JAL-2674 more adjustments to locateVisibleBoundsOfSequence
[jalview.git] / test / jalview / analysis /
2016-08-04 Jim ProcterJAL-2110 comment on failing test (consider skipping...
2016-07-19 gmungocJAL-391 corrected handling of gapped sequences
2016-07-18 gmungocfileFormat enum wip changes
2016-07-12 Jim ProcterJAL-2110 note about use case for when alignAsSameSequen...
2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current imple...
2016-07-11 gmungocfile format enum wip changes
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct...
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds
2016-07-04 gmungocRevert "JAL-2110 use shared alignment dataset when...
2016-07-04 gmungocJAL-2110 use shared alignment dataset when copying...
2016-07-04 gmungocJAL-2110 bug fix / test for searchDataset mappings...
2016-07-01 gmungocJAL-2110 add 'products' parameter to filter results...
2016-06-23 Jim ProcterJAL-2110 JAL-1551 formatting
2016-06-23 Jim ProcterJAL-2110 enable and fix failing tests
2016-06-23 Jim ProcterJAL-2110 enable and fix test
2016-06-22 Jim ProcterJAL-2110 remove hardwired detection of search context...
2016-06-21 gmungocJAL-2110 updated unit test to match code changes
2016-06-20 Jim ProcterJAL-2110 pass dataset to makeCDSalignment
2016-06-16 Jim ProcterJAL-2110 change test for desired behaviour of getCodonF...
2016-06-16 Jim ProcterJAL-2110 throw implementation error if not given a...
2016-06-14 gmungocJAL-2110 fixes to dbref resolution and mappings, use...
2016-06-09 gmungocJAL-2110 work in progress
2016-06-03 gmungocJAL-2110 random stuff
2016-06-02 gmungocMerge branch 'develop' into features/JAL-2110_makeSense...
2016-06-01 Jim ProcterJAL-2038 fix tests for case insensitive eSequenceIdMatcher
2016-05-25 gmungocJAL-2110 wip CrossRefs rewrite of CrossRef
2016-05-20 gmungocJAL-2110 unit tests for and minor refactoring of CrossRef
2016-05-20 gmungocJAL-2049 unit test updated for HGVS syntax, feature...
2016-04-24 Jim ProcterJAL-2075 test showing hidden columns bug in feature...
2016-04-24 Jim ProcterJAL-2075 refactor FeatureScoreModel to native testNG...
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib...
2016-04-14 gmungocJAL-2049 revised computePeptideVariants to transfer...
2016-04-13 Jim ProcterJAL-2046 test to demonstrate feature duplication bug
2016-04-12 gmungocJAL-2049 separate protein variant per dna variant ...
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align...
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
2016-03-11 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h...
2016-03-11 gmungocJAL-1270 unit test for SequenceIdMatcher.SeqIdName
2016-03-11 gmungocJAL-1705 refactoring etc for fetching Ensembl --> Uniprot
2016-03-07 gmungocJAL-2023 CDS sequences added to / share alignment dataset
2016-03-03 gmungocJAL-1705 unit test for aligning with incomplete start...
2016-03-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h...
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts
2016-02-26 tcofoegbuJAL-1994 fix for broken tests
2016-02-12 gmungocJAL-2008 avoid unnecessary repaints; signatures changed...
2016-01-28 gmungocJAL-1705 refine feature copying to including 5' and...
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge
2016-01-21 gmungocJAL-1705 features transferred to CDS sequence; makeExon...
2016-01-05 gmungocJAL-653 updating 'align as' tests to match latest tweak...
2015-12-22 gmungocJAL-391 new Calculate options to Reverse, Reverse Compl...
2015-12-22 gmungocJAL-653 AlignedCodonFrame collections changed from...
2015-11-05 tcofoegbuJAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB...
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-10-08 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-10-08 Jim ProcterJAL-1894 organise imports
2015-09-22 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-09-14 gmungocJAL-1880 handle sequence offsets properly when mapping...
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 licencing for new files in test and utils
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-09-09 gmungocJAL-1619 'align protein as cDNA' now leaves unmapped...
2015-09-07 gmungocJAL-1636 translate stop codon as '*', mouseover * as...
2015-09-07 gmungocJAL-1152 check 'autocalculated' not 'null sequenceRef...
2015-08-17 gmungocJAL-1270 testIsMappable added
2015-07-23 tcofoegbuJAL-1805 modified test setup's so the are ran for group...
2015-07-08 gmungocJAL-1759 merge from develop
2015-07-07 tcofoegbuJAL-1805 test envirionment separation
2015-07-06 gmungocJAL-1081 unit tests added
2015-07-06 gmungocJAL-1782 refactored test to ensure it passes in TestNG
2015-06-26 gmungocMerge branch 'develop' into features/JAL-892varnaToProject
2015-06-26 gmungocMerge branch 'develop' into features/JAL-1759jmolUpdate
2015-06-23 Jim ProcterJAL-1782 JAL-1780 JAL-653 JAL-1892 update patched refac...
2015-06-22 Jim ProcterJAL-1780 JAL-653 Format/AppletFormat import and export...
2015-06-22 Jim ProcterJAL-653 JAL-1780 reorder imports
2015-06-19 tcofoegbuJAL-1270 test suits import order refactor features/JAL-1270_JUnit-to-TestNG features/JAL-1782_JUnit-to-TestNG
2015-06-19 tcofoegbuJAL-1270 JUnit to TestNG refactoring
2015-06-18 gmungocJAL-1270 test added
2015-06-04 gmungocJAL-1750 small tidy of AlignSeq.printMapping (+Junit)
2015-05-18 gmungocJAL-1737 updated JUnit so it creates positional annotations
2015-05-15 gmungocJAL-1270 added test for regex actually used; include...
2015-05-15 gmungocJAL-1270 main methods converted to JUnit
2015-05-13 gmungocJAL-1712 fixes/tests for Castor binding of EMBL XML...
2015-05-12 gmungocJAL-1712 fixes/tests for Castor binding and 'show flank...
2015-04-21 gmungocJAL-1693 mappings added back to the original alignment
2015-04-14 gmungocJAL-1693 generate multiple exon sequences for 1-many...
2015-04-13 gmungocJAL-1693 make exon alignment for get-xref splitframe...
2015-03-30 gmungocJAL-1264 remove broken applet build dependencies
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
2015-02-12 Jim ProcterJAL-1350 forgot to remove empty test
2015-02-12 Jim ProcterJAL-1350 cloned method and tested equivalence for using...
2015-01-07 Jim ProcterJAL-1483 basic test of sequence similarity score model...
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-11-04 gmungocJAL-1152 annotation sort algorithm optimisation
2014-10-31 gmungocJAL-1152 bug fix for 'no sort' case + tests for autocal...
2014-10-31 gmungocJAL-1152 menu tweaks plus new option to put Autocalc...
2014-10-30 gmungocJAL-1152 with sticky annotation sort order that updates...
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