jabaws

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Add untracked dir

Add a file with the runnig command and environment in each wrok dir

Add a file with the runnig command and environment in each wrok dir

Improve coding style

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    /engine/compbio/engine/local/LocalRunner.java
Improve coding style

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    /engine/compbio/engine/local/LocalRunner.java
change header

Change header

change header

Change header

1st working Jpred tester

Check and correct several runner testers

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    /testsrc/compbio/runner/msa/ClustalOTester.java
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    /testsrc/compbio/runner/msa/ClustalWTester.java
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    /testsrc/compbio/runner/msa/TcoffeeTester.java
Remove unused global varibles

Add test of parser of Jpred output

uncomment limit files in order to make some tests successful

Add results of tests of Jpred

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    /binaries/src/jpred/tests/res_d16vpa_.res.fasta
Add Jpred result files

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    /testsrc/testdata/Jpred.test1.fasta
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    /testsrc/testdata/Jpred.test1.fasta.res.align
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    /testsrc/testdata/Jpred.test1.fasta.res.blast.gz
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    /testsrc/testdata/Jpred.test1.fasta.res.hmm
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    /testsrc/testdata/Jpred.test1.fasta.res.jnet
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    /testsrc/testdata/Jpred.test1.fasta.res.profile
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    /testsrc/testdata/Jpred.test1.fasta.res.pssm
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    /testsrc/testdata/Jpred.test1.out
Webservice works! but only supports some parameters. Replacing RNAstuct with String.

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    /conf/settings/RNAalifoldParameters.xml
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    /runner/compbio/runner/structure/RNAalifold.java
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    /testsrc/compbio/ws/client/TestRNAalifoldWS.java
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    /webservices/compbio/data/msa/FoldWS.java
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    /webservices/compbio/data/msa/jaxws/CustomFold.java
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    /webservices/compbio/data/msa/jaxws/CustomFoldResponse.java
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    /webservices/compbio/data/msa/jaxws/Fold.java
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    /webservices/compbio/data/msa/jaxws/FoldResponse.java
  1. … 23 more files in changeset.
Necessary modifications in JABAWS for Jpred

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    /datamodel/compbio/data/sequence/Program.java
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    /runner/compbio/runner/predictors/Jpred.java
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    /testsrc/compbio/runner/predictors/JpredTester.java
Describe new parameters of Jpred

Modify Jpred for JABAWS

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    /binaries/src/jpred/lib/Paths.pm
Simple datamodel for RNAalifold.exe output and method to convert from fasta to clustal format and write clustal input files.

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    /datamodel/compbio/data/sequence/RNAstruct.java
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    /runner/compbio/runner/structure/RNAalifold.java
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    /webservices/compbio/data/structure/FoldWS.java
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    /webservices/compbio/ws/server/WSUtil.java
Parameters Tester updated. Untested webservice code. generate xsd/wsdl?

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    /runner/compbio/runner/structure/RNAalifold.java
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    /webservices/compbio/ws/server/RNAalifoldWS.java
Basic Testing Setup, no getResults method yet

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    /conf/settings/RNAalifoldParameters.xml
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    /runner/compbio/runner/structure/RNAalifold.java
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    /testsrc/testdata/RNAalifoldParameters.xml
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    /testsrc/testdata/unfolded_RF00031.aln
Add Java wrapper class for Jpred

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    /runner/compbio/runner/predictors/Jpred.java
Re-format configuration files

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    /conf/settings/AAConParameters.xml
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    /conf/settings/ClustalLimits.xml
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    /conf/settings/ClustalParameters.xml
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    /conf/settings/ClustalPresets.xml
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    /conf/settings/ClustaloLimits.xml
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    /conf/settings/DisemblLimits.xml
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    /conf/settings/DisemblParameters.xml
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    /conf/settings/GlobPlotLimits.xml
  1. … 7 more files in changeset.
add results of one Jpred test

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    /binaries/src/jpred/tests/res_d16vpa_.align
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    /binaries/src/jpred/tests/res_d16vpa_.concise
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    /binaries/src/jpred/tests/res_d16vpa_.hmm
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    /binaries/src/jpred/tests/res_d16vpa_.jnet
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    /binaries/src/jpred/tests/res_d16vpa_.profile
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    /binaries/src/jpred/tests/res_d16vpa_.pssm
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    /binaries/src/jpred/tests/res_d16vpa_.res
Add converion Jpred output from align/jnet to fasta

Change JABAWS version: 2.0.1 -> 2.5

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Add new artwork

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    /website/images/jabaws25.ai
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    /website/images/jabaws25.png
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    /website/images/jabaws30.ai
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    /website/images/jabaws30.png
Impove coding style

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    /runner/compbio/runner/msa/Mafft.java
Re-format the config files in order to get more readable files

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    /conf/settings/ClustalParameters.xml
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    /conf/settings/ClustaloParameters.xml
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    /conf/settings/MafftParameters.xml
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    /conf/settings/TcoffeeParameters.xml
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    /conf/settings/TcoffeePresets.xml