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2020-10-29	Jim Procter	Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3...	commit \| commitdiff \| tree
2020-10-28	Jim Procter	JAL-3725 fix tests for EMBLFlatFile parser when mapping...	commit \| commitdiff \| tree
2020-10-28	Jim Procter	JAL-3725 patch EMBL flat file to exclude stop codon...	commit \| commitdiff \| tree
2020-10-28	gmungoc	JAL-3725 restrict mapped virtual feature location to...	commit \| commitdiff \| tree
2020-10-28	gmungoc	JAL-3725 helper methods for computing mapped feature...	commit \| commitdiff \| tree
2020-10-28	gmungoc	JAL-3725 exclude stop codon from CDS-to-protein mapping	commit \| commitdiff \| tree
2020-10-28	Jim Procter	Merge branch 'bug/JAL-3760_protsTreatedAsNucleotides...	commit \| commitdiff \| tree
2020-10-27	Jim Procter	JAL-3768 noticed failure of test when run as part of...	commit \| commitdiff \| tree
2020-10-27	Jim Procter	JAL-3700 JAL-3748 JAL-3763 don’t add stop codon via...	commit \| commitdiff \| tree
2020-10-27	Jim Procter	update test for JAL-3763 redact shared DS sequences...	commit \| commitdiff \| tree
2020-10-22	gmungoc	JAL-3763 Javadoc, check for null, additional tests	commit \| commitdiff \| tree
2020-10-22	gmungoc	JAL-3751 only merge strictly contiguous ranges of mappings	commit \| commitdiff \| tree
2020-10-22	gmungoc	JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion	commit \| commitdiff \| tree
2020-10-22	gmungoc	JAL-3700 JAL-3763 create datasets for test sequences	commit \| commitdiff \| tree
2020-10-22	gmungoc	JAL-3763 failsafe check for null	commit \| commitdiff \| tree
2020-10-22	gmungoc	JAL-3763 refactored getCoveringMapping for virtual...	commit \| commitdiff \| tree
2020-10-22	gmungoc	JAL-3763 always make a new dataset sequence for CDS...	commit \| commitdiff \| tree
2020-10-22	gmungoc	JAL-3700 additions and corrections to unit tests	commit \| commitdiff \| tree
2020-10-21	Jim Procter	JAL-3766 release notes for JAL-3611 JAL-3765	commit \| commitdiff \| tree
2020-10-21	Jim Procter	Merge branch 'releases/Release_2_11_1_Branch' of http...	commit \| commitdiff \| tree
2020-10-21	Jim Procter	Merge branch 'bug/JAL-3765_Find_bugs_in_21112' into...	commit \| commitdiff \| tree
2020-10-21	Jim Procter	JAL-3766 cut new patch release	commit \| commitdiff \| tree
2020-10-20	Jim Procter	JAL-3765 fix test	commit \| commitdiff \| tree
2020-10-20	Jim Procter	fix for JAL-3765	commit \| commitdiff \| tree
2020-10-19	Jim Procter	JAL-3765 simple test that findAll finds all matches...	commit \| commitdiff \| tree
2020-09-29	Jim Procter	JAL-3760 fix tests for changed behaviour	commit \| commitdiff \| tree
2020-09-29	Jim Procter	JAL-3760 refactor nucleotide proportion test to per...	commit \| commitdiff \| tree
2020-09-25	Jim Procter	JAL-3758 tweak what’s new for 2.11.1.2!	commit \| commitdiff \| tree
2020-09-25	Jim Procter	JAL-3758 release Fri 25th Sep	commit \| commitdiff \| tree
2020-09-25	Jim Procter	Merge branch 'releases/Release_2_11_1_Branch' of http...	commit \| commitdiff \| tree
2020-09-24	Jim Procter	JAL-3758 2.11.1.2 patch release notes and version bump	commit \| commitdiff \| tree
2020-09-24	Jim Procter	JAL-3757 JAL-3689 use AppletFormat.checkProtocol to...	commit \| commitdiff \| tree
2020-09-23	Jim Procter	JAL-3748 not testing for sequence’s containment in...	commit \| commitdiff \| tree
2020-09-23	Jim Procter	JAL-3748 fix compilation error	commit \| commitdiff \| tree
2020-09-23	Jim Procter	JAL-3748 maximal test for JAL-3748 using covid19 CDS...	commit \| commitdiff \| tree
2020-09-23	Jim Procter	JAL-3748 more tests verifying reconstruction of AlignemntVie...	commit \| commitdiff \| tree
2020-09-23	Jim Procter	JAL-3748 reusable assert to trace specific issues with...	commit \| commitdiff \| tree
2020-09-23	Jim Procter	JAL-3748 allow AlignedCodonFrame.covers to optionally...	commit \| commitdiff \| tree
2020-09-22	Jim Procter	JAL-3748 test data for SplitFrameTest	commit \| commitdiff \| tree
2020-09-22	Jim Procter	JAL-3748 don’t trash start/end on SequenceI reconstructed...	commit \| commitdiff \| tree
2020-09-22	Jim Procter	JAL-3748 simple test for SeqCigar preservation of start...	commit \| commitdiff \| tree
2020-09-22	Jim Procter	JAL-3748 additional asserts to verify start/end after...	commit \| commitdiff \| tree
2020-09-17	Jim Procter	JAL-3675 release notes for JAL-3750 JAL-3751	commit \| commitdiff \| tree
2020-09-17	Jim Procter	Merge branch 'patch/JAL-3750_JAL-3741_https_patch'...	commit \| commitdiff \| tree
2020-09-17	Jim Procter	JAL-3741 http to https (and jar to jvp for exampleFile...	commit \| commitdiff \| tree
2020-09-17	Jim Procter	JAL-3750 parse protocol before checking if argument...	commit \| commitdiff \| tree
2020-09-17	Jim Procter	JAL-3675 patch release date 17th September 2020	commit \| commitdiff \| tree
2020-09-16	Jim Procter	JAL-3748 preserve sequence IDs from original alignment...	commit \| commitdiff \| tree
2020-09-16	Jim Procter	JAL-3748 recover complement alignment from complement...	commit \| commitdiff \| tree
2020-09-16	Jim Procter	JAL-3748 make findAlignedSequence require mapped from...	commit \| commitdiff \| tree
2020-09-16	Jim Procter	JAL-3748 pass a list to findAlignedSequence to return...	commit \| commitdiff \| tree
2020-09-16	Jim Procter	JAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq...	commit \| commitdiff \| tree
2020-09-16	Jim Procter	JAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true...	commit \| commitdiff \| tree
2020-09-16	Jim Procter	Merge branch 'failingTest/JAL-3748_reconstructCDSafterProtei...	commit \| commitdiff \| tree
2020-09-16	gmungoc	JAL-3700 fix for propagation of sort commands	commit \| commitdiff \| tree
2020-09-16	gmungoc	JAL-3700 check for 'covering' mapping when matching...	commit \| commitdiff \| tree
2020-09-16	Jim Procter	JAL-3748 store an AlignmentView for the complement...	commit \| commitdiff \| tree
2020-09-15	Jim Procter	JAL-3675 logged JAL-3748 as known defect	commit \| commitdiff \| tree
2020-09-15	Jim Procter	JAL-3765 JAL-3718 release notes	commit \| commitdiff \| tree
2020-09-15	Jim Procter	Merge branch 'patch/JAL-3718_fixed_getdown_patched_for_Relea...	commit \| commitdiff \| tree
2020-09-15	Jim Procter	JAL-3675 typo in release notes :(	commit \| commitdiff \| tree
2020-09-15	Jim Procter	JAL-3675 update release date and release notes for...	commit \| commitdiff \| tree
2020-09-03	Jim Procter	JAL-3675 update release date and release notes for...	commit \| commitdiff \| tree
2020-09-03	Jim Procter	Merge branch 'improvement/JAL-3280_Migrate_the_VersionChecke...	commit \| commitdiff \| tree
2020-09-03	Jim Procter	JAL-3675 whats new, logging and release notes tidying...	commit \| commitdiff \| tree
2020-09-03	Jim Procter	JAL-3676 rework logging docs.	commit \| commitdiff \| tree
2020-09-03	Jim Procter	Merge branch 'bug/JAL-3718_Getdown_does_not_autoupdate_corre...	commit \| commitdiff \| tree
2020-09-03	Jim Procter	JAL-3676 remove mention of Castor	commit \| commitdiff \| tree
2020-09-03	Jim Procter	JAL-3675 tweak release notes for JAL-3667, JAL-3702	commit \| commitdiff \| tree
2020-09-03	Jim Procter	JAL-3675 update sequence fetcher service documentation...	commit \| commitdiff \| tree
2020-08-31	Jim Procter	JAL-3680 merged description of individual cursor key...	commit \| commitdiff \| tree
2020-08-31	Jim Procter	JAL-3732 - sequences can be moved up/down in cursor...	commit \| commitdiff \| tree
2020-08-25	Jim Procter	report JAL-3127 as known defect (fix targeted for 2...	commit \| commitdiff \| tree
2020-08-25	Jim Procter	JAL-3671 hardwire log4j.root logger to INFO to supress...	commit \| commitdiff \| tree
2020-08-21	Jim Procter	JAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615...	commit \| commitdiff \| tree
2020-08-17	Jim Procter	JAL-3675 release notes for JAL-3691	commit \| commitdiff \| tree
2020-08-17	Jim Procter	Merge branch 'patch/JAL-3691_No_score_models_available...	commit \| commitdiff \| tree
2020-08-17	Jim Procter	JAL-3675 JAL-3561 documented in release notes	commit \| commitdiff \| tree
2020-08-17	Jim Procter	JAL-3675 report JAL-3702 as known defect	commit \| commitdiff \| tree
2020-08-17	Jim Procter	Merge branch 'patch/JAL-3561_JAL-3660_fileformatexport_CLI...	commit \| commitdiff \| tree
2020-08-17	Jim Procter	JAL-3712 fix typos for rebuilding/updating getdown...	commit \| commitdiff \| tree
2020-08-17	Jim Procter	JAL-3490 JAL-3675 release notes, update Find dialog...	commit \| commitdiff \| tree
2020-08-17	Jim Procter	Merge branch 'patch/Release_2_11_1_Branch_patch_JAL...	commit \| commitdiff \| tree
2020-08-17	Jim Procter	JAL-3675 JAL-3597 release notes	commit \| commitdiff \| tree
2020-08-17	Jim Procter	Merge branch 'patch/JAL-3597_for_Release_2_11_1_Branch...	commit \| commitdiff \| tree
2020-08-13	Jim Procter	JAL-3675 brought forward patch to build.gradle for...	commit \| commitdiff \| tree
2020-08-13	Jim Procter	Merge branch 'releases/Release_2_11_1_Branch' of http...	commit \| commitdiff \| tree
2020-08-12	Jim Procter	JAL-3675 added JAL-3576 as known defect (colocated...	commit \| commitdiff \| tree
2020-08-12	Ben Soares	JAL-3608 Changes from code review CR-JAL-236	commit \| commitdiff \| tree
2020-08-11	Jim Procter	JAL-3675 fix issue attribution for JAL-3667 release...	commit \| commitdiff \| tree
2020-08-11	Jim Procter	JAL-3675 update release notes for JAL-3673 and tested...	commit \| commitdiff \| tree
2020-08-11	Jim Procter	JAL-3673 make sure font metrics are updated if dealing...	commit \| commitdiff \| tree
2020-08-11	Jim Procter	Merge branch 'bug/JAL-2983negativeSliderMin' into releases...	commit \| commitdiff \| tree
2020-08-10	gmungoc	JAL-3490 match count independent of contiguous matches...	commit \| commitdiff \| tree
2020-08-10	Jim Procter	JAL-3691 toUpperCase(Locale.ROOT) for all standard...	commit \| commitdiff \| tree
2020-08-10	Jim Procter	Merge branch 'releases/Release_2_11_1_Branch' into...	commit \| commitdiff \| tree
2020-08-10	Jim Procter	JAL-3628 JAL-3708 call Cache.initLogger() before using...	commit \| commitdiff \| tree
2020-08-05	Jim Procter	JAL-3628 init log after loading testProps for each...	commit \| commitdiff \| tree
2020-08-05	Jim Procter	Merge branch 'patch/JAL-3692enaEndpointFlatfile' into...	commit \| commitdiff \| tree
2020-08-05	gmungoc	JAL-3692 unit test updated for ?gzip download endpoint URL	commit \| commitdiff \| tree
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