tcofoegbu [Fri, 8 Jul 2016 16:16:54 +0000 (17:16 +0100)]
JAL-1919 Fixed failing tests, enabled HETATM processing from structure file to be configurable. Minor refactorings (StructureViewSettings class renamed to StructureImportSettings, fileName variables of AlignFile class renamed to dataObject since in realty it could be a file, url or pasted string)
tcofoegbu [Fri, 1 Jul 2016 10:08:43 +0000 (11:08 +0100)]
JAL-2135 bugfix for error preventing processing of secondary structure annotation for model produced by Phyre2
tcofoegbu [Thu, 30 Jun 2016 14:59:00 +0000 (15:59 +0100)]
JAL-2074 Improvement to StructureChooser and FTS interfaces to remember the user preferences for summary table columns, window size & positions
tcofoegbu [Thu, 30 Jun 2016 09:46:51 +0000 (10:46 +0100)]
JAL-1919 updated PDBSequenceFetcherTest and JMol parser config settings to enable proper processing of mmCIF files
tcofoegbu [Wed, 29 Jun 2016 13:58:41 +0000 (14:58 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 29 Jun 2016 13:58:34 +0000 (14:58 +0100)]
JAL-1479 added test case to elaborate getEntityByMostOptimalMatchedId method
gmungoc [Wed, 29 Jun 2016 12:48:58 +0000 (13:48 +0100)]
JAL-1270 avoid overwriting .jalview_properties with test service urls
tcofoegbu [Wed, 29 Jun 2016 11:34:51 +0000 (12:34 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 29 Jun 2016 11:34:41 +0000 (12:34 +0100)]
JAL-1479 improved Sifts PID calculation for determining an Entity to process
gmungoc [Wed, 29 Jun 2016 08:17:29 +0000 (09:17 +0100)]
JAL-1369 fix bug reloading a project with group sequence reps
tcofoegbu [Tue, 28 Jun 2016 15:21:17 +0000 (16:21 +0100)]
JAL-1479 minor refactor and housekeeping
tcofoegbu [Tue, 28 Jun 2016 14:28:28 +0000 (15:28 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 28 Jun 2016 14:28:22 +0000 (15:28 +0100)]
JAL-1479 improved SiftsClient test coverage and implemented previously unimplemented test cases
gmungoc [Mon, 27 Jun 2016 13:04:14 +0000 (14:04 +0100)]
tidied loop with generic iteration / loop variable
gmungoc [Mon, 27 Jun 2016 13:03:09 +0000 (14:03 +0100)]
JAL-2133 refactored duplicated code to AlignmentViewport
gmungoc [Mon, 27 Jun 2016 13:02:15 +0000 (14:02 +0100)]
JAL-1369 additional asserts in testStoreAndRecoverReferenceSeqSettings
gmungoc [Mon, 27 Jun 2016 12:35:51 +0000 (13:35 +0100)]
JAL-1270 unit tests for HiddenSequences
tcofoegbu [Fri, 24 Jun 2016 10:09:15 +0000 (11:09 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 24 Jun 2016 10:08:59 +0000 (11:08 +0100)]
JAL-1960 updated unit test to include the test case where a sequences has no PDBId entry(s) but has Uniprot & PDB dbrefs
gmungoc [Thu, 23 Jun 2016 14:26:03 +0000 (15:26 +0100)]
JAL-2130 now simply viewer.dispose() to close down Jmol threads
tcofoegbu [Thu, 23 Jun 2016 13:47:20 +0000 (14:47 +0100)]
JAL-1996 added notes for an alternative way to view example pages source code
tcofoegbu [Wed, 22 Jun 2016 16:03:00 +0000 (17:03 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 22 Jun 2016 16:02:53 +0000 (17:02 +0100)]
JAL-1996 added link for viewing example source codes, changed release history outline from list to table
gmungoc [Wed, 22 Jun 2016 15:09:00 +0000 (16:09 +0100)]
JAL-2015 fixed bug in copy constructor and added tests
gmungoc [Wed, 22 Jun 2016 13:56:32 +0000 (14:56 +0100)]
JAL-1982 defensive checks for null annotations array
gmungoc [Wed, 22 Jun 2016 13:00:08 +0000 (14:00 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 22 Jun 2016 12:59:35 +0000 (13:59 +0100)]
JAL-1982 defensive test for null array of annotations
tcofoegbu [Wed, 22 Jun 2016 11:54:43 +0000 (12:54 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 22 Jun 2016 11:54:34 +0000 (12:54 +0100)]
JAL-1996 removed quick links in example pages, added one minimal applet embedding example to applet deployment page
Jim Procter [Tue, 21 Jun 2016 14:58:43 +0000 (15:58 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
gmungoc [Tue, 21 Jun 2016 14:27:33 +0000 (15:27 +0100)]
JAL-2074 suppress prompt to save closed Groovy script on Jalview Quit
gmungoc [Tue, 21 Jun 2016 14:26:16 +0000 (15:26 +0100)]
JAL-1270 remove test artefact file after test
Jim Procter [Tue, 21 Jun 2016 13:53:15 +0000 (14:53 +0100)]
Merge branch 'features/JAL-1956_featureStyles' into merge_JAL-1956
Jim Procter [Tue, 21 Jun 2016 13:45:56 +0000 (14:45 +0100)]
JAL-1270 ensure before/after clauses have at least alwaysRun=true in them
gmungoc [Tue, 21 Jun 2016 13:41:43 +0000 (14:41 +0100)]
JAL-1270 added runAlways=true to setUp method
gmungoc [Tue, 21 Jun 2016 13:41:08 +0000 (14:41 +0100)]
JAL-2074 reuse Groovy window when reopening; rebind Cmd-Q to Jalview
when closing
Jim Procter [Tue, 21 Jun 2016 09:54:17 +0000 (10:54 +0100)]
JAL-2089 cleared out old ‘What’s new’
Jim Procter [Tue, 21 Jun 2016 09:53:31 +0000 (10:53 +0100)]
JAL-192 JAL-1369 release notes
Jim Procter [Tue, 21 Jun 2016 09:45:56 +0000 (10:45 +0100)]
Merge branch 'features/JAL-1369_refseqproject' into develop
Jim Procter [Tue, 21 Jun 2016 09:40:47 +0000 (10:40 +0100)]
JAL-1369 make sure desktop is cleared before test starts
Jim Procter [Tue, 21 Jun 2016 09:40:19 +0000 (10:40 +0100)]
JAL-1369 jalview2xml tests need to be run sequentially
Jim Procter [Tue, 21 Jun 2016 09:22:57 +0000 (10:22 +0100)]
JAL-1369 mark reference sequence & view state and restore it
Jim Procter [Tue, 21 Jun 2016 09:22:02 +0000 (10:22 +0100)]
JAL-1369 project XML efficiency TODO
Jim Procter [Tue, 21 Jun 2016 09:21:40 +0000 (10:21 +0100)]
JAL-1369 dead code TODO?
Jim Procter [Tue, 21 Jun 2016 09:21:23 +0000 (10:21 +0100)]
JAL-1369 ensure *real* alignment’s metadata written in Jalview2XML when view contains hidden sequences
Jim Procter [Tue, 21 Jun 2016 09:19:17 +0000 (10:19 +0100)]
JAL-1369 fix the test
Jim Procter [Tue, 21 Jun 2016 09:18:54 +0000 (10:18 +0100)]
JAL-1369 make sure the fake AlignmentI produced by getFullAlignment retains the current reference sequence
Jim Procter [Tue, 21 Jun 2016 09:18:12 +0000 (10:18 +0100)]
JAL-1369 HUGE WARNING: datamodel.HiddenSequences is NOT SAFE
Jim Procter [Mon, 20 Jun 2016 20:38:41 +0000 (21:38 +0100)]
JAL-1369 updated project schema - flag on JSeq to mark view’s reference seq
Jim Procter [Mon, 20 Jun 2016 15:26:16 +0000 (16:26 +0100)]
JAL-1369 failing test
Jim Procter [Mon, 20 Jun 2016 13:35:47 +0000 (14:35 +0100)]
JAL-1989 JAL-1011 release notes
Jim Procter [Mon, 20 Jun 2016 13:22:56 +0000 (14:22 +0100)]
JAL-2086 JAL-2085 release notes
Jim Procter [Mon, 20 Jun 2016 12:52:40 +0000 (13:52 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Mon, 20 Jun 2016 12:52:12 +0000 (13:52 +0100)]
JAL-2065 release notes
Jim Procter [Mon, 20 Jun 2016 12:49:18 +0000 (13:49 +0100)]
Merge branch 'bugs/JAL-2065' into develop
Jim Procter [Mon, 20 Jun 2016 12:48:54 +0000 (13:48 +0100)]
JAL-2065 port patch to applet
Jim Procter [Mon, 20 Jun 2016 12:48:45 +0000 (13:48 +0100)]
JAL-1551 tidy
Jim Procter [Mon, 20 Jun 2016 12:48:33 +0000 (13:48 +0100)]
JAL-1551 tidy
Jim Procter [Mon, 20 Jun 2016 12:48:17 +0000 (13:48 +0100)]
JAL-2065 don’t pass stale group reference
Jim Procter [Mon, 20 Jun 2016 12:47:30 +0000 (13:47 +0100)]
JAL-2068 avoid ArrayIndexOutOfBounds when consensus accessed before calculation has been completed
Jim Procter [Tue, 31 May 2016 14:17:30 +0000 (15:17 +0100)]
JAL-2065 check position lies within group before getting consensus char
tcofoegbu [Mon, 20 Jun 2016 12:10:31 +0000 (13:10 +0100)]
JAL-1996 added JalviewApplet to download list in applet deployment page
tcofoegbu [Mon, 20 Jun 2016 11:07:33 +0000 (12:07 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Mon, 20 Jun 2016 11:07:25 +0000 (12:07 +0100)]
JAL-1823 Deleted two obsolete methods in PopupMenu.java, updated tooltip text for manual PDB entry, and fixed error while manually retrieving some specific PDB chains.
Jim Procter [Mon, 20 Jun 2016 10:44:47 +0000 (11:44 +0100)]
Merge branch 'r291_docs' into develop
Jim Procter [Mon, 20 Jun 2016 10:44:21 +0000 (11:44 +0100)]
JAL-1812 groovy always present
Jim Procter [Mon, 20 Jun 2016 10:43:47 +0000 (11:43 +0100)]
JAL-1812 release notes
Jim Procter [Mon, 20 Jun 2016 10:43:28 +0000 (11:43 +0100)]
JAL-1812 documentation TBC for AlignFrame->Calculate->Run Groovy Script
Jim Procter [Mon, 13 Jun 2016 09:57:03 +0000 (10:57 +0100)]
JAL-2089 typo
Jim Procter [Fri, 10 Jun 2016 14:31:15 +0000 (15:31 +0100)]
JAL-1868 fix typo in test data.
Jim Procter [Mon, 20 Jun 2016 09:54:14 +0000 (10:54 +0100)]
Merge branch 'features/JAL-1812_JAL-2083_groovyBinding' into develop
Jim Procter [Mon, 20 Jun 2016 09:53:46 +0000 (10:53 +0100)]
Merge branch 'develop' into features/JAL-1812_JAL-2083_groovyBinding
gmungoc [Mon, 20 Jun 2016 09:10:24 +0000 (10:10 +0100)]
JAL-2130 call viewer.dispose() on closing Jmol
gmungoc [Mon, 20 Jun 2016 09:07:49 +0000 (10:07 +0100)]
JAL-1667 updated PDB example query to a valid id (without chain code)
tcofoegbu [Fri, 17 Jun 2016 17:08:25 +0000 (18:08 +0100)]
JAL-1823 Updated tooltip to reflect how a specific chain can be retrieved
tcofoegbu [Fri, 17 Jun 2016 14:29:54 +0000 (15:29 +0100)]
JAL-1976 clear message if export is cancelled at 'Rendering options' stage.
tcofoegbu [Fri, 17 Jun 2016 13:43:06 +0000 (14:43 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 17 Jun 2016 13:42:58 +0000 (14:42 +0100)]
JAL-1996 update applet deployment note pages
gmungoc [Fri, 17 Jun 2016 13:23:57 +0000 (14:23 +0100)]
JAL-1557 selection from annotation (and group annotation) added to help
tcofoegbu [Fri, 17 Jun 2016 11:50:43 +0000 (12:50 +0100)]
JAL-1976 improved exception handler.
tcofoegbu [Fri, 17 Jun 2016 11:35:52 +0000 (12:35 +0100)]
JAL-1976 added an intermediate message between a user selecting an export file and export completion.
Jim Procter [Thu, 16 Jun 2016 17:29:40 +0000 (18:29 +0100)]
tests for validating start-end number/sequence length, annotation and metadata for retrieval from PDB via mmCIF and PDB JAL-2007 JAL-2005 JAL-1919
gmungoc [Thu, 16 Jun 2016 13:27:29 +0000 (14:27 +0100)]
JAL-1993 close sequence fetcher when opening database chooser
gmungoc [Thu, 16 Jun 2016 10:29:40 +0000 (11:29 +0100)]
JAL-2124 JAL-1990 additional translations
gmungoc [Thu, 16 Jun 2016 08:49:04 +0000 (09:49 +0100)]
JAL-2112 optimisation of EMBL CDS parsing
gmungoc [Thu, 16 Jun 2016 08:48:13 +0000 (09:48 +0100)]
JAL-1993 hide sequence fetcher dialogue until database selection made
tcofoegbu [Wed, 15 Jun 2016 15:02:30 +0000 (16:02 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 15 Jun 2016 15:02:16 +0000 (16:02 +0100)]
JAL-2002 disabled 'Best Uniport Coverage' filter. JAL-1990 i18n for status messages in the newly introduced progress indicator for Structure Chooser interface
gmungoc [Wed, 15 Jun 2016 10:25:07 +0000 (11:25 +0100)]
JAL-2025 unit tests added
gmungoc [Wed, 15 Jun 2016 08:20:04 +0000 (09:20 +0100)]
JAL-2101 unit test updated to match config file
tcofoegbu [Tue, 14 Jun 2016 16:48:04 +0000 (17:48 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 14 Jun 2016 16:47:55 +0000 (17:47 +0100)]
JAL-2102 right justify 'Mass' in uniprot FTS, and 'Max Observed Residue' in PDB FTS, and correct 'Miscellaneous' spelling
gmungoc [Tue, 14 Jun 2016 13:57:59 +0000 (14:57 +0100)]
JAL-2114 more helpful reporting of parse failures
gmungoc [Tue, 14 Jun 2016 11:31:34 +0000 (12:31 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
tcofoegbu [Tue, 14 Jun 2016 11:24:40 +0000 (12:24 +0100)]
JAL-2047 trapped block that could likely cause ClassCastException
tcofoegbu [Tue, 14 Jun 2016 10:17:44 +0000 (11:17 +0100)]
JAL-2047 resolved structure chooser's displayed column configuration updating, added horizontal scrollbar to structure chooser summary table and minor house keeping
tcofoegbu [Fri, 10 Jun 2016 14:56:48 +0000 (15:56 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 10 Jun 2016 14:56:39 +0000 (15:56 +0100)]
JAL-1479 updated SIFTS FTP download URL, added improvement to ensure that new SIFTS file are successfully downloaded before overwriting the outdated cached ones, and added fix for PDB RESNUM transfer via JMol parser
Jim Procter [Fri, 10 Jun 2016 08:19:28 +0000 (09:19 +0100)]
Merge branch 'r291_docs' into develop
Jim Procter [Fri, 10 Jun 2016 08:18:58 +0000 (09:18 +0100)]
JAL-2089 docs for June 10th
git://source.jalview.org / jalview.git / log