| 2016-04-14 |
gmungoc | JAL-1421 typed map / lists, explicit imports, method...
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commit | commitdiff | tree |
| 2016-04-14 |
gmungoc | JAL-2049 small refactor of constructors to avoid code...
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commit | commitdiff | tree |
| 2016-04-14 |
gmungoc | JAL-1421 type parameter added to some collections
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commit | commitdiff | tree |
| 2016-04-14 |
gmungoc | JAL-2049 revised computePeptideVariants to transfer...
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commit | commitdiff | tree |
| 2016-04-14 |
gmungoc | JAL-1705 refactored/utility methods to detect e.g....
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commit | commitdiff | tree |
| 2016-04-14 |
gmungoc | Merge branch 'develop' of https://source.jalview.org...
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commit | commitdiff | tree |
| 2016-04-14 |
gmungoc | JAL-653 test updated for 'use ID for description'
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commit | commitdiff | tree |
| 2016-04-14 |
gmungoc | JAL-1270 JAL-653 use 'parse immediately' FeaturesFile...
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commit | commitdiff | tree |
| 2016-04-12 |
gmungoc | JAL-2050 only hide introns if exons are present! Removed...
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commit | commitdiff | tree |
| 2016-04-12 |
gmungoc | JAL-2049 separate protein variant per dna variant ...
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commit | commitdiff | tree |
| 2016-04-11 |
gmungoc | JAL-1705 code/comment tidy only
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commit | commitdiff | tree |
| 2016-04-11 |
gmungoc | JAL-2051 fetch Ensembl Gene accessions one at a time
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commit | commitdiff | tree |
| 2016-04-11 |
gmungoc | JAL-391 help for reverse / complement options
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commit | commitdiff | tree |
| 2016-04-11 |
gmungoc | JAL-1705 (new preference option to) hide introns when...
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commit | commitdiff | tree |
| 2016-04-01 |
gmungoc | Merge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport...
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commit | commitdiff | tree |
| 2016-04-01 |
gmungoc | JAL-1705 ensure the right mapping is used to align...
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commit | commitdiff | tree |
| 2016-04-01 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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commit | commitdiff | tree |
| 2016-04-01 |
gmungoc | JAL-2046 fix for broken test for deriveSequence
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commit | commitdiff | tree |
| 2016-04-01 |
gmungoc | JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
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commit | commitdiff | tree |
| 2016-04-01 |
gmungoc | JAL-653 updated test to match parsing of multi-valued...
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commit | commitdiff | tree |
| 2016-04-01 |
gmungoc | JAL-1705 tweak to MapList.toString for debugging
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commit | commitdiff | tree |
| 2016-04-01 |
gmungoc | JAL-1705 generalised getLength() to handle [start1...
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commit | commitdiff | tree |
| 2016-04-01 |
gmungoc | JAL-1705 test updated for canonicalised UNIPROT sequence...
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commit | commitdiff | tree |
| 2016-04-01 |
gmungoc | JAL-1705 include stop codon in mapped CDS range so...
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commit | commitdiff | tree |
| 2016-04-01 |
gmungoc | JAL-2037 set DBRefEntry.version to "0" not "" in EMBL...
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commit | commitdiff | tree |
| 2016-04-01 |
gmungoc | JAL-1705 fetch all Ensembl xrefs (except GO terms)
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commit | commitdiff | tree |
| 2016-03-28 |
gmungoc | JAL-1705 Javadoc / debug output tweaks
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commit | commitdiff | tree |
| 2016-03-28 |
gmungoc | JAL-2016 push getFeatureColourScheme(source) into SequenceFe...
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commit | commitdiff | tree |
| 2016-03-28 |
gmungoc | JAL-2036 update AlignFrame menus when dbreffetcher...
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commit | commitdiff | tree |
| 2016-03-24 |
gmungoc | JAL-1705 removed experimental 'highlight selection...
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commit | commitdiff | tree |
| 2016-03-24 |
gmungoc | JAL-2032 structure follow mouseover in a copy of a...
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commit | commitdiff | tree |
| 2016-03-23 |
gmungoc | Merge branch 'develop' of https://source.jalview.org...
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commit | commitdiff | tree |
| 2016-03-23 |
gmungoc | JAL-1705 add DBRefEntry for 'self' to retrieved transcripts...
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commit | commitdiff | tree |
| 2016-03-23 |
gmungoc | JAL-1997 default empty tooltip required for correct...
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commit | commitdiff | tree |
| 2016-03-22 |
gmungoc | Merge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport...
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commit | commitdiff | tree |
| 2016-03-22 |
gmungoc | JAL-1705 add xref seqs to 'parent' dataset only if...
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commit | commitdiff | tree |
| 2016-03-22 |
gmungoc | JAL-1191 isolated SequenceOntology (BioJava wrapper...
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commit | commitdiff | tree |
| 2016-03-22 |
gmungoc | Merge branch 'develop' of https://source.jalview.org...
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commit | commitdiff | tree |
| 2016-03-21 |
gmungoc | Merge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport...
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commit | commitdiff | tree |
| 2016-03-21 |
gmungoc | Merge branch 'develop' of https://source.jalview.org...
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commit | commitdiff | tree |
| 2016-03-21 |
gmungoc | JAL-2029 further fixes to get correct xrefs and xrefs...
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commit | commitdiff | tree |
| 2016-03-21 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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commit | commitdiff | tree |
| 2016-03-21 |
gmungoc | JAL-1855 dbfetch from /ena_sequence/, /ena_coding/
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commit | commitdiff | tree |
| 2016-03-21 |
gmungoc | JAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings
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commit | commitdiff | tree |
| 2016-03-16 |
gmungoc | Merge branch 'develop' of https://source.jalview.org...
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commit | commitdiff | tree |
| 2016-03-16 |
gmungoc | JAL-1705 xref ENST to correct (ENSP) accession id
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commit | commitdiff | tree |
| 2016-03-15 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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commit | commitdiff | tree |
| 2016-03-15 |
gmungoc | JAL-2016 corrected Javadoc, added test for anonymous...
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commit | commitdiff | tree |
| 2016-03-15 |
gmungoc | JAL-2016 FeatureSettingsI now FeatureSettingsModelI
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commit | commitdiff | tree |
| 2016-03-15 |
gmungoc | JAL-1705 code tidy/comment only
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commit | commitdiff | tree |
| 2016-03-15 |
gmungoc | JAL-1705 compute reverse complement of variants on...
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commit | commitdiff | tree |
| 2016-03-11 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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commit | commitdiff | tree |
| 2016-03-11 |
gmungoc | JAL-1270 unit test for SequenceIdMatcher.SeqIdName
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commit | commitdiff | tree |
| 2016-03-11 |
gmungoc | JAL-1705 check Retry-After response header
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commit | commitdiff | tree |
| 2016-03-11 |
gmungoc | JAL-1705 javadoc added only
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commit | commitdiff | tree |
| 2016-03-11 |
gmungoc | JAL-1705 refactoring etc for fetching Ensembl --> Uniprot
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commit | commitdiff | tree |
| 2016-03-07 |
gmungoc | JAL-2023 CDS sequences added to / share alignment dataset
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commit | commitdiff | tree |
| 2016-03-04 |
gmungoc | JAL-1705 EnsemblGenomes a top level db source
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commit | commitdiff | tree |
| 2016-03-04 |
gmungoc | JAL-1705 parse 'description' from GFF as sequence description
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commit | commitdiff | tree |
| 2016-03-03 |
gmungoc | JAL-1705 unit test for aligning with incomplete start...
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commit | commitdiff | tree |
| 2016-03-03 |
gmungoc | JAL-1705 include stop codons in derived CDS; support...
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commit | commitdiff | tree |
| 2016-03-02 |
gmungoc | JAL-1705 include any unmapped protein start 'X' when...
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commit | commitdiff | tree |
| 2016-03-01 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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commit | commitdiff | tree |
| 2016-03-01 |
gmungoc | JAL-1705 align CDS to transcripts
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commit | commitdiff | tree |
| 2016-03-01 |
gmungoc | JAL-1705 align CDS and peptide products to transcripts
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commit | commitdiff | tree |
| 2016-02-25 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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commit | commitdiff | tree |
| 2016-02-22 |
gmungoc | JAL-1705 first pass at applying preset feature colouring...
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commit | commitdiff | tree |
| 2016-02-20 |
gmungoc | Merge branch 'mungo_develop' into features/JAL-653_JAL...
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commit | commitdiff | tree |
| 2016-02-20 |
gmungoc | Merge branch 'JAL-1956_featureStyles' into features...
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commit | commitdiff | tree |
| 2016-02-20 |
gmungoc | JAL-2016 first draft of pre-set feature colour scheme
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commit | commitdiff | tree |
| 2016-02-20 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 handle case of sequence with no dataset sequence
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 regular expression updates, tests, other refactoring
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 updated for change to CrossRef signature
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 refactor show products, set initial split...
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 more lenient test for 'sequence retrieved'
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 return Ensembl genes for model species for...
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 JAL-1191 more terms added to hard-coded version
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1706 reverted setting start position as too confusing...
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 lenient DBRef matcher added (accession id...
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 helper method for mapping excluding stop codon
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-1270 remove trailing space + test
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-1705 various refactoring towards Uniprot-to-Ensembl...
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-1191 additions to SOLite, tweak to test
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-1705 take feature ID for description if nothing...
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-282 wrap very long id in tooltip
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-1705 JAL-1686 stronger SequenceFeature.equals(...
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-2010 simple prototype of 'Highlight Selection'...
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-2008 updates for String[] to List<String> change
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-2008 avoid unnecessary repaints; signatures changed...
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-265 updated help text
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | Merge branch 'develop' into
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commit | commitdiff | tree |
| 2016-02-05 |
gmungoc | JAL-2006 scale even very small score ranges to a usable...
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | JAL-1544 spelling fix
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | JAL-2005 added (stable) sort methods parameterised by
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | JAL-599 bug fixed so array of visible types is populated
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | JAL-1705 temporary variable to aid inspection in debugger
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | JAL-1705 additional tests, validation regexp tweaks...
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | JAL-2003 export features on alignment, not alignment...
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commit | commitdiff | tree |
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