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

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

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

relevant issue is JAL-3626

relevant issue is JAL-3626

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.

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 ?

Ben Soares reported JAL-3514 about this build

Ben Soares reported JAL-3514 about this build

why are loops in removeAlreadyRetrievedSeqs now backwards?

why are loops in removeAlreadyRetrievedSeqs now backwards?

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

json simple library

    • binary
    /lib/json_simple-1.1.jar
upgrade to latest paradise services model using JSon response.

    • -8
    • +161
    /src/jalview/ext/paradise/Annotate3D.java
    • -6
    • +16
    /src/jalview/ws/jws1/Annotate3D.java
Merge branch 'Release_2_8_Branch' into JAL-1199-Stk_writing

Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch

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

    • -11
    • +104
    /src/jalview/io/StockholmFile.java
JAL-1199 added test for Rfam Stockholm file example

    • -1
    • +6
    /test/jalview/io/StockholmFileTest.java
JAL-1199 refactored stockholm test code from main class and added a Pfam Stockholm file for testing purposes (with new PDB dbref test)

    • -0
    • +523
    /examples/PF00111_seed.stk
    • -200
    • +1
    /src/jalview/io/AppletFormatAdapter.java
    • -0
    • +220
    /test/jalview/io/StockholmFileTest.java
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch

formatting

    • -190
    • +233
    /src/jalview/io/AppletFormatAdapter.java
    • -219
    • +240
    /src/jalview/io/StockholmFile.java
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch

Merge branch 'Dbfetch_hotfix-JAL-1238' into develop

Merge branch 'Dbfetch_hotfix-JAL-1238' into Release_2_8_Branch

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

    • -0
    • +78
    /test/jalview/ws/seqfetcher/DbRefFetcherTest.java
JAL-1238 order to place primary sources before lower tier sources

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

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.

    • -0
    • +6
    /src/jalview/ws/dbsources/EmblCdsSouce.java
    • -0
    • +6
    /src/jalview/ws/dbsources/EmblSource.java
    • -0
    • +5
    /src/jalview/ws/dbsources/GeneDbSource.java
    • -0
    • +5
    /src/jalview/ws/dbsources/PfamFull.java
    • -0
    • +5
    /src/jalview/ws/dbsources/PfamSeed.java
    • -0
    • +5
    /src/jalview/ws/dbsources/RfamFull.java
    • -0
    • +5
    /src/jalview/ws/dbsources/RfamSeed.java
    • -0
    • +6
    /src/jalview/ws/dbsources/Uniprot.java
Merge branch 'JAL-1254-hotfix' into develop

Merge branch 'JAL-1254-hotfix' into Release_2_8_Branch

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

    • -1
    • +1
    /src/jalview/gui/AnnotationLabels.java
JAL-1254 patch for NPE in annotation renderer when no annotations shown in alignment.

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

    • -1
    • +2
    /src/jalview/ws/jws2/Jws2Discoverer.java
JAL-1217 report exception for service when no datastore can be created

    • -1
    • +5
    /src/jalview/ws/jws2/Jws2Discoverer.java
    • -0
    • +2
    /src/jalview/ws/jws2/jabaws2/Jws2Instance.java
revised renderer and annotation model to support different pair-patterns - needs merging and debugging

    • -304
    • +95
    /src/jalview/renderer/AnnotationRenderer.java