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/* $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 = "  ";

  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();

    }

  }

}