// 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 12/21/2015 6:14:59 PM adding typeArray.buffer.slice to be compatible with Safari

// BH 12/20/2015 6:13:52 AM adding Int8Array; streamlining array checking

// BH 12/18/2015 5:02:52 PM adding .slice and also better array copy

// BH 7/24/2015 6:48:50 AM adding optional ?j2sdebug flag on page URL

// -- switches to using j2s/core/corexxx.js, not j2s/core/corexxx.z.js

// -- adds ";//# sourceURL="+file in eval(js)

// -- enables DebugJS.$(msg) call to debugger;

// see https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Statements/debugger

// see https://developer.mozilla.org/en-US/docs/Tools/Debugger/How_to/Debug_eval_sources

// BH 7/23/2015 6:45:55 PM added sourceURL in each js class eval(), allowing full

// breakpoint debugging and code checking in Firefox and Chrome

// BH 7/19/2015 6:18:17 PM added os.name, line.separator, etc. to System.getProperty()

// BH 7/19/2015 5:39:10 PM added java.lang.System = System

// BH 7/19/2015 10:33:10 AM fix for SAEM equating "null" with number or boolean

// BH 7/18/2015 6:08:05 PM for Jmol I was able to remove the $private/$fx business, but now

// I see that in general that cannot be done. Thinking about a strategy...

// 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

// JSmolJavaExt.js

// This library will be wrapped by an additional anonymous function using ANT in

// build_03_tojs.xml. This task will also modify variable names. References

// to Clazz._ will not be changed, but other Clazz.xxx will be changed to

// (local scope) Clazz_xxx, allowing them to be further compressed using

// Google Closure Compiler in that same ANT task.

// BH 6/10/2016 4:20:15 PM removed Clazz.dateToString

// BH 6/10/2016 5:53:20 AM aligned with SwingJS; combined with j2sJmol.js (same as j2sSwingjs)

// BH 3/9/2016 6:25:08 PM at least allow Error() by itself to work as before (inchi.js uses this)

// BH 12/21/2015 1:31:41 PM fixing String.instantialize for generic typed array

// BH 9/19/2015 11:05:45 PM Float.isInfinite(), Float.isNaN(), Double.isInfinite(), Double.isNaN() all not implemented

// BH 5/31/2015 5:53:04 PM Number.compareTo added

// BH 5/21/2015 5:46:30 PM Number("0xFFFFFFFF") is not -1

// BH 4/23/2015 9:08:59 AM xx.getComponentType() is nonfunctional. Array.newInstance now defines a wrapper for .getClass().getComponentType() that works

// BH 4/12/2015 1:37:44 PM adding Math.rint = Math.round

// BH 1/16/2015 10:09:38 AM Chrome failure jqGrig due to new String("x").toString() not being a simple string

// BH 8/14/2014 6:49:22 PM Character class efficiencies

// BH 7/24/2014 9:02:18 AM most browsers do not support String.codePointAt()

// BH 7/11/2014 4:17:22 PM fix for Boolean.valueOf("false") not being false

// BH 5/27/2014 6:29:59 AM ensure floats and doubles have decimal point in toString

// BH 4/1/2014 12:23:41 PM Encoding moved to Clazz._Encoding;

// BH 4/1/2014 7:51:46 AM removing java.lang.B00lean

// BH 3/7/2014 9:17:10 AM removing Array.toString; moving that code here from j2sJmol.js

// BH 1/30/2014 9:04:25 AM adding Throwable.getStackTrace() as a STRING

// BH 12/4/2013 9:20:44 PM fix for reassigning Date.prototype.toString()

// BH 12/3/2013 11:43:10 AM bizarre Safari bug in reassigning Boolean (OK, I admit, we shouldn't have done that...)

// BH 12/1/2013 6:50:16 AM evit Number.prototype.toString assignment removed!

// BH 11/30/2013 1:46:31 PM fixing Byte, Short, Long, Integer, Float, Double to reflect proper bounds and error conditions

// BH 11/29/2013 8:58:49 PM removing Boolean.toString(boolean)

// BH 11/4/2013 7:34:26 AM changing "var nativeClazz" to "var nativeClass" to avoid ANT replacement of "nativeClazz." to "nativeClazz_"

// BH 10/19/2013 1:29:27 PM fixed String.$replace()

// BH 10/18/2013 6:09:23 PM fixed (Double|Float).valueOf(NaN).valueOf(), which should return NaN, not throw an error

// BH 10/12/2013 11:18:44 AM fixed bug in Double(String) and Float(String) that was returning typeof "string"

// BH 10/10/2013 2:40:20 PM added Math.log10

// BH 7/23/2013 7:24:01 AM fixing Number.shortValue() and Number.byteValue() for negative values

// BH 6/16/2013 1:31:30 PM adding /| in String.replace -- thank you David Koes

// BH 3/13/2013 12:49:23 PM setting Boolean.valueOf() "@"

// BH 3/2/2013 10:46:45 PM removed Double.valueOf(String)

// BH 1/7/2013 7:40:06 AM added Clazz.dateToString

// BH 11/6/2012 8:26:33 PM added instanceof Int32Array in String.instantialize

// BH 10/13/2012 11:38:07 PM corrected Integer.parseInt to allow only +-0123456789; created Integer.parseIntRadix

// BH 11/1/2012 added Short

// BH 9/10/2012 6:27:21 AM added java.net.URL... classes