jalview

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first pass at limiting updates of structure to just those that are necessary.

    • -2
    • +3
    /src/jalview/api/AlignmentViewPanel.java
    • -10
    • +10
    /src/jalview/appletgui/APopupMenu.java
    • -31
    • +34
    /src/jalview/appletgui/AlignFrame.java
    • -1
    • +1
    /src/jalview/appletgui/FontChooser.java
    • -1
    • +1
    /src/jalview/appletgui/OverviewPanel.java
  1. … 39 more files in changeset.
JAL-2772 check array bounds for sequence access

    • -0
    • +32
    /test/jalview/datamodel/SequenceTest.java
Merge branch 'bug/JAL-2742' into develop

JAL-2742 set HiddenColumns null for no hidden coluns test to match Jalview usage

JAL-2757 release notes

Merge branch 'bug/JAL-2757_uniprotftsbadquery' into develop

JAL-2757 fix PDB also; suppress stack trace and compiler warnings

JAL-2742 test updates following review

JAL-2742 minor test updates following review

JAL-2742 removed unused getViewAsCigars

    • -11
    • +2
    /src/jalview/api/AlignViewportI.java
JAL-2523 release notes

Merge branch 'features/JAL-2523httpRetries' into develop

JAL-2480 use interface type for sequenceFeatureStore

JAL-2523 basic sleep and retry (3 times) on 429 response code with Retry-After

    • -5
    • +0
    /src/jalview/ext/ensembl/EnsemblInfo.java
    • -1
    • +1
    /src/jalview/ext/ensembl/EnsemblLookup.java
    • -10
    • +10
    /src/jalview/ext/ensembl/EnsemblSymbol.java
    • -6
    • +9
    /src/jalview/ext/ensembl/EnsemblXref.java
JAL-2523 convenience method to get model organisms

    • -0
    • +20
    /src/jalview/ext/ensembl/Species.java
    • -0
    • +30
    /test/jalview/ext/ensembl/SpeciesTest.java
Merge branch 'patch/JAL-2446_mergeconflictmissed' into develop

JAL-2446 remove duplicate code from pulled up method.

Merge branch 'patch/JAL-2116_java9_antjnlpfix' into develop

JAL-2116 fix jnlp file post-processing so java 9 module path and java version added correctly

JAL-2757 reset textbox after a non HTTP 200 response

JAL-2523 start of refactoring...

Merge branch 'releases/Release_2_10_2b1_Branch' into develop

Conflicts:

help/html/releases.html

help/html/whatsNew.html

src/jalview/ws/dbsources/Uniprot.java

JAL-2525 lookup transcript features by Ontology

    • -8
    • +13
    /src/jalview/ext/ensembl/EnsemblGene.java
Merge branch 'documentation/JAL-2751patch2102b2' into releases/Release_2_10_2b1_Branch

JAL-2751 what's new for 2.10.2b2 patch

JAL-2751 patch release notes

JAL-2751 bump version and new releases entry

Merge branch 'feature/JAL-2745ebiHttps' into develop

JAL-2748 JAL-2745 remove uniprot from EBI fetch client test - no longer used in Uniprot fetcher

    • -7
    • +0
    /test/jalview/ws/ebi/EBIFetchClientTest.java
JAL-2748 JAL-2745 remove uniprot from EBI fetch client test - no longer used in Uniprot fetcher

    • -7
    • +0
    /test/jalview/ws/ebi/EBIFetchClientTest.java