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JWS-112 Updated AACon to version 1.1.

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JWS-112 Updated the versions the tool versions that are shown in the ServiceStatus page

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

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Define path to UNIREF database in conf/Executable.properties

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Comment code for future options

Remove still unsupported methods of RegistryWS

Bug Fixg: testing RNAalifold jobs have been considered as real ones

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Add Jabaws version string available in Services

Refactoring (renaming) 2 classes: AsyncJobRunner.java -> AsyncClusterRunner.java and JobRunner.java -> ClusterRunner.java

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Assign JABAService.V2_SERVICE_NAMESPACE to all new services: JpredWS, RNAalifoldWS, MSAprobsWS, GLprobsWS

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Add all needed infrastructure for MSAprobs and GLprobs

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Refactoring: rename duplicated Util classes

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JWS-17 re-design behaviour of Option.toString

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JWS-17: fix problem with undefined URL for the furtherDetails tag

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Final fixing of Jpred problem with casting

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Clean up logging system

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Re-design the ServiceStatus JSP page

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Define proper test for JpredWS

Fix problem with wrong casting Alignment -> JpredAlignment

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Fix problem with the JpredWS service. Now Jws2Client is able to test the service

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Fix problem with unknown services ("forward" compatibility)

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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Switch JpredWS from SequenceAnnotation to MsaWS

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Fix problem with test data for RNAalifold

Roll back JpredWS JABAWS namespace: from V3 to V2. V3 will be a Matrix

  1. … 3 more files in changeset.
Fix a bug with wrong namespace

New version of the JABAWS client

Add method for reporting JABAWS namespace

Changes which allow JpredWS test

  1. … 1 more file in changeset.
Improved help message