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JWS-120 Fixes the exception raised by the ChunkHolder method in GenericMetadataService. This behavior was expected for services which do not support execution statistics. This solution was found in the compbio.ws.server.JronnWS.java.

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

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Google analytics receives message with actual Jabaws version

Roll back some changes in WSDL of RegistryWS for some time: restore back compatibility

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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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    ./resource/GLprobsWS_schema1.xsd
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    ./resource/MSAprobsWS_schema1.xsd
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    ./resource/MsaWS.wsdl
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    ./resource/MsaWS_schema1.xsd
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Add all needed infrastructure for MSAprobs and GLprobs

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    ./MSAprobsWS.java
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    ./resource/GLprobsWS.wsdl
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    ./resource/GLprobsWS_schema1.xsd
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    ./resource/MSAprobsWS.wsdl
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    ./resource/MSAprobsWS_schema1.xsd
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Refactoring: rename duplicated Util classes

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Re-generate WS artefacts: option.furtherDetails is xs:string now

Final fixing of Jpred problem with casting

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Fix probem with metadata

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Clean up logging system

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

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New version of wsdl and xsd files for all services

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    ./resource/ClustalWS_schema1.xsd
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    ./resource/DisemblWS_schema1.xsd
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    ./resource/GlobPlotWS_schema1.xsd
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Add "safe type casting" warnings

Add "safe type cast" warnings

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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Regenerate wsdl-s

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    ./resource/ClustalWS_schema1.xsd
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    ./resource/DisemblWS_schema1.xsd
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    ./resource/GlobPlotWS_schema1.xsd
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    ./resource/JpredWS_schema1.xsd
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Switch to olde namespace

Different code style

Switch JpredWS from SequenceAnnotation to MsaWS

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

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Change JAXWS java code and wsdl for changed methods in RegistryWS

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Other necessary changes

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report both operating and non-operating services

Parameter bug fixed, Jalview will now run some parameters

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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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WSTester updated to work plus hopefully all the other changes that need to go into the remote.

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    ./resource/ClustalWS_schema1.xsd
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    ./resource/DisemblWS_schema1.xsd
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    ./resource/GlobPlotWS_schema1.xsd
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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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