Jim Procter [Thu, 27 Apr 2017 16:34:47 +0000 (17:34 +0100)]
JAL-1933 desktop preferences for occupancy
Jim Procter [Thu, 27 Apr 2017 16:34:29 +0000 (17:34 +0100)]
JAL-1933 action and label for occupancy
Jim Procter [Thu, 27 Apr 2017 15:39:33 +0000 (16:39 +0100)]
JAL-1933 test for SHOW_OCCUPANCY .jalview_properties setting
Jim Procter [Thu, 27 Apr 2017 15:39:12 +0000 (16:39 +0100)]
JAL-1933 showOccupancy applet parameter and SHOW_OCCUPANCY .jalview_properties setting
Jim Procter [Thu, 27 Apr 2017 15:38:22 +0000 (16:38 +0100)]
JAL-1933 only create and add occupancy row to alignment view if showOccupancy viewport attribute is set
Jim Procter [Thu, 27 Apr 2017 15:34:03 +0000 (16:34 +0100)]
JAL-2494 fix: updated behaviour for SequenceGroup.findAnnotations
Jim Procter [Thu, 27 Apr 2017 15:32:53 +0000 (16:32 +0100)]
JAL-2494 fixed behaviour for null parameters in line with test
Jim Procter [Thu, 27 Apr 2017 15:25:24 +0000 (16:25 +0100)]
JAL-2494 javadoc for AnnotatedCollectionI.findAnnotations
Jim Procter [Thu, 27 Apr 2017 15:13:25 +0000 (16:13 +0100)]
JAL-2494 test to cover AnnotatedCollectionI.findAnnotations
Jim Procter [Thu, 27 Apr 2017 14:05:42 +0000 (15:05 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop
Jim Procter [Thu, 27 Apr 2017 13:58:26 +0000 (14:58 +0100)]
JAL-2432 desktop: filter/select columns by threshold as a percentage
Jim Procter [Thu, 27 Apr 2017 13:57:28 +0000 (14:57 +0100)]
JAL-1933 JAL-2432 code tidy
Jim Procter [Thu, 27 Apr 2017 13:57:13 +0000 (14:57 +0100)]
JAL-2432 left justify value shown after adjusting threshold slider
Jim Procter [Thu, 27 Apr 2017 13:56:28 +0000 (14:56 +0100)]
JAL-1933 JAL-2432 percentile filter for select/hide columns by annotation in applet
Jim Procter [Thu, 27 Apr 2017 10:57:50 +0000 (11:57 +0100)]
JAL-1933 shade occupancy from light grey to black for high -> low occupancy
Jim Procter [Thu, 27 Apr 2017 10:56:47 +0000 (11:56 +0100)]
JAL-1933 don’t show symbol counts under histogram (also loses tooltip)
Jim Procter [Thu, 27 Apr 2017 10:55:34 +0000 (11:55 +0100)]
JAL-1933 occupancy row has a space below it for counts
Jim Procter [Thu, 27 Apr 2017 10:11:48 +0000 (11:11 +0100)]
Merge branch 'develop' into features/JAL-1933_occupancy
kiramt [Wed, 26 Apr 2017 13:43:35 +0000 (14:43 +0100)]
Merge remote-tracking branch 'origin/features/JAL-2388hiddencolumnschanges' into features/JAL-2388OverviewWindow
kiramt [Wed, 26 Apr 2017 13:42:59 +0000 (14:42 +0100)]
JAL-2388 Update to hidden columns/column selection changes after merge
kiramt [Wed, 26 Apr 2017 13:41:54 +0000 (14:41 +0100)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges
kiramt [Wed, 26 Apr 2017 13:36:03 +0000 (14:36 +0100)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow
kiramt [Wed, 26 Apr 2017 13:35:49 +0000 (14:35 +0100)]
Merge remote-tracking branch 'origin/features/JAL-2388hiddencolumnschanges' into features/JAL-2388OverviewWindow
kiramt [Wed, 26 Apr 2017 13:35:14 +0000 (14:35 +0100)]
JAL-2388 last separation of hidden columns/col selection
kiramt [Wed, 26 Apr 2017 09:55:48 +0000 (10:55 +0100)]
JAL-2388 Tidies and unit tests
tcofoegbu [Tue, 25 Apr 2017 14:17:58 +0000 (15:17 +0100)]
JAL-2489 edited unit test code comment
tcofoegbu [Tue, 25 Apr 2017 14:14:29 +0000 (15:14 +0100)]
JAL-2489 Unit test for bug
kiramt [Tue, 25 Apr 2017 13:52:45 +0000 (14:52 +0100)]
JAL-2388 Missed file from previous commit
kiramt [Tue, 25 Apr 2017 13:52:11 +0000 (14:52 +0100)]
JAL-2388 Reverted and re-did applet changes
kiramt [Tue, 25 Apr 2017 12:59:18 +0000 (13:59 +0100)]
JAL-2388 Tidies and other corrections so applet compiles
kiramt [Tue, 25 Apr 2017 12:33:37 +0000 (13:33 +0100)]
JAL-2388 And corrected OverviewCanvas for applet
kiramt [Tue, 25 Apr 2017 12:26:21 +0000 (13:26 +0100)]
JAL-2388 Updated applet to show/hide hidden regions in overview
tcofoegbu [Tue, 25 Apr 2017 11:45:44 +0000 (12:45 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 25 Apr 2017 11:45:36 +0000 (12:45 +0100)]
JAL-2489 bug fix
kiramt [Tue, 25 Apr 2017 11:15:50 +0000 (12:15 +0100)]
JAL-2388 Working hidden regions hide/show in desktop
tcofoegbu [Tue, 25 Apr 2017 11:03:10 +0000 (12:03 +0100)]
JAL-1648 enabled caching for Select / Hide columns by annotation window
tcofoegbu [Mon, 24 Apr 2017 15:06:22 +0000 (16:06 +0100)]
JAL-1648 House keeping
gmungoc [Mon, 24 Apr 2017 13:30:45 +0000 (14:30 +0100)]
JAL-2487 remove redundant refreshGUI to minimise threading issues
kiramt [Mon, 24 Apr 2017 13:13:18 +0000 (14:13 +0100)]
Merge remote-tracking branch
'origin/features/JAL-2388hiddencolumnschanges' into
features/JAL-2388OverviewWindow
Conflicts:
src/jalview/appletgui/OverviewPanel.java
src/jalview/gui/OverviewPanel.java
src/jalview/viewmodel/OverviewDimensions.java
kiramt [Mon, 24 Apr 2017 13:01:34 +0000 (14:01 +0100)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow
kiramt [Mon, 24 Apr 2017 13:00:31 +0000 (14:00 +0100)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges
kiramt [Mon, 24 Apr 2017 12:59:47 +0000 (13:59 +0100)]
JAL-2388 Finished split of hidden columns and selected columns
gmungoc [Mon, 24 Apr 2017 11:32:32 +0000 (12:32 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
gmungoc [Mon, 24 Apr 2017 11:19:41 +0000 (12:19 +0100)]
JAL-2424 final contig now an inclusive range
tcofoegbu [Mon, 24 Apr 2017 10:30:03 +0000 (11:30 +0100)]
JAL-1648 added unit test for AppCache
kiramt [Mon, 24 Apr 2017 10:18:26 +0000 (11:18 +0100)]
JAL-2439 Fixed opposite out-by-one problem in wrapped panels
kiramt [Mon, 24 Apr 2017 09:52:12 +0000 (10:52 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
kiramt [Mon, 24 Apr 2017 09:51:39 +0000 (10:51 +0100)]
JAL-2439 Fix to hidden column marker being one row too short
kiramt [Mon, 24 Apr 2017 09:37:33 +0000 (10:37 +0100)]
JAL-2388 Hidden cols separated from column selection (almost complete)
gmungoc [Fri, 21 Apr 2017 15:12:29 +0000 (16:12 +0100)]
JAL-2295 Spanish translations for superposition / errors
gmungoc [Fri, 21 Apr 2017 14:53:55 +0000 (15:53 +0100)]
JAL-2295 Spanish translations added
gmungoc [Fri, 21 Apr 2017 14:34:04 +0000 (15:34 +0100)]
JAL-2361 Spanish text added
gmungoc [Fri, 21 Apr 2017 14:00:20 +0000 (15:00 +0100)]
JAL-2423 tweak tree panel title, add Spanish text
gmungoc [Fri, 21 Apr 2017 13:08:13 +0000 (14:08 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
tcofoegbu [Fri, 21 Apr 2017 11:33:31 +0000 (12:33 +0100)]
JAL-2485 Bug fix to filter out uniprot response header row by excluding the first row
kiramt [Fri, 21 Apr 2017 11:21:23 +0000 (12:21 +0100)]
JAL-2388 Tidies
kiramt [Fri, 21 Apr 2017 09:42:24 +0000 (10:42 +0100)]
JAL-2388 Make sure resizing still works
kiramt [Fri, 21 Apr 2017 09:03:37 +0000 (10:03 +0100)]
JAL-2388 Alignment col and row collections with iterators
tcofoegbu [Thu, 20 Apr 2017 18:15:12 +0000 (19:15 +0100)]
JAL-1648 house-keeping
tcofoegbu [Thu, 20 Apr 2017 18:12:07 +0000 (19:12 +0100)]
JAL-1648 house-keeping
tcofoegbu [Thu, 20 Apr 2017 17:48:28 +0000 (18:48 +0100)]
JAL-2484 minor house-keeping
tcofoegbu [Thu, 20 Apr 2017 17:14:37 +0000 (18:14 +0100)]
JAL-2484 minor house-keeping and code docs
tcofoegbu [Thu, 20 Apr 2017 16:41:50 +0000 (17:41 +0100)]
JAL-2484 added improvement to enable clearing cache items and configuring maximum cache limit
tcofoegbu [Thu, 20 Apr 2017 12:24:32 +0000 (13:24 +0100)]
JAL-1648 refactored and improved caching architecture implementation. The improved design is centred on a custom component(JVCacheableInputBox) which wrapped around JcomoboBox
gmungoc [Wed, 19 Apr 2017 15:16:36 +0000 (16:16 +0100)]
JAL-2435 mirror font changes with middle mouse drag
gmungoc [Wed, 19 Apr 2017 14:07:39 +0000 (15:07 +0100)]
Merge branch 'develop' into features/JAL-2435splitScreenFont
tcofoegbu [Wed, 19 Apr 2017 11:19:45 +0000 (12:19 +0100)]
JAL-2482 added null check
kiramt [Wed, 19 Apr 2017 11:01:30 +0000 (12:01 +0100)]
Merge remote-tracking branch 'origin/develop' into
features/JAL-2388OverviewWindow
Conflicts:
resources/lang/Messages_es.properties
tcofoegbu [Tue, 18 Apr 2017 13:44:19 +0000 (14:44 +0100)]
JAL-2482 Bugfix
gmungoc [Mon, 17 Apr 2017 07:58:24 +0000 (08:58 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
gmungoc [Wed, 12 Apr 2017 15:06:02 +0000 (16:06 +0100)]
JAL-2361 tweak layout of warning message
gmungoc [Wed, 12 Apr 2017 14:46:35 +0000 (15:46 +0100)]
JAL-1632 removed check for aligned sequences for Tree calculation
gmungoc [Wed, 12 Apr 2017 13:43:39 +0000 (14:43 +0100)]
JAL-1632 remove unused check for sequences aligned
gmungoc [Wed, 12 Apr 2017 13:42:11 +0000 (14:42 +0100)]
JAL-2403 ensure array held in Matrix is immutable
gmungoc [Wed, 12 Apr 2017 13:41:45 +0000 (14:41 +0100)]
JAL-2403 public static methods to convert distance/similarity matrices
gmungoc [Wed, 12 Apr 2017 10:30:37 +0000 (11:30 +0100)]
JAL-1632 one PCA/Tree per panel, closed when panel is closed
tcofoegbu [Tue, 11 Apr 2017 14:50:55 +0000 (15:50 +0100)]
JAL-1648 Fix review issue - remove usage of String.join
tcofoegbu [Tue, 11 Apr 2017 14:20:36 +0000 (15:20 +0100)]
Pull from develop
kiramt [Tue, 11 Apr 2017 13:58:08 +0000 (14:58 +0100)]
JAL-2479 Moved some network-dependent unit tests into Network group
gmungoc [Tue, 11 Apr 2017 13:34:50 +0000 (14:34 +0100)]
JAL-2403 improved ScoreModelI hierarchy as per Kira's review suggestions
tcofoegbu [Tue, 11 Apr 2017 12:43:07 +0000 (13:43 +0100)]
JAL-2473 removed unused fields in JalviewDialog
tcofoegbu [Tue, 11 Apr 2017 12:14:33 +0000 (13:14 +0100)]
JAL-1648 minor house keeping
gmungoc [Tue, 11 Apr 2017 10:48:40 +0000 (11:48 +0100)]
JAL-2428 Javadoc
gmungoc [Tue, 11 Apr 2017 07:59:47 +0000 (08:59 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
gmungoc [Mon, 10 Apr 2017 18:24:04 +0000 (19:24 +0100)]
JAL-2403 unit tests for PCA.computeSimilarity, signature simplified
tcofoegbu [Mon, 10 Apr 2017 16:05:21 +0000 (17:05 +0100)]
Merge branch 'bug/JAL-2255_seq-fetcher-broken-on-linux' into develop
tcofoegbu [Mon, 10 Apr 2017 16:04:13 +0000 (17:04 +0100)]
JAL-2255 Bug fix
tcofoegbu [Mon, 10 Apr 2017 15:54:07 +0000 (16:54 +0100)]
Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux
gmungoc [Mon, 10 Apr 2017 15:21:35 +0000 (16:21 +0100)]
JAL-2403 removed remaining jvCalcMode references from PCA
gmungoc [Mon, 10 Apr 2017 14:49:26 +0000 (15:49 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
gmungoc [Mon, 10 Apr 2017 14:49:05 +0000 (15:49 +0100)]
JAL-2416 test updated for reinstatement of '*' row/column in blosum62
tcofoegbu [Mon, 10 Apr 2017 11:44:40 +0000 (12:44 +0100)]
JAL-2473 added improvement to apply default / custom minimum dimension for various Jalview dialogs / windows. This is to prevent some components from disappearing when the dialogs / windows are resized downwards below certain dimensions
gmungoc [Mon, 10 Apr 2017 07:48:59 +0000 (08:48 +0100)]
JAL-2361 option to save on OK of changed named colour scheme
gmungoc [Sun, 9 Apr 2017 07:07:31 +0000 (08:07 +0100)]
JAL-2393 remove unused commented code
gmungoc [Fri, 7 Apr 2017 13:27:45 +0000 (14:27 +0100)]
JAL-2393 code tidying for review comments
gmungoc [Fri, 7 Apr 2017 13:16:55 +0000 (14:16 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
gmungoc [Thu, 6 Apr 2017 15:52:23 +0000 (16:52 +0100)]
JAL-2361 make a modified saved scheme the backout checkpoint for Cancel
gmungoc [Wed, 5 Apr 2017 15:14:39 +0000 (16:14 +0100)]
JAL-2384 JAL-2371 update ResidueShader on change of colour by
conservation / pid
gmungoc [Wed, 5 Apr 2017 14:47:10 +0000 (15:47 +0100)]
JAL-2361 simplify constructors, select unsaved but applied user defined
colour scheme in menu
gmungoc [Wed, 5 Apr 2017 13:21:44 +0000 (14:21 +0100)]
JAL-2361 apply any saved changes to current colour scheme
git://source.jalview.org / jalview.git / log