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Merge branch 'spike/JAL-2040_JAL-2137_phyre2' into features/JAL-2040_JAL-2137_phyre2
[jalview.git]
/
test
/
jalview
/
analysis
/
2016-10-25
gmungoc
JAL-98 minor fixes to / tests for annotation derivation
tree
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commitdiff
2016-10-25
Jim Procter
JAL-2089 patch broken merge to master for Release 2...
releases/Release_2_10_0_Branch
tree
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commitdiff
2016-10-24
gmungoc
JAL-98 ResidueCount 100% test coverage (and bug fixes!)
tree
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commitdiff
2016-10-06
gmungoc
Merge branch 'develop' into bug/JAL-98consensusMemory
tree
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commitdiff
2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
tree
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commitdiff
2016-10-05
Jim Procter
JAL-2189 apply license
tree
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commitdiff
2016-10-05
Jim Procter
JAL-2189 format tests
tree
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commitdiff
2016-10-04
gmungoc
JAL-2232 some fix / partial fix of failing tests
bug/JAL-2210_hack_for_Release_2_10
tree
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commitdiff
2016-10-03
gmungoc
JAL-98 use Profile to store consensus, ResidueCount...
tree
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commitdiff
2016-10-02
Jim Procter
JAL-2210 first pass at attempting to fix CrossRef tests...
tree
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commitdiff
2016-09-27
gmungoc
JAL-2230 JAL-2049 added sequence feature transfer to
tree
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commitdiff
2016-09-21
Jim Procter
JAL-2214 test for strict Watson-Crick pairing
tree
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commitdiff
2016-08-30
Jim Procter
Merge branch 'develop' into merge/develop_bug/JAL-2154p...
tree
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commitdiff
2016-08-29
gmungoc
JAL-1841 robustness fix
bug/JAL-1841rnaSecStr
tree
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commitdiff
2016-08-26
Jim Procter
JAL-2154 patch regression on DbRefFetcher due to PDB...
tree
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commitdiff
2016-08-26
gmungoc
Merge branch 'develop' into bug/JAL-1841rnaSecStr
tree
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commitdiff
2016-08-26
gmungoc
JAL-2049 set Ensembl variant source to ENSEMBL if ...
tree
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commitdiff
2016-08-25
Jim Procter
JAL-2106 JAL-2154 fix test for additional reference...
tree
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commitdiff
2016-08-25
Jim Procter
Merge branch 'trailm' into trial_fixMakeCDSDBRefPropagation
tree
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commitdiff
2016-08-25
Jim Procter
Merge branch 'develop' into refactor/JAL-2106_sourceDbR...
tree
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commitdiff
2016-08-24
Jim Procter
JAL-2106 FIXME for test failure
tree
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commitdiff
2016-08-24
Jim Procter
JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
tree
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commitdiff
2016-08-23
Jim Procter
JAL-2154 updated testMakeCDSAlignment for expected...
tree
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commitdiff
2016-08-22
gmungoc
JAL-2011 adjust method to fix failing unit test
tree
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commitdiff
2016-08-18
gmungoc
Merge branch 'develop' into bug/JAL-1841rnaSecStr
tree
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commitdiff
2016-08-17
gmungoc
JAL-2172 reverted to not sorting column selection
tree
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commitdiff
2016-08-17
gmungoc
JAL-2172 handle case where column selection is not...
tree
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commitdiff
2016-08-16
gmungoc
JAL-2171 matching bracket default character for rna...
tree
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commitdiff
2016-08-12
gmungoc
JAL-1841, bug fix in rna SS consensus, additions to...
tree
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commitdiff
2016-08-04
Jim Procter
JAL-2110 comment on failing test (consider skipping...
tree
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commitdiff
2016-07-19
gmungoc
JAL-391 corrected handling of gapped sequences
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2110 note about use case for when alignAsSameSequen...
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2110 test demonstrating limitation of current imple...
tree
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commitdiff
2016-07-07
gmungoc
JAL-2110 added alignAsSameSequences to handle 'direct...
tree
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commitdiff
2016-07-06
gmungoc
JAL-2110 ensuring mapped dbrefs between protein and cds
tree
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commitdiff
2016-07-04
gmungoc
Revert "JAL-2110 use shared alignment dataset when...
tree
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commitdiff
2016-07-04
gmungoc
JAL-2110 use shared alignment dataset when copying...
tree
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commitdiff
2016-07-04
gmungoc
JAL-2110 bug fix / test for searchDataset mappings...
tree
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commitdiff
2016-07-01
gmungoc
JAL-2110 add 'products' parameter to filter results...
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 JAL-1551 formatting
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 enable and fix failing tests
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 enable and fix test
tree
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commitdiff
2016-06-22
Jim Procter
JAL-2110 remove hardwired detection of search context...
tree
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commitdiff
2016-06-21
gmungoc
JAL-2110 updated unit test to match code changes
tree
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commitdiff
2016-06-20
Jim Procter
JAL-2110 pass dataset to makeCDSalignment
tree
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commitdiff
2016-06-16
Jim Procter
JAL-2110 change test for desired behaviour of getCodonF...
tree
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commitdiff
2016-06-16
Jim Procter
JAL-2110 throw implementation error if not given a...
tree
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commitdiff
2016-06-14
gmungoc
JAL-2110 fixes to dbref resolution and mappings, use...
tree
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commitdiff
2016-06-09
gmungoc
JAL-2110 work in progress
tree
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commitdiff
2016-06-03
gmungoc
JAL-2110 random stuff
tree
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commitdiff
2016-06-02
gmungoc
Merge branch 'develop' into features/JAL-2110_makeSense...
tree
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commitdiff
2016-06-01
Jim Procter
JAL-2038 fix tests for case insensitive eSequenceIdMatcher
tree
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commitdiff
2016-05-25
gmungoc
JAL-2110 wip CrossRefs rewrite of CrossRef
tree
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commitdiff
2016-05-20
gmungoc
JAL-2110 unit tests for and minor refactoring of CrossRef
tree
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commitdiff
2016-05-20
gmungoc
JAL-2049 unit test updated for HGVS syntax, feature...
tree
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commitdiff
2016-04-24
Jim Procter
JAL-2075 test showing hidden columns bug in feature...
tree
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commitdiff
2016-04-24
Jim Procter
JAL-2075 refactor FeatureScoreModel to native testNG...
tree
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commitdiff
2016-04-14
gmungoc
JAL-2041 add ID,clinical_significance to feature attrib...
tree
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commitdiff
2016-04-14
gmungoc
JAL-2049 revised computePeptideVariants to transfer...
tree
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commitdiff
2016-04-13
Jim Procter
JAL-2046 test to demonstrate feature duplication bug
tree
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commitdiff
2016-04-12
gmungoc
JAL-2049 separate protein variant per dna variant ...
tree
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commitdiff
2016-04-01
gmungoc
JAL-1705 ensure the right mapping is used to align...
tree
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commitdiff
2016-04-01
gmungoc
JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
tree
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commitdiff
2016-03-11
gmungoc
Merge branch 'develop' into features/JAL-653_JAL-1766_h...
tree
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commitdiff
2016-03-11
gmungoc
JAL-1270 unit test for SequenceIdMatcher.SeqIdName
tree
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commitdiff
2016-03-11
gmungoc
JAL-1705 refactoring etc for fetching Ensembl --> Uniprot
tree
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commitdiff
2016-03-07
gmungoc
JAL-2023 CDS sequences added to / share alignment dataset
tree
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commitdiff
2016-03-03
gmungoc
JAL-1705 unit test for aligning with incomplete start...
tree
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commitdiff
2016-03-01
gmungoc
Merge branch 'develop' into features/JAL-653_JAL-1766_h...
tree
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commitdiff
2016-03-01
gmungoc
JAL-1705 align CDS and peptide products to transcripts
tree
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commitdiff
2016-02-26
tcofoegbu
JAL-1994 fix for broken tests
tree
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commitdiff
2016-02-12
gmungoc
JAL-2008 avoid unnecessary repaints; signatures changed...
tree
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commitdiff
2016-01-28
gmungoc
JAL-1705 refine feature copying to including 5' and...
tree
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commitdiff
2016-01-28
gmungoc
Merge branch 'develop' into JAL-1705_trialMerge
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 features transferred to CDS sequence; makeExon...
tree
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commitdiff
2016-01-05
gmungoc
JAL-653 updating 'align as' tests to match latest tweak...
tree
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commitdiff
2015-12-22
gmungoc
JAL-391 new Calculate options to Reverse, Reverse Compl...
tree
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commitdiff
2015-12-22
gmungoc
JAL-653 AlignedCodonFrame collections changed from...
tree
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commitdiff
2015-11-05
tcofoegbu
JAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...
tree
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commitdiff
2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
tree
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commitdiff
2015-10-15
tcofoegbu
JAL-1479 refactored SequenceI interface - changed getDB...
tree
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commitdiff
2015-10-08
Jim Procter
JAL-1894 update year/version in copyright
tree
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commitdiff
2015-10-08
Jim Procter
Merge branch 'develop' into Release_2_9_0b1_Branch
tree
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commitdiff
2015-10-08
Jim Procter
JAL-1894 organise imports
tree
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commitdiff
2015-09-22
Jim Procter
Merge branch 'develop' into Release_2_9_0b1_Branch
tree
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commitdiff
2015-09-14
gmungoc
JAL-1880 handle sequence offsets properly when mapping...
tree
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commitdiff
2015-09-10
Jim Procter
JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
tree
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commitdiff
2015-09-10
Jim Procter
JAL-1645 licencing for new files in test and utils
tree
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commitdiff
2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
tree
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commitdiff
2015-09-09
gmungoc
JAL-1619 'align protein as cDNA' now leaves unmapped...
tree
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commitdiff
2015-09-07
gmungoc
JAL-1636 translate stop codon as '*', mouseover * as...
tree
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commitdiff
2015-09-07
gmungoc
JAL-1152 check 'autocalculated' not 'null sequenceRef...
tree
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commitdiff
2015-08-17
gmungoc
JAL-1270 testIsMappable added
tree
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commitdiff
2015-07-23
tcofoegbu
JAL-1805 modified test setup's so the are ran for group...
tree
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commitdiff
2015-07-08
gmungoc
JAL-1759 merge from develop
tree
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commitdiff
2015-07-07
tcofoegbu
JAL-1805 test envirionment separation
tree
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commitdiff
2015-07-06
gmungoc
JAL-1081 unit tests added
tree
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commitdiff
2015-07-06
gmungoc
JAL-1782 refactored test to ensure it passes in TestNG
tree
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commitdiff
2015-06-26
gmungoc
Merge branch 'develop' into features/JAL-892varnaToProject
tree
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commitdiff
2015-06-26
gmungoc
Merge branch 'develop' into features/JAL-1759jmolUpdate
tree
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commitdiff
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