James Procter [Fri, 5 Jun 2015 10:14:48 +0000 (11:14 +0100)]
JAL-1672 fix typo
James Procter [Fri, 5 Jun 2015 10:09:34 +0000 (11:09 +0100)]
JAL-1735 test to ensure uniref90_repid type queries are resolved by uniprot sequence fetcher
James Procter [Fri, 5 Jun 2015 10:08:08 +0000 (11:08 +0100)]
JAL-1551 formatting
James Procter [Fri, 5 Jun 2015 10:04:25 +0000 (11:04 +0100)]
JAL-1601 trial constructor and test for JPred RSBS description
James Procter [Fri, 5 Jun 2015 10:04:04 +0000 (11:04 +0100)]
JAL-1601 organise imports
James Procter [Fri, 5 Jun 2015 10:03:29 +0000 (11:03 +0100)]
JAL-715 JAL-1601 promote parsing errors in Job result data to ERROR log output
James Procter [Fri, 5 Jun 2015 10:02:49 +0000 (11:02 +0100)]
JAL-1601 javadoc
James Procter [Fri, 5 Jun 2015 10:02:25 +0000 (11:02 +0100)]
JAL-1601 JAL-715 allow format to be specified for uploading alignments
James Procter [Fri, 5 Jun 2015 10:00:23 +0000 (11:00 +0100)]
JAL-1601 refactor RSBS description test
James Procter [Fri, 5 Jun 2015 09:58:56 +0000 (10:58 +0100)]
JAl-1601 JAL-715 RestServiceDescription constructor allows specification of a series of URLs for retrieving results
Jim Procter [Wed, 20 May 2015 10:32:27 +0000 (11:32 +0100)]
JAL-1601 todos for this
tcofoegbu [Wed, 20 May 2015 08:53:07 +0000 (09:53 +0100)]
Merge branch 'features/JAL-1541_BioJsMSA' into develop
tcofoegbu [Wed, 20 May 2015 08:52:34 +0000 (09:52 +0100)]
JAL-1541 minor code clean up, and added test for BioJsHTMLOutput
tcofoegbu [Tue, 19 May 2015 10:11:22 +0000 (11:11 +0100)]
Merge branch 'features/JAL-1541_BioJsMSA' into develop
tcofoegbu [Tue, 19 May 2015 10:07:59 +0000 (11:07 +0100)]
JAL-1641 Further refactoring of JSON export option, introduction of Viewport to the File parsing pipe, added ability to retrieve FeatureRenderer from the Viewport api
tcofoegbu [Tue, 19 May 2015 10:03:24 +0000 (11:03 +0100)]
JAL-1541 Modified BioJs exporter to take advantage of the abstracted JSONFile export/import mechanism
gmungoc [Mon, 18 May 2015 12:39:34 +0000 (13:39 +0100)]
JAL-1663 detect tab out of RGB value; correct field tab order
gmungoc [Mon, 18 May 2015 12:38:41 +0000 (13:38 +0100)]
JAL-1663 apply new colour correctly; source formatting
gmungoc [Mon, 18 May 2015 10:29:18 +0000 (11:29 +0100)]
JAL-1652 Escape key now closes Find dialog
gmungoc [Mon, 18 May 2015 08:51:10 +0000 (09:51 +0100)]
JAL-1737 updated JUnit so it creates positional annotations
gmungoc [Fri, 15 May 2015 14:38:42 +0000 (15:38 +0100)]
JAL-1270 main method converted to JUnit test
gmungoc [Fri, 15 May 2015 13:54:23 +0000 (14:54 +0100)]
JAL-1270 main method converted to JUnit test 'as seen'
gmungoc [Fri, 15 May 2015 13:25:56 +0000 (14:25 +0100)]
JAL-1270 main method converted 'as seen' to JUnit
gmungoc [Fri, 15 May 2015 13:13:28 +0000 (14:13 +0100)]
JAL-1737 ignore non-positional annotations for display
gmungoc [Fri, 15 May 2015 13:11:40 +0000 (14:11 +0100)]
JAL-1270 added test for regex actually used; include sequence name in
sysout of extracted scores
gmungoc [Fri, 15 May 2015 09:28:12 +0000 (10:28 +0100)]
JAL-1270 main methods converted to JUnit
gmungoc [Thu, 14 May 2015 11:29:13 +0000 (12:29 +0100)]
JAL-1727 JAL-1270 obsolete DAS registry URL updated in test properties
gmungoc [Thu, 14 May 2015 11:27:56 +0000 (12:27 +0100)]
JAL-1270 set Cache properties in setUp to ensure test success
gmungoc [Wed, 13 May 2015 09:44:28 +0000 (10:44 +0100)]
JAL-1575 no-cache headers added to (empty) rest response
gmungoc [Wed, 13 May 2015 09:39:33 +0000 (10:39 +0100)]
JAL-1712 fixes/tests for Castor binding of EMBL XML / show flanking
region
gmungoc [Wed, 13 May 2015 09:30:37 +0000 (10:30 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
tcofoegbu [Wed, 13 May 2015 08:53:11 +0000 (09:53 +0100)]
Fixed some broken tests
gmungoc [Wed, 13 May 2015 07:26:31 +0000 (08:26 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
tcofoegbu [Tue, 12 May 2015 15:42:44 +0000 (16:42 +0100)]
Merge branch 'features/JAL-793_Embed_data_HTML' into develop
tcofoegbu [Tue, 12 May 2015 15:41:30 +0000 (16:41 +0100)]
JAL_793 implemented embeding source data in exported html
gmungoc [Tue, 12 May 2015 15:35:55 +0000 (16:35 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 12 May 2015 15:35:32 +0000 (16:35 +0100)]
JAL-1712 fixes/tests for Castor binding and 'show flanking regions'
tcofoegbu [Tue, 12 May 2015 10:37:40 +0000 (11:37 +0100)]
JAL_1641 updated test -- added test for annotations
tcofoegbu [Tue, 12 May 2015 10:16:20 +0000 (11:16 +0100)]
Merge branch 'features/JAL-1641_JSON_' into develop
tcofoegbu [Tue, 12 May 2015 10:15:28 +0000 (11:15 +0100)]
JAL_1641 added unit test and minor house keeping
tcofoegbu [Mon, 11 May 2015 09:44:16 +0000 (10:44 +0100)]
Merge branch 'features/JAL-1641_JSON_' into develop
tcofoegbu [Mon, 11 May 2015 09:40:47 +0000 (10:40 +0100)]
JAL-1641 cherry-picked changes into develop compatible 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
git://source.jalview.org / jalview.git / log