jabaws

datamodel

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Tuesday 28 Feb 2017
12:21 pm

Fábio Madeira

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

Options
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    ./compbio/data/sequence/Alignment.java
    • -210
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    ./compbio/data/sequence/JpredAlignment.java
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    • +1
    ./compbio/data/sequence/Program.java
    • -4
    • +4
    ./compbio/data/sequence/SequenceUtil.java
  5. … 11 more files in changeset.
Friday 04 Oct 2013
1:39 pm

Jim Procter <jprocter@compbio.dundee.ac.uk>

JWS-17 regression error - remove unnecessary throws statement

Options
    • -1
    • +1
    ./compbio/metadata/Parameter.java
Wednesday 02 Oct 2013
6:14 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Simplify code

Options
    • -3
    • +3
    ./compbio/metadata/Option.java
Tuesday 24 Sep 2013
3:11 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Add all needed infrastructure for MSAprobs and GLprobs

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    • +1
    ./compbio/data/sequence/ClustalAlignmentUtil.java
    • -0
    • +11
    ./compbio/data/sequence/Program.java
  3. … 33 more files in changeset.
Thursday 19 Sep 2013
2:44 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

JWS-17 re-design behaviour of Option.toString

Options
    • -0
    • +4
    ./compbio/metadata/Option.java
  2. … 1 more file in changeset.
1:46 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

JWS-17: fix problem with undefined URL for the furtherDetails tag

Options
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    ./compbio/metadata/Argument.java
    • -3
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    ./compbio/metadata/Limit.java
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    ./compbio/metadata/LimitsManager.java
    • -9
    • +30
    ./compbio/metadata/Option.java
    • -2
    • +2
    ./compbio/metadata/Parameter.java
    • -2
    • +1
    ./compbio/metadata/Preset.java
    • -2
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    ./compbio/metadata/PresetManager.java
    • -2
    • +2
    ./compbio/metadata/ValueConstrain.java
  9. … 3 more files in changeset.
Tuesday 17 Sep 2013
3:35 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Final fixing of Jpred problem with casting

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    • -1
    • +3
    ./compbio/data/sequence/Alignment.java
  2. … 7 more files in changeset.
3:20 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Fix probem with metadata

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    • +6
    ./compbio/data/sequence/Program.java
  2. … 7 more files in changeset.
11:46 am

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Remove unused imports

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    • -3
    • +1
    ./compbio/data/sequence/RNAStructReader.java
  2. … 1 more file in changeset.
11:22 am

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Clean up logging system

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    • -15
    • +4
    ./compbio/data/sequence/RNAStructReader.java
  2. … 27 more files in changeset.
Friday 13 Sep 2013
4:43 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Fix problem with wrong casting Alignment -> JpredAlignment

Options
    • -1
    • +1
    ./compbio/data/sequence/JpredAlignment.java
  2. … 1 more file in changeset.
Wednesday 11 Sep 2013
5:13 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Fix problem with the JpredWS service. Now Jws2Client is able to test the service

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    • +2
    ./compbio/data/sequence/Alignment.java
    • -81
    • +73
    ./compbio/data/sequence/JpredAlignment.java
  3. … 2 more files in changeset.
Friday 06 Sep 2013
5:23 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

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

Options
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    ./compbio/data/sequence/SequenceUtil.java
  2. … 11 more files in changeset.
3:29 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Switch JpredWS from SequenceAnnotation to MsaWS

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    ./compbio/data/sequence/Alignment.java
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    • +237
    ./compbio/data/sequence/JpredAlignment.java
  3. … 5 more files in changeset.
Friday 30 Aug 2013
10:57 am

Daniel Barton

Clean-up, refactoring, commenting. Parameters file containts only options since Jalview still can't deal with them

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    ./compbio/data/sequence/RNAStructScoreManager.java
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    ./compbio/data/sequence/Range.java
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    ./compbio/data/sequence/Score.java
  4. … 12 more files in changeset.
Wednesday 28 Aug 2013
10:17 pm

Daniel Barton

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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    ./compbio/data/sequence/RNAStructReader.java
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    ./compbio/data/sequence/Score.java
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    ./compbio/data/sequence/ScoreManager.java
  4. … 2 more files in changeset.
Thursday 22 Aug 2013
2:00 pm

Daniel Barton

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

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    ./compbio/data/sequence/RNAStructReader.java
    • -0
    • +2
    ./compbio/data/sequence/RNAStructScoreManager.java
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    ./compbio/data/sequence/ScoreManager.java
  4. … 23 more files in changeset.
Wednesday 21 Aug 2013
11:57 am

Daniel Barton

A third commit where there should have been one.... Everything is here now I hope.

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    ./compbio/data/sequence/RNAStructScoreManager.java
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    ./compbio/data/sequence/ScoreManager.java
11:49 am

Daniel Barton

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

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    ./compbio/data/sequence/RNAStruct.java
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    ./compbio/data/sequence/RNAStructReader.java
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    ./compbio/data/sequence/RNAStructScoreManager.java
  4. … 5 more files in changeset.
Thursday 15 Aug 2013
6:13 pm

Daniel Barton

Alifold results are now parsed and stored in a ScoreManager object

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    • +119
    ./compbio/data/sequence/RNAStruct.java
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    ./compbio/data/sequence/RNAStructReader.java
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    ./compbio/data/sequence/RNAstruct.java
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    ./compbio/data/sequence/Range.java
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    ./compbio/data/sequence/Score.java
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    ./compbio/data/sequence/ScoreManager.java
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    • +5
    ./compbio/data/sequence/SequenceUtil.java
  8. … 8 more files in changeset.
Monday 12 Aug 2013
3:24 pm

Daniel Barton

Webservice which implements FoldWS and returns String. Parameters.xml file updated in line with the RunnerConfig schema.

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    ./compbio/data/sequence/SequenceUtil.java
  2. … 13 more files in changeset.
Thursday 08 Aug 2013
2:15 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

change header

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    ./compbio/data/sequence/SequenceUtil.java
2:13 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Change header

change header

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    ./compbio/data/sequence/SequenceUtil.java
  2. … 2 more files in changeset.
Wednesday 07 Aug 2013
5:28 pm

Sasha Sherstnev <a.sherstnev@dundee.ac.uk>

Necessary modifications in JABAWS for Jpred

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    ./compbio/data/sequence/Program.java
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    ./compbio/data/sequence/SequenceUtil.java
  3. … 2 more files in changeset.
Monday 05 Aug 2013
5:51 pm

Daniel Barton

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

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    ./compbio/data/sequence/RNAstruct.java
    • -0
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    ./compbio/data/sequence/SequenceUtil.java
  3. … 7 more files in changeset.
Friday 08 Mar 2013
5:09 pm

Alexander Sherstnev <asherstnev@main-laptop>

remove unnecessary import

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    • -2
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    ./compbio/data/sequence/FastaReader.java
Friday 01 Jun 2012
12:53 pm

jprocter <jprocter@compbio.dundee.ac.uk>

JWS-29 patch fixes bug - wierd workaround since "^\\s*>" caused scanner to advance to end of file rather than start of next FASTA header

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    • +17
    ./compbio/data/sequence/FastaReader.java
10:57 am

jprocter <jprocter@compbio.dundee.ac.uk>

JWS-36 patched Scores writer to put spaces between ranges and space separated scores

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    ./compbio/data/sequence/Score.java
Thursday 31 May 2012
6:27 pm

jprocter <jprocter@compbio.dundee.ac.uk>

patch fixes JWS-35

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    ./compbio/data/sequence/SequenceUtil.java
6:27 pm

jprocter <jprocter@compbio.dundee.ac.uk>

patch fixes JWS-35

Options
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    • +2
    ./compbio/data/sequence/SequenceUtil.java