Merge branch 'issue71' into new-features (adds line numbering, \label and \ref)

config/default.js

@@ -262,6 +262,13 @@ MathJax.Hub.Config({
     //
     processEnvironments: true,
 
+    //
+    //  Controls whether tex2jax processes \ref{...} commands outside
+    //  of math mode.  Set to "false" to prevent processing of \ref
+    //  except within math mode.
+    //  
+    processRefs: true,
+
     //
     //  Controls whether tex2jax inserts MathJax_Preview spans to make a
     //  preview available, and what preview to use, when it locates in-line
@@ -368,7 +375,20 @@ MathJax.Hub.Config({
     //        bold: ['{\\bf #1}', 1]
     //      }
     //
-    Macros: {}
+    Macros: {},
+    
+    //
+    //  Equation numbering parameters.
+    //  
+    equationNumbers: {
+//    formatNumber: function (n) {return n},            // format for equation number n
+//    formatTag:    function (n) {return '('+n+')'},    // format for \tag and \eqref
+//    formatID:     function (n) {return 'mjx-eqn-'+n}, // element ID to use for reference
+//    formatURL:    function (n) {return '#mjx-eqn-'+escape(n)},   // URL to use for references
+
+      autoNumber: "none"   // "AMS" for standard AMS environment numbering,
+                           //  or "all" to number all displayed equations
+    }
     
   },
 

jax/input/TeX/config.js

@@ -12,5 +12,5 @@
  *      http://www.apache.org/licenses/LICENSE-2.0
  */
 
-MathJax.InputJax.TeX=MathJax.InputJax({id:"TeX",version:"1.1.2",directory:MathJax.InputJax.directory+"/TeX",extensionDir:MathJax.InputJax.extensionDir+"/TeX",config:{TagSide:"right",TagIndent:"0.8em",MultLineWidth:"85%"}});MathJax.InputJax.TeX.Register("math/tex");MathJax.InputJax.TeX.loadComplete("config.js");
+MathJax.InputJax.TeX=MathJax.InputJax({id:"TeX",version:"1.1.3",directory:MathJax.InputJax.directory+"/TeX",extensionDir:MathJax.InputJax.extensionDir+"/TeX",config:{TagSide:"right",TagIndent:"0.8em",MultLineWidth:"85%",equationNumbers:{autoNumber:"none",formatNumber:function(a){return a},formatTag:function(a){return"("+a+")"},formatID:function(a){return"mjx-eqn-"+a},formatURL:function(a){return"#mjx-eqn-"+escape(a)}}}});MathJax.InputJax.TeX.Register("math/tex");MathJax.InputJax.TeX.loadComplete("config.js");
 

jax/output/HTML-CSS/config.js

@@ -12,5 +12,5 @@
  *      http://www.apache.org/licenses/LICENSE-2.0
  */
 
-MathJax.OutputJax["HTML-CSS"]=MathJax.OutputJax({id:"HTML-CSS",version:"1.1.8",directory:MathJax.OutputJax.directory+"/HTML-CSS",extensionDir:MathJax.OutputJax.extensionDir+"/HTML-CSS",autoloadDir:MathJax.OutputJax.directory+"/HTML-CSS/autoload",fontDir:MathJax.OutputJax.directory+"/HTML-CSS/fonts",webfontDir:MathJax.OutputJax.fontDir+"/HTML-CSS",config:{scale:100,minScaleAdjust:50,availableFonts:["STIX","TeX"],preferredFont:"TeX",webFont:"TeX",imageFont:"TeX",undefinedFamily:"STIXGeneral,'Arial Unicode MS',serif",showMathMenu:true,styles:{".MathJax_Display":{"text-align":"center",margin:"1em 0em"},".MathJax .merror":{"background-color":"#FFFF88",color:"#CC0000",border:"1px solid #CC0000",padding:"1px 3px","font-family":"serif","font-style":"normal","font-size":"90%"},".MathJax_Preview":{color:"#888888"},"#MathJax_Tooltip":{"background-color":"InfoBackground",color:"InfoText",border:"1px solid black","box-shadow":"2px 2px 5px #AAAAAA","-webkit-box-shadow":"2px 2px 5px #AAAAAA","-moz-box-shadow":"2px 2px 5px #AAAAAA","-khtml-box-shadow":"2px 2px 5px #AAAAAA",filter:"progid:DXImageTransform.Microsoft.dropshadow(OffX=2, OffY=2, Color='gray', Positive='true')",padding:"3px 4px"}}}});if(MathJax.Hub.Browser.isMSIE&&document.documentMode>=9){delete MathJax.OutputJax["HTML-CSS"].config.styles["#MathJax_Tooltip"].filter}if(!MathJax.Hub.config.delayJaxRegistration){MathJax.OutputJax["HTML-CSS"].Register("jax/mml")}MathJax.Hub.Register.StartupHook("End Config",[function(b,c){var a=b.Insert({minBrowserVersion:{Firefox:3,Opera:9.52,MSIE:6,Chrome:0.3,Safari:2,Konqueror:4},inlineMathDelimiters:["$","$"],displayMathDelimiters:["$$","$$"],multilineDisplay:true,minBrowserTranslate:function(f){var e=b.getJaxFor(f),k=["[Math]"],j;var h=document.createElement("span",{className:"MathJax_Preview"});if(e.inputJax.id==="TeX"){if(e.root.Get("displaystyle")){j=a.displayMathDelimiters;k=[j[0]+e.originalText+j[1]];if(a.multilineDisplay){k=k[0].split(/\n/)}}else{j=a.inlineMathDelimiters;k=[j[0]+e.originalText.replace(/^\s+/,"").replace(/\s+$/,"")+j[1]]}}for(var g=0,d=k.length;g<d;g++){h.appendChild(document.createTextNode(k[g]));if(g<d-1){h.appendChild(document.createElement("br"))}}f.parentNode.insertBefore(h,f)}},(b.config["HTML-CSS"]||{}));if(b.Browser.version!=="0.0"&&!b.Browser.versionAtLeast(a.minBrowserVersion[b.Browser]||0)){c.Translate=a.minBrowserTranslate;b.Config({showProcessingMessages:false});MathJax.Message.Set("Your browser does not support MathJax",null,4000);b.Startup.signal.Post("MathJax not supported")}},MathJax.Hub,MathJax.OutputJax["HTML-CSS"]]);MathJax.OutputJax["HTML-CSS"].loadComplete("config.js");
+MathJax.OutputJax["HTML-CSS"]=MathJax.OutputJax({id:"HTML-CSS",version:"1.1.9",directory:MathJax.OutputJax.directory+"/HTML-CSS",extensionDir:MathJax.OutputJax.extensionDir+"/HTML-CSS",autoloadDir:MathJax.OutputJax.directory+"/HTML-CSS/autoload",fontDir:MathJax.OutputJax.directory+"/HTML-CSS/fonts",webfontDir:MathJax.OutputJax.fontDir+"/HTML-CSS",config:{scale:100,minScaleAdjust:50,availableFonts:["STIX","TeX"],preferredFont:"TeX",webFont:"TeX",imageFont:"TeX",undefinedFamily:"STIXGeneral,'Arial Unicode MS',serif",showMathMenu:true,styles:{".MathJax_Display":{"text-align":"center",margin:"1em 0em"},".MathJax .merror":{"background-color":"#FFFF88",color:"#CC0000",border:"1px solid #CC0000",padding:"1px 3px","font-family":"serif","font-style":"normal","font-size":"90%"},".MathJax_Preview":{color:"#888888"},"#MathJax_Tooltip":{"background-color":"InfoBackground",color:"InfoText",border:"1px solid black","box-shadow":"2px 2px 5px #AAAAAA","-webkit-box-shadow":"2px 2px 5px #AAAAAA","-moz-box-shadow":"2px 2px 5px #AAAAAA","-khtml-box-shadow":"2px 2px 5px #AAAAAA",filter:"progid:DXImageTransform.Microsoft.dropshadow(OffX=2, OffY=2, Color='gray', Positive='true')",padding:"3px 4px"}}}});if(MathJax.Hub.Browser.isMSIE&&document.documentMode>=9){delete MathJax.OutputJax["HTML-CSS"].config.styles["#MathJax_Tooltip"].filter}if(!MathJax.Hub.config.delayJaxRegistration){MathJax.OutputJax["HTML-CSS"].Register("jax/mml")}MathJax.Hub.Register.StartupHook("End Config",[function(b,c){var a=b.Insert({minBrowserVersion:{Firefox:3,Opera:9.52,MSIE:6,Chrome:0.3,Safari:2,Konqueror:4},inlineMathDelimiters:["$","$"],displayMathDelimiters:["$$","$$"],multilineDisplay:true,minBrowserTranslate:function(f){var e=b.getJaxFor(f),k=["[Math]"],j;var h=document.createElement("span",{className:"MathJax_Preview"});if(e.inputJax==="TeX"){if(e.root.Get("displaystyle")){j=a.displayMathDelimiters;k=[j[0]+e.originalText+j[1]];if(a.multilineDisplay){k=k[0].split(/\n/)}}else{j=a.inlineMathDelimiters;k=[j[0]+e.originalText.replace(/^\s+/,"").replace(/\s+$/,"")+j[1]]}}for(var g=0,d=k.length;g<d;g++){h.appendChild(document.createTextNode(k[g]));if(g<d-1){h.appendChild(document.createElement("br"))}}f.parentNode.insertBefore(h,f)}},(b.config["HTML-CSS"]||{}));if(b.Browser.version!=="0.0"&&!b.Browser.versionAtLeast(a.minBrowserVersion[b.Browser]||0)){c.Translate=a.minBrowserTranslate;b.Config({showProcessingMessages:false});MathJax.Message.Set("Your browser does not support MathJax",null,4000);b.Startup.signal.Post("MathJax not supported")}},MathJax.Hub,MathJax.OutputJax["HTML-CSS"]]);MathJax.OutputJax["HTML-CSS"].loadComplete("config.js");
 

jax/output/NativeMML/config.js

@@ -12,5 +12,5 @@
  *      http://www.apache.org/licenses/LICENSE-2.0
  */
 
-MathJax.OutputJax.NativeMML=MathJax.OutputJax({id:"NativeMML",version:"1.1.4",directory:MathJax.OutputJax.directory+"/NativeMML",extensionDir:MathJax.OutputJax.extensionDir+"/NativeMML",config:{scale:100,showMathMenu:true,showMathMenuMSIE:true,styles:{"DIV.MathJax_MathML":{"text-align":"center",margin:".75em 0px"}}}});if(!MathJax.Hub.config.delayJaxRegistration){MathJax.OutputJax.NativeMML.Register("jax/mml")}MathJax.OutputJax.NativeMML.loadComplete("config.js");
+MathJax.OutputJax.NativeMML=MathJax.OutputJax({id:"NativeMML",version:"1.1.5",directory:MathJax.OutputJax.directory+"/NativeMML",extensionDir:MathJax.OutputJax.extensionDir+"/NativeMML",config:{scale:100,showMathMenu:true,showMathMenuMSIE:true,styles:{"DIV.MathJax_MathML":{"text-align":"center",margin:".75em 0px"}}}});if(!MathJax.Hub.config.delayJaxRegistration){MathJax.OutputJax.NativeMML.Register("jax/mml")}MathJax.OutputJax.NativeMML.loadComplete("config.js");
 

unpacked/MathJax.js

@@ -30,7 +30,7 @@ if (!window.MathJax) {window.MathJax= {}}
 if (!MathJax.Hub) {  // skip if already loaded
   
 MathJax.version = "1.1a";
-MathJax.fileversion = "1.1.7";
+MathJax.fileversion = "1.1.8";
 
 /**********************************************************/
 
@@ -366,24 +366,51 @@ MathJax.fileversion = "1.1.7";
   };
 
   //
-  //  Run an array of callbacks passing them the given data.
+  //  An array or priorities hooks that are executed sequentially
+  //  with a given set of data.
+  //
+  var HOOKS = MathJax.Object.Subclass({
+    //
+    //  Initialize the array and the auto-reset status
+    //
+    Init: function (reset) {
+      this.hooks = [];
+      this.reset = reset;
+    },
+    //
+    //  Add a callback to the list, in priority order (default priority is 10)
+    //
+    Add: function (hook,priority) {
+      if (priority == null) {priority = 10}
+      if (!ISCALLBACK(hook)) {hook = USING(hook)}
+      hook.priority = priority;
+      var i = this.hooks.length;
+      while (i > 0 && priority < this.hooks[i-1].priority) {i--}
+      this.hooks.splice(i,0,hook);
+      return hook;
+    },
+    Remove: function (hook) {
+      for (var i = 0, m = this.hooks.length; i < m; i++) {
+        if (this.hooks[i] === hook) {this.hooks.splice(i,1); return}
+      }
+    },
+    //
+    //  Execute the list of callbacks, resetting them if requested.
     //  If any return callbacks, return a callback that will be 
     //  executed when they all have completed.
     //
-  var HOOKS = function (hooks,data,reset) {
+    Execute: function () {
-    if (!hooks) {return null}
-    if (!(hooks instanceof Array)) {hooks = [hooks]}
-    if (!(data instanceof Array))  {data = (data == null ? [] : [data])}
       var callbacks = [{}];
-    for (var i = 0, m = hooks.length; i < m; i++) {
+      for (var i = 0, m = this.hooks.length; i < m; i++) {
-      if (reset) {hooks[i].reset()}
+        if (this.reset) {this.hooks[i].reset()}
-      var result = hooks[i].apply(window,data);
+        var result = this.hooks[i].apply(window,arguments);
         if (ISCALLBACK(result) && !result.called) {callbacks.push(result)}
       }
       if (callbacks.length === 1) {return null}
       if (callbacks.length === 2) {return callbacks[1]}
       return AFTER.apply({},callbacks);
-  };
+    }
+  });
    
   //
   //  Command queue that performs commands in order, waiting when
@@ -448,7 +475,7 @@ MathJax.fileversion = "1.1.7";
       QUEUE.prototype.Init.call(this);
       this.name = name;
       this.posted = [];              // the messages posted so far
-      this.listeners = [];  // those with interest in this signal
+      this.listeners = HOOKS(true);  // those with interest in this signal
     },
     //
     // Post a message to the signal listeners, with callback for when complete
@@ -460,12 +487,9 @@ MathJax.fileversion = "1.1.7";
       } else {
         this.callback = callback; callback.reset();
         if (!forget) {this.posted.push(message)}
-        this.Suspend(); this.posting = 1;
+        this.Suspend(); this.posting = true;
-        for (var i = 0, m = this.listeners.length; i < m; i++) {
+        var result = this.listeners.Execute(message);
-          this.listeners[i].reset();
-          var result = (this.listeners[i])(message);
         if (ISCALLBACK(result) && !result.called) {WAITFOR(result,this)}
-        }
         this.Resume(); delete this.posting;
         if (!this.pending) {this.call()}
       }
@@ -491,11 +515,11 @@ MathJax.fileversion = "1.1.7";
     
     //
     //  A listener calls this to register intrest in the signal (so it will be called
-    //  when posts occur).  If ignorePast is 1, it will not be sent the post history.
+    //  when posts occur).  If ignorePast is true, it will not be sent the post history.
     //
-    Interest: function (callback,ignorePast) {
+    Interest: function (callback,ignorePast,priority) {
       callback = USING(callback);
-      this.listeners[this.listeners.length] = callback;
+      this.listeners.Add(callback,priority);
       if (!ignorePast) {
         for (var i = 0, m = this.posted.length; i < m; i++) {
           callback.reset();
@@ -509,19 +533,17 @@ MathJax.fileversion = "1.1.7";
     //  A listener calls this to remove itself from a signal
     //
     NoInterest: function (callback) {
-      for (var i = 0, m = this.listeners.length; i < m; i++) {
+      this.listeners.Remove(callback);
-        if (this.listeners[i] === callback) {this.listeners.splice(i,1); return}
-      }
     },
     
     //
     //  Hook a callback to a particular message on this signal
     //
-    MessageHook: function (msg,callback) {
+    MessageHook: function (msg,callback,priority) {
       callback = USING(callback);
       if (!this.hooks) {this.hooks = {}; this.Interest(["ExecuteHooks",this])}
-      if (!this.hooks[msg]) {this.hooks[msg] = []}
+      if (!this.hooks[msg]) {this.hooks[msg] = HOOKS(true)}
-      this.hooks[msg].push(callback);
+      this.hooks[msg].Add(callback,priority);
       for (var i = 0, m = this.posted.length; i < m; i++)
         {if (this.posted[i] == msg) {callback.reset(); callback(this.posted[i])}}
       return callback;
@@ -531,7 +553,8 @@ MathJax.fileversion = "1.1.7";
     //
     ExecuteHooks: function (msg,more) {
       var type = ((msg instanceof Array) ? msg[0] : msg);
-      return HOOKS(this.hooks[type],[msg],true);
+      if (!this.hooks[type]) {return null}
+      return this.hooks[type].Execute(msg);
     }
     
   },{
@@ -550,7 +573,7 @@ MathJax.fileversion = "1.1.7";
   BASE.Callback.After = AFTER;
   BASE.Callback.Queue = QUEUE;
   BASE.Callback.Signal = SIGNAL.find;
-  BASE.Callback.ExecuteHooks = HOOKS;
+  BASE.Callback.Hooks = HOOKS;
 })("MathJax");
 
 /**********************************************************/
@@ -635,8 +658,7 @@ MathJax.fileversion = "1.1.7";
         else {type = file.split(/\./).pop().toUpperCase()}
       file = this.fileURL(file);
       if (this.loading[file]) {
-        if (!this.loadHooks[file]) {this.loadHooks[file] = []}
+        this.addHook(file,callback);
-        this.loadHooks[file].push(callback);
       } else {
         this.head = HEAD(this.head);
         if (this.loader[type]) {this.loader[type].call(this,file,callback)}
@@ -649,18 +671,18 @@ MathJax.fileversion = "1.1.7";
     //  Register a load hook for a particular file (it will be called when
     //  loadComplete() is called for that file)
     //
-    LoadHook: function (file,callback) {
+    LoadHook: function (file,callback,priority) {
       callback = BASE.Callback(callback);
       if (file instanceof Object) {for (var i in file) {file = file[i]}}
       file = this.fileURL(file);
-      if (this.loaded[file]) {
+      if (this.loaded[file]) {callback(this.loaded[file])}
-        callback(this.loaded[file]);
+        else {this.addHook(file,callback,priority)}
-      } else {
-        if (!this.loadHooks[file]) {this.loadHooks[file] = []}
-        this.loadHooks[file].push(callback);
-      }
       return callback;
     },
+    addHook: function (file,callback,priority) {
+      if (!this.loadHooks[file]) {this.loadHooks[file] = MathJax.Callback.Hooks()}
+      this.loadHooks[file].Add(callback,priority);
+    },
     
     //
     //  Used when files are combined in a preloading configuration file
@@ -818,13 +840,13 @@ MathJax.fileversion = "1.1.7";
 	  SCRIPTS.push(loading.script);
 	}
         this.loaded[file] = loading.status; delete this.loading[file];
-        if (!this.loadHooks[file]) {this.loadHooks[file] = []}
+        this.addHook(file,loading.callback);
-        this.loadHooks[file].push(loading.callback);
       } else {
         this.loaded[file] = this.STATUS.OK;
         loading = {status: this.STATUS.OK}
       }
-      BASE.Callback.ExecuteHooks(this.loadHooks[file],loading.status);
+      if (!this.loadHooks[file]) {return null}
+      return this.loadHooks[file].Execute(loading.status);
     },
     
     //
@@ -1091,6 +1113,9 @@ MathJax.Message = {
       } else if (text.match(/^Processing /)) {
         if (!this.processing) {this.processing = "Processing "}
         text = this.processing; this.processing += ".";
+      } else if (text.match(/^Typesetting /)) {
+        if (!this.typesetting) {this.typesetting = "Typesetting "}
+        text = this.typesetting; this.typesetting += ".";
       }
     }
     return text;
@@ -1186,10 +1211,6 @@ MathJax.Hub = {
     "v1.0-compatible": true,  // set to false to prevent loading of default configuration file
     elements: [],    // array of elements to process when none is given explicitly
      
-    preProcessors: [], // list of callbacks for preprocessing (initialized by extensions)
-    inputJax: {},      // mime-type mapped to input jax (by registration)
-    outputJax: {order:{}}, // mime-type mapped to output jax list (by registration)
-
     menuSettings: {
       //format: "MathML",  //  the Show Source format (set in MathMenu.js)
       zoom: "None",        //  when to do MathZoom
@@ -1209,6 +1230,10 @@ MathJax.Hub = {
     }
   },
   
+  preProcessors: MathJax.Callback.Hooks(true), // list of callbacks for preprocessing (initialized by extensions)
+  inputJax: {},          // mime-type mapped to input jax (by registration)
+  outputJax: {order:{}}, // mime-type mapped to output jax list (by registration)
+
   processUpdateTime: 250, // time between screen updates when processing math (milliseconds)
 
   signal: MathJax.Callback.Signal("Hub"), // Signal used for Hub events
@@ -1228,7 +1253,7 @@ MathJax.Hub = {
   },
   
   Register: {
-    PreProcessor: function (callback) {MathJax.Hub.config.preProcessors.push(MathJax.Callback(callback))},
+    PreProcessor: function () {MathJax.Hub.preProcessors.Add.apply(MathJax.Hub.preProcessors,arguments)},
     MessageHook: function () {return MathJax.Hub.signal.MessageHook.apply(MathJax.Hub.signal,arguments)},
     StartupHook: function () {return MathJax.Hub.Startup.signal.MessageHook.apply(MathJax.Hub.Startup.signal,arguments)},
     LoadHook: function () {return MathJax.Ajax.LoadHook.apply(MathJax.Ajax,arguments)}
@@ -1275,7 +1300,7 @@ MathJax.Hub = {
     if (element && element.tagName != null && element.tagName.toLowerCase() === 'script') {
       if (element.MathJax) 
         {return (element.MathJax.state === MathJax.ElementJax.STATE.PROCESSED ? 1 : -1)}
-      if (element.type && this.config.inputJax[element.type.replace(/ *;(.|\s)*/,"")]) {return -1}
+      if (element.type && this.inputJax[element.type.replace(/ *;(.|\s)*/,"")]) {return -1}
     }
     // FIXME: check for results of outputJax
     return 0;
@@ -1307,8 +1332,7 @@ MathJax.Hub = {
       if (ec.elements[i]) {
         queue.Push(
           ["Post",this.signal,["Begin PreProcess",ec.elements[i]]],
-          ["ExecuteHooks",MathJax.Callback,
+          (arguments.callee.disabled? {} : ["Execute",this.preProcessors,ec.elements[i]]),
-            (arguments.callee.disabled ? [] : this.config.preProcessors), ec.elements[i], true],
           ["Post",this.signal,["End PreProcess",ec.elements[i]]]
         );
       }
@@ -1330,7 +1354,12 @@ MathJax.Hub = {
           ["Post",this.signal,["Begin "+action,ec.elements[i]]],
           ["Post",this.signal,["Begin Math",ec.elements[i]]],
           ["prepareScripts",this,action,ec.elements[i],scripts],
-          ["processScripts",this,scripts],
+          ["Post",this.signal,["Begin Math Input",ec.elements[i]]],
+          ["processInput",this,scripts],
+          ["Post",this.signal,["End Math Input",ec.elements[i]]],
+          ["Post",this.signal,["Begin Math Output",ec.elements[i]]],
+          ["processOutput",this,scripts],
+          ["Post",this.signal,["End Math Output",ec.elements[i]]],
           ["Post",this.signal,["End Math",ec.elements[i]]],
           ["Post",this.signal,["End "+action,ec.elements[i]]]
         );
@@ -1343,14 +1372,12 @@ MathJax.Hub = {
     Process: function (script) {},
     Update: function (script) {
       var jax = script.MathJax.elementJax;
-      //  FIXME:  Have intputJax determine if things have changed?
+      if (jax && jax.needsUpdate()) {jax.Remove(true); script.MathJax.state = jax.STATE.UPDATE}
-      if (jax && jax.originalText === (script.text == "" ? script.innerHTML : script.text))
+        else {script.MathJax.state = jax.STATE.PROCESSED}
-        {script.MathJax.state = jax.STATE.PROCESSED} else
-        {jax.outputJax.Remove(jax); script.MathJax.state = jax.STATE.UPDATE}
     },
     Reprocess: function (script) {
       var jax = script.MathJax.elementJax;
-      if (jax) {jax.outputJax.Remove(jax); script.MathJax.state = jax.STATE.UPDATE}
+      if (jax) {jax.Remove(true); script.MathJax.state = jax.STATE.UPDATE}
     }
   },
   
@@ -1360,7 +1387,7 @@ MathJax.Hub = {
     var STATE = MathJax.ElementJax.STATE;
     for (var i = 0, m = scripts.length; i < m; i++) {
       var script = scripts[i];
-      if (script.type && this.config.inputJax[script.type.replace(/ *;(.|\n)*/,"")]) {
+      if (script.type && this.inputJax[script.type.replace(/ *;(.|\n)*/,"")]) {
         if (script.MathJax && script.MathJax.state !== STATE.PENDING)
           {this.scriptAction[action](script)}
         if (!script.MathJax) {script.MathJax = {state: STATE.PENDING}}
@@ -1403,13 +1430,12 @@ MathJax.Hub = {
     if (script.MathJax) {script.MathJax.checked = 1}
   },
   
-  processScripts: function (scripts,start,n) {
+  processInput: function (scripts,start,n) {
     if (arguments.callee.disabled) {return null}
-    var result, STATE = MathJax.ElementJax.STATE;
-    var inputJax = this.config.inputJax, outputJax = this.config.outputJax;
-    try {
     if (!start) {start = new Date().getTime()}
+    var result, STATE = MathJax.ElementJax.STATE;
     var i = 0, script, prev;
+    try {
       while (i < scripts.length) {
         script = scripts[i]; if (!script) {i++; continue}
         prev = script.previousSibling;
@@ -1418,46 +1444,68 @@ MathJax.Hub = {
         if (!script.MathJax || script.MathJax.state === STATE.PROCESSED) {i++; continue};
         if (!script.MathJax.elementJax || script.MathJax.state === STATE.UPDATE) {
           this.checkScriptSiblings(script);
-          result = inputJax[type].Process(script);
+          result = this.inputJax[type].Process(script);
           if (typeof result === 'function') {
             if (result.called) continue; // go back and call Process() again
             this.RestartAfter(result);
           }
-          result.Attach(script,inputJax[type]);
+          result.Attach(script,this.inputJax[type].id);
           script.MathJax.state = STATE.OUTPUT;
         }
-        var jax = script.MathJax.elementJax;
-        if (!outputJax[jax.mimeType]) {
-          script.MathJax.state = STATE.UPDATE;
-          throw Error("No output jax registered for "+jax.mimeType);
-        }
-        jax.outputJax = outputJax[jax.mimeType][0];
-        result = jax.outputJax.Process(script);
-        if (typeof result === 'function') {
-          if (result.called) continue; // go back and call Process() again
-          this.RestartAfter(result);
-        }
-        script.MathJax.state = STATE.PROCESSED;
-        this.signal.Post(["New Math",jax.inputID]); // FIXME: wait for this?  (i.e., restart if returns uncalled callback)
         i++;
         if (new Date().getTime() - start > this.processUpdateTime && i < scripts.length)
           {start = 0; this.RestartAfter(MathJax.Callback.Delay(1))}
       }
-    } catch (err) {
+    } catch (err) {return this.processError(err,scripts,i,n,start,"Input")}
-      if (!err.restart) {
+    if ((n || scripts.length) && this.config.showProcessingMessages)
-        if (!this.config.errorSettings.message) {throw err}
+      {MathJax.Message.Set("Processing math: 100%",0)}
-        this.formatError(script,err); i++;
+    return null;
+  },
+
+  processOutput: function (scripts,start,n) {
+    if (arguments.callee.disabled) {return null}
+    if (!start) {start = new Date().getTime()}
+    var result, STATE = MathJax.ElementJax.STATE;
+    var i = 0, script;
+    try {
+      while (i < scripts.length) {
+        script = scripts[i]; if (!script || !script.MathJax) {i++; continue}
+        var jax = script.MathJax.elementJax; if (!jax) {i++; continue}
+        if (!this.outputJax[jax.mimeType]) {
+          script.MathJax.state = STATE.UPDATE;
+          throw Error("No output jax registered for "+jax.mimeType);
         }
-      if (!n) {n = 0}; var m = Math.floor((n+i)/(n+scripts.length)*100); n += i;
+        var outputJax = this.outputJax[jax.mimeType][0];
-      if (this.config.showProcessingMessages) {MathJax.Message.Set("Processing math: "+m+"%",0)}
+        jax.outputJax = outputJax.id;
-      return MathJax.Callback.After(["processScripts",this,scripts.slice(i),start,n],err.restart);
+        result = outputJax.Process(script);
+        if (typeof result === 'function') {
+          if (result.called) continue; // go back and call Process() again
+          this.RestartAfter(result);
         }
+        script.MathJax.state = STATE.PROCESSED; i++;
+        this.signal.Post(["New Math",jax.inputID]); // FIXME: wait for this?  (i.e., restart if returns uncalled callback)
+        if (new Date().getTime() - start > this.processUpdateTime && i < scripts.length)
+          {start = 0; this.RestartAfter(MathJax.Callback.Delay(1))}
+      }
+    } catch (err) {return this.processError(err,scripts,i,n,start,"Output")}
     if ((n || scripts.length) && this.config.showProcessingMessages) {
-      MathJax.Message.Set("Processing Math: 100%",0);
+      MathJax.Message.Set("Typesetting math: 100%",0);
       MathJax.Message.Clear(0);
     }
     return null;
   },
+
+  processError: function (err,scripts,i,n,start,type) {
+    if (!err.restart) {
+      if (!this.config.errorSettings.message) {throw err}
+      this.formatError(scripts[i],err); i++;
+    }
+    if (!n) {n = 0}; var m = Math.floor((n+i)/(n+scripts.length)*100); n += i;
+    var message = (type === "Output" ? "Typesetting" : "Processing");
+    if (this.config.showProcessingMessages) {MathJax.Message.Set(message+" math: "+m+"%",0)}
+    return MathJax.Callback.After(["process"+type,this,scripts.slice(i),start,n],err.restart);
+  },
+  
   formatError: function (script,err) {
     var error = MathJax.HTML.Element("span",{className:"MathJax_Error"},this.config.errorSettings.message);
     script.parentNode.insertBefore(error,script);
@@ -1505,8 +1553,7 @@ MathJax.Hub.Insert(MathJax.Hub.config.styles,MathJax.Message.styles);
 MathJax.Hub.Insert(MathJax.Hub.config.styles,{".MathJax_Error":MathJax.Hub.config.errorSettings.style});
 
 //
-//  Storage area for preprocessors and extensions
+//  Storage area for extensions and preprocessors
-//  (should these be classes?)
 //
 MathJax.Extension = {};
 
@@ -1637,11 +1684,11 @@ MathJax.Hub.Startup = {
   //  Load the input and output jax
   //
   Jax: function () {
-    var config = MathJax.Hub.config;
+    var config = MathJax.Hub.config, jax = MathJax.Hub.outputJax;
     //  Save the order of the output jax since they are loading asynchronously
     for (var i = 0, m = config.jax.length, k = 0; i < m; i++) {
       if (config.jax[i].substr(0,7) === "output/") 
-        {config.outputJax.order[config.jax[i].substr(7)] = k; k++}
+        {jax.order[config.jax[i].substr(7)] = k; k++}
     }
     var queue = MathJax.Callback.Queue();
     return queue.Push(
@@ -1674,7 +1721,7 @@ MathJax.Hub.Startup = {
   //  (this must come after the jax are loaded)
   //
   Menu: function () {
-    var menu = MathJax.Hub.config.menuSettings, jax = MathJax.Hub.config.outputJax, registered;
+    var menu = MathJax.Hub.config.menuSettings, jax = MathJax.Hub.outputJax, registered;
     for (var id in jax) {if (jax.hasOwnProperty(id)) {
       if (jax[id].length) {registered = jax[id]; break}
     }}
@@ -1840,13 +1887,17 @@ MathJax.Hub.Startup = {
       var load = queue.Push(AJAX.Require(this.directory+"/"+this.JAXFILE));
       if (!load.called) {this.constructor.prototype.Process = function () {return load}}
       // Load the associated output jax
-      jax = HUB.config.outputJax["jax/"+jax[0]];
+      jax = HUB.outputJax["jax/"+jax[0]];
       if (jax) {queue.Push(AJAX.Require(jax[0].directory+"/"+this.JAXFILE))}
       return queue.Push({});
     },
+    needsUpdate: function (jax) {
+      var script = jax.SourceElement();
+      return (jax.originalText !== (script.text == "" ? script.innerHTML : script.text));
+    },
     Register: function (mimetype) {
-      if (!HUB.config.inputJax) {HUB.config.inputJax = {}}
+      if (!HUB.inputJax) {HUB.inputJax = {}}
-      HUB.config.inputJax[mimetype] = this;
+      HUB.inputJax[mimetype] = this;
     }
   },{
     version: "1.1",
@@ -1858,7 +1909,7 @@ MathJax.Hub.Startup = {
 
   BASE.OutputJax = JAX.Subclass({
     Register: function (mimetype) {
-      var jax = HUB.config.outputJax;
+      var jax = HUB.outputJax;
       if (!jax[mimetype]) {jax[mimetype] = []}
       //  If the output jax is earlier in the original configuration list, put it first here
       if (jax[mimetype].length && (this.id === HUB.config.menuSettings.renderer ||
@@ -1905,10 +1956,15 @@ MathJax.Hub.Startup = {
       script.MathJax.state = this.STATE.OUTPUT;
       return HUB.Process(script,callback);
     },
-    Remove: function () {
+    Remove: function (keep) {
-      this.outputJax.Remove(this);
+      BASE.OutputJax[this.outputJax].Remove(this);
+      if (!keep) {
         HUB.signal.Post(["Remove Math",this.inputID]); // wait for this to finish?
         this.Detach();
+      }
+    },
+    needsUpdate: function () {
+      return BASE.InputJax[this.inputJax].needsUpdate(this);
     },
 
     SourceElement: function () {return document.getElementById(this.inputID)},

unpacked/config/default.js

@@ -262,6 +262,13 @@ MathJax.Hub.Config({
     //
     processEnvironments: true,
 
+    //
+    //  Controls whether tex2jax processes \ref{...} commands outside
+    //  of math mode.  Set to "false" to prevent processing of \ref
+    //  except within math mode.
+    //  
+    processRefs: true,
+
     //
     //  Controls whether tex2jax inserts MathJax_Preview spans to make a
     //  preview available, and what preview to use, when it locates in-line
@@ -368,7 +375,20 @@ MathJax.Hub.Config({
     //        bold: ['{\\bf #1}', 1]
     //      }
     //
-    Macros: {}
+    Macros: {},
+    
+    //
+    //  Equation numbering parameters.
+    //  
+    equationNumbers: {
+//    formatNumber: function (n) {return n},            // format for equation number n
+//    formatTag:    function (n) {return '('+n+')'},    // format for \tag and \eqref
+//    formatID:     function (n) {return 'mjx-eqn-'+n}, // element ID to use for reference
+//    formatURL:    function (n) {return '#mjx-eqn-'+escape(n)},   // URL to use for references
+
+      autoNumber: "none"   // "AMS" for standard AMS environment numbering,
+                           //  or "all" to number all displayed equations
+    }
     
   },
 

unpacked/extensions/MathZoom.js

@@ -23,7 +23,7 @@
  */
 
 (function (HUB,HTML,AJAX,HTMLCSS,nMML) {
-  var VERSION = "1.1";
+  var VERSION = "1.1.1";
   
   var CONFIG = HUB.CombineConfig("MathZoom",{
     delay: 400,   // mouse must be still this long (milliseconds)
@@ -148,8 +148,8 @@
       if (parent.parentNode.className === "MathJax_MathContainer") {parent = parent.parentNode.parentNode}
       var script = (String(parent.className).match(/^MathJax_(MathML|Display)$/) ? parent : math).nextSibling;
       var jax = HUB.getJaxFor(script), root = jax.root;
-      var JAX = (HTMLCSS && jax.outputJax.isa(HTMLCSS.constructor) ? "HTMLCSS" :
+      var JAX = (HTMLCSS && jax.outputJax === "HTML-CSS" ? "HTMLCSS" :
-                (nMML && jax.outputJax.isa(nMML.constructor) ? "MathML" : null));
+                (nMML && jax.outputJax === "NativeMML" ? "MathML" : null));
       if (!JAX) return; //  FIXME:  report an error?
 
       //

unpacked/extensions/TeX/AMSmath.js

@@ -6,7 +6,7 @@
  *  
  *  ---------------------------------------------------------------------
  *  
- *  Copyright (c) 2009 Design Science, Inc.
+ *  Copyright (c) 2009-2011 Design Science, Inc.
  * 
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.
@@ -21,16 +21,30 @@
  *  limitations under the License.
  */
 
-MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
+MathJax.Extension["TeX/AMSmath"] = {
-  var VERSION = "1.1";
+  version: "1.1.1",
   
-  var MML = MathJax.ElementJax.mml;
+  number: 0,        // current equation number
-  var TEX = MathJax.InputJax.TeX;
+  startNumber: 0,   // current starting equation number (for when equation is restarted)
-  var TEXDEF = TEX.Definitions;
+  labels: {},       // the set of labels
-  var STACKITEM = TEX.Stack.Item;
+  eqlabels: {},     // labels in the current equation
+  refs: []          // array of jax with unresolved references
+};
+
+MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
+  
+  var MML = MathJax.ElementJax.mml,
+      TEX = MathJax.InputJax.TeX,
+      AMS = MathJax.Extension["TeX/AMSmath"];
+
+  var TEXDEF = TEX.Definitions,
+      STACKITEM = TEX.Stack.Item,
+      CONFIG = TEX.config.equationNumbers;
       
   var COLS = function (W) {return W.join("em ") + "em"};
   
+  /******************************************************************************/
+  
   MathJax.Hub.Insert(TEXDEF,{
     macros: {
       mathring:   ['Accent','2DA'],  // or 0x30A
@@ -54,6 +68,9 @@ MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
       
       tag:         'HandleTag',
       notag:       'HandleNoTag',
+      label:       'HandleLabel',
+      ref:         'HandleRef',
+      eqref:       ['HandleRef',true],
       
       substack:   ['Macro','\\begin{subarray}{c}#1\\end{subarray}',1],
       
@@ -101,7 +118,10 @@ MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
       gathered:      ['Array',null,null,null,'c',null,".5em",'D'],
 
       subarray:      ['Array',null,null,null,null,COLS([0,0,0,0]),"0.1em",'S',1],
-      smallmatrix:   ['Array',null,null,null,'c',COLS([1/3]),".2em",'S',1]
+      smallmatrix:   ['Array',null,null,null,'c',COLS([1/3]),".2em",'S',1],
+      
+      'equation':    ['EquationBegin','Equation',true],
+      'equation*':   ['EquationBegin','EquationStar',false]
     },
     
     delimiter: {
@@ -113,21 +133,50 @@ MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
   });
     
 
+  /******************************************************************************/
+  
   TEX.Parse.Augment({
 
     /*
-     *  Add the tag to the environment to be added to the table row later
+     *  Add the tag to the environment (to be added to the table row later)
      */
     HandleTag: function (name) {
-      var arg = this.trimSpaces(this.GetArgument(name));
+      var arg = this.trimSpaces(this.GetArgument(name)), tag = arg;
-      if (arg === "*") {arg = this.GetArgument(name)} else {arg = "("+arg+")"}
+      if (arg === "*") {tag = arg = this.GetArgument(name)} else {arg = CONFIG.formatTag(arg)}
-      if (this.stack.global.notag)
+      var global = this.stack.global; global.tagID = tag;
-        {TEX.Error(name+" not allowed in "+this.stack.global.notag+" environment")}
+      if (global.notags) {TEX.Error(name+" not allowed in "+global.notags+" environment")}
-      if (this.stack.global.tag) {TEX.Error("Multiple "+name)}
+      if (global.tag) {TEX.Error("Multiple "+name)}
-      this.stack.global.tag = MML.mtd.apply(MML,this.InternalMath(arg));
+      global.tag = MML.mtd.apply(MML,this.InternalMath(arg)).With({id:CONFIG.formatID(tag)});
     },
     HandleNoTag: function (name) {
       if (this.stack.global.tag) {delete this.stack.global.tag}
+      this.stack.global.notag = true;  // prevent auto-tagging
+    },
+    
+    /*
+     *  Record a label name for a tag
+     */
+    HandleLabel: function (name) {
+      var global = this.stack.global, label = this.GetArgument(name);
+      if (!AMS.refUpdate) {
+        if (global.label) {TEX.Error("Multiple "+name+"'s")}
+        global.label = label;
+        if (AMS.labels[label] || AMS.eqlabels[label]) {TEX.Error("Label '"+label+"' mutiply defined")}
+        AMS.eqlabels[label] = "???"; // will be replaced by tag value later
+      }
+    },
+    
+    /*
+     *  Handle a label reference
+     */
+    HandleRef: function (name,eqref) {
+      var label = this.GetArgument(name);
+      var ref = AMS.labels[label] || AMS.eqlabels[label];
+      if (!ref) {ref = "??"; AMS.badref = !AMS.refUpdate}
+      var tag = ref; if (eqref) {tag = CONFIG.formatTag(tag)}
+      this.Push(MML.mrow.apply(MML,this.InternalMath(tag)).With({
+        href:CONFIG.formatURL(ref), "class":"MathJax_ref"
+      }));
     },
     
     /*
@@ -202,7 +251,6 @@ MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
         if (STYLE === "D") {frac.displaystyle = true; frac.scriptlevel = 0}
           else {frac.displaystyle = false; frac.scriptlevel = style - 1}
       }
-
       this.Push(frac);
     },
 
@@ -210,8 +258,8 @@ MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
      *  Implements multline environment (mostly handled through STACKITEM below)
      */
     Multline: function (begin,numbered) {
-      this.Push(begin);
+      this.Push(begin); this.checkEqnEnv();
-      return STACKITEM.multline().With({
+      return STACKITEM.multline(numbered,this.stack).With({
         arraydef: {
           displaystyle: true,
           rowspacing: ".5em",
@@ -226,7 +274,7 @@ MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
      *  Handle AMS aligned environments
      */
     AMSarray: function (begin,numbered,taggable,align,spacing) {
-      this.Push(begin);
+      this.Push(begin); if (taggable) {this.checkEqnEnv()}
       align = align.replace(/[^clr]/g,'').split('').join(' ');
       align = align.replace(/l/g,'left').replace(/r/g,'right').replace(/c/g,'center');
       return STACKITEM.AMSarray(begin.name,numbered,taggable,this.stack).With({
@@ -242,6 +290,9 @@ MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
       });
     },
     
+    /*
+     *  Handle alignat environments
+     */
     AlignAt: function (begin,numbered,taggable) {
       var n = this.GetArgument("\\begin{"+begin.name+"}");
       if (n.match(/[^0-9]/)) {TEX.Error("Argument to \\begin{"+begin.name+"} must me a positive integer")}
@@ -252,6 +303,27 @@ MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
       return this.Array(begin,null,null,align,spacing,".5em",'D');
     },
     
+    /*
+     *  Handle equation environment
+     */
+    EquationBegin: function (begin,force) {
+      this.checkEqnEnv();
+      this.stack.global.forcetag = (force && CONFIG.autoNumber !== "none");
+      return begin;
+    },
+    EquationStar: function (begin,row) {
+      this.stack.global.tagged = true; // prevent automatic tagging
+      return row;
+    },
+    
+    /*
+     *  Check for bad nesting of equation environments
+     */
+    checkEqnEnv: function () {
+      if (this.stack.global.eqnenv) {TEX.Error("Erroneous nesting of equation structures")}
+      this.stack.global.eqnenv = true;
+    },
+    
     /*
      *  Handle multiple integrals (make a mathop if followed by limits)
      */
@@ -268,6 +340,9 @@ MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
       this.i = 0;
     },
     
+    /*
+     *  Handle stretchable arrows
+     */
     xArrow: function (name,chr,l,r) {
       var def = {width: "+"+(l+r)+"mu", lspace: l+"mu"};
       var bot = this.GetBrackets(name),
@@ -295,11 +370,43 @@ MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
     }
   });
   
+  /******************************************************************************/
+  
+  STACKITEM.Augment({
+    /*
+     *  Increment equation number and form tag mtd element
+     */
+    autoTag: function () {
+      var global = this.global;
+      if (!global.notag) {
+        AMS.number++; global.tagID = CONFIG.formatNumber(AMS.number.toString());
+        var mml = TEX.Parse("\\text{"+CONFIG.formatTag(global.tagID)+"}",{}).mml();
+        global.tag = MML.mtd(mml.With({id:CONFIG.formatID(global.tagID)}));
+      }
+    },
+  
+    /*
+     *  Get the tag and record the label, if any
+     */
+    getTag: function () {
+      var global = this.global, tag = global.tag; global.tagged = true;
+      if (global.label) {AMS.eqlabels[global.label] = global.tagID}
+      delete global.tag; delete global.tagID; delete global.label;
+      return tag;
+    }
+  });
+  
   /*
    *  Implement multline environment via a STACKITEM
    */
   STACKITEM.multline = STACKITEM.array.Subclass({
     type: "multline",
+    Init: function (numbered,stack) {
+      this.SUPER(arguments).Init.apply(this);
+      this.numbered = (numbered && CONFIG.autoNumber !== "none");
+      this.save = {notag: stack.global.notag};
+      stack.global.tagged = !numbered && !stack.global.forcetag; // prevent automatic tagging in starred environments
+    },
     EndEntry: function () {
       var mtd = MML.mtd.apply(MML,this.data);
       if (this.data.shove) {mtd.columnalign = this.data.shove}
@@ -317,37 +424,46 @@ MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
         if (!this.table[0][0].columnalign) {this.table[0][0].columnalign = MML.ALIGN.LEFT}
         if (!this.table[m][0].columnalign) {this.table[m][0].columnalign = MML.ALIGN.RIGHT}
         var mtr = MML.mtr;
-        if (this.global.tag) {
+        if (!this.global.tag && this.numbered) {this.autoTag()}
-          this.table[0] = [this.global.tag].concat(this.table[0]);
+        if (this.global.tag && !this.global.notags) {
-          delete this.global.tag; mtr = MML.mlabeledtr;
+          this.table[0] = [this.getTag()].concat(this.table[0]);
+          mtr = MML.mlabeledtr;
         }
         this.table[0] = mtr.apply(MML,this.table[0]);
         for (i = 1, m = this.table.length; i < m; i++)
           {this.table[i] = MML.mtr.apply(MML,this.table[i])}
       }
+      this.global.notag  = this.save.notag;
     }
   });
   
+  /*
+   *  Save data about numbering and taging equations, and add
+   *  tags at the ends of rows.
+   */
   STACKITEM.AMSarray = STACKITEM.array.Subclass({
     type: "AMSarray",
     Init: function (name,numbered,taggable,stack) {
       this.SUPER(arguments).Init.apply(this);
-      this.numbered = numbered;
+      this.numbered = (numbered && CONFIG.autoNumber !== "none");
-      this.save_notag = stack.global.notag;
+      this.save = {notags: stack.global.notags, notag: stack.global.notag};
-      stack.global.notag = (taggable ? null : name);
+      stack.global.notags = (taggable ? null : name);
+      stack.global.tagged = !numbered && !stack.global.forcetag; // prevent automatic tagging in starred environments
     },
     EndRow: function () {
       var mtr = MML.mtr;
-      if (this.global.tag) {
+      if (!this.global.tag && this.numbered) {this.autoTag()}
-        this.row = [this.global.tag].concat(this.row);
+      if (this.global.tag &&! this.global.notags) {
+        this.row = [this.getTag()].concat(this.row);
         mtr = MML.mlabeledtr;
-        delete this.global.tag;
       }
+      if (this.numbered) {delete this.global.notag}
       this.table.push(mtr.apply(MML,this.row)); this.row = [];
     },
     EndTable: function () {
       this.SUPER(arguments).EndTable.call(this);
-      this.global.notag = this.save_notag;
+      this.global.notags = this.save.notags;
+      this.global.notag  = this.save.notag;
     }
   });
   
@@ -358,9 +474,11 @@ MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
     oldCheckItem: STACKITEM.start.prototype.checkItem,
     checkItem: function (item) {
       if (item.type === "stop") {
-        var mml = this.mmlData();
+        var mml = this.mmlData(), global = this.global;
-        if (this.global.tag) {
+        if (AMS.display && !global.tag && !global.tagged && !global.isInner &&
-          var row = [this.global.tag,MML.mtd(mml)]; delete this.global.tag;
+            (CONFIG.autoNumber === "all" || global.forcetag)) {this.autoTag()}
+        if (global.tag) {
+          var row = [this.getTag(),MML.mtd(mml)];
           var def = {
             side: TEX.config.TagSide,
             minlabelspacing: TEX.config.TagIndent,
@@ -383,10 +501,44 @@ MathJax.Hub.Register.StartupHook("TeX Jax Ready",function () {
         }
         return STACKITEM.mml(mml);
       }
-      return this.SUPER(arguments).checkItem.call(this,item);
+      return this.oldCheckItem.call(this,item);
     }
   });
   
+  /******************************************************************************/
+
+  /*
+   *  Add pre- and post-filters to handle the equation number maintainance.
+   */
+  TEX.prefilterHooks.Add(function (data) {
+    AMS.display = data.display;
+    AMS.number = AMS.startNumber;  // reset equation numbers (in case the equation restarted)
+    AMS.eqlabels = {}; AMS.badref = false;
+    if (AMS.refUpdate) {AMS.number = data.script.MathJax.startNumber}
+  });
+  TEX.postfilterHooks.Add(function (data) {
+    data.script.MathJax.startNumber = AMS.startNumber;
+    AMS.startNumber = AMS.number;                // equation numbers for next equation
+    MathJax.Hub.Insert(AMS.labels,AMS.eqlabels); // save labels from this equation
+    if (AMS.badref && !data.math.texError) {AMS.refs.push(data.script)}  // reprocess later
+  });
+  
+  MathJax.Hub.Register.MessageHook("Begin Math Input",function () {
+    AMS.refs = [];                 // array of jax with bad references
+    AMS.refUpdate = false;
+  });
+  MathJax.Hub.Register.MessageHook("End Math Input",function (message) {
+    if (AMS.refs.length) {
+      AMS.refUpdate = true;
+      for (var i = 0, m = AMS.refs.length; i < m; i++)
+        {AMS.refs[i].MathJax.state = MathJax.ElementJax.STATE.UPDATE}
+      return MathJax.Hub.processInput(AMS.refs);
+    }
+    return null;
+  });
+
+  /******************************************************************************/
+
   MathJax.Hub.Startup.signal.Post("TeX AMSmath Ready");
   
 });

unpacked/extensions/tex2jax.js

@@ -24,7 +24,7 @@
  */
 
 MathJax.Extension.tex2jax = {
-  version: "1.1.3",
+  version: "1.1.4",
   config: {
     inlineMath: [              // The start/stop pairs for in-line math
 //    ['$','$'],               //  (comment out any you don't want, or add your own, but
@@ -56,6 +56,8 @@ MathJax.Extension.tex2jax = {
     processEnvironments: true, // set to true to process \begin{xxx}...\end{xxx} outside
                                //   of math mode, false to prevent that
 
+    processRefs: true,         // set to true to process \ref{...} outside of math mode
+
     preview: "TeX"             // set to "none" to not insert MathJax_Preview spans
                                //   or set to an array specifying an HTML snippet
                                //   to use the same preview for every equation.
@@ -98,7 +100,8 @@ MathJax.Extension.tex2jax = {
     this.start = new RegExp(
       starts.sort(this.sortLength).join("|") + 
       (config.processEnvironments ? "|\\\\begin\\{([^}]*)\\}" : "") + 
-        (config.processEscapes ? "|\\\\*\\\\\\\$" : ""), "g"
+      (config.processEscapes ? "|\\\\*\\\\\\\$" : "") +
+      (config.processRefs ? "|\\\\(eq)?ref\\{[^}]*\\}" : ""), "g"
     );
     this.skipTags = new RegExp("^("+config.skipTags.join("|")+")$","i");
     this.ignoreClass = new RegExp("(^| )("+config.ignoreClass+")( |$)");
@@ -172,6 +175,12 @@ MathJax.Extension.tex2jax = {
         isBeginEnd: true
       };
       this.switchPattern(this.endPattern(this.search.end));
+    } else if (match[0].substr(0,4) === "\\ref" || match[0].substr(0,6) === "\\eqref") {
+      this.search = {
+        mode: "", end: "", open: element,
+        olen: 0, opos: this.pattern.lastIndex - match[0].length,
+      }
+      return this.endMatch([""],element);
     } else {                                         // escaped dollar signs
       // put $ in a span so it doesn't get processed again
       // split off backslashes so they don't get removed later

unpacked/jax/input/TeX/config.js

@@ -24,14 +24,23 @@
 
 MathJax.InputJax.TeX = MathJax.InputJax({
   id: "TeX",
-  version: "1.1.2",
+  version: "1.1.3",
   directory: MathJax.InputJax.directory + "/TeX",
   extensionDir: MathJax.InputJax.extensionDir + "/TeX",
   
   config: {
     TagSide:       "right",
     TagIndent:     "0.8em",
-    MultLineWidth: "85%"
+    MultLineWidth: "85%",
+    
+    equationNumbers: {
+      autoNumber: "none",  // "AMS" for standard AMS numbering,
+                           //  or "all" for all displayed equations
+      formatNumber: function (n) {return n},
+      formatTag:    function (n) {return '('+n+')'},
+      formatID:     function (n) {return 'mjx-eqn-'+n},
+      formatURL:    function (n) {return '#mjx-eqn-'+escape(n)}
+    }
   }
 });
 MathJax.InputJax.TeX.Register("math/tex");

unpacked/jax/input/TeX/jax.js

@@ -23,13 +23,13 @@
  *  limitations under the License.
  */
 
-(function (TEX) {
+(function (TEX,HUB,AJAX) {
   var TRUE = true, FALSE = false, MML, NBSP = String.fromCharCode(0xA0); 
   
   var STACK = MathJax.Object.Subclass({
-    Init: function (env) {
+    Init: function (env,inner) {
-      this.global = {};
+      this.global = {isInner: inner};
-      this.data = [STACKITEM.start().With({global: this.global})];
+      this.data = [STACKITEM.start(this.global)];
       if (env) {this.data[0].env = env}
       this.env = this.data[0].env;
     },
@@ -102,6 +102,10 @@
 
   STACKITEM.start = STACKITEM.Subclass({
     type: "start", isOpen: TRUE,
+    Init: function (global) {
+      this.SUPER(arguments).Init.call(this);
+      this.global = global;
+    },
     checkItem: function (item) {
       if (item.type === "stop") {return STACKITEM.mml(this.mmlData())}
       return this.SUPER(arguments).checkItem.call(this,item);
@@ -291,7 +295,7 @@
   var TEXDEF = {};
   var STARTUP = function () {
     MML = MathJax.ElementJax.mml;
-    MathJax.Hub.Insert(TEXDEF,{
+    HUB.Insert(TEXDEF,{
   
       // patterns for letters and numbers
       letter:  /[a-z]/i,
@@ -846,8 +850,10 @@
         
         tag:               ['Extension','AMSmath'],
         notag:             ['Extension','AMSmath'],
-        label:             ['Macro','',1],           // not implemented yet
+        label:             ['Extension','AMSmath'],
-        nonumber:          ['Macro',''],             // not implemented yet
+        ref:               ['Extension','AMSmath'],
+        eqref:             ['Extension','AMSmath'],
+        nonumber:          ['Macro','\\notag'],
 
         //  Extensions to TeX
         unicode:           ['Extension','unicode'],
@@ -917,9 +923,8 @@
     Init: function (string,env) {
       this.string = string; this.i = 0; this.macroCount = 0;
       var ENV; if (env) {ENV = {}; for (var id in env) {if (env.hasOwnProperty(id)) {ENV[id] = env[id]}}}
-      this.stack = TEX.Stack(ENV);
+      this.stack = TEX.Stack(ENV,!!env);
-      this.Parse();
+      this.Parse(); this.Push(STACKITEM.stop());
-      this.Push(STACKITEM.stop());
     },
     Parse: function () {
       var c;
@@ -1344,9 +1349,9 @@
       if (name && !typeof(name) === "string") {name = name.name}
       file = TEX.extensionDir+"/"+file;
       if (!file.match(/\.js$/)) {file += ".js"}
-      if (!MathJax.Ajax.loaded[MathJax.Ajax.fileURL(file)]) {
+      if (!AJAX.loaded[AJAX.fileURL(file)]) {
         if (name != null) {delete TEXDEF[array || 'macros'][name.replace(/^\\/,"")]}
-        MathJax.Hub.RestartAfter(MathJax.Ajax.Require(file));
+        HUB.RestartAfter(AJAX.Require(file));
       }
     },
     
@@ -1643,30 +1648,38 @@
     InternalMath: function (text,level) {
       var def = {displaystyle: FALSE}; if (level != null) {def.scriptlevel = level}
       if (this.stack.env.font) {def.mathvariant = this.stack.env.font}
-      if (!text.match(/\$|\\\(/)) {return [this.InternalText(text,def)]}
+      if (!text.match(/\$|\\\(|\\(eq)?ref\s*\{/)) {return [this.InternalText(text,def)]}
       var i = 0, k = 0, c, match = '';
       var mml = [];
       while (i < text.length) {
         c = text.charAt(i++);
         if (c === '$') {
           if (match === '$') {
-            mml.push(MML.TeXAtom(TEX.Parse(text.slice(k,i-1)).mml().With(def)));
+            mml.push(MML.TeXAtom(TEX.Parse(text.slice(k,i-1),{}).mml().With(def)));
             match = ''; k = i;
           } else if (match === '') {
             if (k < i-1) {mml.push(this.InternalText(text.slice(k,i-1),def))}
             match = '$'; k = i;
           }
+        } else if (c === '}' && match === '}') {
+          mml.push(MML.TeXAtom(TEX.Parse(text.slice(k,i),{}).mml().With(def)));
+          match = ''; k = i;
         } else if (c === '\\') {
+          if (match === '' && text.substr(i).match(/^(eq)?ref\s*\{/)) {
+            if (k < i-1) {mml.push(this.InternalText(text.slice(k,i-1),def))}
+            match = '}'; k = i-1;
+          } else {
             c = text.charAt(i++);
             if (c === '(' && match === '') {
               if (k < i-2) {mml.push(this.InternalText(text.slice(k,i-2),def))}
               match = ')'; k = i;
             } else if (c === ')' && match === ')') {
-            mml.push(MML.TeXAtom(TEX.Parse(text.slice(k,i-2)).mml().With(def)));
+              mml.push(MML.TeXAtom(TEX.Parse(text.slice(k,i-2),{}).mml().With(def)));
               match = ''; k = i;
             }
           }
         }
+      }
       if (match !== '') {TEX.Error("Math not terminated in text box")}
       if (k < text.length) {mml.push(this.InternalText(text.slice(k),def))}
       return mml;
@@ -1720,42 +1733,75 @@
       MAXBUFFER: 5*1024    // maximum size of TeX string to process
     },
     
+    prefilterHooks: MathJax.Callback.Hooks(true),    // hooks to run before processing TeX
+    postfilterHooks: MathJax.Callback.Hooks(true),   // hooks to run after processing TeX
+    
+    //
+    //  Check if AMSmath extension must be loaded and push
+    //    it on the extensions array, if needed
+    //
+    Config: function () {
+      this.SUPER(arguments).Config.apply(this,arguments);
+      if (this.config.equationNumbers.autoNumber !== "none") {
+        if (!this.config.extensions) {this.config.extensions = []}
+        this.config.extensions.push("AMSmath.js");
+      }
+    },
+
+    //
+    //  Convert TeX to ElementJax
+    //
     Translate: function (script) {
-      var mml, math = script.innerHTML.replace(/^\s+/,"").replace(/\s+$/,"");
+      var mml, isError = false, math = script.innerHTML.replace(/^\s+/,"").replace(/\s+$/,"");
-      if (MathJax.Hub.Browser.isKonqueror)
+      var display = (script.type.replace(/\n/g," ").match(/(;|\s|\n)mode\s*=\s*display(;|\s|\n|$)/) != null);
-        {math = math.replace(/&lt;/g,"<").replace(/&gt;/g,">").replace(/&amp;/g,"&")}
+      var data = {math:math, display:display, script:script};
-      var displaystyle = 
+      this.prefilterHooks.Execute(data); math = data.math;
-        (script.type.replace(/\n/g," ").match(/(;|\s|\n)mode\s*=\s*display(;|\s|\n|$)/) != null);
-      math = TEX.prefilterMath(math,displaystyle,script);
       try {
         mml = TEX.Parse(math).mml();
 //        mml = MML.semantics(mml,MML.annotation(math).With({encoding:"application:x-tex"}));
       } catch(err) {
         if (!err.texError) {throw err}
-        mml = this.formatError(err,math,displaystyle,script);
+        mml = this.formatError(err,math,display,script);
+        isError = true;
       }
       if (mml.inferred) {mml = MML.apply(MathJax.ElementJax,mml.data)} else {mml = MML(mml)}
-      if (displaystyle) {mml.root.display = "block"}
+      if (display) {mml.root.display = "block"}
-      return this.postfilterMath(mml,displaystyle,script);
+      if (isError) {mml.texError = true}
+      data.math = mml; this.postfilterHooks.Execute(data);
+      return data.math;
     },
-    prefilterMath: function (math,displaystyle,script) {
+    prefilterMath: function (data) {
+      // Konqueror incorrectly quotes these characters in script.innerHTML 
+      if (HUB.Browser.isKonqueror)
+        {data.math = data.math.replace(/&lt;/g,"<").replace(/&gt;/g,">").replace(/&amp;/g,"&")}
       // avoid parsing super- and subscript numbers as a unit
-      return math.replace(/([_^]\s*\d)([0-9.,])/g,"$1 $2");
+      data.math = data.math.replace(/([_^]\s*\d)([0-9.,])/g,"$1 $2");
     },
-    postfilterMath: function (math,displaystyle,script) {
+    postfilterMath: function (data) {
-      this.combineRelations(math.root);
+      this.combineRelations(data.math.root);
-      return math;
     },
-    formatError: function (err,math,displaystyle,script) {
+    formatError: function (err,math,display,script) {
       return MML.merror(err.message.replace(/\n.*/,""));
     },
+
+    //
+    //  Produce an error and stop processing this equation
+    //
     Error: function (message) {
-      throw MathJax.Hub.Insert(Error(message),{texError: TRUE});
+      throw HUB.Insert(Error(message),{texError: TRUE});
     },
+    
+    //
+    //  Add a user-defined macro to the macro list
+    //
     Macro: function (name,def,argn) {
       TEXDEF.macros[name] = ['Macro'].concat([].slice.call(arguments,1));
     },
     
+    //
+    //  Combine adjacent <mo> elements that are relations
+    //    (since MathML treats the spacing very differently)
+    //
     combineRelations: function (mml) {
       for (var i = 0, m = mml.data.length; i < m; i++) {
         if (mml.data[i]) {
@@ -1774,6 +1820,12 @@
     }
   });
 
+  //
+  //  Add the default filters
+  //
+  TEX.prefilterHooks.Add(["prefilterMath",TEX]);
+  TEX.postfilterHooks.Add(["postfilterMath",TEX]);
+
   TEX.loadComplete("jax.js");
   
-})(MathJax.InputJax.TeX);
+})(MathJax.InputJax.TeX,MathJax.Hub,MathJax.Ajax);

unpacked/jax/output/HTML-CSS/config.js

@@ -24,7 +24,7 @@
 
 MathJax.OutputJax["HTML-CSS"] = MathJax.OutputJax({
   id: "HTML-CSS",
-  version: "1.1.8",
+  version: "1.1.9",
   directory: MathJax.OutputJax.directory + "/HTML-CSS",
   extensionDir: MathJax.OutputJax.extensionDir + "/HTML-CSS",
   autoloadDir: MathJax.OutputJax.directory + "/HTML-CSS/autoload",
@@ -110,7 +110,7 @@ MathJax.Hub.Register.StartupHook("End Config",[function (HUB,HTMLCSS) {
     minBrowserTranslate: function (script) {
       var MJ = HUB.getJaxFor(script), text = ["[Math]"], delim;
       var span = document.createElement("span",{className: "MathJax_Preview"});
-      if (MJ.inputJax.id === "TeX") {
+      if (MJ.inputJax === "TeX") {
         if (MJ.root.Get("displaystyle")) {
           delim = CONFIG.displayMathDelimiters;
           text = [delim[0]+MJ.originalText+delim[1]];

unpacked/jax/output/HTML-CSS/jax.js

@@ -433,7 +433,7 @@
           var math = (this.parentNode.className === "MathJax_Display" ? this.parentNode : this)
           MENU.jax = HUB.getJaxFor(math.nextSibling);
           MENU.menu.items[1].menu.items[1].name = 
-            (MENU.jax.inputJax.id === "MathML" ? "Original" : MENU.jax.inputJax.id);
+            (MENU.jax.inputJax === "MathML" ? "Original" : MENU.jax.inputJax);
           return MENU.menu.Post(event);
         } else {
           if (!AJAX.loadingMathMenu) {

unpacked/jax/output/NativeMML/config.js

@@ -24,7 +24,7 @@
 
 MathJax.OutputJax.NativeMML = MathJax.OutputJax({
   id: "NativeMML",
-  version: "1.1.4",
+  version: "1.1.5",
   directory: MathJax.OutputJax.directory + "/NativeMML",
   extensionDir: MathJax.OutputJax.extensionDir + "/NativeMML",
   

unpacked/jax/output/NativeMML/jax.js

@@ -202,7 +202,7 @@
           var script = (isMSIE ? this.parentNode.parentNode.nextSibling : this.parentNode.nextSibling);
           MENU.jax = HUB.getJaxFor(script);
           MENU.menu.items[1].menu.items[1].name = 
-            (MENU.jax.inputJax.id === "MathML" ? "Original" : MENU.jax.inputJax.id);
+            (MENU.jax.inputJax === "MathML" ? "Original" : MENU.jax.inputJax);
           delete nMML.trapClick; delete nMML.trapUp;
           return MENU.menu.Post(event);
         } else {