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2023-10-02	jprocter	JAL-4090 more JAL-3858 docs	commit \| commitdiff \| tree
2023-10-02	jprocter	Merge branch 'develop' into doc/JAL-4090_Release_2_11_3_0	commit \| commitdiff \| tree
2022-03-04	Jim Procter	JAL-3746 JAL-3811 document SHOW_JWS2_SERVICES user...	commit \| commitdiff \| tree
2022-03-04	Jim Procter	JAL-3746 JAL-3812 new argument ‘-nohtmltemplates’ and...	commit \| commitdiff \| tree
2022-03-04	Jim Procter	JAL-3746 JAL-3813 NOIDENTIFIERSSERVICE preference disables...	commit \| commitdiff \| tree
2022-03-04	Jim Procter	JAL-3746 JAL-3814 don’t automatically launch the news...	commit \| commitdiff \| tree
2022-03-04	Jim Procter	JAL-3746 JAL-3814 NONEWS property	commit \| commitdiff \| tree
2021-09-17	Jim Procter	JAL-1260 FileFormat entry for EMBL/GENBANK: TODO: create...	commit \| commitdiff \| tree
2021-09-16	Jim Procter	JAL-3794 X and N are counted as DNA characters, but...	commit \| commitdiff \| tree
2021-09-16	Jim Procter	JAL-3794 new test for recognition of protein or DNA...	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3815 default /etc/jalview_properties under utils...	commit \| commitdiff \| tree
2021-08-30	Jim Procter	JAL-3829 forgot to add in the dummy 3d-beacons db proxy	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
2021-06-09	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
2021-04-06	Jim Procter	JAL-3832 dummy 3d-beacons database client and code...	commit \| commitdiff \| tree
2021-03-15	Jim Procter	Merge branch 'releases/Release_2_11_1_Branch'	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
2021-02-17	Jim Procter	JAL-3821 patch for 2.11.2 to retrieve RNA ENA records...	commit \| commitdiff \| tree
2021-02-17	Jim Procter	Merge branch 'feature/JAL-3692enaEndpoint' into patch...	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
2020-11-13	Jim Procter	JAL-3757 JAL-3689 use AppletFormat.checkProtocol to...	commit \| commitdiff \| tree
2020-10-29	Jim Procter	Merge branch 'releases/Release_2_11_1_Branch'	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	Jim Procter	JAL-3760 fix tests for changed behaviour	commit \| commitdiff \| tree
2020-10-28	Jim Procter	JAL-3760 refactor nucleotide proportion test to per...	commit \| commitdiff \| tree
2020-10-28	Jim Procter	Merge branch 'bug/JAL-3760_protsTreatedAsNucleotides...	commit \| commitdiff \| tree
2020-10-28	Jim Procter	Merge branch 'portforward/JAL-3765_patch_to_2112' into...	commit \| commitdiff \| tree
2020-10-28	Jim Procter	JAL-3765 fix test	commit \| commitdiff \| tree
2020-10-28	Jim Procter	fix for JAL-3765	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
2020-10-21	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
2020-10-21	Jim Procter	Merge branch 'releases/Release_2_11_1_Branch'	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
2020-10-02	Jim Procter	JAL-3762 check for !args \|\| args=="" before overwriting	commit \| commitdiff \| tree
2020-10-02	Jim Procter	JAL-3762 more typo fixing :q	commit \| commitdiff \| tree
2020-10-02	Jim Procter	JAL-3762 syntax error typo	commit \| commitdiff \| tree
2020-10-02	Jim Procter	JAL-3762 check if Info.args already defined before...	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
2020-09-21	Jim Procter	Merge branch 'merge_review/JAL-3490_2_11_2_develop...	commit \| commitdiff \| tree
2020-09-17	Jim Procter	Merge branch 'releases/Release_2_11_1_Branch'	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
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