Jim Procter [Sun, 25 Sep 2016 09:47:00 +0000 (10:47 +0100)]
JAL-2228 base interface for FeatureCounters and factory constructors for FeatureSetCounterI
Jim Procter [Sun, 25 Sep 2016 09:45:56 +0000 (10:45 +0100)]
JAL-2228 interface and worker to allow multiple feature types to be counted simultaneously
Jim Procter [Sat, 24 Sep 2016 12:25:35 +0000 (13:25 +0100)]
Merge branch 'releases/Release_2_10_Branch' into develop
Jim Procter [Sat, 24 Sep 2016 12:23:31 +0000 (13:23 +0100)]
JAL-1919 whats new link
tcofoegbu [Fri, 23 Sep 2016 15:22:13 +0000 (16:22 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 23 Sep 2016 15:22:06 +0000 (16:22 +0100)]
JAL-2164 JAL-1919 fixed failed revert commit
Jim Procter [Fri, 23 Sep 2016 15:02:49 +0000 (16:02 +0100)]
JAL-1957 JAL-1479 tweak SIFTS mappings documentation, add to what’s new section
Jim Procter [Fri, 23 Sep 2016 14:58:55 +0000 (15:58 +0100)]
JAL-1957 JAL-1479 mention SIFTS mappings in PDB Structure viewing instructions
Jim Procter [Fri, 23 Sep 2016 14:57:50 +0000 (15:57 +0100)]
JAL-1957 release notes
Jim Procter [Fri, 23 Sep 2016 14:13:40 +0000 (15:13 +0100)]
JAL-1962 release notes
Jim Procter [Fri, 23 Sep 2016 14:13:24 +0000 (15:13 +0100)]
JAL-2214 fix docs (consistent and correct base pair terminology) and link to ‘sequence logo’ docs for strucConsensus logo
Jim Procter [Fri, 23 Sep 2016 10:29:08 +0000 (11:29 +0100)]
Merge branch 'develop' into releases/Release_2_10_Branch
Jim Procter [Fri, 23 Sep 2016 10:19:40 +0000 (11:19 +0100)]
JAL-2189 JAL-1479 JAL-1491 JAL-1827 release notes
gmungoc [Fri, 23 Sep 2016 09:40:24 +0000 (10:40 +0100)]
JAL-2214 Javadoc
Jim Procter [Thu, 22 Sep 2016 15:28:33 +0000 (16:28 +0100)]
JAL-2275 release notes
Jim Procter [Thu, 22 Sep 2016 15:15:56 +0000 (16:15 +0100)]
JAL-2151 release notes
gmungoc [Thu, 22 Sep 2016 15:00:48 +0000 (16:00 +0100)]
JAL-1421 use declared type of ResidueProperties.propHash
Jim Procter [Thu, 22 Sep 2016 14:51:19 +0000 (15:51 +0100)]
JAL-2168 -news release notes
gmungoc [Thu, 22 Sep 2016 14:49:27 +0000 (15:49 +0100)]
JAL-1421 typed ResidueProperties.propHash; JAL-2176 removed propHash
from Conservation constructor, ResidueProperties.codonHash
Jim Procter [Thu, 22 Sep 2016 14:47:17 +0000 (15:47 +0100)]
JAL-1557 release notes
Jim Procter [Thu, 22 Sep 2016 14:19:08 +0000 (15:19 +0100)]
JAL-2189 bumped date to 27th September \o/
gmungoc [Thu, 22 Sep 2016 14:15:01 +0000 (15:15 +0100)]
JAL-2216 null currentAlignFrame on close all windows; remove action
listener from Window menu item when window closed
Jim Procter [Thu, 22 Sep 2016 14:04:06 +0000 (15:04 +0100)]
JAL-2189 JAL-1812 JAL-2068 new groovy docs (new files add to commit c8c1f2a)
Jim Procter [Thu, 22 Sep 2016 14:01:22 +0000 (15:01 +0100)]
JAL-2189 JAL-2092 popup show/hide cols with feature docs
gmungoc [Thu, 22 Sep 2016 13:50:53 +0000 (14:50 +0100)]
JAL-2216 finalize call super.finalize()
gmungoc [Thu, 22 Sep 2016 13:49:53 +0000 (14:49 +0100)]
JAL-2216 finalise corrected to finalize
gmungoc [Thu, 22 Sep 2016 13:47:11 +0000 (14:47 +0100)]
JAL-2216 explicitly null AnnotationPanel and AnnotationRenderer fields
when closing AlignmentPanel
Jim Procter [Thu, 22 Sep 2016 13:36:40 +0000 (14:36 +0100)]
JAL-2189 JAL-2077 note about CTRL-Click to right click on OSX
Jim Procter [Thu, 22 Sep 2016 13:36:12 +0000 (14:36 +0100)]
JAL-2189 tidy up docs
gmungoc [Thu, 22 Sep 2016 13:33:15 +0000 (14:33 +0100)]
JAL-2216 finalize() refactored so not called programmatically
Jim Procter [Thu, 22 Sep 2016 13:20:38 +0000 (14:20 +0100)]
JAL-1812 JAL-1868 release notes
gmungoc [Thu, 22 Sep 2016 13:19:44 +0000 (14:19 +0100)]
JAL-2216 new dispose() method to null references
Jim Procter [Thu, 22 Sep 2016 13:16:53 +0000 (14:16 +0100)]
JAL-2189 JAL-1812 JAL-2068 new groovy doc section and example featureCounter script
gmungoc [Thu, 22 Sep 2016 13:16:13 +0000 (14:16 +0100)]
JAL-2216 finalize call super.finalize()
Jim Procter [Wed, 21 Sep 2016 15:50:37 +0000 (16:50 +0100)]
JAL-2189 JAL-2171 JAL-2214 JAL-1841 JAL-2215 release notes
Jim Procter [Wed, 21 Sep 2016 15:49:43 +0000 (16:49 +0100)]
JAL-1841 JAL-2214 updated RNA Structure Consensus documentation
Jim Procter [Wed, 21 Sep 2016 15:43:32 +0000 (16:43 +0100)]
JAL-2214 JAL-1841 compute canonical, canonicalAndWobble visually distinguish dominant proportions as (,[,{ in histogram label
Jim Procter [Wed, 21 Sep 2016 15:42:10 +0000 (16:42 +0100)]
JAL-1841 JAL-2215 add the ‘ignore gaps’ structure consensus fraction
Jim Procter [Wed, 21 Sep 2016 15:40:07 +0000 (16:40 +0100)]
JAL-2214 test for strict Watson-Crick pairing
Jim Procter [Wed, 21 Sep 2016 15:39:31 +0000 (16:39 +0100)]
JAL-2215 fix - trigger alignment update when ‘ignore gaps’ setting changed
Jim Procter [Wed, 21 Sep 2016 11:29:49 +0000 (12:29 +0100)]
JAL-2189 reworked annotation docs
JAL-2171 autocomplete RNA ss symbol for interactive annotation
Jim Procter [Wed, 21 Sep 2016 10:13:01 +0000 (11:13 +0100)]
Merge branch 'develop' into releases/Release_2_10_Branch
gmungoc [Tue, 20 Sep 2016 09:46:22 +0000 (10:46 +0100)]
JAL-1306 calculate Quality also when Conservation not enabled
Jim Procter [Mon, 19 Sep 2016 22:02:59 +0000 (23:02 +0100)]
JAL-1577 release notes
Jim Procter [Mon, 19 Sep 2016 21:52:16 +0000 (22:52 +0100)]
JAL-2027 releasenotes
Jim Procter [Mon, 19 Sep 2016 18:11:14 +0000 (19:11 +0100)]
JAL-1563 release notes
Jim Procter [Mon, 19 Sep 2016 17:57:05 +0000 (18:57 +0100)]
JAL-2189 JAL-2002 revised the structure chooser documentation
Jim Procter [Mon, 19 Sep 2016 17:16:26 +0000 (18:16 +0100)]
JAL-2189 Release notes for JAL-2079 JAL-2084 JAL-2054 JAL-2099
Jim Procter [Mon, 19 Sep 2016 16:43:13 +0000 (17:43 +0100)]
JAL-2189 JAL-1369 JAL-192 expand referenceseq documentation
Jim Procter [Mon, 19 Sep 2016 16:40:56 +0000 (17:40 +0100)]
JAL-2189 what’s new - ensembl, new structure stuff, reference seqs
Jim Procter [Mon, 19 Sep 2016 13:17:22 +0000 (14:17 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Mon, 19 Sep 2016 13:16:59 +0000 (14:16 +0100)]
JAL-2175 JAL-2170 fix sense for assertEquals
gmungoc [Mon, 19 Sep 2016 13:10:36 +0000 (14:10 +0100)]
JAL-2118 reorder annotations after add/delete/hide/change name
Jim Procter [Mon, 19 Sep 2016 11:48:17 +0000 (12:48 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
gmungoc [Mon, 19 Sep 2016 10:45:09 +0000 (11:45 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 19 Sep 2016 10:30:37 +0000 (11:30 +0100)]
JAL-2172 test and code updates for readonly selection list
tcofoegbu [Mon, 19 Sep 2016 10:30:00 +0000 (11:30 +0100)]
merge
gmungoc [Mon, 19 Sep 2016 10:29:30 +0000 (11:29 +0100)]
JAL-1353 small tidy of test
gmungoc [Mon, 19 Sep 2016 10:29:08 +0000 (11:29 +0100)]
JAL-1270 use test properties file
Jim Procter [Sun, 18 Sep 2016 11:43:51 +0000 (12:43 +0100)]
JAL-1795 JAL-2206 prevent NPE when no data returned from Ensembl fetch
Jim Procter [Fri, 16 Sep 2016 19:23:07 +0000 (20:23 +0100)]
JAL-2189 clear out old what’s new and add ensembl and uniprot
Jim Procter [Fri, 16 Sep 2016 19:22:49 +0000 (20:22 +0100)]
JAL-2189 JAL-1705 JAL-1795 ensembl fetching docs
Jim Procter [Fri, 16 Sep 2016 16:05:04 +0000 (17:05 +0100)]
JAL-2089 tidied docs for sequence fetcher
Jim Procter [Fri, 16 Sep 2016 15:32:30 +0000 (16:32 +0100)]
JAL-2089 release notes
Jim Procter [Fri, 16 Sep 2016 15:32:02 +0000 (16:32 +0100)]
JAL-2089 zero day for 2.10 - 20th Sep 2016
Jim Procter [Fri, 16 Sep 2016 12:47:32 +0000 (13:47 +0100)]
Merge branch 'patch/JAL-2164_updatesRESNUMtests' into develop
gmungoc [Fri, 16 Sep 2016 11:19:17 +0000 (12:19 +0100)]
JAL-2157 JAL-1803 refactored Sequence.updatePDBIds, parse DBRefs with
chain appended
Jim Procter [Fri, 16 Sep 2016 11:12:24 +0000 (12:12 +0100)]
JAL-2164 update asserts for padded residue numbers in RESNUM tests
gmungoc [Fri, 16 Sep 2016 10:53:32 +0000 (11:53 +0100)]
JAL-2183 don't open two free text panels; give input field focus
gmungoc [Fri, 16 Sep 2016 10:04:03 +0000 (11:04 +0100)]
JAL-2183 avoid duplicate closeDialog()
gmungoc [Fri, 16 Sep 2016 09:31:11 +0000 (10:31 +0100)]
JAL-2164 removed unused parameters from JmolParser constructor
gmungoc [Fri, 16 Sep 2016 08:45:52 +0000 (09:45 +0100)]
JAL-1270 JAL-1919 ensure Temp Factor is OFF for test to pass
Jim Procter [Wed, 14 Sep 2016 18:58:04 +0000 (19:58 +0100)]
JAL-2164 create RESNUM features with padding the same as for pre 2.10 features
Jim Procter [Wed, 14 Sep 2016 14:48:22 +0000 (15:48 +0100)]
JAL-2168 simpler help text re -nonews
tcofoegbu [Tue, 13 Sep 2016 16:18:14 +0000 (17:18 +0100)]
JAL-2164 JAL-1919 disabled PDB file parser configuration option
Jim Procter [Tue, 13 Sep 2016 16:13:13 +0000 (17:13 +0100)]
JAL-2119 keeping gmungoc happy by not running linkcheck on every eclipse build of Jalview
tcofoegbu [Tue, 13 Sep 2016 16:07:44 +0000 (17:07 +0100)]
Revert "JAL-2164 JAL-1919 disabled and removed PDB file parser configuration option, JmolParser is now the sole parser for parsing PDB and mmCIF format files."
This reverts commit
13bc8a3fb89b083922d9fa9dad5050e6aaa1f661.
gmungoc [Tue, 13 Sep 2016 14:52:11 +0000 (15:52 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 13 Sep 2016 14:51:58 +0000 (15:51 +0100)]
JAL-1803 tests added for PDBEntry.Type
tcofoegbu [Tue, 13 Sep 2016 14:25:20 +0000 (15:25 +0100)]
JAL-2164 JAL-1919 disabled and removed PDB file parser configuration option, JmolParser is now the sole parser for parsing PDB and mmCIF format files.
gmungoc [Tue, 13 Sep 2016 14:03:51 +0000 (15:03 +0100)]
JAL-1803 extracted class ChainId to jalview.util.CaseInsensitiveString,
tightened equals(), hashcode(), tests
tcofoegbu [Tue, 13 Sep 2016 09:51:36 +0000 (10:51 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 13 Sep 2016 09:51:27 +0000 (10:51 +0100)]
JAL-2195 bug fix to enable restoring jmol session save on Windows on OSX
gmungoc [Tue, 13 Sep 2016 08:02:10 +0000 (09:02 +0100)]
JAL-2119 use File.separator not "/"
Jim Procter [Mon, 12 Sep 2016 15:50:55 +0000 (16:50 +0100)]
Merge branch 'patch/JAL-2068_JAL-2169_multiviewannotworker' into develop
gmungoc [Mon, 12 Sep 2016 08:59:16 +0000 (09:59 +0100)]
JAL-2119 case-sensitive href filename checking
gmungoc [Mon, 12 Sep 2016 08:12:09 +0000 (09:12 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
tcofoegbu [Fri, 9 Sep 2016 10:49:35 +0000 (11:49 +0100)]
merge
Jim Procter [Fri, 9 Sep 2016 09:29:02 +0000 (10:29 +0100)]
JAL-2119 links must match case on Linux systems
Jim Procter [Thu, 8 Sep 2016 17:15:45 +0000 (18:15 +0100)]
JAL-2119 pass/resolve real help dir in link checker
tcofoegbu [Thu, 8 Sep 2016 16:32:12 +0000 (17:32 +0100)]
JAL-2164 renamed 'DEFAULT_STRUCTURE_FORMAT' property to 'PDB_DOWNLOAD_FORMAT'
Jim Procter [Thu, 8 Sep 2016 14:49:31 +0000 (15:49 +0100)]
Merge branch 'feature/JAL-2119_helplinkchecker' into develop
Jim Procter [Thu, 8 Sep 2016 13:52:16 +0000 (14:52 +0100)]
JAL-1551 formatting
Jim Procter [Thu, 8 Sep 2016 13:51:19 +0000 (14:51 +0100)]
JAL-2119 build fails if invalid links are present
Jim Procter [Thu, 8 Sep 2016 13:51:02 +0000 (14:51 +0100)]
JAL-2119 non-zero exit if any invalid links
Jim Procter [Thu, 8 Sep 2016 13:50:32 +0000 (14:50 +0100)]
JAL-2119 count and report total invalid anchor links
Jim Procter [Thu, 8 Sep 2016 13:35:58 +0000 (14:35 +0100)]
JAL-2089 JAL-2119 help link fixups
Jim Procter [Thu, 8 Sep 2016 13:30:06 +0000 (14:30 +0100)]
JAL-2119 linkcheck target. runs before build indices
Jim Procter [Wed, 7 Sep 2016 14:38:59 +0000 (15:38 +0100)]
Merge branch 'bug/JAL-1803_JAL-2157' into develop
Jim Procter [Wed, 7 Sep 2016 14:38:36 +0000 (15:38 +0100)]
JAL-1670 groundhog day: fix FeaturesFileTest by redacting last commit:
53dd28432308dda9cc73d6887bcd43fcfe17907d
git://source.jalview.org / jalview.git / log