datamodel

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

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    ./compbio/data/sequence/Alignment.java
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    ./compbio/data/sequence/JpredAlignment.java
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    ./compbio/data/sequence/SequenceUtil.java
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JWS-17 regression error - remove unnecessary throws statement

Simplify code

Add all needed infrastructure for MSAprobs and GLprobs

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    ./compbio/data/sequence/Program.java
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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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    ./compbio/metadata/Argument.java
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    ./compbio/metadata/ValueConstrain.java
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Final fixing of Jpred problem with casting

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    ./compbio/data/sequence/Alignment.java
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Fix probem with metadata

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Remove unused imports

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Clean up logging system

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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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    ./compbio/data/sequence/Alignment.java
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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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    ./compbio/data/sequence/SequenceUtil.java
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Switch JpredWS from SequenceAnnotation to MsaWS

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    ./compbio/data/sequence/Alignment.java
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    ./compbio/data/sequence/JpredAlignment.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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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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    ./compbio/data/sequence/ScoreManager.java
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Import RNAalifold removed from RNAStructReader. @XmlSeeAlso line added to ScoreManager.

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    ./compbio/data/sequence/ScoreManager.java
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A third commit where there should have been one.... Everything is here now I hope.

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    ./compbio/data/sequence/ScoreManager.java
RNAStruct replaced by RNAStructScoreManager. Why does webservice getAnnotation method still return a ScoreManager Not an RNAStructScoreManager?!?

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    ./compbio/data/sequence/RNAStruct.java
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    ./compbio/data/sequence/RNAStructReader.java
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    ./compbio/data/sequence/RNAStructScoreManager.java
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Alifold results are now parsed and stored in a ScoreManager object

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    ./compbio/data/sequence/RNAStruct.java
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    ./compbio/data/sequence/RNAStructReader.java
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    ./compbio/data/sequence/RNAstruct.java
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    ./compbio/data/sequence/ScoreManager.java
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    ./compbio/data/sequence/SequenceUtil.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/data/sequence/SequenceUtil.java
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change header

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    ./compbio/data/sequence/SequenceUtil.java
Change header

change header

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    ./compbio/data/sequence/SequenceUtil.java
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Necessary modifications in JABAWS for Jpred

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    ./compbio/data/sequence/SequenceUtil.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/data/sequence/RNAstruct.java
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    ./compbio/data/sequence/SequenceUtil.java
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remove unnecessary import

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    ./compbio/data/sequence/FastaReader.java
JWS-29 patch fixes bug - wierd workaround since "^\\s*>" caused scanner to advance to end of file rather than start of next FASTA header

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    ./compbio/data/sequence/FastaReader.java
JWS-36 patched Scores writer to put spaces between ranges and space separated scores

patch fixes JWS-35

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    ./compbio/data/sequence/SequenceUtil.java
patch fixes JWS-35

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    ./compbio/data/sequence/SequenceUtil.java