Ben Soares [Thu, 5 Jan 2023 13:38:00 +0000 (13:38 +0000)]
JAL-4111 Fixed channel.props to allow replacement of __SUFFIX__. Generic background images with 'branch version' for getdown and DMG
Benedict Soares (Staff) [Thu, 5 Jan 2023 00:19:00 +0000 (00:19 +0000)]
JAL-4111 fixed DMG background image for generic Develop-X.XX app name, and new DS_Store
Ben Soares [Thu, 22 Dec 2022 00:51:44 +0000 (00:51 +0000)]
JAL-4111 Allow -PCHANNEL=DEVELOP-version for new appbase. Add a utils/channel/develop-2.12 dir with new getdown images.
Ben Soares [Mon, 19 Dec 2022 18:18:40 +0000 (18:18 +0000)]
JAL-629 Add image output and quit
Ben Soares [Thu, 15 Dec 2022 14:25:40 +0000 (14:25 +0000)]
JAL-629 move SubId to more logical place. Attempt removal of annotations in a better way (commented out).
Ben Soares [Wed, 14 Dec 2022 10:45:27 +0000 (10:45 +0000)]
JAL-629 Open Structure Viewer from cmdline
Ben Soares [Fri, 9 Dec 2022 13:05:10 +0000 (13:05 +0000)]
JAL-629 null check, fixed tests!
Ben Soares [Thu, 8 Dec 2022 17:29:38 +0000 (17:29 +0000)]
JAL-629 fix opening files
Ben Soares [Thu, 8 Dec 2022 17:08:49 +0000 (17:08 +0000)]
JAL-629 stray code deleted
Ben Soares [Thu, 8 Dec 2022 14:19:23 +0000 (14:19 +0000)]
JAL-629 Allow attachment of pAE file to a particular sequence
Ben Soares [Mon, 5 Dec 2022 09:32:24 +0000 (09:32 +0000)]
JAL-629 implementation of --tempfac options
Jim Procter [Wed, 30 Nov 2022 11:51:02 +0000 (11:51 +0000)]
JAL-4102 bump version number
Jim Procter [Wed, 30 Nov 2022 11:34:45 +0000 (11:34 +0000)]
JAL-4102 2.11.2.6 hotfix release notes - JAL-4101 JAL-2353
Ben Soares [Tue, 29 Nov 2022 13:20:54 +0000 (13:20 +0000)]
JAL-4101 Updated Rfam* tests
Ben Soares [Tue, 29 Nov 2022 13:15:32 +0000 (13:15 +0000)]
JAL-4101 Updated DEFAULT_RFAM_BASEURL
Jim Procter [Sun, 30 Oct 2022 23:19:57 +0000 (23:19 +0000)]
JAL-2353 patch for Ensembl refs from uniprot - needs test and checking !
Ben Soares [Tue, 29 Nov 2022 13:20:54 +0000 (13:20 +0000)]
JAL-4101 Updated Rfam* tests
Ben Soares [Tue, 29 Nov 2022 13:15:32 +0000 (13:15 +0000)]
JAL-4101 Updated DEFAULT_RFAM_BASEURL
Ben Soares [Wed, 23 Nov 2022 17:19:43 +0000 (17:19 +0000)]
JAL-629 Doing things with the command line arguments
Ben Soares [Thu, 17 Nov 2022 09:39:38 +0000 (09:39 +0000)]
JAL-4019 Clarification of position on 'X' in help text
Ben Soares [Wed, 16 Nov 2022 11:52:30 +0000 (11:52 +0000)]
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
Ben Soares [Wed, 16 Nov 2022 11:23:00 +0000 (11:23 +0000)]
JAL-3416 make flatlaf default for linux
Ben Soares [Wed, 16 Nov 2022 09:27:49 +0000 (09:27 +0000)]
JAL-4019 finalised a boolean option and tidied some comments
Ben Soares [Mon, 14 Nov 2022 20:38:04 +0000 (20:38 +0000)]
JAL-4019 Put original test back
Ben Soares [Mon, 14 Nov 2022 09:07:32 +0000 (09:07 +0000)]
JAL-4019 Make diagnostic message debug level
Ben Soares [Sun, 13 Nov 2022 20:35:13 +0000 (20:35 +0000)]
JAL-4019 small colour fix for X in the documentation
Ben Soares [Sun, 13 Nov 2022 20:31:51 +0000 (20:31 +0000)]
JAL-4019 attribution to Suzanne
Ben Soares [Sun, 13 Nov 2022 10:51:22 +0000 (10:51 +0000)]
JAL-4019 Help pages for Nucleotide Ambiguity colour scheme
Ben Soares [Sun, 13 Nov 2022 10:50:57 +0000 (10:50 +0000)]
JAL-4019 small but important corrections to array order, and X colour
Ben Soares [Sun, 13 Nov 2022 00:54:09 +0000 (00:54 +0000)]
JAL-4019 Added tests for new Nucleotide sequence detection
Ben Soares [Sun, 13 Nov 2022 00:53:27 +0000 (00:53 +0000)]
JAL-4019 improvement to short sequence nucleotide detection, and some tidying of unused parameters
Ben Soares [Thu, 10 Nov 2022 15:21:08 +0000 (15:21 +0000)]
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.
Ben Soares [Wed, 9 Nov 2022 18:11:42 +0000 (18:11 +0000)]
JAL-3416 Add necessary logo to non-internal Frames
Ben Soares [Wed, 9 Nov 2022 18:10:20 +0000 (18:10 +0000)]
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
Ben Soares [Wed, 9 Nov 2022 18:10:10 +0000 (18:10 +0000)]
JAL-3416 Add necessary logo to non-internal Frames
Ben Soares [Wed, 9 Nov 2022 17:47:59 +0000 (17:47 +0000)]
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
Ben Soares [Wed, 9 Nov 2022 17:45:21 +0000 (17:45 +0000)]
JAL-3416 Remove all JFrame/JInternalFrame icons (set to null)
Ben Soares [Wed, 9 Nov 2022 15:30:29 +0000 (15:30 +0000)]
Merge branch 'bug/JAL-1988_JAL-3772_improved_quit_handling' into merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
Ben Soares [Wed, 9 Nov 2022 15:30:09 +0000 (15:30 +0000)]
JAL-1988 JAL-3772 Test for FORCE_QUIT whilst saving a file
Ben Soares [Tue, 8 Nov 2022 17:47:25 +0000 (17:47 +0000)]
Merge branch 'bug/JAL-1988_JAL-3772_improved_quit_handling' into ben-big-merge
Ben Soares [Tue, 8 Nov 2022 17:47:14 +0000 (17:47 +0000)]
JAL-1988 JAL-3776 Formatting JvOptionPane
Ben Soares [Tue, 8 Nov 2022 17:42:33 +0000 (17:42 +0000)]
JAL-1988 JAL-3772 Tests for various quitting scenarios
Ben Soares [Tue, 8 Nov 2022 17:39:30 +0000 (17:39 +0000)]
JAL-1988 JAL-3772 Fixes highlighted by tests
Ben Soares [Fri, 4 Nov 2022 17:58:36 +0000 (17:58 +0000)]
Merge branch 'merge/JAL-4054+JAL-4064' into ben-big-merge
Ben Soares [Fri, 4 Nov 2022 17:54:14 +0000 (17:54 +0000)]
JAL-3416 Added logoIcon to quit (and potentially other) dialogs
Ben Soares [Fri, 4 Nov 2022 17:53:36 +0000 (17:53 +0000)]
JAL-1998 JAL-3772 JAL-3416 Merge conflict resolution of JalviewFileChooser and JvOptionPane
Ben Soares [Fri, 4 Nov 2022 09:58:02 +0000 (09:58 +0000)]
JAL-4064 JAL-4054 Combined install4j10 template with new architectures. Added scheme associations for macOS.
Ben Soares [Wed, 2 Nov 2022 21:36:46 +0000 (21:36 +0000)]
JAL-4054 Altered file association templates and generated install4j xml and Info.plist snippets.
Ben Soares [Thu, 3 Nov 2022 19:53:56 +0000 (19:53 +0000)]
JAL-3416 File Chooser iconified, JvOptionPanes iconified, other internal frames and dialogs iconified
Jim Procter [Thu, 3 Nov 2022 16:27:10 +0000 (16:27 +0000)]
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
Ben Soares [Thu, 3 Nov 2022 13:26:20 +0000 (13:26 +0000)]
JAL-1988 JAL-3772 Allow other window closing dialogs to cancel quit handling
Ben Soares [Thu, 3 Nov 2022 13:14:43 +0000 (13:14 +0000)]
JAL-3416 More JInternalFrame icons
Ben Soares [Thu, 3 Nov 2022 09:10:24 +0000 (09:10 +0000)]
JAL-1988 JAL-3772 Tidying of unspecified Callable declarations. Use SwingUtilities.getAncestorOfClass()
Ben Soares [Thu, 3 Nov 2022 08:29:30 +0000 (08:29 +0000)]
JAL-3416 Start to add JInternalFrame icons (to replace default java Duke icon in frame decoration)
Ben Soares [Wed, 2 Nov 2022 14:34:11 +0000 (14:34 +0000)]
JAL-1988 JAL-3772 Moving packages to somewhere more obvious (jbgui -> gui)
Ben Soares [Tue, 1 Nov 2022 18:29:09 +0000 (18:29 +0000)]
JAL-3416 set flatlaf default drag mode to LIVE_DRAG_MODE
Ben Soares [Tue, 1 Nov 2022 16:50:36 +0000 (16:50 +0000)]
JAL-1988 JAL-3772 Change default alignmentviewport saved status and set to true when loaded from file
Ben Soares [Tue, 1 Nov 2022 14:22:21 +0000 (14:22 +0000)]
JAL-4064 tidying build.gradle
Ben Soares [Tue, 1 Nov 2022 14:21:19 +0000 (14:21 +0000)]
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 [Tue, 1 Nov 2022 11:17:16 +0000 (11:17 +0000)]
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.
Ben Soares [Tue, 1 Nov 2022 11:16:06 +0000 (11:16 +0000)]
JAL-4064 Download JRE/JDKs from Azul if not os/arch combination not available from Adoptium
Jim Procter [Sun, 30 Oct 2022 23:22:32 +0000 (23:22 +0000)]
JAL-2349 JAL-3855 bizarre resizing exception when resizing protein alignment for a linked CDS protein alignment
Jim Procter [Sun, 30 Oct 2022 23:21:38 +0000 (23:21 +0000)]
JAL-4091 lines to associate rows sharing same sequence ref - needs some work still ! (And would be great to have more interactivity!)
Jim Procter [Sun, 30 Oct 2022 23:19:57 +0000 (23:19 +0000)]
JAL-2353 patch for Ensembl refs from uniprot - needs test and checking !
Ben Soares [Sat, 29 Oct 2022 18:38:23 +0000 (19:38 +0100)]
JAL-1988 JAL-3772 removed a debugging log line
Jim Procter [Sat, 29 Oct 2022 14:11:58 +0000 (15:11 +0100)]
JAL-4094 shift+click drag up/down to resize all annotation rows with matching calcId and label.
Jim Procter [Sat, 29 Oct 2022 12:08:47 +0000 (13:08 +0100)]
JAL-4091 - noodling about including the names for sequences associated with annotation rows in the annotation row label area
Jim Procter [Sat, 29 Oct 2022 11:20:09 +0000 (12:20 +0100)]
JAL-4090 bump version and set up release notes for 2.11.3
Jim Procter [Sat, 29 Oct 2022 11:16:14 +0000 (12:16 +0100)]
Merge branch 'features/JAL-4061_and_JAL-4062_findselectfeatures' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
Ben Soares [Fri, 28 Oct 2022 23:16:20 +0000 (00:16 +0100)]
JAL-1988 JAL-3772 Removed 'Wait' button from waitDialog, no iterations for GUI. Added bulletpoint to files saving list. Added use of passed in button objects to modal JvOptionPane, so buttons can be controlled (e.g. setEnabled, setVisible) outside of JvOptionPane.
Jim Procter [Fri, 28 Oct 2022 15:30:06 +0000 (16:30 +0100)]
Merge branch 'bug/JAL-4083_exceptions_for_multiple_residue_highlights_in_jmol' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
Jim Procter [Fri, 28 Oct 2022 15:27:00 +0000 (16:27 +0100)]
JAL-2349 allow contact matrix to provide labels for its annotation row
Jim Procter [Fri, 28 Oct 2022 14:49:34 +0000 (15:49 +0100)]
JAL-4086 commented out attempt to create measurement lines between aligned residues in different chains
Jim Procter [Fri, 28 Oct 2022 14:48:32 +0000 (15:48 +0100)]
JAL-4089 use column selection to superpose if 4 or more selected
Jim Procter [Fri, 28 Oct 2022 14:45:22 +0000 (15:45 +0100)]
JAL-2961 centerViewOn command for structure viewers - called after superposition
Jim Procter [Fri, 28 Oct 2022 12:21:41 +0000 (13:21 +0100)]
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into bug/JAL-4083_exceptions_for_multiple_residue_highlights_in_jmol
Ben Soares [Fri, 28 Oct 2022 11:48:56 +0000 (12:48 +0100)]
JAL-1988 JAL-3772 Fixed wait between waitDialog appearances, ensuring all files saving will quit straight away. Goodbye message to user if waitDialog still visible.
Ben Soares [Thu, 27 Oct 2022 17:51:22 +0000 (18:51 +0100)]
JAL-1988 Allow generic Container object in JvOptionPane showDialog. Fix dynamically saving files in the wait for save dialog
Ben Soares [Thu, 27 Oct 2022 15:20:14 +0000 (16:20 +0100)]
Merge branch 'develop' into bug/JAL-1988_JAL-3772_improved_quit_handling
Ben Soares [Thu, 27 Oct 2022 13:43:59 +0000 (14:43 +0100)]
JAL-4083 don't need globalUseScriptWait after all, just a couple of calls to jmolHistory need the flag too
Ben Soares [Thu, 27 Oct 2022 12:23:16 +0000 (13:23 +0100)]
JAL-4083 only set globalUseScriptWait if needed
Ben Soares [Thu, 27 Oct 2022 10:51:01 +0000 (11:51 +0100)]
JAL-4083 Use jmolViewer.scriptWait instead of jmolViewer.evalStringQuiet whilst highlightingt more than one residue
Jim Procter [Wed, 26 Oct 2022 11:37:47 +0000 (12:37 +0100)]
JAL-4086 quick and dirty mouseovers on ruler highlighting all positions highlighted on a particular column..
Ben Soares [Wed, 26 Oct 2022 11:07:43 +0000 (12:07 +0100)]
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into bug/JAL-4083_exceptions_for_multiple_residue_highlights_in_jmol
Ben Soares [Wed, 26 Oct 2022 08:13:24 +0000 (09:13 +0100)]
JAL-3416 (and others) increasing number of STDERR lines used for jalview.bin.CommandLineOperations tests for increased robustness
Ben Soares [Tue, 25 Oct 2022 22:03:17 +0000 (23:03 +0100)]
JAL-3772 silly NPE error fixed
Ben Soares [Tue, 25 Oct 2022 12:07:19 +0000 (13:07 +0100)]
JAL-3416 Making FlatLaF default for macs due to a problem with VAqua not starting on macs
Ben Soares [Mon, 24 Oct 2022 17:08:00 +0000 (18:08 +0100)]
JAL-1988 JAL-3772 wait timer working first time but blocking desktop gui updates
Ben Soares [Mon, 24 Oct 2022 14:41:18 +0000 (15:41 +0100)]
JAL-1988 JAL-3772 Non-blocking modal dialogs for unsaved changes and saving files. Wait timer not working. Wait dialog update/close on files saved not working.
Jim Procter [Sat, 22 Oct 2022 11:40:35 +0000 (12:40 +0100)]
JAL-2349 JAL-3855 highlight residues associated with elements under mouse - Jmol doesn’t like highlighting many residues at once this way.
Jim Procter [Fri, 21 Oct 2022 15:21:51 +0000 (16:21 +0100)]
JAL-2349 JAL-3855 fix failing tests
Jim Procter [Fri, 21 Oct 2022 15:08:23 +0000 (16:08 +0100)]
JAL-2349 JAL-3855 experiment masking hidden columns in contact matrix
Jim Procter [Fri, 21 Oct 2022 15:04:44 +0000 (16:04 +0100)]
JAL-4033 - heuristic threshold for pAE matrix - mark any column where pAE values for column+8.. lie outside threshold - definitely better to do a watershed or other type of clustering
Jim Procter [Thu, 20 Oct 2022 20:00:49 +0000 (21:00 +0100)]
JAL-2349 formatting/pick correct exception
Jim Procter [Thu, 20 Oct 2022 16:14:24 +0000 (17:14 +0100)]
JAL-2349 JAL-3855 off by one and daft return
Jim Procter [Thu, 20 Oct 2022 15:45:16 +0000 (16:45 +0100)]
JAL-2349 avoid div-by-zero when annotation height is zero (though poss better to simply avoid rendering contact at all)
Jim Procter [Thu, 20 Oct 2022 15:29:03 +0000 (16:29 +0100)]
JAL-2349 JAL-3855 adapt renderer for AlignmentI.getContactList(..) mapping to sequence associated reference frame
Jim Procter [Thu, 20 Oct 2022 15:28:00 +0000 (16:28 +0100)]
JAL-2349 JAL-3855 ContactListI.getPosition() to recover original position passed to ContactMatrixI.getContactListFor(..)
Jim Procter [Thu, 20 Oct 2022 14:45:51 +0000 (15:45 +0100)]
JAL-2349 JAL-3855 experimenting with filtering columns based on mean of contact map range
Jim Procter [Thu, 20 Oct 2022 14:14:31 +0000 (15:14 +0100)]
JAL-3855 JAL-2349 AlignmentI.getContactList takes care of mapping columns to sequence positions for sequence associated contact matrices. Need to map selected positions back for drag selects