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JWS-114 Bumped the version of the webservices 'JABAWS_VERSION' to 2.2.

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

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

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Add Jabaws version id as publicly available string in webservices

Add all needed infrastructure for MSAprobs and GLprobs

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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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Use "right" namespace, i.e. the name from JABAService

Change JAXWS java code and wsdl for changed methods in RegistryWS

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    ./jaxws/GetNonoperatedServices.java
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    ./jaxws/GetNonoperatedServicesResponse.java
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Add new method

Add new V3 namespace

Clean-up, refactoring, commenting. Parameters file containts only options since Jalview still can't deal with them

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Category.java updated to include new category for RNA folding. RNAalifoldParameters.xml cut down to a number of parameters which I think are needed and which work easily with Jalview

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Import RNAalifold removed from RNAStructReader. @XmlSeeAlso line added to ScoreManager.

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    ./jaxws/JobSubmissionExceptionBean.java
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    ./jaxws/LimitExceededExceptionBean.java
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Alifold results are now parsed and stored in a ScoreManager object

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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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JpredWS code and codes which provide support for JpredWS

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Regenerated classes. No significant changes

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    ./jaxws/CustomAlignResponse.java
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    ./jaxws/CustomAnalizeResponse.java
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    ./jaxws/GetAnnotationResponse.java
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    ./jaxws/GetJobStatusResponse.java
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Webservice works! but only supports some parameters. Replacing RNAstuct with String.

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    ./jaxws/CustomFold.java
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    ./jaxws/CustomFoldResponse.java
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    ./jaxws/FoldResponse.java
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correct comment

test that methods and fields of Category are publicly accessible

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4707 e3abac25-378b-4346-85de-24260fe3988d

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Fix bug in category class and use Jim's test as a test case

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4703 e3abac25-378b-4346-85de-24260fe3988d

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Move Category into data.msa package from ws.server to get it into min jabaws package.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4700 e3abac25-378b-4346-85de-24260fe3988d

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    ./jaxws/GetServiceCategoriesResponse.java
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Update for web services stubs

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4566 e3abac25-378b-4346-85de-24260fe3988d

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    ./jaxws/GetServiceCategories.java
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    ./jaxws/GetServiceCategoriesResponse.java
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    ./jaxws/GetServiceDescription.java
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    ./jaxws/GetServiceDescriptionResponse.java
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Add an implementation for Services.getServiceInfo method and categorization for services.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4562 e3abac25-378b-4346-85de-24260fe3988d

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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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Change header template for a new version

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4495 e3abac25-378b-4346-85de-24260fe3988d

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Slight refactoring

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4342 e3abac25-378b-4346-85de-24260fe3988d

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    ./jaxws/GetConservationResponse.java
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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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    ./jaxws/JobSubmissionExceptionBean.java
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    ./jaxws/LimitExceededExceptionBean.java
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    ./jaxws/ResultNotAvailableExceptionBean.java
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    ./jaxws/UnsupportedRuntimeExceptionBean.java
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    ./jaxws/WrongParameterExceptionBean.java
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Web service stubs are regenerated to incorporate new the methods. Excveption handling improved for tester

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4231 e3abac25-378b-4346-85de-24260fe3988d

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    ./jaxws/GetLastTested.java
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    ./jaxws/GetLastTestedOn.java
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    ./jaxws/GetLastTestedOnResponse.java
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    ./jaxws/GetLastTestedResponse.java
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    ./jaxws/GetSupportedServices.java
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    ./jaxws/GetSupportedServicesResponse.java
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    ./jaxws/IsOperating.java
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    ./jaxws/IsOperatingResponse.java
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    ./jaxws/JobSubmissionExceptionBean.java
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    ./jaxws/LimitExceededExceptionBean.java
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    ./jaxws/ResultNotAvailableExceptionBean.java
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    ./jaxws/TestAllServices.java
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    ./jaxws/TestAllServicesResponse.java
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    ./jaxws/TestService.java
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    ./jaxws/TestServiceResponse.java
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further work on registry & WSTester nearly there

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4229 e3abac25-378b-4346-85de-24260fe3988d

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