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2016-04-12	gmungoc	JAL-2050 only hide introns if exons are present! Removed...	commit \| commitdiff \| tree
2016-04-12	gmungoc	JAL-2049 separate protein variant per dna variant ...	commit \| commitdiff \| tree
2016-04-11	gmungoc	JAL-1705 code/comment tidy only	commit \| commitdiff \| tree
2016-04-11	gmungoc	JAL-2051 fetch Ensembl Gene accessions one at a time	commit \| commitdiff \| tree
2016-04-11	gmungoc	JAL-391 help for reverse / complement options	commit \| commitdiff \| tree
2016-04-11	gmungoc	JAL-1705 (new preference option to) hide introns when...	commit \| commitdiff \| tree
2016-04-01	gmungoc	Merge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport...	commit \| commitdiff \| tree
2016-04-01	gmungoc	JAL-1705 ensure the right mapping is used to align...	commit \| commitdiff \| tree
2016-04-01	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...	commit \| commitdiff \| tree
2016-04-01	gmungoc	JAL-2046 fix for broken test for deriveSequence	commit \| commitdiff \| tree
2016-04-01	gmungoc	JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...	commit \| commitdiff \| tree
2016-04-01	gmungoc	JAL-653 updated test to match parsing of multi-valued...	commit \| commitdiff \| tree
2016-04-01	gmungoc	JAL-1705 tweak to MapList.toString for debugging	commit \| commitdiff \| tree
2016-04-01	gmungoc	JAL-1705 generalised getLength() to handle [start1...	commit \| commitdiff \| tree
2016-04-01	gmungoc	JAL-1705 test updated for canonicalised UNIPROT sequence...	commit \| commitdiff \| tree
2016-04-01	gmungoc	JAL-1705 include stop codon in mapped CDS range so...	commit \| commitdiff \| tree
2016-04-01	gmungoc	JAL-2037 set DBRefEntry.version to "0" not "" in EMBL...	commit \| commitdiff \| tree
2016-04-01	gmungoc	JAL-1705 fetch all Ensembl xrefs (except GO terms)	commit \| commitdiff \| tree
2016-03-28	gmungoc	JAL-1705 Javadoc / debug output tweaks	commit \| commitdiff \| tree
2016-03-28	gmungoc	JAL-2016 push getFeatureColourScheme(source) into SequenceFe...	commit \| commitdiff \| tree
2016-03-28	gmungoc	JAL-2036 update AlignFrame menus when dbreffetcher...	commit \| commitdiff \| tree
2016-03-24	gmungoc	JAL-1705 removed experimental 'highlight selection...	commit \| commitdiff \| tree
2016-03-24	gmungoc	JAL-2032 structure follow mouseover in a copy of a...	commit \| commitdiff \| tree
2016-03-23	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-03-23	gmungoc	JAL-1705 add DBRefEntry for 'self' to retrieved transcripts...	commit \| commitdiff \| tree
2016-03-23	gmungoc	JAL-1997 default empty tooltip required for correct...	commit \| commitdiff \| tree
2016-03-22	gmungoc	Merge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport...	commit \| commitdiff \| tree
2016-03-22	gmungoc	JAL-1705 add xref seqs to 'parent' dataset only if...	commit \| commitdiff \| tree
2016-03-22	gmungoc	JAL-1191 isolated SequenceOntology (BioJava wrapper...	commit \| commitdiff \| tree
2016-03-22	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-03-21	gmungoc	Merge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport...	commit \| commitdiff \| tree
2016-03-21	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-03-21	gmungoc	JAL-2029 further fixes to get correct xrefs and xrefs...	commit \| commitdiff \| tree
2016-03-21	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...	commit \| commitdiff \| tree
2016-03-21	gmungoc	JAL-1855 dbfetch from /ena_sequence/, /ena_coding/	commit \| commitdiff \| tree
2016-03-21	gmungoc	JAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings	commit \| commitdiff \| tree
2016-03-16	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-03-16	gmungoc	JAL-1705 xref ENST to correct (ENSP) accession id	commit \| commitdiff \| tree
2016-03-15	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...	commit \| commitdiff \| tree
2016-03-15	gmungoc	JAL-2016 corrected Javadoc, added test for anonymous...	commit \| commitdiff \| tree
2016-03-15	gmungoc	JAL-2016 FeatureSettingsI now FeatureSettingsModelI	commit \| commitdiff \| tree
2016-03-15	gmungoc	JAL-1705 code tidy/comment only	commit \| commitdiff \| tree
2016-03-15	gmungoc	JAL-1705 compute reverse complement of variants on...	commit \| commitdiff \| tree
2016-03-11	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...	commit \| commitdiff \| tree
2016-03-11	gmungoc	JAL-1270 unit test for SequenceIdMatcher.SeqIdName	commit \| commitdiff \| tree
2016-03-11	gmungoc	JAL-1705 check Retry-After response header	commit \| commitdiff \| tree
2016-03-11	gmungoc	JAL-1705 javadoc added only	commit \| commitdiff \| tree
2016-03-11	gmungoc	JAL-1705 refactoring etc for fetching Ensembl --> Uniprot	commit \| commitdiff \| tree
2016-03-07	gmungoc	JAL-2023 CDS sequences added to / share alignment dataset	commit \| commitdiff \| tree
2016-03-04	gmungoc	JAL-1705 EnsemblGenomes a top level db source	commit \| commitdiff \| tree
2016-03-04	gmungoc	JAL-1705 parse 'description' from GFF as sequence description	commit \| commitdiff \| tree
2016-03-03	gmungoc	JAL-1705 unit test for aligning with incomplete start...	commit \| commitdiff \| tree
2016-03-03	gmungoc	JAL-1705 include stop codons in derived CDS; support...	commit \| commitdiff \| tree
2016-03-02	gmungoc	JAL-1705 include any unmapped protein start 'X' when...	commit \| commitdiff \| tree
2016-03-01	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...	commit \| commitdiff \| tree
2016-03-01	gmungoc	JAL-1705 align CDS to transcripts	commit \| commitdiff \| tree
2016-03-01	gmungoc	JAL-1705 align CDS and peptide products to transcripts	commit \| commitdiff \| tree
2016-02-25	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...	commit \| commitdiff \| tree
2016-02-22	gmungoc	JAL-1705 first pass at applying preset feature colouring...	commit \| commitdiff \| tree
2016-02-20	gmungoc	Merge branch 'mungo_develop' into features/JAL-653_JAL...	commit \| commitdiff \| tree
2016-02-20	gmungoc	Merge branch 'JAL-1956_featureStyles' into features...	commit \| commitdiff \| tree
2016-02-20	gmungoc	JAL-2016 first draft of pre-set feature colour scheme	commit \| commitdiff \| tree
2016-02-20	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...	commit \| commitdiff \| tree
2016-02-19	gmungoc	JAL-1705 handle case of sequence with no dataset sequence	commit \| commitdiff \| tree
2016-02-19	gmungoc	JAL-1705 regular expression updates, tests, other refactoring	commit \| commitdiff \| tree
2016-02-19	gmungoc	JAL-1705 updated for change to CrossRef signature	commit \| commitdiff \| tree
2016-02-19	gmungoc	JAL-1705 refactor show products, set initial split...	commit \| commitdiff \| tree
2016-02-19	gmungoc	JAL-1705 more lenient test for 'sequence retrieved'	commit \| commitdiff \| tree
2016-02-19	gmungoc	JAL-1705 return Ensembl genes for model species for...	commit \| commitdiff \| tree
2016-02-19	gmungoc	JAL-1705 JAL-1191 more terms added to hard-coded version	commit \| commitdiff \| tree
2016-02-19	gmungoc	JAL-1706 reverted setting start position as too confusing...	commit \| commitdiff \| tree
2016-02-19	gmungoc	JAL-1705 lenient DBRef matcher added (accession id...	commit \| commitdiff \| tree
2016-02-19	gmungoc	JAL-1705 helper method for mapping excluding stop codon	commit \| commitdiff \| tree
2016-02-12	gmungoc	JAL-1270 remove trailing space + test	commit \| commitdiff \| tree
2016-02-12	gmungoc	JAL-1705 various refactoring towards Uniprot-to-Ensembl...	commit \| commitdiff \| tree
2016-02-12	gmungoc	JAL-1191 additions to SOLite, tweak to test	commit \| commitdiff \| tree
2016-02-12	gmungoc	JAL-1705 take feature ID for description if nothing...	commit \| commitdiff \| tree
2016-02-12	gmungoc	JAL-282 wrap very long id in tooltip	commit \| commitdiff \| tree
2016-02-12	gmungoc	JAL-1705 JAL-1686 stronger SequenceFeature.equals(...	commit \| commitdiff \| tree
2016-02-12	gmungoc	JAL-2010 simple prototype of 'Highlight Selection'...	commit \| commitdiff \| tree
2016-02-12	gmungoc	JAL-2008 updates for String[] to List<String> change	commit \| commitdiff \| tree
2016-02-12	gmungoc	JAL-2008 avoid unnecessary repaints; signatures changed...	commit \| commitdiff \| tree
2016-02-12	gmungoc	JAL-265 updated help text	commit \| commitdiff \| tree
2016-02-12	gmungoc	Merge branch 'develop' into	commit \| commitdiff \| tree
2016-02-05	gmungoc	JAL-2006 scale even very small score ranges to a usable...	commit \| commitdiff \| tree
2016-02-04	gmungoc	JAL-1544 spelling fix	commit \| commitdiff \| tree
2016-02-04	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...	commit \| commitdiff \| tree
2016-02-04	gmungoc	JAL-2005 added (stable) sort methods parameterised by	commit \| commitdiff \| tree
2016-02-04	gmungoc	JAL-599 bug fixed so array of visible types is populated	commit \| commitdiff \| tree
2016-02-04	gmungoc	JAL-1705 temporary variable to aid inspection in debugger	commit \| commitdiff \| tree
2016-02-04	gmungoc	JAL-1705 additional tests, validation regexp tweaks...	commit \| commitdiff \| tree
2016-02-04	gmungoc	JAL-2003 export features on alignment, not alignment...	commit \| commitdiff \| tree
2016-02-01	gmungoc	JAL-1705 further unit tests	commit \| commitdiff \| tree
2016-02-01	gmungoc	JAL-1705 set Uniprot xref as 'source dbref' (for SIFTS...	commit \| commitdiff \| tree
2016-02-01	gmungoc	JAL-1191 more terms added to SequenceOntologyLite	commit \| commitdiff \| tree
2016-02-01	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...	commit \| commitdiff \| tree
2016-02-01	gmungoc	JAL-1705 tests added	commit \| commitdiff \| tree
2016-02-01	gmungoc	JAL-1705 JAL-1191 SequenceOntologyLite added as hard...	commit \| commitdiff \| tree
2016-01-30	gmungoc	JAL-1705 refactored cross-reference fetching (CCDS...	commit \| commitdiff \| tree
2016-01-29	gmungoc	JAL-1705 fetch Uniprot and PDB xrefs for Ensembl protein...	commit \| commitdiff \| tree
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