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JWS-128 patch out log4j references in the compbio.FileUtil class, and corresponding calls to methods in the JABAWS client and engine code.

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JWS-128 compbio-utils sources added to compilation tree and log4j logging dependence removed

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JWS-114 Bumping varied config files and jetbrains xmls. Also adding some java classes that are generated during the compilation.

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Refactoring: rename duplicated Util classes

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    ./EngineUtil.java
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Remove unused imports

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Clean up logging system

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Improve coding style

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Improve coding style

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Impove coding style

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JWS-44 - attempt to make a file executable if it is supposed to be executable according to jabaws configuration.

An attempt to automatically make binaries executables - not successful but the code is commented out and let in for future use

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4548 e3abac25-378b-4346-85de-24260fe3988d

Javadoc fixes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4508 e3abac25-378b-4346-85de-24260fe3988d

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Better method for searching JAVA

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4392 e3abac25-378b-4346-85de-24260fe3988d

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remove assert

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4378 e3abac25-378b-4346-85de-24260fe3988d

obtain JAVA executable path from the JAVA_HOME variable. Does not require path to java for jar libraries.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4376 e3abac25-378b-4346-85de-24260fe3988d

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Fix for testcases

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4307 e3abac25-378b-4346-85de-24260fe3988d

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Get rind of NativeClusterJob interface as pretty much every jobs best to use some cluster settings, and they are simply defined in the executable conf file and passed by the SkeletalExecutable.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4294 e3abac25-378b-4346-85de-24260fe3988d

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Refactoring of all SequenceAnnotation web services New version of Metro Definition for IUPred exec Stubs regenerated

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4280 e3abac25-378b-4346-85de-24260fe3988d

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IUPred final touches. All test cases pass

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4274 e3abac25-378b-4346-85de-24260fe3988d

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Adding registry web service and changes to WStester and JWS2Client code. Bugs in input/ouput setup for a few web services fixed

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4223 e3abac25-378b-4346-85de-24260fe3988d

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Changes to return type of Executable.getType() method to make it compile with Oracle javac. A few modifications to statistics package.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4201 e3abac25-378b-4346-85de-24260fe3988d

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Refactor: relocate getLimit() method from Util client to Util engine as SkeletalExecutable (part of the engine depends on it)

Update compile ant task to get rid of warnings.

However, ant still does not complile due to cast issue. TODO later

Updating version of utils and datamodel as it includes the utils

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3967 e3abac25-378b-4346-85de-24260fe3988d

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Centralized statistic collector. All WS are converted to use the same input and output names nano time changed to milliseconds time. Is not finished yet

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3789 e3abac25-378b-4346-85de-24260fe3988d

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Change the way to deal with Limits to simplify wrapper writing and enable couping with null limits

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3751 e3abac25-378b-4346-85de-24260fe3988d

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Change the way to deal with Limits to simplify wrapper writing and enable couping with null limits

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3750 e3abac25-378b-4346-85de-24260fe3988d

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Some refactoring

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2651 e3abac25-378b-4346-85de-24260fe3988d

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Add JRonn runner, tester, methods to parse jronn output files.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2638 e3abac25-378b-4346-85de-24260fe3988d

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Next version of JABA

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2610 e3abac25-378b-4346-85de-24260fe3988d

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    ./ClusterNativeSpecExecutable.java
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    ./CommandBuilder.java
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    ./ConfExecutable.java
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    ./ConfiguredExecutable.java
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    ./EnvVariableProcessor.java
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    ./PathValidator.java
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    ./PipedExecutable.java
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    ./RunConfiguration.java
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    ./SkeletalExecutable.java
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