gmungoc [Wed, 15 Mar 2017 12:49:51 +0000 (12:49 +0000)]
JAL-2438 corrected getFeatureRenderer()
gmungoc [Wed, 15 Mar 2017 12:47:36 +0000 (12:47 +0000)]
JAL-2442 applet feature transparency also on overview or structure
gmungoc [Wed, 15 Mar 2017 11:49:39 +0000 (11:49 +0000)]
JAL-2438 handle null FeatureRenderer in FeatureColourFinder
gmungoc [Wed, 15 Mar 2017 11:29:05 +0000 (11:29 +0000)]
JAL-2438 refactored checks for 'no features displayed'
gmungoc [Wed, 15 Mar 2017 09:19:06 +0000 (09:19 +0000)]
JAL-2438 clarify code and javadoc, reinstate updateFeatures() check
gmungoc [Wed, 15 Mar 2017 08:49:59 +0000 (08:49 +0000)]
Merge branch 'develop' into bug/JAL-2436featureRendererThreading
kiramt [Wed, 15 Mar 2017 07:54:22 +0000 (07:54 +0000)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow
kiramt [Tue, 14 Mar 2017 16:42:01 +0000 (16:42 +0000)]
JAL-2388 Working overview panel
kiramt [Tue, 14 Mar 2017 16:41:33 +0000 (16:41 +0000)]
JAL-2439 Fixes to out-by-one sequence indexing in gui classes
kiramt [Tue, 14 Mar 2017 16:06:34 +0000 (16:06 +0000)]
JAL-2388 New hidden cols/seqs functions to support overview panel
gmungoc [Tue, 14 Mar 2017 15:07:19 +0000 (15:07 +0000)]
JAL-2438 unit test, fixes, Javadoc updates
gmungoc [Tue, 14 Mar 2017 12:25:35 +0000 (12:25 +0000)]
JAL-2438 unit tests for FeatureColourFinder (transparency tbc!)
gmungoc [Tue, 14 Mar 2017 12:25:09 +0000 (12:25 +0000)]
JAL-2438 Javadoc updates
gmungoc [Tue, 14 Mar 2017 09:42:40 +0000 (09:42 +0000)]
JAL-2438 comment/Javadoc tidies
gmungoc [Mon, 13 Mar 2017 17:00:19 +0000 (17:00 +0000)]
JAL-2438 corrected handling of default colour
gmungoc [Mon, 13 Mar 2017 16:42:23 +0000 (16:42 +0000)]
JAL-2438 FeatureColourFinder refactored from FeatureRenderer, fr not
cloned for structure viewers
kiramt [Fri, 10 Mar 2017 16:11:58 +0000 (16:11 +0000)]
JAL-2437 Fixed reordering of sequences when hiding and revealing
kiramt [Fri, 10 Mar 2017 12:08:45 +0000 (12:08 +0000)]
JAL-2388 Moving some alignment panel logic into overview (in progress)
kiramt [Tue, 28 Feb 2017 12:25:11 +0000 (12:25 +0000)]
JAL-2426 Checks on conservation thread in case we are shutting down
kiramt [Tue, 28 Feb 2017 14:50:10 +0000 (14:50 +0000)]
JAL-2426 Removal of NPE in conservation thread when closing Jalview
kiramt [Thu, 9 Mar 2017 10:29:06 +0000 (10:29 +0000)]
JAL-2388 Minor fix for annotation graph, removed unit test dep on gui
gmungoc [Wed, 8 Mar 2017 14:41:45 +0000 (14:41 +0000)]
JAL-2430 colour columns hidden in alignment gray on structure
gmungoc [Wed, 8 Mar 2017 11:15:27 +0000 (11:15 +0000)]
JAL-2295 avoid quotes breaking attribute value parsing
kiramt [Tue, 7 Mar 2017 16:37:11 +0000 (16:37 +0000)]
JAL-2388 Fixed inherited&new out-by-one errors; further unit tests
gmungoc [Tue, 7 Mar 2017 15:53:30 +0000 (15:53 +0000)]
JAL-2295 status messages for Chimera attributes set and for failed
superposition
kiramt [Tue, 7 Mar 2017 14:27:58 +0000 (14:27 +0000)]
JAL-2388 Additional unit tests
kiramt [Tue, 7 Mar 2017 14:27:05 +0000 (14:27 +0000)]
JAL-2388 Missed commit
kiramt [Tue, 7 Mar 2017 10:01:14 +0000 (10:01 +0000)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow
kiramt [Tue, 7 Mar 2017 10:00:37 +0000 (10:00 +0000)]
JAL-2429 Messed something up, merged conflicts
kiramt [Tue, 7 Mar 2017 09:35:14 +0000 (09:35 +0000)]
JAL-2429 findColumnPosition returns 0 for cols in region starting at 0
kiramt [Tue, 7 Mar 2017 09:35:14 +0000 (09:35 +0000)]
JAL-2429 Additional fix to ColumnSelection when hidden cols start at 0
kiramt [Mon, 6 Mar 2017 16:23:53 +0000 (16:23 +0000)]
JAL-2388 Dependency tidy
kiramt [Mon, 6 Mar 2017 16:20:18 +0000 (16:20 +0000)]
JAL-2388 Remove OverviewDimensions dependency on gui classes
kiramt [Mon, 6 Mar 2017 14:29:58 +0000 (14:29 +0000)]
JAL-2388 Corrected overview panel behaviour, updated tests
Jim Procter [Mon, 6 Mar 2017 14:28:06 +0000 (14:28 +0000)]
Merge branch 'merges/develop_JAL2295setChimeraAttributes' into features/JAL-1933_occupancy
update occupancy branch for other changes - will merge in with JAL-2295 and JAL-1933
kiramt [Fri, 3 Mar 2017 15:00:11 +0000 (15:00 +0000)]
JAL-2429 Fix to ColumnSelection::findColumnPosition
kiramt [Fri, 3 Mar 2017 09:46:08 +0000 (09:46 +0000)]
JAL-2388 Initial removal of hidden cols/seqs out of overview
gmungoc [Thu, 2 Mar 2017 10:06:13 +0000 (10:06 +0000)]
JAL-2295 tweak order and wording of Superpose menu items and tooltip
gmungoc [Thu, 2 Mar 2017 09:51:17 +0000 (09:51 +0000)]
JAL-2295 make 'Jmol' menu appear; enable/disable Superpose option for
Chimera
kiramt [Wed, 1 Mar 2017 16:40:07 +0000 (16:40 +0000)]
JAL-2388 Reverted to previous
gmungoc [Wed, 1 Mar 2017 15:19:09 +0000 (15:19 +0000)]
JAL-1264 smarter way to skip autocalc'd annotations in asserts
gmungoc [Wed, 1 Mar 2017 14:38:50 +0000 (14:38 +0000)]
Merge branch 'features/JAL-2295setChimeraAttributes' into
merges/develop_JAL2295setChimeraAttributes
Conflicts:
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/gui/ChimeraViewFrame.java
test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
kiramt [Wed, 1 Mar 2017 08:46:10 +0000 (08:46 +0000)]
JAL-2388 Preliminary refactor check-in, does not compile
kiramt [Tue, 28 Feb 2017 14:50:10 +0000 (14:50 +0000)]
JAL-2426 Removal of NPE in conservation thread when closing Jalview
kiramt [Tue, 28 Feb 2017 14:48:56 +0000 (14:48 +0000)]
JAL-2388 Removing sources of non-determinism in unit tests
kiramt [Tue, 28 Feb 2017 14:48:25 +0000 (14:48 +0000)]
JAL-2388 First move of endRes etc out of AlignmentViewport (in progress)
kiramt [Tue, 28 Feb 2017 12:25:11 +0000 (12:25 +0000)]
JAL-2426 Checks on conservation thread in case we are shutting down
kiramt [Mon, 27 Feb 2017 16:10:21 +0000 (16:10 +0000)]
JAL-2388 Make startRes,startSeq,endRes,endSeq private with get/setters
kiramt [Mon, 27 Feb 2017 11:45:30 +0000 (11:45 +0000)]
JAL-2388 Minor refactoring
kiramt [Mon, 27 Feb 2017 09:31:46 +0000 (09:31 +0000)]
JAL-2388 Unit tests take 2
kiramt [Thu, 23 Feb 2017 18:14:13 +0000 (18:14 +0000)]
JAL-2388 Unit tests for columns, take 1
kiramt [Thu, 23 Feb 2017 10:18:02 +0000 (10:18 +0000)]
JAL-2388 Unit tests in progress
kiramt [Tue, 21 Feb 2017 10:55:07 +0000 (10:55 +0000)]
Merge branch 'bug/JAL-2421overviewboxflicker' into
features/JAL-2388OverviewWindow
Conflicts:
src/jalview/gui/AlignmentPanel.java
kiramt [Tue, 21 Feb 2017 10:53:40 +0000 (10:53 +0000)]
Merge branch 'develop' into features/JAL-2388OverviewWindow
kiramt [Tue, 21 Feb 2017 10:14:01 +0000 (10:14 +0000)]
JAL-2421 Unit test
Jim Procter [Mon, 20 Feb 2017 11:36:39 +0000 (11:36 +0000)]
Merge branch 'features/JAL-2379pcaMemory' into develop
kiramt [Fri, 17 Feb 2017 14:57:39 +0000 (14:57 +0000)]
JAL-2388 Incomplete unit tests
kiramt [Fri, 17 Feb 2017 13:17:32 +0000 (13:17 +0000)]
JAL-2421 incomplete unit test
kiramt [Fri, 17 Feb 2017 07:46:07 +0000 (07:46 +0000)]
JAL-2421 Fix to alignment panel scroll values, and start of unit test.
Jim Procter [Thu, 16 Feb 2017 11:49:57 +0000 (11:49 +0000)]
Merge branch 'bug/JAL-2374_JAL-2419_overlappinggroups_currentselection_popupmenu' into develop
Jim Procter [Wed, 15 Feb 2017 17:13:26 +0000 (17:13 +0000)]
JAL-2374 JAL-2419 - TODO suspiciously redundant nested if clauses probably need a cleanup
Jim Procter [Wed, 15 Feb 2017 17:12:02 +0000 (17:12 +0000)]
fix for JAL-2419 - don’t trash the current selection
Jim Procter [Wed, 15 Feb 2017 16:47:34 +0000 (16:47 +0000)]
JAL-2374 don’t search twice for containing group to assign to stretchGroup
Jim Procter [Wed, 15 Feb 2017 15:45:06 +0000 (15:45 +0000)]
JAL-2374 tests for SequenceGroup.contains
Jim Procter [Wed, 15 Feb 2017 15:43:06 +0000 (15:43 +0000)]
JAL-2374 JAL-1270 assign SequenceGroup tests to ‘Functional’
Jim Procter [Wed, 15 Feb 2017 15:41:58 +0000 (15:41 +0000)]
JAL-2374 new contains methods for seq and seq,apos
Jim Procter [Wed, 15 Feb 2017 15:38:49 +0000 (15:38 +0000)]
JAL-2374 javadoc - qualify that sequence argument to findGroup must be in the Alignment, not share the same dataset sequence
gmungoc [Tue, 14 Feb 2017 14:12:39 +0000 (14:12 +0000)]
JAL-2346 disable 'threshold min/max' when 'use original colours'
selected
gmungoc [Tue, 14 Feb 2017 14:02:03 +0000 (14:02 +0000)]
JAL-2346 remove refactored fields, fix test for above threshold
kiramt [Tue, 14 Feb 2017 13:47:50 +0000 (13:47 +0000)]
JAL-2388 Removed unnecessary CommandListener interface from Viewports
gmungoc [Tue, 14 Feb 2017 12:34:54 +0000 (12:34 +0000)]
Merge branch 'develop' into bug/JAL-2346annotationChoice
Conflicts:
src/jalview/appletgui/AnnotationColourChooser.java
src/jalview/gui/AnnotationRowFilter.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/PopupMenu.java
src/jalview/schemes/AnnotationColourGradient.java
gmungoc [Fri, 10 Feb 2017 11:03:15 +0000 (11:03 +0000)]
JAL-2371 small move of code, typo correction
kiramt [Thu, 9 Feb 2017 15:30:02 +0000 (15:30 +0000)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow
gmungoc [Thu, 9 Feb 2017 13:43:21 +0000 (13:43 +0000)]
JAL-1608 menu entry text; enable/disable Create/Remove Group option
kiramt [Thu, 9 Feb 2017 13:00:32 +0000 (13:00 +0000)]
JAL-2388 Initial refactor of OverviewPanel
Jim Procter [Thu, 9 Feb 2017 12:49:33 +0000 (12:49 +0000)]
Merge branch 'features/JAL-2316' into develop
Jim Procter [Thu, 9 Feb 2017 11:50:07 +0000 (11:50 +0000)]
Merge branch 'develop' into features/JAL-2316
gmungoc [Thu, 9 Feb 2017 11:40:09 +0000 (11:40 +0000)]
JAL-2401 tweaked button text, added Spanish
gmungoc [Thu, 9 Feb 2017 10:39:22 +0000 (10:39 +0000)]
JAL-2401 change 'Lower Case Colour' to checkbox with tooltip
gmungoc [Thu, 9 Feb 2017 10:05:21 +0000 (10:05 +0000)]
JAL-2371 no test for lower case consensus as not expected or handled
gmungoc [Thu, 9 Feb 2017 10:04:13 +0000 (10:04 +0000)]
JAL-2371 ensure some colour scheme (may be None) is set on startup
gmungoc [Thu, 9 Feb 2017 09:05:30 +0000 (09:05 +0000)]
Merge branch 'develop' into features/JAL-2379pcaMemory
gmungoc [Thu, 9 Feb 2017 09:01:13 +0000 (09:01 +0000)]
JAL-2371 skip upper-casing consensus as it already is
gmungoc [Thu, 9 Feb 2017 08:49:38 +0000 (08:49 +0000)]
JAL-2405 check for circular reference in SequenceGroup.context
gmungoc [Thu, 9 Feb 2017 08:41:33 +0000 (08:41 +0000)]
JAL-2405 set initial selection group alignment context
gmungoc [Thu, 9 Feb 2017 08:41:02 +0000 (08:41 +0000)]
JAL-2405 enable nucleotide/peptide colour schemes in applet menus
Jim Procter [Wed, 8 Feb 2017 16:33:51 +0000 (16:33 +0000)]
JAL-2316 tidying preferences help page
Jim Procter [Wed, 8 Feb 2017 16:33:35 +0000 (16:33 +0000)]
JAL-2316 tidied up documentation for Links tab
gmungoc [Wed, 8 Feb 2017 15:30:42 +0000 (15:30 +0000)]
JAL-2405 set context on selection group for tailored colour options
gmungoc [Wed, 8 Feb 2017 14:43:36 +0000 (14:43 +0000)]
JAL-2401 fix for NPE on selectedButtons, tweak for button appearance
gmungoc [Wed, 8 Feb 2017 12:50:41 +0000 (12:50 +0000)]
JAL-2399 JAL-2400 tidy Text Colour wording, behaviour including Cancel
kiramt [Wed, 8 Feb 2017 11:59:19 +0000 (11:59 +0000)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2316
Jim Procter [Wed, 8 Feb 2017 09:53:10 +0000 (09:53 +0000)]
JAL-2366 updated default URL to jalview.org/services/identifiers
Jim Procter [Tue, 7 Feb 2017 18:15:14 +0000 (18:15 +0000)]
Merge branch 'features/JAL-2371collectionColourScheme' into develop
gmungoc [Tue, 7 Feb 2017 15:59:37 +0000 (15:59 +0000)]
JAL-2401 Lower Case Colour toggleable, help text added
gmungoc [Tue, 7 Feb 2017 13:20:31 +0000 (13:20 +0000)]
JAL-2379 removed unused commented code
gmungoc [Tue, 7 Feb 2017 13:20:12 +0000 (13:20 +0000)]
JAL-2397 flag provided for 2.10.1 PCA gap calculation treatment
gmungoc [Tue, 7 Feb 2017 12:50:49 +0000 (12:50 +0000)]
JAL-2398 include 'compatibility mode' for C->R score correction
gmungoc [Tue, 7 Feb 2017 12:44:01 +0000 (12:44 +0000)]
JAL-2397 scripts to toggle 2.10.1 / 2.10.2 PCA calculation mode
gmungoc [Tue, 7 Feb 2017 12:43:19 +0000 (12:43 +0000)]
JAL-2397 PCA gap cost uses last column of score matrix
git://source.jalview.org / jalview.git / log