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2022-01-17	Ben Soares	JAL-3703 fix Gff3 shared InputStream with embedded...	commit \| commitdiff \| tree
2022-01-17	Ben Soares	close filehandles straight after parse, without setting...	commit \| commitdiff \| tree
2022-01-06	Jim Procter	JAL-3934 update whats new	commit \| commitdiff \| tree
2022-01-06	Jim Procter	Merge branch 'task/JAL-3934_update_log4j_again' into...	commit \| commitdiff \| tree
2022-01-06	Jim Procter	JAL-3934 trigger patch release for log4j version bump	commit \| commitdiff \| tree
2021-12-20	Jim Procter	JAL-3842 remove replacement tokens in html text - not...	commit \| commitdiff \| tree
2021-12-20	Jim Procter	JAL-3842 patch what’s new text	commit \| commitdiff \| tree
2021-12-20	Jim Procter	JAL-3842 release 2.11.1.5 release notes	commit \| commitdiff \| tree
2021-12-20	Jim Procter	Merge branch 'critical/JAL-3933_log4shell_mitigation...	commit \| commitdiff \| tree
2021-12-15	Jim Procter	JAL-3933 remove obsolete Castor logging configuration	commit \| commitdiff \| tree
2021-12-15	Jim Procter	JAL-3933 configure root logger console appender to...	commit \| commitdiff \| tree
2021-07-13	Jim Procter	JAL-3842 fix automatic what's new link for custom version...	commit \| commitdiff \| tree
2021-06-30	Jim Procter	JAL-3842 JAL-3746 (need to cherry pick to develop)...	commit \| commitdiff \| tree
2021-06-09	Jim Procter	JAL-3842 2.11.1.5 what’s new, release notes, and version...	commit \| commitdiff \| tree
2021-06-09	Jim Procter	Merge branch 'patch/JAL-3840_2_11_1_4' into releases...	commit \| commitdiff \| tree
2021-06-09	Jim Procter	JAL-3840 don’t update the modal residue count for gaps	commit \| commitdiff \| tree
2021-06-09	Jim Procter	fixes JAL-3840	commit \| commitdiff \| tree
2021-06-09	Jim Procter	JAL-3840 failing test - show that addGaps overflows	commit \| commitdiff \| tree
2021-03-09	Jim Procter	JAL-3816 release date updated to 9th March	commit \| commitdiff \| tree
2021-03-05	Jim Procter	JAL-3816 release date set for 8th March and updated...	commit \| commitdiff \| tree
2021-03-05	Jim Procter	JAL-3816 new known defects JAL-3705 and JAL-3806	commit \| commitdiff \| tree
2021-03-04	Jim Procter	Revert "Merge branch 'bug/JAL-3806_mappingCoversSequence...	commit \| commitdiff \| tree
2021-03-04	Jim Procter	Revert "JAL-3816 release notes for JAL-3806"	commit \| commitdiff \| tree
2021-02-26	Jim Procter	JAL-3816 release notes for JAL-3806	commit \| commitdiff \| tree
2021-02-26	Jim Procter	Merge branch 'bug/JAL-3806_mappingCoversSequence' into...	commit \| commitdiff \| tree
2021-02-26	Jim Procter	JAL-3816 JAL-3814 JAL-3813 JAL-3812 JAL-3811 JAL-3818...	commit \| commitdiff \| tree
2021-02-24	Jim Procter	Merge branch 'bug/JAL-3818_jmolDeadlock' into releases...	commit \| commitdiff \| tree
2021-02-24	Jim Procter	Merge branch 'releases/Release_2_11_1_4_debianpatches...	commit \| commitdiff \| tree
2021-02-07	Jim Procter	JAL-3816 bump version number and cut release notes	commit \| commitdiff \| tree
2021-02-07	Jim Procter	JAL-3815 default /etc/jalview_properties under utils...	commit \| commitdiff \| tree
2021-02-05	Jim Procter	Merge branch 'task/JAL-3521_Slimmed_down_build.gradle_for_de...	commit \| commitdiff \| tree
2021-02-05	Jim Procter	Merge branch 'releases/Release_2_11_1_4_debianpatches...	commit \| commitdiff \| tree
2021-02-05	Jim Procter	JAL-3814 don’t automatically launch the news browser...	commit \| commitdiff \| tree
2021-02-05	Jim Procter	JAL-3813 NOIDENTIFIERSSERVICE preference disables jalview...	commit \| commitdiff \| tree
2021-02-05	Jim Procter	JAL-3812 new argument ‘-nohtmltemplates’ and user preference...	commit \| commitdiff \| tree
2021-02-05	Jim Procter	JAL-3811 document SHOW_JWS2_SERVICES user preference...	commit \| commitdiff \| tree
2021-02-05	Jim Procter	JAL-3814 NONEWS property	commit \| commitdiff \| tree
2020-10-29	Jim Procter	JAL-3766 what’s new and release notes for 2.11.1.3	commit \| commitdiff \| tree
2020-10-29	Jim Procter	JAL-3759 fix compilation error for test	commit \| commitdiff \| tree
2020-10-29	Jim Procter	JAL-3766 release notes for JAL-3759	commit \| commitdiff \| tree
2020-10-29	Jim Procter	JAL-3759 exclude hidden columns when processing...	commit \| commitdiff \| tree
2020-10-29	Jim Procter	Merge branch 'documentation/JAL-3766_relnotes' into...	commit \| commitdiff \| tree
2020-10-29	Jim Procter	JAL-3766 release notes for JAL-3765 JAL-3763 JAL-3760...	commit \| commitdiff \| tree
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
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