Jim Procter [Wed, 31 Aug 2016 14:34:19 +0000 (15:34 +0100)]
JAL-2034 remove todo - answer is yes!
gmungoc [Tue, 30 Aug 2016 14:58:47 +0000 (15:58 +0100)]
JAL-2183 defensive check for openFrameCount < 0 (shouldn't happen but
did)
gmungoc [Tue, 30 Aug 2016 14:49:34 +0000 (15:49 +0100)]
JAL-2183 simplified database tree actionPerformed, accept dbl-click
gmungoc [Tue, 30 Aug 2016 14:45:45 +0000 (15:45 +0100)]
JAL-2183 revised change (= no change)
gmungoc [Tue, 30 Aug 2016 14:27:14 +0000 (15:27 +0100)]
JAL-2183 formatter added @Override (only)
gmungoc [Tue, 30 Aug 2016 14:26:31 +0000 (15:26 +0100)]
JAL-2183 removed redundant (overriden) add panel to container
gmungoc [Mon, 29 Aug 2016 11:31:34 +0000 (12:31 +0100)]
JAL-1854 tweaks to rules and README
gmungoc [Mon, 29 Aug 2016 10:23:58 +0000 (11:23 +0100)]
JAL-1854 checkstyle relocated to /utils, newlines to Unix (?)
gmungoc [Mon, 29 Aug 2016 09:24:23 +0000 (10:24 +0100)]
Merge branch 'bug/JAL-1841rnaSecStr' into develop
gmungoc [Mon, 29 Aug 2016 09:23:59 +0000 (10:23 +0100)]
JAL-1448 updated unit test for last change
gmungoc [Mon, 29 Aug 2016 09:10:20 +0000 (10:10 +0100)]
JAL-1841 robustness fix
gmungoc [Mon, 29 Aug 2016 08:01:06 +0000 (09:01 +0100)]
Merge branch 'develop' into bug/JAL-1841rnaSecStr
gmungoc [Fri, 26 Aug 2016 15:28:53 +0000 (16:28 +0100)]
JAL-1854 two more rules, readme notes
gmungoc [Fri, 26 Aug 2016 11:15:06 +0000 (12:15 +0100)]
Merge branch 'develop' into bug/JAL-1841rnaSecStr
gmungoc [Fri, 26 Aug 2016 11:11:57 +0000 (12:11 +0100)]
JAL-1854 commented FallThrough rule
gmungoc [Fri, 26 Aug 2016 11:11:22 +0000 (12:11 +0100)]
JAL-1854 corrected nested package rule
gmungoc [Fri, 26 Aug 2016 11:09:27 +0000 (12:09 +0100)]
JAL-2049 set Ensembl variant source to ENSEMBL if '.' (not provided) and
in computed peptide variants
gmungoc [Fri, 26 Aug 2016 09:33:38 +0000 (10:33 +0100)]
JAL-1854 comment switch case fallthrough
gmungoc [Thu, 25 Aug 2016 16:19:23 +0000 (17:19 +0100)]
JAL-1854 missing case break statements added
gmungoc [Thu, 25 Aug 2016 16:11:15 +0000 (17:11 +0100)]
JAL-1854 initial checkstyle config
gmungoc [Thu, 25 Aug 2016 08:22:25 +0000 (09:22 +0100)]
JAL-2178 remove duplicate Uniprot db source
gmungoc [Thu, 25 Aug 2016 07:59:59 +0000 (08:59 +0100)]
JAL-1424 duplicate key removed
gmungoc [Wed, 24 Aug 2016 13:39:05 +0000 (14:39 +0100)]
JAL-1355 correct 'thereshold' to 'threshold' in message keys
gmungoc [Wed, 24 Aug 2016 13:31:37 +0000 (14:31 +0100)]
JAL-1424 removed unused and duplicated message keys
gmungoc [Wed, 24 Aug 2016 13:27:22 +0000 (14:27 +0100)]
JAL-1424 tidy / recode MessageManager calls to support code analysis
gmungoc [Wed, 24 Aug 2016 13:24:20 +0000 (14:24 +0100)]
JAL-1854 removed pointless method override
gmungoc [Wed, 24 Aug 2016 13:23:04 +0000 (14:23 +0100)]
JAL-1424 removed two redundant (overwritten) setText() calls
gmungoc [Wed, 24 Aug 2016 13:22:12 +0000 (14:22 +0100)]
JAL-1424 corrected Message bundle lookup key
gmungoc [Wed, 24 Aug 2016 13:21:10 +0000 (14:21 +0100)]
JAL-1424 undo i18n of exception message
gmungoc [Wed, 24 Aug 2016 13:19:34 +0000 (14:19 +0100)]
JAL-1854 declare immutable class as final
gmungoc [Wed, 24 Aug 2016 13:15:05 +0000 (14:15 +0100)]
JAL-1424 recode calls to MessageManager to allow code inspection
gmungoc [Wed, 24 Aug 2016 13:07:26 +0000 (14:07 +0100)]
JAL-2151 port fix to applet
gmungoc [Wed, 24 Aug 2016 13:05:39 +0000 (14:05 +0100)]
JAL-1424 enhanced for cleaner reporting, checks calls to JvSwingUtils
gmungoc [Wed, 24 Aug 2016 09:34:04 +0000 (10:34 +0100)]
JAL-1424 also report (obsolete) keys in translated bundle not in default
gmungoc [Tue, 23 Aug 2016 09:41:15 +0000 (10:41 +0100)]
JAL-2176 unused field / methods removed
gmungoc [Tue, 23 Aug 2016 08:16:51 +0000 (09:16 +0100)]
JAL-2174 markColumns() refactored inside ColumnSelection
gmungoc [Mon, 22 Aug 2016 15:21:38 +0000 (16:21 +0100)]
JAL-1448 corrected for backwards compatibility for UK locale users
gmungoc [Mon, 22 Aug 2016 14:39:43 +0000 (15:39 +0100)]
JAL-2175 code tidying
gmungoc [Mon, 22 Aug 2016 14:38:54 +0000 (15:38 +0100)]
JAL-2175 code/test fixes/tidy for PFAM/MSF/JSON roundtrip
gmungoc [Mon, 22 Aug 2016 08:26:41 +0000 (09:26 +0100)]
JAL-2011 adjust method to fix failing unit test
gmungoc [Fri, 19 Aug 2016 15:52:22 +0000 (16:52 +0100)]
JAL-2174 bug fixes + refactoring to allow + unit tests
tcofoegbu [Fri, 19 Aug 2016 14:13:10 +0000 (15:13 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 19 Aug 2016 14:13:01 +0000 (15:13 +0100)]
JAL-1803 unit test for PDB chainCode save/restore from Jalview project
gmungoc [Thu, 18 Aug 2016 15:33:06 +0000 (16:33 +0100)]
Merge branch 'develop' into bug/JAL-1841rnaSecStr
gmungoc [Thu, 18 Aug 2016 15:20:50 +0000 (16:20 +0100)]
JAL-2077 using Platform method to check for Ctrl-down
gmungoc [Thu, 18 Aug 2016 15:19:01 +0000 (16:19 +0100)]
JAL-1445 status message '...not containing...' for inverted selection
gmungoc [Thu, 18 Aug 2016 15:16:27 +0000 (16:16 +0100)]
JAL-1693 show warning dialog if unable to make CDS for split frame
gmungoc [Thu, 18 Aug 2016 14:25:52 +0000 (15:25 +0100)]
JAL-1855 fail gracefully if XML has no <sequence> element
gmungoc [Thu, 18 Aug 2016 10:08:23 +0000 (11:08 +0100)]
JAL-2077 handling Cmd-click in scale panel for Mac / Windows
gmungoc [Thu, 18 Aug 2016 09:42:28 +0000 (10:42 +0100)]
JAL-2001 return copy of selection in getSelected()
gmungoc [Wed, 17 Aug 2016 13:55:26 +0000 (14:55 +0100)]
JAL-2146 status message now with formatted residue name / code
gmungoc [Wed, 17 Aug 2016 11:30:57 +0000 (12:30 +0100)]
JAL-2173 don't remove annotation from hidden columns
gmungoc [Wed, 17 Aug 2016 11:22:19 +0000 (12:22 +0100)]
JAL-2172 reverted to not sorting column selection
gmungoc [Wed, 17 Aug 2016 11:16:43 +0000 (12:16 +0100)]
JAL-2105 rest versions updated to 4.6, change log link added
gmungoc [Wed, 17 Aug 2016 10:06:04 +0000 (11:06 +0100)]
JAL-2172 handle case where column selection is not ordered
gmungoc [Tue, 16 Aug 2016 15:52:37 +0000 (16:52 +0100)]
Merge branch 'develop' into bug/JAL-1841rnaSecStr
gmungoc [Tue, 16 Aug 2016 15:52:03 +0000 (16:52 +0100)]
JAL-2172 unit test added
gmungoc [Tue, 16 Aug 2016 15:49:47 +0000 (16:49 +0100)]
JAL-2171 matching bracket default character for rna SS entry
gmungoc [Tue, 16 Aug 2016 07:55:26 +0000 (08:55 +0100)]
Merge branch 'develop' into bug/JAL-1841rnaSecStr
gmungoc [Mon, 15 Aug 2016 15:57:06 +0000 (16:57 +0100)]
JAL-1841 better i18n text
tcofoegbu [Mon, 15 Aug 2016 15:54:17 +0000 (16:54 +0100)]
JAL-1128 fix for truncated bottom boarder pixels in figures generated from wrapped alignment
tcofoegbu [Mon, 15 Aug 2016 15:46:00 +0000 (16:46 +0100)]
JAL-1128 fix for truncated bottom boarder pixels in figures generated from wrapped alignment
tcofoegbu [Mon, 15 Aug 2016 13:54:19 +0000 (14:54 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Mon, 15 Aug 2016 13:53:58 +0000 (14:53 +0100)]
JAL-1919 Added improvement to ensure consistence of annotations parsed via JmolParser vs PDBfile parser and fixed unit tests accordingly
gmungoc [Fri, 12 Aug 2016 13:49:08 +0000 (14:49 +0100)]
JAL-1841 count (logo height) is valid pairs only; detect base-gap pair
gmungoc [Fri, 12 Aug 2016 10:33:55 +0000 (11:33 +0100)]
JAL-1841 bug fixes / code tidy for rna SS rendering / parsing
gmungoc [Fri, 12 Aug 2016 10:32:10 +0000 (11:32 +0100)]
JAL-1841, bug fix in rna SS consensus, additions to Rna[Test]
gmungoc [Fri, 12 Aug 2016 09:51:48 +0000 (10:51 +0100)]
JAL-2171 default SS symbol to existing (if present)
gmungoc [Wed, 10 Aug 2016 10:41:20 +0000 (11:41 +0100)]
JAL-2124 i18n of 'All' menu item
gmungoc [Wed, 10 Aug 2016 10:37:01 +0000 (11:37 +0100)]
JAL-2124 i18n of "All" menu item
gmungoc [Wed, 10 Aug 2016 10:34:31 +0000 (11:34 +0100)]
JAL-2146 small optimisation (avoid String creation)
gmungoc [Wed, 10 Aug 2016 10:33:10 +0000 (11:33 +0100)]
JAL-2146 show Column no [Sequence no [Residue / pos]] on mouseover
gmungoc [Mon, 8 Aug 2016 16:16:36 +0000 (17:16 +0100)]
JAL-1577 rebuild menus when secondary structure manually updated
tcofoegbu [Mon, 8 Aug 2016 15:01:32 +0000 (16:01 +0100)]
replaced broken biojsmsa home link in jalveiw help
gmungoc [Mon, 8 Aug 2016 13:42:30 +0000 (14:42 +0100)]
JAL-2119 replaced link with a non-404 alternative
gmungoc [Mon, 8 Aug 2016 13:25:09 +0000 (14:25 +0100)]
JAL-2168 -nonews option also mentioned here
gmungoc [Mon, 8 Aug 2016 13:20:56 +0000 (14:20 +0100)]
JAL-2119 updates to invalid / obsolete help links
gmungoc [Mon, 8 Aug 2016 13:16:44 +0000 (14:16 +0100)]
JAL-2168 document '-nonews' parameter
gmungoc [Fri, 5 Aug 2016 13:53:23 +0000 (14:53 +0100)]
JAL-2168 skip news feed if parameter "-nonews" is supplied
gmungoc [Fri, 5 Aug 2016 13:11:43 +0000 (14:11 +0100)]
JAL-1448 always use UK locale for formatted date properties
gmungoc [Fri, 5 Aug 2016 10:22:14 +0000 (11:22 +0100)]
JAL-2164 add transferred annotation to sequence
gmungoc [Thu, 4 Aug 2016 14:35:18 +0000 (15:35 +0100)]
JAL-2164 changed to be Java 1.7 compliant
gmungoc [Thu, 4 Aug 2016 09:55:50 +0000 (10:55 +0100)]
JAL-2008 handle fast mouse drag of feature ordering correctly
gmungoc [Thu, 4 Aug 2016 09:11:06 +0000 (10:11 +0100)]
JAL-2015 convert Color from colour picker to FeatureColour
Jim Procter [Tue, 2 Aug 2016 15:22:43 +0000 (16:22 +0100)]
JAL-2046 additional logic to suppress spurious implementation-error warnings
Jim Procter [Tue, 2 Aug 2016 14:56:19 +0000 (15:56 +0100)]
Merge branch 'efficiency/JAL-2034_JAL-1421' into develop
Jim Procter [Tue, 2 Aug 2016 14:46:58 +0000 (15:46 +0100)]
JAL-2034 show greyed out image during overview update
Jim Procter [Tue, 2 Aug 2016 13:16:06 +0000 (14:16 +0100)]
Merge branch 'develop' into efficiency/JAL-2034_JAL-1421
Jim Procter [Tue, 2 Aug 2016 13:15:35 +0000 (14:15 +0100)]
JAL-2068 reinstated false return value for notifyWorking
(prevents multiple worker threads starting when new view created)
* documentation for AlignCalcManagerI
Jim Procter [Tue, 2 Aug 2016 10:05:53 +0000 (11:05 +0100)]
Merge branch 'develop' into efficiency/JAL-2034_JAL-1421
Jim Procter [Mon, 1 Aug 2016 20:13:52 +0000 (21:13 +0100)]
JAL-2164 TODO: make test pass for JMOL_PARSER
Jim Procter [Mon, 1 Aug 2016 20:13:22 +0000 (21:13 +0100)]
JAL-2164 JAL-1919 JAL-1270 use structure import settings to properly configure for test
Jim Procter [Mon, 1 Aug 2016 19:16:42 +0000 (20:16 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
tcofoegbu [Mon, 1 Aug 2016 16:21:08 +0000 (17:21 +0100)]
JAL-2164 bugfix to convert insCodes of '\000' to ' ' in JmolParser, this fixes the xml marshalling bug
Jim Procter [Mon, 1 Aug 2016 14:40:24 +0000 (15:40 +0100)]
Merge branch 'bug/JAL-2154projectMappings' into develop
Jim Procter [Mon, 1 Aug 2016 13:00:19 +0000 (14:00 +0100)]
Merge branch 'task/JAL-2164_mcviewforoldjalviewprojects' into develop
Jim Procter [Mon, 1 Aug 2016 12:46:09 +0000 (13:46 +0100)]
JAL-2164 prevent jalview news from opening
Jim Procter [Mon, 1 Aug 2016 12:45:05 +0000 (13:45 +0100)]
JAL-2164 clear the desktop before testStoreAndRecoverExpandedViews
Jim Procter [Mon, 1 Aug 2016 10:54:34 +0000 (11:54 +0100)]
Merge branch 'task/JAL-2164_mcviewforoldjalviewprojects' into develop
Jim Procter [Mon, 1 Aug 2016 07:49:54 +0000 (08:49 +0100)]
JAL-1772 make sure we actually return reference to AlignFrame that is visible after views are gathered
git://source.jalview.org / jalview.git / log