Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
Merge branch 'merge/develop_JAL-3725' into develop

Conflicts:

src/jalview/gui/PopupMenu.java

  1. … 3 more files in changeset.
Merge branch 'bug/JAL-3633_read_proxy_settings_from_jalview_properties_in_getdown' into develop

Conflicts:

src/jalview/bin/MemorySetting.java

  1. … 8 more files in changeset.
Merge branch 'task/JAL-3763_newDatasetForCds' into merge/develop_task/JAL-3763_newDatasetForCds

Conflicts:

src/jalview/analysis/AlignmentUtils.java

src/jalview/util/MapList.java

test/jalview/util/MapListTest.java

test/jalview/util/MappingUtilsTest.java

  1. … 6 more files in changeset.
JAL-3855 JAL-3829 don’t need to make up alphafold model retrieval URL when we’ve been given it

  1. … 1 more file in changeset.
JAL-3616 update messages/tooltips/menu items to use getViewerName() for chimera/x/pymol

  1. … 1 more file in changeset.
JAL-3931 remove % and - from ids so Pymol doesn’t strip them out and truncate the structure identifier that Jalview uses to refer to each file

JAL-3929 URLencode pdbid to remove problematic characters - propagate urlEncoded ID to the features transferred from the structure file

  1. … 2 more files in changeset.
JAL-3904 use new AlignPanel API method

JAL-3904 simple method to make an alignPanel the currently viewed one in the alignframe

JAL-3927 Make url checks asynchronous in preferences dialog

JAL-3878 Add ws menu builder and attach to the align frame.

  1. … 2 more files in changeset.
JAL-3922 convert selection events in Jmol to highlights in Jalview - still need to ignore selection events performed as part of Jalview manipulating Jmol.

  1. … 1 more file in changeset.
JAL-3878 Add javadocs to created classes and reformat code.

  1. … 15 more files in changeset.
JAL-3855 JAL-1731 reuse the StructureViewer.fetchPdbFile(PDBEntry) method in JmolBinding - avoid code duplication for retrieval and import of 3d data

JAL-3921 wait around until session file has been written

JAL-3878 Separate gui elements from operations.

Separation went well for alignment operation but not so much

for the annotations. GUI progress bar needs to be moved outside

the operation and be controlled by the worker listener.

Addition of the results to the frame needs to be moved out from

the #done method, but it's strongly wired to the align frame

code and cannot be nicely packed into AnnotationResult object.

  1. … 14 more files in changeset.
JAL-3829 remove duplicate IDs in 3DBeacons generated PDBFTS query and update mocks

    • -1
    • +2
    ./structurechooser/ThreeDBStructureChooserQuerySource.java
  1. … 3 more files in changeset.
JAL-3829 format and tidy up unused code

    • -34
    • +25
    ./structurechooser/ThreeDBStructureChooserQuerySource.java
JAL-3919 use model format field to ensure we get the file extension correct when creating temp files for structure viewers

    • -5
    • +12
    ./structurechooser/ThreeDBStructureChooserQuerySource.java
  1. … 4 more files in changeset.
JAL-3875 fully reset filter combo-box when fetch 3d-beacons button is pressed, and ensure first 3d-beacons option selected when structures are discovered even when cached structures are present.

JAL-3916 TODO for improved selection of covering structures

    • -0
    • +2
    ./structurechooser/TDBResultAnalyser.java
JAL-3915 remove RNAview opts from preferences. Still present in config file ready for when we have a new RNA structure processing service

  1. … 1 more file in changeset.
JAL-3875 test case and patch to verify the query 3d beacons button is shown for proteins with uniprot ids but no canonical accessions

  1. … 1 more file in changeset.
JAL-3878 Create WebServiceMenuBuilder which will replace PreferredServiceRegistry

    • -0
    • +201
    ./WebServicesMenuBuilder.java
JAL-3904 override buildActionMenu to add in additional menu actions after rebuild

JAL-3904 failing test

  1. … 2 more files in changeset.
JAL-3616 show name of structure viewer in ‘new view’ button

  1. … 2 more files in changeset.
JAL-3616 explicit configure external viewer config

JAL-3829 fetch 3D beacons now started by clicking button shown above the drop-down filter/manual input combo box.

  1. … 2 more files in changeset.
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons