jabaws/runner/compbio

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Tuesday 11 Apr 2017
5:44 pm

Fábio Madeira

JWS-114 Bumping varied config files and jetbrains xmls. Also adding some java classes that are generated during the compilation.

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    • +134
    ./Util.java
  2. … 12 more files in changeset.
Tuesday 28 Feb 2017
12:21 pm

Fábio Madeira

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

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    ./predictors/Jpred.java
  2. … 14 more files in changeset.
Monday 14 Oct 2013
3:20 pm

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

Re-design jpred.pl input options: no -seq for a file with 1 FASTA record only.

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    • +1
    ./predictors/Jpred.java
  2. … 3 more files in changeset.
10:58 am

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

Define path to UNIREF database in conf/Executable.properties

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    • +9
    ./predictors/Jpred.java
  2. … 2 more files in changeset.
Thursday 03 Oct 2013
1:13 pm

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

Fix wrong error message

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    • +8
    ./conservation/AACon.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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    • +95
    ./msa/GLprobs.java
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    ./msa/MSAprobs.java
  3. … 33 more files in changeset.
Friday 20 Sep 2013
3:32 pm

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

Refactoring: rename duplicated Util classes

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    ./RunnerUtil.java
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    ./Util.java
    • -1
    • +2
    ./conservation/AACon.java
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    • +1
    ./disorder/Disembl.java
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    ./disorder/GlobPlot.java
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    • +2
    ./disorder/Jronn.java
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    • +2
    ./msa/ClustalO.java
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    ./msa/ClustalW.java
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    • +2
    ./msa/Mafft.java
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    ./msa/Muscle.java
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    • +2
    ./msa/Probcons.java
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    • +2
    ./msa/Tcoffee.java
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    • +2
    ./structure/RNAalifold.java
  14. … 50 more files in changeset.
Thursday 19 Sep 2013
1:46 pm

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

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

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    • -39
    • +16
    ./Util.java
  2. … 10 more files in changeset.
Tuesday 17 Sep 2013
11:22 am

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

Clean up logging system

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    ./OptionCombinator.java
    • -46
    • +1
    ./Util.java
    • -5
    • +0
    ./conservation/AACon.java
    • -5
    • +2
    ./disorder/Disembl.java
    • -5
    • +1
    ./disorder/GlobPlot.java
    • -8
    • +1
    ./disorder/IUPred.java
    • -3
    • +1
    ./disorder/Jronn.java
    • -8
    • +4
    ./msa/ClustalO.java
    • -1
    • +1
    ./msa/ClustalW.java
    • -1
    • +1
    ./msa/Mafft.java
    • -1
    • +1
    ./msa/Muscle.java
    • -1
    • +1
    ./msa/Probcons.java
    • -2
    • +1
    ./msa/Tcoffee.java
    • -5
    • +2
    ./structure/RNAalifold.java
  15. … 14 more files in changeset.
Friday 06 Sep 2013
3:29 pm

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

Switch JpredWS from SequenceAnnotation to MsaWS

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    • +6
    ./predictors/Jpred.java
  2. … 6 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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    • +1
    ./structure/RNAalifold.java
  2. … 14 more files in changeset.
Wednesday 21 Aug 2013
12:13 pm

Daniel Barton

Reverted some changes I made for testing back to their original states.

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    • -2
    • +3
    ./Util.java
  2. … 3 more files in changeset.
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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    • +75
    ./structure/RNAalifold.java
  2. … 7 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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    • -25
    • +38
    ./Util.java
    • -2
    • +3
    ./structure/RNAalifold.java
  3. … 13 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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    • -4
    • +41
    ./Util.java
    • -7
    • +3
    ./structure/RNAalifold.java
  3. … 12 more files in changeset.
Thursday 08 Aug 2013
10:34 am

Daniel Barton

Webservice works! but only supports some parameters. Replacing RNAstuct with String.

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    • -4
    • +8
    ./structure/RNAalifold.java
  2. … 37 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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    • -7
    • +11
    ./predictors/Jpred.java
  2. … 3 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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    • -0
    • +38
    ./Util.java
    • -39
    • +46
    ./structure/RNAalifold.java
  3. … 7 more files in changeset.
Sunday 04 Aug 2013
10:05 pm

Daniel Barton

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

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    • +63
    ./structure/RNAalifold.java
  2. … 4 more files in changeset.
Saturday 03 Aug 2013
12:18 pm

Daniel Barton

Basic Testing Setup, no getResults method yet

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    • +13
    ./structure/RNAalifold.java
  2. … 8 more files in changeset.
Friday 02 Aug 2013
5:20 pm

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

Add Java wrapper class for Jpred

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    • +143
    ./predictors/Jpred.java
11:41 am

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

Impove coding style

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    ./disorder/Jronn.java
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    • +7
    ./msa/Mafft.java
  3. … 2 more files in changeset.
Thursday 01 Aug 2013
5:29 pm

Daniel Barton

RNAalifold.java runner and RNAalifoldTester incomplete

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    • +60
    ./structure/RNAalifold.java
  2. … 5 more files in changeset.
Tuesday 15 May 2012
4:55 pm

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

remove jabaws 3 development code

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    ./_NativeSpecHelper.java
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    ./_SkeletalCommandBuilder.java
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    ./_impl/BlastAll.java
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    ./_impl/BlastParameters.java
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    ./_impl/Environment.java
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    ./_impl/Mcl.java
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    ./_impl/NetNglyc.java
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    ./_impl/OB.java
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    ./_impl/PSIBlast.java
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    ./_impl/RPSBlast.java
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    ./_impl/Ronn.java
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    ./_impl/Runners.java
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    ./_impl/Tmhmm2.java
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    ./_jpred/JpredParameters.xml
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    ./_jpred/_Jpred.java
  16. … 30 more files in changeset.
Friday 12 Aug 2011
2:35 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Javadoc fixes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4508 e3abac25-378b-4346-85de-24260fe3988d

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    ./_NativeSpecHelper.java
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    ./_SkeletalCommandBuilder.java
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    ./msa/Muscle.java
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    ./msa/Probcons.java
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    ./msa/Tcoffee.java
  6. … 27 more files in changeset.
Thursday 11 Aug 2011
4:00 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Change header template for a new version

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4494 e3abac25-378b-4346-85de-24260fe3988d

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    ./OptionCombinator.java
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    ./Util.java
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    ./_NativeSpecHelper.java
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    ./_SkeletalCommandBuilder.java
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    ./_impl/BlastAll.java
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    ./_impl/BlastParameters.java
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    ./_impl/Environment.java
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    ./_impl/Mcl.java
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    ./_impl/NetNglyc.java
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    ./_impl/OB.java
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    ./_impl/PSIBlast.java
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    ./_impl/RPSBlast.java
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    ./_impl/Ronn.java
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    ./_impl/Runners.java
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    ./_impl/Tmhmm2.java
  16. … 20 more files in changeset.
Thursday 04 Aug 2011
3:32 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Comments

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4473 e3abac25-378b-4346-85de-24260fe3988d

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    • +2
    ./msa/Mafft.java
2:16 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

Clustal Omega web service wrapper and tester

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4462 e3abac25-378b-4346-85de-24260fe3988d

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    ./msa/ClustalO.java
Wednesday 03 Aug 2011
6:06 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

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/ClustalO.java
  2. … 182 more files in changeset.
Thursday 30 Jun 2011
6:22 pm

pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>

obtain JAVA executable path from the JAVA_HOME variable. Does not require path to java for jar libraries.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4376 e3abac25-378b-4346-85de-24260fe3988d

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    ./disorder/Jronn.java
  2. … 3 more files in changeset.