jalview

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-3829 JAL-3855 ignore case when detecting alphafold ID

    • -2
    • +4
    /src/jalview/ws/dbsources/EBIAlfaFold.java
JAL-3855 detect an alphafold model and import its temperature factor as reliability

    • -2
    • +23
    /src/jalview/ext/jmol/JmolParser.java
JAL-3829 move mock query and responses to files

    • -2764
    • +57
    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
    • -2
    • +3
    /test/jalview/gui/StructureChooserTest.java
Merge branch 'develop' into feature/JAL-2422ChimeraX

JAL-2422 Also look in ~/Applications for ChimeraX on macOS

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

Merge branch 'feature/JAL-2422ChimeraX' into develop

JAL-3829 3d-beacons doesn’t work as a sequence source just now

JAL-3829 avoid sending rubbish to PDBe search api

JAL-3829 some providers don’t provide model quality, some experimental methods don’t provide a resolution - try to leave these in their natural order

JAL-3829 allow multiple URL mocks and include P01308 in 3d-beacons mocks

    • -12
    • +21
    /src/jalview/fts/core/FTSRestClient.java
JAL-2422 More helpful highlighting/user guidance of missing structure viewer path

    • -16
    • +45
    /src/jalview/gui/Preferences.java
    • -7
    • +13
    /src/jalview/jbgui/GPreferences.java
JAL-2422 Fixed URL encoding of REST calls (broken paths in Windows due to colon). Better UTF-8 Name call.

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-2422 Fixed URL encoding of REST calls (broken paths in Windows due to colon)

Merge branch 'develop' into feature/JAL-2422ChimeraX

Merge branch 'releases/Release_2_11_2_Branch' into develop

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

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into releases/Release_2_11_2_Branch

JAL-3829 ensure unmock the FTS PDB and TDB clients after mocking for a test

    • -0
    • +4
    /test/jalview/gui/StructureChooserTest.java
JAL-2422 Added linux rpm and deb install locations. Changed macOS to also look for version numbers in Chimera/X (e.g. '/Applications/ChimeraX-1.2.5.app') as this is default macOS installation. Changed macOS preferences to check endswith '.app' and look for '....app/Contents/MacOS/ChimeraX' so user can select the .app folder

JAL-3829 minimal test of additional TDB filters - not at all robust

JAL-3829 select single best TDB structure and select structures from particular provider (this code is horrific !)

    • -5
    • +34
    /src/jalview/gui/StructureChooser.java
    • -4
    • +25
    /src/jalview/jbgui/FilterOption.java
JAL-3829 JalviewJS workarounds/patches

JAL-3829 upgrade Jmol to 14.31.53, SwingJS-JSMol to 14.31.54 and SwingJS to 3.3.1

    • -0
    • +46439
    /j11lib/Jmol-14.31.53.jar
    • -0
    • +46439
    /j8lib/Jmol-14.31.53.jar
    • -0
    • +10
    /swingjs/ver/3.3.1-j11/DEV_NOTES.txt
    • binary
    /swingjs/ver/3.3.1-j11/SwingJS-site.zip
    • -0
    • +412
    /swingjs/ver/3.3.1-j11/_j2sclasslist.txt
    • -0
    • +1526
    /swingjs/ver/3.3.1-j11/differences.txt
    • binary
    /swingjs/ver/3.3.1-j11/net.sf.j2s.core-j11.jar
  1. … 8 more files in changeset.
JAL-3829 ensure tests use mocked service - proper exception for mocked 400 response

    • -0
    • +6
    /test/jalview/gui/StructureChooserTest.java
JAL-3829 patch failing tests and todo for future

    • -1
    • +1
    /src/jalview/jbgui/GStructureChooser.java
    • -3
    • +1
    /test/jalview/gui/StructureChooserTest.java
JAL-3829 provide both PDBe queries and 3D-Beacons queries in the filter combo box

    • -4
    • +13
    /src/jalview/gui/StructureChooser.java
    • -1
    • +13
    /src/jalview/jbgui/FilterOption.java
JAL-3851 changed error response status codes to 201 for jetty reasons. Some example API calls in wget_commands.sh

    • -2
    • +15
    /src/jalview/rest/AbstractEndpoint.java
    • -1
    • +7
    /src/jalview/rest/AbstractEndpointAsync.java
    • -0
    • +2
    /src/jalview/rest/FetchSequencesEndpoint.java
JAL-3829 insert title for structures from PDBe