JAL-1807 update

[jalviewjs.git] / site / swingjs / js / j2sjmol.js

// j2sjmol.js 

// latest author: Bob Hanson, St. Olaf College, hansonr@stolaf.edu
 
// Requires JSmolCore.js and (for now; probably) JSmol.js
// This version of j2slib requires jQuery and works in both Chrome and MSIE locally,
// though Chrome cannot read local data files, and MSIE cannot read local binary data files.

// Java programming notes by Bob Hanson:
//   
//   There are a few motifs to avoid when optimizing Java code to work smoothly
//   with the J2S compiler:
//   
//   arrays: 
//   
// 1. an array with null elements cannot be typed and must be avoided.
// 2. instances of Java "instance of" involving arrays must be found and convered to calls to Clazz.isA...
// 3. new int[n][] must not be used. Use instead JU.AU.newInt2(n);
// 4. new int[] { 1, 2, 3 } has problems because it creates simply [ ] and not IntArray32
//   
//   numbers:
//   
// 1. Remember that EVERY number in JavaScript is a double -- doesn't matter if it is in IntArray32 or not. 
// 2. You cannot reliably use Java long, because doubles consume bits for the exponent which cannot be tested.
// 3. Bit 31 of an integer is unreliable, since (int) -1 is now  , not just 0zFFFFFFFF, and 
//    FFFFFFFF + 1 = 100000000, not 0. In JavaScript, 0xFFFFFFFF is 4294967295, not -1.
//    This means that writeInt(b) will fail if b is negative. What you need is instead
//    writeInt((int)(b & 0xFFFFFFFFl) so that JavaScript knocks off the high bits explicitly. 
//
//   general:
//
// 1. j2sRequireImport xxxx is needed if xxxx is a method used in a static function
// 2. URL.getContent() is not supported. Use other means based on URL.toString()
// 3. It is critical for performance to avoid any significant amount of function overloading.
//    In particular, methods such as xxx(int a, int b) and xxx(float a, int b) MUST be renamed,
//    because JavaScript only has Number, and there is absolutely no way to tell these apart.
//    It's probably bad Java programming, anyway.
// 4. Calls to super(...) can almost always be avoided. These trigger the SAEM
//    (searchAndExecuteMethod) call, and it is very destructive to performance.
//    Just find another way to do it.   

 // NOTES by Bob Hanson: 
 
 // J2S class changes:

 // BH 7/18/2015 4:43:38 PM better handling of TypeError and InternalError for e.getMessage() and e.getStackTrace()
 // BH 7/17/2015 11:51:15 AM adds class.getResource(name) and class.getResourceAsStream(name) 
 // BH 7/16/2015 7:56:49 PM general instantiation using any constructor (in Java here):
 // BH  x = class.forName("my.class.name").newInstance()
 // BH or
 // BH  x = class.forName("my.class.name").getConstructor(String.class,String.class).newInstance(new Object[] {"test", "now"})
 // BH 7/15/2015 11:34:58 PM adding System.lineSeparator()
 // BH 7/15/2015 7:32:41 AM adding class.getCanonicalName == getName
 // BH 5/31/2015 5:38:14 PM  NPEExceptionPredicate fix
 // BH 4/25/2015 9:16:12 AM SAEM misrepresnting Number as Object in parameters and Integer as Number 
 // BH 4/24/2015 7:32:54 AM Object.hashCode() and System.getIdentityHashCode() fail. changed to:     return this._$hashcode || (this._$hashcode = ++Clazz._hashCode)
 // BH 4/23/2015 9:08:59 AM Clazz.instanceOf(a, b) needs to check for a == b.   
 // BH 4/23/2015 9:08:59 AM xx.getContentType() is nonfunctional. Array.newInstance now defines a wrapper for .getClass().getComponentType() that works  
 // BH 4/12/2015 11:48:03 AM added Clazz.getStackTrace(-n) -- reports actual parameter values for n levels
 // BH 4/10/2015 8:23:05 AM adding Int32Array.prototype.clone and Float64.prototype.clone
 // BH 4/5/2015 8:12:57 AM refactoring j2slib (this file) to make private functions really private using var
 // BH 4/3/2015 6:14:34 AM adding anonymous local "ClazzLoader" (Clazz._Loader) --> "_Loader"
 // BH 4/3/2015 6:14:34 AM adding Clazz._Loader._classPending, Clazz._Loader._classCount
 // BH 4/3/2015 6:14:34 AM adding Clazz._Loader._checkLoad 
 //  -- forces asynchronous class loading
 //  -- builds Clazz._Loader._classPending and Clazz._classCount
 //  -- allows reporting 
 
 // BH 3/24/2015 4:11:26 AM better file load failure message in _Loader.evaluate 
 // BH 2/28/2015 7:30:25 AM corrects newIntArray32() and newArray() for pre-defined arrays 
 //             int[] a =  new int[] {1,2,3,343};
 //             int[][] b = new int[][] {new int[]{4,5},new int[]{5,6}}; 

 // BH 9/29/2014 11:34:19 PM removing support for getClass().isArray() 
 // BH 8/29/2014 9:15:57 AM total reworking of Java2Script in preparation for all-asynchronous loading
 //                         (currently sync loading is only for 
 //                                                                                                LOAD command and load() function without ASYNC
 //                            getInterface() 
 //                         see JSmol.js and Jmol._isAsync flag
 // BH 5/11/2015 5:58:42 AM adding __signatures for debugging SAEM issues 
 // BH 3/29/2015 8:12:44 PM System.getProperty(x, "") does not return ""
 // BH 8/23/2014 10:04:19 AM cleaning up a few general methods; Clazz.removeArrayItem
 // BH 6/1/2014 10:58:46 AM fix for Clazz.isAP() not working
 // BH 5/26/2014 5:19:29 PM removing superConstructor call in creating Enum constants
 // BH 4/1/2014 7:55:54 PM removing all $fz references and instances where sub/super classes have same private function names
 // BH 4/1/2014 4:47:30 PM all $_X removed; this is taken care of by Google Closure Compiler
 // BH 4/1/2014 6:40:08 AM removing ClassLoader -- equals Clazz._Loader
 // BH 4/1/2014 6:40:08 AM removing ClassLoaderProgressMonitor -- equals _LoaderProgressMonitor
 // BH 4/1/2014 6:17:21 AM removing Class  -- only used for "Class.forName" in Jmol, which ANT will now change to "Clazz._4Name"
 // BH 3/7/2014 9:05:06 AM Array.prototype.toString should not be aliased. -- http://sourceforge.net/p/jmol/bugs/560/ with Google Visualization

 // BH 1/30/2014 12:54:22 PM gave all field variables prefix underscore. This allows Google Closure Compiler to skip them.  
 // BH 12/3/2013 3:39:57 PM window["j2s.lib"].base implemented
 // BH 12/1/2013 5:34:21 AM removed _LoaderProgressMonitor.initialize and all Clazz.event business; handled by Jmol.clearVars()
 // BH 11/30/2013 12:43:58 PM adding Clazz.arrayIs() -- avoids Number.constructor.toString() infinite recursion
 // BH 11/29/2013 6:33:51 AM adding Clazz._profiler -- reports use of SAEM
 // BH 11/10/2013 9:02:20 AM fixing fading in MSIE  
 // BH 11/3/2013 7:21:39 AM additional wrapping functions for better compressibility
 // BH 10/30/2013 8:10:58 AM added getClass().getResource() -- returning a relative string, not a URL
 // BH 10/30/2013 6:43:00 AM removed second System def and added System.$props and default System.property "line.separator" 
 // BH 6/15/2013 8:02:07 AM corrections to Class.isAS to return true if first element is null
 // BH 6/14/2013 4:41:09 PM corrections to Clazz.isAI and related methods to include check for null object
 // BH 3/17/2013 11:54:28 AM adds stackTrace for ERROR 

 // BH 3/13/2013 6:58:26 PM adds Clazz.clone(me) for BS clone 
 // BH 3/12/2013 6:30:53 AM fixes Clazz.exceptionOf for ERROR condition trapping
 // BH 3/2/2013 9:09:53 AM delete globals c$ and $fz
 // BH 3/2/2013 9:10:45 AM optimizing defineMethod using "look no further" "@" parameter designation (see "\\@" below -- removed 3/23/13)
 // BH 2/27/2013 optimizing Clazz.getParamsType for common cases () and (Number)
 // BH 2/27/2013 optimizing SAEM delegation for hashCode and equals -- disallows overloading of equals(Object)
 
 // BH 2/23/2013 found String.replaceAll does not work -- solution was to never call it.
 // BH 2/9/2013 9:18:03 PM Int32Array/Float64Array fixed for MSIE9
 // BH 1/25/2013 1:55:31 AM moved package.js from j2s/java to j2s/core 
 // BH 1/17/2013 4:37:17 PM String.compareTo() added
 // BH 1/17/2013 4:52:22 PM Int32Array and Float64Array may not have .prototype.sort method
 // BH 1/16/2013 6:20:34 PM Float64Array not available in Safari 5.1
 // BH 1/14/2013 11:28:58 PM  Going to all doubles in JavaScript (Float64Array, not Float32Array)
 //   so that (new float[] {13.48f})[0] == 13.48f, effectively

 // BH 1/14/2013 12:53:41 AM  Fix for Opera 10 not loading any files
 // BH 1/13/2013 11:50:11 PM  Fix for MSIE not loading (nonbinary) files locally
 
 // BH 12/1/2012 9:52:26 AM Compiler note: Thread.start() cannot be executed within the constructor;
 
 // BH 11/24/2012 11:08:39 AM removed unneeded sections
 // BH 11/24/2012 10:23:22 AM  all XHR uses sync loading (_Loader.setLoadingMode)
 // BH 11/21/2012 7:30:06 PM    if (base)       map["@" + pkg] = base;  critical for multiple applets

 // BH 10/8/2012 3:27:41 PM         if (clazzName.indexOf("Array") >= 0) return "Array"; in Clazz.getClassName for function
 // BH removed Clazz.ie$plit = "\\2".split (/\\/).length == 1; unnecessary; using RegEx slows process significantly in all browsers
 // BH 10/6/12 added Int32Array, Float32Array, newArrayBH, upgraded java.lang and java.io
 // BH added Integer.bitCount in core.z.js
 // BH changed alert to Clazz.alert in java.lang.Class.js *.ClassLoader.js, java.lang.thread.js
 // BH removed toString from innerFunctionNames due to infinite recursion
 // BH note: Logger.error(null, e) does not work -- get no constructor for (String) (TypeError)
 // BH added j2s.lib.console
 // BH allowed for alias="."
 // BH removed alert def --> Clazz.alert
 // BH added wrapper at line 2856 
 // BH newArray fix at line 2205
 // BH System.getProperty fix at line 6693
 // BH added Enum .value() method at line 2183
 // BH added System.getSecurityManager() at end
 // BH added String.contains() at end
 // BH added System.gc() at end
 // BH added Clazz.exceptionOf = updated
 // BH added String.getBytes() at end
 

LoadClazz = function() {

// BH This is the ONLY global used in J2S now. I do not think it is necessary,
// but it is created by the compiler, and I have not found a work-around.
// it is used as a local variable in class definitions to point to the 
// current method. See Clazz.p0p and Clazz.pu$h

c$ = null;

if (!window["j2s.clazzloaded"])
        window["j2s.clazzloaded"] = false;

if (window["j2s.clazzloaded"])return;

window["j2s.clazzloaded"] = true;

window["j2s.object.native"] = true;

 // Clazz changes:

 /* http://j2s.sf.net/ *//******************************************************************************
 * Copyright (c) 2007 java2script.org and others.
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 *     Zhou Renjian - initial API and implementation
 *****************************************************************************/
/*******
 * @author zhou renjian
 * @create Nov 5, 2005
 *******/
 

/**
 * Class Clazz. All the methods are static in this class.
 */
/* static */
/*Class = */ Clazz = {
  _isQuiet: false
};

;(function(Clazz, Jmol) {

var __debuggingBH = false;
var _globals = ["j2s.clazzloaded", "j2s.object.native"];
Clazz.setGlobal = function(a, v) {
        _globals.push(a);
        window[a] = v;
}

Clazz.getGlobals = function() {
        return _globals.sort().join("\n");
}

Clazz.setConsoleDiv = function(d) {
        window["j2s.lib"] && (window["j2s.lib"].console = d);
};

// BH Clazz.getProfile monitors exactly what is being delegated with SAEM,
// which could be a bottle-neck for function calling.
// This is critical for performance optimization.

// Jmol.getProfile()

var _profile = (window["j2s.doProfile"]  && self.JSON ? {} : null);

NullObject = function () {};

/* protected */
Clazz._supportsNativeObject = window["j2s.object.native"];

if (Clazz._supportsNativeObject) {
        Clazz._O = function () {};
        Clazz._O.__CLASS_NAME__ = "Object";
        Clazz._O["getClass"] = function () { return Clazz._O; }; 
} else {
        Clazz._O = Object;
}

Clazz.Console = {};
Clazz.dateToString = Date.prototype.toString;
Clazz._hashCode = 0;

var addProto = function(proto, name, func) {
        return proto[name] = func;
};

;(function(proto) {
        addProto(proto, "equals", function (obj) {
                return this == obj;
        });

        addProto(proto, "hashCode", function () {
  
    return this._$hashcode || (this._$hashcode = ++Clazz._hashCode)

  
                try {
                        return this.toString ().hashCode ();
                } catch (e) {
                        var str = ":";
                        for (var s in this) {
                                str += s + ":"
                        }
                        return str.hashCode ();
                }
        });

        addProto(proto, "getClass", function () { return Clazz.getClass (this); });

        addProto(proto, "clone", function () { return Clazz.clone(this); });

        Clazz.clone = function(me) {
                // BH allows @j2sNative access without super constructor
                var o = new me.constructor();
                for (var i in me) {
                        o[i] = me[i];
      }
                return o;
        }
/*
 * Methods for thread in Object
 */
        addProto(proto, "finalize", function () {});
        addProto(proto, "notify", function () {});
        addProto(proto, "notifyAll", function () {});
        addProto(proto, "wait", function () {});
        addProto(proto, "to$tring", Object.prototype.toString);
        addProto(proto, "toString", function () { return (this.__CLASS_NAME__ ? "[" + this.__CLASS_NAME__ + " object]" : this.to$tring.apply(this, arguments)); });
        Clazz._extendedObjectMethods = [ "equals", "hashCode", "getClass", "clone", "finalize", "notify", "notifyAll", "wait", "to$tring", "toString" ];

})(Clazz._O.prototype);

Clazz.extendJO = function(c, name) {  
        if (name)
                c.__CLASS_NAME__ = c.prototype.__CLASS_NAME__ = name;
        if (Clazz._supportsNativeObject) {
                for (var i = 0; i < Clazz._extendedObjectMethods.length; i++) {
                        var p = Clazz._extendedObjectMethods[i];
                        addProto(c.prototype, p, Clazz._O.prototype[p]);
                }
        }
};

/**
 * Try to fix bug on Safari
 */
//InternalFunction = Object;

Clazz.extractClassName = function(clazzStr) {
        // [object Int32Array]
        var clazzName = clazzStr.substring (1, clazzStr.length - 1);
        return (clazzName.indexOf("Array") >= 0 ? "Array" // BH -- for Float64Array and Int32Array
                : clazzName.indexOf ("object ") >= 0 ? clazzName.substring (7) // IE
                : clazzName);
}
/**
 * Return the class name of the given class or object.
 *
 * @param clazzHost given class or object
 * @return class name
 */
/* public */
Clazz.getClassName = function (obj) {
        if (obj == null)
                return "NullObject";
        if (obj instanceof Clazz.CastedNull)
                return obj.clazzName;
        switch(typeof obj) {
        case "number":
                return "n";
        case "boolean":
                return "b";
        case "string":
                // Always treat the constant string as String object.
                // This will be compatiable with Java String instance.
                return "String";
        case "function":
                if (obj.__CLASS_NAME__)
                        return (arguments[1] ? obj.__CLASS_NAME__ : "Class"); /* user defined class name */
                var s = obj.toString();
                var idx0 = s.indexOf("function");
                if (idx0 < 0)
                        return (s.charAt(0) == '[' ? Clazz.extractClassName(s) : s.replace(/[^a-zA-Z0-9]/g, ''));
                var idx1 = idx0 + 8;
                var idx2 = s.indexOf ("(", idx1);
                if (idx2 < 0)
                        return "Object";
                s = s.substring (idx1, idx2);
                if (s.indexOf("Array") >= 0)
                        return "Array"; 
                s = s.replace (/^\s+/, "").replace (/\s+$/, "");
                return (s == "anonymous" || s == "" ? "Function" : s);
        case "object":
                if (obj.__CLASS_NAME__) // user defined class name
                        return obj.__CLASS_NAME__;
                if (!obj.constructor)
                        return "Object"; // For HTML Element in IE
                if (!obj.constructor.__CLASS_NAME__) {
                        if (obj instanceof Number)
                                return "Number";
                        if (obj instanceof Boolean)
                                return "Boolean";
                        if (obj instanceof Array)
                                return "Array";
                        var s = obj.toString();
      // "[object Int32Array]"
                        if (s.charAt(0) == '[')
                                return Clazz.extractClassName(s);
                }
        return Clazz.getClassName (obj.constructor, true);
        }
  // some new, unidentified class
  return "Object";
};
/**
 * Return the class of the given class or object.
 *
 * @param clazzHost given class or object
 * @return class name
 */
/* public */
Clazz.getClass = function (clazzHost) {
        if (!clazzHost)
                return Clazz._O;        // null/undefined is always treated as Object
        if (typeof clazzHost == "function")
                return clazzHost;
        var clazzName;
        if (clazzHost instanceof Clazz.CastedNull) {
                clazzName = clazzHost.clazzName;
        } else {
                switch (typeof clazzHost) {
                case "string":
                        return String;
          case "object":
                        if (!clazzHost.__CLASS_NAME__)
                                return (clazzHost.constructor || Clazz._O);
                        clazzName = clazzHost.__CLASS_NAME__;
                break;
                default:
                        return clazzHost.constructor;
                }
        }
        return Clazz.evalType(clazzName, true);
};


/* private */
var checkInnerFunction = function (hostSuper, funName) {
        for (var k = 0; k < Clazz.innerFunctionNames.length; k++)
                if (funName == Clazz.innerFunctionNames[k] && 
                                Clazz._innerFunctions[funName] === hostSuper[funName])
                        return true;
        return false;
};

var args4InheritClass = function () {};

Clazz.inheritArgs = new args4InheritClass ();

/**
 * Inherit class with "extends" keyword and also copy those static members. 
 * Example, as in Java, if NAME is a static member of ClassA, and ClassB 
 * extends ClassA then ClassB.NAME can be accessed in some ways.
 *
 * @param clazzThis child class to be extended
 * @param clazzSuper super class which is inherited from
 * @param objSuper super class instance
 */
/* protected */
Clazz.inheritClass = function (clazzThis, clazzSuper, objSuper) {
        //var thisClassName = Clazz.getClassName (clazzThis);
        for (var o in clazzSuper) {
                if (o != "b$" && o != "prototype" && o != "superClazz"
                                && o != "__CLASS_NAME__" && o != "implementz"
                                && !checkInnerFunction (clazzSuper, o)) {
                        clazzThis[o] = clazzSuper[o];
                }
        }
        if (Clazz.unloadedClasses[Clazz.getClassName(clazzThis, true)]) {
                // Don't change clazzThis.protoype! Keep it!
        } else if (objSuper) {
                // ! Unsafe reference prototype to an instance!
                // Feb 19, 2006 --josson
                // OK for this reference to an instance, as this is anonymous instance,
                // which is not referenced elsewhere.
                // March 13, 2006
                clazzThis.prototype = objSuper; 
        } else if (clazzSuper !== Number) {
                clazzThis.prototype = new clazzSuper (Clazz.inheritArgs);
        } else { // Number
                clazzThis.prototype = new Number ();
        }
        clazzThis.superClazz = clazzSuper;
        /*
         * Is it necessary to reassign the class name?
         * Mar 10, 2006 --josson
         */
        //clazzThis.__CLASS_NAME__ = thisClassName;
        clazzThis.prototype.__CLASS_NAME__ = clazzThis.__CLASS_NAME__;
};

/**
 * Implementation of Java's keyword "implements".
 * As in JavaScript there are on "implements" keyword implemented, a property
 * of "implementz" is added to the class to record the interfaces the class
 * is implemented.
 * 
 * @param clazzThis the class to implement
 * @param interfacez Array of interfaces
 */
/* public */
Clazz.implementOf = function (clazzThis, interfacez) {
        if (arguments.length >= 2) {
                if (!clazzThis.implementz)
                        clazzThis.implementz = [];
                var impls = clazzThis.implementz;
                if (arguments.length == 2) {
                        if (typeof interfacez == "function") {
                                impls.push(interfacez);
                                copyProperties(clazzThis, interfacez);
                        } else if (interfacez instanceof Array) {
                                for (var i = 0; i < interfacez.length; i++) {
                                        impls.push(interfacez[i]);
                                        copyProperties(clazzThis, interfacez[i]);
                                }
                        }
                } else {
                        for (var i = 1; i < arguments.length; i++) {
                                impls.push(arguments[i]);
                                copyProperties(clazzThis, arguments[i]);
                        }
                }
        }
};

/*
 * Copy members of interface
 */
/* private */
var copyProperties = function(clazzThis, clazzSuper) {
        for (var o in clazzSuper)
                if (o != "b$" 
                                && o != "prototype" && o != "superClazz"
                                && o != "__CLASS_NAME__" && o != "implementz"
                                && (typeof clazzSuper[o] != "function" || !checkInnerFunction(clazzSuper, o)))
                        clazzThis[o] = clazzThis.prototype[o] = clazzSuper[o];
};

/**
 * TODO: More should be done for interface's inheritance
 */
/* public */
Clazz.extendInterface = Clazz.implementOf;

/* protected */
Clazz.equalsOrExtendsLevel = function (clazzThis, clazzAncestor) {
        if (clazzThis === clazzAncestor)
                return 0;
        if (clazzThis.implementz) {
                var impls = clazzThis.implementz;
                for (var i = 0; i < impls.length; i++) {
                        var level = Clazz.equalsOrExtendsLevel (impls[i], clazzAncestor);
                        if (level >= 0)
                                return level + 1;
                }
        }
        return -1;
};

/* protected */
Clazz.getInheritedLevel = function (clazzTarget, clazzBase) {
        if (clazzTarget === clazzBase)
                return 0;
        var isTgtStr = (typeof clazzTarget == "string");
        if (isTgtStr && ("void" == clazzTarget || "unknown" == clazzTarget))
                return -1;
        var isBaseStr = (typeof clazzBase == "string");
        if (isBaseStr && ("void" == clazzBase || "unknown" == clazzBase))
                return -1;
        if (clazzTarget === (isTgtStr ? "NullObject" : NullObject)) {
                switch (clazzBase) {
                case Number:
                case Boolean:
                case NullObject:
                        break;
                default:
                        return 0;
                }
        }
        if (isTgtStr)
                clazzTarget = Clazz.evalType(clazzTarget);
        if (isBaseStr)
                clazzBase = Clazz.evalType(clazzBase);
        if (!clazzBase || !clazzTarget)
                return -1;
        var level = 0;
        var zzalc = clazzTarget; // zzalc <--> clazz
        while (zzalc !== clazzBase && level < 10) {
                /* maybe clazzBase is interface */
                if (zzalc.implementz) {
                        var impls = zzalc.implementz;
                        for (var i = 0; i < impls.length; i++) {
                                var implsLevel = Clazz.equalsOrExtendsLevel (impls[i], clazzBase);
                                if (implsLevel >= 0)
                                        return level + implsLevel + 1;
                        }
                }
                zzalc = zzalc.superClazz;
                if (!zzalc)
                        return (clazzBase === Object || clazzBase === Clazz._O ? 
                                // getInheritedLevel(String, CharSequence) == 1
                                // getInheritedLevel(String, Object) == 1.5
                                // So if both #test(CharSequence) and #test(Object) existed,
                                // #test("hello") will correctly call #test(CharSequence)
                                // instead of #test(Object).
                                level + 1.5 // 1.5! Special!
                        : -1);
                level++;
        }
        return level;
};


/**
 * Implements Java's keyword "instanceof" in JavaScript's way.
 * As in JavaScript part of the object inheritance is implemented in only-
 * JavaScript way.
 *
 * @param obj the object to be tested
 * @param clazz the class to be checked
 * @return whether the object is an instance of the class
 */
/* public */
Clazz.instanceOf = function (obj, clazz) {
  // allows obj to be a class already, from arrayX.getClass().isInstance(y)
        return (obj != null && clazz && (obj == clazz || obj instanceof clazz || Clazz.getInheritedLevel(Clazz.getClassName(obj), clazz) >= 0));
};

/**
 * Call super method of the class. 
 * The same effect as Java's expression:
 * <code> super.* () </code>
 * 
 * @param objThis host object
 * @param clazzThis class of declaring method scope. It's hard to determine 
 * which super class is right class for "super.*()" call when it's in runtime
 * environment. For example,
 * 1. ClasssA has method #run()
 * 2. ClassB extends ClassA overriding method #run() with "super.run()" call
 * 3. ClassC extends ClassB
 * 4. objC is an instance of ClassC
 * Now we have to decide which super #run() method is to be invoked. Without
 * explicit clazzThis parameter, we only know that objC.getClass() is ClassC 
 * and current method scope is #run(). We do not known we are in scope 
 * ClassA#run() or scope of ClassB#run(). if ClassB is given, Clazz can search
 * all super methods that are before ClassB and get the correct super method.
 * This is the reason why there must be an extra clazzThis parameter.
 * @param funName method name to be called
 * @param funParams Array of method parameters
 */
/* public */
Clazz.superCall = function (objThis, clazzThis, funName, funParams) {
        var fx = null;
        var i = -1;
        var clazzFun = objThis[funName];
        if (clazzFun) {
                if (clazzFun.claxxOwner) { 
                        // claxxOwner is a mark for methods that is single.
                        if (clazzFun.claxxOwner !== clazzThis) {
                                // This is a single method, call directly!
                                fx = clazzFun;
        
                        }
                } else if (!clazzFun.stacks && !(clazzFun.lastClaxxRef
                                        && clazzFun.lastClaxxRef.prototype[funName]
                                        && clazzFun.lastClaxxRef.prototype[funName].stacks)) { // super.toString
                        fx = clazzFun;
                } else { // normal wrapped method
                        var stacks = clazzFun.stacks;
                        if (!stacks)
                                stacks = clazzFun.lastClaxxRef.prototype[funName].stacks;
                        for (i = stacks.length; --i >= 0;) {
                                /*
                                 * Once super call is computed precisely, there are no need 
                                 * to calculate the inherited level but just an equals
                                 * comparision
                                 */
                                //var level = Clazz.getInheritedLevel (clazzThis, stacks[i]);
                                if (clazzThis === stacks[i]) { // level == 0
                                        if (i > 0) {
                                                fx = stacks[--i].prototype[funName];
                                        } else {
                                                /*
                                                 * Will this case be reachable?
                                                 * March 4, 2006
                                                 * Should never reach here if all things are converted
                                                 * by Java2Script
                                                 */
                                                fx = stacks[0].prototype[funName]["\\unknown"];
                                        }
                                        break;
                                } else if (Clazz.getInheritedLevel (clazzThis, stacks[i]) > 0) {
                                        fx = stacks[i].prototype[funName];
                                        break;
                                }
                        } // end of for loop
                } // end of normal wrapped method
        } // end of clazzFun
        if (!fx) {
                if (funName != "construct") {
                        Clazz.alert (["j2slib","no class found",(funParams).typeString])
                        throw new MethodNotFoundException(objThis, clazzThis, funName, 
                                        Clazz.getParamsType(funParams).typeString);     
                }
                /* there are members which are initialized out of the constructor */
                /* No super constructor! */
                return;
        }
        /* there are members which are initialized out of the constructor */
        if (i == 0 && funName == "construct") {
                var ss = clazzFun.stacks;
                if (ss && !ss[0].superClazz && ss[0].con$truct)
                        ss[0].con$truct.apply (objThis, []);
        }
        /*# {$no.debug.support} >>x #*/
        /* not used in Jmol
        if (Clazz.tracingCalling) {
                var caller = arguments.callee.caller;
                if (caller === Clazz.superConstructor) {
                        caller = caller.arguments.callee.caller;
                }
                Clazz._callingStackTraces.push(new Clazz.callingStack (caller, clazzThis));
                var ret = fx.apply (objThis, (funParams == null) ? [] : funParams);
                Clazz._callingStackTraces.pop();
                return ret;
        }
        */
        /*# x<< #*/
        return fx.apply (objThis, funParams || []);
};

/**
 * Call super constructor of the class. 
 * The same effect as Java's expression: 
 * <code> super () </code>
 */
/* public */
Clazz.superConstructor = function (objThis, clazzThis, funParams) {
        Clazz.superCall (objThis, clazzThis, "construct", funParams);
        /* If there are members which are initialized out of the constructor */
        if (clazzThis.con$truct) {
                clazzThis.con$truct.apply (objThis, []);
        }
};

/**
 * Class for null with a given class as to be casted.
 * This class will be used as an implementation of Java's casting way.
 * For example,
 * <code> this.call ((String) null); </code>
 */
/* public */
Clazz.CastedNull = function (asClazz) {
        if (asClazz) {
                if (asClazz instanceof String) {
                        this.clazzName = asClazz;
                } else if (asClazz instanceof Function) {
                        this.clazzName = Clazz.getClassName (asClazz, true);
                } else {
                        this.clazzName = "" + asClazz;
                }
        } else {
                this.clazzName = "Object";
        }
        this.toString = function () {
                return null;
        };
        this.valueOf = function () {
                return null;
        };
};

/**
 * API for Java's casting null.
 * @see Clazz.CastedNull
 *
 * @param asClazz given class
 * @return an instance of class Clazz.CastedNull
 */
/* public */
Clazz.castNullAs = function (asClazz) {
        return new Clazz.CastedNull (asClazz);
};

/////////////////////////// Exception handling ////////////////////////////

/*
 * Use to mark that the Throwable instance is created or not.
 * 
 * Called from java.lang.Throwable, as defined in JSmolJavaExt.js
 * 
 * The underscore is important - it tells the JSmol ANT task to NOT 
 * turn this into Clazz_initializingException, because coreBottom2.js does 
 * not include that call, and so Google Closure Compiler does not minify it.
 *        
 */
/* public */
Clazz._initializingException = false;

/**
 * BH: used in Throwable
 *  
 */  
/* public */
Clazz._callingStackTraces = [];

/** 
 * MethodException will be used as a signal to notify that the method is
 * not found in the current clazz hierarchy.
 */
/* private */
var MethodException = function () {
        this.toString = function () {
                return "J2S MethodException";
        };
};
/* private */
var MethodNotFoundException = function () {
        this.toString = function () {
                return "J2S MethodNotFoundException";
        };
};

  var _isNPEExceptionPredicate;

/* super private */
;(function() { 
  /* sgurin: native exception detection mechanism. Only NullPointerException detected and wrapped to java excepions */
  /** private utility method for creating a general regexp that can be used later  
   * for detecting a certain kind of native exceptions. use with error messages like "blabla IDENTIFIER blabla"
   * @param msg String - the error message
   * @param spliterName String, must be contained once in msg
   * spliterRegex String, a string with the regexp literal for identifying the spitter in exception further error messages.
   */
  // reproduce NullPointerException for knowing how to detect them, and create detector function Clazz._isNPEExceptionPredicate
  var $$o$$ = null;
  
  try {
        $$o$$.hello();
  } catch (e) {
    var _ex_reg = function(msg, spliterName, spliterRegex) {
        if(!spliterRegex) 
                spliterRegex="[^\\s]+"; 
        var idx = msg.indexOf (spliterName), 
                str = msg.substring (0, idx) + spliterRegex + msg.substring(idx + spliterName.length), 
                regexp = new RegExp("^"+str+"$");
        return regexp;
    };
        if(/Opera[\/\s](\d+\.\d+)/.test(navigator.userAgent)) {// opera throws an exception with fixed messages like "Statement on line 23: Cannot convert undefined or null to Object Backtrace: Line....long text... " 
                var idx1 = e.message.indexOf(":"), idx2 = e.message.indexOf(":", idx1+2);
                var _NPEMsgFragment = e.message.substr(idx1+1, idx2-idx1-20);
                _isNPEExceptionPredicate = function(e) { return e.message.indexOf(_NPEMsgFragment)!=-1; };
        }       else if(navigator.userAgent.toLowerCase().indexOf("webkit")!=-1) { //webkit, google chrome prints the property name accessed. 
                var _exceptionNPERegExp = _ex_reg(e.message, "hello");
                _isNPEExceptionPredicate = function(e) { return _exceptionNPERegExp.test(e.message); };
        }       else {// ie, firefox and others print the name of the object accessed: 
                var _exceptionNPERegExp = _ex_reg(e.message, "$$o$$");
                _isNPEExceptionPredicate = function(e) { return _exceptionNPERegExp.test(e.message); };
        }               
  };
})();

/**sgurin
 * Implements Java's keyword "instanceof" in JavaScript's way **for exception objects**.
 * 
 * calls Clazz.instanceOf if e is a Java exception. If not, try to detect known native 
 * exceptions, like native NullPointerExceptions and wrap it into a Java exception and 
 * call Clazz.instanceOf again. if the native exception can't be wrapped, false is returned.
 * 
 * @param obj the object to be tested
 * @param clazz the class to be checked
 * @return whether the object is an instance of the class
 * @author: sgurin
 */
Clazz.exceptionOf = function(e, clazz) {
        if(e.__CLASS_NAME__)
                return Clazz.instanceOf(e, clazz);
  if (!e.getMessage) {
    e.getMessage = function() {return "" + this};
  }
  if (!e.printStackTrace) {
    e.printStackTrace = function(){};
    alert(e + " try/catch path:" + Clazz.getStackTrace(-5));
  }
        if(clazz == Error) {
                if (("" + e).indexOf("Error") < 0)
      return false;
                System.out.println (Clazz.getStackTrace());
    return true;
                // everything here is a Java Exception, not a Java Error
        }
        return (clazz == Exception || clazz == Throwable
                || clazz == NullPointerException && _isNPEExceptionPredicate(e));
};

/**
 * BH need to limit this, as JavaScript call stack may be recursive
 */ 
Clazz.getStackTrace = function(n) {
        n || (n = 25);
  // updateNode and updateParents cause infinite loop here
        var s = "\n";
        var c = arguments.callee;
  var showParams = (n < 0);
  if (showParams)
    n = -n;
        for (var i = 0; i < n; i++) {
                if (!(c = c.caller))
      break;
    var sig = (c.toString ? c.toString().substring(0, c.toString().indexOf("{")) : "<native method>");
                s += i + " " + (c.exName ? (c.claxxOwner ? c.claxxOwner.__CLASS_NAME__ + "."  : "") + c.exName  + sig.replace(/function /,""): sig) + "\n";
                if (c == c.caller) {
      s += "<recursing>\n";
      break;
    }
    if (showParams) {
      var args = c.arguments;
      for (var j = 0; j < args.length; j++) {
        var sa = "" + args[j];
        if (sa.length > 60)
          sa = sa.substring(0, 60) + "...";
        s += " args[" + j + "]=" + sa.replace(/\s+/g," ") + "\n";
      }
    }
        }
        return s;
}

///////////////////// method creation ////////////////////////////////

/**
 * Make constructor for the class with the given function body and parameters
 * signature.
 * 
 * @param clazzThis host class
 * @param funBody constructor body
 * @param funParams constructor parameters signature
 */
/* public */
Clazz.makeConstructor = function (clazzThis, funBody, funParams) {
        Clazz.defineMethod (clazzThis, "construct", funBody, funParams);
        if (clazzThis.con$truct) {
                clazzThis.con$truct.index = clazzThis.con$truct.stacks.length;
        }
        //clazzThis.con$truct = clazzThis.prototype.con$truct = null;
};

/**
 * Override constructor for the class with the given function body and
 * parameters signature.
 * 
 * @param clazzThis host class
 * @param funBody constructor body
 * @param funParams constructor parameters signature
 */
/* public */
Clazz.overrideConstructor = function (clazzThis, funBody, funParams) {
        Clazz.overrideMethod (clazzThis, "construct", funBody, funParams);
        if (clazzThis.con$truct) {
                clazzThis.con$truct.index = clazzThis.con$truct.stacks.length;
        }
        //clazzThis.con$truct = clazzThis.prototype.con$truct = null;
};


/*
 * Define method for the class with the given method name and method
 * body and method parameter signature.
 *
 * @param clazzThis host class in which the method to be defined
 * @param funName method name
 * @param funBody function object, e.g function () { ... }
 * @param funParams paramether signature, e.g ["string", "number"]
 * @return method of the given name. The method may be funBody or a wrapper
 * of the given funBody.
 */
/* public */
Clazz.defineMethod = function (clazzThis, funName, funBody, funParams) {
        if (Clazz.assureInnerClass) 
    Clazz.assureInnerClass(clazzThis, funBody);
        funBody.exName = funName;
        var fpName = formatParameters(funParams);
        var proto = clazzThis.prototype;
        var f$ = proto[funName];
  if (Clazz._Loader._checkLoad)
    checkDuplicate(clazzThis, funName, fpName);
        if (!f$ || (f$.claxxOwner === clazzThis && f$.funParams == fpName)) {
                // property "funParams" will be used as a mark of only-one method
                funBody.funParams = fpName; 
                funBody.claxxOwner = clazzThis;
                funBody.exClazz = clazzThis; // make it traceable
                return addProto(proto, funName, funBody);
        }
  // we have found a duplicate
        var oldFun = null;
        var oldStacks = f$.stacks;
                if (!oldStacks) {
                        /* method is not defined by Clazz.defineMethod () */
      oldStacks = [];
                        oldFun = f$;
                        if (f$.claxxOwner) {
                                oldStacks[0] = oldFun.claxxOwner;
                        }
                }
                /*
         * Method that is already defined in super class will be overridden
         * with a new proxy method with class hierarchy stored in a stack.
         * That is to say, the super methods are lost in this class' proxy
         * method. 
         * When method are being called, methods defined in the new proxy 
         * method will be searched through first. And if no method fitted,
         * it will then try to search method in the super class stacks.
         */
        if (!f$.stacks || f$.claxxReference !== clazzThis) {
                //Generate a new delegating method for the class                
    var id = ++SAEMid;
        var delegate = function () {
                return searchAndExecuteMethod(id, this, arguments.callee.claxxReference, arguments.callee.methodName, arguments);
        };
        delegate.methodName = funName;
        delegate.claxxReference = clazzThis;
                f$ = addProto(proto, funName, delegate);                                
                // Keep the class inheritance stacks
                var arr = [];
                for (var i = 0; i < oldStacks.length; i++)
                        arr[i] = oldStacks[i];
                f$.stacks = arr;
        }
        var ss = f$.stacks;
        if (findArrayItem(ss, clazzThis) < 0) ss.push(clazzThis);

        if (oldFun) {
                if (oldFun.claxxOwner === clazzThis) {
                        f$[oldFun.funParams] = oldFun;
                        oldFun.claxxOwner = null;
                        // property "funParams" will be used as a mark of only-one method
                        oldFun.funParams = null; // null ? safe ? // safe for != null
                } else if (!oldFun.claxxOwner) {
                        /*
                         * The function is not defined Clazz.defineMethod ().
                         * Try to fixup the method ...
                         * As a matter of lost method information, I just suppose
                         * the method to be fixed is with void parameter!
                         */
                        f$["\\unknown"] = oldFun;
                }
        }
        funBody.exClazz = clazzThis; // make it traceable
        f$[fpName] = funBody;
        return f$;
};                                                

duplicatedMethods = {};

var checkDuplicate = function(clazzThis, funName, fpName) {
        var proto = clazzThis.prototype;
        var f$ = proto[funName];
  if (f$ && (f$.claxxOwner || f$.claxxReference) === clazzThis) {
    key = clazzThis.__CLASS_NAME__ + "." + funName + fpName;
    var m = duplicatedMethods[key];
    if (m) {
      var s = "Warning! Duplicate method found for " + key;
      System.out.println(s);
      Clazz.alert(s);
      duplicatedMethods[key] = m + 1; 
    } else {
      duplicatedMethods[key] = 1;
    }
  }
}

Clazz.showDuplicates = function(quiet) {
  var s = "";
  var a = duplicatedMethods;
  var n = 0;
  for (var key in a)
    if (a[key] > 1) {
      s += a[key] + "\t" + key + "\n";
      n++;
    }
  s = "Duplicates: " + n + "\n\n" + s;
  System.out.println(s);
  if (!quiet)
    alert(s);
}

var findArrayItem = function(arr, item) {
        if (arr && item)
                for (var i = arr.length; --i >= 0;)
                        if (arr[i] === item)
                                return i;
        return -1;
}

var removeArrayItem = function(arr, item) {
        var i = findArrayItem(arr, item);
        if (i >= 0) {
                var n = arr.length - 1;
                for (; i < n; i++)
                        arr[i] = arr[i + 1];
                arr.length--;
                return true;
        }
}

/*
 * Other developers may need to extend this formatParameters method
 * to deal complicated situation.
 */
/* protected */
var formatParameters = function (funParams) {
        return (funParams ? funParams.replace (/~([NABSO])/g, 
      function ($0, $1) {
        switch ($1) {
        case 'N':
                return "n";
        case 'B':
                return "b";
        case 'S':
                return "String";
        case 'O':
                return "Object";
        case 'A':
                return "Array";
        }
        return "Unknown";
      }).replace (/\s+/g, "").replace (/^|,/g, "\\").replace (/\$/g, "org.eclipse.s") : "\\void");
};

/*
 * Override the existed methods which are in the same name.
 * Overriding methods is provided for the purpose that the JavaScript
 * does not need to search the whole hierarchied methods to find the
 * correct method to execute.
 * Be cautious about this method. Incorrectly using this method may
 * break the inheritance system.
 *
 * @param clazzThis host class in which the method to be defined
 * @param funName method name
 * @param funBody function object, e.g function () { ... }
 * @param funParams paramether signature, e.g ["string", "number"]
 */
/* public */
Clazz.overrideMethod = function(clazzThis, funName, funBody, funParams) {
        if (Clazz.assureInnerClass) Clazz.assureInnerClass (clazzThis, funBody);
        funBody.exName = funName;
        var fpName = formatParameters(funParams);
  if (Clazz._Loader._checkLoad)
    checkDuplicate(clazzThis, funName, fpName);
        /*
         * Replace old methods with new method. No super methods are kept.
         */
        funBody.funParams = fpName; 
        funBody.claxxOwner = clazzThis;
        return addProto(clazzThis.prototype, funName, funBody);
};

//////////////  Overridden and Overloaded Java Method Handling //////////////////
//                       SAEM (SearchAndExecuteMethod)
// adapted by BH
//

/*
 * BH Clazz.getProfile monitors exactly what is being delegated with SAEM,
 * which could be a bottle-neck for function calling.
 * This is critical for performance optimization.
 */ 

  var __signatures = ""; 

Clazz.getProfile = function() {
        var s = "";
        if (_profile) {
                var l = [];
                for (var i in _profile) {
                        var n = "" + _profile[i];
                        l.push("        ".substring(n.length) + n + "\t" + i);
                }
                s = l.sort().reverse().join("\r\n");
                _profile = {};
        }
        return s + __signatures;
}

var addProfile = function(c, f, p, id) {
        var s = id + " " + c.__CLASS_NAME__ + " " + f + " ";// + JSON.stringify(p);
  if (__signatures.indexOf(s) < 0)
    __signatures += s + "\n";    
        _profile[s] || (_profile[s] = 0);
        _profile[s]++;
}

/**
 * Called also by Throwable
 *  
/* public */
Clazz.getParamsType = function (funParams) {
        // bh: optimization here for very common cases
        var n = funParams.length;
        switch (n) {
        case 0:
                var params = ["void"];
                params.typeString = "\\void";
                return params;
        case 1:
          // BH just so common
    switch (typeof obj) {
    case "number":
                        var params = ["n"];
                        params.typeString = "\\n";
                        return params;
    case "boolean":
                        var params = ["b"];
                        params.typeString = "\\b";
                        return params;
                }
        }

        var params = [];
        params.hasCastedNull = false;
        if (funParams) {
                for (var i = 0; i < n; i++) {
                        params[i] = Clazz.getClassName (funParams[i]);
                        if (funParams[i] instanceof Clazz.CastedNull) {
                                params.hasCastedNull = true;
                        }
                }
        }
        params.typeString = "\\" + params.join ('\\');
        return params;
};

var SAEMid = 0;
//var SAEMarray = [];
/**
 * BH: OK, this was an idea that doesn't work. The idea was to tag SAEM calls
 * and then refer back to an array. But the id number cannot be put in the right place.
 * 
 * Say we have this:
 * 
 * StringBuffer sb = new StringBuffer(); 
 * sb.append("").append(1);
 * 
 * Here we have two different append methods to call. They are saved under two
 * names:  StringBuffer.prototype.append["\\String"] 
 *     and StringBuffer.prototype.append["\\Number"]
 * 
 * The job of generateDelegatingMethod is to discriminate between those two. We can do
 * that, but the real issue is that we have to do that EVERY time a call is made.
 * This is a problem that must be handled at compile time. There is no way to 
 * make .append("") to go one way the first time and another way the second time. 
 * What we need at run time is something like this:
 * 
 * Clazz.delegate(sb.append,1,[""]) and Clazz.delegate(sb.append,2,[1])
 * The we would be able to log those numbers at run time and refer to them.
 *                     
 * The only real way to avoid SAEM is: 
 * 
 * 1) to never call super() -- always call a differently named function in a superclass.
 * 2) don't overload functions 
 *  
 */   


/**
 * Search the given class prototype, find the method with the same
 * method name and the same parameter signatures by the given 
 * parameters, and then run the method with the given parameters.
 *
 * @param objThis the current host object
 * @param claxxRef the current host object's class
 * @param fxName the method name
 * @param funParams the given arguments
 * @return the result of the specified method of the host object,
 * the return maybe void.
 * @throws MethodNotFoundException if no matched method is found
 */
/* protected */
var searchAndExecuteMethod = function (id, objThis, claxxRef, fxName, args) {

//  var fx = SAEMarray[id];
//  if (fx) {
//    return fx.apply(objThis, args);
//  }

        fx = objThis[fxName];
        var params = Clazz.getParamsType(args);
  if (!fx)    
    try {System.out.println(Clazz.getStackTrace(5))} catch (e){}
        _profile && addProfile(claxxRef, fxName, params, id);
        // Cache last matched method
        if (fx.lastParams == params.typeString && fx.lastClaxxRef === claxxRef) {
                var methodParams;
                if (params.hasCastedNull) {
                        methodParams = [];
                        // For Clazz.CastedNull instances, the type name is
                        // already used to indentified the method in searchMethod.
                        for (var k = 0; k < args.length; k++)
                                methodParams[k] = (args[k] instanceof Clazz.CastedNull ? null : args[k]);
                } else {
//      if (fx.lastMethod) SAEMarray[id] = fx.lastMethod;
                        methodParams = args;
                }
                return (fx.lastMethod ? fx.lastMethod.apply(objThis, methodParams) : null);
        }
        fx.lastParams = params.typeString;
        fx.lastClaxxRef = claxxRef;

        var stacks = fx.stacks;
        if (!stacks)
                stacks = claxxRef.prototype[fxName].stacks;
        var length = stacks.length;

        /*
         * Search the inheritance stacks to get the given class' function
         */
        var began = false; // began to search its super classes
        for (var i = length; --i >= 0;) {
                if (began || stacks[i] === claxxRef) {
                        /*
                         * First try to search method within the same class scope
                         * with stacks[i] === claxxRef
                         */
                        var clazzFun = stacks[i].prototype[fxName];
                        var ret = tryToSearchAndExecute(id, fxName, objThis, clazzFun, params,
                                        args, fx);
                        if (!(ret instanceof MethodException)) {
                                return ret;
                        }
                        /*
                         * As there are no such methods in current class, Clazz will try 
                         * to search its super class stacks. Here variable began indicates
                         * that super searchi is began, and there is no need checking
                         * <code>stacks[i] === claxxRef</code>
                         */
                        began = true; 
                } // end of if
        } // end of for
        if ("construct" == fxName) {
                /*
                 * For non existed constructors, just return without throwing
                 * exceptions. In Java codes, extending Object can call super
                 * default Object#constructor, which is not defined in JS.
                 */
                return;
        }
        // TODO: should be java.lang.NoSuchMethodException
        throw new MethodNotFoundException(objThis, claxxRef, 
                        fxName, params.typeString);
};


/* private */
var tryToSearchAndExecute = function(id, fxName, objThis, clazzFun, params, args, fx) {
        var method = [];
        var generic = true;
        for (var fn in clazzFun) {
                if (fn.charCodeAt(0) == 92) { // 92 == '\\'.charCodeAt (0)
                        var ps = fn.substring(1).split("\\");
                        (ps.length == params.length) && method.push(ps);
                generic = false;
                        continue;
                }
                /*
                 * When there is only one method in the class, use the args
                 * to identify the parameter type.
                 *
                 * AbstractCollection.remove (Object)
                 * AbstractList.remove (int)
                 * ArrayList.remove (int)
                 *
                 * Then calling #remove (Object) method on ArrayList instance will 
                 * need to search up to the AbstractCollection.remove (Object),
                 * which contains only one method.
                 */
                /*
                 * See Clazz#defineMethod --Mar 10, 2006, josson
                 */
                if (generic && fn == "funParams" && clazzFun.funParams) {
                        fn = clazzFun.funParams;
                        var ps = fn.substring(1).split ("\\");
                        (ps.length == params.length) && (method[0] = ps);
                        break;
                }
        }
  if (method.length == 0 || !(method = searchMethod(method, params)))
          return new MethodException();
        var f = (generic ? clazzFun : clazzFun["\\" + method]);
        //if (generic) 
  //{ /* Use the generic method */
                /*
                 * Will this case be reachable?
                 * March 4, 2006 josson
                 * 
                 * Reachable for calling #remove (Object) method on 
                 * ArrayList instance
                 * May 5, 2006 josson
                 */
        var methodParams = null;
        if (params.hasCastedNull) {
                methodParams = [];
                for (var k = 0; k < args.length; k++) {
                        if (args[k] instanceof Clazz.CastedNull) {
                                /*
                                 * For Clazz.CastedNull instances, the type name is
                                 * already used to indentify the method in searchMethod.
                                 */
                                methodParams[k] = null;
                        } else {
                                methodParams[k] = args[k];
                        }
                }
        } else {
                methodParams = args;
        }
        fx.lastMethod = f;
  //if (!params.hasCastedNull) SAEMarray[id] = f;
        return f.apply(objThis, methodParams);
};

/**
 * Search the existed polymorphic methods to get the matched method with
 * the given parameter types.
 *
 * @param existedMethods Array of string which contains method parameters
 * @param paramTypes Array of string that is parameter type.
 * @return string of method parameters seperated by "\\"
 */
/* private */
var searchMethod = function(roundOne, paramTypes) {
        // Filter out all the fitted methods for the given parameters
        var roundTwo = [];
        var len = roundOne.length;
        for (var i = 0; i < len; i++) {
                var fittedLevel = [];
                var isFitted = true;
                var len2 = roundOne[i].length;
                for (var j = 0; j < len2; j++) {
                        fittedLevel[j] = Clazz.getInheritedLevel (paramTypes[j], 
                                        roundOne[i][j]);
                        if (fittedLevel[j] < 0) {
                                isFitted = false;
                                break;
                        }
                }
                if (isFitted) {
                        fittedLevel[paramTypes.length] = i; // Keep index for later use
                        roundTwo.push(fittedLevel);
                }
        }
        if (roundTwo.length == 0)
                return null;
        // Find out the best method according to the inheritance.
        var resultTwo = roundTwo;
        var min = resultTwo[0];
        for (var i = 1; i < resultTwo.length; i++) {
                var isVectorLesser = true;
                for (var j = 0; j < paramTypes.length; j++) {
                        if (min[j] < resultTwo[i][j]) {
                                isVectorLesser = false;;
                                break;
                        }
                }
                if (isVectorLesser)
                        min = resultTwo[i];
        }
        var index = min[paramTypes.length]; // Get the previously stored index
        /*
         * Return the method parameters' type string as indentifier of the
         * choosen method.
         */
        return roundOne[index].join ('\\');
};

////////////////////////////////// package loading ///////////////////////

/*
 * all root packages. e.g. java.*, org.*, com.*
 */
/* protected */
Clazz.allPackage = {};

/**
 * Will be used to keep value of whether the class is defined or not.
 */
/* protected */
Clazz.allClasses = {};

Clazz.lastPackageName = null;
Clazz.lastPackage = null;

/* protected */
Clazz.unloadedClasses = [];

/* public */
Clazz.declarePackage = function (pkgName) {
        if (Clazz.lastPackageName == pkgName)
                return Clazz.lastPackage;
        if (pkgName && pkgName.length) {
                var pkgFrags = pkgName.split (/\./);
                var pkg = Clazz.allPackage;
                for (var i = 0; i < pkgFrags.length; i++) {
                        if (!pkg[pkgFrags[i]]) {
                                pkg[pkgFrags[i]] = { 
                                        __PKG_NAME__ : (pkg.__PKG_NAME__ ? 
                                                pkg.__PKG_NAME__ + "." + pkgFrags[i] : pkgFrags[i])
                                }; 
                                // pkg[pkgFrags[i]] = {};
                                if (i == 0) {
                                        // eval ...
                                        Clazz.setGlobal(pkgFrags[i], pkg[pkgFrags[i]]);
                                }
                        }
                        pkg = pkg[pkgFrags[i]]
                }
                Clazz.lastPackageName = pkgName;
                Clazz.lastPackage = pkg;
                return pkg;
        }
};

/* protected */
Clazz.evalType = function (typeStr, isQualified) {
        var idx = typeStr.lastIndexOf(".");
        if (idx != -1) {
                var pkgName = typeStr.substring (0, idx);
                var pkg = Clazz.declarePackage (pkgName);
                var clazzName = typeStr.substring (idx + 1);
                return pkg[clazzName];
        } 
        if (isQualified)
                return window[typeStr];
        switch (typeStr) {
        case "string":
                return String;
        case "number":
                return Number;
  case "object":
                return Clazz._O;
        case "boolean":
                return Boolean;
        case "function":
                return Function;
  case "void":
  case "undefined":
  case "unknown":
                return typeStr;
        case "NullObject":
                return NullObject;
        default:
                return window[typeStr];
        }
};

/**
 * Define a class or interface.
 *
 * @param qClazzName String presents the qualified name of the class
 * @param clazzFun Function of the body
 * @param clazzParent Clazz to inherit from, may be null
 * @param interfacez Clazz may implement one or many interfaces
 *   interfacez can be Clazz object or Array of Clazz objects.
 * @return Ruturn the modified Clazz object
 */
/* public */
Clazz.defineType = function (qClazzName, clazzFun, clazzParent, interfacez) {
        var cf = Clazz.unloadedClasses[qClazzName];
        if (cf) {
                clazzFun = cf;
        }
        var idx = qClazzName.lastIndexOf (".");
        if (idx != -1) {
                var pkgName = qClazzName.substring (0, idx);
                var pkg = Clazz.declarePackage (pkgName);
                var clazzName = qClazzName.substring (idx + 1);
                if (pkg[clazzName]) {
                        // already defined! Should throw exception!
                        return pkg[clazzName];
                }
                pkg[clazzName] = clazzFun;
        } else {
                if (window[qClazzName]) {
                        // already defined! Should throw exception!
                        return window[qClazzName];
                }
                Clazz.setGlobal(qClazzName, clazzFun);
        }
        Clazz.decorateAsType(clazzFun, qClazzName, clazzParent, interfacez);
        /*# {$no.javascript.support} >>x #*/
        var iFun = Clazz._innerFunctions;
        clazzFun.defineMethod = iFun.defineMethod;
        clazzFun.defineStaticMethod = iFun.defineStaticMethod;
        clazzFun.makeConstructor = iFun.makeConstructor;
        /*# x<< #*/
        return clazzFun;
};

var isSafari = (navigator.userAgent.indexOf ("Safari") != -1);
var isSafari4Plus = false;
if (isSafari) {
        var ua = navigator.userAgent;
        var verIdx = ua.indexOf("Version/");
        if (verIdx  != -1) {
                var verStr = ua.substring(verIdx + 8);
                var verNumber = parseFloat(verStr);
                isSafari4Plus = verNumber >= 4.0;
        }
}

/* public */
Clazz.instantialize = function (objThis, args) {


        if (args && args.length == 1 && args[0] 
                        && args[0] instanceof args4InheritClass) {
                return;
        }
        if (objThis instanceof Number) {
                objThis.valueOf = function () {
                        return this;
                };
        }
        if (isSafari4Plus) { // Fix bug of Safari 4.0+'s over-optimization
                var argsClone = [];
                for (var k = 0; k < args.length; k++) {
                        argsClone[k] = args[k];
                }
                args = argsClone;
        }

        var c = objThis.construct;
        if (c) {
                if (!objThis.con$truct) { // no need to init fields
                        c.apply (objThis, args);
                } else if (!objThis.getClass ().superClazz) { // the base class
                        objThis.con$truct.apply (objThis, []);
                        c.apply (objThis, args);
                } else if ((c.claxxOwner 
                                && c.claxxOwner === objThis.getClass ())
                                || (c.stacks 
                                && c.stacks[c.stacks.length - 1] == objThis.getClass ())) {
                        /*
                         * This #construct is defined by this class itself.
                         * #construct will call Clazz.superConstructor, which will
                         * call #con$truct back
                         */
                        c.apply (objThis, args);
                } else { // constructor is a super constructor
                        if (c.claxxOwner && !c.claxxOwner.superClazz 
                                                && c.claxxOwner.con$truct) {
                                c.claxxOwner.con$truct.apply (objThis, []);
                        } else if (c.stacks && c.stacks.length == 1
                                        && !c.stacks[0].superClazz) {
                                c.stacks[0].con$truct.apply (objThis, []);
                        }
                        c.apply (objThis, args);
                        objThis.con$truct.apply (objThis, []);
                }
        } else if (objThis.con$truct) {
                objThis.con$truct.apply (objThis, []);
        }
};

/**
 * Once there are other methods registered to the Function.prototype, 
 * those method names should be add to the following Array.
 */
/*
 * static final member of interface may be a class, which may
 * be function.
 */
/* protected */
Clazz.innerFunctionNames = [
        "isInstance", "equals", "hashCode", /*"toString",*/ "getName", "getCanonicalName", "getClassLoader", "getResource", "getResourceAsStream" /*# {$no.javascript.support} >>x #*/, "defineMethod", "defineStaticMethod",
        "makeConstructor" /*# x<< #*/
];

/*
 * Static methods
 */
Clazz._innerFunctions = {
        /*
         * Similar to Object#equals
         */
   
  isInstance: function(c) {
    return Clazz.instanceOf(c, this);
  },
  
        equals : function (aFun) {
                return this === aFun;
        },

        hashCode : function () {
                return this.getName ().hashCode ();
        },

        toString : function () {
                return "class " + this.getName ();
        },

        /*
         * Similar to Class#getName
         */
        getName : function () {
                return Clazz.getClassName (this, true);
        },
        getCanonicalName : function () {
                return this.__CLASS_NAME__;
        },
        getClassLoader : function () {
                var clazzName = this.__CLASS_NAME__;
                var baseFolder = Clazz._Loader.getClasspathFor(clazzName);
                var x = baseFolder.lastIndexOf (clazzName.replace (/\./g, "/"));
                if (x != -1) {
                        baseFolder = baseFolder.substring (0, x);
                } else {
                        baseFolder = Clazz._Loader.getClasspathFor(clazzName, true);
                }
                var loader = Clazz._Loader.requireLoaderByBase(baseFolder);
                loader.getResourceAsStream = Clazz._innerFunctions.getResourceAsStream;
                loader.getResource = Clazz._innerFunctions.getResource; // BH
                return loader;
        },

        getResource : function(name) {
                var stream = this.getResourceAsStream(name);
    return (stream ? stream.url : null);
        },

        getResourceAsStream : function (name) {
                if (!name)
                        return null;
                name = name.replace (/\\/g, '/');
                var baseFolder = null;
    var fname = name;
                var clazzName = this.__CLASS_NAME__;
                if (arguments.length == 2 && name.indexOf ('/') != 0) { // additional argument
                        name = "/" + name;
                }
                if (name.indexOf ('/') == 0) {
                        //is.url = name.substring (1);
                        if (arguments.length == 2) { // additional argument
                                baseFolder = arguments[1];
                                if (!baseFolder)
                                        baseFolder = Clazz.binaryFolders[0];
                        } else if (Clazz._Loader) {
                                baseFolder = Clazz._Loader.getClasspathFor(clazzName, true);
                        }
                        if (!baseFolder) {
                                fname = name.substring (1);
                        } else {
                                baseFolder = baseFolder.replace (/\\/g, '/');
                                var length = baseFolder.length;
                                var lastChar = baseFolder.charAt (length - 1);
                                if (lastChar != '/') {
                                        baseFolder += "/";
                                }
                                fname = baseFolder + name.substring (1);
                        }
                } else {
                        if (this.base) {
                                baseFolder = this.base;
                        } else if (Clazz._Loader) {
                                baseFolder = Clazz._Loader.getClasspathFor(clazzName);
                                var x = baseFolder.lastIndexOf (clazzName.replace (/\./g, "/"));
                                if (x != -1) {
                                        baseFolder = baseFolder.substring (0, x);
                                } else {
                                        //baseFolder = null;
                                        var y = -1;
                                        if (baseFolder.indexOf (".z.js") == baseFolder.length - 5
                                                        && (y = baseFolder.lastIndexOf ("/")) != -1) {
                                                baseFolder = baseFolder.substring (0, y + 1);
                                                var pkgs = clazzName.split (/\./);
                                                for (var k = 1; k < pkgs.length; k++) {
                                                        var pkgURL = "/";
                                                        for (var j = 0; j < k; j++) {
                                                                pkgURL += pkgs[j] + "/";
                                                        }
                                                        if (pkgURL.length > baseFolder.length) {
                                                                break;
                                                        }
                                                        if (baseFolder.indexOf (pkgURL) == baseFolder.length - pkgURL.length) {
                                                                baseFolder = baseFolder.substring (0, baseFolder.length - pkgURL.length + 1);
                                                                break;
                                                        }
                                                }
                                        } else {
                                                baseFolder = Clazz._Loader.getClasspathFor(clazzName, true);
                                        }
                                }
                        } else {
                                var bins = Clazz.binaryFolders;
                                if (bins && bins.length) {
                                        baseFolder = bins[0];
                                }
                        }
                        if (!baseFolder)
                                baseFolder = "j2s/";
                        baseFolder = baseFolder.replace (/\\/g, '/');
                        var length = baseFolder.length;
                        var lastChar = baseFolder.charAt (length - 1);
                        if (lastChar != '/') {
                                baseFolder += "/";
                        }
                        if (this.base) {
                                fname = baseFolder + name;
                        } else {
                                var idx = clazzName.lastIndexOf ('.');
                                if (idx == -1 || this.base) {
                                        fname = baseFolder + name;
                                } else {
                                        fname = baseFolder + clazzName.substring (0, idx)
                                                        .replace (/\./g, '/') +  "/" + name;
                                }
                        }            
                }
    var url = null;
    try {
      if (fname.indexOf(":/") < 0) {
        var d = document.location.href.split("?")[0].split("/");
        d[d.length - 1] = fname;
        fname = d.join("/");
      }
      url = new java.net.URL(fname);
    } catch (e) {
    }
                var data = (url == null ? null : Jmol._getFileData(fname.toString()));
    if (!data || data == "error" || data.indexOf("[Exception") == 0)
      return null;
    var bytes = new java.lang.String(data).getBytes();      
    var is = new java.io.BufferedInputStream ( new java.io.ByteArrayInputStream (bytes)); 
    is.url = url;
                return is;
        }/*# {$no.javascript.support} >>x #*/,

        /*
         * For JavaScript programmers
         */
        defineMethod : function (methodName, funBody, paramTypes) {
                Clazz.defineMethod (this, methodName, funBody, paramTypes);
        },

        /*
         * For JavaScript programmers
         */
        defineStaticMethod : function (methodName, funBody, paramTypes) {
                Clazz.defineMethod (this, methodName, funBody, paramTypes);
                this[methodName] = this.prototype[methodName];
        },

        /*
         * For JavaScript programmers
         */
        makeConstructor : function (funBody, paramTypes) {
                Clazz.makeConstructor (this, funBody, paramTypes);
        }
        /*# x<< #*/
};


var cStack = [];

/**
 * BH: I would like to be able to remove "self.c$" here, but that is tricky.
 */
  
Clazz.pu$h = function (c) {
  c || (c = self.c$); // old style
        c && cStack.push(c);
};

Clazz.p0p = function () {
        return cStack.pop();
};

/* protected */
Clazz.decorateAsClass = function (clazzFun, prefix, name, clazzParent, 
                interfacez, parentClazzInstance, _decorateAsClass) {
    
        var prefixName = null;
        if (prefix) {
                prefixName = prefix.__PKG_NAME__;
                if (!prefixName)
                        prefixName = prefix.__CLASS_NAME__;      
        }
        var qName = (prefixName ? prefixName + "." : "") + name;
  
    if (Clazz._Loader._classPending[qName]) {
      delete Clazz._Loader._classPending[qName];
      Clazz._Loader._classCountOK++;
      Clazz._Loader._classCountPending--;
    }
  if (Clazz._Loader && Clazz._Loader._checkLoad) {
    System.out.println("decorating class " + prefixName + "." + name);
  }
        var cf = Clazz.unloadedClasses[qName];
        if (cf) {
                clazzFun = cf;
        }
        var qName = null;
        decorateFunction(clazzFun, prefix, name);
        if (parentClazzInstance) {
                Clazz.inheritClass (clazzFun, clazzParent, parentClazzInstance);
        } else if (clazzParent) {
                Clazz.inheritClass (clazzFun, clazzParent);
        }
        if (interfacez) {
                Clazz.implementOf (clazzFun, interfacez);
        }
        return clazzFun;
};

/* private */
var decorateFunction = function (clazzFun, prefix, name, _decorateFunction) {
        var qName;
        if (!prefix) {
                // e.g. Clazz.declareInterface (null, "ICorePlugin", org.eclipse.ui.IPlugin);
                qName = name;
                Clazz.setGlobal(name, clazzFun);
        } else if (prefix.__PKG_NAME__) {
                // e.g. Clazz.declareInterface (org.eclipse.ui, "ICorePlugin", org.eclipse.ui.IPlugin);
                qName = prefix.__PKG_NAME__ + "." + name;
                prefix[name] = clazzFun;
                if (prefix === java.lang)
                        Clazz.setGlobal(name, clazzFun);
        } else {
                // e.g. Clazz.declareInterface (org.eclipse.ui.Plugin, "ICorePlugin", org.eclipse.ui.IPlugin);
                qName = prefix.__CLASS_NAME__ + "." + name;
                prefix[name] = clazzFun;
        }
        Clazz.extendJO(clazzFun, qName);
        var inF = Clazz.innerFunctionNames;
        for (var i = 0; i < inF.length; i++) {
                clazzFun[inF[i]] = Clazz._innerFunctions[inF[i]];
        }

        if (Clazz._Loader) 
    Clazz._Loader.updateNodeForFunctionDecoration(qName);
};

/* protected */
Clazz.declareInterface = function (prefix, name, interfacez, _declareInterface) {
        var clazzFun = function () {};
        decorateFunction(clazzFun, prefix, name);
        if (interfacez) {
                Clazz.implementOf (clazzFun, interfacez);
        }
        return clazzFun;
};

/* public */
Clazz.declareType = function (prefix, name, clazzParent, interfacez, 
                parentClazzInstance, _declareType) {
        var f = function () {
                Clazz.instantialize (this, arguments);
        };
        return Clazz.decorateAsClass (f, prefix, name, clazzParent, interfacez, 
                        parentClazzInstance);
};

/* public */
Clazz.declareAnonymous = function (prefix, name, clazzParent, interfacez, 
                parentClazzInstance, _declareAnonymous) {
        var f = function () {
                Clazz.prepareCallback(this, arguments);
                Clazz.instantialize (this, arguments);
        };
        return Clazz.decorateAsClass (f, prefix, name, clazzParent, interfacez, 
                        parentClazzInstance);
};

/* public */
Clazz.decorateAsType = function (clazzFun, qClazzName, clazzParent, 
                interfacez, parentClazzInstance, inheritClazzFuns, _decorateAsType) {
        Clazz.extendJO(clazzFun, qClazzName);
        clazzFun.equals = Clazz._innerFunctions.equals;
        clazzFun.getName = Clazz._innerFunctions.getName;
        if (inheritClazzFuns) {
                for (var i = 0; i < Clazz.innerFunctionNames.length; i++) {
                        var methodName = Clazz.innerFunctionNames[i];
                        clazzFun[methodName] = Clazz._innerFunctions[methodName];
                }
        }
        if (parentClazzInstance) {
                Clazz.inheritClass (clazzFun, clazzParent, parentClazzInstance);
        } else if (clazzParent) {
                Clazz.inheritClass (clazzFun, clazzParent);
        }
        if (interfacez) {
                Clazz.implementOf (clazzFun, interfacez);
        }
        return clazzFun;
};


////////////////////////// default package declarations ////////////////////////

/* sgurin: preserve Number.prototype.toString */
Number.prototype._numberToString=Number.prototype.toString;


Clazz.declarePackage ("java.io");
//Clazz.declarePackage ("java.lang");
Clazz.declarePackage ("java.lang.annotation"); // java.lang
Clazz.declarePackage ("java.lang.instrument"); // java.lang
Clazz.declarePackage ("java.lang.management"); // java.lang
Clazz.declarePackage ("java.lang.reflect"); // java.lang
Clazz.declarePackage ("java.lang.ref");  // java.lang.ref
java.lang.ref.reflect = java.lang.reflect;
Clazz.declarePackage ("java.util");
//var reflect = Clazz.declarePackage ("java.lang.reflect");
Clazz.declarePackage ("java.security");


/*
 * Consider these interfaces are basic!
 */
Clazz.declareInterface (java.io,"Closeable");
Clazz.declareInterface (java.io,"DataInput");
Clazz.declareInterface (java.io,"DataOutput");
Clazz.declareInterface (java.io,"Externalizable");
Clazz.declareInterface (java.io,"Flushable");
Clazz.declareInterface (java.io,"Serializable");
Clazz.declareInterface (java.lang,"Iterable");
Clazz.declareInterface (java.lang,"CharSequence");
Clazz.declareInterface (java.lang,"Cloneable");
Clazz.declareInterface (java.lang,"Appendable");
Clazz.declareInterface (java.lang,"Comparable");
Clazz.declareInterface (java.lang,"Runnable");
Clazz.declareInterface (java.util,"Comparator");

java.lang.ClassLoader = {
        __CLASS_NAME__ : "ClassLoader"
};

/******************************************************************************
 * Copyright (c) 2007 java2script.org and others.
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 *     Zhou Renjian - initial API and implementation
 *****************************************************************************/
/*******
 * @author zhou renjian
 * @create March 10, 2006
 *******/

/**
 * Once ClassExt.js is part of Class.js.
 * In order to make the Class.js as small as possible, part of its content
 * is moved into this ClassExt.js.
 *
 * See also http://j2s.sourceforge.net/j2sclazz/
 */
 
/**
 * Clazz.MethodNotFoundException is used to notify the developer about calling
 * methods with incorrect parameters.
 */
/* protected */
// Override the Clazz.MethodNotFoundException in Class.js to give details
var MethodNotFoundException = function (obj, clazz, method, params) {
        var paramStr = "";
        if (params) {
                paramStr = params.substring (1).replace (/\\/g, ",");
        }
        var leadingStr = "";
        if (method && method != "construct") {
                leadingStr = "Method";
        } else {
                leadingStr = "Constructor";
        }
        this.message = leadingStr + " " + Clazz.getClassName (clazz, true) + "." 
                                        + method + "(" + paramStr + ") is not found!";
        this.toString = function () {
                return "MethodNotFoundException:" + this.message;
        }
};

/**
 * Prepare "callback" for instance of anonymous Class.
 * For example for the callback:
 *     this.callbacks.MyEditor.sayHello();
 *     
 * This is specifically for inner classes that are referring to 
 * outer class methods and fields.   
 *
 * @param objThis the host object for callback
 * @param args arguments object. args[0] will be classThisObj -- the "this"
 * object to be hooked
 * 
 * Attention: parameters should not be null!
 */
/* protected */
Clazz.prepareCallback = function (innerObj, args) {
        var outerObj = args[0];
        var cbName = "b$"; // "callbacks";
        if (innerObj && outerObj && outerObj !== window) {
                var className = Clazz.getClassName(outerObj, true);             
                var obs = {};
                if (innerObj[cbName]) // must make a copy!
                        for (var s in innerObj[cbName])
                                obs[s] = innerObj[cbName][s];
                innerObj[cbName] = obs;
                
                /*
                 * TODO: the following line is SWT-specific! Try to move it out!
                 */
                //                      obs[className.replace (/org\.eclipse\.swt\./, "$wt.")] = outerObj;

        // all references to outer class and its superclass objects must be here as well
                obs[className] = outerObj;
                var clazz = Clazz.getClass(outerObj);
                while (clazz.superClazz) {
                        clazz = clazz.superClazz;
                        /*
                         * TODO: the following line is SWT-specific! Try to move it out!
                         */
                        //                              obs[Clazz.getClassName (clazz, true)
                        //                                              .replace (/org\.eclipse\.swt\./, "$wt.")] = outerObj;
                        obs[Clazz.getClassName(clazz, true)] = outerObj;
                }
                var cbs = outerObj[cbName];
                if (cbs)
                        for (var s in cbs)
                                obs[s] = cbs[s];
        }
        // remove "this" argument
        // note that args is an instance of arguments -- NOT an array; does not have the .shift() method!
        for (var i = 0; i < args.length - 1; i++)
                args[i] = args[i + 1];
        args.length--;
};

/**
 * Construct instance of the given inner class.
 *
 * @param classInner given inner class, alway with name like "*$*"
 * @param innerObj this instance which can be used to call back.
 * @param finalVars final variables which the inner class may use
 * @return the constructed object
 *
 * @see Clazz#cloneFinals
 */
/* public */
Clazz.innerTypeInstance = function (clazzInner, innerObj, finalVars) {
        if (!clazzInner)
                clazzInner = arguments.callee.caller;
        var obj;
        if (finalVars || innerObj.$finals) {
                        obj = new clazzInner(innerObj, Clazz.inheritArgs);
                // f$ is short for the once choosen "$finals"
                if (finalVars) {
                        if (innerObj.f$) {
                                var o = {};
                                for (var attr in innerObj.f$)
                                        o[attr] = innerObj.f$[attr];
                                for (var attr in finalVars)
                                        o[attr] = finalVars[attr];
                                obj.f$ = o;
                        } else {
                                obj.f$ = finalVars;
                        }
                } else if (innerObj.f$) {
                        obj.f$ = innerObj.f$;
                }
        } else {
                switch (arguments.length) {
                case 3:
                        return new clazzInner(innerObj);
                case 4:
                        return (innerObj.__CLASS_NAME__ == clazzInner.__CLASS_NAME__
                                        && arguments[3] === Clazz.inheritArgs ? innerObj : new clazzInner(innerObj, arguments[3]));
                case 5:
                        return new clazzInner(innerObj, arguments[3], arguments[4]);
                case 6:
                        return new clazzInner(innerObj, arguments[3], arguments[4], 
                                        arguments[5]);
                case 7:
                        return new clazzInner(innerObj, arguments[3], arguments[4], 
                                        arguments[5], arguments[6]);
                case 8:
                        return new clazzInner(innerObj, arguments[3], arguments[4], 
                                        arguments[5], arguments[6], arguments[7]);
                case 9:
                        return new clazzInner(innerObj, arguments[3], arguments[4], 
                                        arguments[5], arguments[6], arguments[7], arguments[8]);
                case 10:
                        return new clazzInner(innerObj, arguments[3], arguments[4], 
                                        arguments[5], arguments[6], arguments[7], arguments[8],
                                        arguments[9]);
                default:
                        //Should construct instance manually.
                        obj = new clazzInner(innerObj, Clazz.inheritArgs);
                        break;
                }
        }
        var n = arguments.length - 3;
        var args = new Array(n);
        for (var i = n; --i >= 0;)
                args[i] = arguments[i + 3];
        Clazz.instantialize(obj, args);
        return obj;
};

/**
 * Clone variables whose modifier is "final".
 * Usage: var o = Clazz.cloneFinals ("name", name, "age", age);
 *
 * @return Object with all final variables
 */
/* public */
Clazz.cloneFinals = function () {
        var o = {};
        var len = arguments.length / 2;
        for (var i = len; --i >= 0;)
                o[arguments[i + i]] = arguments[i + i + 1];
        return o;
};

/* public */
Clazz.isClassDefined = Clazz.isDefinedClass = function(clazzName) {
        if (!clazzName) 
                return false;           /* consider null or empty name as non-defined class */
        if (Clazz.allClasses[clazzName])
                return true;
        var pkgFrags = clazzName.split (/\./);
        var pkg = null;
        for (var i = 0; i < pkgFrags.length; i++)
                if (!(pkg = (pkg ? pkg[pkgFrags[i]] : Clazz.allPackage[pkgFrags[0]]))) {
                        return false;
    }
  return (pkg && (Clazz.allClasses[clazzName] = true));
};
/**
 * Define the enum constant.
 * @param classEnum enum type
 * @param enumName enum constant
 * @param enumOrdinal enum ordinal
 * @param initialParams enum constant constructor parameters
 * @return return defined enum constant
 */
/* public */
Clazz.defineEnumConstant = function (clazzEnum, enumName, enumOrdinal, initialParams, clazzEnumExt) {
        var o = (clazzEnumExt ? new clazzEnumExt() : new clazzEnum());
        // BH avoids unnecessary calls to SAEM
        o.$name = enumName;
        o.$ordinal = enumOrdinal;
        //Clazz.superConstructor (o, clazzEnum, [enumName, enumOrdinal]);
        if (initialParams && initialParams.length)
                o.construct.apply (o, initialParams);
        clazzEnum[enumName] = o;
        clazzEnum.prototype[enumName] = o;
        if (!clazzEnum["$ values"]) {         // BH added
                clazzEnum["$ values"] = []          // BH added
                clazzEnum.values = function() {     // BH added
                        return this["$ values"];          // BH added
                };                                  // BH added
        }
        clazzEnum["$ values"].push(o);
        return o;
};

//////// (int) conversions //////////

Clazz.floatToInt = function (x) {
        return x < 0 ? Math.ceil(x) : Math.floor(x);
};

Clazz.floatToByte = Clazz.floatToShort = Clazz.floatToLong = Clazz.floatToInt;
Clazz.doubleToByte = Clazz.doubleToShort = Clazz.doubleToLong = Clazz.doubleToInt = Clazz.floatToInt;

Clazz.floatToChar = function (x) {
        return String.fromCharCode (x < 0 ? Math.ceil(x) : Math.floor(x));
};

Clazz.doubleToChar = Clazz.floatToChar;



///////////////////////////////// Array additions //////////////////////////////
//
// BH: these are necessary for integer processing, especially
//
//

var getArrayClone = function(nbits) {
  return function() {
    var me = this;
    var n = me.length;
    var a = (nbits == 32 ? new Int32Array(n) : new Float64Array(n));
    for (var i = n; --i >= 0;)
      a[i] = me[i];
    return a; 
  }
}

if (self.Int32Array && self.Int32Array != Array) {
        Clazz.haveInt32 = true;
        if (!Int32Array.prototype.sort)
                Int32Array.prototype.sort = Array.prototype.sort
        if (!Int32Array.prototype.clone)
                Int32Array.prototype.clone = getArrayClone(32);
} else {
        Int32Array = function(n) {
                if (!n) n = 0;
                var b = new Array(n);
                b.toString = function(){return "[object Int32Array]"}
                for (var i = 0; i < n; i++)b[i] = 0
                return b;
        }
        Clazz.haveInt32 = false;
        Int32Array.prototype.sort = Array.prototype.sort
        Int32Array.prototype.clone = getArrayClone(32);
        Int32Array.prototype.int32Fake = function(){};
}

if (self.Float64Array && self.Float64Array != Array) {
        Clazz.haveFloat64 = true;
        if (!Float64Array.prototype.sort)
                Float64Array.prototype.sort = Array.prototype.sort
        if (!Float64Array.prototype.clone)
                Float64Array.prototype.clone = getArrayClone(64);
} else {
        Clazz.haveFloat64 = false;
        Float64Array = function(n) {
                if (!n) n = 0;
                var b = new Array(n);
                for (var i = 0; i < n; i++)b[i] = 0.0
                return b;
        };
        Float64Array.prototype.sort = Array.prototype.sort
        Float64Array.prototype.clone = getArrayClone(64);
        Float64Array.prototype.float64Fake = function() {}; // "present"
        Float64Array.prototype.toString = function() {return "[object Float64Array]"};
// Darn! Mozilla makes this a double, not a float. It's 64-bit.
// and Safari 5.1 doesn't have Float64Array 
}

/**
 * Make arrays.
 *
 * @return the created Array object
 */
/* public */
Clazz.newArray  = function () {
        if (arguments[0] instanceof Array) {
                // recursive, from newArray(n,m,value)
                // as newArray([m, value], newInt32Array)
                var args = arguments[0];
                var f = arguments[1];
        } else {
                var args = arguments;
                var f = Array;
        }
        var dim = args[0];
        if (typeof dim == "string") {
                dim = dim.charCodeAt (0); // char
        }
        var len = args.length - 1;
        var val = args[len];
  switch (args.length) {
  case 0: // never
  case 1:
                return []; // maybe never?
  case 2:
                if (val == null)
                return new Array(dim);
          if (f === true && Clazz.haveInt32) return new Int32Array(dim);
          if (f === false && Clazz.haveFloat64) return new Float64Array(dim);
                var arr = (f === true ? new Int32Array() : f === false ? new Float64Array() : dim < 0 ? val : new Array(dim));
                for (var i = dim; --i >= 0;)
                arr[i] = val;
          return arr;
  default:
        var xargs = new Array (len);
        for (var i = 0; i < len; i++) {
                xargs[i] = args[i + 1];
        }
        var arr = new Array (dim);
        if (val == null || val >= 0 || len > 2)
                for (var i = 0; i < dim; i++) {
                // Call recursively!
                        arr[i] = Clazz.newArray (xargs, f);
                }
        return arr;
        }
};

Clazz.newArray32 = function(args, isInt32) {
        var dim = args[0];
        if (typeof dim == "string")
                dim = dim.charCodeAt (0); // char
        var len = args.length - 1;
        var val = args[len];
        switch (args.length) {
        case 0:
        case 1:  
                alert ("ERROR IN newArray32 -- args.length < 2");
                return new Array(0);
        case 2:
    var isDefined = (dim < 0);
    if (isDefined)
      dim = val.length;
    var a = (val < 0 ? new Array(dim) : isInt32 ? new Int32Array(dim) : new Float64Array(dim));
    if (isDefined)
      for (var i = dim; --i >= 0;)
        a[i] = val[i];
    return a;
        }
        var xargs = new Array(len);
        for (var i = len; --i >= 0;) {
                xargs[i] = args[i + 1];
        }
        var arr = new Array (dim);
        for (var i = 0; i < dim; i++) {
                // Call newArray referencing this array type
                // only for the final iteration, and only if val === 0
                arr[i] = Clazz.newArray (xargs, isInt32);
        }
        return arr;
};


/**
 * Make arrays.
 *
 * @return the created Array object
 */
/* public */
Clazz.newInt32Array  = function () {
        return Clazz.newArray32(arguments, true);
}

/**
 * Make arrays.
 *
 * @return the created Array object
 */
/* public */
Clazz.newFloat64Array  = function () {
        return Clazz.newArray32(arguments, false);
}

Clazz.newFloatArray = Clazz.newDoubleArray = Clazz.newFloat64Array;
Clazz.newIntArray = Clazz.newLongArray = Clazz.newShortArray = Clazz.newByteArray = Clazz.newInt32Array;
Clazz.newCharArray = Clazz.newBooleanArray = Clazz.newArray;

//$_AI=Clazz.newIntArray;
//$_AF=Clazz.newFloatArray;
//$_AD=Clazz.newDoubleArray;
//$_AL=Clazz.newLongArray;
//$_AS=Clazz.newShortArray;
//$_AB=Clazz.newByteArray;
//$_AC=Clazz.newCharArray;
//$_Ab=Clazz.newBooleanArray;


var arrayIs = function(a, what) {
        // for some reason, Number.constructor.toString() now gives "too much recursion"
        return a.constructor && a.constructor != Number && a.constructor.toString().indexOf(what) >= 0
}

Clazz.isAS = function(a) { // just checking first parameter
        return (a && typeof a == "object" && arrayIs(a, " Array") && (typeof a[0] == "string" || typeof a[0] == "undefined"));
}

Clazz.isASS = function(a) {
        return (a && typeof a == "object" && Clazz.isAS(a[0]));
}

Clazz.isAP = function(a) {
        return (a && Clazz.getClassName(a[0]) == "JU.P3");
}

Clazz.isAI = function(a) {
        return (a && typeof a == "object" && (Clazz.haveInt32 ? arrayIs(a, "Int32Array") : a.int32Fake ? true : false));
}

Clazz.isAII = function(a) { // assumes non-null a[0]
        return (a && typeof a == "object" && Clazz.isAI(a[0]));
}

Clazz.isAF = function(a) {
        return (a && typeof a == "object" && (Clazz.haveFloat64 ? arrayIs(a, "Float64Array") : a.float64Fake ? true : false));
}

Clazz.isAFF = function(a) { // assumes non-null a[0]
        return (a && typeof a == "object" && Clazz.isAF(a[0]));
}

Clazz.isAFFF = function(a) { // assumes non-null a[0]
        return (a && typeof a == "object" && Clazz.isAFF(a[0]));
}

Clazz.isAFloat = function(a) { // just checking first parameter
        return (a && typeof a == "object" && arrayIs(a, " Array") && Clazz.instanceOf(a[0], Float));
}


/**
 * Make the RunnableCompatiability instance as a JavaScript function.
 *
 * @param jsr Instance of RunnableCompatiability
 * @return JavaScript function instance represents the method run of jsr.
 */
/* public */
/*
Clazz.makeFunction = function (jsr) {
// never used in Jmol -- called by Enum, but not accessible to it -- part of SWT
        return function(e) {
                if (!e)
                        e = window.event;
                if (jsr.setEvent)
                        jsr.setEvent(e);
                jsr.run();
                switch (jsr.returnSet) {
                case 1: 
                        return jsr.returnNumber;
                case 2:
                        return jsr.returnBoolean;
                case 3:
                        return jsr.returnObject;
                }
        };
};
*/

/* protected */
Clazz.defineStatics = function (clazz) {
        for (var j = arguments.length, i = (j - 1) / 2; --i >= 0;) {
                var val = arguments[--j]
                var name = arguments[--j];
                clazz[name] = clazz.prototype[name] = val;
        }
};

/* public */
Clazz.prepareFields = function (clazz, fieldsFun) {
        var stacks = [];
        if (clazz.con$truct) {
                var ss = clazz.con$truct.stacks;
                var idx = 0;//clazz.con$truct.index;
                for (var i = idx; i < ss.length; i++) {
                        stacks[i] = ss[i];
                }
        }
        addProto(clazz.prototype, "con$truct", clazz.con$truct = function () {
                var stacks = arguments.callee.stacks;
                if (stacks) {
                        for (var i = 0; i < stacks.length; i++) {
                                stacks[i].apply (this, []);
                        }
                }
        });
        stacks.push(fieldsFun);
        clazz.con$truct.stacks = stacks;
        clazz.con$truct.index = 0;
};

/*
 * Serialize those public or protected fields in class 
 * net.sf.j2s.ajax.SimpleSerializable.
 */
/* protected */
/*
Clazz.registerSerializableFields = function (clazz) {
        var args = arguments;
        var length = args.length;
        var newArr = [];
        if (clazz.declared$Fields) {
                for (var i = 0; i < clazz.declared$Fields.length; i++) {
                        newArr[i] = clazz.declared$Fields[i];
                }
        }
        clazz.declared$Fields = newArr;

        if (length > 0 && length % 2 == 1) {
                var fs = clazz.declared$Fields;
                var n = (length - 1) / 2;
                for (var i = 1; i <= n; i++) {
                        var o = { name : args[i + i - 1], type : args[i + i] };
                        var existed = false;
                        for (var j = 0; j < fs.length; j++) {
                                if (fs[j].name == o.name) { // reloaded classes
                                        fs[j].type = o.type; // update type
                                        existed = true;
                                        break;
                                }
                        }
                        if (!existed)
                                fs.push(o);
                }
        }
};
*/
/*
 * Get the caller method for those methods that are wrapped by 
 * Clazz.searchAndExecuteMethod.
 *
 * @param args caller method's arguments
 * @return caller method, null if there is not wrapped by 
 * Clazz.searchAndExecuteMethod or is called directly.
 */
/* protected */
/*
Clazz.getMixedCallerMethod = function (args) {
        var o = {};
        var argc = args.callee.caller; // tryToSearchAndExecute
        if (argc && argc !== tryToSearchAndExecute) // inherited method's apply
                argc = argc.arguments.callee.caller;
        if (argc !== tryToSearchAndExecute
                || (argc = argc.arguments.callee.caller) !== Clazz.searchAndExecuteMethod)
                return null;
        o.claxxRef = argc.arguments[1];
        o.fxName = argc.arguments[2];
        o.paramTypes = Clazz.getParamsType(argc.arguments[3]);  
        argc = argc.arguments.callee.caller // Clazz.generateDelegatingMethod 
                                        && argc.arguments.callee.caller; // the private method's caller
        if (!argc)
                return null;
        o.caller = argc;
        return o;
};
*/
/* BH -- The issue here is a subclass calling its private method FOO when
 *       there is also a private method of the same name in its super class.
 *       This can ALWAYS be avoided and, one could argue, is bad 
 *       program design anyway. In Jmol, the presence of this possibility
 *       creates over 8000 references to the global $fx, which was only
 *       checked in a few rare cases. We can then also remove $fz references.
 *         
 */

/*
 * Check and return super private method.
 * In order make private methods be executed correctly, some extra javascript
 * must be inserted into the beggining of the method body of the non-private 
 * methods that with the same method signature as following:
 * <code>
 *                      var $private = Clazz.checkPrivateMethod (arguments);
 *                      if ($private) {
 *                              return $private.apply (this, arguments);
 *                      }
 * </code>
 * Be cautious about this. The above codes should be insert by Java2Script
 * compiler or with double checks to make sure things work correctly.
 *
 * @param args caller method's arguments
 * @return private method if there are private method fitted for the current 
 * calling environment
 */
/* public */

/*** BH
Clazz.checkPrivateMethod = function (args) {
        var m = Clazz.getMixedCallerMethod (args);
        if (m == null) return null;
        var callerFx = m.claxxRef.prototype[m.caller.exName];
        if (callerFx == null) return null; // may not be in the class hierarchies
        var ppFun = null;
        if (callerFx.claxxOwner ) {
                ppFun = callerFx.claxxOwner.prototype[m.fxName];
        } else {
                var stacks = callerFx.stacks;
                for (var i = stacks.length - 1; i >= 0; i--) {
                        var fx = stacks[i].prototype[m.caller.exName];
                        if (fx === m.caller) {
                                ppFun = stacks[i].prototype[m.fxName];
                        } else if (fx ) {
                                for (var fn in fx) {
                                        if (fn.indexOf ('\\') == 0 && fx[fn] === m.caller) {
                                                ppFun = stacks[i].prototype[m.fxName];
                                                break;
                                        }
                                }
                        }
                        if (ppFun) {
                                break;
                        }
                }
        }
        if (ppFun && ppFun.claxxOwner == null) {
                ppFun = ppFun["\\" + m.paramTypes];
        }
        if (ppFun && ppFun.isPrivate && ppFun !== args.callee) {
                return ppFun;
        }
        return null;
};
*****/


//$fz = null; // for private method declaration


// /*# {$no.debug.support} >>x #*/
// /*
//  * Option to switch on/off of stack traces.
//  */
// /* protect */
//Clazz.tracingCalling = false;

// /* private */
// Clazz.callingStack = function (caller, owner) {
//      this.caller = caller;
//      this.owner = owner;
// };

/*# x<< #*/

/**
 * The first folder is considered as the primary folder.
 * And try to be compatiable with _Loader system.
 */
/* private */


/*** not used in Jmol
 * *
if (window["_Loader"] && _Loader.binaryFolders) {
        Clazz.binaryFolders = _Loader.binaryFolders;
} else {
        Clazz.binaryFolders = ["j2s/", "", "j2slib/"];
}

Clazz.addBinaryFolder = function (bin) {
        if (bin) {
                var bins = Clazz.binaryFolders;
                for (var i = 0; i < bins.length; i++) {
                        if (bins[i] == bin) {
                                return ;
                        }
                }
                bins[bins.length] = bin;
        }
};
Clazz.removeBinaryFolder = function (bin) {
        if (bin) {
                var bins = Clazz.binaryFolders;
                for (var i = 0; i < bins.length; i++) {
                        if (bins[i] == bin) {
                                for (var j = i; j < bins.length - 1; j++) {
                                        bins[j] = bins[j + 1];
                                }
                                bins.length--;
                                return bin;
                        }
                }
        }
        return null;
};
Clazz.setPrimaryFolder = function (bin) {
        if (bin) {
                Clazz.removeBinaryFolder (bin);
                var bins = Clazz.binaryFolders;
                for (var i = bins.length - 1; i >= 0; i--) {
                        bins[i + 1] = bins[i];
                }
                bins[0] = bin;
        }
};

***/


///////////////// special definitions of standard Java class methods ///////////

/**
 * This is a simple implementation for Clazz#load. It just ignore dependencies
 * of the class. This will be fine for jar *.z.js file.
 * It will be overriden by _Loader#load.
 * For more details, see _Loader.js
 */
/* protected */
/*
Clazz.load = function (musts, clazz, optionals, declaration) {
        // not used in Jmol
        if (declaration)
                declaration ();
};
*/

/*
 * Invade the Object prototype!
 * TODO: make sure that invading Object prototype does not affect other
 * existed library, such as Dojo, YUI, Prototype, ...
 */
java.lang.Object = Clazz._O;

Clazz._O.getName = Clazz._innerFunctions.getName;


System = {
        props : null, //new java.util.Properties (),
        $props : {},
        arraycopy : function (src, srcPos, dest, destPos, length) {
                if (src !== dest) {
                        for (var i = 0; i < length; i++) {
                                dest[destPos + i] = src[srcPos + i];
                        }
                } else {
                        var swap = [];
                        for (var i = 0; i < length; i++) {
                                swap[i] = src[srcPos + i];
                        }
                        for (var i = 0; i < length; i++) {
                                dest[destPos + i] = swap[i];
                        }
                }
        },
        currentTimeMillis : function () {
                return new Date ().getTime ();
        },
        gc : function() {}, // bh
        getProperties : function () {
                return System.props;
        },
        getProperty : function (key, def) {
                if (System.props)
                        return System.props.getProperty (key, def);
                var v = System.$props[key];
    
                return (typeof v != "undefined" ? v : arguments.length == 1 ? null : def == null ? key : def); // BH
        },
        getSecurityManager : function() { return null },  // bh
        setProperties : function (props) {
                System.props = props;
        },
  lineSeparator : function() { return '\n' }, // bh
        setProperty : function (key, val) {
                if (!System.props)
                        return System.$props[key] = val; // BH
                System.props.setProperty (key, val);
        }
};

System.setProperty("line.separator", navigator.userAgent.indexOf("Windows")>=0?"\r\n" : "\n") //BH
System.setProperty("os.name", navigator.userAgent) //BH
System.identityHashCode=function(obj){
  if(obj==null)
    return 0;
    
        return obj._$hashcode || (obj._$hashcode = ++Clazz._hashCode)

/*    
  try{
    return obj.toString().hashCode();
  }catch(e){
    var str=":";
    for(var s in obj){
     str+=s+":"
    }
    return str.hashCode();
  }
*/  
}

System.out = new Clazz._O ();
System.out.__CLASS_NAME__ = "java.io.PrintStream";
System.out.print = function () {};
System.out.printf = function () {};
System.out.println = function () {};
System.out.write = function () {};

System.err = new Clazz._O ();
System.err.__CLASS_NAME__ = "java.io.PrintStream";
System.err.print = function () {};
System.err.printf = function () {};
System.err.println = function () {};
System.err.write = function () {};

Clazz.popup = Clazz.assert = Clazz.log = Clazz.error = window.alert;

Thread = function () {};
Thread.J2S_THREAD = Thread.prototype.J2S_THREAD = new Thread ();
Thread.currentThread = Thread.prototype.currentThread = function () {
        return this.J2S_THREAD;
};

/* not used in Jmol
Clazz.intCast = function (n) { // 32bit
        var b1 = (n & 0xff000000) >> 24;
        var b2 = (n & 0xff0000) >> 16;
        var b3 = (n & 0xff00) >> 8;
        var b4 = n & 0xff;
        if ((b1 & 0x80) != 0) {
                return -(((b1 & 0x7f) << 24) + (b2 << 16) + (b3 << 8) + b4 + 1);
        } else {
                return (b1 << 24) + (b2 << 16) + (b3 << 8) + b4;
        }
};
Clazz.shortCast = function (s) { // 16bit
        var b1 = (n & 0xff00) >> 8;
        var b2 = n & 0xff;
        if ((b1 & 0x80) != 0) {
                return -(((b1 & 0x7f) << 8) + b2 + 1);
        } else {
                return (b1 << 8) + b4;
        }
};

Clazz.byteCast = function (b) { // 8bit
        if ((b & 0x80) != 0) {
                return -((b & 0x7f) + 1);
        } else {
                return b & 0xff;
        }
};

Clazz.charCast = function (c) { // 8bit
        return String.fromCharCode (c & 0xff).charAt (0);
};

Clazz.floatCast = function (f) { // 32bit
        return f;
};

*/


/*
 * Try to fix JavaScript's shift operator defects on long type numbers.
 */

/* not used in Jmol

Clazz.longMasks = [];

Clazz.longReverseMasks = [];

Clazz.longBits = [];

;(function () {
        var arr = [1];
        for (var i = 1; i < 53; i++) {
                arr[i] = arr[i - 1] + arr[i - 1]; // * 2 or << 1
        }
        Clazz.longBits = arr;
        Clazz.longMasks[52] = arr[52];
        for (var i = 51; i >= 0; i--) {
                Clazz.longMasks[i] = Clazz.longMasks[i + 1] + arr[i];
        }
        Clazz.longReverseMasks[0] = arr[0];
        for (var i = 1; i < 52; i++) {
                Clazz.longReverseMasks[i] = Clazz.longReverseMasks[i - 1] + arr[i];
        }
}) ();


Clazz.longLeftShift = function (l, o) { // 64bit
        if (o == 0) return l;
        if (o >= 64) return 0;
        if (o > 52) {
                error ("[Java2Script] Error : JavaScript does not support long shift!");
                return l;
        }
        if ((l & Clazz.longMasks[o - 1]) != 0) {
                error ("[Java2Script] Error : Such shift operator results in wrong calculation!");
                return l;
        }
        var high = l & Clazz.longMasks[52 - 32 + o];
        if (high != 0) {
                return high * Clazz.longBits[o] + (l & Clazz.longReverseMasks[32 - o]) << 0;
        } else {
                return l << o;
        }
};

Clazz.intLeftShift = function (n, o) { // 32bit
        return (n << o) & 0xffffffff;
};

Clazz.longRightShift = function (l, o) { // 64bit
        if ((l & Clazz.longMasks[52 - 32]) != 0) {
                return Math.round((l & Clazz.longMasks[52 - 32]) / Clazz.longBits[32 - o]) + (l & Clazz.longReverseMasks[o]) >> o;
        } else {
                return l >> o;
        }
};

Clazz.intRightShift = function (n, o) { // 32bit
        return n >> o; // no needs for this shifting wrapper
};

Clazz.long0RightShift = function (l, o) { // 64bit
        return l >>> o;
};

Clazz.int0RightShift = function (n, o) { // 64bit
        return n >>> o; // no needs for this shifting wrapper
};

*/
// Compress the common public API method in shorter name
//$_L=Clazz.load;
//$_W=Clazz.declareAnonymous;$_T=Clazz.declareType;
//$_J=Clazz.declarePackage;$_C=Clazz.decorateAsClass;
//$_Z=Clazz.instantialize;$_I=Clazz.declareInterface;$_D=Clazz.isClassDefined;
//$_H=Clazz.pu$h;$_P=Clazz.p0p;$_B=Clazz.prepareCallback;
//$_N=Clazz.innerTypeInstance;$_K=Clazz.makeConstructor;$_U=Clazz.superCall;$_R=Clazz.superConstructor;
//$_M=Clazz.defineMethod;$_V=Clazz.overrideMethod;$_S=Clazz.defineStatics;
//$_E=Clazz.defineEnumConstant;
//$_F=Clazz.cloneFinals;
//$_Y=Clazz.prepareFields;$_A=Clazz.newArray;$_O=Clazz.instanceOf;
//$_G=Clazz.inheritArgs;$_X=Clazz.checkPrivateMethod;$_Q=Clazz.makeFunction;
//$_s=Clazz.registerSerializableFields;
//$_k=Clazz.overrideConstructor;


/////////////////////// inner function support /////////////////////////////////

/* public */
Clazz.innerFunctionNames = Clazz.innerFunctionNames.concat ([
    "getSuperclass", "isAssignableFrom", 
    "getConstructor", 
    "getDeclaredMethod", "getDeclaredMethods",
    "getMethod", "getMethods",   
                "getModifiers", /*"isArray",*/ "newInstance"]);

/* public */
Clazz._innerFunctions.getSuperclass = function () {
        return this.superClazz; 
};

/* public */
Clazz._innerFunctions.isAssignableFrom = function (clazz) {
        return Clazz.getInheritedLevel (clazz, this) >= 0;      
};

/* public */
Clazz._innerFunctions.getConstructor = function () {
        return new java.lang.reflect.Constructor (this, [], [], 
                        java.lang.reflect.Modifier.PUBLIC);
};
/**
 * TODO: fix bug for polymorphic methods!
 */
/* public */
Clazz._innerFunctions.getDeclaredMethods = Clazz._innerFunctions.getMethods = function () {
        var ms = [];
        var p = this.prototype;
        for (var attr in p) {
                if (typeof p[attr] == "function" && !p[attr].__CLASS_NAME__) {
                        /* there are polynormical methods. */
                        ms.push(new java.lang.reflect.Method (this, attr,
                                        [], java.lang.Void, [], java.lang.reflect.Modifier.PUBLIC));
                }
        }
        p = this;
        for (var attr in p) {
                if (typeof p[attr] == "function" && !p[attr].__CLASS_NAME__) {
                        ms.push(new java.lang.reflect.Method (this, attr,
                                        [], java.lang.Void, [], java.lang.reflect.Modifier.PUBLIC
                                        | java.lang.reflect.Modifier.STATIC));
                }
        }
        return ms;
};
/* public */
Clazz._innerFunctions.getDeclaredMethod = Clazz._innerFunctions.getMethod = function (name, clazzes) {
        var p = this.prototype;
        for (var attr in p) {
                if (name == attr && typeof p[attr] == "function" 
                                && !p[attr].__CLASS_NAME__) {
                        /* there are polynormical methods. */
                        return new java.lang.reflect.Method (this, attr,
                                        [], java.lang.Void, [], java.lang.reflect.Modifier.PUBLIC);
                }
        }
        p = this;
        for (var attr in p) {
                if (name == attr && typeof p[attr] == "function" 
                                && !p[attr].__CLASS_NAME__) {
                        return new java.lang.reflect.Method (this, attr,
                                        [], java.lang.Void, [], java.lang.reflect.Modifier.PUBLIC
                                        | java.lang.reflect.Modifier.STATIC);
                }
        }
        return null;
};
/* public */
Clazz._innerFunctions.getModifiers = function () {
        return java.lang.reflect.Modifier.PUBLIC;
};

Clazz._innerFunctions.newInstance = function (a) {
        var clz = this;
  switch(a == null ? 0 : a.length) {
  case 0:
    return new clz();
  case 1:
        return new clz(a[0]);
  case 2:
        return new clz(a[0], a[1]);
  case 3:
        return new clz(a[0], a[1], a[2]);
  case 4:
        return new clz(a[0], a[1], a[2], a[3]);
  default:
    var x = "new " + clz.__CLASS_NAME__ + "(";
    for (var i = 0; i < a.length; i++)
     x += (i == 0 ? "" : ",") + "a[" + i + "]";
    x += ")";
    return eval(x);
  }
};

//Object.newInstance = Clazz._innerFunctions.newInstance;
;(function(){  // BH added wrapper here
        var inF = Clazz.innerFunctionNames;
        for (var i = 0; i < inF.length; i++) {
                Clazz._O[inF[i]] = Clazz._innerFunctions[inF[i]];
                Array[inF[i]] = Clazz._innerFunctions[inF[i]];
        }
        //Array["isArray"] = function () {
        //      return true;
        //};
})();

//////////////////////////// hotspot and unloading /////////////////////////////
/* For hotspot and unloading */

if (window["Clazz"] && !window["Clazz"].unloadClass) {

/* public */
Clazz.unloadClass = function (qClazzName) {
        var cc = Clazz.evalType (qClazzName);
        if (cc) {
                Clazz.unloadedClasses[qClazzName] = cc;
                var clazzName = qClazzName;
                var pkgFrags = clazzName.split (/\./);
                var pkg = null;
                for (var i = 0; i < pkgFrags.length - 1; i++)
                        pkg = (pkg ? pkg[pkgFrags[i]] : Clazz.allPackage[pkgFrags[0]]);
                if (!pkg) {
                        Clazz.allPackage[pkgFrags[0]] = null;
                        window[pkgFrags[0]] = null;
                        // also try to unload inner or anonymous classes
                        for (var c in window) {
                                if (c.indexOf (qClazzName + "$") == 0) {
                                        Clazz.unloadClass (c);
                                        window[c] = null;
                                }
                        }
                } else {
                        pkg[pkgFrags[pkgFrags.length - 1]] = null;
                        // also try to unload inner or anonymous classes
                        for (var c in pkg) {
                                if (c.indexOf (pkgFrags[pkgFrags.length - 1] + "$") == 0) {
                                        Clazz.unloadClass (pkg.__PKG_NAME__ + "." + c);
                                        pkg[c] = null;
                                }
                        }
                }

                if (Clazz.allClasses[qClazzName]) {
                        Clazz.allClasses[qClazzName] = false;
                        // also try to unload inner or anonymous classes
                        for (var c in Clazz.allClasses) {
                                if (c.indexOf (qClazzName + "$") == 0) {
                                        Clazz.allClasses[c] = false;
                                }
                        }
                }

                for (var m in cc) {
                        cleanDelegateMethod (cc[m]);
                }
                for (var m in cc.prototype) {
                        cleanDelegateMethod (cc.prototype[m]);
                }

                if (Clazz._Loader) {
                        Clazz._Loader.unloadClassExt(qClazzName);
                }

                return true;
        }
        return false;
};

/* private */
var cleanDelegateMethod = function (m) {
        if (!m) 
                return;
        if (typeof m == "function" && m.lastMethod
                        && m.lastParams && m.lastClaxxRef) {
                m.lastMethod = null;
                m.lastParams = null;
                m.lastClaxxRef = null;
        }
};

} // if (window["Clazz"] && !window["Clazz"].unloadClass)

/******************************************************************************
 * Copyright (c) 2007 java2script.org and others.
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 *     Zhou Renjian - initial API and implementation
 *****************************************************************************/
/*******
 * @author zhou renjian
 * @create July 10, 2006
 *******/

//if (window["ClazzNode"] == null) {
/**
 * TODO:
 * Make optimization over class dependency tree.
 */

/*
 * ClassLoader Summary
 * 
 * ClassLoader creates SCRIPT elements and setup class path and onload 
 * callback to continue class loading.
 *
 * In the onload callbacks, _Loader will try to calculate the next-to-be-
 * load *.js and load it. In *.js, it will contains some codes like
 * Clazz.load (..., "$wt.widgets.Control", ...);
 * to provide information to build up the class dependency tree.
 *
 * Some known problems of different browsers:
 * 1. In IE, loading *.js through SCRIPT will first triggers onreadstatechange 
 * event, and then executes inner *.js source.
 * 2. In Firefox, loading *.js will first executes *.js source and then 
 * triggers onload event.
 * 3. In Opera, similar to IE, but trigger onload event. (TODO: More details 
 * should be studied. Currently, Opera supports no multiple-thread-loading)
 * 
 * For class dependency tree, actually, it is not a tree. It is a reference
 * net with nodes have n parents and n children. There is a root, which 
 * ClassLoader knows where to start searching and loading classes, for such
 * a net. Each node is a class. Each class may require a set of must-classes, 
 * which must be loaded before itself getting initialized, and also need a set
 * of optional classes, which also be loaded before being called.
 *
 * The class loading status will be in 6 stages.
 * 1. Unknown, the class is newly introduced by other class.
 * 2. Known, the class is already mentioned by other class.
 * 3. Loaded, *.js source is in memory, but may not be initialized yet. It 
 * requires all its must-classes be intiailized, which is in the next stage.
 * 4. Musts loaded, all must classes is already loaded and declared.
 * 5. Delcared, the class is already declared (_Loader#isClassDefined).
 * 6. Optionals loaded, all optional classes is loaded and declared.
 *
 * The ClassLoader tries to load all necessary classes in order, and intialize
 * them in order. For such job, it will traverse the dependency tree, and try 
 * to next class to-be-loaded. Sometime, the class dependencies may be in one
 * or more cycles, which must be broken down so classes is loaded in correct
 * order.
 *
 * Loading order and intializing order is very important for the ClassLoader.
 * The following technical options are considered:
 * 1. SCRIPT is loading asynchronously, which means controling order must use
 * callback methods to continue.
 * 2. Multiple loading threads are later introduced, which requires the 
 * ClassLoader should use variables to record the class status.
 * 3. Different browsers have different loading orders, which means extra tests
 * should be tested to make sure loading order won't be broken.
 * 4. Java2Script simulator itself have some loading orders that must be 
 * honored, which means it should be integrated seamlessly to Clazz system.
 * 5. Packed *.z.js is introduced to avoid lots of small *.js which requires 
 * lots of HTTP connections, which means that packed *.z.js should be treated
 * specially (There will be mappings for such packed classes).
 * 6. *.js or *.css loading may fail according to network status, which means
 * another loading try should be performed, so _Loader is more robust.
 * 7. SWT lazy loading is later introduced, which means that class loading
 * process may be paused and should be resumed later.
 *
 * Some known bugs:
 * <code>$_L(["$wt.graphics.Drawable","$wt.widgets.Widget"],
 *  "$wt.widgets.Control", ...</code>
 * has errors while must classes in different order such as
 * <code>$_L(["$wt.widgets.Widget", "$wt.graphics.Drawable"],
 *  "$wt.widgets.Control", ...</code>
 * has no error.
 * 
 * Other maybe bug scenarios:
 * 1. In <code>_Loader.maxLoadingThreads = 1;</code> single loading thread 
 * mode, there are no errors, but in default multiple thread loading mode, 
 * there are errors.
 * 2. No errors in one browser, but has errors on other browsers (Browser 
 * script loading order differences).
 * 3. First time loading has errors, but reloading it gets no errors (Maybe 
 * HTTP connections timeout, but should not accur in local file system, or it
 * is a loading bug by using JavaScript timeout thread).
 */

/*
 * The following comments with "#" are special configurations for a much
 * smaller *.js file size.
 *
 * @see net.sf.j2s.lib/src/net/sf/j2s/lib/build/SmartJSCompressor.java
 */
/**
 * Static class loader class
 */
Clazz._Loader = Clazz.ClazzLoader = function () {};

/**
 * Class dependency tree node
 */
/* private */
var Node = function () {
        this.parents = [];
        this.musts = [];
        this.optionals = [];
        this.declaration = null;
        this.name = null; // id
        this.path = null;
//      this.requires = null;
//      this.requiresMap = null;
        this.onLoaded = null;
        this.status = 0;
        this.random = 0.13412;
};


;(function(Clazz, _Loader) {

_Loader._checkLoad = Jmol._checkLoad;
 
_Loader.updateNodeForFunctionDecoration = function(qName) {
        var node = findNode(qName);
        if (node && node.status == Node.STATUS_KNOWN) {
                window.setTimeout((function(nnn) {
                        return function() {
                                updateNode(nnn);
                        };
                })(node), 1);
        }
}

Node.prototype.toString = function() {
        return this.name || this.path || "ClazzNode";
}

Node.STATUS_UNKNOWN = 0;
Node.STATUS_KNOWN = 1;
Node.STATUS_CONTENT_LOADED = 2;
Node.STATUS_MUSTS_LOADED = 3;
Node.STATUS_DECLARED = 4;
Node.STATUS_LOAD_COMPLETE = 5;

                                                 
var loaders = [];

/* public */
_Loader.requireLoaderByBase = function (base) {
        for (var i = 0; i < loaders.length; i++) {
                if (loaders[i].base == base) {
                        return loaders[i];
                }
        }
        var loader = new _Loader ();
        loader.base = base; 
        loaders.push(loader);
        return loader;
};

/**
 * Class dependency tree
 */
var clazzTreeRoot = new Node();

/**
 * Used to keep the status whether a given *.js path is loaded or not.
 */
/* private */
var loadedScripts = {};

/**
 * Multiple threads are used to speed up *.js loading.
 */
/* private */
var inLoadingThreads = 0;

/**
 * Maximum of loading threads
 */
/* private */
var maxLoadingThreads = 6;

var userAgent = navigator.userAgent.toLowerCase ();
var isOpera = (userAgent.indexOf ("opera") != -1);
var isIE = (userAgent.indexOf ("msie") != -1) && !isOpera;
var isGecko = (userAgent.indexOf ("gecko") != -1);

/*
 * Opera has different loading order which will result in performance degrade!
 * So just return to single thread loading in Opera!
 *
 * FIXME: This different loading order also causes bugs in single thread!
 */
if (isOpera) {
        maxLoadingThreads = 1;
        var index = userAgent.indexOf ("opera/");
        if (index != -1) {
                var verNumber = 9.0;
                try {
                        verNumber = parseFloat(userAgent.subString (index + 6));
                } catch (e) {}
                if (verNumber >= 9.6) {
                        maxLoadingThreads = 6;
                }
        } 
}

/**
 * Try to be compatiable with Clazz system.
 * In original design _Loader and Clazz are independent!
 *  -- zhourenjian @ December 23, 2006
 */
var isClassdefined;
var definedClasses;

if (self.Clazz && Clazz.isClassDefined) {
        isClassDefined = Clazz.isClassDefined;
} else {
        definedClasses = {};
        isClassDefined = function (clazzName) {
                return definedClasses[clazzName] == true;
        };
}

/**
 * Expand the shortened list of class names.
 * For example:
 * JU.Log, $.Display, $.Decorations
 * will be expanded to 
 * JU.Log, JU.Display, JU.Decorations
 * where "$." stands for the previous class name's package.
 *
 * This method will be used to unwrap the required/optional classes list and 
 * the ignored classes list.
 */
/* private */
var unwrapArray = function (arr) {
        if (!arr || arr.length == 0)
                return [];
        var last = null;
        for (var i = 0; i < arr.length; i++) {
                if (!arr[i])
                        continue;
                if (arr[i].charAt (0) == '$') {
                        if (arr[i].charAt (1) == '.') {
                                if (!last)
                                        continue;
                                var idx = last.lastIndexOf (".");
                                if (idx != -1) {
                                        var prefix = last.substring (0, idx);
                                        arr[i] = prefix + arr[i].substring (1);
                                }
                        } else {
                                arr[i] = "org.eclipse.s" + arr[i].substring (1);
                        }
                }
                last = arr[i];
        }
        return arr;
};

/**
 * Used to keep to-be-loaded classes.
 */
/* private */
var classQueue = [];

/* private */
var classpathMap = {};

/* private */
var pkgRefCount = 0;

/* public */
_Loader.loadPackageClasspath = function (pkg, base, isIndex, fSuccess, mode, pt) {
        var map = classpathMap;
        mode || (mode = 0);
        fSuccess || (fSuccess = null);
        pt || (pt = 0);

        /*
         * In some situation, maybe,
         * _Loader.packageClasspath ("java", ..., true);
         * is called after other _Loader#packageClasspath, e.g.
         * <code>
         * _Loader.packageClasspath ("org.eclipse.swt", "...", true);
         * _Loader.packageClasspath ("java", "...", true);
         * </code>
         * which is not recommended. But _Loader should try to adjust orders
         * which requires "java" to be declared before normal _Loader
         * #packageClasspath call before that line! And later that line
         * should never initialize "java/package.js" again!
         */
        var isPkgDeclared = (isIndex && map["@" + pkg]);
        if (mode == 0 && isIndex && !map["@java"] && pkg.indexOf ("java") != 0 && needPackage("java")) {
                _Loader.loadPackage("java", fSuccess ? function(_package){_Loader.loadPackageClasspath(pkg, base, isIndex, fSuccess, 1)} : null);
                if (fSuccess)
                        return;
        }
        if (pkg instanceof Array) {
                unwrapArray(pkg);
                if (fSuccess) {
                        if (pt < pkg.length)
                                _Loader.loadPackageClasspath(pkg[pt], base, isIndex, function(_loadPackageClassPath){_Loader.loadPackageClasspath(pkg, base, isIndex, fSuccess, 1, pt + 1)}, 1);
                        else
                                fSuccess();
                } else {
                        for (var i = 0; i < pkg.length; i++)
                                _Loader.loadPackageClasspath(pkg[i], base, isIndex, null);
                }
                return;
        }
        switch (pkg) {
        case "java.*":
                pkg = "java";
                // fall through
        case "java":
                if (base) {
                        // support ajax for default
                        var key = "@net.sf.j2s.ajax";
                        if (!map[key])
                                map[key] = base;
                        key = "@net.sf.j2s";
                        if (!map[key])
                                map[key] = base;
                }               
                break;
        case "swt":
                pkg = "org.eclipse.swt";
                break;
        case "ajax":
                pkg = "net.sf.j2s.ajax";
                break;
        case "j2s":
                pkg = "net.sf.j2s";
                break;
        default:
                if (pkg.lastIndexOf(".*") == pkg.length - 2)
                        pkg = pkg.substring(0, pkg.length - 2);
                break;
        }
        if (base) // critical for multiple applets
                map["@" + pkg] = base;
        if (isIndex && !isPkgDeclared && !window[pkg + ".registered"]) {
                pkgRefCount++;
                if (pkg == "java")
                        pkg = "core" // JSmol -- moves java/package.js to core/package.js
                _Loader.loadClass(pkg + ".package", function () {
                                        if (--pkgRefCount == 0)
                                                runtimeLoaded();
                                        //fSuccess && fSuccess();
                                }, true, true, 1);
                return;
        }
        fSuccess && fSuccess();
};

/**
 * BH: allows user/developer to load classes even though wrapping and Google
 * Closure Compiler has not been run on the class.
 *   
 */
Clazz.loadClass = function (name, onLoaded, async) {
  if (!self.Class) {
    Class = Clazz;
    Class.forName = Clazz._4Name;
    JavaObject = Clazz._O;
    // maybe more here
  }
  return (name && _Loader.loadClass(name, onLoaded, true, async, 1));
}

/**
 * Load the given class ant its related classes.
 */
/* public */
_Loader.loadClass = function (name, onLoaded, forced, async, mode) {

  mode || (mode = 0); // BH: not implemented
  (async == null) && (async = false);
  
        if (typeof onLoaded == "boolean")
                return Clazz.evalType(name);

  System.out.println("loadClass " + name)

        // Make sure that packageClasspath ("java", base, true); 
        // is called before any _Loader#loadClass is called.

        if (needPackage("java"))
                _Loader.loadPackage("java");
        if (needPackage("core"))
                _Loader.loadPackage("core");    

//      var swtPkg = "org.eclipse.swt";
//      if (name.indexOf (swtPkg) == 0 || name.indexOf ("$wt") == 0) {
//              _Loader.assurePackageClasspath (swtPkg);
//      }
//      if (name.indexOf ("junit") == 0) {
//              _Loader.assurePackageClasspath ("junit");
//      }

        // Any _Loader#loadClass calls will be queued until java.* core classes are loaded.

        _Loader.keepOnLoading = true;
        
        if (!forced && (pkgRefCount && name.lastIndexOf(".package") != name.length - 8
                        || name.indexOf("java.") != 0 && !isClassDefined(runtimeKeyClass)
                 )) {   
                queueBe4KeyClazz.push([name, onLoaded]);
    
    
  System.out.println("loadclass-queuing" + name+ runtimeKeyClass + " "+ isClassDefined(runtimeKeyClass))

                return;    
        }
        var b;
        if ((b = isClassDefined(name)) || isClassExcluded(name)) {
                if (b && onLoaded) {
                        var nn = findNode(name);
                        if (!nn || nn.status >= Node.STATUS_LOAD_COMPLETE) {
                                if (async) {
                                        window.setTimeout(onLoaded, 25);
                                } else {
                                        onLoaded();
                                }
                        }
                }
                return;
        }
        var path = _Loader.getClasspathFor(name);
  var existed = loadedScripts[path];
        var qq = classQueue;
        if (!existed)
                for (var i = qq.length; --i >= 0;)
                        if (qq[i].path == path || qq[i].name == name) {
                                existed = true;
                                break;
                        }
        if (existed) {
                if (onLoaded) {
                        var n = findNode(name);
                        if (n) {
                                if (!n.onLoaded) {
                                        n.onLoaded = onLoaded;
                                } else if (onLoaded != n.onLoaded) {
                                        n.onLoaded = (function (nF, oF) { return function () { nF(); oF() };    }) (n.onLoaded, onLoaded);
                                }
                        }
                }
                return;
        }

        var n = (Clazz.unloadedClasses[name] && findNode(name) || new Node());
        n.name = name;
        n.path = path;
        n.isPackage = (path.lastIndexOf("package.js") == path.length - 10);
        mappingPathNameNode(path, name, n);
        n.onLoaded = onLoaded;
        n.status = Node.STATUS_KNOWN;
        var needBeingQueued = false;
        for (var i = qq.length; --i >= 0;) {
                if (qq[i].status != Node.STATUS_LOAD_COMPLETE) {
                        needBeingQueued = true;
                        break;
                }
        }
        
        if (n.isPackage) {//forced
                // push class to queue
                var pt = qq.length;
                for (; --pt >= 0;) {
                        if (qq[pt].isPackage) 
                                break;
                        qq[pt + 1] = qq[pt];
                }
                qq[++pt] = n;
        } else if (needBeingQueued) {
                qq.push(n);
        }
        if (!needBeingQueued) { // can be loaded directly
                var bSave = false;
                if (onLoaded) { 
                        bSave = isLoadingEntryClass;
                        isLoadingEntryClass = true;
                }
    if (forced)onLoaded = null;
                addChildClassNode(clazzTreeRoot, n, true);
                loadScript(n, n.path, n.requiredBy, false, onLoaded ? function(_loadClass){ isLoadingEntryClass = bSave; onLoaded()}: null);
        }
};

/*
 * Check whether given package's classpath is setup or not.
 * Only "java" and "org.eclipse.swt" are accepted in argument.
 */
/* private */
var needPackage = function(pkg) {
  // note that false != null and true != null
        return (window[pkg + ".registered"] != null && !classpathMap["@" + pkg]);
}

/* private */
_Loader.loadPackage = function(pkg, fSuccess) {
        fSuccess || (fSuccess = null);
        window[pkg + ".registered"] = false;
        _Loader.loadPackageClasspath(pkg, 
                (_Loader.J2SLibBase || (_Loader.J2SLibBase = (_Loader.getJ2SLibBase() || "j2s/"))), 
                true, fSuccess);
};

/**
 * Register classes to a given *.z.js path, so only a single *.z.js is loaded
 * for all those classes.
 */
/* public */
_Loader.jarClasspath = function (jar, clazzes) {
        if (!(clazzes instanceof Array))
                clazzes = [classes];
        unwrapArray(clazzes);
        for (var i = clazzes.length; --i >= 0;)
                classpathMap["#" + clazzes[i]] = jar;
        classpathMap["$" + jar] = clazzes;
};

/**
 * Usually be used in .../package.js. All given packages will be registered
 * to the same classpath of given prefix package.
 */
/* public */
_Loader.registerPackages = function (prefix, pkgs) {
        //_Loader.checkInteractive ();
        var base = _Loader.getClasspathFor (prefix + ".*", true);
        for (var i = 0; i < pkgs.length; i++) {
                if (window["Clazz"]) {
                        Clazz.declarePackage (prefix + "." + pkgs[i]);
                }
                _Loader.loadPackageClasspath (prefix + "." + pkgs[i], base);
        }
};

/**
 * Using multiple sites to load *.js in multiple threads. Using multiple
 * sites may avoid 2 HTTP 1.1 connections recommendation limit.
 * Here is a default implementation for http://archive.java2script.org.
 * In site archive.java2script.org, there are 6 sites:
 * 1. http://archive.java2script.org or http://a.java2script.org
 * 2. http://erchive.java2script.org or http://e.java2script.org
 * 3. http://irchive.java2script.org or http://i.java2script.org
 * 4. http://orchive.java2script.org or http://o.java2script.org
 * 5. http://urchive.java2script.org or http://u.java2script.org
 * 6. http://yrchive.java2script.org or http://y.java2script.org
 */
/* protected */
        /*
_Loader.multipleSites = function (path) {
        var deltas = window["j2s.update.delta"];
        if (deltas && deltas instanceof Array && deltas.length >= 3) {
                var lastOldVersion = null;
                var lastNewVersion = null;
                for (var i = 0; i < deltas.length / 3; i++) {
                        var oldVersion = deltas[i + i + i];
                        if (oldVersion != "$") {
                                lastOldVersion = oldVersion;
                        }
                        var newVersion = deltas[i + i + i + 1];
                        if (newVersion != "$") {
                                lastNewVersion = newVersion;
                        }
                        var relativePath = deltas[i + i + i + 2];
                        var key = lastOldVersion + "/" + relativePath;
                        var idx = path.indexOf (key);
                        if (idx != -1 && idx == path.length - key.length) {
                                path = path.substring (0, idx) + lastNewVersion + "/" + relativePath;
                                break;
                        }
                }
        }
        var length = path.length;
        if (maxLoadingThreads > 1 
                        && ((length > 15 && path.substring (0, 15) == "http://archive.")
                        || (length > 9 && path.substring (0, 9) == "http://a."))) {
                var index = path.lastIndexOf("/");
                if (index < length - 3) {
                        var arr = ['a', 'e', 'i', 'o', 'u', 'y'];
                        var c1 = path.charCodeAt (index + 1);
                        var c2 = path.charCodeAt (index + 2);
                        var idx = (length - index) * 3 + c1 * 5 + c2 * 7; // Hash
                        return path.substring (0, 7) + arr[idx % 6] + path.substring (8);
                }
        }
        return path;
};
        */

/**
 * Return the *.js path of the given class. Maybe the class is contained
 * in a *.z.js jar file.
 * @param clazz Given class that the path is to be calculated for. May
 * be java.package, or java.lang.String
 * @param forRoot Optional argument, if true, the return path will be root
 * of the given classs' package root path.
 * @param ext Optional argument, if given, it will replace the default ".js"
 * extension.
 */
/* public */
_Loader.getClasspathFor = function (clazz, forRoot, ext) {
        var path = classpathMap["#" + clazz];
        if (!path || forRoot || ext) {
                var base;
                var idx;
                if (path) {
                        clazz = clazz.replace(/\./g, "/");      
                        if ((idx = path.lastIndexOf(clazz)) >= 0 
                                || (idx = clazz.lastIndexOf("/")) >= 0 
                                        && (idx = path.lastIndexOf(clazz.substring(0, idx))) >= 0)
                                base = path.substring(0, idx);
                } else {
                        idx = clazz.length + 2;
                        while ((idx = clazz.lastIndexOf(".", idx - 2)) >= 0)
                                if ((base = classpathMap["@" + clazz.substring(0, idx)]))
                                        break;
                        if (!forRoot)
                                clazz = clazz.replace (/\./g, "/");     
                }
                if (base == null) {
                        var bins = "binaryFolders";
                        base = (window["Clazz"] && Clazz[bins] && Clazz[bins].length ? Clazz[bins][0] 
                                : _Loader[bins] && _Loader[bins].length ? _Loader[bins][0]
                                : "j2s");
                }
                path = (base.lastIndexOf("/") == base.length - 1 ? base : base + "/") + (forRoot ? ""
                        : clazz.lastIndexOf("/*") == clazz.length - 2 ? clazz.substring(0, idx + 1)
                        : clazz + (!ext ? ".js" : ext.charAt(0) != '.' ? "." + ext : ext));
        }               
        return path;//_Loader.multipleSites(path);
};

/**
 * To ignore some classes.
 */
/* public */
_Loader.ignore = function () {
        var clazzes = (arguments.length == 1 && arguments[0] instanceof Array ?
                        clazzes = arguments[0] : null);
        var n = (clazzes ? clazzes.length : arguments.length);
        if (!clazzes) {
                clazzes = new Array(n);
                for (var i = 0; i < n; i++)
                        clazzes[i] = arguments[i];
        }
        unwrapArray(clazzes);
        for (var i = 0; i < n; i++)
                excludeClassMap["@" + clazzes[i]] = 1;
};

/**
 * The following *.script* can be overriden to indicate the 
 * status of classes loading.
 *
 * TODO: There should be a Java interface with name like INativeLoaderStatus
 */
/* public */
_Loader.onScriptLoading = function (file){};

/* public */
_Loader.onScriptLoaded = function (file, isError){};

/* public */
_Loader.onScriptInitialized = function (file){};

/* public */
_Loader.onScriptCompleted = function (file){};

/* public */
_Loader.onClassUnloaded = function (clazz){};

/**
 * After all the classes are loaded, this method will be called.
 * Should be overriden to run *.main([]).
 */
/* public */
_Loader.onGlobalLoaded = function () {};

/* public */
_Loader.keepOnLoading = true; // never set false in this code


/* private */
var mapPath2ClassNode = {};

/* private */
var isClassExcluded = function (clazz) {
        return excludeClassMap["@" + clazz];
};

/* Used to keep ignored classes */
/* private */
var excludeClassMap = {};

/* private */
var evaluate = function(file, js) {
                try {
                        eval(js);
                } catch (e) {      
      if (Clazz._isQuiet) 
        return;
                        var s = "[Java2Script] The required class file \n\n" + file + (js.indexOf("[Exception") == 0 && js.indexOf("data: no") ? 
         "\nwas not found.\n"
        : "\ncould not be loaded. Script error: " + e.message + " \n\ndata:\n\n" + js) + "\n\n" + Clazz.getStackTrace();
                alert(s)
                        Clazz.alert(s);
                        throw e;
                }
                _Loader.onScriptLoaded(file, false);
                tryToLoadNext(file);
}

/* private */
var failedHandles = {};

/* private */
var generateRemovingFunction = function (node) {
        return function () {
                if (node.readyState != "interactive") {
                        try {
                                if (node.parentNode)
                                        node.parentNode.removeChild (node);
                        } catch (e) { }
                        node = null;
                }
        };
};

/* private */
var removeScriptNode = function (n) {
        if (window["j2s.script.debugging"]) {
                return;
        }
        // lazily remove script nodes.
        window.setTimeout (generateRemovingFunction (n), 1);
};

/* public */
Clazz._4Name = function(clazzName, applet, state) {
        if (Clazz.isClassDefined(clazzName))
                return Clazz.evalType(clazzName);
        var f = (Jmol._isAsync && applet ? applet._restoreState(clazzName, state) : null);
        if (f == 1)
                return null; // must be already being created
        if (_Loader.setLoadingMode(f ? _Loader.MODE_SCRIPT : "xhr.sync")) {
                _Loader.loadClass(clazzName, f, false, true, 1);
                return null; // this will surely throw an error, but that is OK
        }
        //alert ("Using Java reflection: " + clazzName + " for " + applet._id + " \n"+ Clazz.getStackTrace());
        _Loader.loadClass(clazzName);
        return Clazz.evalType(clazzName);
};

/**
 * BH: possibly useful for debugging
 */ 
Clazz.currentPath= "";

/**
 * Load *.js by adding script elements into head. Hook the onload event to
 * load the next class in dependency tree.
 */
/* private */
var loadScript = function (node, file, why, ignoreOnload, fSuccess, _loadScript) {
                Clazz.currentPath = file;
        if (ignoreOnload)alert("WHY>>")
//BH removed    // maybe some scripts are to be loaded without needs to know onload event.
//      if (!ignoreOnload && loadedScripts[file]) {
//              _Loader.tryToLoadNext(file);
//              return;
//      }
        loadedScripts[file] = true;
        // also remove from queue
        removeArrayItem(classQueue, file);

    // forces not-found message
    isUsingXMLHttpRequest = true;
    isAsynchronousLoading = false;
  if (_Loader._checkLoad) {
    System.out.println("\t" + file + (why ? "\n -- required by " + why : "") + "  ajax=" + isUsingXMLHttpRequest + " async=" + isAsynchronousLoading)
  }

        _Loader.onScriptLoading(file);
        if (isUsingXMLHttpRequest && !isAsynchronousLoading) {
                // alert("\t" + file + (why ? "\n -- required by " + why : "") + "  ajax=" + isUsingXMLHttpRequest + " async=" + isAsynchronousLoading + " " + Clazz.getStackTrace())
                // synchronous loading
                // works in MSIE locally unless a binary file :)
                // from Jmol.api.Interface only
                var data = Jmol._getFileData(file);
    try{
                  evaluate(file, data);
    }catch(e) {
      alert(e + " loading file " + file + " " + node.name + " " + Clazz.getStackTrace());
    }
    if (fSuccess) {
//      System.out.println("firing in loadScript " + file + " " + (fSuccess && fSuccess.toString()))
      fSuccess(); 
    }
                return;
        }
  
  
System.out.println("for file " + file +" fSuccess = " + (fSuccess ? fSuccess.toString() : ""))
        var info = {
                dataType:"script",
                async:true, 
                type:"GET", 
                url:file,
                success:W3CScriptOnCallback(file, false, fSuccess),
                error:W3CScriptOnCallback(file, true, fSuccess)
        };
        inLoadingThreads++;
        Jmol.$ajax(info);
};

/* private */
var W3CScriptOnCallback = function (path, forError, fSuccess) {
  var s = Clazz.getStackTrace();
  // if (!fSuccess)alert("why no fSuccess?" + s)
        return function () {
  //System.out.println("returning " + (fSuccess ? fSuccess.toString() : "no function ") + s) 
                if (forError && __debuggingBH)Clazz.alert ("############ forError=" + forError + " path=" + path + " ####" + (forError ? "NOT" : "") + "LOADED###");
                if (isGecko && this.timeoutHandle)
                        window.clearTimeout(this.timeoutHandle), this.timeoutHandle = null;
                if (inLoadingThreads > 0)
                        inLoadingThreads--;
                //System.out.println("w3ccalback for " + path + " " + inLoadingThreads + " threads")
                this.onload = null;
                this.onerror = null;
                if (forError) 
                        alert ("There was a problem loading " + path);
                _Loader.onScriptLoaded(path, true);
                var node = this;                        
                var f;
    if (fSuccess)
      f = function(_W3scriptFS){removeScriptNode(node);tryToLoadNext(path, fSuccess); };
    else
      f = function(_W3script){removeScriptNode(node);tryToLoadNext(path)};
                if (loadingTimeLag >= 0)
                        window.setTimeout(function() { tryToLoadNext(path, f); }, loadingTimeLag);
                else
                        tryToLoadNext(path, f);
        };
};

/* private */
var isLoadingEntryClass = true;

/* private */
var besidesJavaPackage = false;

/**
 * After class is loaded, this method will be executed to check whether there
 * are classes in the dependency tree that need to be loaded.
 */
/* private */
var tryToLoadNext = function (file, fSuccess) {
        var node = mapPath2ClassNode["@" + file];
        if (!node) // maybe class tree root
                return;
        var n;
  // check for content loaded
        var clazzes = classpathMap["$" + file];
        if (clazzes) {
                for (var i = 0; i < clazzes.length; i++) {
                        var name = clazzes[i];
                        if (name != node.name && (n = findNode(name))) {
                                if (n.status < Node.STATUS_CONTENT_LOADED) {
                                        n.status = Node.STATUS_CONTENT_LOADED;
                                        updateNode(n);
                                }
                        } else {
                                n = new Node();
                                n.name = name;
                                var pp = classpathMap["#" + name];
                                if (!pp) {
                                        alert (name + " J2S error in tryToLoadNext");
                                        error("Java2Script implementation error! Please report this bug!");
                                }
                                n.path = pp;
                                mappingPathNameNode (n.path, name, n);
                                n.status = Node.STATUS_CONTENT_LOADED;
                                addChildClassNode(clazzTreeRoot, n, false);
                                updateNode(n);
                        }
                }
        }
        if (node instanceof Array) {
                for (var i = 0; i < node.length; i++) {
                        if (node[i].status < Node.STATUS_CONTENT_LOADED) {
                                node[i].status = Node.STATUS_CONTENT_LOADED;
                                updateNode(node[i]);
                        }
                }
        } else if (node.status < Node.STATUS_CONTENT_LOADED) {
                var stillLoading = false;
                var ss = document.getElementsByTagName ("SCRIPT");
                for (var i = 0; i < ss.length; i++) {
                        if (isIE) {
                                if (ss[i].onreadystatechange && ss[i].onreadystatechange.path == node.path
                                                && ss[i].readyState == "interactive") {
                                        stillLoading = true;
                                        break;
                                }
                        } else if (ss[i].onload && ss[i].onload.path == node.path) {
                                stillLoading = true;
                                break;
                        }
                }
                if (!stillLoading) {
                        node.status = Node.STATUS_CONTENT_LOADED;
                        updateNode(node);
                }
        }
        /*
         * Maybe in #optinalLoaded inside above _Loader#updateNode calls, 
         * _Loader.keepOnLoading is set false (Already loaded the wanted
         * classes), so here check to stop.
         */
         
        if (!_Loader.keepOnLoading) // set externally
                return;

 // check for a "must" class that has content and load it
        var cq;
        var working = true;
        if ((n = findNextMustClass(Node.STATUS_KNOWN))) {
                loadClassNode(n);
                while (inLoadingThreads < maxLoadingThreads) {
                        if (!(n = findNextMustClass(Node.STATUS_KNOWN)))
                                break;
                        loadClassNode(n); // will increase inLoadingThreads!
                }
        } else if ((cq = classQueue).length != 0) { 
                /* queue must be loaded in order! */
                n = cq.shift();
                if (!loadedScripts[n.path] 
                                || cq.length != 0 
                                || !isLoadingEntryClass
                                || n.musts.length
                                || n.optionals.length) {
                        addChildClassNode(clazzTreeRoot, n, true);
                        loadScript(n, n.path, n.requiredBy, false);
                } else if (isLoadingEntryClass) {
                        /*
                         * The first time reaching here is the time when ClassLoader
                         * is trying to load entry class. Class with #main method and
                         * is to be executed is called Entry Class.
                         *
                         * Here when loading entry class, ClassLoader should not call
                         * the next following loading script. This is because, those
                         * scripts will try to mark the class as loaded directly and
                         * then continue to call #onLoaded callback method,
                         * which results in an script error!
                         */
                        isLoadingEntryClass = false;
                }
        } else if ((n = findNextRequiredClass(Node.STATUS_KNOWN))) {
                loadClassNode(n);
                while (inLoadingThreads < maxLoadingThreads) {
                        if (!(n = findNextRequiredClass(Node.STATUS_KNOWN)))
                                break;
                        loadClassNode(n); // will increase inLoadingThreads!
                }
        } else {
                working = false;
        }
        if (working || inLoadingThreads > 0)
                return;
  // 
  // now check all classes that MUST be loaded prior to initialization 
  // of some other class (static calls, extends, implements)
  // and all classes REQUIRED somewhere in that class, possibly by the constructor
  // (that is, "new xxxx()" called somewhere in code) and update them
  // that have content but are not declared already 
        var f = [findNextMustClass,findNextRequiredClass];
        var lastNode = null;
        for (var i = 0; i < 2; i++)
                while ((n = f[i](Node.STATUS_CONTENT_LOADED))) {
                        if (i == 1 && lastNode === n) // Already existed cycle ?
                                n.status = Node.STATUS_LOAD_COMPLETE;
                        updateNode(n);
                        lastNode = n;
                }
    
  // check for load cycles
  
        while (true) {
                tracks = [];
                if (!checkCycle(clazzTreeRoot, file))
                        break;
        }
  
  // and update all MUST and REQUIRED classes that are declared already 
  
        for (var i = 0; i < 2; i++) {
                lastNode = null;
                while ((n = f[i](Node.STATUS_DECLARED))) {
                        if (lastNode === n) 
                                break;
                        updateNode(lastNode = n);
                }
        }
        var done = [];
        for (var i = 0; i < 2; i++) 
                while ((n = f[i](Node.STATUS_DECLARED)))
                        done.push(n), n.status = Node.STATUS_LOAD_COMPLETE;
        if (done.length) {
                for (var i = 0; i < done.length; i++)
                        destroyClassNode(done[i]);
                for (var i = 0; i < done.length; i++)
                        if ((f = done[i].onLoaded))
                                done[i].onLoaded = null, f();
        }
  
  
  
  
  
  
  
        //System.out.println(node.name + " loaded completely" + _Loader.onGlobalLoaded + "\n\n")
  if (fSuccess) {
    //System.out.println("tryToLoadNext firing " + _Loader._classCountOK + "/" + _Loader._classCountPending + " "   + fSuccess.toString() + " " + Clazz.getStackTrace())
          fSuccess();
  } else if (_Loader._classCountPending) {
    for (var name in _Loader._classPending) {
      var n = findNode(name);
      System.out.println("class left pending " + name + " " + n);
      if (n) {
        updateNode(n);
        break;
      }
    }
  } else {
    
 // System.out.println("I think I'm done " 
  // + _Loader._classCountOK + "/" + _Loader._classCountPending + " " 
   //+ _Loader.onGlobalLoaded.toString() + " " + Clazz.getStackTrace()
 //  )
    if (_Loader._checkLoad) {
      System.out.println("I think I'm done: SAEM call count: " + SAEMid);
      Clazz.showDuplicates(true);
    }
  }
        _Loader.onGlobalLoaded();
};


var tracks = [];

/*
 * There are classes reference cycles. Try to detect and break those cycles.
 */
/* private */
var checkCycle = function (node, file) {
        var ts = tracks;
        var len = ts.length;
  // add this node to tracks
        ts.push(node);
        var i = len;
        for (; --i >= 0;)
                if (ts[i] === node && ts[i].status >= Node.STATUS_DECLARED) 
                        break;
        if (i >= 0) {
    // this node is already in tracks, and it has been declared already
    // for each node in tracks, set its status to "LOAD_COMPLETE"
    // update all parents, remove all parents, and fire its onLoaded function
    // then clear tracks and return true (keep checking)  
    if (_Loader._checkLoad) {
      var msg = "cycle found loading " + file + " for " + node;
      System.out.println(msg)
    } 
                for (; i < len; i++) {
      var n = ts[i];
                        n.status = Node.STATUS_LOAD_COMPLETE;
                        destroyClassNode(n); // Same as above
                        for (var k = 0; k < n.parents.length; k++)
                                updateNode(n.parents[k]);
                        n.parents = [];
      var f = n.onLoaded;
      if (_Loader._checkLoad) {
        var msg = "cycle setting status to LOAD_COMPLETE for " + n.name + (f ? " firing " + f.toString() : "");
        System.out.println(msg)
      } 
                        if (f)
                                n.onLoaded = null, f();
                }
                ts.length = 0;
                return true;
        }
        var a = [node.musts, node.optionals];
        for (var j = 0; j < 2; j++)
                for (var r = a[j], i = r.length; --i >= 0;)
                        if (r[i].status == Node.STATUS_DECLARED && checkCycle(r[i], file)) 
                                return true;
  // reset _tracks to its original length      
        ts.length = len;
        return false; // done 
};


_Loader._classCountPending = 0;
_Loader._classCountOK = 0;
_Loader._classPending = {};

_Loader.showPending = function() {
  var a = [];
  for (var name in _Loader._classPending) {
    var n = findNode(name);
    if (!n) {
      alert("No node for " + name);
      continue;
    }
    a.push(n);
    System.out.println(showNode("", "", n, "", 0));     
  }  
  return a;
}

var showNode = function(s, names, node, inset, level) {
  names += "--" + node.name;
  s += names + "\n";
  if (level > 5) {
    s += inset + " ...\n";
    return s;
  }
  inset += "\t";
  s += inset + "status: " + node.status + "\n";
  if (node.parents && node.parents.length && node.parents[0] && node.parents[0].name) {
    s += inset + "parents: " + node.parents.length + "\n";
    for (var i = 0; i < node.parents.length; i++) {
      s = showNode(s, names, node.parents[i], inset + "\t", level+1);
    }
    s += "\n";
  }
//  if (node.requiredBy) {
//    s += inset + "requiredBy:\n";
//    s = showNode(s, names, node.requiredBy, inset + "\t", level+1);
//    s += "\n";
//  }
  return s;    
}     

/**
 * Update the dependency tree nodes recursively.
 */
/* private */
updateNode = function(node, _updateNode) {
        if (!node.name || node.status >= Node.STATUS_LOAD_COMPLETE) {
                destroyClassNode(node);
                return;
        }
        var ready = true;
  // check for declared and also having MUSTS
        if (node.musts.length && node.declaration) {
                for (var mustLength = node.musts.length, i = mustLength; --i >= 0;) {
                        var n = node.musts[i];
                        n.requiredBy = node;
                        if (n.status < Node.STATUS_DECLARED && isClassDefined (n.name)) {
                                var nns = []; // a stack for onLoaded events
                                n.status = Node.STATUS_LOAD_COMPLETE;
                                destroyClassNode(n); // Same as above
                                if (n.declaration       && n.declaration.clazzList) {
                                        // For those classes within one *.js file, update them synchronously.
                                        for (var j = 0, list = n.declaration.clazzList, l = list.length; j < l; j++) {
                                                var nn = findNode (list[j]);
                                                if (nn && nn.status != Node.STATUS_LOAD_COMPLETE
                                                                && nn !== n) {
                                                        nn.status = n.status;
                                                        nn.declaration = null;
                                                        destroyClassNode(nn);
                                                        nn.onLoaded && nns.push(nn);
                                                }
                                        }
                                        n.declaration = null;
                                }
        // fire all onLoaded events
                                if (n.onLoaded)
                                        nns.push(n);
                                for (var j = 0; j < nns.length; j++) {
                                        var onLoaded = nns[j].onLoaded;
                                        if (onLoaded) {
                                                nns[j].onLoaded = null;
                                                onLoaded();
                                        }
                                }
                        } else {
                                (n.status == Node.STATUS_CONTENT_LOADED) && updateNode(n); // musts may be changed
                                if (n.status < Node.STATUS_DECLARED)
                                        ready = false;
                        }
                        if (node.musts.length != mustLength) {
                                // length changed -- restart!
                                i = mustLength = node.musts.length;
                                ready = true;
                        }
                }
        }
        if (!ready)
                return;
        if (node.status < Node.STATUS_DECLARED) {
                var decl = node.declaration;
                if (decl)
                        decl(), decl.executed = true;
    if(_Loader._checkLoad) {
            if (_Loader._classPending[node.name]) {
              delete _Loader._classPending[node.name];
              _Loader._classCountOK;
              _Loader._classCountPending--;
//              System.out.println("OK " + (_Loader._classCountOK) + " FOR " + node.name)
            }
    }
                node.status = Node.STATUS_DECLARED;
                if (definedClasses)
                        definedClasses[node.name] = true;
                _Loader.onScriptInitialized(node.path);
                if (node.declaration && node.declaration.clazzList) {
                        // For those classes within one *.js file, update them synchronously.
                        for (var j = 0, list = node.declaration.clazzList, l = list.length; j < l; j++) {
                                var nn = findNode(list[j]);
                                if (nn && nn.status != Node.STATUS_DECLARED
                                                && nn !== node) {
                                        nn.status = Node.STATUS_DECLARED;
                                        if (definedClasses)
                                                definedClasses[nn.name] = true;
                                        _Loader.onScriptInitialized(nn.path);
                                }
                        }
                }
        }
        var level = Node.STATUS_DECLARED;
        if (node.optionals.length == 0 && node.musts.length == 0
                        || node.status > Node.STATUS_KNOWN && !node.declaration
                        || checkStatusIs(node.musts, Node.STATUS_LOAD_COMPLETE)
                                        && checkStatusIs(node.optionals, Node.STATUS_LOAD_COMPLETE)) { 
                level = Node.STATUS_LOAD_COMPLETE;
                if (!doneLoading(node, level))
                        return false;
                        // For those classes within one *.js file, update them synchronously.
                if (node.declaration && node.declaration.clazzList) {
                        for (var j = 0, list = node.declaration.clazzList, l = list.length; j < l; j++) {
                                var nn = findNode(list[j]);
                                if (nn && nn.status != level && nn !== node) {
                                        nn.declaration = null;
                                        if (!doneLoading(nn, level))
                                                return false;
                                }
                        }
                }
        }
  // _Loader.updateParents = function (node, level, _updateParents)
        if (node.parents && node.parents.length) {
        for (var i = 0; i < node.parents.length; i++) {
                var p = node.parents[i];
                if (p.status < level) 
                        updateNode(p, p.name);
        }
        if (level == Node.STATUS_LOAD_COMPLETE)
                node.parents = [];
  }
};

/* private */
var checkStatusIs = function(arr, status){
        for (var i = arr.length; --i >= 0;)
                if (arr[i].status < status)
                        return false;
        return true;
}
/* private */
var doneLoading = function(node, level, _doneLoading) {
        node.status = level;
        _Loader.onScriptCompleted(node.path);
  
        var onLoaded = node.onLoaded;
        if (onLoaded) {
                node.onLoaded = null;
                onLoaded();
                if (!_Loader.keepOnLoading)
                        return false;
        }
  
        destroyClassNode(node);
        return true;
}

/*
 * Be used to record already used random numbers. And next new random
 * number should not be in the property set.
 */
/* private */
var usedRandoms = {
  "r0.13412" : 1
};

/* private */
var getRnd = function() {
        while (true) { // get a unique random number
                var rnd = Math.random();
                var s = "r" + rnd;
                if (!usedRandoms[s])
                        return (usedRandoms[s] = 1, clazzTreeRoot.random = rnd);
        }
}

/* protected */
var findNode = function(clazzName) {
        getRnd();
        return findNodeUnderNode(clazzName, clazzTreeRoot);
};

/* private */
var findNextRequiredClass = function(status) {
        getRnd();
        return findNextRequiredNode(clazzTreeRoot, status);
};

/* private */
var findNextMustClass = function(status) {
        return findNextMustNode(clazzTreeRoot, status);
};

/* private */
var findNodeUnderNode = function(clazzName, node) {
        var n;
        // node, then musts then optionals
        return (node.name == clazzName ? node 
                : (n = findNodeWithin(clazzName, node.musts))
                || (n = findNodeWithin(clazzName, node.optionals)) 
                ? n : null);
};

/* private */
var findNodeWithin = function(name, arr) {
        var rnd = clazzTreeRoot.random;
        for (var i = arr.length; --i >= 0;) {
                var n = arr[i];
                if (n.name == name)
                        return n;
                if (n.random != rnd) {
                        n.random = rnd;
                        if ((n = findNodeUnderNode(name, n)))
                                return n;
                }
        }
        return null;
}

/* private */
var checkStatus = function(n, status) {
        return (n.status == status 
                        && (status != Node.STATUS_KNOWN || !loadedScripts[n.path])
                        && (status == Node.STATUS_DECLARED      || !isClassDefined (n.name)));
}

/* private */
var findNextMustNode = function(node, status) {
        for (var i = node.musts.length; --i >= 0;) {
                var n = node.musts[i];
                if (checkStatus(n, status) || (n = findNextMustNode(n, status)))
                        return n;       
        }
        return (checkStatus(node, status) ? node : null); 
};

/* private */
var findNextRequiredNode = function (node, status) {
        // search musts first
        // search optionals second
        // search itself last
        var n;
        return ((n = searchClassArray(node.musts, status))
                || (n = searchClassArray(node.optionals, status))
                || checkStatus(n = node, status) ? n : null);
};

/* private */
var searchClassArray = function (arr, status) {
        if (arr) {
                var rnd = clazzTreeRoot.random;
                for (var i = 0; i < arr.length; i++) {
                        var n = arr[i];
                        if (checkStatus(n, status))
                                return n;
                        if (n.random != rnd) {
                                n.random = rnd; // mark as visited!
                                if ((n = findNextRequiredNode(n, status)))
                                        return n;
                        }
                }
        }
        return null;
};

/**
 * This map variable is used to mark that *.js is correctly loaded.
 * In IE, _Loader has defects to detect whether a *.js is correctly
 * loaded or not, so inner loading mark is used for detecting.
 */
/* private */
var innerLoadedScripts = {};

/**
 * This method will be called in almost every *.js generated by Java2Script
 * compiler.
 */
/* public */
var load = function (musts, name, optionals, declaration) {
  // called as name.load in Jmol
        if (name instanceof Array) {
                unwrapArray(name);
                for (var i = 0; i < name.length; i++)
                        load(musts, name[i], optionals, declaration, name);
                return;
        }       

  if (_Loader._checkLoad) {
    if (_Loader._classPending[name]) {
      //alert("duplicate load for " + name)
    } else {
      _Loader._classPending[name] = 1;
      if (_Loader._classCountPending++ == 0)
        _Loader._classCountOK = 0;
      System.out.println("Loading class " + name);
    }
  }

//      if (clazz.charAt (0) == '$')
//              clazz = "org.eclipse.s" + clazz.substring (1);
        var node = mapPath2ClassNode["#" + name];
        if (!node) { // load called inside *.z.js?
                var n = findNode(name);
                node = (n ? n : new Node());
                node.name = name;
                node.path = classpathMap["#" + name] || "unknown";
                mappingPathNameNode(node.path, name, node);
                node.status = Node.STATUS_KNOWN;
                addChildClassNode(clazzTreeRoot, node, false);
        }
        processRequired(node, musts, true);
        if (arguments.length == 5 && declaration) {
                declaration.status = node.status;
                declaration.clazzList = arguments[4];
        }
        node.declaration = declaration;
        if (declaration) 
                node.status = Node.STATUS_CONTENT_LOADED;
        processRequired(node, optionals, false);
};

/* private */
var processRequired = function(node, arr, isMust) {
        if (arr && arr.length) {
                unwrapArray(arr);
                for (var i = 0; i < arr.length; i++) {
                        var name = arr[i];
                        if (!name)
                                continue;
                        if (isClassDefined(name)
                                        || isClassExcluded(name))
                                continue;
                        var n = findNode(name);
                        if (!n) {
                                n = new Node();
                                n.name = name;
                                n.status = Node.STATUS_KNOWN;
                        }
                        n.requiredBy = node;
                        addChildClassNode(node, n, isMust);
                }
        }
}

/*
 * Try to be compatiable of Clazz
 */
if (window["Clazz"]) {
        Clazz.load = load;
} else {
  _Loader.load = load;
}  
/**
 * Map different class to the same path! Many classes may be packed into
 * a *.z.js already.
 *
 * @path *.js path
 * @name class name
 * @node Node object
 */
/* private */
var mappingPathNameNode = function (path, name, node) {
        var map = mapPath2ClassNode;
        var keyPath = "@" + path;
        var v = map[keyPath];
        if (v) {
                if (v instanceof Array) {
                        var existed = false;
                        for (var i = 0; i < v.length; i++) {
                                if (v[i].name == name) {
                                        existed = true;
                                        break;
                                }
                        }
                        if (!existed)
                                v.push(node);
                } else {
                        map[keyPath] = [v, node];
                }
        } else {
                map[keyPath] = node;
        }
        map["#" + name] = node;
};

/* protected */
var loadClassNode = function (node) {
        var name = node.name;
        if (!isClassDefined (name) 
                        && !isClassExcluded (name)) {
                var path = _Loader.getClasspathFor (name/*, true*/);
                node.path = path;
                mappingPathNameNode (path, name, node);
                if (!loadedScripts[path]) {
                        loadScript(node, path, node.requiredBy, false);
                        return true;
                }
        }
        return false;
};


/**
 * Used in package
/* public */
var runtimeKeyClass = _Loader.runtimeKeyClass = "java.lang.String";

/**
 * Queue used to store classes before key class is loaded.
 */
/* private */
var queueBe4KeyClazz = [];

/* private */
var J2sLibBase;

/**
 * Return J2SLib base path from existed SCRIPT src attribute.
 */
/* public */
_Loader.getJ2SLibBase = function () {
        var o = window["j2s.lib"];
        return (o ? o.base + (o.alias == "." ? "" : (o.alias ? o.alias : (o.version ? o.version : "1.0.0")) + "/") : null);
};

/**
 * Indicate whether _Loader is loading script synchronously or 
 * asynchronously.
 */
/* private */
var isAsynchronousLoading = true;

/* private */
var isUsingXMLHttpRequest = false;

/* private */
var loadingTimeLag = -1;

_Loader.MODE_SCRIPT = 4;
_Loader.MODE_XHR = 2;
_Loader.MODE_SYNC = 1;

/**
 * String mode:
 * asynchronous modes:
 * async(...).script, async(...).xhr, async(...).xmlhttprequest,
 * script.async(...), xhr.async(...), xmlhttprequest.async(...),
 * script
 * 
 * synchronous modes:
 * sync(...).xhr, sync(...).xmlhttprequest,
 * xhr.sync(...), xmlhttprequest.sync(...),
 * xmlhttprequest, xhr
 *                                                    
 * Integer mode:
 * Script 4; XHR 2; SYNC bit 1; 
 */
/* public */
_Loader.setLoadingMode = function (mode, timeLag) {
        var async = true;
        var ajax = true;
        if (typeof mode == "string") {
                mode = mode.toLowerCase();
                if (mode.indexOf("script") >= 0)
                        ajax = false;
                else
                        async = (mode.indexOf("async") >=0);
                async = false; // BH
        } else {
                if (mode & _Loader.MODE_SCRIPT)
                        ajax = false;
                else
                        async = !(mode & _Loader.MODE_SYNC);
        }
        isUsingXMLHttpRequest = ajax;
        isAsynchronousLoading = async;
        loadingTimeLag = (async && timeLag >= 0 ? timeLag: -1);
        return async;
};

/* private */
var runtimeLoaded = function () {
        if (pkgRefCount || !isClassDefined(runtimeKeyClass))
                return;
        var qbs = queueBe4KeyClazz;
        for (var i = 0; i < qbs.length; i++)
                _Loader.loadClass(qbs[i][0], qbs[i][1]);
        queueBe4KeyClazz = [];
};

/*
 * Load those key *.z.js. This *.z.js will be surely loaded before other 
 * queued *.js.
 */
/* public */
_Loader.loadZJar = function (zjarPath, keyClass) {
// used only by package.js for core.z.js
        var f = null;
        var isArr = (keyClass instanceof Array);
        if (isArr)
                keyClass = keyClass[keyClass.length - 1];
        else
                f = (keyClass == runtimeKeyClass ? runtimeLoaded : null);                       
        _Loader.jarClasspath(zjarPath, isArr ? keyClass : [keyClass]);
        // BH note: runtimeKeyClass is java.lang.String 
        _Loader.loadClass(keyClass, f, true);
};

var NodeMap = {};
var _allNodes = [];

/**
 * The method help constructing the multiple-binary class dependency tree.
 */
/* private */
var addChildClassNode = function (parent, child, isMust) {
        var existed = false;
        var arr;
        if (isMust) {
                arr = parent.musts;
                if (!child.requiredBy)
                        child.requiredBy = parent;
//              if (!parent.requiresMap){
//                      parent.requires = [];
//                      parent.requiresMap = {};
//              }
//              if (!parent.requiresMap[child.name]) {
//                      parent.requiresMap[child.name] = 1;
//                      parent.requires.push[child];
//              }
        } else {
                arr = parent.optionals;
        }
        if (!NodeMap[child.name]) {
                _allNodes.push(child)
                NodeMap[child.name]=child
        }
        for (var i = 0; i < arr.length; i++) {
                if (arr[i].name == child.name) {
                        existed = true;
                        break;
                }
        }
        if (!existed) {
                arr.push(child);
                if (isLoadingEntryClass 
                                && child.name.indexOf("java") != 0 
                                && child.name.indexOf("net.sf.j2s.ajax") != 0) {
                        if (besidesJavaPackage)
                                isLoadingEntryClass = false;
                        besidesJavaPackage = true;
//              } else if (child.name.indexOf("org.eclipse.swt") == 0 
//                              || child.name.indexOf("$wt") == 0) {
//                      window["swt.lazy.loading.callback"] = swtLazyLoading;
//                      if (needPackage("org.eclipse.swt"))
//                              return _Loader.loadPackage("org.eclipse.swt", function() {addParentClassNode(child, parent)});
                }
        }
        addParentClassNode(child, parent);
};

/* private */
var addParentClassNode = function(child, parent) {
        if (parent.name && parent != clazzTreeRoot && parent != child)
                for (var i = 0; i < child.parents.length; i++)
                        if (child.parents[i].name == parent.name)
                                return;
        child.parents.push(parent);
}

/* private */
var destroyClassNode = function (node) {
        var parents = node.parents;
        if (parents)
                for (var k = parents.length; --k >= 0;)
                        removeArrayItem(parents[k].musts, node) || removeArrayItem(parents[k].optionals, node);
};

/* public */
_Loader.unloadClassExt = function (qClazzName) {
        if (definedClasses)
                definedClasses[qClazzName] = false;
        if (classpathMap["#" + qClazzName]) {
                var pp = classpathMap["#" + qClazzName];
                classpathMap["#" + qClazzName] = null;
                var arr = classpathMap["$" + pp];
                removeArrayItem(arr, qClazzName) && (classpathMap["$" + pp] = arr);
        }
        var n = findNode(qClazzName);
        if (n) {
                n.status = Node.STATUS_KNOWN;
                loadedScripts[n.path] = false;
        }
        var path = _Loader.getClasspathFor (qClazzName);
        loadedScripts[path] = false;
        innerLoadedScripts[path] && (innerLoadedScripts[path] = false);
        _Loader.onClassUnloaded(qClazzName);
};

/* private */
var assureInnerClass = function (clzz, fun) {
        clzz = clzz.__CLASS_NAME__;
        if (Clazz.unloadedClasses[clzz]) {
                if (clzz.indexOf("$") >= 0)
                        return;
                var list = [];
                var key = clzz + "$";
                for (var s in Clazz.unloadedClasses)
                        if (Clazz.unloadedClasses[s] && s.indexOf(key) == 0)
                                list.push(s);
                if (!list.length) 
                        return;
                fun = "" + fun;
                var idx1, idx2;
                if ((idx1 = fun.indexOf(key)) < 0 || (idx2 = fun.indexOf("\"", idx1 + key.length)) < 0) 
                        return;
                clzz = fun.substring(idx1, idx2);
                if (!Clazz.unloadedClasses[clzz] || (idx1 = fun.indexOf("{", idx2) + 1) == 0)
                        return;
                if ((idx2 = fun.indexOf("(" + clzz + ",", idx1 + 3)) < 0
                        || (idx2 = fun.lastIndexOf("}", idx2 - 1)) < 0)
                                return;
                eval(fun.substring(idx1, idx2));
                Clazz.unloadedClasses[clzz] = null;
        }
};

Clazz.binaryFolders =  _Loader.binaryFolders = [ _Loader.getJ2SLibBase() ];

})(Clazz, Clazz._Loader);

//}
/******************************************************************************
 * Copyright (c) 2007 java2script.org and others.
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 *     Zhou Renjian - initial API and implementation
 *****************************************************************************/
/*******
 * @author zhou renjian
 * @create Jan 11, 2007
 *******/

Clazz._LoaderProgressMonitor = {};

;(function(CLPM, Jmol) {

var fadeOutTimer = null;
var fadeAlpha = 0;
var monitorEl = null;
var lastScrollTop = 0;
var bindingParent = null;

CLPM.DEFAULT_OPACITY = (Jmol && Jmol._j2sLoadMonitorOpacity ? Jmol._j2sLoadMonitorOpacity : 55);

/* public */
/*CLPM.initialize = function (parent) {
        bindingParent = parent;
        if (parent && !attached) {
                attached = true;
                //Clazz.addEvent (window, "unload", cleanup);
                // window.attachEvent ("onunload", cleanup);
        }
};
*/

/* public */
CLPM.hideMonitor = function () {
        monitorEl.style.display = "none";
}

/* public */
CLPM.showStatus = function (msg, fading) {
        if (!monitorEl) {
                createHandle ();
                if (!attached) {
                        attached = true;
                        //Clazz.addEvent (window, "unload", cleanup);
                        // window.attachEvent ("onunload", cleanup);
                }
        }
        clearChildren(monitorEl);
  if (msg == null) {
    if (fading) {
      fadeOut();
    } else {
        CLPM.hideMonitor();
    }
    return;
  }
  
        monitorEl.appendChild(document.createTextNode ("" + msg));
        if (monitorEl.style.display == "none") {
                monitorEl.style.display = "";
        }
        setAlpha(CLPM.DEFAULT_OPACITY);
        var offTop = getFixedOffsetTop();
        if (lastScrollTop != offTop) {
                lastScrollTop = offTop;
                monitorEl.style.bottom = (lastScrollTop + 4) + "px";
        }
        if (fading) {
                fadeOut();
        }
};

/* private static */ 
var clearChildren = function (el) {
        if (!el)
                return;
        for (var i = el.childNodes.length; --i >= 0;) {
                var child = el.childNodes[i];
                if (!child)
                        continue;
                if (child.childNodes && child.childNodes.length)
                        clearChildren (child);
                try {
                        el.removeChild (child);
                } catch (e) {};
        }
};
/* private */ 
var setAlpha = function (alpha) {
        if (fadeOutTimer && alpha == CLPM.DEFAULT_OPACITY) {
                window.clearTimeout (fadeOutTimer);
                fadeOutTimer = null;
        }
        fadeAlpha = alpha;
        var ua = navigator.userAgent.toLowerCase();
        monitorEl.style.filter = "Alpha(Opacity=" + alpha + ")";
        monitorEl.style.opacity = alpha / 100.0;
};
/* private */ 
var hidingOnMouseOver = function () {
  CLPM.hideMonitor();
};

/* private */ 
var attached = false;
/* private */ 
var cleanup = function () {
        //if (monitorEl) {
        //      monitorEl.onmouseover = null;
        //}
        monitorEl = null;
        bindingParent = null;
        //Clazz.removeEvent (window, "unload", cleanup);
        //window.detachEvent ("onunload", cleanup);
        attached = false;
};
/* private */ 
var createHandle = function () {
        var div = document.createElement ("DIV");
        div.id = "_Loader-status";
        div.style.cssText = "position:absolute;bottom:4px;left:4px;padding:2px 8px;"
                        + "z-index:" + (window["j2s.lib"].monitorZIndex || 10000) + ";background-color:#8e0000;color:yellow;" 
                        + "font-family:Arial, sans-serif;font-size:10pt;white-space:nowrap;";
        div.onmouseover = hidingOnMouseOver;
        monitorEl = div;
        if (bindingParent) {
                bindingParent.appendChild(div);
        } else {
                document.body.appendChild(div);
        }
        return div;
};
/* private */ 

var fadeOut = function () {
        if (monitorEl.style.display == "none") return;
        if (fadeAlpha == CLPM.DEFAULT_OPACITY) {
                fadeOutTimer = window.setTimeout(function () {
                                        fadeOut();
                                }, 750);
                fadeAlpha -= 5;
        } else if (fadeAlpha - 10 >= 0) {
                setAlpha(fadeAlpha - 10);
                fadeOutTimer = window.setTimeout(function () {
                                        fadeOut();
                                }, 40);
        } else {
                monitorEl.style.display = "none";
        }
};
/* private */
var getFixedOffsetTop = function (){
        if (bindingParent) {
                var b = bindingParent;
                return b.scrollTop;
        }
        var dua = navigator.userAgent;
        var b = document.body;
        var p = b.parentNode;
        var pcHeight = p.clientHeight;
        var bcScrollTop = b.scrollTop + b.offsetTop;
        var pcScrollTop = p.scrollTop + p.offsetTop;
        return (dua.indexOf("Opera") < 0 && document.all ? (pcHeight == 0 ? bcScrollTop : pcScrollTop)
                : dua.indexOf("Gecko") < 0 ? (pcHeight == p.offsetHeight 
                                && pcHeight == p.scrollHeight ? bcScrollTop : pcScrollTop) : bcScrollTop);
};

/* not used in Jmol
if (window["ClazzLoader"]) {
        _Loader.onScriptLoading = function(file) {
                CLPM.showStatus("Loading " + file + "...");
        };
        _Loader.onScriptLoaded = function(file, isError) {
                CLPM.showStatus(file + (isError ? " loading failed." : " loaded."), true);
        };
        _Loader.onGlobalLoaded = function(file) {
                CLPM.showStatus("Application loaded.", true);
        };
        _Loader.onClassUnloaded = function(clazz) {
                CLPM.showStatus("Class " + clazz + " is unloaded.", true);
  };
}
*/

})(Clazz._LoaderProgressMonitor, Jmol);

//}
/******************************************************************************
 * Copyright (c) 2007 java2script.org and others.
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 *     Zhou Renjian - initial API and implementation
 *****************************************************************************/
/*******
 * @author zhou renjian
 * @create Nov 5, 2005
 *******/

;(function(Con, Sys) {
/**
 * Setting maxTotalLines to -1 will not limit the console result
 */
/* protected */
Con.maxTotalLines =     10000;

/* protected */
Con.setMaxTotalLines = function (lines) {
        Con.maxTotalLines = (lines > 0 ? lines : 999999);
}

/* protected */
Con.maxLatency = 40;

/* protected */
Con.setMaxLatency = function (latency) {
        Con.maxLatency = (latency > 0 ? latency : 40);
};

/* protected */
Con.pinning  = false;

/* protected */
Con.enablePinning = function (enabled) {
        Con.pinning = enabled;
};

/* private */
Con.linesCount = 0;

/* private */
Con.metLineBreak = false;


/*
 * Give an extension point so external script can create and bind the console
 * themself.
 *
 * TODO: provide more template of binding console window to browser.
 */
/* protected */
Con.createConsoleWindow = function (parentEl) {
        var console = document.createElement ("DIV");
        console.style.cssText = "font-family:monospace, Arial, sans-serif;";
        document.body.appendChild (console);
        return console;
};

var c160 = String.fromCharCode(160); //nbsp;
c160 += c160+c160+c160;

/* protected */
Con.consoleOutput = function (s, color) {
        var o = window["j2s.lib"];
        var console = (o && o.console);
        if (console && typeof console == "string")
                console = document.getElementById(console)
        if (!console)
                return false; // BH this just means we have turned off all console action
        if (Con.linesCount > Con.maxTotalLines) {
                for (var i = 0; i < Con.linesCount - Con.maxTotalLines; i++) {
                        if (console && console.childNodes.length > 0) {
                                console.removeChild (console.childNodes[0]);
                        }
                }
                Con.linesCount = Con.maxTotalLines;
        }

        var willMeetLineBreak = false;
        s = (typeof s == "undefined" ? "" : s == null ? "null" : "" + s);
        s = s.replace (/\t/g, c160);
        if (s.length > 0)
                switch (s.charAt(s.length - 1)) {
                case '\n':
                case '\r':
                        s = (s.length > 1 ? s.substring (0, s.length - (s.charAt (s.length - 2) == '\r' ? 2 : 1)) : "");
                        willMeetLineBreak = true;
                        break;
                }

        var lines = null;
        s = s.replace (/\t/g, c160);
        lines = s.split(/\r\n|\r|\n/g);
        for (var i = 0, last = lines.length - 1; i <= last; i++) {
                var lastLineEl = null;
                if (Con.metLineBreak || Con.linesCount == 0 
                                || console.childNodes.length < 1) {
                        lastLineEl = document.createElement ("DIV");
                        console.appendChild (lastLineEl);
                        lastLineEl.style.whiteSpace = "nowrap";
                        Con.linesCount++;
                } else {
                        try {
                                lastLineEl = console.childNodes[console.childNodes.length - 1];
                        } catch (e) {
                                lastLineEl = document.createElement ("DIV");
                                console.appendChild (lastLineEl);
                                lastLineEl.style.whiteSpace = "nowrap";
                                Con.linesCount++;
                        }
                }
                var el = document.createElement ("SPAN");
                lastLineEl.appendChild (el);
                el.style.whiteSpace = "nowrap";
                if (color)
                        el.style.color = color;
                var l = lines[i]
                if (l.length == 0)
                        l = c160;
                el.appendChild(document.createTextNode(l));
                if (!Con.pinning)
                        console.scrollTop += 100;
                Con.metLineBreak = (i != last || willMeetLineBreak);
        }

        var cssClazzName = console.parentNode.className;
        if (!Con.pinning && cssClazzName
                        && cssClazzName.indexOf ("composite") != -1) {
                console.parentNode.scrollTop = console.parentNode.scrollHeight;
        }
        Con.lastOutputTime = new Date ().getTime ();
};

/*
 * Clear all contents inside the console.
 */
/* public */
Con.clear = function () {
        try {
                Con.metLineBreak = true;
                var o = window["j2s.lib"];
                var console = o && o.console;
                if (!console || !(console = document.getElementById (console)))
                        return;
                var childNodes = console.childNodes;
                for (var i = childNodes.length; --i >= 0;)
                        console.removeChild (childNodes[i]);
                Con.linesCount = 0;
        } catch(e){};
};

/* public */
Clazz.alert = function (s) {
        Con.consoleOutput (s + "\r\n");
};


/* public */
Sys.out.print = function (s) { 
        Con.consoleOutput (s);
};
/* public */
Sys.out.println = function(s) { 
        Con.consoleOutput(typeof s == "undefined" ? "\r\n" : s == null ?  s = "null\r\n" : s + "\r\n");
};

Sys.out.write = function (buf, offset, len) {
        Sys.out.print(String.instantialize(buf).substring(offset, offset+len));
};

/* public */
Sys.err.__CLASS_NAME__ = "java.io.PrintStream";

/* public */
Sys.err.print = function (s) { 
        Con.consoleOutput (s, "red");
};

/* public */
Sys.err.println = function (s) {
        Con.consoleOutput (typeof s == "undefined" ? "\r\n" : s == null ?  s = "null\r\n" : s + "\r\n", "red");
};

Sys.err.write = function (buf, offset, len) {
        Sys.err.print(String.instantialize(buf).substring(offset, offset+len));
};

})(Clazz.Console, System);

})(Clazz, Jmol); // requires JSmolCore.js

}; // called by external application