tcofoegbu [Fri, 5 Jun 2015 16:08:15 +0000 (17:08 +0100)]
JAL-1760 JAL-1641 Serialisation of Hidden Seqs and Cols in JSON output. Added ability to retrieve hidden Seqs
gmungoc [Thu, 4 Jun 2015 10:51:47 +0000 (11:51 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 4 Jun 2015 10:51:28 +0000 (11:51 +0100)]
JAL-1757 match only first altloc CA in PDB structure for superposition
tcofoegbu [Thu, 4 Jun 2015 10:45:31 +0000 (11:45 +0100)]
JAL-1641 added some JSON libraries to appletlib
tcofoegbu [Thu, 4 Jun 2015 10:20:42 +0000 (11:20 +0100)]
clean up
tcofoegbu [Thu, 4 Jun 2015 10:12:03 +0000 (11:12 +0100)]
JAL-1756 fix failed test as a result of runing the BioJS updater from a new thread
gmungoc [Thu, 4 Jun 2015 10:07:28 +0000 (11:07 +0100)]
JAL-1421 generic collections in MCView package (+unit tests)
tcofoegbu [Thu, 4 Jun 2015 09:52:06 +0000 (10:52 +0100)]
Merge branch 'features/JAL-1641_JSON-extension' into develop
tcofoegbu [Thu, 4 Jun 2015 09:42:08 +0000 (10:42 +0100)]
JAL-1756 bug-fix
tcofoegbu [Thu, 4 Jun 2015 09:04:47 +0000 (10:04 +0100)]
JAL-1641 updated json schema to make it more generic in order to accomodate more dynamic parameters
tcofoegbu [Tue, 2 Jun 2015 16:59:23 +0000 (17:59 +0100)]
fixed bug in build.xml
tcofoegbu [Tue, 2 Jun 2015 15:51:56 +0000 (16:51 +0100)]
Merge branch 'features/JAL-1641_JSON-extension' into develop
tcofoegbu [Tue, 2 Jun 2015 15:51:30 +0000 (16:51 +0100)]
JAL-1641 updated build.xml
tcofoegbu [Tue, 2 Jun 2015 14:54:44 +0000 (15:54 +0100)]
JAL-1641 updated examples/applets.html
tcofoegbu [Tue, 2 Jun 2015 14:12:45 +0000 (15:12 +0100)]
Merge branch 'features/JAL-1641_JSON-extension' into develop
tcofoegbu [Tue, 2 Jun 2015 14:11:50 +0000 (15:11 +0100)]
JAL-1641 applet build fix
tcofoegbu [Mon, 1 Jun 2015 15:59:19 +0000 (16:59 +0100)]
Merge branch 'features/JAL-1641_JSON-extension' into develop
tcofoegbu [Mon, 1 Jun 2015 15:58:38 +0000 (16:58 +0100)]
JAL-1641 remove all refs/imports from gui package
tcofoegbu [Mon, 1 Jun 2015 14:23:16 +0000 (15:23 +0100)]
Merge branch 'bug/JAL-1703_hint_select_by_annot' into develop
tcofoegbu [Mon, 1 Jun 2015 14:19:06 +0000 (15:19 +0100)]
JAL-1703 added tooltip hints to components of the Select by Annotation UI
tcofoegbu [Mon, 1 Jun 2015 10:15:34 +0000 (11:15 +0100)]
Merge branch 'bug/JAL-1734_misleading-progress-bar' into develop
tcofoegbu [Mon, 1 Jun 2015 10:15:04 +0000 (11:15 +0100)]
JAL-1734 updated progress bar messages
tcofoegbu [Fri, 29 May 2015 15:41:21 +0000 (16:41 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 29 May 2015 15:41:10 +0000 (16:41 +0100)]
JAL-1748 house keeping
gmungoc [Fri, 29 May 2015 13:56:48 +0000 (14:56 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 29 May 2015 13:56:36 +0000 (14:56 +0100)]
JAL-1753 declare field with interface type; check for null dereference
Jim Procter [Fri, 29 May 2015 13:23:34 +0000 (14:23 +0100)]
Merge branch 'JAL-1755_npe_groupconsensus' into develop
Jim Procter [Fri, 29 May 2015 13:22:38 +0000 (14:22 +0100)]
JAL-1755 fix for NPE when setting up temporary variables
gmungoc [Fri, 29 May 2015 13:07:56 +0000 (14:07 +0100)]
JAL-1753 Junit for new class
gmungoc [Fri, 29 May 2015 11:06:20 +0000 (12:06 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Fri, 29 May 2015 11:01:09 +0000 (12:01 +0100)]
JAL-1753 duplicated code refactored to new class ProgressBar
tcofoegbu [Fri, 29 May 2015 10:22:37 +0000 (11:22 +0100)]
Merge branch 'bug/JAL-1748_extend-pdb-query-opt' into develop
tcofoegbu [Fri, 29 May 2015 10:21:04 +0000 (11:21 +0100)]
JAL-1748 and employ preprocessing routine when return action event is triggered
tcofoegbu [Fri, 29 May 2015 08:53:50 +0000 (09:53 +0100)]
validate PDB selections on mouse release event
tcofoegbu [Thu, 28 May 2015 15:47:25 +0000 (16:47 +0100)]
JAL-1700 made PDB service error mechanism more user friendly
tcofoegbu [Thu, 28 May 2015 10:46:35 +0000 (11:46 +0100)]
Merge branch 'bug/JAL-1751_make-table-uneditable' into develop
tcofoegbu [Thu, 28 May 2015 10:45:50 +0000 (11:45 +0100)]
JAL-1751 provided method to overide isCellEditable for the PDB response table model
tcofoegbu [Thu, 28 May 2015 10:05:00 +0000 (11:05 +0100)]
Merge branch 'bug/JAL-1749_reinstate-rna-viewing' into develop
tcofoegbu [Thu, 28 May 2015 10:03:04 +0000 (11:03 +0100)]
JAL-1749 reinstated the ability to view RNA structures
tcofoegbu [Thu, 28 May 2015 08:20:33 +0000 (09:20 +0100)]
JAL-1740 minor house keeping
tcofoegbu [Wed, 27 May 2015 17:01:16 +0000 (18:01 +0100)]
Removed redundant classes and dependencies pulled in from last merge of features/JAL-1740_Decoup-BioJS branch
tcofoegbu [Wed, 27 May 2015 16:55:38 +0000 (17:55 +0100)]
Merge branch 'features/JAL-1740_Decoup-BioJS' into develop
tcofoegbu [Wed, 27 May 2015 16:49:47 +0000 (17:49 +0100)]
JAL-1740 updated synch codes to use a git repo rather than FTP
tcofoegbu [Tue, 26 May 2015 11:44:16 +0000 (12:44 +0100)]
JAL-1627 bug fix to remove wierd space in Sequence Features/Sequence Group tooltip on windows
tcofoegbu [Mon, 25 May 2015 15:04:22 +0000 (16:04 +0100)]
build fix
tcofoegbu [Fri, 22 May 2015 16:03:32 +0000 (17:03 +0100)]
Merge branch 'features/JAL-1745_PDB-redownload' into develop
tcofoegbu [Fri, 22 May 2015 16:02:55 +0000 (17:02 +0100)]
JAL-1745, JAL-1717 improvement to ensure cached PDB entries are unique within a sequence. Also only truly downloaded files should be shown in the cache view
tcofoegbu [Fri, 22 May 2015 11:09:58 +0000 (12:09 +0100)]
Merge branch 'features/JAL-1745_PDB-redownload' into develop
tcofoegbu [Fri, 22 May 2015 11:09:09 +0000 (12:09 +0100)]
JAL-1745 improvement to retreive already downloaded pdb structure file from cache
tcofoegbu [Thu, 21 May 2015 10:37:29 +0000 (11:37 +0100)]
JAL-1740 implemented auto-update of BioJsMSA, introduced FTP client for downloading remote BioJs Templates
gmungoc [Wed, 20 May 2015 13:41:54 +0000 (14:41 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 20 May 2015 13:41:38 +0000 (14:41 +0100)]
JAL-1741 nucleotide-aware colour schemes applied to structures
tcofoegbu [Wed, 20 May 2015 09:40:21 +0000 (10:40 +0100)]
Merge branch 'features/JAL-1739_JSON-versioning' into develop
tcofoegbu [Wed, 20 May 2015 09:39:39 +0000 (10:39 +0100)]
JAL-1739 added svid - serial version id to hold version info for all the json objects
gmungoc [Wed, 20 May 2015 09:35:03 +0000 (10:35 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 20 May 2015 09:34:42 +0000 (10:34 +0100)]
JAL-796 JAL-1652 better implementation (key binding not KeyListener)
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 11:25:37 +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
git://source.jalview.org / jalview.git / log