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
gmungoc [Fri, 12 Feb 2016 16:58:15 +0000 (16:58 +0000)]
JAL-1270 remove trailing space + test
gmungoc [Fri, 12 Feb 2016 16:55:19 +0000 (16:55 +0000)]
JAL-1705 various refactoring towards Uniprot-to-Ensembl fetching
gmungoc [Fri, 12 Feb 2016 16:53:14 +0000 (16:53 +0000)]
JAL-1191 additions to SOLite, tweak to test
gmungoc [Fri, 12 Feb 2016 16:51:14 +0000 (16:51 +0000)]
JAL-1705 take feature ID for description if nothing better found
gmungoc [Fri, 12 Feb 2016 16:47:48 +0000 (16:47 +0000)]
JAL-282 wrap very long id in tooltip
gmungoc [Fri, 12 Feb 2016 16:42:34 +0000 (16:42 +0000)]
JAL-1705 JAL-1686 stronger SequenceFeature.equals() test
gmungoc [Fri, 12 Feb 2016 15:03:51 +0000 (15:03 +0000)]
JAL-2010 simple prototype of 'Highlight Selection' onto Chimera view
gmungoc [Fri, 12 Feb 2016 14:53:02 +0000 (14:53 +0000)]
JAL-2008 updates for String[] to List<String> change
gmungoc [Fri, 12 Feb 2016 14:51:28 +0000 (14:51 +0000)]
JAL-2008 avoid unnecessary repaints; signatures changed from String[] to
List<String>
gmungoc [Fri, 12 Feb 2016 14:37:11 +0000 (14:37 +0000)]
JAL-265 updated help text
gmungoc [Fri, 12 Feb 2016 14:11:34 +0000 (14:11 +0000)]
Merge branch 'develop' into
features/JAL-653_JAL-1766_htslib_refseqsupport
Conflicts:
resources/lang/Messages.properties
src/jalview/gui/FeatureColourChooser.java
tcofoegbu [Tue, 9 Feb 2016 16:57:16 +0000 (16:57 +0000)]
merge develop
tcofoegbu [Tue, 9 Feb 2016 13:11:08 +0000 (13:11 +0000)]
JAL-1976 catch and handle OOM Error
tcofoegbu [Tue, 9 Feb 2016 13:05:31 +0000 (13:05 +0000)]
JAL-1976 Added progress indicators for HTML_SVG and BioJS export operations
tcofoegbu [Tue, 9 Feb 2016 11:56:17 +0000 (11:56 +0000)]
JAL-1975 updated image export pipeline to produce more informative messages.
tcofoegbu [Tue, 9 Feb 2016 10:28:59 +0000 (10:28 +0000)]
JAL-1957 deleted stale comment
tcofoegbu [Tue, 9 Feb 2016 10:25:37 +0000 (10:25 +0000)]
merge
tcofoegbu [Tue, 9 Feb 2016 10:25:14 +0000 (10:25 +0000)]
JAL-1957 enabled multi-chain mapping and highlight for Chimera viewer
gmungoc [Fri, 5 Feb 2016 14:56:13 +0000 (14:56 +0000)]
JAL-2006 scale even very small score ranges to a usable threshold slider
gmungoc [Thu, 4 Feb 2016 15:26:24 +0000 (15:26 +0000)]
JAL-1544 spelling fix
gmungoc [Thu, 4 Feb 2016 14:49:17 +0000 (14:49 +0000)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Thu, 4 Feb 2016 14:41:35 +0000 (14:41 +0000)]
JAL-2005 added (stable) sort methods parameterised by
ascending/descending
gmungoc [Thu, 4 Feb 2016 14:02:16 +0000 (14:02 +0000)]
JAL-599 bug fixed so array of visible types is populated
gmungoc [Thu, 4 Feb 2016 10:29:42 +0000 (10:29 +0000)]
JAL-1705 temporary variable to aid inspection in debugger
gmungoc [Thu, 4 Feb 2016 10:29:09 +0000 (10:29 +0000)]
JAL-1705 additional tests, validation regexp tweaks, javadoc
gmungoc [Thu, 4 Feb 2016 10:28:29 +0000 (10:28 +0000)]
JAL-2003 export features on alignment, not alignment dataset
gmungoc [Mon, 1 Feb 2016 16:44:17 +0000 (16:44 +0000)]
JAL-1705 further unit tests
gmungoc [Mon, 1 Feb 2016 12:54:13 +0000 (12:54 +0000)]
JAL-1705 set Uniprot xref as 'source dbref' (for SIFTS mapping)
gmungoc [Mon, 1 Feb 2016 12:53:46 +0000 (12:53 +0000)]
JAL-1191 more terms added to SequenceOntologyLite
gmungoc [Mon, 1 Feb 2016 10:23:29 +0000 (10:23 +0000)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Mon, 1 Feb 2016 10:18:03 +0000 (10:18 +0000)]
JAL-1705 tests added
gmungoc [Mon, 1 Feb 2016 10:17:49 +0000 (10:17 +0000)]
JAL-1705 JAL-1191 SequenceOntologyLite added as hard-coded alternative
gmungoc [Sat, 30 Jan 2016 06:33:01 +0000 (06:33 +0000)]
JAL-1705 refactored cross-reference fetching (CCDS, Uniprot, PDB)
tcofoegbu [Fri, 29 Jan 2016 16:52:55 +0000 (16:52 +0000)]
merge from develop
tcofoegbu [Fri, 29 Jan 2016 16:24:29 +0000 (16:24 +0000)]
JAL-1979 refactor out duplicated similar block of code in StructureSelectionManger to a single method
gmungoc [Fri, 29 Jan 2016 16:11:36 +0000 (16:11 +0000)]
JAL-1705 fetch Uniprot and PDB xrefs for Ensembl protein products
gmungoc [Fri, 29 Jan 2016 16:10:56 +0000 (16:10 +0000)]
JAL-1705 copy feature settings when opening a split frame for show
product
gmungoc [Thu, 28 Jan 2016 16:44:10 +0000 (16:44 +0000)]
JAL-1705 more correct title (CDS not cDNA) on split frame
gmungoc [Thu, 28 Jan 2016 16:43:51 +0000 (16:43 +0000)]
JAL-1705 refine feature copying to including 5' and 3' overlaps
gmungoc [Thu, 28 Jan 2016 15:00:17 +0000 (15:00 +0000)]
JAL-1705 tests added, minor bugfix and refactoring
gmungoc [Thu, 28 Jan 2016 12:07:40 +0000 (12:07 +0000)]
Merge branch 'develop' into JAL-1705_trialMerge
Conflicts:
src/jalview/analysis/AlignmentUtils.java
src/jalview/analysis/CrossRef.java
src/jalview/structure/StructureSelectionManager.java
src/jalview/ws/dbsources/Uniprot.java
test/jalview/analysis/AlignmentUtilsTests.java
test/jalview/util/MappingUtilsTest.java
test/jalview/ws/seqfetcher/DbRefFetcherTest.java
gmungoc [Thu, 28 Jan 2016 10:17:03 +0000 (10:17 +0000)]
JAL-1551 wrap enum declarations
gmungoc [Thu, 28 Jan 2016 09:39:21 +0000 (09:39 +0000)]
JAL-1705 merge contiguous ranges when constructing a MapList (e.g. for
exons in cDNA)
gmungoc [Wed, 27 Jan 2016 16:57:11 +0000 (16:57 +0000)]
JAL-1705 add exon name to features and render on peptide (to show
boundaries)
tcofoegbu [Wed, 27 Jan 2016 12:24:27 +0000 (12:24 +0000)]
JAL-1479 fixed off-by-one error in SIFTS mapping output and added the flag 'isGetEntityIdDirectly' to control how an entity to process is determined.
gmungoc [Wed, 27 Jan 2016 11:59:35 +0000 (11:59 +0000)]
JAL-1705 use GET for single queries; set gene name as description on
transcript
gmungoc [Tue, 26 Jan 2016 16:36:03 +0000 (16:36 +0000)]
JAL-1705 derive transcript sequences from gene sequence/GFF; handle CDS
phase != 0
tcofoegbu [Tue, 26 Jan 2016 14:28:31 +0000 (14:28 +0000)]
develop merge
tcofoegbu [Tue, 26 Jan 2016 12:56:22 +0000 (12:56 +0000)]
JAL-1999 JAL-1479 implemented configurable fail-safe mechanism for SIFTS mapping based on a PID threshold. Also added config threshold parameter for auto-computing time-based caching of downloaded SIFTS
tcofoegbu [Mon, 25 Jan 2016 15:06:26 +0000 (15:06 +0000)]
JAL-1998 bugfix for division by zero error for PDB entries with chain(s) consisiting of a single residue
gmungoc [Mon, 25 Jan 2016 10:45:02 +0000 (10:45 +0000)]
JAL-1705 EnsemblGene added, and related refactoring
gmungoc [Mon, 25 Jan 2016 10:43:06 +0000 (10:43 +0000)]
JAL-1997 database browser support tooltip if available
gmungoc [Sat, 23 Jan 2016 06:15:20 +0000 (06:15 +0000)]
JAL-1355 get dialog title from message bundle
gmungoc [Sat, 23 Jan 2016 06:13:18 +0000 (06:13 +0000)]
JAL-1705 copy 'show sequence features' setting in 'show products'
gmungoc [Sat, 23 Jan 2016 06:12:13 +0000 (06:12 +0000)]
JAL-1705 todo comment re writing DBRefEntry/SequenceFeature to dataset
gmungoc [Sat, 23 Jan 2016 06:11:30 +0000 (06:11 +0000)]
JAL-1705 compute peptide variants from dna; add "consequence" feature on
CDS
tcofoegbu [Thu, 21 Jan 2016 17:00:16 +0000 (17:00 +0000)]
JAL-1479 JAL-1979 bugfix to check entire annotation property of a resDetail object for NOT_OBSERVED rather than just the topmost value. Intially thought the multiplicity was 0..1 rather than 0..* which it turned out to be following the N2NScan test
gmungoc [Thu, 21 Jan 2016 16:25:55 +0000 (16:25 +0000)]
JAL-1705 transfer features to the dataset sequence if there is one
gmungoc [Thu, 21 Jan 2016 16:01:19 +0000 (16:01 +0000)]
JAL-1705 reworked Ensembl clients now fetching and mapping features &
peptide
gmungoc [Thu, 21 Jan 2016 15:58:15 +0000 (15:58 +0000)]
JAL-653 refactor / tidy
gmungoc [Thu, 21 Jan 2016 15:57:43 +0000 (15:57 +0000)]
JAL-653 JAL-1705 set strand for GFF sequence feature
gmungoc [Thu, 21 Jan 2016 15:56:06 +0000 (15:56 +0000)]
JAL-1705 removed (only) usage of otherwise unused constant
gmungoc [Thu, 21 Jan 2016 15:55:20 +0000 (15:55 +0000)]
JAL-653 comments/javadoc tidy only
gmungoc [Thu, 21 Jan 2016 15:49:08 +0000 (15:49 +0000)]
JAL-1796 parse ensembl genomic coordinates to set start position
gmungoc [Thu, 21 Jan 2016 15:33:18 +0000 (15:33 +0000)]
JAL-1705 AlignmentUtils method renamed
gmungoc [Thu, 21 Jan 2016 15:31:11 +0000 (15:31 +0000)]
JAL-1705 ENSEMBL added, unused constants removed
gmungoc [Thu, 21 Jan 2016 15:23:20 +0000 (15:23 +0000)]
JAL-1705 features transferred to CDS sequence; makeExon renamed makeCds
gmungoc [Thu, 21 Jan 2016 15:20:43 +0000 (15:20 +0000)]
JAL-1705 redundant comment removed
gmungoc [Thu, 21 Jan 2016 15:18:59 +0000 (15:18 +0000)]
JAL-1705 suppress jvsuffix (for sequence id matching to work)
gmungoc [Thu, 21 Jan 2016 15:18:13 +0000 (15:18 +0000)]
JAL-1705 unused import removed
gmungoc [Thu, 21 Jan 2016 15:17:12 +0000 (15:17 +0000)]
JAL-1705 include dummy sequences in returned alignment
tcofoegbu [Thu, 21 Jan 2016 14:59:40 +0000 (14:59 +0000)]
JAL-1479 JAL-1979 updated the modified-aminoacid triplet code dictionary in Jalview using data from SCOP/PDB provided by Fabio
gmungoc [Thu, 21 Jan 2016 14:56:27 +0000 (14:56 +0000)]
JAL-1705 tidy and todo comment, no functional change
gmungoc [Thu, 21 Jan 2016 14:54:41 +0000 (14:54 +0000)]
JAL-1705 tests for amended toString
git://source.jalview.org / jalview.git / log