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

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857 commits
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  • First commit: 17 May 2011
  • Last commit: 11 February 2013
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Monday 19 Oct 2020
11:59 am

Jim Procter

not related to JAL-3765 ! Actually related to JAL-3675!

not related to JAL-3765 ! Actually related to JAL-3675!

Friday 22 May 2020
11:37 am

Jim Procter

relevant issue is JAL-3626

relevant issue is JAL-3626

Thursday 09 Apr 2020
2:34 pm

Ben Soares

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with. This seemed like a quick way to achieve almost the same, but longer term a ...

Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created with.
This seemed like a quick way to achieve almost the same, but longer term a getdown created visibile indicator would be ideal. I'll create an issue.

12:07 pm

Jim Procter

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?

Wednesday 05 Feb 2020
11:50 am

Jim Procter

Ben Soares reported JAL-3514 about this build

Ben Soares reported JAL-3514 about this build

Friday 01 Feb 2019
2:23 pm

Mungo Carstairs

why are loops in removeAlreadyRetrievedSeqs now backwards?

why are loops in removeAlreadyRetrievedSeqs now backwards?

Monday 11 Feb 2013
5:07 pm

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

patch for 'This parser does not support specification "null" version "null"' error

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    /src/jalview/io/RnamlFile.java
4:12 pm

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

json simple library

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    /lib/json_simple-1.1.jar
4:09 pm

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

upgrade to latest paradise services model using JSon response.

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    /.classpath
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    /.gitignore
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    /THIRDPARTYLIBS
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    /src/jalview/ext/paradise/Annotate3D.java
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    /src/jalview/ws/jws1/Annotate3D.java
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    /test/jalview/ext/paradise/TestAnnotate3D.java
Wednesday 06 Feb 2013
5:04 pm

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

Merge branch 'Release_2_8_Branch' into JAL-1199-Stk_writing

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4:49 pm

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

Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch

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4:43 pm

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

JAL-1265 basic support for parsing database accessions from Stockholm JAL-851 - guess the primary sequence accession based on RFAM or PFAM alignment accession code

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    /src/jalview/io/StockholmFile.java
4:41 pm

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

JAL-1199 added test for Rfam Stockholm file example

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    /test/jalview/io/StockholmFileTest.java
3:43 pm

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

JAL-1199 refactored stockholm test code from main class and added a Pfam Stockholm file for testing purposes (with new PDB dbref test)

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    /examples/PF00111_seed.stk
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    /src/jalview/io/AppletFormatAdapter.java
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    /test/jalview/io/StockholmFileTest.java
Tuesday 05 Feb 2013
3:18 pm

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

Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch

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3:17 pm

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

formatting

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    /src/jalview/io/AppletFormatAdapter.java
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    /src/jalview/io/StockholmFile.java
3:00 pm

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

Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch

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Sunday 20 Jan 2013
2:29 pm

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

Merge branch 'Dbfetch_hotfix-JAL-1238' into develop

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    /src/jalview/ws/dbsources/Pdb.java
2:28 pm

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

Merge branch 'Dbfetch_hotfix-JAL-1238' into Release_2_8_Branch

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Friday 18 Jan 2013
3:56 pm

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

JAL-1238 test to see if the primary Uniprot source is placed first in list of Uniprot sources

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    /test/jalview/ws/seqfetcher/DbRefFetcherTest.java
3:55 pm

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

JAL-1238 order to place primary sources before lower tier sources

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    /src/jalview/ws/seqfetcher/ASequenceFetcher.java
3:55 pm

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

JAL-1238 method to test if DAS source is a primary reference source

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    /src/jalview/ws/dbsources/das/api/jalviewSourceI.java
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    /src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
3:52 pm

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

JAL-1238 tier index indicating distance of a source from the primary source for that database - level 0 sources are the only ones that should be used to validate sequences.

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    /src/jalview/ws/dbsources/EmblCdsSouce.java
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    /src/jalview/ws/dbsources/EmblSource.java
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    /src/jalview/ws/dbsources/GeneDbSource.java
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    /src/jalview/ws/dbsources/Pdb.java
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    /src/jalview/ws/dbsources/PfamFull.java
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    /src/jalview/ws/dbsources/PfamSeed.java
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    /src/jalview/ws/dbsources/RfamFull.java
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    /src/jalview/ws/dbsources/RfamSeed.java
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    /src/jalview/ws/dbsources/Uniprot.java
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    /src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
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    /src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
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    /src/jalview/ws/seqfetcher/DbSourceProxy.java
10:50 am

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

Merge branch 'JAL-1254-hotfix' into develop

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    /src/jalview/renderer/AnnotationRenderer.java
8:09 am

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

Merge branch 'JAL-1254-hotfix' into Release_2_8_Branch

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8:01 am

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

JAL-1255 don't show 'Right click to add annotations' message in wrapped mode

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    /src/jalview/appletgui/AnnotationLabels.java
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    /src/jalview/gui/AnnotationLabels.java
7:51 am

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

JAL-1254 patch for NPE in annotation renderer when no annotations shown in alignment.

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    /src/jalview/renderer/AnnotationRenderer.java
Tuesday 11 Dec 2012
5:27 pm

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

JAL-1217 check and avoid NPE if no datastore object instantiated

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    /src/jalview/ws/jws2/Jws2Discoverer.java
5:27 pm

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

JAL-1217 report exception for service when no datastore can be created

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    /src/jalview/ws/jws2/Jws2Discoverer.java
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    /src/jalview/ws/jws2/jabaws2/Jws2Instance.java
Friday 07 Dec 2012
3:53 pm

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

revised renderer and annotation model to support different pair-patterns - needs merging and debugging

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    /src/jalview/datamodel/AlignmentAnnotation.java
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    /src/jalview/renderer/AnnotationRenderer.java
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    /src/jalview/schemes/ResidueProperties.java