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

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    ./sequence/SequenceUtilTester.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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    ./sequence/SequenceUtilTester.java
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Change header

change header

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Change header

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Add test of parser of Jpred output

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    ./sequence/SequenceUtilTester.java
Simple datamodel for RNAalifold.exe output and method to convert from fasta to clustal format and write clustal input files.

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test demonstrating JWS-29 assertion failure

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test for JWS-35 - check that range and first value of prediction for each method matches expected values

test for JWS-35 - check that range and first value of prediction for each method matches expected values

A few minor changes to the test

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4706 e3abac25-378b-4346-85de-24260fe3988d

Assign a test to an appropriate test category

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4704 e3abac25-378b-4346-85de-24260fe3988d

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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    ./msa/CategoryTester.java
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Fixes for failed test cases (most was due to the data being used or problems with test cases themselves)

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4303 e3abac25-378b-4346-85de-24260fe3988d

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IUPred final touches. All test cases pass

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4274 e3abac25-378b-4346-85de-24260fe3988d

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IUPred wrapper, tester and new binary for X64 linux systems

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4265 e3abac25-378b-4346-85de-24260fe3988d

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IUPred result readers. IUpred binaries compilation scripts. IUpred executable description. IUPred output files for testing

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4263 e3abac25-378b-4346-85de-24260fe3988d

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More work to disorder prediction client & services.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4236 e3abac25-378b-4346-85de-24260fe3988d

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    ./sequence/ClustalAlignmentUtilTester.java
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Add method to SequenceUtil to clean the protein sequence

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4047 e3abac25-378b-4346-85de-24260fe3988d

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New FastaReader implementing iterator & test case for it

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4041 e3abac25-378b-4346-85de-24260fe3988d

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    ./sequence/FastaReaderTester.java
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Finally, the new web services are working

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3738 e3abac25-378b-4346-85de-24260fe3988d

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Replace Map<String, HashSet<Score>> with ScoreManager and ScoreHolder classes to compensate for JAXB inability to serialize Maps. Propagate the changes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3733 e3abac25-378b-4346-85de-24260fe3988d

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DisEMBL and GlobProt web services further work

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3727 e3abac25-378b-4346-85de-24260fe3988d

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Further work on GlobPlot

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3718 e3abac25-378b-4346-85de-24260fe3988d

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GlobPlot service, runner and result parser Some rearrangements for disembl to reuse methods

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3709 e3abac25-378b-4346-85de-24260fe3988d

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    ./sequence/SequenceUtilTester.java
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Parser for DisEMBL results and finished runner, few test cases. DisemblTester has all tests "green"

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3695 e3abac25-378b-4346-85de-24260fe3988d

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    ./sequence/SequenceUtilTester.java
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Disembl further implementation

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3663 e3abac25-378b-4346-85de-24260fe3988d

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Remove Annotated and MuptiAnnotated Sequence use Score instead

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3660 e3abac25-378b-4346-85de-24260fe3988d

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AAConWS is working

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3416 e3abac25-378b-4346-85de-24260fe3988d

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AAConWS further work

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3406 e3abac25-378b-4346-85de-24260fe3988d

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Tests for AACon loader

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3387 e3abac25-378b-4346-85de-24260fe3988d

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