/* 

Jmol2.js   (JSmol version)
author: Bob Hanson hansonr@stolaf.edu 5/24/2013 12:06:25 PM

Script replacement for legacy Jmol.js that uses JSmol instead.
Can be used to turn most legacy Jmol.js-based sites to JSmol.

BH 1/16/2014 10:33:46 PM adding serverURL indication, more notes
BH 1/13/2014 11:14:12 AM incorrect default for missing jmolInitialize() (should be ".")
BH 1/8/2014 5:56:15 AM simplified instructions; removed option for self.Info
BH 11/12/2013 6:34:22 AM adds jmolAppletInline()
BH 9/23/2013 10:07:16 PM adds set of loadInline functions
BH 9/19/2013 7:09:41 AM  fixed jmolSetTarget() to accept "0" as a suffix; use of undefined --> null

Summary:

You should not have to change any of your HTML pages.
You are going to replace Jmol.js, wherever that is, with this file.
You are going to replace all your JAR file with the ones in this distribution.
You are going to add about 1000 files in the jsmol/j2s directory to your website. 
	Don't worry; only a few will be called. But you won't know which ones.
You will be able to switch from HTML5 to JAVA using ?_USE=SIGNED in the URL

Procedure:

1a) If you want to use HTML5, copy all jsmol/j2s/* files into a j2s subdirectory 
		in the directory that contains Jmol.js and your old Jmol jar files.

1b) If you are not using HTML5, change the "use" parameter below from "HTML5" to "JAVA" and save this file.
		Copy all the jsmol/java/* files into the directory containing your current JAR files. This adds
		four JNLP files as well and will replace all your JAR files.

2) Rename your current Jmol.js file Jmol_old.js in case you want to undo this.

3) Concatenate Jmol.min.js if you are not using jQuery (or Jmol.min.nojq.js if you are)
	 with this file to form a new file (Jmol.min.js first, then Jmol2.js) and replace your
	 current Jmol.js with it. Note that if you are using your own version of jQuery, it
	 must be version 1.9 or higher, and note that 2.0 or higher will not work with MSIE
	 used locally but accessing remote resources. See http://bugs.jquery.com/ticket/14876
	 
4) Try your page and see how it goes. You may still have some problems, because not all of the 
	 methods in the original Jmol.js are included here. Let me know if that's the case.

If you wish to change the directories your j2s or JAR files and override the default settings
(old JAR file location; j2s directory in the directory of those JAR files) and thus override
your current settings in your HTML files, then you can to that three ways:

a) You can change the parameters below to override what your pages already use by uncommenting
	 one or the other of the jarPath and j2sPath definitions. This will override jmolInitialize
	 in ALL your HTML files. 
	 
b) You can change your jmolInitialization call in an individual HTML file. This sets both 
	 the JAR path and the j2s path (as [jarPath]/j2s) together.

c) You can add lines to an individual HTML file along the lines of:

		Jmol.Info.jarPath = "../../Jmol"
		Jmol.Info.j2sPath = "../../JSmol"

	 or whatever. This will override jmolInitialize in that specific HTML file only. 
 
Note that: 

 -- FireFox works great. You will be able to read binary files from your local machine
 -- Chrome can only read local files if started with the  --allow-file-access-from-files  flag
		and even then the files must be ASCII, not binary.
 -- MSIE and Safari cannot work with local pages

*/
/* $RCSfile: Jmol.js,v $
 * $Author: migueljmol $
 * $Date: 2004/12/11 22:22:10 $
 * $Revision: 1.28 $
 *
 * Copyright (C) 2004  The Jmol Development Team
 *
 * Contact: jmol-developers@lists.sf.net
 *
 *  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

var undefined; // for IE 5 ... wherein undefined is undefined

////////////////////////////////////////////////////////////////
// Basic Scripting infrastruture
////////////////////////////////////////////////////////////////

function jmolInitialize(codebaseDirectory) {
  if (_jmol.initialized) {
    alert("jmolInitialize() should only be called *ONCE* within a page");
    return;
  }
  if (! codebaseDirectory) {
    alert("codebaseDirectory is a required parameter to jmolInitialize");
    codebaseDirectory = ".";
  }
  if (codebaseDirectory.indexOf("http://") == 0 ||
      codebaseDirectory.indexOf("https://") == 0)
    alert("codebaseDirectory should be directory relative,\n" +
	  "not be an absolute URL : " + codebaseDirectory);
  else if (codebaseDirectory.charAt(0) == '/')
    alert("codebaseDirectory should be directory relative,\n" +
	  "not relative to the root of the web server : " + codebaseDirectory);
  _jmolSetCodebase(codebaseDirectory);
  _jmolOnloadResetForms();
  _jmol.initialized = true;
}

function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {
  _jmolInitCheck();
  _jmol.boxbgcolor = boxbgcolor;
  if (boxfgcolor)
    _jmol.boxfgcolor = boxfgcolor
  else if (boxbgcolor == "white" || boxbgcolor == "#FFFFFF")
    _jmol.boxfgcolor = "black";
  else
    _jmol.boxfgcolor = "white";
  if (progresscolor)
    _jmol.progresscolor = progresscolor;
  if (_jmol.debugAlert)
    alert(" boxbgcolor=" + _jmol.boxbgcolor +
          " boxfgcolor=" + _jmol.boxfgcolor +
          " progresscolor=" + _jmol.progresscolor);
}

function jmolApplet(size, script, nameSuffix) {
  _jmolInitCheck();
  _jmolApplet(size, null, script, nameSuffix);
}

////////////////////////////////////////////////////////////////
// Basic controls
////////////////////////////////////////////////////////////////

function jmolButton(script, label, id) {
  _jmolInitCheck();
  var scriptIndex = _jmolAddScript(script);
  if (label == undefined || label == null)
    label = script.substring(0, 32);
  if (id == undefined || id == null)
    id = "jmolButton" + _jmol.buttonCount;
  ++_jmol.buttonCount;
  var t = "<input type='button' name='" + id + "' id='" + id +
          "' value='" + label +
          "' onClick='_jmolClick(" + scriptIndex + _jmol.targetText +
          ")' onMouseover='_jmolMouseOver(" + scriptIndex +
          ");return true' onMouseout='_jmolMouseOut()' " +
          _jmol.buttonCssText + "/>";
  if (_jmol.debugAlert)
    alert(t);
  document.write(t);
}

function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked,
                      labelHtml, isChecked, id) {
  _jmolInitCheck();
  if (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 t = "<input type='checkbox' name='" + id + "' id='" + id +
          "' onClick='_jmolCbClick(this," +
          indexChecked + "," + indexUnchecked + _jmol.targetText +
          ")' onMouseover='_jmolCbOver(this," + indexChecked + "," +
          indexUnchecked +
          ");return true' onMouseout='_jmolMouseOut()' " +
	  (isChecked ? "checked " : "") + _jmol.checkboxCssText + "/>" +
          labelHtml;
  if (_jmol.debugAlert)
    alert(t);
  document.write(t);
}

function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName) {
  _jmolInitCheck();
  var type = typeof arrayOfRadioButtons;
  if (type != "object" || type == null || ! arrayOfRadioButtons.length) {
    alert("invalid arrayOfRadioButtons");
    return;
  }
  if (separatorHtml == undefined || separatorHtml == null)
    separatorHtml = "&nbsp; ";
  var length = arrayOfRadioButtons.length;
  var t = "";
  jmolStartNewRadioGroup();
  for (var i = 0; i < length; ++i) {
    var radio = arrayOfRadioButtons[i];
    type = typeof radio;
    if (type == "object") {
      t += _jmolRadio(radio[0], radio[1], radio[2], separatorHtml, groupName);
    } else {
      t += _jmolRadio(radio, null, null, separatorHtml, groupName);
    }
  }
  if (_jmol.debugAlert)
    alert(t);
  document.write(t);
}

function jmolLink(script, text, id) {
  _jmolInitCheck();
  if (id == undefined || id == null)
    id = "jmolLink" + _jmol.linkCount;
  ++_jmol.linkCount;
  var scriptIndex = _jmolAddScript(script);
  var t = "<a name='" + id + "' id='" + id + 
          "' href='javascript:_jmolClick(" + scriptIndex +
          _jmol.targetText +
          ");' onMouseover='_jmolMouseOver(" + scriptIndex +
          ");return true;' onMouseout='_jmolMouseOut()' " +
          _jmol.linkCssText + ">" + text + "</a>";
  if (_jmol.debugAlert)
    alert(t);
  document.write(t);
}

function jmolMenu(arrayOfMenuItems, size, id) {
  _jmolInitCheck();
  if (id == undefined || id == null)
    id = "jmolMenu" + _jmol.menuCount;
  ++_jmol.menuCount;
  var type = typeof arrayOfMenuItems;
  if (type != null && type == "object" && arrayOfMenuItems.length) {
    var length = arrayOfMenuItems.length;
    if (typeof size != "number" || size == 1)
      size = null;
    else if (size < 0)
      size = length;
    var sizeText = size ? " size='" + size + "' " : "";
    var t = "<select name='" + id + "' id='" + id +
            "' onChange='_jmolMenuSelected(this" +
            _jmol.targetText + ")'" +
            sizeText + _jmol.menuCssText + ">";
    for (var i = 0; i < length; ++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;
      }
      if (text == undefined || text == null)
        text = script;
      var scriptIndex = _jmolAddScript(script);
      var selectedText = isSelected ? "' selected>" : "'>";
      t += "<option value='" + scriptIndex + selectedText + text + "</option>";
    }
    t += "</select>";
    if (_jmol.debugAlert)
      alert(t);
    document.write(t);
  }
}

function jmolHtml(html) {
  document.write(html);
}

function jmolBr() {
  document.write("<br />");
}

////////////////////////////////////////////////////////////////
// advanced scripting functions
////////////////////////////////////////////////////////////////

function jmolDebugAlert(enableAlerts) {
  _jmol.debugAlert = (enableAlerts == undefined || enableAlerts)
}

function jmolAppletInline(size, inlineModel, script, nameSuffix) {
  _jmolApplet(size, _jmolConvertInline(inlineModel), script, nameSuffix);
}

function jmolSetTarget(targetSuffix) {
  _jmol.targetSuffix = targetSuffix;
  _jmol.targetText = targetSuffix ? ",\"" + targetSuffix + "\"" : "";
}

function jmolScript(script, targetSuffix) {
  if (script) {
    _jmolCheckBrowser();
    var target = "jmolApplet" + (targetSuffix ? targetSuffix : "0");
    var applet = _jmolFindApplet(target);
    if (applet)
      return applet.script(script);
    else
      alert("could not find applet " + target);
  }
}

function jmolLoadInline(model, targetSuffix) {
  if (model) {
    var target = "jmolApplet" + (targetSuffix ? targetSuffix : "0");
//    while (! _jmol.ready[target])
//      alert("The Jmol applet " + target + " is not loaded yet");
//    if (! _jmol.ready[target])
//      alert("The Jmol applet " + target + " is not loaded yet");
//    if (document.applets[target] && ! document.applets[target].isActive())
//       alert("The Jmol applet " + target + " is not yet active");
//    else {
      var applet = _jmolFindApplet(target);
      if (applet)
        return applet.loadInline(model);
      else
        alert("could not find applet " + target);
//    }
  }
}

function jmolStartNewRadioGroup() {
  ++_jmol.radioGroupCount;
}

function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName) {
  _jmolInitCheck();
  if (_jmol.radioGroupCount == 0)
    ++_jmol.radioGroupCount;
  var t = _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName);
  if (_jmol.debugAlert)
    alert(t);
  document.write(t);
}

function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {
  if (typeof action == "string") {
    action = action.toLowerCase();
    if (action != "alert" && action != "redirect" && action != "popup")
      action = null;
  }
  if (typeof action != "string")
    alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
          "action must be 'alert', 'redirect', or 'popup'");
  else {
    if (typeof urlOrMessage != "string")
      alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
            "urlOrMessage must be a string");
    else {
      _jmol.checkBrowserAction = action;
      _jmol.checkBrowserUrlOrMessage = urlOrMessage;
    }
  }
  if (typeof nowOrLater == "string" && nowOrLater.toLowerCase() == "now")
    _jmolCheckBrowser();
}

////////////////////////////////////////////////////////////////
// Cascading Style Sheet Class support
////////////////////////////////////////////////////////////////

function jmolSetAppletCssClass(appletCssClass) {
  if (_jmol.hasGetElementById) {
    _jmol.appletCssClass = appletCssClass;
    _jmol.appletCssText = appletCssClass ? "class='" + appletCssClass + "' " : "";
  }
}

function jmolSetButtonCssClass(buttonCssClass) {
  if (_jmol.hasGetElementById) {
    _jmol.buttonCssClass = buttonCssClass;
    _jmol.buttonCssText = buttonCssClass ? "class='" + buttonCssClass + "' " : "";
  }
}

function jmolSetCheckboxCssClass(checkboxCssClass) {
  if (_jmol.hasGetElementById) {
    _jmol.checkboxCssClass = checkboxCssClass;
    _jmol.checkboxCssText = checkboxCssClass ? "class='" + checkboxCssClass + "' " : "";
  }
}

function jmolSetRadioCssClass(radioCssClass) {
  if (_jmol.hasGetElementById) {
    _jmol.radioCssClass = radioCssClass;
    _jmol.radioCssText = radioCssClass ? "class='" + radioCssClass + "' " : "";
  }
}

function jmolSetLinkCssClass(linkCssClass) {
  if (_jmol.hasGetElementById) {
    _jmol.linkCssClass = linkCssClass;
    _jmol.linkCssText = linkCssClass ? "class='" + linkCssClass + "' " : "";
  }
}

function jmolSetMenuCssClass(menuCssClass) {
  if (_jmol.hasGetElementById) {
    _jmol.menuCssClass = menuCssClass;
    _jmol.menuCssText = menuCssClass ? "class='" + menuCssClass + "' " : "";
  }
}

////////////////////////////////////////////////////////////////
// functions for INTERNAL USE ONLY which are subject to change
// use at your own risk ... you have been WARNED!
////////////////////////////////////////////////////////////////

var _jmol = {

debugAlert: false,
bgcolor: "black",
progresscolor: "blue",
boxbgcolor: "black",
boxfgcolor: "white",
boxmessage: "Downloading JmolApplet ...",

codebase: ".",
modelbase: ".",

appletCount: 0,

buttonCount: 0,
checkboxCount: 0,
linkCount: 0,
menuCount: 0,
radioCount: 0,
radioGroupCount: 0,

appletCssClass: null,
appletCssText: "",
buttonCssClass: null,
buttonCssText: "",
checkboxCssClass: null,
checkboxCssText: "",
radioCssClass: null,
radioCssText: "",
linkCssClass: null,
linkCssText: "",
menuCssClass: null,
menuCssText: "",

targetSuffix: 0,
targetText: "",
scripts: [""],

ua: navigator.userAgent.toLowerCase(),
uaVersion: parseFloat(navigator.appVersion),

os: "unknown",
browser: "unknown",
browserVersion: 0,
hasGetElementById: !!document.getElementById,
isJavaEnabled: navigator.javaEnabled(),
isNetscape47Win: false,

isBrowserCompliant: false,
isJavaCompliant: false,
isFullyCompliant: false,

initialized: false,
initChecked: false,

browserChecked: false,
checkBrowserAction: "alert",
checkBrowserUrlOrMessage: null,

previousOnloadHandler: null,
ready: {}
}

with (_jmol) {
  function _jmolTestUA(candidate) {
    var ua = _jmol.ua;
    var index = ua.indexOf(candidate);
    if (index < 0)
      return false;
    _jmol.browser = candidate;
    _jmol.browserVersion = parseFloat(ua.substring(index + candidate.length+1));
    return true;
  }
  
  function _jmolTestOS(candidate) {
    if (_jmol.ua.indexOf(candidate) < 0)
      return false;
    _jmol.os = candidate;
    return true;
  }
  
  _jmolTestUA("konqueror") ||
  _jmolTestUA("safari") ||
  _jmolTestUA("omniweb") ||
  _jmolTestUA("opera") ||
  _jmolTestUA("webtv") ||
  _jmolTestUA("icab") ||
  _jmolTestUA("msie") ||
  (_jmol.ua.indexOf("compatible") < 0 && _jmolTestUA("mozilla"));
  
  _jmolTestOS("linux") ||
  _jmolTestOS("unix") ||
  _jmolTestOS("mac") ||
  _jmolTestOS("win");

  isNetscape47Win = (os == "win" && browser == "mozilla" &&
                     browserVersion >= 4.78 && browserVersion <= 4.8);

  if (os == "win") {
    isBrowserCompliant = hasGetElementById || isNetscape47Win;
  } else if (os == "mac") { // mac is the problem child :-(
    if (browser == "mozilla" && browserVersion >= 5) {
      // miguel 2004 11 17
      // checking the plugins array does not work because
      // Netscape 7.2 OS X still has Java 1.3.1 listed even though
      // javaplugin.sf.net is installed to upgrade to 1.4.2
      eval("try {var v = java.lang.System.getProperty('java.version');" +
           " _jmol.isBrowserCompliant = v >= '1.4.2';" +
           " } catch (e) { }");
    } else if (browser == "opera" && browserVersion <= 7.54) {
      isBrowserCompliant = false;
    } else {
      isBrowserCompliant = hasGetElementById &&
        !((browser == "msie") ||
          (browser == "safari" && browserVersion < 125.1));
    }
  } else if (os == "linux" || os == "unix") {
    if (browser == "konqueror" && browserVersion <= 3.3)
      isBrowserCompliant = false;
    else
      isBrowserCompliant = hasGetElementById;
  } else { // other OS
    isBrowserCompliant = hasGetElementById;
  }

  // possibly more checks in the future for this
  isJavaCompliant = isJavaEnabled;

  isFullyCompliant = isBrowserCompliant && isJavaCompliant;
}

function _jmolApplet(size, inlineModel, script, nameSuffix) {
  with (_jmol) {
    if (! nameSuffix)
      nameSuffix = appletCount;
    ++appletCount;
    if (! script)
      script = "select *";
    var sz = _jmolGetAppletSize(size);
    var t;
    t = "<applet name='jmolApplet" + nameSuffix + "' id='jmolApplet" + nameSuffix +
        "' " + appletCssText +
        " code='JmolApplet' archive='JmolApplet.jar'\n" +
        " codebase='" + codebase + "'\n" +
        " width='" + sz[0] + "' height='" + sz[1] +
        "' mayscript='true'>\n" +
        "  <param name='progressbar' value='true' />\n" +
        "  <param name='progresscolor' value='" +
        progresscolor + "' />\n" +
        "  <param name='boxmessage' value='" +
        boxmessage + "' />\n" +
        "  <param name='boxbgcolor' value='" +
        boxbgcolor + "' />\n" +
        "  <param name='boxfgcolor' value='" +
        boxfgcolor + "' />\n" +
        "  <param name='ReadyCallback' value='_jmolReadyCallback' />\n";

    if (inlineModel)
      t += "  <param name='loadInline' value='" + inlineModel + "' />\n";
    if (script)
      t += "  <param name='script' value='" + script + "' />\n";
    t += "</applet>";
    jmolSetTarget(nameSuffix);
    ready["jmolApplet" + nameSuffix] = false;
    if (_jmol.debugAlert)
      alert(t);
    document.write(t);
  }
}

function _jmolInitCheck() {
  if (_jmol.initChecked)
    return;
  _jmol.initChecked = true;
  if (_jmol.initialized)
    return;
  alert("jmolInitialize({codebase}, {badBrowseURL}, {badJavaURL})\n" +
        "  must be called before any other Jmol.js functions");
}

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" +
              "brower: " + browser +
              "   version: " + browserVersion +
              "   os: " + os +
              "\n\n" + ua;
      alert(msg);
    }
  }
  return false;
}

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 _jmolConvertInline(model) {
  var inlineModel = model.replace(/\r|\n|\r\n/g, "|");
  if (_jmol.debugAlert)
    alert("inline model:\n" + inlineModel);
  return inlineModel;
}

function _jmolGetAppletSize(size) {
  var width, height;
  var type = typeof size;
  if (type == "number")
    width = height = size;
  else if (type == "object" && size != null) {
    width = size[0]; height = size[1];
  }
  if (! (width >= 25 && width <= 2000))
    width = 300;
  if (! (height >= 25 && height <= 2000))
    height = 300;
  return [width, height];
}

function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName) {
  ++_jmol.radioCount;
  if (groupName == undefined || groupName == null)
    groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1);
  if (!script)
    return "";
  if (labelHtml == undefined || labelHtml == null)
    labelHtml = script.substring(0, 32);
  if (! separatorHtml)
    separatorHtml = "";
  var scriptIndex = _jmolAddScript(script);
  return "<input name='" + groupName +
         "' type='radio' onClick='_jmolClick(" +
         scriptIndex + _jmol.targetText +
         ");return true;' onMouseover='_jmolMouseOver(" +
         scriptIndex +
         ");return true;' onMouseout='_jmolMouseOut()' " +
	 (isChecked ? "checked " : "") + _jmol.radioCssText + "/>" +
         labelHtml + separatorHtml;
}

function _jmolFindApplet(target) {
  // first look for the target in the current window
  var applet = _jmolSearchFrames(window, target);
  if (applet == undefined)
    applet = _jmolSearchFrames(top, target); // look starting in top frame
  return applet;
}

function _jmolSearchFrames(win, target) {
  var applet;
  var frames = win.frames;
  if (frames && frames.length) { // look in all the frames below this window
    for (var i = 0; i < frames.length; ++i) {
      applet = _jmolSearchFrames(frames[i++], target);
      if (applet)
        break;
    }
  } else { // look for the applet in this window
    var doc = win.document;
// getElementById fails on MacOSX Safari & Mozilla	
    if (doc.applets)
      applet = doc.applets[target];
    else
      applet = doc[target];
  }
  return applet;
}

function _jmolAddScript(script) {
  if (! script)
    return 0;
  var index = _jmol.scripts.length;
  _jmol.scripts[index] = script;
  return index;
}

function _jmolClick(scriptIndex, targetSuffix) {
  jmolScript(_jmol.scripts[scriptIndex], targetSuffix);
}

function _jmolMenuSelected(menuObject, targetSuffix) {
  var scriptIndex = menuObject.value;
  if (scriptIndex != undefined) {
    jmolScript(_jmol.scripts[scriptIndex], targetSuffix);
    return;
  }
  var length = menuObject.length;
  if (typeof length == "number") {
    for (var i = 0; i < length; ++i) {
      if (menuObject[i].selected) {
        _jmolClick(menuObject[i].value, targetSuffix);
	return;
      }
    }
  }
  alert("?Que? menu selected bug #8734");
}

function _jmolCbClick(ckbox, whenChecked, whenUnchecked, targetSuffix) {
  _jmolClick(ckbox.checked ? whenChecked : whenUnchecked, targetSuffix);
}

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() {
  _jmol.previousOnloadHandler = window.onload;
  window.onload =
  function() {
//    alert("onloadResetForms");
    with (_jmol) {
      if (buttonCount+checkboxCount+menuCount+radioCount+radioGroupCount > 0) {
        var forms = document.forms;
        if (!forms || forms.length == 0) {
          alert("<form> tags seem to be missing\n" +
                "Jmol/HTML input controls must be contained " +
                "within form tags"
//                + "\n\n" + forms + " forms.length=" + forms.length +
//                " typeof=" + (typeof forms)
                );
        } else {
          for (var i = forms.length; --i >= 0; )
            forms[i].reset();
        }
      }
      if (previousOnloadHandler)
        previousOnloadHandler();
    }
  }
}


Jmol.Info = {      
			// uncomment one or more of these next lines only if you want to override jmolInitialize()
			//jarPath: "java", 
			//jarFile: "JmolAppletSigned0.jar", 
			//j2sPath: "j2s", 
			use: "JAVA", // could be JAVA or HTML5
			// the serverURL path is only used to load binary files in Safari, Chrome, and MSIE
			serverURL: "https://www.chem.wisc.edu/deptfiles/genchem/netorial/modules/biomolecules/jmol-10.00/php/jsmol.php", // required for binary file loading (Spartan, .gz, .map, etc.)
	disableJ2SLoadMonitor: false,
	disableInitialConsole: true

}

////////// private functions /////////////

var _jmol = {
	appletCount: 0,
	applets: {},
	allowedJmolSize: [25, 2048, 300],   // min, max, default (pixels)
	codebase: ".",
	targetSuffix: 0,
	target: "jmolApplet0",
	buttonCount: 0,
	checkboxCount: 0,
	linkCount: 0,
	cmdCount: 0,
	menuCount: 0,
	radioCount: 0,
	radioGroupCount: 0,
	initialized: false,
	initChecked: false,
	archivePath: "JmolAppletSigned0.jar"
}

function _jmolApplet(size, inlineModel, script, nameSuffix) {
		nameSuffix == null && (nameSuffix = _jmol.appletCount);
		var id = "jmolApplet" + nameSuffix;
		jmolSetTarget(nameSuffix);
		++_jmol.appletCount;
		script || (script = "select *");
		inlineModel && (script = 'load DATA "inline"\n' + inlineModel + '\nEND "inline";' + script); 
		var Info = {}
		for (var i in Jmol.Info)
			Info[i] = Jmol.Info[i]
		Info.jarFile || (Info.jarFile = _jmol.archivePath);
		Info.jarPath || (Info.jarPath = _jmol.codebase);
		Info.j2sPath || (Info.j2sPath = Info.jarPath + "/j2s");    
		var sz = _jmolGetAppletSize(size);
		Info.width || (Info.width = sz[0]);
		Info.height || (Info.height = sz[1]);  
		Info.script || (Info.script = script);
		Info.isSigned == null && (Info.isSigned = (Info.jarFile.indexOf("Signed") >= 0));
		for (var i in _jmol.params)
			if(_jmol.params[i]!="")
				Info[i] || (Info[i] = _jmol.params[i]);
//  alert(JSON.stringify(Info).replace(/\,/g,"\n\n\n\n"))
		return _jmol.applets[id] = Jmol.getApplet(id, Info)
}

function _jmolGetJarFilename(fileNameOrFlag) {
	_jmol.archivePath =
		(typeof(fileNameOrFlag) == "string"  ? fileNameOrFlag : (fileNameOrFlag ?  "JmolAppletSigned" : "JmolApplet") + "0.jar");
}

////////////////////////////////////////////////////////////////
// Legacy Scripting API
////////////////////////////////////////////////////////////////

function jmolSetParameter(key,value) {
	Jmol.Info[key] = value;
}

function jmolSetXHTML(id) {
	Jmol.setXHTML(id);
}

function jmolSetTranslation(TF) {
	// n/a
}

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;
		}
	}
	_jmol.codebase = codebaseDirectory;
	_jmolGetJarFilename(fileNameOrUseSignedApplet);
}

function jmolSetDocument(doc) {
	_jmol.currentDocument = doc;
}

function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {
	Jmol.Info.color = boxbgcolor ? boxbgcolor : "black";
}

function jmolSetAppletWindow(w) {
	_jmol.appletWindow = w;
}

function jmolApplet(size, script, nameSuffix) {
	return _jmolApplet(size, null, script, nameSuffix);
}

function jmolAppletInline(size, inlineModel, script, nameSuffix) {
	return _jmolApplet(size, inlineModel, script, nameSuffix);
}



////////////////////////////////////////////////////////////////
// Basic controls
////////////////////////////////////////////////////////////////

function jmolButton(script, label, id, title) {
	return Jmol.jmolButton(_jmol.target, script, label, id, title);
}

function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked, labelHtml, isChecked, id, title) {
	return Jmol.jmolCheckbox(_jmol.target, scriptWhenChecked, scriptWhenUnchecked, labelHtml, isChecked, id, title)
}

function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) {
	return Jmol.jmolRadioGroup(_jmol.target, arrayOfRadioButtons, separatorHtml, groupName, id, title)
}


function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
	return  Jmol.jmolRadio(_jmol.target, script, labelHtml, isChecked, separatorHtml, groupName, id, title)
}

function jmolLink(script, label, id, title) {
	return Jmol.jmolLink(_jmol.target, script, label, id, title)
}

function jmolCommandInput(label, size, id, title) {
	return Jmol.jmolCommandInput(_jmol.target, label, size, id, title);
}

function jmolMenu(arrayOfMenuItems, size, id, title) {
	return Jmol.jmolMenu(_jmol.target, arrayOfMenuItems, size, id, title);
}

function jmolHtml(html) {
	return Jmol._documentWrite(html);
}

function jmolBr() {
	return Jmol._documentWrite("<br />");
}

////////////////////////////////////////////////////////////////
// advanced scripting functions
////////////////////////////////////////////////////////////////

function jmolDebugAlert(enableAlerts) {
	// n/a
}


function jmolLoadInline(model, targetSuffix) {
	return jmolLoadInlineScript(model, null, targetSuffix, false)
}

function jmolLoadInlineArray(ModelArray, script, targetSuffix) {
	return jmolLoadInlineScript(ModelArray.join("\n"), script, targetSuffix, false)
}

function jmolAppendInlineArray(ModelArray, script, targetSuffix) {
	return jmolLoadInlineScript(ModelArray.join("\n"), script, targetSuffix, true)
}

function jmolAppendInlineScript(model, script, targetSuffix) {
	return jmolLoadInlineScript(model, script, targetSuffix, true)
}

function jmolLoadInlineScript(model, script, targetSuffix, isAppend) {
	Jmol.script(jmolFindTarget(targetSuffix),
		 "load " 
		 + (isAppend ? "APPEND " : "") 
		 + "DATA 'mydata'\n" + model.replace(/\"/g,'\\"') + "\nEND 'mydata'\n")
}

function jmolSetTarget(targetSuffix) {
	targetSuffix == null || (_jmol.targetSuffix = targetSuffix);
	return _jmol.target = "jmolApplet" + _jmol.targetSuffix;
}

function jmolFindTarget(targetSuffix) {
	return _jmol.applets[jmolSetTarget(targetSuffix)];
}

function jmolScript(script, targetSuffix) {
	Jmol.script(jmolFindTarget(targetSuffix), script)
}

function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {
	// unnecessary
}

////////////////////////////////////////////////////////////////
// Cascading Style Sheet Class support
////////////////////////////////////////////////////////////////

function jmolSetAppletCssClass(appletCssClass) {
	Jmol.setAppletCss(appletCssClass)
}

function jmolSetButtonCssClass(s) {
	Jmol.setButtonCss(s)
}

function jmolSetCheckboxCssClass(s) {
	Jmol.setCheckboxCss(s)
}

function jmolSetRadioCssClass(s) {
	Jmol.setRadioCss(s)
}

function jmolSetLinkCssClass(s) {
	Jmol.setLinkCss(s)
}

function jmolSetMenuCssClass(s) {
	Jmol.setMenuCss(s)
}

function jmolSetMemoryMb(nMb) {
	// n/a
}


function jmolSetCallback(callbackName,funcName) {
//if(!self[funcName])alert(funcName + " is not defined yet in jmolSetCallback")
	Jmol.Info[callbackName] = funcName
	//document.title=("jmolSetCallback " + callbackName + "/" + funcName + " must be included in Info definition")
}

function jmolSetSyncId(n) {
	alert("jmolSetSyncId " + n + " must be included in Info definition")
}

function jmolSetLogLevel(n) {
	Jmol.script(_jmol.target, "set loglevel " + n)
}

function _jmolGetAppletSize(size, units) {
	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 : ""));
}

//////////user property/status functions/////////

function jmolGetStatus(strStatus,targetSuffix){
	return Jmol.getStatus(jmolFindTarget(targetSuffix), strStatus)
}

function jmolGetPropertyAsArray(sKey,sValue,targetSuffix) {
	return Jmol.getPropertyAsArray(jmolFindTarget(targetSuffix), sKey, sValue)
}

function jmolGetPropertyAsString(sKey,sValue,targetSuffix) {
	return Jmol.getPropertyAsString(jmolFindTarget(targetSuffix), sKey, sValue)
}

function jmolGetPropertyAsJSON(sKey,sValue,targetSuffix) {
	return Jmol.getPropertyAsJSON(jmolFindTarget(targetSuffix), sKey, sValue)
}

function jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix) {
	return Jmol.getPropertyAsJavaObject(jmolFindTarget(targetSuffix), sKey, sValue)
}

///////// synchronous scripting ////////

function jmolScriptWait(script, targetSuffix) {
	return Jmol.scriptWait(jmolFindTarget(targetSuffix), script)
}

function jmolScriptWaitOutput(script, targetSuffix) {
	return Jmol.scriptWaitOutput(jmolFindTarget(targetSuffix), script)
}

function jmolEvaluate(molecularMath, targetSuffix) {
	return Jmol.evaluate(jmolFindTarget(targetSuffix), molecularMath)
}

function jmolScriptEcho(script, targetSuffix) {
	return Jmol.scriptEcho(jmolFindTarget(targetSuffix), script)
}


function jmolScriptMessage(script, targetSuffix) {
	return Jmol.scriptMessage(jmolFindTarget(targetSuffix), script)
}


function jmolScriptWaitAsArray(script, targetSuffix) {
	return Jmol.scriptWait(jmolFindTarget(targetSuffix), script)
}



////////////   save/restore orientation   /////////////

function jmolSaveOrientation(id, targetSuffix) {
	return Jmol.saveOrientation(jmolFindTarget(targetSuffix), id)
}

function jmolRestoreOrientation(id, targetSuffix) {
	return Jmol.restoreOrientation(jmolFindTarget(targetSuffix), id)
}

function jmolRestoreOrientationDelayed(id, delay, targetSuffix) {
	return Jmol.restoreOrientationDelayed(jmolFindTarget(targetSuffix), id, delay)
}

function jmolResizeApplet(size, targetSuffix) {
	return Jmol.resizeApplet(jmolFindTarget(targetSuffix), size);
}


////////////  add parameter /////////////

function jmolAppletAddParam(appletCode,name,value){
	alert ("use Info to add a parameter: " + name + "/" + value)
}