Jim Procter [Sun, 2 Oct 2016 11:22:20 +0000 (12:22 +0100)]
JAL-2210 try to merge all sequences referenced by a sequence with a matching xref with ones already in dataset (rather than just ones matching the source sequence) before adding the xrefed sequence to the returned sequence set.
Jim Procter [Sun, 2 Oct 2016 11:17:14 +0000 (12:17 +0100)]
JAL-2210 comments
Jim Procter [Sun, 2 Oct 2016 11:15:21 +0000 (12:15 +0100)]
JAL-2210 discover candidate dataset sequences for an xref based on primaryDBRefs first, and only fall back to sequence name match if none are found
Jim Procter [Sun, 2 Oct 2016 11:05:44 +0000 (12:05 +0100)]
JAL-2079 pass server name when reporting FTS ‘warning/error’ messages
Jim Procter [Sat, 1 Oct 2016 16:00:05 +0000 (17:00 +0100)]
Merge branch 'develop' into bug/JAL-2210_ensembl_uniprot_primaryrefs_alternate
Jim Procter [Sat, 1 Oct 2016 12:21:29 +0000 (13:21 +0100)]
JAL-2210 factored out code for processing cross-referenced sequences retrieved via a dbref on source sequence
Jim Procter [Sat, 1 Oct 2016 12:00:34 +0000 (13:00 +0100)]
JAL-2210 refactor code to remove from a list of dbrefs those which match primary dbrefs for sequences in the dataset
Jim Procter [Fri, 30 Sep 2016 16:44:32 +0000 (17:44 +0100)]
JAL-2210 some DBRef xref/ref correspondences may add sequence but have no mapping (e.g. ENSG->Uniprot), so always check if mappings have been added even if xref’ed sequence has already been added to set to be shown to user.
Jim Procter [Fri, 30 Sep 2016 16:42:57 +0000 (17:42 +0100)]
JAL-2210 CrossRef.findInDataset should search for presence of SequenceI in dataset before anything more fancy or fuzzy.
Jim Procter [Fri, 30 Sep 2016 16:40:19 +0000 (17:40 +0100)]
JAL-2210 add uniprot+mapping between ENST and ENSP seqs
gmungoc [Fri, 30 Sep 2016 12:51:59 +0000 (13:51 +0100)]
JAL-2236 code restored (and some compiler warnings addressed)
gmungoc [Fri, 30 Sep 2016 11:39:08 +0000 (12:39 +0100)]
Merge branch 'develop' into features/JAL-1856dbRefFetcherMessages
gmungoc [Fri, 30 Sep 2016 11:32:24 +0000 (12:32 +0100)]
JAL-2234 FER1_ARATH renamed FER2_ARATH and vice versa
gmungoc [Fri, 30 Sep 2016 08:08:17 +0000 (09:08 +0100)]
JAL-2236 fixes for desktop and applet implementation of 'append seqname'
gmungoc [Thu, 29 Sep 2016 15:45:28 +0000 (16:45 +0100)]
JAL-1856 better warning messages for sequence matching in DBRefFetcher
gmungoc [Thu, 29 Sep 2016 12:20:30 +0000 (13:20 +0100)]
JAL-2213 code warnings addressed (typed collections, string / magic
number constants)
gmungoc [Thu, 29 Sep 2016 12:18:42 +0000 (13:18 +0100)]
JAL-2213 removed PDB from db sources list; also code tidy (typed
collections,
gmungoc [Thu, 29 Sep 2016 12:17:53 +0000 (13:17 +0100)]
JAL-2213 made RESNUM constant private (not used elsewhere) to reduce
confusion
gmungoc [Thu, 29 Sep 2016 12:15:53 +0000 (13:15 +0100)]
JAL-2213 corrected wait for files to load in Jmol; extract method
refactoring of run()
gmungoc [Thu, 29 Sep 2016 11:56:51 +0000 (12:56 +0100)]
JAL-2237 apply default filter as sort in initial search
gmungoc [Thu, 29 Sep 2016 11:49:56 +0000 (12:49 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
Jim Procter [Thu, 29 Sep 2016 11:21:39 +0000 (12:21 +0100)]
JAL-2089 fix broken help link
Jim Procter [Thu, 29 Sep 2016 10:58:55 +0000 (11:58 +0100)]
Merge branch 'patch/JAL-2236_filtercolumns_seqassoc' into develop
Jim Procter [Thu, 29 Sep 2016 10:58:24 +0000 (11:58 +0100)]
JAL-2236 include associated sequence id for annotation’s label in filter/select combobox
Jim Procter [Thu, 29 Sep 2016 10:53:51 +0000 (11:53 +0100)]
Merge branch 'patch/JAL-2238_tcoffee_subgroups' into develop
Jim Procter [Thu, 29 Sep 2016 10:53:21 +0000 (11:53 +0100)]
JAL-2236 fix: bail if no context available for subgroup
gmungoc [Thu, 29 Sep 2016 10:03:27 +0000 (11:03 +0100)]
JAL-2047 allow title to be shrunk; spelling fix
gmungoc [Thu, 29 Sep 2016 09:57:08 +0000 (10:57 +0100)]
JAL-1544 typo
gmungoc [Thu, 29 Sep 2016 09:30:19 +0000 (10:30 +0100)]
JAL-1903 increase REST reply timeout from 5 to 15 seconds
Jim Procter [Wed, 28 Sep 2016 21:30:16 +0000 (22:30 +0100)]
JAL-2210 patch network test for additional refs
Jim Procter [Wed, 28 Sep 2016 14:57:58 +0000 (15:57 +0100)]
JAL-2210 JAL-2235 fix deriveSequence test for tightened up setDBRefs and addDBRef behaviour (always add to dataset sequence if present)
Jim Procter [Wed, 28 Sep 2016 14:56:38 +0000 (15:56 +0100)]
JAL-1270 read test props before manipulating config for this test
Jim Procter [Wed, 28 Sep 2016 14:26:52 +0000 (15:26 +0100)]
JAL-2235 patch tests where self-reference was used for dataset sequence ref
Jim Procter [Wed, 28 Sep 2016 14:26:08 +0000 (15:26 +0100)]
JAL-2235 implicit test to check that exception is raised for non-dataset reference
Jim Procter [Wed, 28 Sep 2016 14:25:29 +0000 (15:25 +0100)]
JAL-2235 raise exceptions if self reference or reference to non-ds sequence is passed to setDatasetSequence
Jim Procter [Wed, 28 Sep 2016 14:20:46 +0000 (15:20 +0100)]
JAL-2210 patch for when no DBRefs on sequence
Jim Procter [Wed, 28 Sep 2016 13:24:48 +0000 (14:24 +0100)]
JAL-2210 instrument setDBRefs to call ensurePrimaries
JAL-2210 defer setDBRefs to datasetSequence if available
Jim Procter [Wed, 28 Sep 2016 06:52:08 +0000 (07:52 +0100)]
JAL-2210 JAL-2232 check response code before attempting to get the content to avoid IO error raised for HTTP 400
Jim Procter [Wed, 28 Sep 2016 06:49:30 +0000 (07:49 +0100)]
JAL-2232 extract EMBLCDS refs from EMBL refs on Uniprot XML.
gmungoc [Tue, 27 Sep 2016 15:53:03 +0000 (16:53 +0100)]
JAL-2233 less verbose logging for Jmol
Jim Procter [Tue, 27 Sep 2016 15:07:01 +0000 (16:07 +0100)]
Merge branch 'develop' into bug/JAL-2210_ensembl_uniprot_primaryrefs_alternate
Jim Procter [Tue, 27 Sep 2016 14:17:43 +0000 (15:17 +0100)]
JAL-2210 formatting
Jim Procter [Tue, 27 Sep 2016 14:16:58 +0000 (15:16 +0100)]
JAL-2210 report stack trace for unexpected exceptions
Jim Procter [Tue, 27 Sep 2016 14:16:34 +0000 (15:16 +0100)]
JAL-2210 promote direct dbrefs from verified sources to primary for a sequence
Jim Procter [Tue, 27 Sep 2016 14:14:56 +0000 (15:14 +0100)]
JAL-2210 resolve todo - addDBRef adds to dataset sequence. test needed
gmungoc [Tue, 27 Sep 2016 10:06:44 +0000 (11:06 +0100)]
JAL-2231 save preferred scroll height _without_ progress bar message
gmungoc [Tue, 27 Sep 2016 09:04:50 +0000 (10:04 +0100)]
JAL-2230 JAL-2049 added sequence feature transfer to
testMakeCdsAlignment
gmungoc [Tue, 27 Sep 2016 08:23:55 +0000 (09:23 +0100)]
JAL-2230 use correct mapping to transfer features to CDS!
Jim Procter [Sat, 24 Sep 2016 12:25:35 +0000 (13:25 +0100)]
Merge branch 'releases/Release_2_10_Branch' into develop
Jim Procter [Sat, 24 Sep 2016 12:23:31 +0000 (13:23 +0100)]
JAL-1919 whats new link
tcofoegbu [Fri, 23 Sep 2016 15:22:13 +0000 (16:22 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 23 Sep 2016 15:22:06 +0000 (16:22 +0100)]
JAL-2164 JAL-1919 fixed failed revert commit
Jim Procter [Fri, 23 Sep 2016 15:02:49 +0000 (16:02 +0100)]
JAL-1957 JAL-1479 tweak SIFTS mappings documentation, add to what’s new section
Jim Procter [Fri, 23 Sep 2016 14:58:55 +0000 (15:58 +0100)]
JAL-1957 JAL-1479 mention SIFTS mappings in PDB Structure viewing instructions
Jim Procter [Fri, 23 Sep 2016 14:57:50 +0000 (15:57 +0100)]
JAL-1957 release notes
Jim Procter [Fri, 23 Sep 2016 14:13:40 +0000 (15:13 +0100)]
JAL-1962 release notes
Jim Procter [Fri, 23 Sep 2016 14:13:24 +0000 (15:13 +0100)]
JAL-2214 fix docs (consistent and correct base pair terminology) and link to ‘sequence logo’ docs for strucConsensus logo
Jim Procter [Fri, 23 Sep 2016 10:29:08 +0000 (11:29 +0100)]
Merge branch 'develop' into releases/Release_2_10_Branch
Jim Procter [Fri, 23 Sep 2016 10:19:40 +0000 (11:19 +0100)]
JAL-2189 JAL-1479 JAL-1491 JAL-1827 release notes
gmungoc [Fri, 23 Sep 2016 09:40:24 +0000 (10:40 +0100)]
JAL-2214 Javadoc
Jim Procter [Thu, 22 Sep 2016 15:28:33 +0000 (16:28 +0100)]
JAL-2275 release notes
Jim Procter [Thu, 22 Sep 2016 15:15:56 +0000 (16:15 +0100)]
JAL-2151 release notes
gmungoc [Thu, 22 Sep 2016 15:00:48 +0000 (16:00 +0100)]
JAL-1421 use declared type of ResidueProperties.propHash
Jim Procter [Thu, 22 Sep 2016 14:51:19 +0000 (15:51 +0100)]
JAL-2168 -news release notes
gmungoc [Thu, 22 Sep 2016 14:49:27 +0000 (15:49 +0100)]
JAL-1421 typed ResidueProperties.propHash; JAL-2176 removed propHash
from Conservation constructor, ResidueProperties.codonHash
Jim Procter [Thu, 22 Sep 2016 14:47:17 +0000 (15:47 +0100)]
JAL-1557 release notes
Jim Procter [Thu, 22 Sep 2016 14:19:08 +0000 (15:19 +0100)]
JAL-2189 bumped date to 27th September \o/
gmungoc [Thu, 22 Sep 2016 14:15:01 +0000 (15:15 +0100)]
JAL-2216 null currentAlignFrame on close all windows; remove action
listener from Window menu item when window closed
Jim Procter [Thu, 22 Sep 2016 14:04:06 +0000 (15:04 +0100)]
JAL-2189 JAL-1812 JAL-2068 new groovy docs (new files add to commit c8c1f2a)
Jim Procter [Thu, 22 Sep 2016 14:01:22 +0000 (15:01 +0100)]
JAL-2189 JAL-2092 popup show/hide cols with feature docs
gmungoc [Thu, 22 Sep 2016 13:50:53 +0000 (14:50 +0100)]
JAL-2216 finalize call super.finalize()
gmungoc [Thu, 22 Sep 2016 13:49:53 +0000 (14:49 +0100)]
JAL-2216 finalise corrected to finalize
gmungoc [Thu, 22 Sep 2016 13:47:11 +0000 (14:47 +0100)]
JAL-2216 explicitly null AnnotationPanel and AnnotationRenderer fields
when closing AlignmentPanel
Jim Procter [Thu, 22 Sep 2016 13:36:40 +0000 (14:36 +0100)]
JAL-2189 JAL-2077 note about CTRL-Click to right click on OSX
Jim Procter [Thu, 22 Sep 2016 13:36:12 +0000 (14:36 +0100)]
JAL-2189 tidy up docs
gmungoc [Thu, 22 Sep 2016 13:33:15 +0000 (14:33 +0100)]
JAL-2216 finalize() refactored so not called programmatically
Jim Procter [Thu, 22 Sep 2016 13:20:38 +0000 (14:20 +0100)]
JAL-1812 JAL-1868 release notes
gmungoc [Thu, 22 Sep 2016 13:19:44 +0000 (14:19 +0100)]
JAL-2216 new dispose() method to null references
Jim Procter [Thu, 22 Sep 2016 13:16:53 +0000 (14:16 +0100)]
JAL-2189 JAL-1812 JAL-2068 new groovy doc section and example featureCounter script
gmungoc [Thu, 22 Sep 2016 13:16:13 +0000 (14:16 +0100)]
JAL-2216 finalize call super.finalize()
Jim Procter [Wed, 21 Sep 2016 15:50:37 +0000 (16:50 +0100)]
JAL-2189 JAL-2171 JAL-2214 JAL-1841 JAL-2215 release notes
Jim Procter [Wed, 21 Sep 2016 15:49:43 +0000 (16:49 +0100)]
JAL-1841 JAL-2214 updated RNA Structure Consensus documentation
Jim Procter [Wed, 21 Sep 2016 15:43:32 +0000 (16:43 +0100)]
JAL-2214 JAL-1841 compute canonical, canonicalAndWobble visually distinguish dominant proportions as (,[,{ in histogram label
Jim Procter [Wed, 21 Sep 2016 15:42:10 +0000 (16:42 +0100)]
JAL-1841 JAL-2215 add the ‘ignore gaps’ structure consensus fraction
Jim Procter [Wed, 21 Sep 2016 15:40:07 +0000 (16:40 +0100)]
JAL-2214 test for strict Watson-Crick pairing
Jim Procter [Wed, 21 Sep 2016 15:39:31 +0000 (16:39 +0100)]
JAL-2215 fix - trigger alignment update when ‘ignore gaps’ setting changed
Jim Procter [Wed, 21 Sep 2016 11:29:49 +0000 (12:29 +0100)]
JAL-2189 reworked annotation docs
JAL-2171 autocomplete RNA ss symbol for interactive annotation
Jim Procter [Wed, 21 Sep 2016 10:13:01 +0000 (11:13 +0100)]
Merge branch 'develop' into releases/Release_2_10_Branch
gmungoc [Tue, 20 Sep 2016 09:46:22 +0000 (10:46 +0100)]
JAL-1306 calculate Quality also when Conservation not enabled
Jim Procter [Mon, 19 Sep 2016 22:02:59 +0000 (23:02 +0100)]
JAL-1577 release notes
Jim Procter [Mon, 19 Sep 2016 21:52:16 +0000 (22:52 +0100)]
JAL-2027 releasenotes
Jim Procter [Mon, 19 Sep 2016 18:11:14 +0000 (19:11 +0100)]
JAL-1563 release notes
Jim Procter [Mon, 19 Sep 2016 17:57:05 +0000 (18:57 +0100)]
JAL-2189 JAL-2002 revised the structure chooser documentation
Jim Procter [Mon, 19 Sep 2016 17:16:26 +0000 (18:16 +0100)]
JAL-2189 Release notes for JAL-2079 JAL-2084 JAL-2054 JAL-2099
Jim Procter [Mon, 19 Sep 2016 16:43:13 +0000 (17:43 +0100)]
JAL-2189 JAL-1369 JAL-192 expand referenceseq documentation
Jim Procter [Mon, 19 Sep 2016 16:40:56 +0000 (17:40 +0100)]
JAL-2189 what’s new - ensembl, new structure stuff, reference seqs
Jim Procter [Mon, 19 Sep 2016 13:17:22 +0000 (14:17 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Mon, 19 Sep 2016 13:16:59 +0000 (14:16 +0100)]
JAL-2175 JAL-2170 fix sense for assertEquals
gmungoc [Mon, 19 Sep 2016 13:10:36 +0000 (14:10 +0100)]
JAL-2118 reorder annotations after add/delete/hide/change name
Jim Procter [Mon, 19 Sep 2016 11:48:17 +0000 (12:48 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
git://source.jalview.org / jalview.git / log