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
Jim Procter [Thu, 20 Oct 2022 13:00:49 +0000 (14:00 +0100)]
JAL-4033 fix drag selections and distinguish row/columnwise highlights from intersections on matrix
Jim Procter [Thu, 20 Oct 2022 10:23:36 +0000 (11:23 +0100)]
JAL-2349 (still buggy) interactive selection - time to write tests!
Jim Procter [Thu, 20 Oct 2022 09:50:49 +0000 (10:50 +0100)]
JAL-2349 tooltip reports value from contact range
Jim Procter [Thu, 20 Oct 2022 09:50:42 +0000 (10:50 +0100)]
JAL-2349 adjusted range calculation to be inclusive rather than inclusive, exclusive of bounds
Jim Procter [Thu, 20 Oct 2022 09:49:21 +0000 (10:49 +0100)]
JAL-2349 debugged click/drag and added yellow rubber banding (like Alphafold)
Jim Procter [Thu, 20 Oct 2022 09:08:39 +0000 (10:08 +0100)]
JAL-2349 JAL-3855 - interactive point-wise row/column selection, and first attempt at alt-drag for region selections (not yet working!)
Jim Procter [Thu, 20 Oct 2022 09:07:57 +0000 (10:07 +0100)]
JAL-3855 RGB colours from the alphafold paE scale.
Jim Procter [Wed, 19 Oct 2022 12:10:58 +0000 (13:10 +0100)]
JAL-2349 JAL-4033 refactored contact matrix geom calc to allow reporting of mapped positions in tooltip
Jim Procter [Mon, 17 Oct 2022 16:56:51 +0000 (17:56 +0100)]
JAL-2349 JAL-3855 column selection highlighting
Jim Procter [Mon, 17 Oct 2022 11:49:02 +0000 (12:49 +0100)]
JAL-3855 bump AF version to 3 - keep contact renderer happy by filling out maxcols and maxrows attribute in PAE
Jim Procter [Mon, 17 Oct 2022 11:19:34 +0000 (12:19 +0100)]
JAL-1551 formatting
Jim Procter [Mon, 17 Oct 2022 11:19:24 +0000 (12:19 +0100)]
JAL-2349 JAL-3855 tests that probably should be part of Functional..
Jim Procter [Mon, 17 Oct 2022 11:18:44 +0000 (12:18 +0100)]
JAL-3855 report download errors as errors!
Jim Procter [Mon, 17 Oct 2022 11:18:22 +0000 (12:18 +0100)]
JAL-2349 JAL-3855 Integrate pAE retrieval in StructureFile so it can be transferred as reference annotation
Jim Procter [Sat, 15 Oct 2022 12:00:00 +0000 (13:00 +0100)]
JAL-2349 reusable contact map holder for SequenceI and AnnotatedCollectionI
Jim Procter [Sat, 15 Oct 2022 11:40:17 +0000 (12:40 +0100)]
JAL-3855 2349 TODO
Jim Procter [Sat, 15 Oct 2022 10:11:34 +0000 (11:11 +0100)]
JAL-3855 import pAE when StructureSelectionManager parses an alphaFold structure. Works but AlignmentI holding the contact matrices prevents transfer.
Jim Procter [Sat, 15 Oct 2022 10:09:52 +0000 (11:09 +0100)]
JAL-3855 pAE v2 import
Jim Procter [Fri, 14 Oct 2022 16:05:06 +0000 (17:05 +0100)]
JAL-3855 refactor the pAE retrieval code so it can be called via structureselectionmanager
Jim Procter [Fri, 14 Oct 2022 15:40:16 +0000 (16:40 +0100)]
Merge branch 'features/JAL-3895_alphafoldcolours' into features/r2_11_2_alphafold/JAL-2349_JAL-3855
Jim Procter [Fri, 14 Oct 2022 15:38:56 +0000 (16:38 +0100)]
Merge branch 'develop' into features/JAL-3895_alphafoldcolours
Jim Procter [Tue, 11 Oct 2022 15:54:16 +0000 (16:54 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 15:53:25 +0000 (16:53 +0100)]
JAL-4065 final fix for 2.11.2.5 - 5pm BST release
Jim Procter [Tue, 11 Oct 2022 15:16:37 +0000 (16:16 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 15:16:01 +0000 (16:16 +0100)]
JAL-4065 revised to avoid a visit from the apostrophe police
Jim Procter [Tue, 11 Oct 2022 14:44:01 +0000 (15:44 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 14:43:36 +0000 (15:43 +0100)]
JAL-4073 update tests
Jim Procter [Tue, 11 Oct 2022 14:28:03 +0000 (15:28 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 14:26:59 +0000 (15:26 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Jim Procter [Tue, 11 Oct 2022 14:24:32 +0000 (15:24 +0100)]
JAL-4073 fix PEBCAK failure
Ben Soares [Tue, 11 Oct 2022 13:43:10 +0000 (14:43 +0100)]
JAL-4014 Changed gecos display names to match labels in help
Jim Procter [Tue, 11 Oct 2022 12:10:56 +0000 (13:10 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 12:10:29 +0000 (13:10 +0100)]
JAL-4065 revised whatsNew to make sense !
Jim Procter [Tue, 11 Oct 2022 10:32:29 +0000 (11:32 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Tue, 11 Oct 2022 10:32:05 +0000 (11:32 +0100)]
JAL-4065 release 2.11.2.5 date is 11th Oct
Jim Procter [Fri, 7 Oct 2022 15:32:43 +0000 (16:32 +0100)]
Fix for JAL-4075 - don’t write a label in secondary structure annotation element
Jim Procter [Fri, 7 Oct 2022 14:53:01 +0000 (15:53 +0100)]
JAL-4065 update citations for Pfam and Rfam and added the Interpro citation
Jim Procter [Fri, 7 Oct 2022 14:19:54 +0000 (15:19 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 7 Oct 2022 14:19:21 +0000 (15:19 +0100)]
JAL-4065 2.11.2.5 release version bump
Jim Procter [Fri, 7 Oct 2022 14:14:42 +0000 (15:14 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Fri, 7 Oct 2022 14:14:08 +0000 (15:14 +0100)]
JAL-4065 release notes and updated release date for 2.11.2.5
Jim Procter [Thu, 6 Oct 2022 17:14:19 +0000 (18:14 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 6 Oct 2022 17:13:09 +0000 (18:13 +0100)]
stable url for PFAM retrieval via interpro api :) JAL-4073
Jim Procter [Thu, 6 Oct 2022 17:08:26 +0000 (18:08 +0100)]
JAL-1551 formatting
Jim Procter [Thu, 6 Oct 2022 16:25:53 +0000 (17:25 +0100)]
JAL-3895 alphafold colours via pluggable annotation row builder. Also ensures min/max set correctly
Jim Procter [Thu, 6 Oct 2022 11:36:33 +0000 (12:36 +0100)]
Merge branch 'develop' into releases/Release_2_11_2_Branch
Jim Procter [Thu, 6 Oct 2022 11:31:14 +0000 (12:31 +0100)]
JAL-1551 formatting
Jim Procter [Thu, 6 Oct 2022 11:22:09 +0000 (12:22 +0100)]
JAL-4065 release notes for JAL-4073 JAL-4074
Jim Procter [Thu, 6 Oct 2022 11:21:28 +0000 (12:21 +0100)]
JAL-4073 Pfam retrieval now works via a template including $PFAMID$ and $ALTYPE$ (full, seed, etc). Also changed name of PFAM_BASEURL_KEY to PFAM_INTERPRO_URL_TEMPLATE to avoid misconfiguration