Daniel Barton

Brief html documentation entry for RNAalifold under webServices

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    /help/html/webServices/RNAalifold.html
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    /help/html/webServices/RNAalifoldAnnotationRows.png
merged conf/Executable.properties

Parameter bug fixed, Jalview will now run some parameters

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    /conf/settings/RNAalifoldOptionsOnly.xml
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    /conf/settings/RNAalifoldParameters.xml
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    /webservices/compbio/ws/server/WSUtil.java
A secondary parameters file with some Jalview friendly parameters

Colour be RNA helices bug fixed

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    /src/jalview/schemes/RNAHelicesColourChooser.java
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    /src/jalview/ws/jws2/RNAalifoldClient.java
JAL-1358 Cleaned up RNAalifoldClient.java. RNA helices colouring bug and parameters bug unsolved

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    /src/jalview/ws/jws2/RNAalifoldClient.java
Clean-up, refactoring, commenting. Parameters file containts only options since Jalview still can't deal with them

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    /conf/settings/RNAalifoldOptionsOnly.xml
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    /conf/settings/RNAalifoldParameters.xml
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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/structure/RNAalifold.java
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    /webservices/compbio/data/msa/FoldWS.java
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    /webservices/compbio/ws/client/Services.java
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    /webservices/compbio/ws/client/WSTester.java
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    /webservices/compbio/ws/server/WSUtil.java
JWS-69 RNAalifold Linux Binary

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    /binaries/src/ViennaRNA/Progs/RNAalifold
RNAalifoldClient updated to be more like AAConClient and now (attempts) to support all the output from RNAalifold

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    /src/jalview/ws/jws2/JabaWsServerQuery.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
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    /src/jalview/ws/jws2/RNAalifoldClient.java
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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    /conf/settings/RNAalifoldParameters.xml
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    /datamodel/compbio/data/sequence/Score.java
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    /webservices/compbio/data/msa/Category.java
JAL-1358 jalview displays some RNA struture annotation but the format is very messed up

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    /lib/min-jabaws-client-3.0.0.jar
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    /src/jalview/ws/jws2/RNAalifoldClient.java
Merge remote-tracking branch 'origin/Release_2_8_1_Branch' into RNAalifold

JAL-1358 RNAStructExportImport test file mirrors DisorderAnnotExportImport file. RNAalifoldClient updated to basic working state.

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    /examples/unfolded_RF00031.aln
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    /src/jalview/ws/jws2/RNAalifoldClient.java
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    /test/jalview/ws/jabaws/RNAStructExportImport.java
JAL-1358 Just the eclipse project/classpath files so that I can stash changes and demonstrate DisorderAnnotExportImport failure

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    /src/jalview/ws/jws2/RNAalifoldClient.java
WSTester updated to work plus hopefully all the other changes that need to go into the remote.

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    /binaries/src/ViennaRNA/AUTHORS
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    /binaries/src/ViennaRNA/COPYING
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    /binaries/src/ViennaRNA/ChangeLog
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    /binaries/src/ViennaRNA/Cluster/AD_main.c
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    /binaries/src/ViennaRNA/Cluster/AS_main.c
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    /binaries/src/ViennaRNA/Cluster/AnalyseDists.1
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    /binaries/src/ViennaRNA/Cluster/AnalyseSeqs.1
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    /binaries/src/ViennaRNA/Cluster/Makefile.am
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    /binaries/src/ViennaRNA/Cluster/Makefile.in
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    /binaries/src/ViennaRNA/Cluster/PS3D.c
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    /binaries/src/ViennaRNA/Cluster/PS3D.h
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Jalview builds sucessfully and runs from eclipse

Import RNAalifold removed from RNAStructReader. @XmlSeeAlso line added to ScoreManager.

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Reverted some testing changes in TestRNAalifoldWS so that it will run successfully.

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    /testsrc/compbio/ws/client/TestRNAalifoldWS.java
Reverted some changes I made for testing back to their original states.

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    /webservices/compbio/ws/server/WSUtil.java
A third commit where there should have been one.... Everything is here now I hope.

Update the last commit which missed some files. RNAStructScoreManager replacing RNAStruct. Webservices returns ScoreManager!?!-

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    /webservices/compbio/ws/server/WSUtil.java
RNAStruct replaced by RNAStructScoreManager. Why does webservice getAnnotation method still return a ScoreManager Not an RNAStructScoreManager?!?

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    /datamodel/compbio/data/sequence/RNAStructScoreManager.java
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    /runner/compbio/runner/structure/RNAalifold.java
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    /testsrc/compbio/ws/client/TestRNAalifoldWS.java
Webservices Actually working with ScoreManager

Webservice working with ScoreManager

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    /webservices/compbio/ws/server/WSUtil.java
Webservice Updated for scoremanager but I think I broke something on the way.

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    /webservices/compbio/ws/client/Services.java
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    /webservices/compbio/ws/server/RNAalifoldWS.java
Alifold results are now parsed and stored in a ScoreManager object

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    /datamodel/compbio/data/sequence/RNAStruct.java
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    /datamodel/compbio/data/sequence/RNAStructReader.java
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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/Util.java
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    /runner/compbio/runner/structure/RNAalifold.java
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    /webservices/compbio/data/msa/FoldWS.java
Webservice which implements FoldWS and returns String. Parameters.xml file updated in line with the RunnerConfig schema.

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    /conf/settings/RNAalifoldParameters.xml
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    /runner/compbio/runner/structure/RNAalifold.java
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    /webservices/compbio/data/msa/FoldWS.java
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    /webservices/compbio/ws/client/WSTester.java
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
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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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    /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