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
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
kiramt [Wed, 1 Mar 2017 16:40:07 +0000 (16:40 +0000)]
JAL-2388 Reverted to previous
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
kiramt [Tue, 14 Feb 2017 13:47:50 +0000 (13:47 +0000)]
JAL-2388 Removed unnecessary CommandListener interface from Viewports
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
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
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
gmungoc [Tue, 7 Feb 2017 11:50:00 +0000 (11:50 +0000)]
JAL-2398 corrected entry for C->R in Blosum62 matrix
gmungoc [Mon, 6 Feb 2017 14:50:11 +0000 (14:50 +0000)]
JAL-2379 computePairwiseScores() moved to ScoreMatrix
gmungoc [Fri, 3 Feb 2017 16:13:24 +0000 (16:13 +0000)]
JAL-2379 'direct' pairwise score calculation for PCA (no encoding)
gmungoc [Wed, 1 Feb 2017 13:02:56 +0000 (13:02 +0000)]
JAL-2371 (slight!) simplification of isApplicableTo()
gmungoc [Wed, 1 Feb 2017 11:37:04 +0000 (11:37 +0000)]
JAL-2383 and Spanish!
gmungoc [Tue, 31 Jan 2017 15:23:06 +0000 (15:23 +0000)]
JAL-2371 commented code removed only
gmungoc [Tue, 31 Jan 2017 14:40:51 +0000 (14:40 +0000)]
JAL-2371 rename global/viewportColourScheme to residueShading
gmungoc [Tue, 31 Jan 2017 14:38:38 +0000 (14:38 +0000)]
JAL-2385 more tests/bug fixes mostly for gui.SliderPanel and some
JAL-2371 tidying
gmungoc [Fri, 27 Jan 2017 15:46:02 +0000 (15:46 +0000)]
JAL-2379 commented out code removed
gmungoc [Fri, 27 Jan 2017 15:37:30 +0000 (15:37 +0000)]
JAL-2371 CollectionColourScheme renamed ResidueShader and moved to
jalview.renderer
gmungoc [Fri, 27 Jan 2017 15:30:49 +0000 (15:30 +0000)]
JAL-2099 belated unit test
gmungoc [Fri, 27 Jan 2017 10:40:43 +0000 (10:40 +0000)]
JAL-2360 JAL-2371 updates from review CR-JAL-1
kiramt [Fri, 27 Jan 2017 09:52:40 +0000 (09:52 +0000)]
JAL-2366 Removed unneeded setEnabled calls
gmungoc [Thu, 26 Jan 2017 14:35:28 +0000 (14:35 +0000)]
JAL-2360 corrected comment
gmungoc [Thu, 26 Jan 2017 14:24:38 +0000 (14:24 +0000)]
JAL-2360 C is Pink with consensus > 85% (not 100%)
kiramt [Thu, 26 Jan 2017 11:40:39 +0000 (11:40 +0000)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2316
gmungoc [Thu, 26 Jan 2017 11:34:46 +0000 (11:34 +0000)]
Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371collectionColourScheme
gmungoc [Thu, 26 Jan 2017 11:34:04 +0000 (11:34 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
Conflicts:
src/jalview/gui/UserDefinedColours.java
kiramt [Thu, 26 Jan 2017 11:27:08 +0000 (11:27 +0000)]
JAL-2316 Updated to use identifiers jalview service
gmungoc [Thu, 26 Jan 2017 09:47:42 +0000 (09:47 +0000)]
Merge branch 'develop' into features/JAL-2379pcaMemory
Conflicts:
src/jalview/analysis/PCA.java
src/jalview/math/Matrix.java
test/jalview/math/MatrixTest.java
gmungoc [Thu, 26 Jan 2017 09:38:31 +0000 (09:38 +0000)]
JAL-2344 test fix and code tidy for review comments
gmungoc [Thu, 26 Jan 2017 09:20:46 +0000 (09:20 +0000)]
JAL-2380 code tidy after review
gmungoc [Wed, 25 Jan 2017 12:15:43 +0000 (12:15 +0000)]
JAL-2344 push Cache.getProperty("LAST_DIRECTORY") inside method
gmungoc [Mon, 23 Jan 2017 20:25:42 +0000 (20:25 +0000)]
JAL-2379 made SparseMatrix.divide() so as to exactly match
Matrix.divide()
gmungoc [Mon, 23 Jan 2017 13:26:24 +0000 (13:26 +0000)]
JAL-2386 unit tests for change colour (and minor refactoring for
testability)
gmungoc [Mon, 23 Jan 2017 09:11:36 +0000 (09:11 +0000)]
JAL-2386 simplify changeColour (doesn't change colour thresholds)
gmungoc [Fri, 20 Jan 2017 14:49:29 +0000 (14:49 +0000)]
Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371collectionColourScheme
gmungoc [Fri, 20 Jan 2017 14:48:43 +0000 (14:48 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
gmungoc [Fri, 20 Jan 2017 14:48:16 +0000 (14:48 +0000)]
JAL-2385 tweak to applet 'switch colour slider context'
gmungoc [Fri, 20 Jan 2017 14:44:02 +0000 (14:44 +0000)]
Merge branch 'features/JAL-2360colourSchemeApplicability' into
features/JAL-2371collectionColourScheme
Conflicts:
src/jalview/appletgui/SliderPanel.java
src/jalview/gui/SliderPanel.java
gmungoc [Fri, 20 Jan 2017 14:25:58 +0000 (14:25 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
gmungoc [Fri, 20 Jan 2017 14:20:48 +0000 (14:20 +0000)]
JAL-2385 update slider settings when switching slider panel focus
gmungoc [Fri, 20 Jan 2017 12:21:42 +0000 (12:21 +0000)]
Merge branch 'features/JAL-2360colourSchemeApplicability' into
features/JAL-2371collectionColourScheme
Conflicts:
src/jalview/appletgui/SliderPanel.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/SliderPanel.java
gmungoc [Fri, 20 Jan 2017 12:03:39 +0000 (12:03 +0000)]
JAL-2383 fixup from last merge
gmungoc [Fri, 20 Jan 2017 11:56:07 +0000 (11:56 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
Conflicts:
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/SliderPanel.java
src/jalview/gui/PopupMenu.java
gmungoc [Fri, 20 Jan 2017 10:55:50 +0000 (10:55 +0000)]
JAL-2383 check for null, spelling
gmungoc [Fri, 20 Jan 2017 10:55:24 +0000 (10:55 +0000)]
JAL-2383 make popup colour menu order and wording consistent
git://source.jalview.org / jalview.git / log