unknown [Sat, 9 May 2015 11:25:37 +0000 (12:25 +0100)]
Merge branch 'develop' into Release_2_9_Branch
unknown [Sat, 9 May 2015 11:25:15 +0000 (12:25 +0100)]
JAL-1601 bugfix on previous commit
unknown [Sat, 9 May 2015 08:55:38 +0000 (09:55 +0100)]
JAL-1601 patch burial display for prediction loaded to full alignment
gmungoc [Thu, 7 May 2015 15:58:15 +0000 (16:58 +0100)]
JAL-1575 bare bones RestHandler added
Jim Procter [Thu, 7 May 2015 14:17:00 +0000 (15:17 +0100)]
JAL-1731 fix JPred4 citation in legacy client code
Jim Procter [Thu, 7 May 2015 13:55:52 +0000 (14:55 +0100)]
JAL-1551 formatting
Jim Procter [Thu, 7 May 2015 13:55:11 +0000 (14:55 +0100)]
JAL-1601 migrated the JABAWS 2.1 jpred burial representation to the core jpred concise parser
gmungoc [Wed, 6 May 2015 14:58:26 +0000 (15:58 +0100)]
Merge branch 'Release_2_9_Branch' of https://source.jalview.org/git/jalview.git into Release_2_9_Branch
gmungoc [Wed, 6 May 2015 14:31:59 +0000 (15:31 +0100)]
JAL-1725 broadcast empty selection (to clear selection)
gmungoc [Wed, 6 May 2015 14:30:00 +0000 (15:30 +0100)]
JAL-1725 limit thread pool size; prefix /jalview to paths
gmungoc [Wed, 6 May 2015 11:50:25 +0000 (12:50 +0100)]
JAL-1725 parse atomSpec with submodel; debug output removed
gmungoc [Wed, 6 May 2015 09:57:34 +0000 (10:57 +0100)]
JAL-1725 fix for redirect of POST to GET, debug output removed
gmungoc [Tue, 5 May 2015 15:33:06 +0000 (16:33 +0100)]
JAL-1725 jetty libraries added to classpath
gmungoc [Tue, 5 May 2015 15:27:16 +0000 (16:27 +0100)]
JAL-1725 first version of Jetty server / chimera selection listener
tcofoegbu [Fri, 1 May 2015 16:32:41 +0000 (17:32 +0100)]
Merge branch 'bug/JAL-1700_PDB-rest-api-error-handling' into Release_2_9_Branch
tcofoegbu [Fri, 1 May 2015 16:28:02 +0000 (17:28 +0100)]
JAL-1700 Improved the error handling mechanism for the PDB Rest client
tcofoegbu [Fri, 1 May 2015 11:04:18 +0000 (12:04 +0100)]
Merge branch 'bug/JAL-1726_External-integration-test_PDB' into Release_2_9_Branch
tcofoegbu [Fri, 1 May 2015 11:02:17 +0000 (12:02 +0100)]
JAL-1726 Added external integration test for PDB Rest API
gmungoc [Fri, 1 May 2015 08:12:18 +0000 (09:12 +0100)]
JAL-1684 hook added to test for fields ignored in copy constructor
gmungoc [Fri, 1 May 2015 08:11:29 +0000 (09:11 +0100)]
JAL-1690 refining 'copy format from' as applied to splitframe panels
gmungoc [Fri, 1 May 2015 08:04:56 +0000 (09:04 +0100)]
JAL-1690 unused fields removed
Mungo Carstairs [Thu, 30 Apr 2015 20:12:42 +0000 (21:12 +0100)]
JAL-845 reduced height to allow for Desktop decorators on Windows
tcofoegbu [Thu, 30 Apr 2015 11:47:58 +0000 (12:47 +0100)]
Merge branch 'bug/JAL-1717_make-pbd-id-case_insensitive' into Release_2_9_Branch
tcofoegbu [Thu, 30 Apr 2015 11:47:08 +0000 (12:47 +0100)]
JAL-1717 updated the PDBEntry model and updated the method use for its equality test. Furthermore, a couple of other methods where modified to ensure PDB entries are always unique
gmungoc [Wed, 29 Apr 2015 15:00:27 +0000 (16:00 +0100)]
JAL-1690 preserve scaling in New View, synch id width changes
gmungoc [Wed, 29 Apr 2015 08:13:08 +0000 (09:13 +0100)]
JAL-1686 ViewStyle.hashCode implemented
gmungoc [Tue, 28 Apr 2015 15:55:30 +0000 (16:55 +0100)]
Merge branch 'Release_2_9_Branch' of https://source.jalview.org/git/jalview.git into Release_2_9_Branch
gmungoc [Tue, 28 Apr 2015 15:55:17 +0000 (16:55 +0100)]
JAL-1684 removed reflection from ViewStyle (to Junit), and removed
duplications with AlignViewportI
tcofoegbu [Tue, 28 Apr 2015 10:50:01 +0000 (11:50 +0100)]
Merge branch 'features/JAL-1714_specify-mulitple-id_PDB-query' into Release_2_9_Branch
tcofoegbu [Tue, 28 Apr 2015 10:49:30 +0000 (11:49 +0100)]
JAL-1711 and JAL-1714 documentation updated
tcofoegbu [Tue, 28 Apr 2015 10:46:38 +0000 (11:46 +0100)]
Merge branch 'features/JAL-1714_specify-mulitple-id_PDB-query' into Release_2_9_Branch
tcofoegbu [Tue, 28 Apr 2015 10:45:42 +0000 (11:45 +0100)]
JAL-1711 and JAL-1714 documentation updated
tcofoegbu [Mon, 27 Apr 2015 16:01:41 +0000 (17:01 +0100)]
Merge branch 'bug/JAL-1715_PDB-Search-selection-validation' into Release_2_9_Branch
tcofoegbu [Mon, 27 Apr 2015 16:00:33 +0000 (17:00 +0100)]
JAL-1715 implemented selection validation for the new PDB Query interface
tcofoegbu [Mon, 27 Apr 2015 14:56:15 +0000 (15:56 +0100)]
Merge branch 'features/JAL-1714_specify-mulitple-id_PDB-query' into Release_2_9_Branch
tcofoegbu [Mon, 27 Apr 2015 14:24:09 +0000 (15:24 +0100)]
JAL-1714 improved the new PDB Sequence fetcher by enabling it query multiple PDB entries in one operation
Jim Procter [Mon, 27 Apr 2015 10:28:04 +0000 (11:28 +0100)]
JAL-1645 Release_2_9 branch build tag
gmungoc [Mon, 27 Apr 2015 10:04:05 +0000 (11:04 +0100)]
Merge branch 'Release_2_8_3_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_3_Branch
gmungoc [Mon, 27 Apr 2015 10:03:48 +0000 (11:03 +0100)]
JAL-1691 more stable linked scrolling across split frame (+javadoc)
tcofoegbu [Fri, 24 Apr 2015 15:06:38 +0000 (16:06 +0100)]
Merge branch 'features/JAL-1711_PDB-specify-chain' into Release_2_8_3_Branch
tcofoegbu [Fri, 24 Apr 2015 15:06:05 +0000 (16:06 +0100)]
Merge branch 'Release_2_8_3_Branch' of https://source.jalview.org/git/jalview into Release_2_8_3_Branch
tcofoegbu [Fri, 24 Apr 2015 15:05:24 +0000 (16:05 +0100)]
JAL-1710, JAL-1711 Bug fix for exception thrown when a request containing a colon (:) is sent to the PDB Rest API and Implementation to allow selection of a specific PDB chain
gmungoc [Fri, 24 Apr 2015 14:42:10 +0000 (15:42 +0100)]
JAL-1691 prevent propagation of scrolling on mouseover follow highlight
tcofoegbu [Fri, 24 Apr 2015 13:53:01 +0000 (14:53 +0100)]
Merge branch 'bug/JAL-1707_retrieve-pdb-structure-for-rna' into Release_2_8_3_Branch
tcofoegbu [Fri, 24 Apr 2015 13:51:32 +0000 (14:51 +0100)]
JAL-1707 bug fix - also search using sequence name
gmungoc [Thu, 23 Apr 2015 10:44:50 +0000 (11:44 +0100)]
JAL-1702 corrected check for 'no colours selected'
gmungoc [Thu, 23 Apr 2015 09:47:30 +0000 (10:47 +0100)]
JAL-1706 distinguish between 'font too small' and 'font does not have
letters'
gmungoc [Thu, 23 Apr 2015 08:24:02 +0000 (09:24 +0100)]
JAL-1681 create mappings before AlignFrame to ensure cDNA consensus
added
gmungoc [Thu, 23 Apr 2015 08:23:17 +0000 (09:23 +0100)]
JAL-845 only 'follow' sort command in coding complement alignment
gmungoc [Thu, 23 Apr 2015 08:21:53 +0000 (09:21 +0100)]
JAL-845 set split frame divider safely for eXpand Views
gmungoc [Thu, 23 Apr 2015 08:10:15 +0000 (09:10 +0100)]
Merge branch 'Release_2_8_3_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_3_Branch
gmungoc [Thu, 23 Apr 2015 08:09:57 +0000 (09:09 +0100)]
JAL-1706 fixed to correctly restore the last dialog selection after
warning
tcofoegbu [Wed, 22 Apr 2015 15:56:20 +0000 (16:56 +0100)]
JAL-1667_1668 updated help doc
tcofoegbu [Wed, 22 Apr 2015 15:47:55 +0000 (16:47 +0100)]
Merge branch 'features/JAL-1667_1668-documentation' into Release_2_8_3_Branch
tcofoegbu [Wed, 22 Apr 2015 15:46:46 +0000 (16:46 +0100)]
JAL-1667_1668 added help documentation for PDB Sequence fetcher
gmungoc [Wed, 22 Apr 2015 14:21:22 +0000 (15:21 +0100)]
JAL-845 fix SplitFrame sizing on eXpand Views
gmungoc [Wed, 22 Apr 2015 13:28:44 +0000 (14:28 +0100)]
'Test' added to help identify "too small" font families/sizes
gmungoc [Wed, 22 Apr 2015 12:21:59 +0000 (13:21 +0100)]
JAL-1690 fix NPE on Cancel when not in split frame
tcofoegbu [Tue, 21 Apr 2015 15:42:28 +0000 (16:42 +0100)]
JAL-1667_1668 Updated documentation
gmungoc [Tue, 21 Apr 2015 12:54:13 +0000 (13:54 +0100)]
JAL-1693 mappings added back to the original alignment
gmungoc [Tue, 21 Apr 2015 11:45:53 +0000 (12:45 +0100)]
JAL-1702 wording improved; also some duplicate entries removed
tcofoegbu [Tue, 21 Apr 2015 10:28:48 +0000 (11:28 +0100)]
JAL-1667_1668 Documentation - Added a separate help file for the Structure Chooser interface
gmungoc [Mon, 20 Apr 2015 14:41:58 +0000 (15:41 +0100)]
JAL-1690 shorter text to fit in FontChooser dialog
gmungoc [Mon, 20 Apr 2015 14:41:27 +0000 (15:41 +0100)]
JAL-1701 first draft of help page for Split View (not linked in)
tcofoegbu [Fri, 17 Apr 2015 15:35:03 +0000 (16:35 +0100)]
Merge branch 'bug/JAL-1697_browse-local-structures' into Release_2_8_3_Branch
tcofoegbu [Fri, 17 Apr 2015 15:33:52 +0000 (16:33 +0100)]
JAL-1697 added ablity to select/view cached structures in the new structure chooser interface
tcofoegbu [Fri, 17 Apr 2015 09:39:13 +0000 (10:39 +0100)]
Merge branch 'bug/JAL-1698_Append-Structures' into Release_2_8_3_Branch
tcofoegbu [Fri, 17 Apr 2015 09:34:35 +0000 (10:34 +0100)]
JAL-1698 bug fix to enable addition of a single structure to an already launched structure viewer
tcofoegbu [Fri, 17 Apr 2015 09:19:52 +0000 (10:19 +0100)]
JAL-1668 updated documentation
gmungoc [Tue, 14 Apr 2015 19:56:29 +0000 (20:56 +0100)]
JAL-1693 generate multiple exon sequences for 1-many dna-protein
mappings
tcofoegbu [Tue, 14 Apr 2015 13:28:04 +0000 (14:28 +0100)]
Merge branch 'bug/Jal-1696_disable-pdb_id-field-settings' into Release_2_8_3_Branch
tcofoegbu [Tue, 14 Apr 2015 13:26:29 +0000 (14:26 +0100)]
JAL-1696 disabled editing of PDB Id field from settings
tcofoegbu [Tue, 14 Apr 2015 08:54:31 +0000 (09:54 +0100)]
Merge branch 'Release_2_8_3_Branch' of https://source.jalview.org/git/jalview into Release_2_8_3_Branch
gmungoc [Mon, 13 Apr 2015 15:57:16 +0000 (16:57 +0100)]
JAL-1695 enableSplitFrame=true for applet example
gmungoc [Mon, 13 Apr 2015 15:36:31 +0000 (16:36 +0100)]
JAL-1690 adjusted wording
gmungoc [Mon, 13 Apr 2015 15:22:35 +0000 (16:22 +0100)]
JAL-1693 make exon alignment for get-xref splitframe (with CDS xref)
gmungoc [Mon, 13 Apr 2015 15:03:23 +0000 (16:03 +0100)]
JAL-1681 work around ConcurrentModificationException on startup
gmungoc [Mon, 13 Apr 2015 14:59:59 +0000 (15:59 +0100)]
JAL-1690 show 'scale protein' in protein _and_ dna menus; default true
gmungoc [Mon, 13 Apr 2015 14:58:02 +0000 (15:58 +0100)]
JAL-1695 new property ENABLE_SPLIT_FRAME
gmungoc [Mon, 13 Apr 2015 14:56:31 +0000 (15:56 +0100)]
JAL-1695 parameter controls whether SplitFrame is enabled
gmungoc [Wed, 8 Apr 2015 14:24:29 +0000 (15:24 +0100)]
JAL-1684 adjusting parameters for split frame applet example
gmungoc [Wed, 8 Apr 2015 14:23:17 +0000 (15:23 +0100)]
JAL-1690 scaleProteinAsCdna new applet parameter documented
gmungoc [Wed, 8 Apr 2015 14:22:08 +0000 (15:22 +0100)]
JAL-1270 protection against NullPointer when run as JUnit
gmungoc [Wed, 8 Apr 2015 14:21:23 +0000 (15:21 +0100)]
JAL-1691 applet SplitFrame scrolling; pull up of 5 fields to
AlignmentViewport
gmungoc [Wed, 8 Apr 2015 14:17:55 +0000 (15:17 +0100)]
JAL-1270 separated standalone tests out of Jws2ParamView, interactive
test marked @Ignore
gmungoc [Tue, 7 Apr 2015 08:18:49 +0000 (09:18 +0100)]
JAL-1270 test added
gmungoc [Tue, 7 Apr 2015 08:18:26 +0000 (09:18 +0100)]
JAL-1691 linked scrollling in split frame (Desktop)
gmungoc [Tue, 7 Apr 2015 08:17:00 +0000 (09:17 +0100)]
JAL-1691 defensive check for null
gmungoc [Thu, 2 Apr 2015 14:37:06 +0000 (15:37 +0100)]
JAL-1690 'scale protein as cDNA' options in Preferences, FontChooser
gmungoc [Wed, 1 Apr 2015 13:59:27 +0000 (14:59 +0100)]
JAL-845 fixed start/end range of a mapped SequenceGroup
gmungoc [Wed, 1 Apr 2015 13:57:24 +0000 (14:57 +0100)]
JAL-1264 reinstate Show annotations menu item
gmungoc [Mon, 30 Mar 2015 14:18:25 +0000 (15:18 +0100)]
JAL-1264 remove broken applet build dependencies
gmungoc [Mon, 30 Mar 2015 09:57:40 +0000 (10:57 +0100)]
JAL-1270 fall back on compbio if no localhost:8080/jabaws
gmungoc [Mon, 30 Mar 2015 09:05:22 +0000 (10:05 +0100)]
JAL-1596 refactoring to allow unit tests to start and shut down Chimera
gmungoc [Mon, 30 Mar 2015 09:01:02 +0000 (10:01 +0100)]
JAL-1270 Cache.logger initialisation added
tcofoegbu [Fri, 27 Mar 2015 13:23:42 +0000 (13:23 +0000)]
Merge branch 'merge/JAL-1667_PDBe_Search_API' into Release_2_8_3_Branch
tcofoegbu [Fri, 27 Mar 2015 13:22:09 +0000 (13:22 +0000)]
JAL-1667 updated the collection type for searchSummaryFields and structureSummaryFields preferences
tcofoegbu [Fri, 27 Mar 2015 11:43:50 +0000 (11:43 +0000)]
Merge branch 'merge/JAL-1667_PDBe_Search_API' into Release_2_8_3_Branch
tcofoegbu [Fri, 27 Mar 2015 11:37:34 +0000 (11:37 +0000)]
merge commit
tcofoegbu [Thu, 26 Mar 2015 15:15:39 +0000 (15:15 +0000)]
JAL-1667 updated parseJsonExceptionString method in PDBRestClient.java and its equivalent test case in PDBRestClientTest.java
git://source.jalview.org / jalview.git / log