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Merge branch 'develop' into bug/JAL-1803_JAL-2157
[jalview.git]
/
test
/
jalview
/
analysis
/
AlignmentUtilsTests.java
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 fix test for additional reference...
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2016-08-25
Jim Procter
Merge branch 'trailm' into trial_fixMakeCDSDBRefPropagation
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2016-08-25
Jim Procter
Merge branch 'develop' into refactor/JAL-2106_sourceDbR...
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2016-08-24
Jim Procter
JAL-2106 FIXME for test failure
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2016-08-24
Jim Procter
JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
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2016-08-23
Jim Procter
JAL-2154 updated testMakeCDSAlignment for expected...
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2016-08-22
gmungoc
JAL-2011 adjust method to fix failing unit test
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2016-08-04
Jim Procter
JAL-2110 comment on failing test (consider skipping...
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2016-07-12
Jim Procter
JAL-2110 note about use case for when alignAsSameSequen...
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2016-07-12
Jim Procter
JAL-2110 test demonstrating limitation of current imple...
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2016-07-07
gmungoc
JAL-2110 added alignAsSameSequences to handle 'direct...
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2016-07-06
gmungoc
JAL-2110 ensuring mapped dbrefs between protein and cds
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2016-07-04
gmungoc
Revert "JAL-2110 use shared alignment dataset when...
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2016-07-04
gmungoc
JAL-2110 use shared alignment dataset when copying...
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diff to current
2016-07-01
gmungoc
JAL-2110 add 'products' parameter to filter results...
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2016-06-21
gmungoc
JAL-2110 updated unit test to match code changes
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2016-06-20
Jim Procter
JAL-2110 pass dataset to makeCDSalignment
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2016-06-16
Jim Procter
JAL-2110 change test for desired behaviour of getCodonF...
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2016-06-16
Jim Procter
JAL-2110 throw implementation error if not given a...
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2016-06-14
gmungoc
JAL-2110 fixes to dbref resolution and mappings, use...
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2016-05-20
gmungoc
JAL-2049 unit test updated for HGVS syntax, feature...
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2016-04-14
gmungoc
JAL-2041 add ID,clinical_significance to feature attrib...
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2016-04-14
gmungoc
JAL-2049 revised computePeptideVariants to transfer...
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2016-04-12
gmungoc
JAL-2049 separate protein variant per dna variant ...
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2016-04-01
gmungoc
JAL-1705 ensure the right mapping is used to align...
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2016-04-01
gmungoc
JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
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2016-03-11
gmungoc
JAL-1705 refactoring etc for fetching Ensembl --> Uniprot
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2016-03-07
gmungoc
JAL-2023 CDS sequences added to / share alignment dataset
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2016-03-03
gmungoc
JAL-1705 unit test for aligning with incomplete start...
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2016-03-01
gmungoc
JAL-1705 align CDS and peptide products to transcripts
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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
Merge branch 'develop' into JAL-1705_trialMerge
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2016-01-21
gmungoc
JAL-1705 features transferred to CDS sequence; makeExon...
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2016-01-05
gmungoc
JAL-653 updating 'align as' tests to match latest tweak...
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2015-12-22
gmungoc
JAL-653 AlignedCodonFrame collections changed from...
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2015-11-05
tcofoegbu
JAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...
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2015-10-15
tcofoegbu
JAL-1479 refactored SequenceI interface - changed getDB...
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2015-09-14
gmungoc
JAL-1880 handle sequence offsets properly when mapping...
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2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
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2015-09-09
gmungoc
JAL-1619 'align protein as cDNA' now leaves unmapped...
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2015-09-07
gmungoc
JAL-1636 translate stop codon as '*', mouseover * as...
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2015-08-17
gmungoc
JAL-1270 testIsMappable added
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2015-07-08
gmungoc
JAL-1759 merge from develop
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2015-07-07
tcofoegbu
JAL-1805 test envirionment separation
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2015-06-23
Jim Procter
JAL-1782 JAL-1780 JAL-653 JAL-1892 update patched refac...
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2015-06-22
Jim Procter
JAL-1780 JAL-653 Format/AppletFormat import and export...
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2015-06-22
Jim Procter
JAL-653 JAL-1780 reorder imports
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2015-06-19
tcofoegbu
JAL-1270 test suits import order refactor
features/JAL-1270_JUnit-to-TestNG
features/JAL-1782_JUnit-to-TestNG
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2015-06-19
tcofoegbu
JAL-1270 JUnit to TestNG refactoring
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2015-05-13
gmungoc
JAL-1712 fixes/tests for Castor binding of EMBL XML...
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2015-05-12
gmungoc
JAL-1712 fixes/tests for Castor binding and 'show flank...
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2015-04-21
gmungoc
JAL-1693 mappings added back to the original alignment
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2015-04-14
gmungoc
JAL-1693 generate multiple exon sequences for 1-many...
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2015-04-13
gmungoc
JAL-1693 make exon alignment for get-xref splitframe...
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2015-03-30
gmungoc
JAL-1264 remove broken applet build dependencies
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2015-03-26
gmungoc
Merge develop to Release_2_8_3_Branch
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2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
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2014-12-15
Jim Procter
JAL-1620 version bump and release notes
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2014-06-06
Jim Procter
JAL-1517 fix copyright for 2.8.2
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2014-04-21
Jim Procter
JAL-1466 improved test and patched off by one that...
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2014-04-21
Jim Procter
JAL-1466 new calculation menu option to recover the...
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