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

-/* $RCSfile: Jmol.js,v $
+/* Jmol 11.7 script library Jmol.js  15:32 06.12.2008 Bob Hanson
- * $Author: migueljmol $
- * $Date: 2004/12/11 22:22:10 $
+ checkbox heirarchy -- see http://chemapps.stolaf.edu/jmol/docs/examples-11/check.htm
- * $Revision: 1.28 $
+    based on:
+ *
- * Copyright (C) 2004  The Jmol Development Team
+ * Copyright (C) 2004-2005  Miguel, Jmol Development, www.jmol.org
+ *
- * Contact: jmol-developers@lists.sf.net
+ * 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.
  *  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%)
+// 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 <span> 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 <label> 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
+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 allowJMOLJAR = true
 var undefined; // for IE 5 ... wherein undefined is undefined
 ////////////////////////////////////////////////////////////////
 // Basic Scripting infrastruture
 ////////////////////////////////////////////////////////////////
-function jmolInitialize(codebaseDirectory) {
+function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {
-  if (_jmol.initialized) {
+  if (_jmol.initialized)
-    alert("jmolInitialize() should only be called *ONCE* within a page");
     return;
+  _jmol.initialized = true;
+  if(allowJMOLJAR && document.location.search.indexOf("JMOLJAR=")>=0) {
+    var f = document.location.search.split("JMOLJAR=")[1].split("&")[0];
+    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;
+    }
+  }
-  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);
+  _jmolGetJarFilename(fileNameOrUseSignedApplet);
   _jmolOnloadResetForms();
+}
+function jmolSetTranslation(TF) {
+  _jmol.params.doTranslate = ''+TF;
+}
+function _jmolGetJarFilename(fileNameOrFlag) {
+  _jmol.archivePath =
+    (typeof(fileNameOrFlag) == "string"  ? fileNameOrFlag : (fileNameOrFlag ?  "JmolAppletSigned" : "JmolApplet") + "0.jar");
+}
+function jmolSetDocument(doc) {
-  _jmol.initialized = true;
+  _jmol.currentDocument = doc;
+}
 function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {
   _jmolInitCheck();
-  _jmol.boxbgcolor = boxbgcolor;
+  _jmol.params.boxbgcolor = boxbgcolor;
   if (boxfgcolor)
-    _jmol.boxfgcolor = boxfgcolor
+    _jmol.params.boxfgcolor = boxfgcolor
   else if (boxbgcolor == "white" || boxbgcolor == "#FFFFFF")
-    _jmol.boxfgcolor = "black";
+    _jmol.params.boxfgcolor = "black";
   else
-    _jmol.boxfgcolor = "white";
+    _jmol.params.boxfgcolor = "white";
   if (progresscolor)
-    _jmol.progresscolor = progresscolor;
+    _jmol.params.progresscolor = progresscolor;
   if (_jmol.debugAlert)
-    alert(" boxbgcolor=" + _jmol.boxbgcolor +
+    alert(" boxbgcolor=" + _jmol.params.boxbgcolor +
-          " boxfgcolor=" + _jmol.boxfgcolor +
+          " boxfgcolor=" + _jmol.params.boxfgcolor +
-          " progresscolor=" + _jmol.progresscolor);
+          " progresscolor=" + _jmol.params.progresscolor);
+}
+function jmolSetAppletWindow(w) {
+  _jmol.appletWindow = w;
+}
 function jmolApplet(size, script, nameSuffix) {
   _jmolInitCheck();
-  _jmolApplet(size, null, script, nameSuffix);
+  return _jmolApplet(size, null, script, nameSuffix);
+}
 ////////////////////////////////////////////////////////////////
 // Basic controls
 ////////////////////////////////////////////////////////////////
-function jmolButton(script, label, id) {
+function jmolButton(script, label, id, title) {
   _jmolInitCheck();
-  var scriptIndex = _jmolAddScript(script);
-  if (label == undefined || label == null)
-    label = script.substring(0, 32);
   if (id == undefined || id == null)
     id = "jmolButton" + _jmol.buttonCount;
+  if (label == undefined || label == null)
+    label = script.substring(0, 32);
   ++_jmol.buttonCount;
+  var scriptIndex = _jmolAddScript(script);
-  var t = "<input type='button' name='" + id + "' id='" + id +
+  var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input type='button' name='" + id + "' id='" + id +
           "' value='" + label +
           "' onClick='_jmolClick(" + scriptIndex + _jmol.targetText +
           ")' onMouseover='_jmolMouseOver(" + scriptIndex +
           ");return true' onMouseout='_jmolMouseOut()' " +
-          _jmol.buttonCssText + "/>";
+          _jmol.buttonCssText + "/></span>";
   if (_jmol.debugAlert)
     alert(t);
-  document.write(t);
+  return _jmolDocumentWrite(t);
 }
 function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked,
-                      labelHtml, isChecked, id) {
+                      labelHtml, isChecked, id, title) {
   _jmolInitCheck();
   if (id == undefined || id == null)
     id = "jmolCheckbox" + _jmol.checkboxCount;
   ++_jmol.checkboxCount;
   if (scriptWhenChecked == undefined || scriptWhenChecked == null ||
     alert("jmolCheckbox requires a label");
     return;
+  }
   var indexChecked = _jmolAddScript(scriptWhenChecked);
   var indexUnchecked = _jmolAddScript(scriptWhenUnchecked);
+  var eospan = "</span>"
-  var t = "<input type='checkbox' name='" + id + "' id='" + id +
+  var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><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 + "/>" +
+          (isChecked ? "checked " : "") + _jmol.checkboxCssText + "/>"
+  if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
+        t += eospan
-          labelHtml;
+        eospan = "";
+  }
+  t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan;
   if (_jmol.debugAlert)
     alert(t);
-  document.write(t);
+  return _jmolDocumentWrite(t);
+}
+function jmolStartNewRadioGroup() {
+  ++_jmol.radioGroupCount;
 }
-function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName) {
+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;
   }
   if (separatorHtml == undefined || separatorHtml == null)
     separatorHtml = "&nbsp; ";
-  var length = arrayOfRadioButtons.length;
+  var len = arrayOfRadioButtons.length;
-  var t = "";
   jmolStartNewRadioGroup();
+  if (!groupName)
+    groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1);
+  var t = "<span id='"+(id ? id : groupName)+"'>";
-  for (var i = 0; i < length; ++i) {
+  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);
+      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);
+      t += _jmolRadio(radio, null, null, separatorHtml, groupName, (id ? id : groupName)+"_"+i, title);
+    }
+  }
+  t+="</span>"
   if (_jmol.debugAlert)
     alert(t);
-  document.write(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, text, id) {
+function jmolLink(script, label, id, title) {
+  _jmolInitCheck();
+  if (id == undefined || id == null)
+    id = "jmolLink" + _jmol.linkCount;
+  if (label == undefined || label == null)
+    label = script.substring(0, 32);
+  ++_jmol.linkCount;
+  var scriptIndex = _jmolAddScript(script);
+  var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><a name='" + id + "' id='" + id +
+          "' href='javascript:_jmolClick(" + scriptIndex + _jmol.targetText + ");' onMouseover='_jmolMouseOver(" + scriptIndex +
+          ");return true;' onMouseout='_jmolMouseOut()' " +
+          _jmol.linkCssText + ">" + label + "</a></span>";
+  if (_jmol.debugAlert)
+    alert(t);
+  return _jmolDocumentWrite(t);
+}
+function jmolCommandInput(label, size, id, title) {
   _jmolInitCheck();
   if (id == undefined || id == null)
-    id = "jmolLink" + _jmol.linkCount;
+    id = "jmolCmd" + _jmol.cmdCount;
-  ++_jmol.linkCount;
+  if (label == undefined || label == null)
-  var scriptIndex = _jmolAddScript(script);
+    label = "Execute";
-  var t = "<a name='" + id + "' id='" + id +
+  if (size == undefined || isNaN(size))
-          "' href='javascript:_jmolClick(" + scriptIndex +
+    size = 60;
-          _jmol.targetText +
+  ++_jmol.cmdCount;
-          ");' onMouseover='_jmolMouseOver(" + scriptIndex +
+  var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input name='" + id + "' id='" + id +
-          ");return true;' onMouseout='_jmolMouseOut()' " +
+          "' size='"+size+"'><input type=button value = '"+label+"' onClick='jmolScript(document.getElementById(\""+id+"\").value" + _jmol.targetText + ")'/></span>";
-          _jmol.linkCssText + ">" + text + "</a>";
   if (_jmol.debugAlert)
     alert(t);
-  document.write(t);
+  return _jmolDocumentWrite(t);
+}
-function jmolMenu(arrayOfMenuItems, size, id) {
+function jmolMenu(arrayOfMenuItems, size, id, title) {
   _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;
+    var len = arrayOfMenuItems.length;
     if (typeof size != "number" || size == 1)
       size = null;
     else if (size < 0)
-      size = length;
+      size = len;
     var sizeText = size ? " size='" + size + "' " : "";
-    var t = "<select name='" + id + "' id='" + id +
+    var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><select name='" + id + "' id='" + id +
-            "' onChange='_jmolMenuSelected(this" +
+            "' onChange='_jmolMenuSelected(this" + _jmol.targetText + ")'" +
-            _jmol.targetText + ")'" +
             sizeText + _jmol.menuCssText + ">";
-    for (var i = 0; i < length; ++i) {
+    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) {
         isSelected = menuItem[2];
       } else {
         script = text = menuItem;
+      }
       if (text == undefined || text == null)
         text = script;
+          if (script=="#optgroup") {
+        t += "<optgroup label='" + text + "'>";
+          } else if (script=="#optgroupEnd") {
+        t += "</optgroup>";
+          } else {
-      var scriptIndex = _jmolAddScript(script);
+        var scriptIndex = _jmolAddScript(script);
-      var selectedText = isSelected ? "' selected>" : "'>";
+        var selectedText = isSelected ? "' selected>" : "'>";
-      t += "<option value='" + scriptIndex + selectedText + text + "</option>";
+        t += "<option value='" + scriptIndex + selectedText + text + "</option>";
+          }
+    }
-    t += "</select>";
+    t += "</select></span>";
     if (_jmol.debugAlert)
       alert(t);
-    document.write(t);
+    return _jmolDocumentWrite(t);
+  }
+}
 function jmolHtml(html) {
-  document.write(html);
+  return _jmolDocumentWrite(html);
+}
 function jmolBr() {
-  document.write("<br />");
+  return _jmolDocumentWrite("<br />");
+}
 ////////////////////////////////////////////////////////////////
 // advanced scripting functions
 ////////////////////////////////////////////////////////////////
 function jmolDebugAlert(enableAlerts) {
   _jmol.debugAlert = (enableAlerts == undefined || enableAlerts)
+}
 function jmolAppletInline(size, inlineModel, script, nameSuffix) {
+  _jmolInitCheck();
-  _jmolApplet(size, _jmolConvertInline(inlineModel), script, nameSuffix);
+  return _jmolApplet(size, _jmolSterilizeInline(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");
+    if (targetSuffix == "all") {
+      with (_jmol) {
-    var applet = _jmolFindApplet(target);
+        for (var i = 0; i < appletSuffixes.length; ++i) {
-    if (applet)
+          var applet = _jmolGetApplet(appletSuffixes[i]);
-      return applet.script(script);
+          if (applet) applet.script(script);
+        }
+      }
-    else
+    } else {
+      var applet=_jmolGetApplet(targetSuffix);
-      alert("could not find applet " + target);
+      if (applet) applet.script(script);
+    }
   }
 }
 function jmolLoadInline(model, targetSuffix) {
-  if (model) {
+  if (!model)return "ERROR: NO MODEL"
-    var target = "jmolApplet" + (targetSuffix ? targetSuffix : "0");
+  var applet=_jmolGetApplet(targetSuffix);
+  if (!applet)return "ERROR: NO APPLET"
-//    while (! _jmol.ready[target])
+  if (typeof(model) == "string")
-//      alert("The Jmol applet " + target + " is not loaded yet");
+    return applet.loadInlineString(model, "", false);
+  else
+    return applet.loadInlineArray(model, "", false);
+}
+function jmolLoadInlineScript(model, script, targetSuffix) {
+  if (!model)return "ERROR: NO MODEL"
-//    if (! _jmol.ready[target])
+  var applet=_jmolGetApplet(targetSuffix);
+  if (!applet)return "ERROR: NO APPLET"
-//      alert("The Jmol applet " + target + " is not loaded yet");
+  return applet.loadInlineString(model, script, false);
+}
-//    if (document.applets[target] && ! document.applets[target].isActive())
+function jmolLoadInlineArray(ModelArray, script, targetSuffix) {
+  if (!model)return "ERROR: NO MODEL"
+  if (!script)script=""
-//       alert("The Jmol applet " + target + " is not yet active");
+  var applet=_jmolGetApplet(targetSuffix);
+  if (!applet)return "ERROR: NO APPLET"
-//    else {
+  try {
-      var applet = _jmolFindApplet(target);
+    return applet.loadInlineArray(ModelArray, script, false);
-      if (applet)
+  } catch (err) {
+    //IE 7 bug
-        return applet.loadInline(model);
+    return applet.loadInlineString(ModelArray.join("\n"), script, false);
+  }
+}
+function jmolAppendInlineArray(ModelArray, script, targetSuffix) {
+  if (!model)return "ERROR: NO MODEL"
+  if (!script)script=""
+  var applet=_jmolGetApplet(targetSuffix);
+  if (!applet)return "ERROR: NO APPLET"
-      else
+  try {
-        alert("could not find applet " + target);
+    return applet.loadInlineArray(ModelArray, script, true);
+  } catch (err) {
-//    }
+    //IE 7 bug
+    return applet.loadInlineString(ModelArray.join("\n"), script, true);
+  }
+}
-function jmolStartNewRadioGroup() {
-  ++_jmol.radioGroupCount;
-}
-function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName) {
+function jmolAppendInlineScript(model, script, targetSuffix) {
-  _jmolInitCheck();
-  if (_jmol.radioGroupCount == 0)
+  if (!model)return "ERROR: NO MODEL"
-    ++_jmol.radioGroupCount;
+  var applet=_jmolGetApplet(targetSuffix);
-  var t = _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName);
-  if (_jmol.debugAlert)
+  if (!applet)return "ERROR: NO APPLET"
-    alert(t);
-  document.write(t);
+  return applet.loadInlineString(model, script, true);
+}
 function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {
   if (typeof action == "string") {
     action = action.toLowerCase();
 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 = {
+  currentDocument: document,
-debugAlert: false,
+  debugAlert: false,
-bgcolor: "black",
-progresscolor: "blue",
-boxbgcolor: "black",
-boxfgcolor: "white",
-boxmessage: "Downloading JmolApplet ...",
-codebase: ".",
+  codebase: "",
-modelbase: ".",
+  modelbase: ".",
-appletCount: 0,
+  appletCount: 0,
+  appletSuffixes: [],
+  appletWindow: null,
-buttonCount: 0,
+  buttonCount: 0,
-checkboxCount: 0,
+  checkboxCount: 0,
-linkCount: 0,
+  linkCount: 0,
+  cmdCount: 0,
-menuCount: 0,
+  menuCount: 0,
-radioCount: 0,
+  radioCount: 0,
-radioGroupCount: 0,
+  radioGroupCount: 0,
-appletCssClass: null,
+  appletCssClass: null,
-appletCssText: "",
+  appletCssText: "",
-buttonCssClass: null,
+  buttonCssClass: null,
-buttonCssText: "",
+  buttonCssText: "",
-checkboxCssClass: null,
+  checkboxCssClass: null,
-checkboxCssText: "",
+  checkboxCssText: "",
-radioCssClass: null,
+  radioCssClass: null,
-radioCssText: "",
+  radioCssText: "",
-linkCssClass: null,
+  linkCssClass: null,
-linkCssText: "",
+  linkCssText: "",
-menuCssClass: null,
+  menuCssClass: null,
-menuCssText: "",
+  menuCssText: "",
-targetSuffix: 0,
+  targetSuffix: 0,
-targetText: "",
+  targetText: "",
-scripts: [""],
+  scripts: [""],
+  params: {
+        syncId: ("" + Math.random()).substring(3),
+        progressbar: "true",
+        progresscolor: "blue",
+        boxbgcolor: "black",
+        boxfgcolor: "white",
+        boxmessage: "Downloading JmolApplet ..."
+  },
-ua: navigator.userAgent.toLowerCase(),
+  ua: navigator.userAgent.toLowerCase(),
-uaVersion: parseFloat(navigator.appVersion),
+  uaVersion: parseFloat(navigator.appVersion),
-os: "unknown",
+  os: "unknown",
-browser: "unknown",
+  browser: "unknown",
-browserVersion: 0,
+  browserVersion: 0,
-hasGetElementById: !!document.getElementById,
+  hasGetElementById: !!document.getElementById,
-isJavaEnabled: navigator.javaEnabled(),
+  isJavaEnabled: navigator.javaEnabled(),
-isNetscape47Win: false,
+  isNetscape47Win: false,
+  isIEWin: false,
+  useIEObject: false,
+  useHtml4Object: false,
+  windowsClassId: "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93",
+  windowsCabUrl:
+   "http://java.sun.com/update/1.5.0/jinstall-1_5_0_05-windows-i586.cab",
-isBrowserCompliant: false,
+  isBrowserCompliant: false,
-isJavaCompliant: false,
+  isJavaCompliant: false,
-isFullyCompliant: false,
+  isFullyCompliant: false,
-initialized: false,
+  initialized: false,
-initChecked: false,
+  initChecked: false,
-browserChecked: false,
+  browserChecked: false,
-checkBrowserAction: "alert",
+  checkBrowserAction: "alert",
-checkBrowserUrlOrMessage: null,
+  checkBrowserUrlOrMessage: null,
+  archivePath: null, // JmolApplet0.jar OR JmolAppletSigned0.jar
-previousOnloadHandler: null,
+  previousOnloadHandler: null,
-ready: {}
+  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));
+    _jmol.browserVersion = parseFloat(ua.substring(index+candidate.length+1));
     return true;
+  }
   function _jmolTestOS(candidate) {
     if (_jmol.ua.indexOf(candidate) < 0)
   isNetscape47Win = (os == "win" && browser == "mozilla" &&
                      browserVersion >= 4.78 && browserVersion <= 4.8);
   if (os == "win") {
-    isBrowserCompliant = hasGetElementById || isNetscape47Win;
+    isBrowserCompliant = hasGetElementById;
   } 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
     } else if (browser == "opera" && browserVersion <= 7.54) {
       isBrowserCompliant = false;
     } else {
       isBrowserCompliant = hasGetElementById &&
         !((browser == "msie") ||
-          (browser == "safari" && browserVersion < 125.1));
+          (browser == "safari" && browserVersion < 125.12));
+    }
   } else if (os == "linux" || os == "unix") {
     if (browser == "konqueror" && browserVersion <= 3.3)
       isBrowserCompliant = false;
     else
   // possibly more checks in the future for this
   isJavaCompliant = isJavaEnabled;
   isFullyCompliant = isBrowserCompliant && isJavaCompliant;
+  // IE5.5 works just fine ... but let's push them to Sun Java
+  isIEWin = (os == "win" && browser == "msie" && browserVersion >= 5.5);
+  useIEObject = isIEWin;
+  useHtml4Object =
+   (os != "mac" && browser == "mozilla" && browserVersion >= 5) ||
+   (os == "win" && browser == "opera" && browserVersion >= 8) ||
+   (os == "mac" && browser == "safari" && browserVersion >= 412.2);
+ doTranslate = true;
+ haveSetTranslate = false;
+}
+function jmolSetCallback(callbackName,funcName) {
+  _jmol.params[callbackName] = funcName
+}
+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.<br />\n" +
+        "Check the warning message from your browser and/or enable Java applets in<br />\n" +
+        "your web browser preferences, or install the Java Runtime Environment from <a href='http://www.java.com'>www.java.com</a><br />";
+if (noJavaMsg2==undefined) var noJavaMsg2 =
+        "You do not have the<br />\n" +
+        "Java Runtime Environment<br />\n" +
+        "installed for applet support.<br />\n" +
+        "Visit <a href='http://www.java.com'>www.java.com</a>";
 function _jmolApplet(size, inlineModel, script, nameSuffix) {
+        /*  AngelH, mar2007
+                Fixed percent / pixel business, to avoid browser errors:
+                put "px" where needed, avoid where not.
+        */
   with (_jmol) {
     if (! nameSuffix)
       nameSuffix = appletCount;
+    appletSuffixes.push(nameSuffix);
     ++appletCount;
     if (! script)
       script = "select *";
     var sz = _jmolGetAppletSize(size);
+    var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' ";
+    var tHeader, tFooter;
+    if (!codebase)
+        jmolInitialize(".");
+    if (useIEObject || useHtml4Object) {
+      params.name = 'jmolApplet' + nameSuffix;
+      params.archive = archivePath;
+      params.mayscript = 'true';
+      params.codebase = codebase;
+    }
+    if (useIEObject) { // use MSFT IE6 object tag with .cab file reference
+      winCodebase = (windowsCabUrl ? " codebase='" + windowsCabUrl + "'\n" : "");
+      params.code = 'JmolApplet';
-    var t;
+      tHeader =
+        "<object name='jmolApplet" + nameSuffix +
+        "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
+        " classid='" + windowsClassId + "'\n" + winCodebase + widthAndHeight + ">\n";
+      tFooter = "</object>";
+    } else if (useHtml4Object) { // use HTML4 object tag
+      tHeader =
+        "<object name='jmolApplet" + nameSuffix +
-    t = "<applet name='jmolApplet" + nameSuffix + "' id='jmolApplet" + nameSuffix +
+        "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
+        " classid='java:JmolApplet'\n" +
+        " type='application/x-java-applet'\n" +
+        widthAndHeight + ">\n";
+      tFooter = "</object>";
+    } else { // use applet tag
+      tHeader =
+        "<applet name='jmolApplet" + nameSuffix +
+        "' id='jmolApplet" + nameSuffix +
         "' " + appletCssText +
-        " code='JmolApplet' archive='JmolApplet.jar'\n" +
+        " code='JmolApplet'" +
-        " codebase='" + codebase + "'\n" +
+        " archive='" + archivePath + "' codebase='" + codebase + "'\n" +
-        " width='" + sz[0] + "' height='" + sz[1] +
+                widthAndHeight +
-        "' mayscript='true'>\n" +
+        " mayscript='true'>\n";
-        "  <param name='progressbar' value='true' />\n" +
+      tFooter = "</applet>";
+    }
+    var visitJava;
-        "  <param name='progresscolor' value='" +
+    if (isIEWin || useHtml4Object) {
-        progresscolor + "' />\n" +
+                var szX = "width:" + sz[0]
-        "  <param name='boxmessage' value='" +
+                if ( szX.indexOf("%")==-1 ) szX+="px"
-        boxmessage + "' />\n" +
+                var szY = "height:" + sz[1]
-        "  <param name='boxbgcolor' value='" +
+                if ( szY.indexOf("%")==-1 ) szY+="px"
-        boxbgcolor + "' />\n" +
+      visitJava =
-        "  <param name='boxfgcolor' value='" +
+        "<p style='background-color:yellow; color:black; " +
-        boxfgcolor + "' />\n" +
+                szX + ";" + szY + ";" +
-        "  <param name='ReadyCallback' value='_jmolReadyCallback' />\n";
+        // why doesn't this vertical-align work?
+        "text-align:center;vertical-align:middle;'>\n" +
+                noJavaMsg +
+        "</p>";
+    } else {
-    if (inlineModel)
+      visitJava =
+        "<table bgcolor='yellow'><tr>" +
-      t += "  <param name='loadInline' value='" + inlineModel + "' />\n";
+        "<td align='center' valign='middle' " + widthAndHeight + "><font color='black'>\n" +
-    if (script)
+                noJavaMsg2 +
+        "</font></td></tr></table>";
+    }
+    params.loadInline = (inlineModel ? inlineModel : "");
-      t += "  <param name='script' value='" + script + "' />\n";
+    params.script = (script ? _jmolSterilizeScript(script) : "");
-    t += "</applet>";
+    var t = tHeader + _jmolParams() + visitJava + tFooter;
     jmolSetTarget(nameSuffix);
     ready["jmolApplet" + nameSuffix] = false;
     if (_jmol.debugAlert)
       alert(t);
-    document.write(t);
+    return _jmolDocumentWrite(t);
+  }
+}
+function _jmolParams() {
+ var t = "";
+ for (i in _jmol.params)
+        if(_jmol.params[i]!="")
+                 t+="  <param name='"+i+"' value='"+_jmol.params[i]+"' />\n";
+ return t
+}
 function _jmolInitCheck() {
   if (_jmol.initChecked)
     return;
   _jmol.initChecked = true;
-  if (_jmol.initialized)
-    return;
-  alert("jmolInitialize({codebase}, {badBrowseURL}, {badJavaURL})\n" +
+  jmolInitialize(defaultdir, defaultjar)
-        "  must be called before any other Jmol.js functions");
+}
 function _jmolCheckBrowser() {
   with (_jmol) {
     if (browserChecked)
       _jmolPopup(checkBrowserUrlOrMessage);
     else {
       var msg = checkBrowserUrlOrMessage;
       if (msg == null)
         msg = "Your web browser is not fully compatible with Jmol\n\n" +
-              "brower: " + browser +
+              "browser: " + browser +
               "   version: " + browserVersion +
               "   os: " + os +
               "\n\n" + ua;
       alert(msg);
+    }
+  }
   return false;
+}
+function _jmolDocumentWrite(text) {
+  if (_jmol.currentDocument)
+    _jmol.currentDocument.write(text);
+  return text;
+}
 function _jmolPopup(url) {
   var popup = window.open(url, "JmolPopup",
                           "left=150,top=150,height=400,width=600," +
 function _jmolReadyCallback(name) {
   if (_jmol.debugAlert)
     alert(name + " is ready");
   _jmol.ready["" + name] = true;
 }
+function _jmolSterilizeScript(script) {
+  var inlineScript = script.replace(/'/g, "&#39;");
+  if (_jmol.debugAlert)
+    alert("script:\n" + inlineScript);
+  return inlineScript;
+}
-function _jmolConvertInline(model) {
+function _jmolSterilizeInline(model) {
+  var inlineModel =
-  var inlineModel = model.replace(/\r|\n|\r\n/g, "|");
+    model.replace(/\r|\n|\r\n/g, "|").replace(/'/g, "&#39;");
   if (_jmol.debugAlert)
     alert("inline model:\n" + inlineModel);
   return inlineModel;
+}
+        /*  AngelH, mar2007:
+                By (re)setting this variable in the webpage before calling jmolApplet(), limits for applet size can be overriden.
+        */
+        /* hansonr, jun2007:
+standard for GeoWall (http://geowall.geo.lsa.umich.edu/home.html)
+        */
+if (allowedJmolSize==undefined) var allowedJmolSize = [1, 2048, 300]   // min, max, default (pixels)
 function _jmolGetAppletSize(size) {
+        /*  AngelH, mar2007
+                Accepts single number or 2-value array, each one can be either:
+           percent (text string ending %), decimal 0 to 1 (percent/100), number, or text string (interpreted as nr.)
+           Size is now returned as string or number, no "px".
+        */
   var width, height;
-  var type = typeof size;
-  if (type == "number")
-    width = height = size;
-  else if (type == "object" && size != null) {
+  if ( (typeof size) == "object" && size != null ) {
     width = size[0]; height = size[1];
+  } else {
+    width = height = size;
+  }
+  // if percent, leave it as it is:
+  if ( width.toString().charAt(width.toString().length-1) != "%" ) {
+    width = parseFloat(width);  // convert to nr., or strip text, or make zero
+        if ( width <= 1 && width > 0 ) { width = (width*100)+"%" }      // decimal: convert to percent and quit
+        else if ( width >= allowedJmolSize[0] && width <= allowedJmolSize[1] ) { width = parseInt(width) }      // accept only that range (pixels)
+        else { width = allowedJmolSize[2] }     // default size 300 pixels
+  }
+  if ( height.toString().charAt(height.toString().length-1) != "%" ) {
+    height = parseFloat(height);
+        if ( height <= 1 && height > 0 ) { height = (height*100)+"%" }
+        else if ( height >= allowedJmolSize[0] && height <= allowedJmolSize[1] ) { height = parseInt(height) }
+        else { height = allowedJmolSize[2] }
+  }
-  if (! (width >= 25 && width <= 2000))
-    width = 300;
-  if (! (height >= 25 && height <= 2000))
-    height = 300;
   return [width, height];
 }
-function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName) {
+function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
   ++_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 +
+  var eospan = "</span>"
+  var t = "<span id=\"span_"+id+"\""+(title ? " title =\"" + title + "\"":"")+"><input name='"
-         "' type='radio' onClick='_jmolClick(" +
+        + groupName + "' id='"+id+"' type='radio' onClick='_jmolClick(" +
-         scriptIndex + _jmol.targetText +
-         ");return true;' onMouseover='_jmolMouseOver(" +
+         scriptIndex + _jmol.targetText + ");return true;' onMouseover='_jmolMouseOver(" +
-         scriptIndex +
-         ");return true;' onMouseout='_jmolMouseOut()' " +
+         scriptIndex + ");return true;' onMouseout='_jmolMouseOut()' " +
-         (isChecked ? "checked " : "") + _jmol.radioCssText + "/>" +
+         (isChecked ? "checked " : "") + _jmol.radioCssText + "/>"
+  if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
+        t += eospan
+        eospan = "";
+  }
-         labelHtml + separatorHtml;
+  t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +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)
-  var applet = _jmolSearchFrames(window, target);
+    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
+ if(!_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);
+      applet = _jmolSearchFrames(frames[i], target);
       if (applet)
-        break;
+        return applet;
+    }
+   }catch(e) {
+        if (_jmol.debugAlert)
+                alert("Jmol.js _jmolSearchFrames cannot access " + win.name + ".frame[" + i + "] consider using jmolSetAppletWindow()")
+   }
+  }
-  } else { // look for the applet in this window
+  return applet = _jmolFindAppletInWindow(win, target)
+}
+function _jmolFindAppletInWindow(win, target) {
     var doc = win.document;
-// getElementById fails on MacOSX Safari & Mozilla
+    // getElementById fails on MacOSX Safari & Mozilla
+    if (_jmol.useHtml4Object || _jmol.useIEObject)
+      return doc.getElementById(target);
-    if (doc.applets)
+    else if (doc.applets)
-      applet = doc.applets[target];
+      return doc.applets[target];
     else
-      applet = doc[target];
+      return 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) {
+function _jmolClick(scriptIndex, targetSuffix, elementClicked) {
+  _jmol.element = elementClicked;
   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;
+  var len = menuObject.length;
-  if (typeof length == "number") {
+  if (typeof len == "number") {
-    for (var i = 0; i < length; ++i) {
+    for (var i = 0; i < len; ++i) {
       if (menuObject[i].selected) {
         _jmolClick(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.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;
+}
   if (_jmol.debugAlert)
     alert("jmolCodebase=" + _jmol.codebase);
+}
 function _jmolOnloadResetForms() {
+  // must be evaluated ONLY once
   _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; )
+        for (var i = forms.length; --i >= 0; )
-            forms[i].reset();
+          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;i<A.length;i++){
+        sout+="\n"
+        if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){
+                sout+=_jmolEnumerateObject(A[i],key+"["+i+"]")
+        }else{
+                sout+=key+"["+i+"]="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])
+        }
+    }
+ }else{
+    if(key != ""){
+        sout+=key+"={}"
+        key+="."
+    }
+    for(var i in A){
+        sout+="\n"
+        if(typeof(A[i]) == "object"||typeof(A[i]) == "array"){
+                sout+=_jmolEnumerateObject(A[i],key+i)
+        }else{
+                sout+=key+i+"="+(typeof(A[i]) == "string" && A[i]!="null"?"\""+A[i].replace(/\"/g,"\\\"")+"\"":A[i])
+        }
+    }
+ }
+ return sout
+}
+function _jmolSortKey0(a,b){
+ return (a[0]<b[0]?1:a[0]>b[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<A[i].length;j++)B[B.length]=A[i][j]
+ if(B.length == 0) return
+ B=B.sort(_jmolSortKey0)
+ return B
+}
+/////////additional extensions //////////
+function _jmolDomScriptLoad(URL){
+ //open(URL) //to debug
+ _jmol.servercall=URL
+ var node = document.getElementById("_jmolScriptNode")
+ if (node && _jmol.browser!="msie"){
+    document.getElementsByTagName("HEAD")[0].removeChild(node)
+    node=null
+ }
+ if (node) {
+   node.setAttribute("src",URL)
+ } else {
+   node=document.createElement("script")
+   node.setAttribute("id","_jmolScriptNode")
+   node.setAttribute("type","text/javascript")
+   node.setAttribute("src",URL)
+   document.getElementsByTagName("HEAD")[0].appendChild(node)
+ }
+}
+function _jmolExtractPostData(url){
+ S=url.split("&POST:")
+ var s=""
+ for(var i=1;i<S.length;i++){
+        KV=S[i].split("=")
+        s+="&POSTKEY"+i+"="+KV[0]
+        s+="&POSTVALUE"+i+"="+KV[1]
+ }
+ return "&url="+escape(S[0])+s
+}
+function _jmolLoadModel(targetSuffix,remoteURL,array,isError,errorMessage){
+ //called by server, but in client
+ //overload this function to customize return
+ _jmol.remoteURL=remoteURL
+ if(isError)alert(errorMessage)
+ jmolLoadInlineScript(array.join("\n"),_jmol.optionalscript,targetSuffix)
+}
+//////////user property/status functions/////////
+function jmolGetStatus(strStatus,targetSuffix){
+ return _jmolSortMessages(jmolGetPropertyAsArray("jmolStatus",strStatus,targetSuffix))
+}
+function jmolGetPropertyAsArray(sKey,sValue,targetSuffix) {
+ return _jmolEvalJSON(jmolGetPropertyAsJSON(sKey,sValue,targetSuffix),sKey)
+}
+function jmolGetPropertyAsString(sKey,sValue,targetSuffix) {
+ var applet = _jmolGetApplet(targetSuffix);
+ if(!sValue)sValue=""
+ return (applet ? applet.getPropertyAsString(sKey,sValue) + "" : "")
+}
+function jmolGetPropertyAsJSON(sKey,sValue,targetSuffix) {
+ if(!sValue)sValue = ""
+ var applet = _jmolGetApplet(targetSuffix);
+ try {
+  return (applet ? applet.getPropertyAsJSON(sKey,sValue) + "" : "")
+ } catch(e) {
+  return ""
+ }
+}
+function jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix) {
+ if(!sValue)sValue = ""
+ var applet = _jmolGetApplet(targetSuffix);
+ return (applet ? applet.getProperty(sKey,sValue) : null)
+}
+function jmolDecodeJSON(s) {
+ return _jmolEnumerateObject(_jmolEvalJSON(s),"")
+}
+///////// synchronous scripting ////////
+function jmolScriptWait(script, targetSuffix) {
+  if(!targetSuffix)targetSuffix="0"
+  var Ret=jmolScriptWaitAsArray(script, targetSuffix)
+  var s = ""
+  for(var i=Ret.length;--i>=0;)
+  for(var j=0;j< Ret[i].length;j++)
+        s+=Ret[i][j]+"\n"
+  return s
+}
+function jmolScriptWaitOutput(script, targetSuffix) {
+  if(!targetSuffix)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
+  if(!targetSuffix)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
+  if(!targetSuffix)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"
+  if(!targetSuffix)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) {
+ if(!targetSuffix)targetSuffix="0"
+  return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo
+}
+function jmolRestoreOrientation(id, targetSuffix) {
+ if(!targetSuffix)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) {
+ if(arguments.length < 2)delay=1;
+ if(!targetSuffix)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){
+  if(value == "")return appletCode
+  return appletCode.replace(/\<param/,"\n<param name='"+name+"' value='"+value+"' />\n<param")
+}
+///////////////auto load Research Consortium for Structural Biology (RCSB) data ///////////
+function jmolLoadAjax_STOLAF_RCSB(fileformat,pdbid,optionalscript,targetSuffix){
+ if(!_jmol.thismodel)_jmol.thismodel = "1crn"
+ if(!_jmol.serverURL)_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm"
+ if(!_jmol.RCSBserver)_jmol.RCSBserver="http://www.rcsb.org"
+ if(!_jmol.defaultURL_RCSB)_jmol.defaultURL_RCSB=_jmol.RCSBserver+"/pdb/files/1CRN.CIF"
+ if(!fileformat)fileformat="PDB"
+ if(!pdbid)pdbid=prompt("Enter a 4-digit PDB ID:",_jmol.thismodel)
+ if(!pdbid || pdbid.length != 4)return ""
+ if(!targetSuffix)targetSuffix="0"
+ if(!optionalscript)optionalscript=""
+ var url=_jmol.defaultURL_RCSB.replace(/1CRN/g,pdbid.toUpperCase())
+ if(fileformat!="CIF")url=url.replace(/CIF/,fileformat)
+ _jmol.optionalscript=optionalscript
+ _jmol.thismodel=pdbid
+ _jmol.thistargetsuffix=targetSuffix
+ _jmol.thisurl=url
+ _jmol.modelArray = []
+ url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
+ _jmolDomScriptLoad(url)
+ return url
+}
+/////////////// St. Olaf College AJAX server -- ANY URL ///////////
+function jmolLoadAjax_STOLAF_ANY(url, userid, optionalscript,targetSuffix){
+ _jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm"
+ if(!_jmol.thisurlANY)_jmol.thisurlANY = "http://www.stolaf.edu/depts/chemistry/mo/struc/data/ycp3-1.mol"
+ if(!url)url=prompt("Enter any (uncompressed file) URL:", _jmol.thisurlANY)
+ if(!userid)userid="0"
+ if(!targetSuffix)targetSuffix="0"
+ if(!optionalscript)optionalscript=""
+ _jmol.optionalscript=optionalscript
+ _jmol.thistargetsuffix=targetSuffix
+ _jmol.modelArray = []
+ _jmol.thisurl = url
+ url=_jmol.serverURL+"?returnfunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix+_jmolExtractPostData(url)
+ _jmolDomScriptLoad(url)
+}
+/////////////// Mineralogical Society of America (MSA) data /////////
+function jmolLoadAjax_MSA(key,value,optionalscript,targetSuffix){
+ if(!_jmol.thiskeyMSA)_jmol.thiskeyMSA = "mineral"
+ if(!_jmol.thismodelMSA)_jmol.thismodelMSA = "quartz"
+ if(!_jmol.ajaxURL_MSA)_jmol.ajaxURL_MSA="http://rruff.geo.arizona.edu/AMS/result.php?mineral=quartz&viewing=ajaxjs"
+ if(!key)key=prompt("Enter a field:", _jmol.thiskeyMSA)
+ if(!key)return ""
+ if(!value)value=prompt("Enter a "+key+":", _jmol.thismodelMSA)
+ if(!value)return ""
+ if(!targetSuffix)targetSuffix="0"
+ if(!optionalscript)optionalscript=""
+ if(optionalscript == 1)optionalscript='load "" {1 1 1}'
+ var url=_jmol.ajaxURL_MSA.replace(/mineral/g,key).replace(/quartz/g,value)
+ _jmol.optionalscript=optionalscript
+ _jmol.thiskeyMSA=key
+ _jmol.thismodelMSA=value
+ _jmol.thistargetsuffix=targetSuffix
+ _jmol.thisurl=url
+ _jmol.modelArray = []
+ loadModel=_jmolLoadModel
+ _jmolDomScriptLoad(url)
+ return url
+}
+function jmolLoadAjaxJS(url, userid, optionalscript,targetSuffix){
+ if(!userid)userid="0"
+ if(!targetSuffix)targetSuffix="0"
+ if(!optionalscript)optionalscript=""
+ _jmol.optionalscript=optionalscript
+ _jmol.thismodel=userid
+ _jmol.thistargetsuffix=targetSuffix
+ _jmol.modelArray = []
+ _jmol.thisurl = url
+ url+="&returnFunction=_jmolLoadModel&returnArray=_jmol.modelArray&id="+targetSuffix
+ _jmolDomScriptLoad(url)
+}
+//// in case Jmol library has already been loaded:
+}catch(e){}
+///////////////moving atoms //////////////
+// HIGHLY experimental!!
+function jmolSetAtomCoord(i,x,y,z,targetSuffix){
+    _jmolCheckBrowser();
+      var applet=_jmolGetApplet(targetSuffix);
+      if (applet) applet.getProperty('jmolViewer').setAtomCoord(i,x,y,z)
+}
+function jmolSetAtomCoordRelative(i,x,y,z,targetSuffix){
+    _jmolCheckBrowser();
+      var applet=_jmolGetApplet(targetSuffix);
+      if (applet) applet.getProperty('jmolViewer').setAtomCoordRelative(i,x,y,z)
+}
+///////////////applet fake for testing buttons/////////////
+if(document.location.search.indexOf("NOAPPLET")>=0){
+        jmolApplet = function(w){
+                var s="<table style='background-color:black' width="+w+"><tr height="+w+">"
+                +"<td align=center valign=center style='background-color:white'>"
+                +"Applet would be here"
+                +"<p><textarea id=fakeApplet rows=5 cols=50></textarea>"
+                +"</td></tr></table>"
+                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}
+        }
+}
+///////////////////////////////////////////
+//new 9:49 AM 3/6/2007:
+//both w and h are optional.
+//if either is between 0 and 1, then it is taken as percent/100.
+//if either is greater than 1, then it is taken as a size.
+function jmolResize(w,h) {
+ _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(0);
+ if(!applet)return;
+ applet.style.width = (percentW ? width * percentW/100 : w)+"px"
+ applet.style.height = (percentH ? height * percentH/100 : h)+"px"
+ title=width +  " " + height + " " + (new Date())
+}

Subversion Repositories wimsdev

(root)/trunk/wims/public_html/java/jmol/Jmol.js – Rev 17 → 1365