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JAL-3616 update messages/tooltips/menu items to use getViewerName() for chimera/x/pymol

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JAL-3919 use model format field to ensure we get the file extension correct when creating temp files for structure viewers

  1. … 4 more files in changeset.
Merge branch 'develop' into features/JAL-2909_bamImport_2_11_2

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

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JAL-3829 3d beacons logo - misi varadi gave permission to re-use but most likely it is CC-0

    • binary
    ./images/3d-beacons-logo-transparent.png
JAL-3829 fetch 3D beacons now started by clicking button shown above the drop-down filter/manual input combo box.

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JAL-2909 mininal merge of bam import demo to Jalview 2.11.2 develop Merge remote-tracking branch 'origin/features/JAL-2909_bamImport2_11' into features/JAL-2909_bamImport_2_11_2

Conflicts:

src/jalview/io/AlignmentFileReaderI.java

src/jalview/io/AppletFormatAdapter.java

src/jalview/io/FileFormat.java

src/jalview/io/FileLoader.java

  1. … 9 more files in changeset.
JAL-3829 report when 3d-beacons doesn’t provide any models

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

  1. … 2 more files in changeset.
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. … 4 more files in changeset.
JAL-3774 combined changes from bug/JAL-3774_splitFrameFinder: i) fixed focus Finder from split frame. ii) missing i18n added, overlong translation shortened. iii) better translation.

  1. … 3 more files in changeset.
JAL-3739 (combined) commits from feature/JAL-3739_useFormFieldText

  1. … 5 more files in changeset.
JAL-3829 update for v1.0 3d-beacons api spec

    • -10
    • +14
    ./fts/tdbeacons_data_columns.txt
  1. … 2 more files in changeset.
JAL-3829 proof in principle 3d-beacons sequence fetcher - still some TODOs !

    • -17
    • +18
    ./fts/tdbeacons_data_columns.txt
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JAL-3929 proof in principle 3d-beacons sequence fetcher - still some TODOs !

    • -17
    • +18
    ./fts/tdbeacons_data_columns.txt
  1. … 2 more files in changeset.
JAL-3829 fixed up the 3d-beacons data columns definitions, tests and client.

  1. … 2 more files in changeset.
JAL-3929 fixed up the 3d-beacons data columns definitions, tests and client.

  1. … 2 more files in changeset.
JAL-3929 tidying up PDBFTSRestClient test responses - still one failing external test which expects to raise a server exception

  1. … 1 more file in changeset.
JAL-3829 tidying up PDBFTSRestClient test responses - still one failing external test which expects to raise a server exception

  1. … 1 more file in changeset.
remove debugging printlns

remove debugging printlns

aim is normally to avoid creating query-specific data containers on the core query response class

aim is normally to avoid creating query-specific data containers on the core query response class

? not sure this is correct

? not sure this is correct

Needs additionally: model_category created sequence_identity uniprot_start uniprot_end resolution coverage qmean_version ? model_version

Needs additionally:
model_category
created
sequence_identity
uniprot_start
uniprot_end
resolution
coverage
qmean_version ?
model_version

Evaluate 3D-Beacons dev path based on Arnaud's ERASMUS+ project code
Evaluate 3D-Beacons dev path based on Arnaud's ERASMUS+ project code
JAL-3948 - temporarily add the ojdk8 calendardata file (GPL licensed)

    • -0
    • +1488
    ./sun/util/resources/CalendarData.properties
JAL-3832 Gui working, with 3DBeacons parameters

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JAL-3832 Gui working, with 3DBeacons parameters

  1. … 2 more files in changeset.
JAL-3829 more testing wit tdbeacons data columns and FTSclient

  1. … 5 more files in changeset.