gmungoc [Mon, 27 Mar 2017 18:13:20 +0000 (19:13 +0100)]
JAL-2416 amended to (as near as possible) strict NCBI format
gmungoc [Mon, 27 Mar 2017 13:27:35 +0000 (14:27 +0100)]
JAL-2416 class Javadoc updates prior to parsing changes
gmungoc [Mon, 27 Mar 2017 13:25:59 +0000 (14:25 +0100)]
JAL-2468 change score model in PCAModel when switching
peptide/nucleotide
gmungoc [Mon, 27 Mar 2017 12:49:06 +0000 (13:49 +0100)]
JAL-2416 tidy up after switch from ' ' to '-' in score matrices
gmungoc [Mon, 27 Mar 2017 12:12:37 +0000 (13:12 +0100)]
JAL-2416 score matrix gap symbol (if any) dynamically determined
gmungoc [Mon, 27 Mar 2017 11:40:35 +0000 (12:40 +0100)]
JAL-2416 tooltip with descriptions for score models drop-down list
gmungoc [Mon, 27 Mar 2017 10:48:49 +0000 (11:48 +0100)]
JAL-2416 add score model description field for tooltip in PCA panel
gmungoc [Mon, 27 Mar 2017 10:02:47 +0000 (11:02 +0100)]
JAL-2403 SWDistanceModel now SmithWatermanModel - a similarity model
gmungoc [Mon, 27 Mar 2017 09:16:21 +0000 (10:16 +0100)]
JAL-2416 use '-' not space for gap in score matrices
gmungoc [Mon, 27 Mar 2017 09:10:13 +0000 (10:10 +0100)]
JAL-2428 unused method deleted
gmungoc [Mon, 27 Mar 2017 09:09:22 +0000 (10:09 +0100)]
JAL-2403 PIDDistanceModel deleted as superseded by PIDModel
gmungoc [Mon, 27 Mar 2017 08:11:47 +0000 (09:11 +0100)]
JAL-2428 pass AlignmentView to TreeModel so Show Input Data works
gmungoc [Fri, 24 Mar 2017 16:59:32 +0000 (16:59 +0000)]
Merge branch 'develop' into features/JAL-2393customMatrices
gmungoc [Fri, 24 Mar 2017 16:30:04 +0000 (16:30 +0000)]
JAL-2428 simplify TreeModel constructors, add getOriginalData
gmungoc [Fri, 24 Mar 2017 16:28:29 +0000 (16:28 +0000)]
JAL-2428 use 'correct' name for selected score model
Jim Procter [Fri, 24 Mar 2017 15:28:49 +0000 (15:28 +0000)]
JAL-2360 fix applet build by separating castor XML dependency from jalview.schemes.ColourSchemes to jalview.schemes.ColourSchemeLoader
gmungoc [Fri, 24 Mar 2017 14:47:49 +0000 (14:47 +0000)]
JAL-1632 TreeChooser renamed CalculationChooser, text improved, i18n
gmungoc [Fri, 24 Mar 2017 12:21:33 +0000 (12:21 +0000)]
JAL-1632 named parameters
gmungoc [Fri, 24 Mar 2017 09:58:15 +0000 (09:58 +0000)]
JAL-2398 corrected BLOSUM62 C -> R score in resource file!
gmungoc [Fri, 24 Mar 2017 09:57:31 +0000 (09:57 +0000)]
JAL-2416 tests added for ScoreMatrix
gmungoc [Fri, 24 Mar 2017 09:30:47 +0000 (09:30 +0000)]
JAL-838 move two callers off Comparison.PID and deprecate it
kiramt [Thu, 23 Mar 2017 20:40:10 +0000 (20:40 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
kiramt [Thu, 23 Mar 2017 20:39:51 +0000 (20:39 +0000)]
JAL-2388 unit test initialisation fix for running full suite
gmungoc [Thu, 23 Mar 2017 16:39:46 +0000 (16:39 +0000)]
JAL-2397 scale PCA by PID to alignment width to match SeqSpace
gmungoc [Thu, 23 Mar 2017 16:12:14 +0000 (16:12 +0000)]
JAL-2397 formatting only
gmungoc [Thu, 23 Mar 2017 16:11:37 +0000 (16:11 +0000)]
JAL-1632 suppress PID parameter options in Tree/PCA chooser for now
gmungoc [Thu, 23 Mar 2017 16:10:21 +0000 (16:10 +0000)]
JAL-838 class javadoc added
gmungoc [Thu, 23 Mar 2017 15:10:52 +0000 (15:10 +0000)]
JAL-2464 fix cancel tree print behaviour
gmungoc [Thu, 23 Mar 2017 15:01:29 +0000 (15:01 +0000)]
JAL-2393 code tidy and comments, PIDDistanceModel deprecated
gmungoc [Thu, 23 Mar 2017 15:00:59 +0000 (15:00 +0000)]
JAL-2393 updated test for removal of PIDDistanceModel
gmungoc [Thu, 23 Mar 2017 09:17:31 +0000 (09:17 +0000)]
Merge branch 'develop' into features/JAL-2393customMatrices
kiramt [Wed, 22 Mar 2017 14:12:50 +0000 (14:12 +0000)]
JAL-2388 Reinstated original overview checks for annotation display
kiramt [Wed, 22 Mar 2017 13:53:57 +0000 (13:53 +0000)]
Merge remote-tracking branch
'origin/bug/JAL-2436featureRendererThreading' into develop
Conflicts:
src/jalview/appletgui/OverviewPanel.java
src/jalview/gui/OverviewPanel.java
kiramt [Wed, 22 Mar 2017 12:36:24 +0000 (12:36 +0000)]
Merge remote-tracking branch 'origin/develop' into
bug/JAL-2436featureRendererThreading
Conflicts:
src/jalview/appletgui/OverviewPanel.java
src/jalview/gui/OverviewPanel.java
gmungoc [Wed, 22 Mar 2017 10:51:23 +0000 (10:51 +0000)]
JAL-2311 suppress autocalc'd annotation to isolate the 'real' failure
kiramt [Tue, 21 Mar 2017 19:42:32 +0000 (19:42 +0000)]
JAL-2307 Fixed SiftsClient unit test
gmungoc [Tue, 21 Mar 2017 12:41:01 +0000 (12:41 +0000)]
JAL-2306 assert no DAS sources
gmungoc [Tue, 21 Mar 2017 10:22:57 +0000 (10:22 +0000)]
JAL-2438 removed (non-functional) lastSeq, lastSequenceFeatures
gmungoc [Tue, 21 Mar 2017 09:44:08 +0000 (09:44 +0000)]
JAL-2243 update discovered features on opening structure in Chimera
gmungoc [Tue, 21 Mar 2017 09:43:32 +0000 (09:43 +0000)]
JAL-2438 check for null FeatureRenderer
Jim Procter [Tue, 21 Mar 2017 09:05:53 +0000 (09:05 +0000)]
Merge branch 'features/JAL-2388OverviewWindow' into develop
Jim Procter [Mon, 20 Mar 2017 16:05:00 +0000 (16:05 +0000)]
Merge branch 'bug/JAL-2421overviewboxflicker' into develop
kiramt [Mon, 20 Mar 2017 08:12:15 +0000 (08:12 +0000)]
JAL-2388 Comment typo
kiramt [Fri, 17 Mar 2017 14:11:11 +0000 (14:11 +0000)]
JAL-2388 ViewportRanges unit test
kiramt [Fri, 17 Mar 2017 13:47:15 +0000 (13:47 +0000)]
JAL-2437 Synchronization corrections and unit tests
kiramt [Fri, 17 Mar 2017 07:24:00 +0000 (07:24 +0000)]
JAL-2388 Renamed column and row subtraction functions
Jim Procter [Thu, 16 Mar 2017 18:15:03 +0000 (18:15 +0000)]
Merge branch 'merges/develop_JAL2295setChimeraAttributes' into develop
Jim Procter [Thu, 16 Mar 2017 17:42:25 +0000 (17:42 +0000)]
JAL-1933 refactor parameter for code clarity
kiramt [Thu, 16 Mar 2017 17:30:14 +0000 (17:30 +0000)]
JAL-2388 Applied ViewportRanges to code
kiramt [Thu, 16 Mar 2017 13:32:40 +0000 (13:32 +0000)]
JAL-2388 Renamed viewport position props to viewport ranges
kiramt [Thu, 16 Mar 2017 12:13:05 +0000 (12:13 +0000)]
JAL-2388 Unit test update
kiramt [Thu, 16 Mar 2017 12:12:52 +0000 (12:12 +0000)]
JAL-2388 Applet update for overview panel
kiramt [Thu, 16 Mar 2017 12:12:31 +0000 (12:12 +0000)]
JAL-2439 Out-by-one in setting endRes/endSeq
kiramt [Wed, 15 Mar 2017 14:58:36 +0000 (14:58 +0000)]
JAL-2388 Unit tests and tidies
gmungoc [Wed, 15 Mar 2017 12:55:25 +0000 (12:55 +0000)]
JAL-2443 push getResidueBoxColour inside getResidueColour
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
gmungoc [Mon, 6 Mar 2017 14:39:42 +0000 (14:39 +0000)]
JAL-2428 correct order of processing in joinClusters()
kiramt [Mon, 6 Mar 2017 14:29:58 +0000 (14:29 +0000)]
JAL-2388 Corrected overview panel behaviour, updated tests
gmungoc [Mon, 6 Mar 2017 09:45:54 +0000 (09:45 +0000)]
JAL-2428 separate TreeModel from TreeBuilder/NJTree/AverageDistanceTree
(first pass)
kiramt [Fri, 3 Mar 2017 15:00:11 +0000 (15:00 +0000)]
JAL-2429 Fix to ColumnSelection::findColumnPosition
gmungoc [Fri, 3 Mar 2017 10:01:34 +0000 (10:01 +0000)]
JAL-2428 use BitSet for clusters and done flags
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
git://source.jalview.org / jalview.git / log