gmungoc [Mon, 20 Feb 2017 10:35:32 +0000 (10:35 +0000)]
JAL-2416 remove unused pep, dna alphabets, unused methods, code format
tidy
gmungoc [Sat, 18 Feb 2017 08:21:41 +0000 (08:21 +0000)]
JAL-2416 better encapsulated 'constants' for BLOSUM62, PAM250
gmungoc [Fri, 17 Feb 2017 19:26:26 +0000 (19:26 +0000)]
JAL-2416 BLOSUM62 removed from ResidueProperties
gmungoc [Fri, 17 Feb 2017 17:44:56 +0000 (17:44 +0000)]
JAL-2416 removed DNA and PAM250 matrices from ResidueProperties
gmungoc [Fri, 17 Feb 2017 16:28:44 +0000 (16:28 +0000)]
JAL-2416 scoreMatrices removed from ResidueProperties
gmungoc [Fri, 17 Feb 2017 15:41:39 +0000 (15:41 +0000)]
JAL-2413 extracted new method SetUtils.countDisjunction()
gmungoc [Fri, 17 Feb 2017 15:14:19 +0000 (15:14 +0000)]
JAL-2423 refactored method to build panel title for tree either
calculated or read from file
gmungoc [Fri, 17 Feb 2017 13:31:49 +0000 (13:31 +0000)]
JAL-2416 SeqSpace PCA now provided as an alternative score matrix rather
than an alternative method (+code tidying)
gmungoc [Fri, 17 Feb 2017 13:30:39 +0000 (13:30 +0000)]
JAL-2416 score models now held in order added
gmungoc [Fri, 17 Feb 2017 13:30:01 +0000 (13:30 +0000)]
JAL-2416 allow space in score matrix name
gmungoc [Fri, 17 Feb 2017 13:27:33 +0000 (13:27 +0000)]
JAL-2416 order score models by order of addition rather than name
gmungoc [Fri, 17 Feb 2017 13:26:39 +0000 (13:26 +0000)]
JAL-2403 redundant 'implements' removed
gmungoc [Fri, 17 Feb 2017 13:25:42 +0000 (13:25 +0000)]
JAL-2403 extract method refactoring of FeatureScoreModel + test
gmungoc [Fri, 17 Feb 2017 10:31:11 +0000 (10:31 +0000)]
JAL-2403 constants for "NJ", "AV"
gmungoc [Tue, 14 Feb 2017 16:48:32 +0000 (16:48 +0000)]
JAL-2393 example (unvalidated) blosum80 matrix to play with drag and
drop
gmungoc [Tue, 14 Feb 2017 16:47:52 +0000 (16:47 +0000)]
Parsing moved to (new) ScoreMatrixFile, drag and drop to alignment now
supported
gmungoc [Mon, 13 Feb 2017 17:00:37 +0000 (17:00 +0000)]
JAL-2416 allow alphabet symbol (optional) in first column of score table
gmungoc [Mon, 13 Feb 2017 16:00:59 +0000 (16:00 +0000)]
JAL-1632 JAL-2416 load score matrices from file, as float[][]
gmungoc [Mon, 13 Feb 2017 09:01:54 +0000 (09:01 +0000)]
JAL-1632 first cut of Tree chooser dialog and ScoreModels singleton
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 09:01:13 +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 [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 15:37:30 +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 09:38:31 +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 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 [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 [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
gmungoc [Wed, 11 Jan 2017 16:06:01 +0000 (16:06 +0000)]
JAL-2344 groovy script that registers a new file format
gmungoc [Wed, 11 Jan 2017 16:05:41 +0000 (16:05 +0000)]
JAL-2344 FileFormats singleton for formats, FileFormatI simplified
gmungoc [Wed, 11 Jan 2017 15:38:34 +0000 (15:38 +0000)]
JAL-2344 addSequence() method added to support Groovy parser
kiramt [Wed, 11 Jan 2017 14:58:14 +0000 (14:58 +0000)]
JAL-2316 Spanish message translations
gmungoc [Tue, 10 Jan 2017 14:38:48 +0000 (14:38 +0000)]
JAL-2377 avoid infinite loop formatting 1.0E-310
kiramt [Tue, 10 Jan 2017 13:40:32 +0000 (13:40 +0000)]
JAL-2316 Separate label/db name in UrlProviders. Unit test updates.
kiramt [Mon, 9 Jan 2017 13:15:30 +0000 (13:15 +0000)]
JAL-2316 Prevent applet from loading null links into Link menu
gmungoc [Mon, 9 Jan 2017 12:02:33 +0000 (12:02 +0000)]
JAL-2371 pull up isNucleotide to SequenceCollectionI
gmungoc [Mon, 9 Jan 2017 11:54:27 +0000 (11:54 +0000)]
JAL-2371 remove ColourSchemeI.findColour(c), pure interface groovy
script
kiramt [Mon, 9 Jan 2017 11:47:12 +0000 (11:47 +0000)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2316
gmungoc [Fri, 6 Jan 2017 15:21:58 +0000 (15:21 +0000)]
JAL-2371 slight simplification of findColour overrides
gmungoc [Fri, 6 Jan 2017 14:42:40 +0000 (14:42 +0000)]
JAL-2371 correct Clustal, Blosum, PID colouring of consensus logo
gmungoc [Fri, 6 Jan 2017 14:11:24 +0000 (14:11 +0000)]
Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371collectionColourScheme
gmungoc [Fri, 6 Jan 2017 14:10:44 +0000 (14:10 +0000)]
JAL-2360 findColour() with no args removed from ColourSchemeI
gmungoc [Fri, 6 Jan 2017 09:04:18 +0000 (09:04 +0000)]
Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371collectionColourScheme
gmungoc [Fri, 6 Jan 2017 09:03:27 +0000 (09:03 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
git://source.jalview.org / jalview.git / log