Jim Procter [Thu, 16 Mar 2017 17:42:25 +0000 (17:42 +0000)]
JAL-1933 refactor parameter for code clarity
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
gmungoc [Tue, 7 Mar 2017 15:53:30 +0000 (15:53 +0000)]
JAL-2295 status messages for Chimera attributes set and for failed
superposition
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
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
Jim Procter [Mon, 20 Feb 2017 11:36:39 +0000 (11:36 +0000)]
Merge branch 'features/JAL-2379pcaMemory' into develop
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 [Fri, 10 Feb 2017 11:03:15 +0000 (11:03 +0000)]
JAL-2371 small move of code, typo correction
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
gmungoc [Fri, 20 Jan 2017 10:52:29 +0000 (10:52 +0000)]
JAL-2383 restore group conservation slider setting from project
gmungoc [Fri, 20 Jan 2017 09:47:20 +0000 (09:47 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
Conflicts:
src/jalview/appletgui/APopupMenu.java
src/jalview/gui/AlignFrame.java
src/jalview/gui/PopupMenu.java
src/jalview/jbgui/GAlignFrame.java
gmungoc [Thu, 19 Jan 2017 16:37:02 +0000 (16:37 +0000)]
JAL-2383 restore PID colour threshold from project; enable/disable
modify PID/Conservation (and add to popup menus)
gmungoc [Thu, 19 Jan 2017 10:29:04 +0000 (10:29 +0000)]
JAL-2370 unit tests for extracted ColumnSelection.stretchGroup()
gmungoc [Thu, 19 Jan 2017 09:40:06 +0000 (09:40 +0000)]
JAL-2370 corrected applet mouse drag, refactored into ColumnSelection
gmungoc [Wed, 18 Jan 2017 09:14:12 +0000 (09:14 +0000)]
JAL-2379 more realistic matrices for unit tests
gmungoc [Tue, 17 Jan 2017 16:20:55 +0000 (16:20 +0000)]
JAL-1933 update threshold on focus lost in text field
gmungoc [Tue, 17 Jan 2017 16:07:49 +0000 (16:07 +0000)]
Merge branch 'develop' into features/JAL-2295setChimeraAttributes
gmungoc [Tue, 17 Jan 2017 15:01:01 +0000 (15:01 +0000)]
JAL-2370 fix bug when hiding a range including two or more hidden ranges
gmungoc [Tue, 17 Jan 2017 13:32:33 +0000 (13:32 +0000)]
Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371collectionColourScheme
gmungoc [Tue, 17 Jan 2017 13:31:55 +0000 (13:31 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
Conflicts:
src/jalview/gui/PopupMenu.java
src/jalview/jbgui/GAlignFrame.java
gmungoc [Tue, 17 Jan 2017 13:21:12 +0000 (13:21 +0000)]
JAL-2379 use SparseMatrix for encoded sequences, tidy unneeded code
gmungoc [Tue, 17 Jan 2017 13:20:37 +0000 (13:20 +0000)]
JAL-2379 SparseMatrix alternative to Matrix, both MatrixI
gmungoc [Tue, 17 Jan 2017 13:18:45 +0000 (13:18 +0000)]
JAL-2379 SparseDoubleArray added (for use by SparseMatrix)
gmungoc [Mon, 16 Jan 2017 09:02:52 +0000 (09:02 +0000)]
JAL-1270 class renamed
gmungoc [Mon, 16 Jan 2017 09:02:34 +0000 (09:02 +0000)]
JAL-2380 fix Matrix.postMultiply()
gmungoc [Mon, 16 Jan 2017 08:52:20 +0000 (08:52 +0000)]
JAL-1270 tweaks to AlignmentGenerator / client class
gmungoc [Thu, 12 Jan 2017 17:10:00 +0000 (17:10 +0000)]
JAL-1270 renamed AlignmentGenerator, and added peptide option
gmungoc [Thu, 12 Jan 2017 16:44:09 +0000 (16:44 +0000)]
JAL-2379 null references to PCA model when panel is closed
gmungoc [Thu, 12 Jan 2017 09:05:56 +0000 (09:05 +0000)]
JAL-2344 now flagging formats as 'identifiable' instead of 'dynamic'
gmungoc [Wed, 11 Jan 2017 16:48:28 +0000 (16:48 +0000)]
JAL-2344 separated AlignmentFileI into AlignmentFileReaderI,
AlignmentFileWriterI
git://source.jalview.org / jalview.git / log