2023-11-03 |
James Procter | JAL-4090 JAL-1551 spotlessApply |
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2023-08-10 |
Ben Soares | JAL-629 Change all stdout and stderr output to use... |
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2022-03-08 |
Jim Procter | JAL-3438 spotless for 2.11.2.0 |
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2022-02-11 |
Jim Procter | JAL-3949 - refactor logging from jalview.bin.Cache... |
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2022-02-11 |
Ben Soares | JAL-3949 Complete new abstracted logging framework... |
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2020-03-30 |
gmungoc | JAL-3210 debug logging commented out |
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2020-03-30 |
gmungoc | Merge branch 'develop' into Jalview-JS/develop |
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2019-10-08 |
gmungoc | Merge branch 'develop' into Jalview-JS/develop |
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2019-08-22 |
gmungoc | JAL-3121 round trip GFF attributes including map-valued... |
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2019-02-20 |
gmungoc | Merge branch 'feature/JAL-3143ensemblJSON' into feature... |
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2019-01-29 |
hansonr | time check, iterators |
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2019-01-29 |
hansonr | more iterators out; some time checks |
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2019-01-26 |
hansonr | Platform.timecheck calls removed or commented out. |
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2019-01-26 |
hansonr | Jalview.isJS() --> Platform.isJS(), DBRefEntry[] -... |
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2019-01-25 |
hansonr | JSON refactoring |
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2019-01-25 |
gmungoc | JAL-3187 don't compute variant features on peptide... |
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2018-11-12 |
gmungoc | JAL-3076 JalviewJS requires lower case content-type... |
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2018-10-25 |
gmungoc | JAL-3143 comma-delimited feature attributes for alleles, |
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2018-10-25 |
gmungoc | JAL-3143 fetch Ensembl(Genomes) features as JSON not GFF |
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2018-09-03 |
gmungoc | JAL-3076 fetch Ensembl sequence as JSON instead of... |
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2018-09-03 |
Jim Procter | JAL-3076 clarify javadoc handling single sequence respo... bug/JAL-3076ensemblGeneId |
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2018-08-10 |
gmungoc | JAL-3076 refactor for more efficient scan of 'gene... |
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2018-08-10 |
gmungoc | JAL-3076 fetch Ensembl sequence as JSON instead of... |
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2018-01-30 |
gmungoc | JAL-1793 update spike build to latest incl stop and... |
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2018-01-26 |
gmungoc | Merge branch 'develop' into features/JAL-1793VCF |
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2018-01-17 |
gmungoc | JAL-2679 case-insensitive comparison of query and retri... |
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2018-01-16 |
gmungoc | JAL-2679 use object_type=Transcript for lookup of Paren... |
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2017-10-03 |
gmungoc | JAL-2738 copy to spikes/mungo |
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2017-09-25 |
gmungoc | JAL-2738 one constant in codebase for "alleles" attribu... |
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2017-08-25 |
gmungoc | JAL-2480 suppress debug timing output that got left in |
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2017-08-21 |
gmungoc | Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList |
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2017-08-16 |
Jim Procter | JAL-2418 source formatting |
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2017-06-09 |
gmungoc | JAL-2446 merged to spike branch |
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2017-05-25 |
gmungoc | JAL-2050 make SequenceFeature.score final, adjust const... |
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2017-05-24 |
gmungoc | JAL-2529 add object_type=cdna to EnsemblCdna parameters |
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2017-05-12 |
gmungoc | JAL-2480 renamed java.util.RangeComparator to IntRangeC... |
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2017-05-09 |
gmungoc | JAL-2505 use constructors to set (what will be) final... |
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2016-12-08 |
gmungoc | Merge branch 'develop' into features/JAL-2295setChimera... |
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2016-12-07 |
gmungoc | JAL-2354 handle error response when fetching features |
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2016-11-08 |
gmungoc | JAL-2295 make RangeComparator a top level class for... |
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2016-10-05 |
Jim Procter | JAL-2189 apply license |
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2016-10-05 |
Jim Procter | JAL-2189 source formatting |
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2016-10-03 |
gmungoc | JAL-2110 JAL-1705 handle not found (400) better |
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2016-09-30 |
Jim Procter | JAL-2210 add uniprot+mapping between ENST and ENSP... |
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2016-09-27 |
Jim Procter | JAL-2210 report stack trace for unexpected exceptions |
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2016-08-30 |
Jim Procter | Merge branch 'develop' into merge/develop_bug/JAL-2154p... |
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2016-08-26 |
gmungoc | JAL-2049 set Ensembl variant source to ENSEMBL if ... |
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2016-08-25 |
Jim Procter | JAL-2106 JAL-2154 cross-refs from Ensembl should verify... |
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2016-08-24 |
Jim Procter | JAL-2106 removed setSourceDBRef, refactor getSourceDBRe... |
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2016-07-06 |
gmungoc | JAL-2110 ensuring mapped dbrefs between protein and cds |
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2016-05-13 |
gmungoc | JAL-2105 capture Ensembl data version, check REST versi... |
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2016-04-14 |
gmungoc | JAL-1705 refactored/utility methods to detect e.g.... |
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2016-04-11 |
gmungoc | JAL-1705 code/comment tidy only |
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2016-04-01 |
gmungoc | JAL-1705 fetch all Ensembl xrefs (except GO terms) |
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2016-03-23 |
gmungoc | JAL-1705 add DBRefEntry for 'self' to retrieved transcr... |
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2016-03-16 |
gmungoc | JAL-1705 xref ENST to correct (ENSP) accession id |
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2016-03-15 |
gmungoc | JAL-1705 compute reverse complement of variants on... |
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2016-03-11 |
gmungoc | JAL-1705 refactoring etc for fetching Ensembl --> Uniprot |
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2016-03-04 |
gmungoc | JAL-1705 parse 'description' from GFF as sequence descr... |
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2016-03-03 |
gmungoc | JAL-1705 include stop codons in derived CDS; support... |
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2016-03-01 |
gmungoc | JAL-1705 align CDS and peptide products to transcripts |
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2016-02-19 |
gmungoc | JAL-1705 regular expression updates, tests, other refac... |
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2016-02-12 |
gmungoc | JAL-1705 various refactoring towards Uniprot-to-Ensembl... |
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2016-02-04 |
gmungoc | JAL-1705 additional tests, validation regexp tweaks... |
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2016-02-01 |
gmungoc | JAL-1705 further unit tests |
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2016-02-01 |
gmungoc | JAL-1705 set Uniprot xref as 'source dbref' (for SIFTS... |
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2016-02-01 |
gmungoc | JAL-1705 JAL-1191 SequenceOntologyLite added as hard... |
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2016-01-30 |
gmungoc | JAL-1705 refactored cross-reference fetching (CCDS... |
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2016-01-29 |
gmungoc | JAL-1705 fetch Uniprot and PDB xrefs for Ensembl protei... |
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2016-01-28 |
gmungoc | JAL-1705 refine feature copying to including 5' and... |
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2016-01-28 |
gmungoc | JAL-1705 tests added, minor bugfix and refactoring |
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2016-01-27 |
gmungoc | JAL-1705 add exon name to features and render on peptid... |
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2016-01-27 |
gmungoc | JAL-1705 use GET for single queries; set gene name... |
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2016-01-26 |
gmungoc | JAL-1705 derive transcript sequences from gene sequence... |
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2016-01-25 |
gmungoc | JAL-1705 EnsemblGene added, and related refactoring |
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2016-01-23 |
gmungoc | JAL-1705 compute peptide variants from dna; add "conseq... |
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2016-01-21 |
gmungoc | JAL-1705 reworked Ensembl clients now fetching and... |
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2016-01-08 |
gmungoc | JAL-1705 DbSourceProxy properties converted to methods... |
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2015-06-28 |
Jim Procter | JAL-1705 renamed SeqFetcherTest to EnsemblSeqProxyTest |
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