = codebase;
params.code = 'JmolApplet';
tHeader =
"\n";
} else if (useHtml4Object) { // use HTML4 object tag
tHeader += " type='application/x-java-applet'\n>\n";
/* " classid='java:JmolApplet'\n" + AH removed this
Chromium Issue 62076: Java Applets using an with a classid paramater don't load.
http://code.google.com/p/chromium/issues/detail?id=62076
They say this is the correct behavior according to the spec, and there's no indication at this point
that WebKit will be changing the handling, so eventually Safari will acquire this behavior too.
Removing the classid parameter seems to be well tolerated by all browsers (even IE!).
*/
} else { // use applet tag
tHeader =
"\n";
tFooter = " ";
}
var visitJava;
if (useIEObject || useHtml4Object) {
var szX = "width:" + sz[0]
if ( szX.indexOf("%")==-1 ) szX+="px"
var szY = "height:" + sz[1]
if ( szY.indexOf("%")==-1 ) szY+="px"
visitJava =
"\n" +
noJavaMsg +
"
";
} else {
visitJava =
"" +
"\n" +
noJavaMsg2 +
"
";
}
params.loadInline = (inlineModel ? inlineModel : "");
params.script = (script ? _jmolSterilizeScript(script) : "");
var t = tHeader + _jmolParams() + visitJava + tFooter;
jmolSetTarget(nameSuffix);
ready["jmolApplet" + nameSuffix] = false;
if (_jmol.debugAlert)
alert(t);
return _jmolDocumentWrite(t);
}
}
function _jmolParams() {
var t = "";
for (var i in _jmol.params)
if(_jmol.params[i]!="")
t+=" \n";
return t
}
function _jmolInitCheck() {
if (_jmol.initChecked)
return;
_jmol.initChecked = true;
jmolInitialize(defaultdir, defaultjar)
}
function _jmolCheckBrowser() {
with (_jmol) {
if (browserChecked)
return;
browserChecked = true;
if (isFullyCompliant)
return true;
if (checkBrowserAction == "redirect")
location.href = checkBrowserUrlOrMessage;
else if (checkBrowserAction == "popup")
_jmolPopup(checkBrowserUrlOrMessage);
else {
var msg = checkBrowserUrlOrMessage;
if (msg == null)
msg = "Your web browser is not fully compatible with Jmol\n\n" +
"browser: " + browser +
" version: " + browserVersion +
" os: " + os +
" isBrowserCompliant: " + isBrowserCompliant +
" isJavaCompliant: " + isJavaCompliant +
"\n\n" + ua;
alert(msg);
}
}
return false;
}
function jmolSetXHTML(id) {
_jmol.isXHTML = true
_jmol.XhtmlElement = null
_jmol.XhtmlAppendChild = false
if (id){
_jmol.XhtmlElement = document.getElementById(id)
_jmol.XhtmlAppendChild = true
}
}
function _jmolDocumentWrite(text) {
if (_jmol.currentDocument) {
if (_jmol.isXHTML && !_jmol.XhtmlElement) {
var s = document.getElementsByTagName("script")
_jmol.XhtmlElement = s.item(s.length - 1)
_jmol.XhtmlAppendChild = false
}
if (_jmol.XhtmlElement) {
_jmolDomDocumentWrite(text)
} else {
_jmol.currentDocument.write(text);
}
}
return text;
}
function _jmolDomDocumentWrite(data) {
var pt = 0
var Ptr = []
Ptr[0] = 0
while (Ptr[0] < data.length) {
var child = _jmolGetDomElement(data, Ptr)
if (!child)break
if (_jmol.XhtmlAppendChild)
_jmol.XhtmlElement.appendChild(child)
else
_jmol.XhtmlElement.parentNode.insertBefore(child, _jmol.XhtmlElement);
}
}
function _jmolGetDomElement(data, Ptr, closetag, lvel) {
var e = document.createElement("span")
e.innerHTML = data
Ptr[0] = data.length
return e
//unnecessary?
closetag || (closetag = "")
lvel || (lvel = 0)
var pt0 = Ptr[0]
var pt = pt0
while (pt < data.length && data.charAt(pt) != "<") pt++
if (pt != pt0) {
var text = data.substring(pt0, pt)
Ptr[0] = pt
return document.createTextNode(text)
}
pt0 = ++pt
var ch
while (pt < data.length && "\n\r\t >".indexOf(ch = data.charAt(pt)) < 0) pt++
var tagname = data.substring(pt0, pt)
var e = (tagname == closetag || tagname == "/" ? ""
: document.createElementNS ? document.createElementNS('http://www.w3.org/1999/xhtml', tagname)
: document.createElement(tagname));
if (ch == ">") {
Ptr[0] = ++pt
return e
}
while (pt < data.length && (ch = data.charAt(pt)) != ">") {
while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) pt++
pt0 = pt
while (pt < data.length && "\n\r\t =/>".indexOf(ch = data.charAt(pt)) < 0) pt++
var attrname = data.substring(pt0, pt).toLowerCase()
if (attrname && ch != "=")
e.setAttribute(attrname, "true")
while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) pt++
if (ch == "/") {
Ptr[0] = pt + 2
return e
} else if (ch == "=") {
var quote = data.charAt(++pt)
pt0 = ++pt
while (pt < data.length && (ch = data.charAt(pt)) != quote) pt++
var attrvalue = data.substring(pt0, pt)
e.setAttribute(attrname, attrvalue)
pt++
}
}
Ptr[0] = ++pt
while (Ptr[0] < data.length) {
var child = _jmolGetDomElement(data, Ptr, "/" + tagname, lvel+1)
if (!child)break
e.appendChild(child)
}
return e
}
function _jmolPopup(url) {
var popup = window.open(url, "JmolPopup",
"left=150,top=150,height=400,width=600," +
"directories=yes,location=yes,menubar=yes," +
"toolbar=yes," +
"resizable=yes,scrollbars=yes,status=yes");
if (popup.focus)
poup.focus();
}
function _jmolReadyCallback(name) {
if (_jmol.debugAlert)
alert(name + " is ready");
_jmol.ready["" + name] = true;
}
function _jmolSterilizeScript(script) {
script = script.replace(/'/g, "'");
if (_jmol.debugAlert)
alert("script:\n" + script);
return script;
}
function _jmolSterilizeInline(model) {
model = model.replace(/\r|\n|\r\n/g, (model.indexOf("|") >= 0 ? "\\/n" : "|")).replace(/'/g, "'");
if (_jmol.debugAlert)
alert("inline model:\n" + model);
return model;
}
function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
++_jmol.radioCount;
groupName != undefined && groupName != null || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));
if (!script)
return "";
labelHtml != undefined && labelHtml != null || (labelHtml = script.substring(0, 32));
separatorHtml || (separatorHtml = "")
var scriptIndex = _jmolAddScript(script);
var eospan = " "
var t = " "
if (labelHtml.toLowerCase().indexOf(" ")>=0) {
t += eospan
eospan = "";
}
t += "" + labelHtml + " " +eospan + separatorHtml;
return t;
}
function _jmolFindApplet(target) {
// first look for the target in the current window
var applet = _jmolFindAppletInWindow(_jmol.appletWindow != null ? _jmol.appletWindow : window, target);
// THEN look for the target in child frames
if (applet == undefined)
applet = _jmolSearchFrames(window, target);
// FINALLY look for the target in sibling frames
if (applet == undefined)
applet = _jmolSearchFrames(top, target); // look starting in top frame
return applet;
}
function _jmolGetApplet(targetSuffix){
var target = "jmolApplet" + (targetSuffix ? targetSuffix : "0");
var applet = _jmolFindApplet(target);
if (applet) return applet
_jmol.alerted || alert("could not find applet " + target);
_jmol.alerted = true;
return null
}
function _jmolSearchFrames(win, target) {
var applet;
var frames = win.frames;
if (frames && frames.length) { // look in all the frames below this window
try{
for (var i = 0; i < frames.length; ++i) {
applet = _jmolSearchFrames(frames[i], target);
if (applet)
return applet;
}
}catch(e) {
if (_jmol.debugAlert)
alert("Jmol.js _jmolSearchFrames cannot access " + win.name + ".frame[" + i + "] consider using jmolSetAppletWindow()")
}
}
return applet = _jmolFindAppletInWindow(win, target)
}
function _jmolFindAppletInWindow(win, target) {
var doc = win.document;
if (doc.getElementById(target))
return doc.getElementById(target);
else if (doc.applets)
return doc.applets[target];
else
return doc[target];
}
function _jmolAddScript(script) {
if (!script)
return 0;
var index = _jmol.scripts.length;
_jmol.scripts[index] = script;
return index;
}
function _jmolClick(elementClicked, scriptIndex, targetSuffix) {
_jmol.element = elementClicked;
_jmolScriptExecute(elementClicked, _jmol.scripts[scriptIndex], targetSuffix);
}
function _jmolMenuSelected(menuObject, targetSuffix) {
var scriptIndex = menuObject.value;
if (scriptIndex != undefined) {
_jmolScriptExecute(menuObject, _jmol.scripts[scriptIndex], targetSuffix);
return;
}
var len = menuObject.length;
if (typeof len == "number") {
for (var i = 0; i < len; ++i) {
if (menuObject[i].selected) {
_jmolClick(menuObject[i], menuObject[i].value, targetSuffix);
return;
}
}
}
alert("?Que? menu selected bug #8734");
}
_jmol.checkboxMasters = {};
_jmol.checkboxItems = {};
function jmolSetCheckboxGroup(chkMaster,chkBox) {
var id = chkMaster;
if(typeof(id)=="number")id = "jmolCheckbox" + id;
chkMaster = document.getElementById(id);
if (!chkMaster)alert("jmolSetCheckboxGroup: master checkbox not found: " + id);
var m = _jmol.checkboxMasters[id] = {};
m.chkMaster = chkMaster;
m.chkGroup = {};
for (var i = 1; i < arguments.length; i++){
var id = arguments[i];
if(typeof(id)=="number")id = "jmolCheckbox" + id;
checkboxItem = document.getElementById(id);
if (!checkboxItem)alert("jmolSetCheckboxGroup: group checkbox not found: " + id);
m.chkGroup[id] = checkboxItem;
_jmol.checkboxItems[id] = m;
}
}
function _jmolNotifyMaster(m){
//called when a group item is checked
var allOn = true;
var allOff = true;
for (var chkBox in m.chkGroup){
if(m.chkGroup[chkBox].checked)
allOff = false;
else
allOn = false;
}
if (allOn)m.chkMaster.checked = true;
if (allOff)m.chkMaster.checked = false;
if ((allOn || allOff) && _jmol.checkboxItems[m.chkMaster.id])
_jmolNotifyMaster(_jmol.checkboxItems[m.chkMaster.id])
}
function _jmolNotifyGroup(m, isOn){
//called when a master item is checked
for (var chkBox in m.chkGroup){
var item = m.chkGroup[chkBox]
item.checked = isOn;
if (_jmol.checkboxMasters[item.id])
_jmolNotifyGroup(_jmol.checkboxMasters[item.id], isOn)
}
}
function _jmolCbClick(ckbox, whenChecked, whenUnchecked, targetSuffix) {
_jmol.control = ckbox
_jmolClick(ckbox, ckbox.checked ? whenChecked : whenUnchecked, targetSuffix);
if(_jmol.checkboxMasters[ckbox.id])
_jmolNotifyGroup(_jmol.checkboxMasters[ckbox.id], ckbox.checked)
if(_jmol.checkboxItems[ckbox.id])
_jmolNotifyMaster(_jmol.checkboxItems[ckbox.id])
}
function _jmolCbOver(ckbox, whenChecked, whenUnchecked) {
window.status = _jmol.scripts[ckbox.checked ? whenUnchecked : whenChecked];
}
function _jmolMouseOver(scriptIndex) {
window.status = _jmol.scripts[scriptIndex];
}
function _jmolMouseOut() {
window.status = " ";
return true;
}
function _jmolSetCodebase(codebase) {
_jmol.codebase = codebase ? codebase : ".";
if (_jmol.debugAlert)
alert("jmolCodebase=" + _jmol.codebase);
}
function _jmolOnloadResetForms() {
// must be evaluated ONLY once
_jmol.previousOnloadHandler = window.onload;
window.onload =
function() {
with (_jmol) {
if (buttonCount+checkboxCount+menuCount+radioCount+radioGroupCount > 0) {
var forms = document.forms;
for (var i = forms.length; --i >= 0; )
forms[i].reset();
}
if (previousOnloadHandler)
previousOnloadHandler();
}
}
}
////////////////////////////////////
/////extensions for getProperty/////
////////////////////////////////////
function _jmolEvalJSON(s,key){
s=s+""
if(!s)return []
if(s.charAt(0)!="{"){
if(s.indexOf(" | ")>=0)s=s.replace(/\ \|\ /g, "\n")
return s
}
var A = eval("("+s+")")
if(!A)return
if(key && A[key])A=A[key]
return A
}
function _jmolEnumerateObject(A,key){
var sout=""
if(typeof(A) == "string" && A!="null"){
sout+="\n"+key+"=\""+A+"\""
}else if(!isNaN(A)||A==null){
sout+="\n"+key+"="+(A+""==""?"null":A)
}else if(A.length){
sout+=key+"=[]"
for(var i=0;ib[0]?-1:0)
}
function _jmolSortMessages(A){
if(!A || typeof(A)!="object")return []
var B = []
for(var i=A.length-1;i>=0;i--)for(var j=0;j=0;)
for(var j=0;j< Ret[i].length;j++)
s+=Ret[i][j]+"\n"
return s
}
function jmolScriptWaitOutput(script, targetSuffix) {
targetSuffix == undefined && (targetSuffix="0")
var ret = ""
try{
if (script) {
_jmolCheckBrowser();
var applet=_jmolGetApplet(targetSuffix);
if (applet) ret += applet.scriptWaitOutput(script);
}
}catch(e){
}
return ret;
}
function jmolEvaluate(molecularMath, targetSuffix) {
//carries out molecular math on a model
targetSuffix == undefined && (targetSuffix="0")
var result = "" + jmolGetPropertyAsJavaObject("evaluate", molecularMath, targetSuffix);
var s = result.replace(/\-*\d+/,"")
if (s == "" && !isNaN(parseInt(result)))return parseInt(result);
var s = result.replace(/\-*\d*\.\d*/,"")
if (s == "" && !isNaN(parseFloat(result)))return parseFloat(result);
return result;
}
function jmolScriptEcho(script, targetSuffix) {
// returns a newline-separated list of all echos from a script
targetSuffix == undefined && (targetSuffix="0")
var Ret=jmolScriptWaitAsArray(script, targetSuffix)
var s = ""
for(var i=Ret.length;--i>=0;)
for(var j=Ret[i].length;--j>=0;)
if (Ret[i][j][1] == "scriptEcho")s+=Ret[i][j][3]+"\n"
return s.replace(/ \| /g, "\n")
}
function jmolScriptMessage(script, targetSuffix) {
// returns a newline-separated list of all messages from a script, ending with "script completed\n"
targetSuffix == undefined && (targetSuffix="0")
var Ret=jmolScriptWaitAsArray(script, targetSuffix)
var s = ""
for(var i=Ret.length;--i>=0;)
for(var j=Ret[i].length;--j>=0;)
if (Ret[i][j][1] == "scriptStatus")s+=Ret[i][j][3]+"\n"
return s.replace(/ \| /g, "\n")
}
function jmolScriptWaitAsArray(script, targetSuffix) {
var ret = ""
try{
jmolGetStatus("scriptEcho,scriptMessage,scriptStatus,scriptError",targetSuffix)
if (script) {
_jmolCheckBrowser();
var applet=_jmolGetApplet(targetSuffix);
if (applet) ret += applet.scriptWait(script);
ret = _jmolEvalJSON(ret,"jmolStatus")
if(typeof ret == "object")
return ret
}
}catch(e){
}
return [[ret]]
}
//////////// save/restore orientation /////////////
function jmolSaveOrientation(id, targetSuffix) {
targetSuffix == undefined && (targetSuffix="0")
return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo
}
function jmolRestoreOrientation(id, targetSuffix) {
targetSuffix == undefined && (targetSuffix="0")
var s=_jmol["savedOrientation"+id]
if (!s || s == "")return
s=s.replace(/1\.0/,"0")
return jmolScriptWait(s,targetSuffix)
}
function jmolRestoreOrientationDelayed(id, delay, targetSuffix) {
arguments.length < 2 && (delay=1)
targetSuffix == undefined && (targetSuffix="0")
var s=_jmol["savedOrientation"+id]
if (!s || s == "")return
s=s.replace(/1\.0/,delay)
return jmolScriptWait(s,targetSuffix)
}
//////////// add parameter /////////////
/*
* for adding callbacks or other parameters. Use:
jmolSetDocument(0)
var s= jmolApplet(....)
s = jmolAppletAddParam(s,"messageCallback", "myFunctionName")
document.write(s)
jmolSetDocument(document) // if you want to then write buttons and such normally
*/
function jmolAppletAddParam(appletCode,name,value){
return (value == "" ? appletCode : appletCode.replace(/\ \n"
+""
+"Applet would be here"
+""
+"
"
return _jmolDocumentWrite(s)
}
_jmolFindApplet = function(){return jmolApplet0}
jmolApplet0 = {
script: function(script){document.getElementById("fakeApplet").value="\njmolScript:\n"+script}
,scriptWait: function(script){document.getElementById("fakeApplet").value="\njmolScriptWait:\n"+script}
,loadInline: function(data,script){document.getElementById("fakeApplet").value="\njmolLoadInline data:\n"+data+"\n\nscript:\n"+script}
}
}
///////////////////////////////////////////
// This should no longer be needed, jmolResizeApplet() is better; kept for backwards compatibility
/*
Resizes absolutely (pixels) or by percent of window (w or h 0.5 means 50%).
targetSuffix is optional and defaults to zero (first applet in page).
Both w and h are optional, but needed if you want to use targetSuffix.
h defaults to w
w defaults to 100% of window
If either w or h is between 0 and 1, then it is taken as percent/100.
If either w or h is greater than 1, then it is taken as a size (pixels).
*/
function jmolResize(w,h,targetSuffix) {
_jmol.alerted = true;
var percentW = (!w ? 100 : w <= 1 && w > 0 ? w * 100 : 0);
var percentH = (!h ? percentW : h <= 1 && h > 0 ? h * 100 : 0);
if (_jmol.browser=="msie") {
var width=document.body.clientWidth;
var height=document.body.clientHeight;
} else {
var netscapeScrollWidth=15;
var width=window.innerWidth - netscapeScrollWidth;
var height=window.innerHeight-netscapeScrollWidth;
}
var applet = _jmolGetApplet(targetSuffix);
if(!applet)return;
applet.style.width = (percentW ? width * percentW/100 : w)+"px";
applet.style.height = (percentH ? height * percentH/100 : (h ? h : w))+"px";
//title=width + " " + height + " " + (new Date());
}
// 13 Jun 09 -- makes jmolResize() obsolete (kept for backwards compatibility)
function jmolResizeApplet(size,targetSuffix) {
// See _jmolGetAppletSize() for the formats accepted as size [same used by jmolApplet()]
// Special case: an empty value for width or height is accepted, meaning no change in that dimension.
_jmol.alerted = true;
var applet = _jmolGetApplet(targetSuffix);
if(!applet)return;
var sz = _jmolGetAppletSize(size, "px");
sz[0] && (applet.style.width = sz[0]);
sz[1] && (applet.style.height = sz[1]);
}
function _jmolGetAppletSize(size, units) {
/* Accepts single number or 2-value array, each one can be one of:
percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.)
[width, height] array of strings is returned, with units added if specified.
Percent is relative to container div or element (which should have explicitly set size).
*/
var width, height;
if ( (typeof size) == "object" && size != null ) {
width = size[0]; height = size[1];
} else {
width = height = size;
}
return [_jmolFixDim(width, units), _jmolFixDim(height, units)];
}
function _jmolFixDim(x, units) {
var sx = "" + x;
return (sx.length == 0 ? (units ? "" : _jmol.allowedJmolSize[2])
: sx.indexOf("%") == sx.length-1 ? sx
: (x = parseFloat(x)) <= 1 && x > 0 ? x * 100 + "%"
: (isNaN(x = Math.floor(x)) ? _jmol.allowedJmolSize[2]
: x < _jmol.allowedJmolSize[0] ? _jmol.allowedJmolSize[0]
: x > _jmol.allowedJmolSize[1] ? _jmol.allowedJmolSize[1]
: x) + (units ? units : ""));
}