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

-/* Jmol 11.7 script library Jmol.js  12:17 AM 4/20/2009 Bob Hanson
+/* Jmol 11.9 script library Jmol.js  6:56 AM 1/20/2010 Bob Hanson
  checkbox heirarchy -- see http://chemapps.stolaf.edu/jmol/docs/examples-11/check.htm
     based on:
+ *
 // bh 12/2008 -- jmolLoadInline, jmolLoadInlineArray, jmolLoadInlineScript, jmolAppendInlineScript, jmolAppendInlineArray all return error message or null (Jmol 11.7.16)
 // bh 12/2008 -- jmolScriptWaitOutput() -- waits for script to complete and delivers output normally sent to console
 // bh 5/2009  -- Support for XHTML using jmolSetXHTML(id)
 // ah & bh 6/2009 -- New jmolResizeApplet() more flexible, similar to jmolApplet() size syntax
+// bh 11/2009 -- care in accessing top.document
+// bh 12/2009 -- added jmolSetParameter(name, value)
+// bh 12/2009 -- added PARAMS=name:value;name:value;name:value... for command line
+// bh 12/2009 -- overhaul of target checking
+// bh 1/2010  -- all _xxxx() methods ALWAYS have complete argument list
+// bh 1/2010  -- adds option to run a JavaScript function from any Jmol control.
+//               This is accomplished by passing an array rather than a script:
+//               jmolHref([myfunc,"my param 1", "my param 2"], "testing")
+//               function myfunc(jmolControlObject, [myfunc,"my param 1", "my param 2"], target){...}
+//               and allows much more flexibility with responding to controls
 var defaultdir = "."
 var defaultjar = "JmolApplet.jar"
 // 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
 ////////////////////////////////////////////////////////////////
 function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) {
   if (_jmol.initialized)
     return;
   _jmol.initialized = true;
-  if(allowJMOLJAR && document.location.search.indexOf("JMOLJAR=")>=0) {
+  if(_jmol.jmoljar) {
-    var f = document.location.search.split("JMOLJAR=")[1].split("&")[0];
+    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("/"));
+    }
+  }
   _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.currentDocument = doc;
 }
 function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) {
   _jmolInitCheck();
   _jmol.params.boxbgcolor = boxbgcolor;
   if (boxfgcolor)
     _jmol.params.boxfgcolor = boxfgcolor
+}
 function jmolApplet(size, script, nameSuffix) {
   _jmolInitCheck();
   return _jmolApplet(size, null, script, nameSuffix);
 }
 ////////////////////////////////////////////////////////////////
 // Basic controls
 ////////////////////////////////////////////////////////////////
+// undefined means it wasn't there; null means it was explicitly listed as null (so as to skip it)
 function jmolButton(script, label, id, title) {
   _jmolInitCheck();
-  if (id == undefined || id == null)
-    id = "jmolButton" + _jmol.buttonCount;
+  id != undefined && id != null || (id = "jmolButton" + _jmol.buttonCount);
-  if (label == undefined || label == null)
-    label = script.substring(0, 32);
+  label != undefined && label != null || (label = script.substring(0, 32));
   ++_jmol.buttonCount;
   var scriptIndex = _jmolAddScript(script);
   var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input type='button' name='" + id + "' id='" + id +
           "' value='" + label +
-          "' onclick='_jmolClick(" + scriptIndex + _jmol.targetText +
+          "' onclick='_jmolClick(this," + scriptIndex + _jmol.targetText +
           ")' onmouseover='_jmolMouseOver(" + scriptIndex +
           ");return true' onmouseout='_jmolMouseOut()' " +
           _jmol.buttonCssText + " /></span>";
   if (_jmol.debugAlert)
     alert(t);
+}
 function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked,
                       labelHtml, isChecked, id, title) {
   _jmolInitCheck();
-  if (id == undefined || id == null)
-    id = "jmolCheckbox" + _jmol.checkboxCount;
+  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;
           indexChecked + "," + indexUnchecked + _jmol.targetText +
           ")' onmouseover='_jmolCbOver(this," + indexChecked + "," +
           indexUnchecked +
           ");return true' onmouseout='_jmolMouseOut()' " +
           (isChecked ? "checked='true' " : "")+ _jmol.checkboxCssText + " />"
   if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
         t += eospan
         eospan = "";
+  }
   t += "<label for=\"" + id + "\">" + labelHtml + "</label>" +eospan;
   if (_jmol.debugAlert)
     alert(t);
   return _jmolDocumentWrite(t);
+}
 function jmolStartNewRadioGroup() {
   ++_jmol.radioGroupCount;
 }
 function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) {
   /*
     array: [radio1,radio2,radio3...]
   var type = typeof arrayOfRadioButtons;
   if (type != "object" || type == null || ! arrayOfRadioButtons.length) {
     alert("invalid arrayOfRadioButtons");
     return;
+  }
-  if (separatorHtml == undefined || separatorHtml == null)
+  separatorHtml != undefined && separatorHtml != null || (separatorHtml = "&nbsp; ");
-    separatorHtml = "&nbsp; ";
   var len = arrayOfRadioButtons.length;
   jmolStartNewRadioGroup();
-  if (!groupName)
-    groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1);
+  groupName || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));
   var t = "<span id='"+(id ? id : groupName)+"'>";
   for (var i = 0; i < len; ++i) {
     if (i == len - 1)
       separatorHtml = "";
     var radio = arrayOfRadioButtons[i];
     } else {
       t += _jmolRadio(radio, null, null, separatorHtml, groupName, (id ? id : groupName)+"_"+i, title);
+    }
+  }
   t+="</span>"
   if (_jmol.debugAlert)
     alert(t);
   return _jmolDocumentWrite(t);
+}
 function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
   _jmolInitCheck();
   if (_jmol.radioGroupCount == 0)
     ++_jmol.radioGroupCount;
   var t = _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, (id ? id : groupName + "_" + _jmol.radioCount), title ? title : 0);
   if (_jmol.debugAlert)
     alert(t);
   return _jmolDocumentWrite(t);
+}
 function jmolLink(script, label, id, title) {
   _jmolInitCheck();
-  if (id == undefined || id == null)
-    id = "jmolLink" + _jmol.linkCount;
+  id != undefined && id != null || (id = "jmolLink" + _jmol.linkCount);
-  if (label == undefined || label == null)
-    label = script.substring(0, 32);
+  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 +
+          "' href='javascript:_jmolClick(this," + 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 = "jmolCmd" + _jmol.cmdCount;
+  id != undefined && id != null || (id = "jmolCmd" + _jmol.cmdCount);
-  if (label == undefined || label == null)
+  label != undefined && label != null || (label = "Execute");
-    label = "Execute";
-  if (size == undefined || isNaN(size))
+  size != undefined && !isNaN(size) || (size = 60);
-    size = 60;
   ++_jmol.cmdCount;
   var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input name='" + id + "' id='" + id +
           "' size='"+size+"' onkeypress='_jmolCommandKeyPress(event,\""+id+"\"" + _jmol.targetText + ")'><input type=button value = '"+label+"' onclick='jmolScript(document.getElementById(\""+id+"\").value" + _jmol.targetText + ")' /></span>";
   if (_jmol.debugAlert)
     alert(t);
+}
 function _jmolCommandKeyPress(e, id, target) {
         var keycode = (window.event ? window.event.keyCode : e ? e.which : 0);
         if (keycode == 13) {
+                var inputBox = document.getElementById(id)
-                jmolScript(document.getElementById(id).value, target)
+                _jmolScriptExecute(inputBox, inputBox.value, target)
+        }
+}
+function _jmolScriptExecute(element,script,target) {
+        if (typeof(script) == "object")
+                script[0](element, script, target)
+        else
+                jmolScript(script, target)
+}
 function jmolMenu(arrayOfMenuItems, size, id, title) {
   _jmolInitCheck();
-  if (id == undefined || id == null)
-    id = "jmolMenu" + _jmol.menuCount;
+  id != undefined && id != null || (id = "jmolMenu" + _jmol.menuCount);
   ++_jmol.menuCount;
   var type = typeof arrayOfMenuItems;
   if (type != null && type == "object" && arrayOfMenuItems.length) {
     var len = arrayOfMenuItems.length;
     if (typeof size != "number" || size == 1)
         text = menuItem[1];
         isSelected = menuItem[2];
       } else {
         script = text = menuItem;
+      }
-      if (text == undefined || text == null)
+      text != undefined && text != null || (text = script);
-        text = script;
-          if (script=="#optgroup") {
+      if (script=="#optgroup") {
         t += "<optgroup label='" + text + "'>";
           } else if (script=="#optgroupEnd") {
         t += "</optgroup>";
           } else {
         var scriptIndex = _jmolAddScript(script);
         var selectedText = isSelected ? "' selected='true'>" : "'>";
         t += "<option value='" + scriptIndex + selectedText + text + "</option>";
-          }
+      }
+    }
     t += "</select></span>";
     if (_jmol.debugAlert)
       alert(t);
     return _jmolDocumentWrite(t);
                      script, nameSuffix);
+}
 function jmolSetTarget(targetSuffix) {
   _jmol.targetSuffix = targetSuffix;
-  _jmol.targetText = targetSuffix ? ",\"" + targetSuffix + "\"" : "";
+  _jmol.targetText = targetSuffix ? ",\"" + targetSuffix + "\"" : ",0";
+}
 function jmolScript(script, targetSuffix) {
   if (script) {
     _jmolCheckBrowser();
+}
 function jmolLoadInlineArray(ModelArray, script, targetSuffix) {
   if (!model)return "ERROR: NO MODEL"
-  if (!script)script=""
+  script || (script="")
   var applet=_jmolGetApplet(targetSuffix);
   if (!applet)return "ERROR: NO APPLET"
   try {
     return applet.loadInlineArray(ModelArray, script, false);
   } catch (err) {
+  }
+}
 function jmolAppendInlineArray(ModelArray, script, targetSuffix) {
   if (!model)return "ERROR: NO MODEL"
-  if (!script)script=""
+  script || (script="")
   var applet=_jmolGetApplet(targetSuffix);
   if (!applet)return "ERROR: NO APPLET"
   try {
     return applet.loadInlineArray(ModelArray, script, true);
   } catch (err) {
+}
 function jmolCheckBrowser(action, urlOrMessage, nowOrLater) {
   if (typeof action == "string") {
     action = action.toLowerCase();
-    if (action != "alert" && action != "redirect" && action != "popup")
+    action == "alert" || action == "redirect" || action == "popup" || (action = null);
-      action = null;
+  }
   if (typeof action != "string")
     alert("jmolCheckBrowser(action, urlOrMessage, nowOrLater)\n\n" +
           "action must be 'alert', 'redirect', or 'popup'");
   else {
   linkCssText: "",
   menuCssClass: null,
   menuCssText: "",
   targetSuffix: 0,
-  targetText: "",
+  targetText: ",0",
   scripts: [""],
   params: {
         syncId: ("" + Math.random()).substring(3),
         progressbar: "true",
         progresscolor: "blue",
   checkBrowserUrlOrMessage: null,
   archivePath: null, // JmolApplet0.jar OR JmolAppletSigned0.jar
   previousOnloadHandler: null,
+  jmoljar: null,
+  useNoApplet: false,
   ready: {}
+}
 with (_jmol) {
   function _jmolTestUA(candidate) {
   _jmolTestOS("mac") ||
   _jmolTestOS("win");
   isNetscape47Win = (os == "win" && browser == "mozilla" &&
                      browserVersion >= 4.78 && browserVersion <= 4.8);
   if (os == "win") {
     isBrowserCompliant = hasGetElementById;
   } else if (os == "mac") { // mac is the problem child :-(
     if (browser == "mozilla" && browserVersion >= 5) {
       // miguel 2004 11 17
     isBrowserCompliant = hasGetElementById;
+  }
   // 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);
+ try {
+  if (top.location.search.indexOf("JMOLJAR=")>=0)
+    jmoljar = top.location.search.split("JMOLJAR=")[1].split("&")[0];
+ } catch(e) {
+  // can't access top.location
+ }
+ try {
+  useNoApplet = (top.location.search.indexOf("NOAPPLET")>=0);
- doTranslate = true;
+ } catch(e) {
- haveSetTranslate = false;
+  // can't access top.document
+ }
 }
+function jmolSetParameter(name,value) {
+  _jmol.params[name] = value
+}
 function jmolSetCallback(callbackName,funcName) {
   _jmol.params[callbackName] = funcName
+}
+ try {
+// note this is done FIRST, so it cannot override a setting done by the developer
+  if (top.location.search.indexOf("PARAMS=")>=0) {
+    var pars = unescape(top.location.search.split("PARAMS=")[1].split("&")[0]).split(";");
+    for (var i = 0; i < pars.length; i++) {
+      var p = pars[i].split(":");
+      jmolSetParameter(p[0],p[1]);
+    }
+  }
+ } catch(e) {
+  // can't access top.location
+ }
 function jmolSetSyncId(n) {
   return _jmol.params["syncId"] = n
+}
         "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.
+            Bob Hanson, 1/2010
+                Fixed inline escape changing returns to |
         */
   with (_jmol) {
-    if (! nameSuffix)
-      nameSuffix = appletCount;
+    nameSuffix == undefined && (nameSuffix = appletCount);
     appletSuffixes.push(nameSuffix);
     ++appletCount;
-    if (! script)
-      script = "select *";
+    script || (script = "select *");
     var sz = _jmolGetAppletSize(size);
     var widthAndHeight = " width='" + sz[0] + "' height='" + sz[1] + "' ";
     var tHeader, tFooter;
-    if (!codebase)
-        jmolInitialize(".");
+    codebase || jmolInitialize(".");
     if (useIEObject || useHtml4Object) {
       params.name = 'jmolApplet' + nameSuffix;
       params.archive = archivePath;
       params.mayscript = 'true';
       params.codebase = codebase;
         "<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 +
         "' id='jmolApplet" + nameSuffix + "' " + appletCssText + "\n" +
         " classid='java:JmolApplet'\n" +
         " type='application/x-java-applet'\n" +
         widthAndHeight + ">\n";
  var t = "";
  for (var 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;
   jmolInitialize(defaultdir, defaultjar)
         Ptr[0] = data.length
         return e
 //unnecessary?
-        if (!closetag)closetag = ""
+        closetag || (closetag = "")
-        if (!lvel) lvel = 0
+        lvel || (lvel = 0)
         var pt0 = Ptr[0]
         var pt = pt0
         while (pt < data.length && data.charAt(pt) != "<") pt++
         if (pt != pt0) {
                 var text = data.substring(pt0, pt)
     alert(name + " is ready");
   _jmol.ready["" + name] = true;
+}
 function _jmolSterilizeScript(script) {
-  var inlineScript = script.replace(/'/g, "&#39;");
+  script = script.replace(/'/g, "&#39;");
   if (_jmol.debugAlert)
-    alert("script:\n" + inlineScript);
+    alert("script:\n" + script);
-  return inlineScript;
+  return script;
+}
 function _jmolSterilizeInline(model) {
-  var inlineModel =
-    model.replace(/\r|\n|\r\n/g, "|").replace(/'/g, "&#39;");
+  model = model.replace(/\r|\n|\r\n/g, (model.indexOf("|") >= 0 ? "\\/n" : "|")).replace(/'/g, "&#39;");
   if (_jmol.debugAlert)
-    alert("inline model:\n" + inlineModel);
+    alert("inline model:\n" + model);
-  return inlineModel;
+  return model;
+}
 function _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) {
   ++_jmol.radioCount;
-  if (groupName == undefined || groupName == null)
-    groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1);
+  groupName != undefined && groupName != null || (groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1));
   if (!script)
     return "";
-  if (labelHtml == undefined || labelHtml == null)
+  labelHtml != undefined && labelHtml != null || (labelHtml = script.substring(0, 32));
-    labelHtml = script.substring(0, 32);
-  if (! separatorHtml)
-    separatorHtml = "";
+  separatorHtml || (separatorHtml = "")
   var scriptIndex = _jmolAddScript(script);
   var eospan = "</span>"
   var t = "<span id=\"span_"+id+"\""+(title ? " title=\"" + title + "\"":"")+"><input name='"
-        + groupName + "' id='"+id+"' type='radio' onclick='_jmolClick(" +
+        + groupName + "' id='"+id+"' type='radio' onclick='_jmolClick(this," +
          scriptIndex + _jmol.targetText + ");return true;' onmouseover='_jmolMouseOver(" +
          scriptIndex + ");return true;' onmouseout='_jmolMouseOut()' " +
          (isChecked ? "checked='true' " : "") + _jmol.radioCssText + " />"
   if (labelHtml.toLowerCase().indexOf("<td>")>=0) {
         t += eospan
 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 || alert("could not find applet " + target);
  _jmol.alerted = true;
  return null
+}
 function _jmolSearchFrames(win, target) {
     else
       return doc[target];
+}
 function _jmolAddScript(script) {
-  if (! script)
+  if (!script)
     return 0;
   var index = _jmol.scripts.length;
   _jmol.scripts[index] = script;
   return index;
+}
-function _jmolClick(scriptIndex, targetSuffix, elementClicked) {
+function _jmolClick(elementClicked, scriptIndex, targetSuffix) {
   _jmol.element = elementClicked;
-  jmolScript(_jmol.scripts[scriptIndex], targetSuffix);
+  _jmolScriptExecute(elementClicked, _jmol.scripts[scriptIndex], targetSuffix);
+}
 function _jmolMenuSelected(menuObject, targetSuffix) {
   var scriptIndex = menuObject.value;
   if (scriptIndex != undefined) {
-    jmolScript(_jmol.scripts[scriptIndex], targetSuffix);
+    _jmolScriptExecute(menuObject, _jmol.scripts[scriptIndex], targetSuffix);
     return;
+  }
   var len = menuObject.length;
   if (typeof len == "number") {
     for (var i = 0; i < len; ++i) {
       if (menuObject[i].selected) {
-        _jmolClick(menuObject[i].value, targetSuffix);
+        _jmolClick(menuObject[i], menuObject[i].value, targetSuffix);
         return;
+      }
+    }
+  }
   alert("?Que? menu selected bug #8734");
+        }
+}
 function _jmolCbClick(ckbox, whenChecked, whenUnchecked, targetSuffix) {
   _jmol.control = ckbox
-  _jmolClick(ckbox.checked ? whenChecked : whenUnchecked, targetSuffix);
+  _jmolClick(ckbox, ckbox.checked ? whenChecked : whenUnchecked, targetSuffix);
   if(_jmol.checkboxMasters[ckbox.id])
         _jmolNotifyGroup(_jmol.checkboxMasters[ckbox.id], ckbox.checked)
   if(_jmol.checkboxItems[ckbox.id])
         _jmolNotifyMaster(_jmol.checkboxItems[ckbox.id])
+}
 function _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)
+ isError && alert(errorMessage)
  jmolLoadInlineScript(array.join("\n"),_jmol.optionalscript,targetSuffix)
+}
 //////////user property/status functions/////////
  return _jmolEvalJSON(jmolGetPropertyAsJSON(sKey,sValue,targetSuffix),sKey)
+}
 function jmolGetPropertyAsString(sKey,sValue,targetSuffix) {
  var applet = _jmolGetApplet(targetSuffix);
- if(!sValue)sValue=""
+ sValue == undefined && (sValue="");
  return (applet ? applet.getPropertyAsString(sKey,sValue) + "" : "")
+}
 function jmolGetPropertyAsJSON(sKey,sValue,targetSuffix) {
- if(!sValue)sValue = ""
+ sValue == undefined && (sValue = "")
  var applet = _jmolGetApplet(targetSuffix);
  try {
   return (applet ? applet.getPropertyAsJSON(sKey,sValue) + "" : "")
  } catch(e) {
   return ""
+ }
+}
 function jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix) {
- if(!sValue)sValue = ""
+ sValue == undefined && (sValue = "")
  var applet = _jmolGetApplet(targetSuffix);
  return (applet ? applet.getProperty(sKey,sValue) : null)
+}
 ///////// synchronous scripting ////////
 function jmolScriptWait(script, targetSuffix) {
-  if(!targetSuffix)targetSuffix="0"
+  targetSuffix == undefined && (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"
+  targetSuffix == undefined && (targetSuffix="0")
   var ret = ""
   try{
    if (script) {
     _jmolCheckBrowser();
     var applet=_jmolGetApplet(targetSuffix);
 function jmolEvaluate(molecularMath, targetSuffix) {
   //carries out molecular math on a model
-  if(!targetSuffix)targetSuffix="0"
+  targetSuffix == undefined && (targetSuffix="0")
   var result = "" + jmolGetPropertyAsJavaObject("evaluate", molecularMath, targetSuffix);
   var s = result.replace(/\-*\d+/,"")
   if (s == "" && !isNaN(parseInt(result)))return parseInt(result);
   var s = result.replace(/\-*\d*\.\d*/,"")
   if (s == "" && !isNaN(parseFloat(result)))return parseFloat(result);
   return result;
+}
 function jmolScriptEcho(script, targetSuffix) {
   // returns a newline-separated list of all echos from a script
-  if(!targetSuffix)targetSuffix="0"
+  targetSuffix == undefined && (targetSuffix="0")
   var Ret=jmolScriptWaitAsArray(script, targetSuffix)
   var s = ""
   for(var i=Ret.length;--i>=0;)
   for(var j=Ret[i].length;--j>=0;)
         if (Ret[i][j][1] == "scriptEcho")s+=Ret[i][j][3]+"\n"
+}
 function jmolScriptMessage(script, targetSuffix) {
   // returns a newline-separated list of all messages from a script, ending with "script completed\n"
-  if(!targetSuffix)targetSuffix="0"
+  targetSuffix == undefined && (targetSuffix="0")
   var Ret=jmolScriptWaitAsArray(script, targetSuffix)
   var s = ""
   for(var i=Ret.length;--i>=0;)
   for(var j=Ret[i].length;--j>=0;)
         if (Ret[i][j][1] == "scriptStatus")s+=Ret[i][j][3]+"\n"
 ////////////   save/restore orientation   /////////////
 function jmolSaveOrientation(id, targetSuffix) {
- if(!targetSuffix)targetSuffix="0"
+ targetSuffix == undefined && (targetSuffix="0")
-  return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo
+ return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo
+}
 function jmolRestoreOrientation(id, targetSuffix) {
- if(!targetSuffix)targetSuffix="0"
+ targetSuffix == undefined && (targetSuffix="0")
  var s=_jmol["savedOrientation"+id]
  if (!s || s == "")return
  s=s.replace(/1\.0/,"0")
  return jmolScriptWait(s,targetSuffix)
+}
 function jmolRestoreOrientationDelayed(id, delay, targetSuffix) {
- if(arguments.length < 2)delay=1;
+ arguments.length < 2 && (delay=1)
- if(!targetSuffix)targetSuffix="0"
+ targetSuffix == undefined && (targetSuffix="0")
  var s=_jmol["savedOrientation"+id]
  if (!s || s == "")return
  s=s.replace(/1\.0/,delay)
  return jmolScriptWait(s,targetSuffix)
+}
    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")
+  return (value == "" ? appletCode : 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"
+ _jmol.thismodel || (_jmol.thismodel = "1crn")
- if(!_jmol.serverURL)_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm"
+ _jmol.serverURL || (_jmol.serverURL="http://fusion.stolaf.edu/chemistry/jmol/getajaxjs.cfm")
- if(!_jmol.RCSBserver)_jmol.RCSBserver="http://www.rcsb.org"
+ _jmol.RCSBserver || (_jmol.RCSBserver="http://www.rcsb.org")
- if(!_jmol.defaultURL_RCSB)_jmol.defaultURL_RCSB=_jmol.RCSBserver+"/pdb/files/1CRN.CIF"
+ _jmol.defaultURL_RCSB || (_jmol.defaultURL_RCSB=_jmol.RCSBserver+"/pdb/files/1CRN.CIF")
- if(!fileformat)fileformat="PDB"
+ fileformat || (fileformat="PDB")
- if(!pdbid)pdbid=prompt("Enter a 4-digit PDB ID:",_jmol.thismodel)
+ pdbid || (pdbid=prompt("Enter a 4-digit PDB ID:",_jmol.thismodel))
  if(!pdbid || pdbid.length != 4)return ""
- if(!targetSuffix)targetSuffix="0"
+ targetSuffix || (targetSuffix="0")
- if(!optionalscript)optionalscript=""
+ optionalscript || (optionalscript="")
  var url=_jmol.defaultURL_RCSB.replace(/1CRN/g,pdbid.toUpperCase())
- if(fileformat!="CIF")url=url.replace(/CIF/,fileformat)
+ fileformat=="CIF" || (url=url.replace(/CIF/,fileformat))
  _jmol.optionalscript=optionalscript
  _jmol.thismodel=pdbid
  _jmol.thistargetsuffix=targetSuffix
  _jmol.thisurl=url
  _jmol.modelArray = []
 /////////////// 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"
+ _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)
+ url || (url=prompt("Enter any (uncompressed file) URL:", _jmol.thisurlANY))
- if(!userid)userid="0"
+ userid || (userid="0")
- if(!targetSuffix)targetSuffix="0"
+ targetSuffix || (targetSuffix="0")
- if(!optionalscript)optionalscript=""
+ 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)
 /////////////// Mineralogical Society of America (MSA) data /////////
 function jmolLoadAjax_MSA(key,value,optionalscript,targetSuffix){
- if(!_jmol.thiskeyMSA)_jmol.thiskeyMSA = "mineral"
+ _jmol.thiskeyMSA || (_jmol.thiskeyMSA = "mineral")
- if(!_jmol.thismodelMSA)_jmol.thismodelMSA = "quartz"
+ _jmol.thismodelMSA || (_jmol.thismodelMSA = "quartz")
- if(!_jmol.ajaxURL_MSA)_jmol.ajaxURL_MSA="http://rruff.geo.arizona.edu/AMS/result.php?mineral=quartz&viewing=ajaxjs"
+ _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)
+ key || (key=prompt("Enter a field:", _jmol.thiskeyMSA))
  if(!key)return ""
- if(!value)value=prompt("Enter a "+key+":", _jmol.thismodelMSA)
+ value || (value=prompt("Enter a "+key+":", _jmol.thismodelMSA))
  if(!value)return ""
- if(!targetSuffix)targetSuffix="0"
+ targetSuffix || (targetSuffix="0")
- if(!optionalscript)optionalscript=""
+ optionalscript || (optionalscript="")
- if(optionalscript == 1)optionalscript='load "" {1 1 1}'
+ 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
+}
 function jmolLoadAjaxJS(url, userid, optionalscript,targetSuffix){
- if(!userid)userid="0"
+ userid || (userid="0")
- if(!targetSuffix)targetSuffix="0"
+ targetSuffix || (targetSuffix="0")
- if(!optionalscript)optionalscript=""
+ optionalscript || (optionalscript="")
  _jmol.optionalscript=optionalscript
  _jmol.thismodel=userid
  _jmol.thistargetsuffix=targetSuffix
  _jmol.modelArray = []
  _jmol.thisurl = url
 ///////////////applet fake for testing buttons/////////////
-if(document.location.search.indexOf("NOAPPLET")>=0){
+if(_jmol.useNoApplet){
         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>"

Subversion Repositories wimsdev

(root)/trunk/wims/public_html/java/jmol/Jmol.js – Rev 2876 → 2989