jalview

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-3746 release notes and what’s new for 2.11.2 - in progress

    • -8
    • +6
    /help/help/html/features/preferences.html
Merge branch 'doc/JAL-3746_Release_2_11_2' into develop

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop

JAL-3829 - callback finessing - leave DBRefFetcher to do progress updates itself

    • -28
    • +21
    /src/jalview/gui/StructureChooser.java
JAL-3829 prefix PDBe filters with PDBe to make clear what they search

JAL-3829 alternative UX: need to select 3d-beacons from dropdown if db-refs need to be fetched

    • -121
    • +246
    /src/jalview/gui/StructureChooser.java
JAL-3521 'Debian-safe' version of minimal build.gradle and patch. Using existing doc/*.html and build_properties from source tarball.

    • -55
    • +225
    /utils/debian/build_gradle.patch
    • -141
    • +10
    /utils/debian/debian_build.gradle
JAL-3829 ignore the fake ID generated when a PDB format file without embedded ID is imported for an existing PDBEntry

    • -1
    • +37
    /src/jalview/datamodel/PDBEntry.java
    • -0
    • +15
    /test/jalview/datamodel/SequenceTest.java
    • -0
    • +4
    /test/jalview/ext/jmol/JmolParserTest.java
JAL-3521 Created a patch file to transform build.gradle into debian_build.gradle

    • -0
    • +2739
    /utils/debian/build_gradle.patch
JAL-3878 Implement AlignmentOperation WIP

    • -0
    • +380
    /src/jalview/ws2/operations/AlignmentOperation.java
JAL-3878 Create interface for web service operations

    • -0
    • +13
    /src/jalview/ws2/operations/Operation.java
JAL-3878 Implement slivka web service and discoverer.

    • -175
    • +0
    /src/jalview/ws2/slivka/SlivkaWS.java
    • -0
    • +175
    /src/jalview/ws2/slivka/SlivkaWSDiscoverer.java
    • -0
    • +215
    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Add web service executor class and instantiate for each alignment viewport.

    • -50
    • +86
    /src/jalview/ws2/WebServiceExecutor.java
JAL-3878 Create base interfaces for new web services.

    • -67
    • +0
    /src/jalview/ws2/JalviewWebServiceI.java
    • -2
    • +1
    /src/jalview/ws2/MenuEntryProviderI.java
    • -211
    • +0
    /src/jalview/ws2/MsaMenuEntryProvider.java
    • -0
    • +9
    /src/jalview/ws2/ResultSupplier.java
    • -0
    • +198
    /src/jalview/ws2/WSJob.java
    • -0
    • +103
    /src/jalview/ws2/WSJobStatus.java
    • -0
    • +58
    /src/jalview/ws2/WebServiceDiscoverer.java
    • -0
    • +53
    /src/jalview/ws2/WebServiceI.java
    • -0
    • +89
    /src/jalview/ws2/WebServiceInfoUpdater.java
    • -0
    • +14
    /src/jalview/ws2/WebServiceThreadListenerI.java
    • -53
    • +17
    /src/jalview/ws2/WebServiceWorkerI.java
    • -0
    • +64
    /src/jalview/ws2/utils/WSJobList.java
JAL-3878 Remove throws declaration from param store construction.

    • -1
    • +1
    /src/jalview/ws/slivkaws/SlivkaParamSet.java
JAL-3829 updated response for P01308

JAL-3829 tests need to wait for dialog to be closed and background processes to finish before they can check functionality

    • -32
    • +52
    /src/jalview/gui/StructureChooser.java
    • -0
    • +22
    /test/jalview/gui/StructureChooserTest.java
JAL-3829 TDBeacons fetcher needs a sequence with at least one canonical uniprot accession

JAL-3829 throw the exception even if it has no message

JAL-3829 ensure nulls are not wildcards when retrieving annotation by calcId/label/description

JAL-3521 working minimal build.gradle for debian and 2.11.2. Flexmark plugin might be a problem

JAL-3521 not quite working minimal build.gradle for debian and 2.11.2

    • -0
    • +620
    /utils/debian/debian_build.gradle
JAL-3829 do better at detecting structure type, prompt to retrieve Uniprot ids for proteins without canonical Ids and show provider in the Structure Chooser’s cache view

    • -1
    • +1
    /resources/fts/tdbeacons_data_columns.txt
    • -11
    • +86
    /src/jalview/gui/StructureChooser.java
JAL-3829 make sure structure data type reflects actual format identified

    • -5
    • +42
    /src/jalview/ext/jmol/JmolParser.java
JAL-3829 store 3db metadata on PDBEntry so it can be shown in Cache/etc

    • -3
    • +61
    /src/jalview/datamodel/PDBEntry.java
JAL-3829 allow PDBEntry with file and ID with mismatching case to override one without a file

    • -9
    • +25
    /src/jalview/datamodel/PDBEntry.java
    • -1
    • +1
    /test/jalview/datamodel/PDBEntryTest.java
Merge branch 'merge/develop_JAL-1260' into develop

JAL-1260 rudimentary parsing of LOCUS line to at least get accession id

    • -32
    • +14
    /src/jalview/io/GenBankFile.java
JAL-1260 rudimentary parsing of LOCUS line to at least get accession id

    • -32
    • +14
    /src/jalview/io/GenBankFile.java
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons