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

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    ./data/sequence/SequenceUtilTester.java
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    ./runner/predictors/JpredTester.java
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Fix problems with tests

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    ./engine/conf/RunnerConfigMarshallerTester.java
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    ./metadata/OptionMarshallerTester.java
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    ./metadata/RunnerConfigTester.java
Refactoring (renaming) 2 classes: AsyncJobRunner.java -> AsyncClusterRunner.java and JobRunner.java -> ClusterRunner.java

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    ./engine/cluster/drmaa/ClusterSessionTester.java
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    ./runner/conservation/AAConTester.java
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Refactoring: rename duplicated Util classes

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    ./engine/cluster/drmaa/UtilTester.java
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    ./engine/local/AsyncLocalRunnerTester.java
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    ./runner/conservation/AAConTester.java
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    ./runner/msa/TcoffeeParametersTester.java
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add lost exception

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    ./engine/conf/RunnerConfigMarshallerTester.java
Fix problems with tests

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    ./engine/conf/RunnerConfigMarshallerTester.java
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    ./metadata/OptionMarshallerTester.java
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    ./metadata/RunnerConfigTester.java
Merge branch 'JABAWS_Release_2_5' into develop

Conflicts:

.project

WEB-INF/sun-jaxws.xml

conf/Executable.properties

testsrc/compbio/data/sequence/SequenceUtilTester.java

webservices/compbio/data/msa/Category.java

webservices/compbio/ws/client/Jws2Client.java

webservices/compbio/ws/client/Services.java

webservices/compbio/ws/client/WSTester.java

webservices/compbio/ws/server/WSUtil.java

webservices/compbio/ws/server/resource/AAConWS.wsdl

webservices/compbio/ws/server/resource/AAConWS_schema1.xsd

webservices/compbio/ws/server/resource/ClustalWS.wsdl

webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd

webservices/compbio/ws/server/resource/DisemblWS.wsdl

webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd

webservices/compbio/ws/server/resource/GlobPlotWS.wsdl

webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd

webservices/compbio/ws/server/resource/IUPredWS.wsdl

webservices/compbio/ws/server/resource/IUPredWS_schema1.xsd

webservices/compbio/ws/server/resource/JronnWS.wsdl

webservices/compbio/ws/server/resource/JronnWS_schema1.xsd

webservices/compbio/ws/server/resource/MafftWS.wsdl

webservices/compbio/ws/server/resource/MafftWS_schema1.xsd

webservices/compbio/ws/server/resource/MuscleWS.wsdl

webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd

webservices/compbio/ws/server/resource/RegistryWS.wsdl

webservices/compbio/ws/server/resource/RegistryWS_schema1.xsd

webservices/compbio/ws/server/resource/TcoffeeWS.wsdl

webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd

wsbuild.xml

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    ./data/sequence/SequenceUtilTester.java
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Switch JpredWS from SequenceAnnotation to MsaWS

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    ./runner/predictors/JpredTester.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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Import RNAalifold removed from RNAStructReader. @XmlSeeAlso line added to ScoreManager.

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Reverted some testing changes in TestRNAalifoldWS so that it will run successfully.

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    ./ws/client/TestRNAalifoldWS.java
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RNAStruct replaced by RNAStructScoreManager. Why does webservice getAnnotation method still return a ScoreManager Not an RNAStructScoreManager?!?

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    ./runner/structure/RNAalifoldParametersTester.java
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    ./runner/structure/RNAalifoldTester.java
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    ./ws/client/TestRNAalifoldWS.java
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Webservice working with ScoreManager

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Alifold results are now parsed and stored in a ScoreManager object

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    ./runner/structure/RNAalifoldTester.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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    ./runner/structure/RNAalifoldParametersTester.java
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    ./ws/client/TestRNAalifoldWS.java
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Fix problem with unknown global constants

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    ./runner/msa/TcoffeeParametersTester.java
Change header

change header

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    ./data/sequence/SequenceUtilTester.java
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Change header

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    ./data/sequence/SequenceUtilTester.java
1st working Jpred tester

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    ./runner/predictors/JpredTester.java
Check and correct several runner testers

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    ./runner/conservation/AAConTester.java
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    ./runner/disorder/JronnTester.java
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    ./runner/msa/ClustalOTester.java
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    ./runner/msa/ClustalWTester.java
Remove unused global varibles

Add test of parser of Jpred output

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    ./data/sequence/SequenceUtilTester.java
Webservice works! but only supports some parameters. Replacing RNAstuct with String.

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    ./ws/client/TestRNAalifoldWS.java
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Necessary modifications in JABAWS for Jpred

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    ./runner/predictors/JpredTester.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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    ./data/sequence/SequenceUtilTester.java
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    ./runner/structure/RNAalifoldTester.java
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Parameters Tester updated. Untested webservice code. generate xsd/wsdl?

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

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    ./runner/structure/RNAalifoldParametersTester.java
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    ./runner/structure/RNAalifoldTester.java
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RNAalifold.java runner and RNAalifoldTester incomplete

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    ./runner/structure/RNAalifoldTester.java
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change code style

JWS-50 patch AAConWS test for refactoring of calculation parameters to a series of options