Jim Procter [Fri, 25 Mar 2016 15:33:38 +0000 (15:33 +0000)]
JAL-2034 JAL-1421 use ArrayLists, and make ‘selection’ group an ScGroup
Jim Procter [Fri, 25 Mar 2016 15:31:53 +0000 (15:31 +0000)]
JAL-2034 notes on efficiency
Jim Procter [Fri, 25 Mar 2016 15:31:22 +0000 (15:31 +0000)]
JAL-2034 break out of redraw loop early if another update has already been requested
Jim Procter [Fri, 25 Mar 2016 15:21:53 +0000 (15:21 +0000)]
JAL-2034 disable overview updates when extent of a transient selection group is changed
Jim Procter [Fri, 25 Mar 2016 15:19:32 +0000 (15:19 +0000)]
JAL-2034 make Escape/select/deselect operations not trigger an overview repaint (which will also disable updates to structure views)
Note: this needs to be done systematically, and ideally decided by current editing state of the alignmentPanel
Jim Procter [Fri, 25 Mar 2016 14:52:04 +0000 (14:52 +0000)]
JAL-2034 make colour scheme update optional when group conservation is calculated, and pass back a ‘change’ flag
Jim Procter [Fri, 25 Mar 2016 14:49:52 +0000 (14:49 +0000)]
JAL-1551
Jim Procter [Fri, 25 Mar 2016 14:48:02 +0000 (14:48 +0000)]
JAL-2034 flag for triggering redraw of overview window for a view
tcofoegbu [Thu, 24 Mar 2016 11:12:27 +0000 (11:12 +0000)]
merge
tcofoegbu [Thu, 24 Mar 2016 11:11:44 +0000 (11:11 +0000)]
fixed applet build
gmungoc [Thu, 24 Mar 2016 11:02:11 +0000 (11:02 +0000)]
JAL-1705 removed experimental 'highlight selection on structure'
gmungoc [Thu, 24 Mar 2016 10:50:48 +0000 (10:50 +0000)]
JAL-2032 structure follow mouseover in a copy of a mapped sequence
tcofoegbu [Thu, 24 Mar 2016 10:22:34 +0000 (10:22 +0000)]
JAL-1919 set DEFUALT_STRUCTURE_FORMAT to PDB
tcofoegbu [Wed, 23 Mar 2016 18:17:49 +0000 (18:17 +0000)]
merge
tcofoegbu [Wed, 23 Mar 2016 18:06:46 +0000 (18:06 +0000)]
JAL-2009 added programmatic custom feature setting to show insertion position for PDB sequences fetched via SequenceFetcher, Paste and File (url, drag'n'drop, File dialog)
gmungoc [Wed, 23 Mar 2016 15:37:53 +0000 (15:37 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 23 Mar 2016 15:36:25 +0000 (15:36 +0000)]
JAL-1705 add DBRefEntry for 'self' to retrieved transcripts so they are
not reported as failed when fetching a gene
gmungoc [Wed, 23 Mar 2016 15:34:38 +0000 (15:34 +0000)]
JAL-1997 default empty tooltip required for correct behaviour
tcofoegbu [Tue, 22 Mar 2016 17:02:10 +0000 (17:02 +0000)]
resolve conflict with Mungo's merge
tcofoegbu [Tue, 22 Mar 2016 16:58:53 +0000 (16:58 +0000)]
JAL-1919 code improvement to make PDB sequence fetcher file format configurable. Also fixed issue preventing viewing large structures
gmungoc [Tue, 22 Mar 2016 16:29:45 +0000 (16:29 +0000)]
Merge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport' into develop
gmungoc [Tue, 22 Mar 2016 16:29:08 +0000 (16:29 +0000)]
JAL-1705 add xref seqs to 'parent' dataset only if same type (nuc/prot)
gmungoc [Tue, 22 Mar 2016 13:57:29 +0000 (13:57 +0000)]
JAL-1191 isolated SequenceOntology (BioJava wrapper) to /ext/so folder
gmungoc [Tue, 22 Mar 2016 08:42:26 +0000 (08:42 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
tcofoegbu [Mon, 21 Mar 2016 17:14:17 +0000 (17:14 +0000)]
JAL-1919 refactor moved StructureViewerSettings
gmungoc [Mon, 21 Mar 2016 16:46:57 +0000 (16:46 +0000)]
Merge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport' into develop
gmungoc [Mon, 21 Mar 2016 16:46:41 +0000 (16:46 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 21 Mar 2016 16:46:10 +0000 (16:46 +0000)]
JAL-2029 further fixes to get correct xrefs and xrefs on xrefs...
tcofoegbu [Mon, 21 Mar 2016 16:18:26 +0000 (16:18 +0000)]
merged features/JAL-1919_mmCIF-Support to develop
tcofoegbu [Mon, 21 Mar 2016 16:08:17 +0000 (16:08 +0000)]
develop merge
gmungoc [Mon, 21 Mar 2016 14:49:08 +0000 (14:49 +0000)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Mon, 21 Mar 2016 14:46:40 +0000 (14:46 +0000)]
JAL-1855 dbfetch from /ena_sequence/, /ena_coding/
gmungoc [Mon, 21 Mar 2016 14:42:51 +0000 (14:42 +0000)]
JAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings
tcofoegbu [Mon, 21 Mar 2016 14:34:34 +0000 (14:34 +0000)]
JAL-2028 added improvement for preconfigured ordering of custom display options
tcofoegbu [Mon, 21 Mar 2016 11:27:39 +0000 (11:27 +0000)]
develop merge
tcofoegbu [Mon, 21 Mar 2016 11:22:50 +0000 (11:22 +0000)]
merge
tcofoegbu [Mon, 21 Mar 2016 11:21:58 +0000 (11:21 +0000)]
mungo merge
tcofoegbu [Mon, 21 Mar 2016 11:14:26 +0000 (11:14 +0000)]
develop merge
tcofoegbu [Mon, 21 Mar 2016 10:11:19 +0000 (10:11 +0000)]
JAL-1667 Changed PDBSearchPanel's search result layout to CardLayout to provide a better resize behaviour
gmungoc [Wed, 16 Mar 2016 14:12:06 +0000 (14:12 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 16 Mar 2016 14:11:54 +0000 (14:11 +0000)]
JAL-1705 xref ENST to correct (ENSP) accession id
tcofoegbu [Wed, 16 Mar 2016 12:24:24 +0000 (12:24 +0000)]
JAL-2028 improvment to the displayed column customisation
gmungoc [Tue, 15 Mar 2016 15:37:39 +0000 (15:37 +0000)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Tue, 15 Mar 2016 15:19:46 +0000 (15:19 +0000)]
JAL-2016 corrected Javadoc, added test for anonymous instance
gmungoc [Tue, 15 Mar 2016 14:49:13 +0000 (14:49 +0000)]
JAL-2016 FeatureSettingsI now FeatureSettingsModelI
gmungoc [Tue, 15 Mar 2016 14:27:12 +0000 (14:27 +0000)]
JAL-1705 code tidy/comment only
gmungoc [Tue, 15 Mar 2016 14:26:45 +0000 (14:26 +0000)]
JAL-1705 compute reverse complement of variants on reverse strand
tcofoegbu [Tue, 15 Mar 2016 12:19:29 +0000 (12:19 +0000)]
JAL-1919 refined structure view annotation settings to work for both PDB and mmCIF
tcofoegbu [Fri, 11 Mar 2016 18:03:21 +0000 (18:03 +0000)]
JAL-1478 Fixed ArrayIndexOutOfBoundsException while performing NW mapping
tcofoegbu [Fri, 11 Mar 2016 17:14:04 +0000 (17:14 +0000)]
merge
tcofoegbu [Fri, 11 Mar 2016 17:04:56 +0000 (17:04 +0000)]
JAL-2026 Bug fix for best quality filter
gmungoc [Fri, 11 Mar 2016 12:15:22 +0000 (12:15 +0000)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Fri, 11 Mar 2016 12:14:34 +0000 (12:14 +0000)]
JAL-1270 unit test for SequenceIdMatcher.SeqIdName
gmungoc [Fri, 11 Mar 2016 12:08:06 +0000 (12:08 +0000)]
JAL-1705 check Retry-After response header
gmungoc [Fri, 11 Mar 2016 12:07:15 +0000 (12:07 +0000)]
JAL-1705 javadoc added only
gmungoc [Fri, 11 Mar 2016 12:06:31 +0000 (12:06 +0000)]
JAL-1705 refactoring etc for fetching Ensembl --> Uniprot
cross-references
tcofoegbu [Fri, 11 Mar 2016 11:59:38 +0000 (11:59 +0000)]
JAL-1818 reimplemented sequence and annotation processing for JmolParser and further refactoring to improve codes
tcofoegbu [Thu, 10 Mar 2016 15:53:56 +0000 (15:53 +0000)]
develop merge
tcofoegbu [Thu, 10 Mar 2016 15:17:37 +0000 (15:17 +0000)]
JAL-2025 added code to stanitise query for structure by sequence name which contains special characters
tcofoegbu [Thu, 10 Mar 2016 11:43:59 +0000 (11:43 +0000)]
JAL-2024 code to enforce case insensitivity for manual pdb structure querying
gmungoc [Mon, 7 Mar 2016 13:25:06 +0000 (13:25 +0000)]
JAL-2023 CDS sequences added to / share alignment dataset
gmungoc [Fri, 4 Mar 2016 09:59:04 +0000 (09:59 +0000)]
JAL-1705 EnsemblGenomes a top level db source
gmungoc [Fri, 4 Mar 2016 09:58:42 +0000 (09:58 +0000)]
JAL-1705 parse 'description' from GFF as sequence description
tcofoegbu [Thu, 3 Mar 2016 14:46:00 +0000 (14:46 +0000)]
JAL-1919 fixed bug causing PDBfile test failure
gmungoc [Thu, 3 Mar 2016 11:02:10 +0000 (11:02 +0000)]
JAL-1705 unit test for aligning with incomplete start codon
tcofoegbu [Thu, 3 Mar 2016 10:08:21 +0000 (10:08 +0000)]
develop merge
tcofoegbu [Thu, 3 Mar 2016 10:00:10 +0000 (10:00 +0000)]
JAL-1919 updated unicode mapping symbol
tcofoegbu [Thu, 3 Mar 2016 09:55:58 +0000 (09:55 +0000)]
JAL-1919 updated unicode symbol for mapping
gmungoc [Thu, 3 Mar 2016 09:53:40 +0000 (09:53 +0000)]
JAL-1705 include stop codons in derived CDS; support ensemblgenomes
tcofoegbu [Thu, 3 Mar 2016 09:23:40 +0000 (09:23 +0000)]
JAL-1919 PDBfile and JmolParser refactor
gmungoc [Wed, 2 Mar 2016 16:35:00 +0000 (16:35 +0000)]
JAL-1705 include any unmapped protein start 'X' when aligning to dna
gmungoc [Tue, 1 Mar 2016 12:12:09 +0000 (12:12 +0000)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Tue, 1 Mar 2016 12:10:25 +0000 (12:10 +0000)]
JAL-1705 align CDS to transcripts
gmungoc [Tue, 1 Mar 2016 12:09:47 +0000 (12:09 +0000)]
JAL-1705 align CDS and peptide products to transcripts
tcofoegbu [Fri, 26 Feb 2016 14:26:46 +0000 (14:26 +0000)]
develop merge
tcofoegbu [Fri, 26 Feb 2016 14:18:43 +0000 (14:18 +0000)]
JAL-2009 reverted 'RES NUM' feature back to 'RESNUM'
tcofoegbu [Fri, 26 Feb 2016 10:55:02 +0000 (10:55 +0000)]
JAL-1994 updated implementation for broken tests
tcofoegbu [Fri, 26 Feb 2016 10:41:27 +0000 (10:41 +0000)]
JAL-1994 fix for broken tests
tcofoegbu [Thu, 25 Feb 2016 16:50:05 +0000 (16:50 +0000)]
JAL-1919 initial support for mmCIF using JMol API. Created an Abstract class - StructureFile and refactored PDBfile class and JmolParser class to extend from it.
gmungoc [Thu, 25 Feb 2016 16:14:57 +0000 (16:14 +0000)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
tcofoegbu [Tue, 23 Feb 2016 10:06:19 +0000 (10:06 +0000)]
develop merge
tcofoegbu [Tue, 23 Feb 2016 10:03:34 +0000 (10:03 +0000)]
JAL-1720 renamed Structure Chooser filters according to suggestions from Jim. Also made improvements which enables automatic listing of selected filter meta-data in the summary table
tcofoegbu [Mon, 22 Feb 2016 17:12:36 +0000 (17:12 +0000)]
JAL-1720 JAL-2002 improvement for 'uniprot coverage' filter using facet pivot query
tcofoegbu [Mon, 22 Feb 2016 15:38:01 +0000 (15:38 +0000)]
JAL-1944 bugfix for error when exporting hidden sequences but not hidden columns
gmungoc [Mon, 22 Feb 2016 14:32:42 +0000 (14:32 +0000)]
JAL-1705 first pass at applying preset feature colouring for EnsemblGene
gmungoc [Sat, 20 Feb 2016 14:00:13 +0000 (14:00 +0000)]
Merge branch 'mungo_develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Sat, 20 Feb 2016 13:55:43 +0000 (13:55 +0000)]
Merge branch 'JAL-1956_featureStyles' into features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Sat, 20 Feb 2016 13:54:56 +0000 (13:54 +0000)]
JAL-2016 first draft of pre-set feature colour scheme
gmungoc [Sat, 20 Feb 2016 13:05:48 +0000 (13:05 +0000)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Fri, 19 Feb 2016 17:00:55 +0000 (17:00 +0000)]
JAL-1705 handle case of sequence with no dataset sequence
gmungoc [Fri, 19 Feb 2016 17:00:19 +0000 (17:00 +0000)]
JAL-1705 regular expression updates, tests, other refactoring
gmungoc [Fri, 19 Feb 2016 16:59:42 +0000 (16:59 +0000)]
JAL-1705 updated for change to CrossRef signature
gmungoc [Fri, 19 Feb 2016 16:58:45 +0000 (16:58 +0000)]
JAL-1705 refactor show products, set initial split frame divider
gmungoc [Fri, 19 Feb 2016 16:51:48 +0000 (16:51 +0000)]
JAL-1705 more lenient test for 'sequence retrieved'
gmungoc [Fri, 19 Feb 2016 16:49:46 +0000 (16:49 +0000)]
JAL-1705 return Ensembl genes for model species for a gene name
gmungoc [Fri, 19 Feb 2016 16:46:01 +0000 (16:46 +0000)]
JAL-1705 JAL-1191 more terms added to hard-coded version
gmungoc [Fri, 19 Feb 2016 16:45:10 +0000 (16:45 +0000)]
JAL-1706 reverted setting start position as too confusing for -ve strand
gmungoc [Fri, 19 Feb 2016 16:42:34 +0000 (16:42 +0000)]
JAL-1705 lenient DBRef matcher added (accession id only)
gmungoc [Fri, 19 Feb 2016 16:37:02 +0000 (16:37 +0000)]
JAL-1705 helper method for mapping excluding stop codon
tcofoegbu [Fri, 19 Feb 2016 15:57:10 +0000 (15:57 +0000)]
JAL-2009 Codes to enable storing inserted residues as features to their base residue position
git://source.jalview.org / jalview.git / log