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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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    ./compbio/runner/Util.java
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JWS-113 Commented Jpred entries in the datamodel, runner and webservices java source code.

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    ./compbio/runner/predictors/Jpred.java
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Re-design jpred.pl input options: no -seq for a file with 1 FASTA record only.

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    ./compbio/runner/predictors/Jpred.java
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Define path to UNIREF database in conf/Executable.properties

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    ./compbio/runner/predictors/Jpred.java
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Fix wrong error message

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    ./compbio/runner/conservation/AACon.java
Add all needed infrastructure for MSAprobs and GLprobs

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    ./compbio/runner/msa/GLprobs.java
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    ./compbio/runner/msa/MSAprobs.java
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Refactoring: rename duplicated Util classes

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    ./compbio/runner/RunnerUtil.java
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    ./compbio/runner/conservation/AACon.java
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    ./compbio/runner/disorder/Disembl.java
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    ./compbio/runner/disorder/GlobPlot.java
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    ./compbio/runner/structure/RNAalifold.java
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JWS-17: fix problem with undefined URL for the furtherDetails tag

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Clean up logging system

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    ./compbio/runner/OptionCombinator.java
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    ./compbio/runner/conservation/AACon.java
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    ./compbio/runner/disorder/Disembl.java
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    ./compbio/runner/disorder/GlobPlot.java
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    ./compbio/runner/structure/RNAalifold.java
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Switch JpredWS from SequenceAnnotation to MsaWS

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    ./compbio/runner/predictors/Jpred.java
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Clean-up, refactoring, commenting. Parameters file containts only options since Jalview still can't deal with them

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    ./compbio/runner/structure/RNAalifold.java
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Reverted some changes I made for testing back to their original states.

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RNAStruct replaced by RNAStructScoreManager. Why does webservice getAnnotation method still return a ScoreManager Not an RNAStructScoreManager?!?

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    ./compbio/runner/structure/RNAalifold.java
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Alifold results are now parsed and stored in a ScoreManager object

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    ./compbio/runner/structure/RNAalifold.java
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Webservice which implements FoldWS and returns String. Parameters.xml file updated in line with the RunnerConfig schema.

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    ./compbio/runner/structure/RNAalifold.java
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Webservice works! but only supports some parameters. Replacing RNAstuct with String.

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    ./compbio/runner/structure/RNAalifold.java
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Necessary modifications in JABAWS for Jpred

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    ./compbio/runner/predictors/Jpred.java
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Simple datamodel for RNAalifold.exe output and method to convert from fasta to clustal format and write clustal input files.

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    ./compbio/runner/structure/RNAalifold.java
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Parameters Tester updated. Untested webservice code. generate xsd/wsdl?

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    ./compbio/runner/structure/RNAalifold.java
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Basic Testing Setup, no getResults method yet

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    ./compbio/runner/structure/RNAalifold.java
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Add Java wrapper class for Jpred

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    ./compbio/runner/predictors/Jpred.java
Impove coding style

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    ./compbio/runner/disorder/Jronn.java
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RNAalifold.java runner and RNAalifoldTester incomplete

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    ./compbio/runner/structure/RNAalifold.java
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delete wronigly located log4j.properties

remove jabaws 3 development code

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    ./compbio/data/_structure/JpredResult.java
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    ./compbio/pipeline/_jpred/BlastParser.java
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    ./compbio/pipeline/_jpred/JackHmmerHitParser.java
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    ./compbio/pipeline/_jpred/Jpred4.java
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    ./compbio/pipeline/_jpred/PScore.java
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    ./compbio/pipeline/_jpred/Pairwise.java
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    ./compbio/pipeline/_jpred/Requirements
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    ./compbio/runner/_NativeSpecHelper.java
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    ./compbio/runner/_SkeletalCommandBuilder.java
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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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    ./compbio/runner/_NativeSpecHelper.java
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Change header template for a new version

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4494 e3abac25-378b-4346-85de-24260fe3988d

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    ./compbio/data/_structure/JpredResult.java
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    ./compbio/pipeline/_jpred/BlastParser.java
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    ./compbio/pipeline/_jpred/JackHmmerHitParser.java
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    ./compbio/pipeline/_jpred/Pairwise.java
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    ./compbio/runner/OptionCombinator.java
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    ./compbio/runner/_NativeSpecHelper.java
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Comments

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4473 e3abac25-378b-4346-85de-24260fe3988d

Clustal Omega web service wrapper and tester

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4462 e3abac25-378b-4346-85de-24260fe3988d

Wrapper for Clustal Omega.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4458 e3abac25-378b-4346-85de-24260fe3988d

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    ./compbio/runner/msa/ClustalO.java
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