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

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

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Refactoring: rename duplicated Util classes

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Switch JpredWS from SequenceAnnotation to MsaWS

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RNAStruct replaced by RNAStructScoreManager. Why does webservice getAnnotation method still return a ScoreManager Not an RNAStructScoreManager?!?

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    ./structure/RNAalifoldParametersTester.java
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    ./structure/RNAalifoldTester.java
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Alifold results are now parsed and stored in a ScoreManager object

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    ./structure/RNAalifoldParametersTester.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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    ./structure/RNAalifoldParametersTester.java
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Fix problem with unknown global constants

1st working Jpred tester

Check and correct several runner testers

Necessary modifications in JABAWS for Jpred

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    ./predictors/JpredTester.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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Parameters Tester updated. Untested webservice code. generate xsd/wsdl?

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    ./structure/RNAalifoldParametersTester.java
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Basic Testing Setup, no getResults method yet

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    ./structure/RNAalifoldParametersTester.java
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RNAalifold.java runner and RNAalifoldTester incomplete

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    ./structure/RNAalifoldTester.java
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remove jabaws 3 development code

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Clustal Omega web service wrapper and tester

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4464 e3abac25-378b-4346-85de-24260fe3988d

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Wrapper for Clustal Omega.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4458 e3abac25-378b-4346-85de-24260fe3988d

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    ./msa/ClustalOTester.java
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Build script improvements & updated util

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4337 e3abac25-378b-4346-85de-24260fe3988d

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annotate test with appropriate groups

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4308 e3abac25-378b-4346-85de-24260fe3988d

A few more tests for IUPred

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4275 e3abac25-378b-4346-85de-24260fe3988d

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

  1. … 11 more files in changeset.
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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    ./disorder/IUPredTester.java
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Fixes to test cases

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3734 e3abac25-378b-4346-85de-24260fe3988d

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Fix a test case for jronn parameters

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3724 e3abac25-378b-4346-85de-24260fe3988d

GlobPlot and DIsembl execs all test passed

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3722 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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    ./disorder/GlobPlotTester.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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Disembl further implementation

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

  1. … 5 more files in changeset.
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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    ./disorder/DisemblTester.java
  1. … 13 more files in changeset.