JAL-3933 configure root logger console appender to stderr (2.11.2 version)
[jalview.git] / src / jalview / ext /
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-10-05 gmungocJAL-1191 use full SO in desktop application
2016-10-05 gmungocJAL-2105 update Ensembl REST version to 4.7
2016-10-03 gmungocJAL-2110 JAL-1705 handle not found (400) better
2016-10-03 gmungocJAL-98 throw exception (unhandled) for int overthrow...
2016-10-03 gmungocJAL-98 use Profile to store consensus, ResidueCount...
2016-10-01 Jim ProcterMerge branch 'develop' into bug/JAL-2210_ensembl_unipro...
2016-09-30 Jim ProcterJAL-2210 add uniprot+mapping between ENST and ENSP...
2016-09-30 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory
2016-09-28 Jim ProcterJAL-2210 JAL-2232 check response code before attempting...
2016-09-27 gmungocJAL-2233 less verbose logging for Jmol
2016-09-27 Jim ProcterJAL-2210 report stack trace for unexpected exceptions
2016-09-26 gmungocJAL-98 generalised increment() to add() and made faster
2016-09-23 gmungocJAL-98 performance tweaks to use of SparseIntArray
2016-09-23 gmungocJAL-98 Android SparseIntArray added
2016-09-18 Jim ProcterJAL-1795 JAL-2206 prevent NPE when no data returned...
2016-09-16 gmungocJAL-2164 removed unused parameters from JmolParser...
2016-09-14 Jim ProcterJAL-2164 create RESNUM features with padding the same...
2016-09-07 Jim ProcterMerge branch 'develop' into bug/JAL-1803_JAL-2157
2016-09-07 Jim ProcterJAL-1803 JAL-1919 set type when structure file is parsed
2016-08-31 tcofoegbuJAL-2148 further enhancment to CA HETATM processing
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p...
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum
2016-08-26 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ...
2016-08-25 Jim ProcterJAL-2106 JAL-2154 cross-refs from Ensembl should verify...
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR...
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-08-17 gmungocJAL-2105 rest versions updated to 4.6, change log link...
2016-08-15 tcofoegbuJAL-1919 Added improvement to ensure consistence of...
2016-08-01 tcofoegbuJAL-2164 bugfix to convert insCodes of '\000' to '...
2016-07-22 tcofoegbuJAL-2148 Bugfix in structureImportSettings string-to...
2016-07-21 tcofoegbuResolve merge conflict for StructureImportSettings
2016-07-21 tcofoegbuJAL-2148 fix to heuristically determine chain terminati...
2016-07-21 Jim ProcterMerge branch 'apifix/JAL-1926_JAL-2106' into develop
2016-07-20 Jim ProcterJAL-1926 JAL-2106 fix name for flag controlling additio...
2016-07-19 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-07-19 tcofoegbuJAL-1919 set default structure file format to mmCIF...
2016-07-18 gmungocJAL-2105 check content of Ensembl REST ping response
2016-07-13 Jim ProcterMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-07-13 tcofoegbuJAL-2135 minor house-keeping
2016-07-12 gmungocFileFormat enum wip changes
2016-07-12 tcofoegbuJAL-2135 NPE bugfix when parsing a structure file with...
2016-07-11 gmungocfile format enum wip changes
2016-07-09 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... features/JAL-2110_crossRefDuplications
2016-07-08 tcofoegbuJAL-1919 Fixed failing tests, enabled HETATM processing...
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds
2016-07-01 tcofoegbuJAL-2135 bugfix for error preventing processing of...
2016-06-30 tcofoegbuJAL-1919 updated PDBSequenceFetcherTest and JMol parser...
2016-06-23 gmungocJAL-2130 now simply viewer.dispose() to close down...
2016-06-21 Jim ProcterMerge branch 'features/JAL-1956_featureStyles' into...
2016-06-20 gmungocJAL-2130 call viewer.dispose() on closing Jmol
2016-06-10 Jim ProcterJAL-1941 added test URL and notes about PyRNA restclient
2016-05-31 gmungocJAL-2123 use "rlabel" command to highlight with label...
2016-05-13 gmungocJAL-2105 capture Ensembl data version, check REST versi...
2016-05-10 gmungocMerge branch 'develop' into features/JAL-1956_featureStyles
2016-04-29 gmungocJAL-2051 better checking of retrieved / duplicated...
2016-04-14 gmungocJAL-1705 refactored/utility methods to detect e.g....
2016-04-11 gmungocJAL-1705 code/comment tidy only
2016-04-11 gmungocJAL-2051 fetch Ensembl Gene accessions one at a time
2016-04-06 tcofoegbumerge
2016-04-06 tcofoegbuJAL-2047 JAL-1919 fixed empty tooltip text when a cell...
2016-04-04 Jim ProcterJAL-2010 refactoring todo
2016-04-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h...
2016-04-01 gmungocJAL-1705 fetch all Ensembl xrefs (except GO terms)
2016-03-24 tcofoegbuJAL-1919 Added ability to generate temprature factor...
2016-03-23 gmungocMerge branch 'develop' of https://source.jalview.org...
2016-03-23 gmungocJAL-1705 add DBRefEntry for 'self' to retrieved transcr...
2016-03-22 tcofoegburesolve conflict with Mungo's merge
2016-03-22 tcofoegbuJAL-1919 code improvement to make PDB sequence fetcher...
2016-03-22 gmungocJAL-1191 isolated SequenceOntology (BioJava wrapper...
2016-03-21 tcofoegbudevelop merge
2016-03-16 gmungocJAL-1705 xref ENST to correct (ENSP) accession id
2016-03-15 gmungocJAL-2016 FeatureSettingsI now FeatureSettingsModelI
2016-03-15 gmungocJAL-1705 code tidy/comment only
2016-03-15 gmungocJAL-1705 compute reverse complement of variants on...
2016-03-15 tcofoegbuJAL-1919 refined structure view annotation settings...
2016-03-11 gmungocJAL-1705 check Retry-After response header
2016-03-11 gmungocJAL-1705 refactoring etc for fetching Ensembl --> Uniprot
2016-03-11 tcofoegbuJAL-1818 reimplemented sequence and annotation processi...
2016-03-04 gmungocJAL-1705 EnsemblGenomes a top level db source
2016-03-04 gmungocJAL-1705 parse 'description' from GFF as sequence descr...
2016-03-03 gmungocJAL-1705 include stop codons in derived CDS; support...
2016-03-03 tcofoegbuJAL-1919 PDBfile and JmolParser refactor
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts
2016-02-25 tcofoegbuJAL-1919 initial support for mmCIF using JMol API....
2016-02-22 gmungocJAL-1705 first pass at applying preset feature colourin...
2016-02-19 gmungocJAL-1705 regular expression updates, tests, other refac...
2016-02-19 gmungocJAL-1705 return Ensembl genes for model species for...
2016-02-12 gmungocJAL-1705 various refactoring towards Uniprot-to-Ensembl...
2016-02-12 gmungocJAL-2010 simple prototype of 'Highlight Selection'...
2016-02-12 gmungocMerge branch 'develop' into
2016-02-09 tcofoegbumerge develop
2016-02-09 tcofoegbuJAL-1957 deleted stale comment
2016-02-09 tcofoegbuJAL-1957 enabled multi-chain mapping and highlight...
2016-02-04 gmungocJAL-1705 additional tests, validation regexp tweaks...
2016-02-04 gmungocJAL-2003 export features on alignment, not alignment...
2016-02-01 gmungocJAL-1705 further unit tests
2016-02-01 gmungocJAL-1705 set Uniprot xref as 'source dbref' (for SIFTS...
2016-02-01 gmungocJAL-1705 JAL-1191 SequenceOntologyLite added as hard...
2016-01-30 gmungocJAL-1705 refactored cross-reference fetching (CCDS...
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