jalview

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-3692 unit test updated for ?gzip download endpoint URL

    • -2
    • +2
    /test/jalview/ws/ebi/EBIFetchClientTest.java
JAL-3692 unit test updated for ?gzip download endpoint URL

    • -2
    • +2
    /test/jalview/ws/ebi/EBIFetchClientTest.java
JAL-3692 parse multiline feature qualifiers and escaped quotes

    • -32
    • +90
    /src/jalview/io/EmblFlatFile.java
    • -3
    • +2
    /src/jalview/ws/ebi/EBIFetchClient.java
    • -2
    • +15
    /test/jalview/io/EmblFlatFileTest.java
JAL-3692 parse multiline feature qualifiers and escaped quotes

    • -32
    • +90
    /src/jalview/io/EmblFlatFile.java
    • -3
    • +2
    /src/jalview/ws/ebi/EBIFetchClient.java
    • -2
    • +15
    /test/jalview/io/EmblFlatFileTest.java
JAL-3692 parse multiline feature qualifiers and escaped quotes

    • -32
    • +90
    /src/jalview/io/EmblFlatFile.java
    • -3
    • +2
    /src/jalview/ws/ebi/EBIFetchClient.java
    • -2
    • +15
    /test/jalview/io/EmblFlatFileTest.java
JAL-3675 release notes for JAL-3477, JAL-3667, JAL-3541, JAL-3685, JAL-3676, JAL-3677 and bumped release date for 2.11.1.1 to next Tuesday(ish)

Merge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into releases/Release_2_11_1_Branch

    • -11
    • +16
    /resources/lang/Messages.properties
    • -0
    • +5
    /resources/lang/Messages_es.properties
    • -92
    • +109
    /src/jalview/bin/Jalview.java
JAL-3700 fix for propagation of sort commands

    • -7
    • +11
    /src/jalview/util/MappingUtils.java
JAL-3700 fix for propagation of sort commands

    • -7
    • +11
    /src/jalview/util/MappingUtils.java
JAL-3477 Improved command line arguments description in memory.html

JAL-3477 Improved command line arguments description in memory.html

JAL-3477 Added -help text for jvmmempc and jvmmemmax. Fixed typo and slight rewording in help/memory.html

    • -3
    • +3
    /help/help/html/features/clarguments.html
JAL-3477 Added -help text for jvmmempc and jvmmemmax. Fixed typo and slight rewording in help/memory.html

    • -3
    • +3
    /help/help/html/features/clarguments.html
JAL-3700 check for 'covering' mapping when matching CDS to peptides

    • -55
    • +49
    /src/jalview/util/MappingUtils.java
JAL-3700 check for 'covering' mapping when matching CDS to peptides

    • -55
    • +49
    /src/jalview/util/MappingUtils.java
JAL-3675 report JAL-3701 as known defect

JAL-3675 release notes for JAL-3692

JAL-1260 FileFormat entry for EMBL/GENBANK: TODO: create tests and IdentifyFile routine for this format

JAL-1260 FileFormat entry for EMBL/GENBANK: TODO: create tests and IdentifyFile routine for this format

Merge branch 'patch/JAL-3692enaEndpointFlatfile' into releases/Release_2_11_1_Branch

JAL-3692 fix up test for 2.11.1 series datamodel API

    • -4
    • +4
    /test/jalview/io/EmblFlatFileTest.java
JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax

    • -0
    • +19
    /help/help/html/features/clarguments.html
JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax

    • -0
    • +19
    /help/help/html/features/clarguments.html
Merge branch 'bug/JAL-2983negativeSliderMin' into develop

Conflicts:

src/jalview/gui/FeatureSettings.java

src/jalview/gui/FeatureTypeSettings.java

    • -20
    • +13
    /src/jalview/gui/AnnotationColourChooser.java
    • -15
    • +13
    /src/jalview/gui/AnnotationColumnChooser.java
    • -34
    • +28
    /src/jalview/gui/FeatureTypeSettings.java
JAL - 3690 AlignCalc rebuilt - WIP

    • -0
    • +11
    /src/jalview/api/AlignCalcListener.java
    • -2
    • +2
    /src/jalview/api/AlignCalcManagerI.java
    • -0
    • +26
    /src/jalview/api/AlignCalcManagerI2.java
    • -2
    • +21
    /src/jalview/api/AlignCalcWorkerI.java
    • -0
    • +321
    /src/jalview/workers/AlignCalcManager2.java
    • -2
    • +4
    /src/jalview/workers/AlignCalcWorker.java
    • -1
    • +1
    /src/jalview/workers/ConsensusThread.java
    • -1
    • +1
    /src/jalview/ws/jws2/Jws2ClientFactory.java
JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

    • -0
    • +11
    /src/jalview/api/AlignCalcListener.java
    • -2
    • +2
    /src/jalview/api/AlignCalcManagerI.java
    • -0
    • +26
    /src/jalview/api/AlignCalcManagerI2.java
    • -2
    • +21
    /src/jalview/api/AlignCalcWorkerI.java
    • -1
    • +1
    /src/jalview/appletgui/AlignViewport.java
    • -2
    • +4
    /src/jalview/workers/AlignCalcWorker.java
    • -32
    • +10
    /src/jalview/workers/ColumnCounterSetWorker.java
    • -56
    • +18
    /src/jalview/workers/ConsensusThread.java
    • -59
    • +29
    /src/jalview/workers/ConservationThread.java
  1. … 5 more files in changeset.
JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

    • -0
    • +11
    /src/jalview/api/AlignCalcListener.java
    • -2
    • +2
    /src/jalview/api/AlignCalcManagerI.java
    • -0
    • +26
    /src/jalview/api/AlignCalcManagerI2.java
    • -2
    • +21
    /src/jalview/api/AlignCalcWorkerI.java
    • -1
    • +1
    /src/jalview/appletgui/AlignViewport.java
    • -2
    • +4
    /src/jalview/workers/AlignCalcWorker.java
    • -32
    • +10
    /src/jalview/workers/ColumnCounterSetWorker.java
    • -56
    • +18
    /src/jalview/workers/ConsensusThread.java
    • -59
    • +29
    /src/jalview/workers/ConservationThread.java
  1. … 5 more files in changeset.
Merge branch 'releases/Release_2_11_1_Branch' into bug/JAL-3509hideResnum

Merge branch 'releases/Release_2_11_1_Branch' into merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch

JAL-3633 last minute refinement so password box doesn't get focus all the time