Jim Procter [Tue, 5 Apr 2016 17:30:57 +0000 (18:30 +0100)]
JAL-2046 explicit contract for get/set SequenceFeatures on SequenceI
Jim Procter [Tue, 5 Apr 2016 17:26:23 +0000 (18:26 +0100)]
JAL-2046 remove javadoc
Jim Procter [Tue, 5 Apr 2016 17:25:27 +0000 (18:25 +0100)]
JAL-2046 simpler deriveSequence - promote to dataset and initSeqFrom or defer to copy constructor
Jim Procter [Tue, 5 Apr 2016 17:17:03 +0000 (18:17 +0100)]
JAL-2046 clarify contract for copy constructor and initSeqFrom implementation
- with existing dataset sequence reference, no sequence features are cloned
Jim Procter [Tue, 5 Apr 2016 17:14:42 +0000 (18:14 +0100)]
JAL-2046 explicitly copy char[] when cloning sequence data for copy-constructor/deriveSequence
Jim Procter [Tue, 5 Apr 2016 17:12:59 +0000 (18:12 +0100)]
JAL-2046 safer createDatasetSequence manipulates private fields and moves sequenceFeatures to dataset
Jim Procter [Mon, 4 Apr 2016 16:02:43 +0000 (17:02 +0100)]
JAL-2046 basic test to make sure any derived sequence has a null sequence feature array
Jim Procter [Mon, 4 Apr 2016 15:15:07 +0000 (16:15 +0100)]
Merge branch 'optimisation/JAL-2001' into develop
Jim Procter [Mon, 4 Apr 2016 15:13:21 +0000 (16:13 +0100)]
JAL-2001 drop isSelected(int) in favour of original ‘contains(int)’ method
Jim Procter [Mon, 4 Apr 2016 15:12:48 +0000 (16:12 +0100)]
JAL-2001 catch -ve column values
(fixes failing test jalview.util.MappingUtilsTest.testMapColumnSelection)
Jim Procter [Mon, 4 Apr 2016 14:49:37 +0000 (15:49 +0100)]
JAL-2001 TODO for new ColumnSelection API
Jim Procter [Mon, 4 Apr 2016 14:49:02 +0000 (15:49 +0100)]
JAL-1551 formatting
Jim Procter [Mon, 4 Apr 2016 14:48:42 +0000 (15:48 +0100)]
JAL-2001 - note about possible side effect on JalviewLite.selectIn due to refactored columnSelection - maybe need a test here
Jim Procter [Mon, 4 Apr 2016 14:45:09 +0000 (15:45 +0100)]
JAL-2010 refactoring todo
Jim Procter [Mon, 4 Apr 2016 14:23:52 +0000 (15:23 +0100)]
JAL-2001 use fast column selection test
Jim Procter [Mon, 4 Apr 2016 14:22:56 +0000 (15:22 +0100)]
JAL-969 refactor columnselection operation (during JAL-2001)
Jim Procter [Mon, 4 Apr 2016 14:21:04 +0000 (15:21 +0100)]
JAL-2001 faster check for a column being selected
TODO: consider deprecate Integer variant ?
Jim Procter [Mon, 4 Apr 2016 14:19:52 +0000 (15:19 +0100)]
JAL-2001 javadoc
Jim Procter [Mon, 4 Apr 2016 14:19:27 +0000 (15:19 +0100)]
JAL-2001 faster getMax/getMin selected column, with tests
Jim Procter [Mon, 4 Apr 2016 13:13:08 +0000 (14:13 +0100)]
JAL-2001 JAL-1722 - store selection as ArrayList and BitSet for fast addition of very large numbers of columns - all tests pass but needs verification
gmungoc [Fri, 1 Apr 2016 20:02:08 +0000 (21:02 +0100)]
Merge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport' into develop
gmungoc [Fri, 1 Apr 2016 20:00:26 +0000 (21:00 +0100)]
JAL-1705 ensure the right mapping is used to align CDS to cDNA
tcofoegbu [Fri, 1 Apr 2016 16:03:12 +0000 (17:03 +0100)]
JAL-2048 Update to structureviz2 package from cytoscape
gmungoc [Fri, 1 Apr 2016 15:52:19 +0000 (16:52 +0100)]
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
gmungoc [Fri, 1 Apr 2016 15:46:53 +0000 (16:46 +0100)]
JAL-2046 fix for broken test for deriveSequence
gmungoc [Fri, 1 Apr 2016 15:46:20 +0000 (16:46 +0100)]
JAL-1705 reworked AlignmentUtils.makeCdsAlignment and associated code
gmungoc [Fri, 1 Apr 2016 10:57:02 +0000 (11:57 +0100)]
JAL-653 updated test to match parsing of multi-valued GFF attribute
gmungoc [Fri, 1 Apr 2016 10:51:02 +0000 (11:51 +0100)]
JAL-1705 tweak to MapList.toString for debugging
gmungoc [Fri, 1 Apr 2016 10:44:04 +0000 (11:44 +0100)]
JAL-1705 generalised getLength() to handle [start1, end1, start2,
end2..]
gmungoc [Fri, 1 Apr 2016 10:42:08 +0000 (11:42 +0100)]
JAL-1705 test updated for canonicalised UNIPROT sequence name
gmungoc [Fri, 1 Apr 2016 10:34:58 +0000 (11:34 +0100)]
JAL-1705 include stop codon in mapped CDS range so it is included in the
generated CDS sequence
gmungoc [Fri, 1 Apr 2016 10:33:33 +0000 (11:33 +0100)]
JAL-2037 set DBRefEntry.version to "0" not "" in EMBL xrefs
gmungoc [Fri, 1 Apr 2016 10:26:16 +0000 (11:26 +0100)]
JAL-1705 fetch all Ensembl xrefs (except GO terms)
tcofoegbu [Fri, 1 Apr 2016 10:07:14 +0000 (11:07 +0100)]
JAL-2045 JAL-2047 improvement for sorting PDB quality measure numerically, and improvment to make PDB Search and Structure Chooser table column rendering smarter
tcofoegbu [Thu, 31 Mar 2016 11:36:25 +0000 (12:36 +0100)]
JAL-2035 improvement to add binding to multiple model
tcofoegbu [Wed, 30 Mar 2016 15:47:44 +0000 (16:47 +0100)]
JAL-1668 further clean-up of popup menu and NPE check while transfering ResNum features in PDBChain
tcofoegbu [Wed, 30 Mar 2016 10:14:06 +0000 (11:14 +0100)]
JAL-2038 bug fix for NPE while setting progress message during d'n'd PDB files association
tcofoegbu [Mon, 28 Mar 2016 14:37:00 +0000 (15:37 +0100)]
merge
tcofoegbu [Mon, 28 Mar 2016 13:16:17 +0000 (14:16 +0100)]
JAL-1919 Fixed broken test in DBRefUtilsTest
tcofoegbu [Mon, 28 Mar 2016 13:13:25 +0000 (14:13 +0100)]
JAL-1668 removed redundant UI elements in PopupMenu class associated with the old structure selection mechanism
gmungoc [Mon, 28 Mar 2016 09:12:36 +0000 (10:12 +0100)]
JAL-1705 Javadoc / debug output tweaks
gmungoc [Mon, 28 Mar 2016 09:02:46 +0000 (10:02 +0100)]
JAL-2016 push getFeatureColourScheme(source) into SequenceFetcher
gmungoc [Mon, 28 Mar 2016 08:47:54 +0000 (09:47 +0100)]
JAL-2036 update AlignFrame menus when dbreffetcher is complete
tcofoegbu [Fri, 25 Mar 2016 16:12:42 +0000 (16:12 +0000)]
JAL-2035 improvement to bind Jalview to Chimera model when opening an mmCIF file
tcofoegbu [Thu, 24 Mar 2016 16:08:59 +0000 (16:08 +0000)]
JAL-1919 Settings to disable duplicate generation of sequence features via reflection
tcofoegbu [Thu, 24 Mar 2016 15:56:55 +0000 (15:56 +0000)]
JAL-1479 Commented out debug sysout's for SiftsClient
tcofoegbu [Thu, 24 Mar 2016 15:55:28 +0000 (15:55 +0000)]
JAL-1919 Added ability to generate temprature factor annotation via JmolParser
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
git://source.jalview.org / jalview.git / log