gmungoc [Tue, 2 May 2017 14:35:39 +0000 (15:35 +0100)]
JAL-1933 Spanish for Occupancy
Jim Procter [Tue, 2 May 2017 13:17:23 +0000 (14:17 +0100)]
JAL-2424 fixme’s removed
Jim Procter [Tue, 2 May 2017 13:16:25 +0000 (14:16 +0100)]
JAL-2424 update assert to correct width for normalising similarity scores
Jim Procter [Tue, 2 May 2017 13:15:52 +0000 (14:15 +0100)]
JAL-2424 resolved, assert updated to pass (1f != 1d)
Jim Procter [Tue, 2 May 2017 12:46:06 +0000 (13:46 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
Jim Procter [Tue, 2 May 2017 12:37:58 +0000 (13:37 +0100)]
Merge branch 'bug/JAL-2424getVisibleContigs' into develop
gmungoc [Tue, 2 May 2017 09:42:13 +0000 (10:42 +0100)]
JAL-2499 inlined two 1-line methods
gmungoc [Tue, 2 May 2017 09:30:58 +0000 (10:30 +0100)]
JAL-2499 JAL-2403 push 'configure for view' inside ScoreModels, defer
creating model for PCA/Tree, tidy Javadoc
gmungoc [Tue, 2 May 2017 08:28:30 +0000 (09:28 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
tcofoegbu [Mon, 1 May 2017 17:16:56 +0000 (18:16 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Mon, 1 May 2017 17:13:55 +0000 (18:13 +0100)]
JAL-2482 bug fix
tcofoegbu [Mon, 1 May 2017 17:08:05 +0000 (18:08 +0100)]
JAL-2482 unit test for bug fix
gmungoc [Mon, 1 May 2017 15:44:23 +0000 (16:44 +0100)]
JAL-2489 JAL-2371 reinstate calls to
ColourSchemeProperty.getColourName() to handle null case
gmungoc [Mon, 1 May 2017 13:18:38 +0000 (14:18 +0100)]
Merge remote-tracking branch
'origin/bug/JAL-2479unitteststoNetworkGroup' into develop
tcofoegbu [Mon, 1 May 2017 13:16:43 +0000 (14:16 +0100)]
JAL-2376 copied out patch from Phyre branch
gmungoc [Fri, 28 Apr 2017 09:07:55 +0000 (10:07 +0100)]
Merge branch 'develop' into features/JAL-2393customMatrices
Jim Procter [Thu, 27 Apr 2017 17:29:17 +0000 (18:29 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop
Jim Procter [Thu, 27 Apr 2017 17:22:47 +0000 (18:22 +0100)]
JAL-1933 patch jalview/io/testProps.jvprops to show occupancy by default (allows jalview.gui.AnnotationChooserTest to pass)
Jim Procter [Thu, 27 Apr 2017 17:21:29 +0000 (18:21 +0100)]
JAL-1933 patch jalview/io/testProps.jvprops to show occupancy by default
Jim Procter [Thu, 27 Apr 2017 17:04:05 +0000 (18:04 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop
Jim Procter [Thu, 27 Apr 2017 17:02:54 +0000 (18:02 +0100)]
JAL-1933 don't show occupancy row when testing conservation thread runs even when only quality calculation is enabled in preferences (JAL-1306)
Jim Procter [Thu, 27 Apr 2017 16:49:30 +0000 (17:49 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop
Jim Procter [Thu, 27 Apr 2017 16:48:46 +0000 (17:48 +0100)]
JAL-1933 applet doc for showOccupancy parameter
Jim Procter [Thu, 27 Apr 2017 16:48:30 +0000 (17:48 +0100)]
JAL-1933 desktop documentation for show occupancy preference
Jim Procter [Thu, 27 Apr 2017 16:43:32 +0000 (17:43 +0100)]
JAL-1933 use constant for preference token
Jim Procter [Thu, 27 Apr 2017 16:40:56 +0000 (17:40 +0100)]
Merge branch 'features/JAL-1933_occupancy' into develop
Jim Procter [Thu, 27 Apr 2017 16:39:38 +0000 (17:39 +0100)]
JAL-1933 consensus calculation doesn’t depend on occupancy row being materialised
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
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
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
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 14:20:36 +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
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
git://source.jalview.org / jalview.git / log