Jim Procter [Thu, 23 Jun 2016 13:02:38 +0000 (14:02 +0100)]
JAL-2110 use SequenceI.isProtein()
Jim Procter [Thu, 23 Jun 2016 13:01:36 +0000 (14:01 +0100)]
JAL-2110 SequenceI.isProtein method
Jim Procter [Wed, 22 Jun 2016 10:41:24 +0000 (11:41 +0100)]
JAL-2110 remove hardwired detection of search context from the dataset ‘isNucleotide()’ flag
Jim Procter [Tue, 21 Jun 2016 15:13:05 +0000 (16:13 +0100)]
Merge branch 'features/JAL-2110_crossRefDuplications' into merge_JAL-2110
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
gmungoc [Tue, 21 Jun 2016 09:38:48 +0000 (10:38 +0100)]
JAL-2110 updated unit test to match code changes
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
gmungoc [Tue, 21 Jun 2016 09:08:48 +0000 (10:08 +0100)]
JAL-2113 tidy up canonicalisation of Uniprot xrefs in EMBL data
gmungoc [Tue, 21 Jun 2016 08:57:36 +0000 (09:57 +0100)]
JAL-2113 tidy up canonicalisation of Uniprot xrefs in EMBL data
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)
Jim Procter [Mon, 20 Jun 2016 09:00:17 +0000 (10:00 +0100)]
JAL-2110 pass dataset to makeCDSalignment
Jim Procter [Mon, 20 Jun 2016 08:59:58 +0000 (09:59 +0100)]
JAL-2110 catch case when updateDBRef argument has null version string
Jim Procter [Mon, 20 Jun 2016 08:02:29 +0000 (09:02 +0100)]
JAL-2110 List now used for AlignCodonFrame references
Jim Procter [Mon, 20 Jun 2016 07:58:10 +0000 (08:58 +0100)]
JAL-2110 copy alcodonframes only if copy constructor called on dataset alignmentI instance
Jim Procter [Sun, 19 Jun 2016 10:55:19 +0000 (11:55 +0100)]
JAL-2110 distinct alignedcodonframe entries for tests
Jim Procter [Sun, 19 Jun 2016 10:19:45 +0000 (11:19 +0100)]
JAL-2110 test alcodonframes must be distinct
Jim Procter [Sun, 19 Jun 2016 07:29:58 +0000 (08:29 +0100)]
JAL-2110 JAL-2131 JAL-1765 remove reference to jalview.datamodel.Alignment from AlignmentI
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
Jim Procter [Thu, 16 Jun 2016 12:50:55 +0000 (13:50 +0100)]
JAL-2110 todo - select mappings involving sequences in alignment
Jim Procter [Thu, 16 Jun 2016 12:50:16 +0000 (13:50 +0100)]
JAL-2110 change test for desired behaviour of getCodonFrame()
Jim Procter [Thu, 16 Jun 2016 12:47:05 +0000 (13:47 +0100)]
JAL-2110 equals and hashcode should check fromSeq
Jim Procter [Thu, 16 Jun 2016 12:38:33 +0000 (13:38 +0100)]
JAL-2110 throw implementation error if not given a dataset for CDS alignment synthesis
Jim Procter [Thu, 16 Jun 2016 12:18:36 +0000 (13:18 +0100)]
JAL-2110 typo caused infinite loop
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
Jim Procter [Wed, 15 Jun 2016 15:49:21 +0000 (16:49 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications
@gmungoc verified correct to raise exceptions for unsupported join grammar expressions
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 12:44:53 +0000 (13:44 +0100)]
Merge branch 'develop' into features/JAL-2110_crossRefDuplications
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
gmungoc [Tue, 14 Jun 2016 11:28:11 +0000 (12:28 +0100)]
JAL-2110 fixes to dbref resolution and mappings, use same dataset for
dna/cds/protein
gmungoc [Tue, 14 Jun 2016 11:26:04 +0000 (12:26 +0100)]
JAL-2110 ensure "UniProtKB/Swiss-Prot" dbrefs canonicalised to UNIPROT
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
gmungoc [Tue, 14 Jun 2016 07:05:53 +0000 (08:05 +0100)]
JAL-1686 JAL-2110 equals and/or hashCode method added
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
Jim Procter [Wed, 8 Jun 2016 15:38:56 +0000 (16:38 +0100)]
JAL-2089 signed off bug release notes
Jim Procter [Wed, 8 Jun 2016 15:37:51 +0000 (16:37 +0100)]
JAL-1941 remove improper test tag from Annotate3D test helper
Jim Procter [Mon, 6 Jun 2016 08:48:31 +0000 (09:48 +0100)]
JAL-2089 documenting for 8th june RC1
Jim Procter [Fri, 10 Jun 2016 08:01:03 +0000 (09:01 +0100)]
JAL-1941 added test URL and notes about PyRNA restclient
Jim Procter [Fri, 10 Jun 2016 08:00:41 +0000 (09:00 +0100)]
JAL-1941 Annotate3d tests should be in network group
git://source.jalview.org / jalview.git / log