jabaws

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Refactor: relocate getLimit() method from Util client to Util engine as SkeletalExecutable (part of the engine depends on it)

Update compile ant task to get rid of warnings.

However, ant still does not complile due to cast issue. TODO later

Updating version of utils and datamodel as it includes the utils

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3967 e3abac25-378b-4346-85de-24260fe3988d

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    /engine/compbio/engine/client/PathValidator.java
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    /engine/compbio/engine/client/Util.java
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    /webservices/compbio/ws/server/AAConWS.java
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    /webservices/compbio/ws/server/JronnWS.java
  1. … 5 more files in changeset.
Adding new website from r3934 JABA_r1 branch

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3936 e3abac25-378b-4346-85de-24260fe3988d

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    /website/contacts.html
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Remove old web site to replace with the new web site from JABA_r1 branch

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3935 e3abac25-378b-4346-85de-24260fe3988d

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    /website/archive/TO1381.fasta
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    /website/archive/full-jaba-client.jar
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    /website/archive/out.txt
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Doc update

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3855 e3abac25-378b-4346-85de-24260fe3988d

Fix to JABAWS web.xml file to make it work with tomcat 7

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3829 e3abac25-378b-4346-85de-24260fe3988d

statistics processor further work

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3818 e3abac25-378b-4346-85de-24260fe3988d

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Add exec statistics processor & derby database

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3806 e3abac25-378b-4346-85de-24260fe3988d

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    /ExecutionStatistic/seg0/c10.dat
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Centralized statistic collector. All WS are converted to use the same input and output names nano time changed to milliseconds time. Is not finished yet

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3789 e3abac25-378b-4346-85de-24260fe3988d

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    /engine/compbio/engine/ExecutionStatCollector.java
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    /engine/compbio/engine/client/Util.java
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    /webservices/compbio/ws/server/AAConWS.java
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    /webservices/compbio/ws/server/JronnWS.java
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    /webservices/compbio/ws/server/MafftWS.java
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    /webservices/compbio/ws/server/MuscleWS.java
Add limits for presets from jws2 branch

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3752 e3abac25-378b-4346-85de-24260fe3988d

Change the way to deal with Limits to simplify wrapper writing and enable couping with null limits

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3751 e3abac25-378b-4346-85de-24260fe3988d

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    /webservices/compbio/ws/server/AAConWS.java
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    /webservices/compbio/ws/server/JronnWS.java
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    /webservices/compbio/ws/server/MafftWS.java
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    /webservices/compbio/ws/server/MuscleWS.java
Change the way to deal with Limits to simplify wrapper writing and enable couping with null limits

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3750 e3abac25-378b-4346-85de-24260fe3988d

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    /runner/compbio/runner/conservation/AACon.java
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    /runner/compbio/runner/disorder/Disembl.java
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    /runner/compbio/runner/disorder/GlobPlot.java
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    /runner/compbio/runner/msa/ClustalW.java
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    /runner/compbio/runner/msa/Mafft.java
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    /runner/compbio/runner/msa/Muscle.java
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    /runner/compbio/runner/msa/Probcons.java
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    /runner/compbio/runner/msa/Tcoffee.java
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    /runner/compbio/runner/psiblast/PsiBlast.java
  1. … 11 more files in changeset.
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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    /datamodel/compbio/data/sequence/Range.java
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    /datamodel/compbio/data/sequence/Score.java
Fixes to test cases

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

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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    /testsrc/compbio/ws/client/TestAAConWS.java
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@3731 e3abac25-378b-4346-85de-24260fe3988d

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    /datamodel/compbio/data/sequence/ScoreManager.java
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    /testsrc/compbio/ws/client/TestAAConWS.java
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    /webservices/compbio/ws/client/IOHelper.java
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    /webservices/compbio/ws/server/AAConWS.java
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    /webservices/compbio/ws/server/JronnWS.java
new services are registered in wsbuild

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3728 e3abac25-378b-4346-85de-24260fe3988d

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    /datamodel/compbio/data/sequence/Score.java
  1. … 22 more files in changeset.
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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    /webservices/compbio/ws/client/Services.java
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

Disable jronn parameter

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3723 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

Copying Bio-python to globplot to satisfy the dependency

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3719 e3abac25-378b-4346-85de-24260fe3988d

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    /binaries/src/globplot/biopython-1.50/Bio/Alphabet/IUPAC.py
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    /binaries/src/globplot/biopython-1.50/Bio/Alphabet/Reduced.py
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    /binaries/src/globplot/biopython-1.50/Bio/Alphabet/__init__.py
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    /binaries/src/globplot/biopython-1.50/Bio/Application/__init__.py
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    /binaries/src/globplot/biopython-1.50/Bio/Data/CodonTable.py
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    /binaries/src/globplot/biopython-1.50/Bio/Data/__init__.py
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    /binaries/src/globplot/biopython-1.50/Bio/Decode.py
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    /binaries/src/globplot/biopython-1.50/Bio/DocSQL.py
  1. … 74 more files in changeset.
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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    /binaries/src/globplot/GlobPipe.py
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    /binaries/src/globplot/GlobPlot.py
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    /conf/settings/GlobPlotLimits.xml
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    /how_to_add_new_webservice.txt
Add globplot and disembl to web services descriptors

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3710 e3abac25-378b-4346-85de-24260fe3988d

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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    /binaries/src/disembl/DisEMBL.py
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    /datamodel/compbio/data/sequence/Range.java
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    /datamodel/compbio/data/sequence/Score.java
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    /runner/compbio/runner/disorder/GlobPlot.java
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    /testsrc/compbio/runner/disorder/GlobPlotTester.java
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    /testsrc/testdata/globplot.out
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    /webservices/compbio/ws/server/GlobPlotWS.java
git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3705 e3abac25-378b-4346-85de-24260fe3988d

Disembl and Jronn web services work. Modified to produce raw scores Globplot script is added into binaries. Annotation IF renamed to SequenceAnnotation and getAnnotation() method returns Map<String, Set<Score>> result instead of Set<Score> to unify. Changes cause by this is propagated.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3704 e3abac25-378b-4346-85de-24260fe3988d

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    /binaries/src/globplot/GlobPipe.py.original
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    /binaries/src/globplot/LICENSE
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    /binaries/src/globplot/README
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    /runner/compbio/runner/disorder/Disembl.java
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    /runner/compbio/runner/disorder/GlobProt.java
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    /webservices/compbio/data/msa/SequenceAnnotation.java
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    /webservices/compbio/ws/client/IOHelper.java
  1. … 4 more files in changeset.
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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    /testsrc/testdata/scores.out
Add py script to executable too

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3694 e3abac25-378b-4346-85de-24260fe3988d

got rid of all disembl parameters as they were pointless to change dues to the fact that underlaying executable refuses to accept values or they have no impact

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3693 e3abac25-378b-4346-85de-24260fe3988d

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    /binaries/src/disembl/DisEMBL.py
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add disembl limits

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3688 e3abac25-378b-4346-85de-24260fe3988d

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    /conf/settings/DisemblLimits.xml