Build: #11 was successful
Job: Default Job was successful
Code commits
Jalview Git
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Ben Soares <b.soares@dundee.ac.uk> e6e897ddf845d4e79ff5e6c7afddf66766c7d31d
JAL-4128 Catch RasterFormatException caused whilst resizing Overview window, recalculate OverviewDimensions od instead. Prevent negative OverviewDimensions being set to avoid problem with vertically fully shrunk overview window 'losing' the alignement canvas.
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Ben Soares <b.soares@dundee.ac.uk> a327fd39320e482fad4b57f256f3e3c8ebcf015b
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
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James Procter <j.procter@dundee.ac.uk> d6eab72955158d1e070b45dfd93e55c64a47ff86
JAL-1713 don’t close an automatically created overview window for projects from Jalview versions older than 2.11.3
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James Procter <j.procter@dundee.ac.uk> 284b555bcff969e2b92d32241ede65e4c7e538bb
Merge branch 'develop' into feature/JAL-1713_overviewInProject
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James Procter <j.procter@dundee.ac.uk> 164a8192345f622c2f9c62d3b0c6e593b5f08af4
Passing test for JAL-4127 failing on the JAL-1713 branch
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James Procter <j.procter@dundee.ac.uk> 17863d983fe946ec642e3d6d86cabd2e01be3b19
JAL-4090 move 2.11.3 series release notes to 2.11.3.0 release and premptively list issues already or nearly addressed in this version
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Ben Soares <b.soares@dundee.ac.uk> 75509b3431c75337de94bb92c74d0cc35701ee52
Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
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Ben Soares <b.soares@dundee.ac.uk> 23886ff208184dbdb811ea445cfd6dbad7087fab
JAL-4125 Spanish translations
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Ben Soares <b.soares@dundee.ac.uk> 5a166386ec498f9887de88dc3221fa48f9287d4c
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
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Ben Soares <b.soares@dundee.ac.uk> 9b943e6d79fd92f78a61916a6f6eb047ba0a9755
JAL-4125 Move confirmation of closing external viewer windows into the quit handler, and allow all to close or not in closeViewer whilst quitting.
- resources/lang/Messages.properties (version 9b943e6d79fd92f78a61916a6f6eb047ba0a9755) (diffs)
- src/jalview/api/structures/JalviewStructureDisplayI.java (version 9b943e6d79fd92f78a61916a6f6eb047ba0a9755) (diffs)
- src/jalview/gui/Desktop.java (version 9b943e6d79fd92f78a61916a6f6eb047ba0a9755) (diffs)
- src/jalview/gui/QuitHandler.java (version 9b943e6d79fd92f78a61916a6f6eb047ba0a9755) (diffs)
- src/jalview/gui/StructureViewerBase.java (version 9b943e6d79fd92f78a61916a6f6eb047ba0a9755) (diffs)
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James Procter <j.procter@dundee.ac.uk> b303b657375dee5ac79e2f52ef96803652a2fbd1
Merge branch 'develop' into feature/JAL-1713_overviewInProject
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James Procter <j.procter@dundee.ac.uk> 421c0cd3daea00db58f42af499c8415608fb0aaa
JAL-3077 broken conflict resolve resulted in failing test (nb - still not resolved the issue of (promoted) dbrefs!)
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James Procter <j.procter@dundee.ac.uk> e7623d0a250b5d4908c45d50f52a78be4e339ce7
Fix for JAL-4126 - don’t automatically create a threshold line when no threshold line is needed when reconstructing the annotation colour scheme from a project file
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James Procter <j.procter@dundee.ac.uk> a473afe5d67b0368c7627c001c65fe9a6117dd16
JAL-4126 comment out closeAll - so we can visually check the alignment frame as it is restored
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James Procter <j.procter@dundee.ac.uk> dcb4c919fdf50dd481eb411c11a657611ab4f63b
JAL-4126 failing test - colour scheme appears to be being created and configured, but the renderer is not actually using the colour scheme to shade the sequence when the project is restored.
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Ben Soares <b.soares@dundee.ac.uk> b865b46f6f34e82f5d10fccfe646f00b8ae2e7a1
JAL-4125 Additions to JvOptionPane and QuitHandler with StructureViewerBase handling closed frame during quit differently. Still not working as dialog content does not appear until after quithandling thread has finished (it's blocking EDT). Need to break the doDesktopQuit Callable up into sections, that add another bit to the end when necessary.
- src/jalview/gui/Desktop.java (version b865b46f6f34e82f5d10fccfe646f00b8ae2e7a1) (diffs)
- src/jalview/gui/JvOptionPane.java (version b865b46f6f34e82f5d10fccfe646f00b8ae2e7a1) (diffs)
- src/jalview/gui/QuitHandler.java (version b865b46f6f34e82f5d10fccfe646f00b8ae2e7a1) (diffs)
- src/jalview/gui/StructureViewerBase.java (version b865b46f6f34e82f5d10fccfe646f00b8ae2e7a1) (diffs)
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James Procter <j.procter@dundee.ac.uk> 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35
JAL-1551 remove temp file in src
- src/jalview/appletgui/#OverviewPanel.java# (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/datamodel/Profile.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/datamodel/ProfileI.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/datamodel/Profiles.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/datamodel/ProfilesI.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/datamodel/ResidueCount.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/datamodel/SearchResultMatchI.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/datamodel/SearchResultsI.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/ext/jmol/JmolParser.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/gui/#OverviewPanel.java# (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/gui/StructureChooser.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/gui/TreeCanvas.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/structure/StructureSelectionManager.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/util/SparseCount.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
- src/jalview/ws/dbsources/Pdb.java~ (version 17b7d054cf7faa5ee57ad8c8c4c9daa495d8cb35) (diffs)
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James Procter <j.procter@dundee.ac.uk> 4a59f639cf5769d9ec66142ebecfa4961c5d3b04
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
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James Procter <j.procter@dundee.ac.uk> 3659ecfe7bb17dd25a0a6b5c94a7d9dab4525136
JAL-1713 update from Jalview 2.11.3 develop Merge branch 'develop' into feature/JAL-1713_overviewInProject regenerated jaxb classes to resolve conflicts
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Ben Soares <b.soares@dundee.ac.uk> 140b350c1bb78f0d6b46f9fcbfc523a05c32beba
JAL-1988 Make sensible choices if only the opening file has been opened, and alter the message if an alignment has been fetched but not changed
- resources/lang/Messages.properties (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
- resources/lang/Messages_es.properties (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
- src/jalview/bin/Jalview.java (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
- src/jalview/gui/QuitHandler.java (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
- src/jalview/io/DataSourceType.java (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
- src/jalview/io/FileLoader.java (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
- src/jalview/viewmodel/AlignmentViewport.java (version 140b350c1bb78f0d6b46f9fcbfc523a05c32beba) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> dbdd2bd3493e0aef8aa3c0fe054c6bceedc31316
JAL-4118 remove unnecessary sleep from QuitHandlerTest
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Ben Soares <b.soares@dundee.ac.uk> cd443f0faad6561791b4ae9a617bed680036959a
JAL-4118 fix a small buglet in BackupFiles exhibited in tests on build server. Possible problem with filename with dirs in passed to BackupFiles.
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Ben Soares <b.soares@dundee.ac.uk> f205bfec471719e5735229689cab62e9b675ee2a
JAL-1988 Add a sleep to file save test to give time for file to save
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James Procter <j.procter@dundee.ac.uk> 15a605b8a12026b453e252477b416b2c82b6344a
JAL-4116 relegate the failed to promote warning to Console.debug so most users won’t even see it (or be slowed down by it).
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James Procter <j.procter@dundee.ac.uk> 09be4c7dd6a31d9a39e5317cc8dc9eb21e8e6ebf
Merge branch 'new_feature/JAL-4019_ambiguous_base_colourscheme' into develop
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James Procter <j.procter@dundee.ac.uk> f09ab2df2e8be8cdcf2e21d3e962470815743ff4
JAL-4090 Release 2.11.3.0 release notes and version bump
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James Procter <j.procter@dundee.ac.uk> 6ff51fcc01238abb8f337aca7b6984fdc0b8368a
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064' into develop
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James Procter <j.procter@dundee.ac.uk> a8c998b5e5debd0dc8a17daa8005a1cc3ca07078
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphafold/JAL-2349_JAL-3855
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James Procter <j.procter@dundee.ac.uk> d5bd34eb49f43735e240058f8875ab0bfcae4441
JAL-4104 JAL-4102 update help docs with script to add jalview command line tool to osx path
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Jim Procter <j.procter@dundee.ac.uk> c3eb495269d836f7a8a2addf402425acbcc53c7b
JAL-4102 whatsNew for 2.11.2.6
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Jim Procter <j.procter@dundee.ac.uk> bd30c068414c3dcd87312befe7249202108b78e1
Merge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop
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Jim Procter <j.procter@dundee.ac.uk> 456e7b01bf201167e0063d0e8b56d4717322d6c0
JAL-4114 model_page_url not required in v2.0 response
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Jim Procter <j.procter@dundee.ac.uk> 3d3cc73c14a48c9af73bf0a33a4897b37a66856b
JAL-4102 update date and release notes for 2.11.2.6
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Jim Procter <j.procter@dundee.ac.uk> 49702354dac6b1b590030070690c0737d31e3766
Merge branch 'patch/JAL-4114_updated_3dbeacons_api' into develop
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Jim Procter <j.procter@dundee.ac.uk> da11f432f67f80f1848d75f862495e5e9dd9076b
Merge branch 'patch/Release_2_11_2_6_Branch' into develop
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Jim Procter <j.procter@dundee.ac.uk> 5faac1104c41690e38e259fae5bb700236021360
JAL-2353 primary ref candidates that should be promoted should preserve original version string
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Jim Procter <j.procter@dundee.ac.uk> fdb8d739d02975e003eaa044bc299c843e474a0c
JAL-4114 missing mock server response
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Jim Procter <j.procter@dundee.ac.uk> 1a80985facca80167fb54ca70d9778b1c3bcf9f1
JAL-4114 only rank model qualities that are computed with the same method, and uprank models with pLDDT over other types of models in the same model type category
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Jim Procter <j.procter@dundee.ac.uk> a3f8f05c73d08184254a8751c99824cfd126c4be
JAL-4114 alphafold now marked as AB-INITIO so adjust ranking in categories
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Jim Procter <j.procter@dundee.ac.uk> 4314e53ec6134b03f48578bf3e78d1bd7eaec6a9
JAL-4114 additional warnings when PDBe doesn’t return as many responses as queries made to it when adding in additional metadata
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Jim Procter <j.procter@dundee.ac.uk> 66270dda280788c15956c7a0485f0b9adf03c62a
JAL-4114 patch REST client for changed JSON schema in 3D beacons v2 API
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Jim Procter <j.procter@dundee.ac.uk> 1bf6c31ad57e146c40fb46ac471caa0cb3b9b975
JAL-4114 formatting
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Jim Procter <j.procter@dundee.ac.uk> c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a
JAL-4114 updated mock tests and responses for v2.0 api
- test/jalview/fts/service/pdb/PDBFTSRestClientTest.java (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p01308_pdbfts_query.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p01308_pdbfts_query_pt1.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p01308_pdbfts_query_pt1_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p01308_pdbfts_query_pt2.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p01308_pdbfts_query_pt2_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p01308_pdbfts_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p01308_tdb_fts_query_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt1.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt1_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt2.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt2_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt3.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt3_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt4.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt4_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt5.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p0dtd1_tdb_fts_query_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p27787_tdb_fts_query_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/fts/threedbeacons/p38398_tdb_fts_query_resp.txt (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
- test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java (version c10fb1cf26cf04916561a8f729fc9ccdb81c3f0a) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> a0fed91447e5411f87869be995666b88b59302ea
JAL-3416 No longer needed
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Ben Soares <b.soares@dundee.ac.uk> 6f5ac0e759db06db212ea8025f1db8c2b0092d89
Merge branch 'develop' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
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Ben Soares <b.soares@dundee.ac.uk> 9b3bed72df9fa38b8f8007b87a019356d55a030b
JAL-3416 More tweaking of FlatLaf. Problem with macOS themed FlatLaf solved with new DesktopManager
- j11lib/VAqua5-patch.jar (version 9b3bed72df9fa38b8f8007b87a019356d55a030b) (diffs)
- j11lib/quaqua-filechooser-only-8.0.jar (version 9b3bed72df9fa38b8f8007b87a019356d55a030b) (diffs)
- j8lib/VAqua5-patch.jar (version 9b3bed72df9fa38b8f8007b87a019356d55a030b) (diffs)
- j8lib/quaqua-filechooser-only-8.0.jar (version 9b3bed72df9fa38b8f8007b87a019356d55a030b) (diffs)
- src/jalview/bin/Jalview.java (version 9b3bed72df9fa38b8f8007b87a019356d55a030b) (diffs)
- src/jalview/gui/Desktop.java (version 9b3bed72df9fa38b8f8007b87a019356d55a030b) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> a800086bf169fc6495fef3effa56338f5cff4804
JAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as 'all saved' after initial opening
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Ben Soares <b.soares@dundee.ac.uk> 614526a57b61c771de369d422407eb993454bd72
JAL-3416 More explicit setting of FlatLaf macOS theme
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Ben Soares <b.soares@dundee.ac.uk> 6da716e5be79482b04d4582004c3317de53999ac
JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme for macOS
- j11lib/flatlaf-2.3.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
- j11lib/flatlaf-3.0.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
- j11lib/flatlaf-extras-2.3.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
- j11lib/flatlaf-extras-3.0.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
- j8lib/flatlaf-2.3.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
- j8lib/flatlaf-3.0.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
- j8lib/flatlaf-extras-2.3.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
- j8lib/flatlaf-extras-3.0.jar (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
- src/jalview/bin/Jalview.java (version 6da716e5be79482b04d4582004c3317de53999ac) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> 77c09ec649cf7f3e9152d93431ff30121885af57
JAL-3416 remove a missed panel titlebar icon in TreePanel
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Ben Soares <b.soares@dundee.ac.uk> 24b2b95d1aa552dbf4a0c98aa6d18bdaf1e22e4d
JAL-3416 Fix file permissions on bundled macOS JREs
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Jim Procter <j.procter@dundee.ac.uk> 16a3176b683e8d2d2de218e21c4c7c1369812ddf
JAL-4102 bump version number
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Jim Procter <j.procter@dundee.ac.uk> e9afa3f0a258083c2f5d1d007d671dd150333aec
JAL-4102 2.11.2.6 hotfix release notes - JAL-4101 JAL-2353
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Ben Soares <b.soares@dundee.ac.uk> 3052eba3a08674ff6720c3db6305ab899af9510d
JAL-4101 Updated Rfam* tests
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Ben Soares <b.soares@dundee.ac.uk> d3a15179b5d50068f4458e2130a648a88181e2de
JAL-4101 Updated DEFAULT_RFAM_BASEURL
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Jim Procter <j.procter@dundee.ac.uk> c8b686c24ab8806bc89b9ef7e8aeee88a8c83943
JAL-2353 patch for Ensembl refs from uniprot - needs test and checking !
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Ben Soares <b.soares@dundee.ac.uk> cd7f028b24e8fccbcab05cf68acbea55da941943
JAL-4101 Updated Rfam* tests
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Ben Soares <b.soares@dundee.ac.uk> 40892424a98ce7583cfb2f56c18840aa891c1304
JAL-4101 Updated DEFAULT_RFAM_BASEURL
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Ben Soares <b.soares@dundee.ac.uk> 7723baa88fa4f365c01e9f0ee9551e278219d2e5
JAL-4019 Clarification of position on 'X' in help text
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Ben Soares <b.soares@dundee.ac.uk> 3b0aa1a072e9c18ce9b7040204584ce810803bb6
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
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Ben Soares <b.soares@dundee.ac.uk> 7f0c5c453a345a700b9e19caebaf7a3b55783759
JAL-3416 make flatlaf default for linux
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Ben Soares <b.soares@dundee.ac.uk> f23edb1da574ceea56f2570996698ab29e61e129
JAL-4019 finalised a boolean option and tidied some comments
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Ben Soares <b.soares@dundee.ac.uk> 698b9fdaf44386a5e6773b85c24cbf864f442c47
JAL-4019 Put original test back
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Ben Soares <b.soares@dundee.ac.uk> f8d5b1deab2f7a25be7f77adeaefdd23c188dbcf
JAL-4019 Make diagnostic message debug level
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Ben Soares <b.soares@dundee.ac.uk> a6e5f10e2efb8cfad7a0dd844b50dd0f4dcaab0e
JAL-4019 small colour fix for X in the documentation
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Ben Soares <b.soares@dundee.ac.uk> 10f902599b98a57f377eb2bee57f37304c69553d
JAL-4019 attribution to Suzanne
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Ben Soares <b.soares@dundee.ac.uk> 184fb2cb4f0420156e2601a7187b77b41406b52d
JAL-4019 Help pages for Nucleotide Ambiguity colour scheme
- help/help/help.jhm (version 184fb2cb4f0420156e2601a7187b77b41406b52d) (diffs)
- help/help/helpTOC.xml (version 184fb2cb4f0420156e2601a7187b77b41406b52d) (diffs)
- help/help/html/colourSchemes/index.html (version 184fb2cb4f0420156e2601a7187b77b41406b52d) (diffs)
- help/help/html/colourSchemes/nucleotideambiguity.html (version 184fb2cb4f0420156e2601a7187b77b41406b52d) (diffs)
- help/help/html/menus/alignmentMenu.html (version 184fb2cb4f0420156e2601a7187b77b41406b52d) (diffs)
- help/help/html/menus/alwcolour.html (version 184fb2cb4f0420156e2601a7187b77b41406b52d) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> aeaf52866c6d5e82a38cc438a66fa0a4b8b36309
JAL-4019 small but important corrections to array order, and X colour
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Ben Soares <b.soares@dundee.ac.uk> dd2762def4e4db097c1b829debd49550c5cb191e
JAL-4019 Added tests for new Nucleotide sequence detection
- test/jalview/analysis/CrossRefTest.java (version dd2762def4e4db097c1b829debd49550c5cb191e) (diffs)
- test/jalview/datamodel/SequenceTest.java (version dd2762def4e4db097c1b829debd49550c5cb191e) (diffs)
- test/jalview/schemes/ResiduePropertiesTest.java (version dd2762def4e4db097c1b829debd49550c5cb191e) (diffs)
- test/jalview/util/ComparisonTest.java (version dd2762def4e4db097c1b829debd49550c5cb191e) (diffs)
- test/jalview/util/comparisonTestProps.jvprops (version dd2762def4e4db097c1b829debd49550c5cb191e) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> 6fc54333dcca130b378144b067a9a016c9e1cc41
JAL-4019 improvement to short sequence nucleotide detection, and some tidying of unused parameters
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Ben Soares <b.soares@dundee.ac.uk> e134aeee6802ab52748920ec07220c6a6431b77c
JAL-4019 Nucleotide Ambiguity Colour Scheme added. Test for nucleotide sequence adapted to recognise nucleotide sequences with (more than 15%) ambiguity codes. Two tests fixed.
- resources/lang/Messages.properties (version e134aeee6802ab52748920ec07220c6a6431b77c) (diffs)
- resources/lang/Messages_es.properties (version e134aeee6802ab52748920ec07220c6a6431b77c) (diffs)
- src/jalview/schemes/JalviewColourScheme.java (version e134aeee6802ab52748920ec07220c6a6431b77c) (diffs)
- src/jalview/schemes/NucleotideAmbiguityColourScheme.java (version e134aeee6802ab52748920ec07220c6a6431b77c) (diffs)
- src/jalview/schemes/ResidueProperties.java (version e134aeee6802ab52748920ec07220c6a6431b77c) (diffs)
- src/jalview/util/Comparison.java (version e134aeee6802ab52748920ec07220c6a6431b77c) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> a87e70e6c8fd8e899a42becd0dc6a3bfdf317613
JAL-3416 Add necessary logo to non-internal Frames
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Ben Soares <b.soares@dundee.ac.uk> 4de17e621110fe9f4f57d67aa30af47d9db5bf31
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
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Ben Soares <b.soares@dundee.ac.uk> e16a6f83e4f08e8cfc30afb534b506496d383b9c
JAL-3416 Add necessary logo to non-internal Frames
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Ben Soares <b.soares@dundee.ac.uk> 737dc271c809d911ea69c423f1525c3c41c68ded
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
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Ben Soares <b.soares@dundee.ac.uk> c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862
JAL-3416 Remove all JFrame/JInternalFrame icons (set to null)
- resources/images/windowIcons/alignmentIcon.png (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- resources/images/windowIcons/annotationIcon.png (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- resources/images/windowIcons/featuresIcon.png (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- resources/images/windowIcons/fetchIcon.png (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- resources/images/windowIcons/overviewIcon.png (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- resources/images/windowIcons/plainIcon.png (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- resources/images/windowIcons/preferencesIcon.png (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- resources/images/windowIcons/splitIcon.png (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- resources/images/windowIcons/structureIcon.png (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- resources/images/windowIcons/treeIcon.png (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/AlignFrame.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/AnnotationChooser.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/AnnotationColourChooser.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/AnnotationColumnChooser.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/AnnotationExporter.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/CalculationChooser.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/CutAndPasteHtmlTransfer.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/FeatureSettings.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/Finder.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/FontChooser.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/JvOptionPane.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/PCAPanel.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/Preferences.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/RedundancyPanel.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/SequenceFetcher.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/SliderPanel.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/SplitFrame.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/StructureViewerBase.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/TreePanel.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/UserDefinedColours.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/WebserviceInfo.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/gui/WindowIcons.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
- src/jalview/io/JalviewFileChooser.java (version c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> c3ddfbdfabb6a5613a2850175cdd8d1a24195ca0
Merge branch 'bug/JAL-1988_JAL-3772_improved_quit_handling' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
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Ben Soares <b.soares@dundee.ac.uk> 0d37fef8a89c67845c14f2383e89003c9a2c5b62
JAL-1988 JAL-3772 Test for FORCE_QUIT whilst saving a file
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Ben Soares <b.soares@dundee.ac.uk> 678fc0aaa829b3c433845ecb9bbebe7c8fd0fee5
Merge branch 'bug/JAL-1988_JAL-3772_improved_quit_handling' into ben-big-merge
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Ben Soares <b.soares@dundee.ac.uk> 12098b3de3f7a7858cdf50bbcc51a2afc7568e76
JAL-1988 JAL-3776 Formatting JvOptionPane
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Ben Soares <b.soares@dundee.ac.uk> 21fae6296551b02a5f89c55261d0205b42d4e14f
JAL-1988 JAL-3772 Tests for various quitting scenarios
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Ben Soares <b.soares@dundee.ac.uk> cb74c47e3bcfd8b7349da1f25b1f8685db1bca46
JAL-1988 JAL-3772 Fixes highlighted by tests
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Ben Soares <b.soares@dundee.ac.uk> 51c011768a77932d6c0aebd2d686a04fabaa2589
Merge branch 'merge/JAL-4054+JAL-4064' into ben-big-merge
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Ben Soares <b.soares@dundee.ac.uk> 26cd0e575e86884dee2d8cafab1effa05c3842d3
JAL-3416 Added logoIcon to quit (and potentially other) dialogs
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Ben Soares <b.soares@dundee.ac.uk> 952d6b6fecfb976c0c113f013ed2b8980af3d190
JAL-1998 JAL-3772 JAL-3416 Merge conflict resolution of JalviewFileChooser and JvOptionPane
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Ben Soares <b.soares@dundee.ac.uk> 931bd79285961f259c0c6b9bcfc4166465054423
JAL-4064 JAL-4054 Combined install4j10 template with new architectures. Added scheme associations for macOS.
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Ben Soares <b.soares@dundee.ac.uk> b831a65e06cb39cac1de962e75c92f4a7946c423
JAL-4054 Altered file association templates and generated install4j xml and Info.plist snippets.
- build.gradle (version b831a65e06cb39cac1de962e75c92f4a7946c423) (diffs)
- gradle.properties (version b831a65e06cb39cac1de962e75c92f4a7946c423) (diffs)
- utils/install4j/auto_file_associations-i4j10.pl (version b831a65e06cb39cac1de962e75c92f4a7946c423) (diffs)
- utils/install4j/file_associations_auto-Info_plist.xml (version b831a65e06cb39cac1de962e75c92f4a7946c423) (diffs)
- utils/install4j/file_associations_auto-install4j10.xml (version b831a65e06cb39cac1de962e75c92f4a7946c423) (diffs)
- utils/install4j/file_associations_template-Info_plist.xml (version b831a65e06cb39cac1de962e75c92f4a7946c423) (diffs)
- utils/install4j/file_associations_template-install4j10.xml (version b831a65e06cb39cac1de962e75c92f4a7946c423) (diffs)
- utils/install4j/install4j10_template.install4j (version b831a65e06cb39cac1de962e75c92f4a7946c423) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> 071a00a0f8ce9892254630595696c1c9d7c39ec7
JAL-3416 File Chooser iconified, JvOptionPanes iconified, other internal frames and dialogs iconified
- resources/images/windowIcons/preferencesIcon.png (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/AlignFrame.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/CutAndPasteHtmlTransfer.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/CutAndPasteTransfer.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/EditNameDialog.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/Finder.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/FontChooser.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/JvOptionPane.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/PCAPanel.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/PopupMenu.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/Preferences.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/RedundancyPanel.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/SliderPanel.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/TreePanel.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/UserDefinedColours.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/WebserviceInfo.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/gui/WindowIcons.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
- src/jalview/io/JalviewFileChooser.java (version 071a00a0f8ce9892254630595696c1c9d7c39ec7) (diffs)
-
Jim Procter <j.procter@dundee.ac.uk> 5221c772a071266446c5c959f34ec89c8e874201
JAL-3855 JAL-4095 simple picking of ranges adjacent to a clicked region of the pAE that score less than the max pAE observed under the mouse
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Ben Soares <b.soares@dundee.ac.uk> bfc2ccc01fd77463a3edb1265e3ee6db5741f917
JAL-1988 JAL-3772 Allow other window closing dialogs to cancel quit handling
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Ben Soares <b.soares@dundee.ac.uk> 29625ee998523520e87bb88643247b3723e908bd
JAL-3416 More JInternalFrame icons
- resources/images/windowIcons/splitIcon.png (version 29625ee998523520e87bb88643247b3723e908bd) (diffs)
- src/jalview/gui/AnnotationChooser.java (version 29625ee998523520e87bb88643247b3723e908bd) (diffs)
- src/jalview/gui/AnnotationColourChooser.java (version 29625ee998523520e87bb88643247b3723e908bd) (diffs)
- src/jalview/gui/AnnotationColumnChooser.java (version 29625ee998523520e87bb88643247b3723e908bd) (diffs)
- src/jalview/gui/AnnotationExporter.java (version 29625ee998523520e87bb88643247b3723e908bd) (diffs)
- src/jalview/gui/AppVarna.java (version 29625ee998523520e87bb88643247b3723e908bd) (diffs)
- src/jalview/gui/CalculationChooser.java (version 29625ee998523520e87bb88643247b3723e908bd) (diffs)
- src/jalview/gui/SplitFrame.java (version 29625ee998523520e87bb88643247b3723e908bd) (diffs)
- src/jalview/gui/StructureViewerBase.java (version 29625ee998523520e87bb88643247b3723e908bd) (diffs)
- src/jalview/gui/WindowIcons.java (version 29625ee998523520e87bb88643247b3723e908bd) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> d90302c57e61e425f6a8fc52f6ab59ac28d32310
JAL-1988 JAL-3772 Tidying of unspecified Callable declarations. Use SwingUtilities.getAncestorOfClass()
- src/jalview/gui/Desktop.java (version d90302c57e61e425f6a8fc52f6ab59ac28d32310) (diffs)
- src/jalview/gui/JvOptionPane.java (version d90302c57e61e425f6a8fc52f6ab59ac28d32310) (diffs)
- src/jalview/gui/QuitHandler.java (version d90302c57e61e425f6a8fc52f6ab59ac28d32310) (diffs)
- src/jalview/util/dialogrunner/DialogRunnerI.java (version d90302c57e61e425f6a8fc52f6ab59ac28d32310) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> 2f8f4850cd8437b7c2a2450df2391426aaa3e1b8
JAL-3416 Start to add JInternalFrame icons (to replace default java Duke icon in frame decoration)
- resources/images/windowIcons/alignmentIcon.png (version 2f8f4850cd8437b7c2a2450df2391426aaa3e1b8) (diffs)
- resources/images/windowIcons/annotationIcon.png (version 2f8f4850cd8437b7c2a2450df2391426aaa3e1b8) (diffs)
- resources/images/windowIcons/featuresIcon.png (version 2f8f4850cd8437b7c2a2450df2391426aaa3e1b8) (diffs)
- resources/images/windowIcons/fetchIcon.png (version 2f8f4850cd8437b7c2a2450df2391426aaa3e1b8) (diffs)
- resources/images/windowIcons/overviewIcon.png (version 2f8f4850cd8437b7c2a2450df2391426aaa3e1b8) (diffs)
- resources/images/windowIcons/plainIcon.png (version 2f8f4850cd8437b7c2a2450df2391426aaa3e1b8) (diffs)
- resources/images/windowIcons/structureIcon.png (version 2f8f4850cd8437b7c2a2450df2391426aaa3e1b8) (diffs)
- resources/images/windowIcons/treeIcon.png (version 2f8f4850cd8437b7c2a2450df2391426aaa3e1b8) (diffs)
- src/jalview/gui/AlignFrame.java (version 2f8f4850cd8437b7c2a2450df2391426aaa3e1b8) (diffs)
- src/jalview/gui/FeatureSettings.java (version 2f8f4850cd8437b7c2a2450df2391426aaa3e1b8) (diffs)
- src/jalview/gui/SequenceFetcher.java (version 2f8f4850cd8437b7c2a2450df2391426aaa3e1b8) (diffs)
- src/jalview/gui/WindowIcons.java (version 2f8f4850cd8437b7c2a2450df2391426aaa3e1b8) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> 4c007a518fc7e2fdaa863f16cb715f8e45e6cfbf
JAL-1988 JAL-3772 Moving packages to somewhere more obvious (jbgui -> gui)
- src/jalview/bin/Jalview.java (version 4c007a518fc7e2fdaa863f16cb715f8e45e6cfbf) (diffs)
- src/jalview/gui/APQHandlers.java (version 4c007a518fc7e2fdaa863f16cb715f8e45e6cfbf) (diffs)
- src/jalview/gui/Desktop.java (version 4c007a518fc7e2fdaa863f16cb715f8e45e6cfbf) (diffs)
- src/jalview/gui/QuitHandler.java (version 4c007a518fc7e2fdaa863f16cb715f8e45e6cfbf) (diffs)
- src/jalview/jbgui/APQHandlers.java (version 4c007a518fc7e2fdaa863f16cb715f8e45e6cfbf) (diffs)
- src/jalview/jbgui/GDesktop.java (version 4c007a518fc7e2fdaa863f16cb715f8e45e6cfbf) (diffs)
- src/jalview/jbgui/QuitHandler.java (version 4c007a518fc7e2fdaa863f16cb715f8e45e6cfbf) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> 7bb1887834cefc1a39ffd5b034b77c7984a13009
JAL-3416 set flatlaf default drag mode to LIVE_DRAG_MODE
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Ben Soares <b.soares@dundee.ac.uk> 193fda2755ccc72dce5175fa5445348b6fdcc92e
JAL-1988 JAL-3772 Change default alignmentviewport saved status and set to true when loaded from file
-
Ben Soares <b.soares@dundee.ac.uk> 62796f8131afc22f3916a15c67dcc06a3ac4ea7c
JAL-4064 tidying build.gradle
-
Ben Soares <b.soares@dundee.ac.uk> 5a9e223e17c5b12aa876da0ddd12b63b95cd5526
JAL-4064 re-added bundled macOS JREs as Filesets, which is the only way to get them in the DMG where we want them
-
Ben Soares <b.soares@dundee.ac.uk> 1a1ef26885c32c5e79012f638c5b0f96f59b8c96
JAL-4064 Cleaned up file sets in install4j template. New media installers for AARCH64 JVMs for macOS and Linux in install4j template. New variables passed to install4j by gradle.
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Ben Soares <b.soares@dundee.ac.uk> 80458cd593a992843a8eee1651ca489b6bfdfbb9
JAL-4064 Download JRE/JDKs from Azul if not os/arch combination not available from Adoptium
