tcofoegbu [Tue, 28 Mar 2017 18:02:33 +0000 (19:02 +0100)]
clean up mistake in the test file allhits.ann
tcofoegbu [Tue, 28 Mar 2017 17:20:10 +0000 (18:20 +0100)]
JAL-2136 JAL-2137 Added improvement to enable explicit and dynamic definition of STRUCTMODEL data via HEADER_STRUCT_MODEL annotation, updated test annotation file, and added unit test accordingly
tcofoegbu [Tue, 28 Mar 2017 17:12:43 +0000 (18:12 +0100)]
JAL-2136 fixed failing unit test for Phyre2Client
tcofoegbu [Tue, 28 Mar 2017 17:08:15 +0000 (18:08 +0100)]
JAL-2465 missed commit for refactore renaming of getPdbFile() method to getStructureFile()
tcofoegbu [Tue, 28 Mar 2017 17:04:46 +0000 (18:04 +0100)]
JAL-2465 unit test for bugfix
tcofoegbu [Tue, 28 Mar 2017 17:03:41 +0000 (18:03 +0100)]
JAL-2465 bugfix and rerefactor renamed getPdbFile() method to getStructureFile()
tcofoegbu [Thu, 23 Mar 2017 12:02:33 +0000 (12:02 +0000)]
JAL-2463 bugfix
tcofoegbu [Mon, 20 Mar 2017 15:14:27 +0000 (15:14 +0000)]
Merge JAL-2136_phyre2_integration to develop
tcofoegbu [Fri, 17 Mar 2017 15:41:01 +0000 (15:41 +0000)]
JAL-2136 JAL-2137 Improvements: enable STRUCTMODEL annotation statement to be less stringent and backwards compatible, Link query and template sequences, transfer annotation from model to template sequence
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
tcofoegbu [Tue, 14 Mar 2017 15:35:50 +0000 (15:35 +0000)]
JAL-2136 JAL-2137 Improved STRUCTMODEL annotation syntax to reinstated fasta file specification, improved implementation to link the Fasta mapping file to Phyre2 model entry, and moved Phyre2 model info from sequence detail to PDBEntry properties
tcofoegbu [Fri, 10 Mar 2017 14:29:21 +0000 (14:29 +0000)]
JAL-2136 JAL-2137 Modified STRUCTMODEL annotation format and added implementation to register Phyre2 model file from AnnotationFile such that it could be properly processed Phyre2 client on structure viewing.
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
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
tcofoegbu [Tue, 28 Feb 2017 12:49:20 +0000 (12:49 +0000)]
JAL-2136 added improvement to parse crudelist file instead of scrapping 'summary.html' and renamed testfiles accordingly
tcofoegbu [Mon, 20 Feb 2017 12:25:32 +0000 (12:25 +0000)]
JAL-2136 merged and resolved conflicts with
80edaa84d6d9beac9f0d2c71b50b7b56fd393427
Jim Procter [Mon, 20 Feb 2017 11:36:39 +0000 (11:36 +0000)]
Merge branch 'features/JAL-2379pcaMemory' into develop
tcofoegbu [Mon, 20 Feb 2017 10:17:44 +0000 (10:17 +0000)]
Merge branch 'reviews/features/JAL-2136_phyre2_integration_withJims' into merge/JAL-2136_phyre2_integration
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
Jim Procter [Wed, 8 Feb 2017 15:01:21 +0000 (15:01 +0000)]
JAL-2136 update merged code for JAL-2040 for new FileFormat/Protocol interface (JAL-2344)
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
tcofoegbu [Mon, 30 Jan 2017 11:37:55 +0000 (11:37 +0000)]
Merge branch 'reviews/features/JAL-2136_phyre2_integration_withJims' into merge/JAL-2136_phyre2_integration
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()
Jim Procter [Mon, 23 Jan 2017 15:13:33 +0000 (15:13 +0000)]
Merge branch 'features/JAL-2040_JAL-2137_phyre2' into reviews/features/JAL-2136_phyre2_integration_withJims
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)
tcofoegbu [Fri, 20 Jan 2017 19:43:20 +0000 (19:43 +0000)]
JAL-2375 JAL-2376 First commit of implementation for Phyre2 result browsing, template parsing and structure mapping. Added fix for failing tests in SiftsClientTest, added improvement to un-offer cached option when cached data is unavailable, added improvement to include horizontal separator between structure filter options and manual input options, and other minor refactoring
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