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)
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
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
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
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
gmungoc [Thu, 21 Jan 2016 14:44:15 +0000 (14:44 +0000)]
JAL-1705 added isSequenceVariant(), commonly used SO terms as constants
gmungoc [Thu, 21 Jan 2016 14:40:17 +0000 (14:40 +0000)]
JAL-1705 isFromForwardStrand added; toString (for debug) tweaked
gmungoc [Thu, 21 Jan 2016 14:38:21 +0000 (14:38 +0000)]
JAL-1705 canonicalise ENSEMBL name; code tidy
gmungoc [Thu, 21 Jan 2016 14:34:54 +0000 (14:34 +0000)]
JAL-1705 get xrefs only for dna/peptide; code tidy
gmungoc [Thu, 21 Jan 2016 14:30:31 +0000 (14:30 +0000)]
JAL-1705 toString() added (for debugging)
gmungoc [Thu, 21 Jan 2016 14:29:42 +0000 (14:29 +0000)]
JAL-1705 isEmpty() and (debug) toString() methods added
gmungoc [Tue, 12 Jan 2016 08:58:01 +0000 (08:58 +0000)]
JAL-1191 cache isA (great-)grandparents as well for fast isA testing
gmungoc [Mon, 11 Jan 2016 14:58:24 +0000 (14:58 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Mon, 11 Jan 2016 12:37:52 +0000 (12:37 +0000)]
JAL-1989 additional ways to 'mirror' show/hide columns in split frame
tcofoegbu [Mon, 11 Jan 2016 12:37:07 +0000 (12:37 +0000)]
JAL-1990 added a progress indicator for Structure Chooser interface
tcofoegbu [Mon, 11 Jan 2016 11:18:30 +0000 (11:18 +0000)]
merge
tcofoegbu [Mon, 11 Jan 2016 11:16:03 +0000 (11:16 +0000)]
JAL-1991 bug fix for some flat-file printers to check for exact modulus in order to avoid outputing an extra redundant header line with empty sequences
gmungoc [Mon, 11 Jan 2016 11:04:40 +0000 (11:04 +0000)]
JAL-1989 map hidden column ranges
gmungoc [Mon, 11 Jan 2016 11:03:50 +0000 (11:03 +0000)]
JAL-1989 more unit tests and encapsulation for ColumnSelection
gmungoc [Mon, 11 Jan 2016 10:51:36 +0000 (10:51 +0000)]
JAL-1544 "more than" not "more that"
gmungoc [Fri, 8 Jan 2016 10:03:40 +0000 (10:03 +0000)]
JAL-1705 DbSourceProxy properties converted to methods, tidy/format code
tcofoegbu [Thu, 7 Jan 2016 14:51:48 +0000 (14:51 +0000)]
merge
tcofoegbu [Thu, 7 Jan 2016 14:50:06 +0000 (14:50 +0000)]
JAL-1479 implemented timestamp based caching of SIFTS by providing code which checks if an already downloaded SIFTS file has exceeded a certain threshold upon processing. Also added a method to handle SIFTS entries for cases when an 'entityId' is NOT EQUAL TO 'chainId', this is a heuristic measure achieved using greedy search.
gmungoc [Tue, 5 Jan 2016 13:40:12 +0000 (13:40 +0000)]
JAL-653 updating 'align as' tests to match latest tweaks to algorithm
gmungoc [Tue, 5 Jan 2016 13:09:44 +0000 (13:09 +0000)]
Merge remote-tracking branch 'origin/features/JAL-1705_ensembl' into
features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Tue, 5 Jan 2016 10:15:22 +0000 (10:15 +0000)]
JAL-653 typed map for feature colours in method signature
gmungoc [Tue, 5 Jan 2016 10:12:09 +0000 (10:12 +0000)]
JAL-1191 check for obsolete term when descriptions are duplicated
gmungoc [Wed, 23 Dec 2015 09:48:26 +0000 (09:48 +0000)]
JAL-1191 unzipped OBO file removed
gmungoc [Wed, 23 Dec 2015 09:47:52 +0000 (09:47 +0000)]
JAL-1191 zipped SO OBO file added to /resources, more tests added
gmungoc [Tue, 22 Dec 2015 16:24:02 +0000 (16:24 +0000)]
JAL-1191 more test cases
gmungoc [Tue, 22 Dec 2015 16:01:20 +0000 (16:01 +0000)]
JAL-1191 and provide the SO OBO file in /resources :-)
gmungoc [Tue, 22 Dec 2015 15:49:33 +0000 (15:49 +0000)]
JAL-1191 SequenceOntology wrapping/caching SO.OBO via BioJava library
gmungoc [Tue, 22 Dec 2015 09:28:04 +0000 (09:28 +0000)]
JAL-1191 stub class for a SequenceOntology wrapper
gmungoc [Tue, 22 Dec 2015 09:24:49 +0000 (09:24 +0000)]
JAL-1551 don't autoformat /* comments */
gmungoc [Tue, 22 Dec 2015 09:22:57 +0000 (09:22 +0000)]
JAL-1421 parameterised map constructor used
gmungoc [Tue, 22 Dec 2015 09:21:58 +0000 (09:21 +0000)]
JAL-653 encapsulate Strand, Attributes, Status of SequenceFeature
gmungoc [Tue, 22 Dec 2015 09:21:22 +0000 (09:21 +0000)]
JAL-653 realise virtual mappings and align when adding sequences
gmungoc [Tue, 22 Dec 2015 09:15:40 +0000 (09:15 +0000)]
JAL-391 new Calculate options to Reverse, Reverse Complement nucleotide
gmungoc [Tue, 22 Dec 2015 09:14:08 +0000 (09:14 +0000)]
JAL-653 AlignedCodonFrame collections changed from Set to List
gmungoc [Tue, 22 Dec 2015 09:11:48 +0000 (09:11 +0000)]
JAL-653 set showSequenceFeatures=true on loading a FeaturesSourceI
gmungoc [Tue, 22 Dec 2015 09:10:07 +0000 (09:10 +0000)]
JAL-653 GFF new/refactored helper classes
gmungoc [Tue, 22 Dec 2015 09:03:03 +0000 (09:03 +0000)]
JAL-653 AlignedCodonFrame internal refactor, merge ranges with
MapList.addMapList
gmungoc [Tue, 22 Dec 2015 08:58:50 +0000 (08:58 +0000)]
JAL-653 hold AlignedCodonFrame collections as list rather than set
Jim Procter [Wed, 9 Dec 2015 16:03:51 +0000 (16:03 +0000)]
JAL-1982 hotfix to prevent NPE with applet launch on Jpred4 site
gmungoc [Thu, 3 Dec 2015 16:27:57 +0000 (16:27 +0000)]
JAL-653 code tidy / tests for 'realise gff mappings'
gmungoc [Thu, 3 Dec 2015 16:26:51 +0000 (16:26 +0000)]
JAL-653 handle reverse strand mapping in SearchResults matches
gmungoc [Thu, 3 Dec 2015 16:26:08 +0000 (16:26 +0000)]
JAL-653 mappings always reside on the dataset alignment if there is one
gmungoc [Thu, 3 Dec 2015 14:46:53 +0000 (14:46 +0000)]
JAL-653 handle reverse strand mappings also
gmungoc [Thu, 3 Dec 2015 10:05:22 +0000 (10:05 +0000)]
JAL-1827 code and comment tidy up
gmungoc [Wed, 2 Dec 2015 16:52:41 +0000 (16:52 +0000)]
JAL-1827 refactored to handle missing residues better
gmungoc [Wed, 2 Dec 2015 16:43:32 +0000 (16:43 +0000)]
JAL-1827 added overloaded method for convenience
gmungoc [Wed, 2 Dec 2015 16:42:23 +0000 (16:42 +0000)]
JAL-1827 reverted text on generic sequence fetcher to not refer to PDB
gmungoc [Mon, 30 Nov 2015 10:05:57 +0000 (10:05 +0000)]
JAL-1421 generics loop syntax; 'bug?' comment added
gmungoc [Mon, 30 Nov 2015 10:04:40 +0000 (10:04 +0000)]
JAL-653 test for 'resolving GFF mappings to sequences' (wip)
gmungoc [Mon, 30 Nov 2015 10:03:15 +0000 (10:03 +0000)]
JAL-653 small comment change only
gmungoc [Mon, 30 Nov 2015 09:51:08 +0000 (09:51 +0000)]
JAL-652 refactored to remove one method
gmungoc [Mon, 30 Nov 2015 09:33:36 +0000 (09:33 +0000)]
JAL-653 (experimental) 'realise' dummy sequences in add alignment
gmungoc [Mon, 30 Nov 2015 09:31:51 +0000 (09:31 +0000)]
JAL-1980 check for null alignment; JAL-1551 @Override's added
gmungoc [Mon, 30 Nov 2015 09:30:20 +0000 (09:30 +0000)]
JAL-653 (experimental) methods to resolve dummy to real sequence
gmungoc [Mon, 30 Nov 2015 09:28:43 +0000 (09:28 +0000)]
JAL-1270 constructor test added
gmungoc [Mon, 30 Nov 2015 09:27:47 +0000 (09:27 +0000)]
JAL-653 getStrand javadoc/refactor/test
gmungoc [Mon, 30 Nov 2015 09:19:11 +0000 (09:19 +0000)]
JAL-1421 use generics JAL-1551 @Override annotations added
gmungoc [Mon, 30 Nov 2015 09:16:49 +0000 (09:16 +0000)]
JAL-1270 constructor tests added, compiler warnings removed
gmungoc [Mon, 30 Nov 2015 09:14:34 +0000 (09:14 +0000)]
JAL-652 further refactoring / tests
gmungoc [Mon, 30 Nov 2015 09:11:48 +0000 (09:11 +0000)]
JAL-652 correct case for test file name
gmungoc [Mon, 30 Nov 2015 09:10:47 +0000 (09:10 +0000)]
JAL-653 MapList constructor merges any contiguous ranges
tcofoegbu [Wed, 25 Nov 2015 15:29:41 +0000 (15:29 +0000)]
JAL-1479 refactored DBRef fetching code to StructureChooser to enable applet build
tcofoegbu [Wed, 25 Nov 2015 15:13:40 +0000 (15:13 +0000)]
JAL-1479 applet build debug
tcofoegbu [Wed, 25 Nov 2015 14:24:04 +0000 (14:24 +0000)]
JAL-1479 bugfix after decoupling SIFTS preference settings
tcofoegbu [Mon, 23 Nov 2015 18:04:25 +0000 (18:04 +0000)]
JAL-1479 commented out DBRef fetching code from SIFTS to test applet build
gmungoc [Mon, 23 Nov 2015 10:16:13 +0000 (10:16 +0000)]
JAL-653 Gff tests moved back in to FeaturesFileTest
gmungoc [Sun, 22 Nov 2015 18:24:26 +0000 (18:24 +0000)]
JAL-653 test for 'groups file' and mixed Jalview/GFF
gmungoc [Sat, 21 Nov 2015 19:33:37 +0000 (19:33 +0000)]
JAL-1968 remove feature links
gmungoc [Sat, 21 Nov 2015 19:24:24 +0000 (19:24 +0000)]
JAL-653 JAL-1968 FeaturesFile now handles Jalview or GFF2 or GFF3
(partially); feature links option removed
git://source.jalview.org / jalview.git / log