James Procter [Mon, 20 Mar 2023 16:26:18 +0000 (16:26 +0000)]
JAL-4150 test and quick patch copying code from AlignFrame.paste() to Desktop.paste() so internal paste works from popup menu
James Procter [Mon, 20 Mar 2023 15:30:39 +0000 (15:30 +0000)]
JAL-2349 JAL-4134 Console log messages for contact matrix selection
James Procter [Mon, 20 Mar 2023 15:29:34 +0000 (15:29 +0000)]
JAL-4134 propagate column selection changes in tree and alignment views
James Procter [Mon, 20 Mar 2023 15:28:52 +0000 (15:28 +0000)]
JAL-4134 fix off-by-one in selection
James Procter [Mon, 20 Mar 2023 15:28:33 +0000 (15:28 +0000)]
JAL-4134 fix NPEs when matrix not resolved or alignment view is closed
James Procter [Mon, 20 Mar 2023 15:25:17 +0000 (15:25 +0000)]
JAL-4134 better popup menu name ‘Tree for Contact Matrix’
James Procter [Mon, 20 Mar 2023 15:23:50 +0000 (15:23 +0000)]
JAL-2349 test TODOs
James Procter [Mon, 20 Mar 2023 15:23:38 +0000 (15:23 +0000)]
JAL-2349 fix off by one when resolving columns for sequence associated contact matrix
Ben Soares [Sat, 18 Mar 2023 22:37:10 +0000 (22:37 +0000)]
JAL-629 restore original tests memory settings
Ben Soares [Sat, 18 Mar 2023 22:36:00 +0000 (22:36 +0000)]
JAL-629 restore original tests memory settings
Ben Soares [Sat, 18 Mar 2023 22:12:31 +0000 (22:12 +0000)]
JAL-629 Check for new commandsSuccess before quit
Ben Soares [Sat, 18 Mar 2023 21:59:10 +0000 (21:59 +0000)]
JAL-629 move getdown update to earlier stage
Ben Soares [Sat, 18 Mar 2023 20:48:50 +0000 (20:48 +0000)]
JAL-629 Back to forking tests
Ben Soares [Fri, 17 Mar 2023 21:15:30 +0000 (21:15 +0000)]
JAL-629 All applications System.exits going through Jalview.exit
Ben Soares [Fri, 17 Mar 2023 18:16:12 +0000 (18:16 +0000)]
JAL-629 whittling down options for successful tests
Ben Soares [Fri, 17 Mar 2023 18:09:46 +0000 (18:09 +0000)]
JAL-629 whittling down options for successful tests
James Procter [Fri, 17 Mar 2023 17:33:05 +0000 (17:33 +0000)]
JAL-4134 fix up column selection when hidden regions are present. Needs tests!
James Procter [Fri, 17 Mar 2023 17:32:40 +0000 (17:32 +0000)]
JAL-4134 store/restore Newick tree for PAE annotation row
Ben Soares [Fri, 17 Mar 2023 12:50:21 +0000 (12:50 +0000)]
JAL-629 whittling down options for successful tests
Ben Soares [Fri, 17 Mar 2023 12:40:12 +0000 (12:40 +0000)]
JAL-629 whittling down options for successful tests
Ben Soares [Fri, 17 Mar 2023 11:33:55 +0000 (11:33 +0000)]
JAL-629 more memory to tests task
Ben Soares [Fri, 17 Mar 2023 10:40:03 +0000 (10:40 +0000)]
JAL-629 add in jvmArgs for memory for tests and keep increased clover memory
Ben Soares [Fri, 17 Mar 2023 10:32:29 +0000 (10:32 +0000)]
JAL-629 remove jvmArgs for memory for tests. Increase clover memory
Ben Soares [Fri, 17 Mar 2023 10:25:53 +0000 (10:25 +0000)]
JAL-629 Add in jvmArgs for memory for tests
Ben Soares [Thu, 16 Mar 2023 21:31:12 +0000 (21:31 +0000)]
JAL-629 closer to normal gradle settings with just increased test memory
Ben Soares [Thu, 16 Mar 2023 18:51:13 +0000 (18:51 +0000)]
JAL-629 increase test JVM size
Ben Soares [Thu, 16 Mar 2023 18:36:54 +0000 (18:36 +0000)]
JAL-629 failFast and new threads for each test
Ben Soares [Thu, 16 Mar 2023 16:46:49 +0000 (16:46 +0000)]
JAL-629 increased memory for clover
Ben Soares [Thu, 16 Mar 2023 16:41:00 +0000 (16:41 +0000)]
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/r2_11_2_alphafold/JAL-629-new_temp_test_branch
Ben Soares [Thu, 16 Mar 2023 16:40:50 +0000 (16:40 +0000)]
JAL-629 revert metal laf
Ben Soares [Thu, 16 Mar 2023 14:22:51 +0000 (14:22 +0000)]
JAL-629 Set Metal as default LAF for build server tests
Ben Soares [Thu, 16 Mar 2023 10:41:20 +0000 (10:41 +0000)]
JAL-629 fixed a test failing when run without a Jalview.main() having been started in another task
James Procter [Wed, 15 Mar 2023 17:30:48 +0000 (17:30 +0000)]
JAL-4091 JAL-4147 - revised annotation label display so consecutive runs of rows with the same label have their description shown instead of the bare label
James Procter [Wed, 15 Mar 2023 17:28:43 +0000 (17:28 +0000)]
JAL-4091 JAL-629 ‘Add Reference Annotations’ takes description into account when looking for potential addees - reverts change in
8fce85002e6f6a5957dc95662c6a3d80fcce8e82 so PAEContactMatrix annotation labels are consistent.
James Procter [Wed, 15 Mar 2023 10:56:34 +0000 (10:56 +0000)]
JAL-2349 don’t clobber existing label/description for an annotation when associating it with a contact matrix
James Procter [Wed, 15 Mar 2023 10:54:19 +0000 (10:54 +0000)]
JAL-4134 JAL-3855 store/restore groups, tree and threshold used to cluster a PAE matrix
Ben Soares [Wed, 15 Mar 2023 01:00:21 +0000 (01:00 +0000)]
JAL-3833 fixed HiDPI test for macOS
Ben Soares [Wed, 15 Mar 2023 00:48:45 +0000 (00:48 +0000)]
JAL-629 Commands more objecty, less classy. FileLoader with sync option (or rather default async flag). Tests adjusted.
Ben Soares [Mon, 13 Mar 2023 19:52:26 +0000 (19:52 +0000)]
JAL-629 teardown in CommandsTest
Ben Soares [Sun, 12 Mar 2023 01:13:59 +0000 (01:13 +0000)]
JAL-629 Allow substitutions of {} = defaultCounter, {n} = autoCounter, {++n} = incremented autoCounter on args involving an output filename.
Ben Soares [Sat, 11 Mar 2023 12:45:18 +0000 (12:45 +0000)]
JAL-629 --substitutions --nosubstitutions flags, --nil[{++n}] just in case needed
Ben Soares [Sat, 11 Mar 2023 00:43:01 +0000 (00:43 +0000)]
JAL-629 Auto and Default count incrementer args. Flags for output filename replacements.
Ben Soares [Sat, 11 Mar 2023 00:12:45 +0000 (00:12 +0000)]
JAL-629 start of CommandsTest. More ArgParserTests.
Ben Soares [Fri, 10 Mar 2023 14:53:23 +0000 (14:53 +0000)]
JAL-629 start of tests and more examples
Ben Soares [Thu, 9 Mar 2023 23:56:15 +0000 (23:56 +0000)]
JAL-629 start of tests
Ben Soares [Thu, 9 Mar 2023 16:29:19 +0000 (16:29 +0000)]
JAL-629 --argfile=glob implemented. Remove reference seq from pAE Matrix annotation label
Ben Soares [Wed, 8 Mar 2023 15:56:02 +0000 (15:56 +0000)]
JAL-629 --close individually for each AlignFrame opened now allows batch processing of jobs in one jalview instance
Ben Soares [Wed, 8 Mar 2023 15:12:50 +0000 (15:12 +0000)]
JAL-629 improved comment and return speed of StringUtils.replaceLast()
James Procter [Wed, 8 Mar 2023 15:08:57 +0000 (15:08 +0000)]
JAL-2349 handle matrix_clicked on mouse_release rather than mouse_pressed so click-drag to resize the annotation row doesn’t trigger a selection event as well.
Ben Soares [Wed, 8 Mar 2023 15:06:39 +0000 (15:06 +0000)]
JAL-629 --quiet [no stdout], --quiet --quiet [no stderr]. Tidied up BootstrapArgs. Multiple --argfile=... can be used.
James Procter [Wed, 8 Mar 2023 13:45:11 +0000 (13:45 +0000)]
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-4134_treeviewerforcolumns
Ben Soares [Wed, 8 Mar 2023 13:32:44 +0000 (13:32 +0000)]
JAL-629 Fix --headless for new args. Fix progressbar for non-headless commands. Add an --argfile=... feature
Ben Soares [Wed, 8 Mar 2023 13:31:23 +0000 (13:31 +0000)]
JAL-629 stash some TFType and PAEFile info into a PDBEntry
Ben Soares [Mon, 6 Mar 2023 20:43:45 +0000 (20:43 +0000)]
JAL-629 Fix null AlignPanel. More descriptive label of pAE Matrix allows 'Add reference annotation' to be enabled for subsequent PDB+PAE files.
Ben Soares [Fri, 3 Mar 2023 22:59:11 +0000 (22:59 +0000)]
JAL-629 Improved consistency of ArgParser classes (use of ArgValuesMap). Added setting, checking and fetching ID value for ArgValues to allow easier linking of arguments. Added argIndex for boolean Args. Made noDuplicates (no duplicate values) an Arg Option.
Ben Soares [Thu, 2 Mar 2023 23:02:27 +0000 (23:02 +0000)]
JAL-629 slight tidy up
Ben Soares [Thu, 2 Mar 2023 22:22:09 +0000 (22:22 +0000)]
JAL-629 Removal of unnecessary methods. Set pLTTD tempfac for EBIAlfafold. Simplify adding cmannot.
Ben Soares [Thu, 2 Mar 2023 13:31:03 +0000 (13:31 +0000)]
JAL-629 Some refactoring to allow more flexible use of PAE files. Not working as desired yet
James Procter [Wed, 1 Mar 2023 17:31:26 +0000 (17:31 +0000)]
JAL-4134 hold ctrl to select groups containing rows and columns under mouse over a PAE
Ben Soares [Tue, 28 Feb 2023 18:29:20 +0000 (18:29 +0000)]
JAL-629 Firm up bootstrapArgs. Correct '-colour' in test. Separate --headless and -headless for now to avoid premature exit for -headless (fixes tests).
Ben Soares [Mon, 27 Feb 2023 23:54:45 +0000 (23:54 +0000)]
JAL-629 add AF examples for FER1_SPIOL. Link and display PAE matrix annotation
James Procter [Mon, 27 Feb 2023 18:51:21 +0000 (18:51 +0000)]
JAL-2349 TODO consider caching contactRanges from getContactRange to improve efficiency
James Procter [Mon, 27 Feb 2023 18:44:12 +0000 (18:44 +0000)]
JAL-4134 tree panel shouldn’t try to redraw before tree is calculated..
James Procter [Mon, 27 Feb 2023 18:43:58 +0000 (18:43 +0000)]
JAL-4134 fix more of the egregious SeqNode/BinaryNode casting
James Procter [Mon, 27 Feb 2023 18:43:23 +0000 (18:43 +0000)]
JAL-4134 leaves marked when columns are selected - doesn’t refresh automatically from alignment yet (only when tree panel repainted)
James Procter [Mon, 27 Feb 2023 17:58:09 +0000 (17:58 +0000)]
JAL-4134 TODO: alternative way of performing interactive picking using threshold
James Procter [Mon, 27 Feb 2023 17:57:44 +0000 (17:57 +0000)]
JAL-4134 use average distance between PAE elements as distance for tree calculation
James Procter [Mon, 27 Feb 2023 17:27:44 +0000 (17:27 +0000)]
JAL-4134 display tree for columns - selecting an internal node selects column in alignment
James Procter [Mon, 27 Feb 2023 17:26:46 +0000 (17:26 +0000)]
JAL-4134 compute normalised dot product for contact matrix similarities
James Procter [Mon, 27 Feb 2023 17:18:44 +0000 (17:18 +0000)]
JAL-4134 allow tree groups to be stored/recovered on contact matrix for groupwise column selection
Ben Soares [Mon, 27 Feb 2023 15:05:09 +0000 (15:05 +0000)]
JAL-629 Fix Exceptions when running with CLI not headless
Ben Soares [Mon, 27 Feb 2023 14:16:00 +0000 (14:16 +0000)]
JAL-629 Guesstimate whether to set pLDDT with PDB file
Ben Soares [Mon, 27 Feb 2023 10:04:43 +0000 (10:04 +0000)]
JAL-629 JAL-4124 JAL-3855 remove deleted debugging test file from tests
Ben Soares [Mon, 27 Feb 2023 09:52:13 +0000 (09:52 +0000)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
Ben Soares [Mon, 27 Feb 2023 09:47:23 +0000 (09:47 +0000)]
JAL-629 removed debug prints. added .cif. added some comments/code-markers
James Procter [Mon, 27 Feb 2023 09:28:31 +0000 (09:28 +0000)]
Merge branch 'develop' into features/JAL-4134_treeviewerforcolumns
Ben Soares [Sun, 26 Feb 2023 19:43:10 +0000 (19:43 +0000)]
JAL-629 PAE matrix file guesstimate from filename
Ben Soares [Fri, 24 Feb 2023 17:23:52 +0000 (17:23 +0000)]
JAL-629 Position GUI widgets for PDF file options. Remove icon from StructureChooser frame.
James Procter [Fri, 24 Feb 2023 17:10:02 +0000 (17:10 +0000)]
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - additional test case
James Procter [Fri, 24 Feb 2023 16:44:48 +0000 (16:44 +0000)]
JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - and fix up a casting issue (again?)
Ben Soares [Fri, 24 Feb 2023 16:23:09 +0000 (16:23 +0000)]
Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
Ben Soares [Fri, 24 Feb 2023 15:54:38 +0000 (15:54 +0000)]
JAL-629 add widgets to StructureChooser for tempfac choice and pae matrix file
James Procter [Fri, 24 Feb 2023 15:26:30 +0000 (15:26 +0000)]
Merge branch 'features/JAL-3858_PAEsInProjects' into develop
James Procter [Fri, 24 Feb 2023 15:13:37 +0000 (15:13 +0000)]
Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects
Conflicts:
src/jalview/bin/Jalview.java
Ben Soares [Fri, 24 Feb 2023 14:43:38 +0000 (14:43 +0000)]
JAL-629 helper function for getting sensible structure (or other arg value)
Ben Soares [Fri, 24 Feb 2023 12:54:35 +0000 (12:54 +0000)]
JAL-629 better test fixes. --props=... instead of --debug
Ben Soares [Fri, 24 Feb 2023 11:52:19 +0000 (11:52 +0000)]
JAL-629 Made ArgValuesMap helper class, simplifies readability/writing of the code and will allow arg position lookups
Ben Soares [Thu, 23 Feb 2023 19:21:24 +0000 (19:21 +0000)]
JAL-629 test fixing
James Procter [Thu, 23 Feb 2023 17:01:13 +0000 (17:01 +0000)]
JAL-4134 group columns using a tree cut - seems to work after more egregiousness
Ben Soares [Thu, 23 Feb 2023 17:01:05 +0000 (17:01 +0000)]
JAL-629 Add debug messages for more failing tests
James Procter [Thu, 23 Feb 2023 16:38:04 +0000 (16:38 +0000)]
JAL-4134 - brutal hack to build a tree clustering columns of PAE Matrix
Ben Soares [Thu, 23 Feb 2023 16:21:49 +0000 (16:21 +0000)]
JAL-629 fixed a Log4j test by adding --debug arg
Ben Soares [Thu, 23 Feb 2023 16:21:19 +0000 (16:21 +0000)]
JAL-629 bootstrap args and properties. Remember index of args for 'previous structure' defaulting of other args
Ben Soares [Thu, 23 Feb 2023 16:19:25 +0000 (16:19 +0000)]
JAL-629 nf-core sample alignment files and a2m versions
Ben Soares [Thu, 23 Feb 2023 16:18:40 +0000 (16:18 +0000)]
JAL-629 fix a PAEMatrix casting error
James Procter [Thu, 23 Feb 2023 12:24:39 +0000 (12:24 +0000)]
JAL-4134 tidied up refactoring and fix compilation errrors
James Procter [Thu, 23 Feb 2023 12:10:53 +0000 (12:10 +0000)]
Merge branch 'features/JAL-3858_PAEsInProjects' into features/JAL-4134_treeviewerforcolumns
James Procter [Thu, 23 Feb 2023 12:08:00 +0000 (12:08 +0000)]
JAL-3858 new MatrixType JAX-RI POJO
James Procter [Thu, 23 Feb 2023 12:06:43 +0000 (12:06 +0000)]
JAL-4134 - refactor tree calculation code to work with binaryNode base type.
James Procter [Thu, 23 Feb 2023 11:58:09 +0000 (11:58 +0000)]
JAL-4133 update validChar width when font is changed so characters are suppressed for small widths