Jim Procter [Thu, 23 Jun 2016 13:58:42 +0000 (14:58 +0100)]
Merge branch 'develop' into merge_JAL-2110
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
Jim Procter [Thu, 23 Jun 2016 13:16:55 +0000 (14:16 +0100)]
JAL-1270 test group fix
Jim Procter [Thu, 23 Jun 2016 13:15:05 +0000 (14:15 +0100)]
JAL-2110 make indirect xref searches work by not filtering refs on candidates after selecting them by molecule type (direct==same, indirect==different)
Jim Procter [Thu, 23 Jun 2016 13:12:09 +0000 (14:12 +0100)]
JAL-2110 warning message when routine finds non-ds sequences in the dataset (seems to happen with alignments returned from Ensembl sequence fetcher)
Jim Procter [Thu, 23 Jun 2016 13:11:27 +0000 (14:11 +0100)]
JAL-2110 clarify javadoc
Jim Procter [Thu, 23 Jun 2016 13:11:10 +0000 (14:11 +0100)]
JAL-2110 refactor to split SequenceFetcher from x-ref resolution routine
Jim Procter [Thu, 23 Jun 2016 13:09:44 +0000 (14:09 +0100)]
JAL-2110 JAL-1551 formatting
Jim Procter [Thu, 23 Jun 2016 13:09:36 +0000 (14:09 +0100)]
JAL-2110 enable and fix failing tests
Jim Procter [Thu, 23 Jun 2016 13:06:10 +0000 (14:06 +0100)]
JAL-2110 enable and fix test
Jim Procter [Thu, 23 Jun 2016 13:04:47 +0000 (14:04 +0100)]
JAL-2110 refactor sequenceFetcherTest to allow verifying cross-reference retrieval for a single sequence sourc
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
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 [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
git://source.jalview.org / jalview.git / log