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