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jalview.git
2022-01-17 Jim ProcterJAL-3940 bump version and update release notes - releas... commit | commitdiff | tree | snapshot
2022-01-17 Jim ProcterJAL-3940 update release notes for JAL-3702,JAL-3935... commit | commitdiff | tree | snapshot
2022-01-17 Ben SoaresJAL-3703 Test that fails in Windows only, and only... commit | commitdiff | tree | snapshot
2022-01-17 Ben SoaresJAL-3703 fix Gff3 shared InputStream with embedded... commit | commitdiff | tree | snapshot
2022-01-17 Ben Soaresclose filehandles straight after parse, without setting... commit | commitdiff | tree | snapshot
2022-01-11 Ben SoaresJAL-3937 update releases.html commit | commitdiff | tree | snapshot
2022-01-10 Ben SoaresJAL-3937 enable AIA download of intermediate certificat... commit | commitdiff | tree | snapshot
2022-01-06 Jim ProcterJAL-3934 update whats new Release_2_11_1_6 commit | commitdiff | tree | snapshot
2022-01-06 Jim ProcterMerge branch 'task/JAL-3934_update_log4j_again' into... commit | commitdiff | tree | snapshot
2022-01-06 Jim ProcterJAL-3934 trigger patch release for log4j version bump commit | commitdiff | tree | snapshot
2021-12-22 Ben SoaresJAL-3934 updated log4j from 2.16.0 to 2.17.0 commit | commitdiff | tree | snapshot
2021-12-20 Jim ProcterJAL-3842 remove replacement tokens in html text - not... Release_2_11_1_5 commit | commitdiff | tree | snapshot
2021-12-20 Jim ProcterJAL-3842 patch what’s new text commit | commitdiff | tree | snapshot
2021-12-20 Jim ProcterJAL-3842 release 2.11.1.5 release notes commit | commitdiff | tree | snapshot
2021-12-20 Jim ProcterMerge branch 'critical/JAL-3933_log4shell_mitigation... commit | commitdiff | tree | snapshot
2021-12-15 Ben SoaresJAL-3933 updated THIRDPARTYLIBS commit | commitdiff | tree | snapshot
2021-12-15 Ben SoaresJAL-3933 updated THIRDPARTYLIBS commit | commitdiff | tree | snapshot
2021-12-15 Jim ProcterJAL-3933 remove obsolete Castor logging configuration commit | commitdiff | tree | snapshot
2021-12-15 Jim ProcterJAL-3933 configure root logger console appender to... commit | commitdiff | tree | snapshot
2021-12-14 Ben SoaresJAL-3933 updated slf4j to 1.7.32 commit | commitdiff | tree | snapshot
2021-12-14 Ben SoaresJAL-3933 Updated log4j jars with log4j-2.16.0 and compa... commit | commitdiff | tree | snapshot
2021-07-13 Jim ProcterJAL-3842 fix automatic what's new link for custom versi... commit | commitdiff | tree | snapshot
2021-06-30 Jim ProcterJAL-3842 JAL-3746 (need to cherry pick to develop)... commit | commitdiff | tree | snapshot
2021-06-09 Jim ProcterJAL-3842 2.11.1.5 what’s new, release notes, and versio... commit | commitdiff | tree | snapshot
2021-06-09 Jim ProcterMerge branch 'patch/JAL-3840_2_11_1_4' into releases... commit | commitdiff | tree | snapshot
2021-06-09 Jim ProcterJAL-3840 don’t update the modal residue count for gaps patch/JAL-3840_2_11_1_4 commit | commitdiff | tree | snapshot
2021-06-09 Jim Procterfixes JAL-3840 commit | commitdiff | tree | snapshot
2021-06-09 Jim ProcterJAL-3840 failing test - show that addGaps overflows commit | commitdiff | tree | snapshot
2021-04-26 Ben SoaresJAL-3248 Archived old README. Added new README to point... commit | commitdiff | tree | snapshot
2021-04-26 Ben SoaresJAL-3743 Fixed NullPointerExceptions happening with... commit | commitdiff | tree | snapshot
2021-04-19 Ben SoaresJAL-3833 cap the scaling used by HiDPISetting for incor... commit | commitdiff | tree | snapshot
2021-03-09 Jim ProcterJAL-3816 release date updated to 9th March Release_2_11_1_4 commit | commitdiff | tree | snapshot
2021-03-05 Jim ProcterJAL-3816 release date set for 8th March and updated... commit | commitdiff | tree | snapshot
2021-03-05 Jim ProcterJAL-3816 new known defects JAL-3705 and JAL-3806 commit | commitdiff | tree | snapshot
2021-03-04 Jim ProcterRevert "Merge branch 'bug/JAL-3806_mappingCoversSequenc... commit | commitdiff | tree | snapshot
2021-03-04 Jim ProcterRevert "JAL-3816 release notes for JAL-3806" commit | commitdiff | tree | snapshot
2021-02-26 Jim ProcterJAL-3816 release notes for JAL-3806 commit | commitdiff | tree | snapshot
2021-02-26 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence' into... bug/JAL-3806_mappingCoversSequence commit | commitdiff | tree | snapshot
2021-02-26 Jim ProcterJAL-3816 JAL-3814 JAL-3813 JAL-3812 JAL-3811 JAL-3818... commit | commitdiff | tree | snapshot
2021-02-24 Jim ProcterMerge branch 'bug/JAL-3818_jmolDeadlock' into releases... commit | commitdiff | tree | snapshot
2021-02-24 Jim ProcterMerge branch 'releases/Release_2_11_1_4_debianpatches... commit | commitdiff | tree | snapshot
2021-02-12 Ben SoaresJAL-3521 High quality file icons for jalview associated... releases/Release_2_11_1_4_debianpatches commit | commitdiff | tree | snapshot
2021-02-11 gmungocJAL-3818 process Jmol callbacks in AWT thread bug/JAL-3818_jmolDeadlock commit | commitdiff | tree | snapshot
2021-02-10 Ben SoaresJAL-3521 Change grouped Jalview windows on linux taskba... commit | commitdiff | tree | snapshot
2021-02-10 Ben SoaresJAL-3521 Changed wording of INSTALLATION in source... commit | commitdiff | tree | snapshot
2021-02-08 Ben SoaresJAL-3521 Adding a build_properties into sourceDist... commit | commitdiff | tree | snapshot
2021-02-08 Ben SoaresJAL-3521 Adjusted wrapper shell script and .desktop... commit | commitdiff | tree | snapshot
2021-02-07 Jim ProcterJAL-3816 bump version number and cut release notes commit | commitdiff | tree | snapshot
2021-02-07 Jim ProcterJAL-3815 default /etc/jalview_properties under utils... commit | commitdiff | tree | snapshot
2021-02-06 Ben SoaresJAL-3251 debian build using maven, simplified build... commit | commitdiff | tree | snapshot
2021-02-06 Ben SoaresJAL-3521 Moved the debian build.gradle to utils/debian... commit | commitdiff | tree | snapshot
2021-02-05 Jim ProcterMerge branch 'task/JAL-3521_Slimmed_down_build.gradle_f... commit | commitdiff | tree | snapshot
2021-02-05 Jim ProcterMerge branch 'releases/Release_2_11_1_4_debianpatches... commit | commitdiff | tree | snapshot
2021-02-05 Jim ProcterJAL-3814 don’t automatically launch the news browser... commit | commitdiff | tree | snapshot
2021-02-05 Jim ProcterJAL-3813 NOIDENTIFIERSSERVICE preference disables jalvi... commit | commitdiff | tree | snapshot
2021-02-05 Jim ProcterJAL-3812 new argument ‘-nohtmltemplates’ and user prefe... commit | commitdiff | tree | snapshot
2021-02-05 Jim ProcterJAL-3811 document SHOW_JWS2_SERVICES user preference... commit | commitdiff | tree | snapshot
2021-02-05 Jim ProcterJAL-3814 NONEWS property commit | commitdiff | tree | snapshot
2021-02-04 gmungocJAL-3806 fix and test for one-to-many sequence mapping... bug/JAL-3806_mappingCoversCDS_reprise commit | commitdiff | tree | snapshot
2021-01-28 gmungocJAL-3806 more lax allowance (3 positions) for stop... commit | commitdiff | tree | snapshot
2021-01-26 Ben SoaresJAL-3521 Updating file opening marker to %u commit | commitdiff | tree | snapshot
2021-01-26 Ben SoaresJAL-3521 Debian mime-type and desktop helper files... commit | commitdiff | tree | snapshot
2020-11-19 Ben SoaresJAL-3521 removed unnecessary parts of the ext project... task/JAL-3521_Slimmed_down_build.gradle_for_debian commit | commitdiff | tree | snapshot
2020-11-19 Ben SoaresJAL-3521 Minimal plugins and tasks needed to run tests... commit | commitdiff | tree | snapshot
2020-10-29 Jim ProcterJAL-3766 what’s new and release notes for 2.11.1.3 Release_2_11_1_3 commit | commitdiff | tree | snapshot
2020-10-29 Jim ProcterJAL-3759 fix compilation error for test commit | commitdiff | tree | snapshot
2020-10-29 Jim ProcterJAL-3766 release notes for JAL-3759 commit | commitdiff | tree | snapshot
2020-10-29 Jim Procter JAL-3759 exclude hidden columns when processing... commit | commitdiff | tree | snapshot
2020-10-29 Jim ProcterMerge branch 'documentation/JAL-3766_relnotes' into... commit | commitdiff | tree | snapshot
2020-10-29 Jim ProcterJAL-3766 release notes for JAL-3765 JAL-3763 JAL-3760... commit | commitdiff | tree | snapshot
2020-10-29 Jim ProcterMerge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11... commit | commitdiff | tree | snapshot
2020-10-29 Ben SoaresJAL-3248 Fixed path typos in building.md/html and corre... commit | commitdiff | tree | snapshot
2020-10-29 gmungocJAL-3700 mapped sequence group includes short (or all... patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3 commit | commitdiff | tree | snapshot
2020-10-28 Jim ProcterJAL-3725 fix tests for EMBLFlatFile parser when mapping... commit | commitdiff | tree | snapshot
2020-10-28 Jim ProcterJAL-3725 patch EMBL flat file to exclude stop codon... commit | commitdiff | tree | snapshot
2020-10-28 gmungocJAL-3725 restrict mapped virtual feature location to... commit | commitdiff | tree | snapshot
2020-10-28 gmungocJAL-3725 helper methods for computing mapped feature... commit | commitdiff | tree | snapshot
2020-10-28 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping commit | commitdiff | tree | snapshot
2020-10-28 Jim ProcterMerge branch 'bug/JAL-3760_protsTreatedAsNucleotides... commit | commitdiff | tree | snapshot
2020-10-28 Ben SoaresJAL-3248 Added step to create the eclipse files before... commit | commitdiff | tree | snapshot
2020-10-27 Jim ProcterJAL-3768 noticed failure of test when run as part of... commit | commitdiff | tree | snapshot
2020-10-27 Jim ProcterJAL-3700 JAL-3748 JAL-3763 don’t add stop codon via... commit | commitdiff | tree | snapshot
2020-10-27 Jim Procterupdate test for JAL-3763 redact shared DS sequences... commit | commitdiff | tree | snapshot
2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests commit | commitdiff | tree | snapshot
2020-10-22 gmungocJAL-3751 only merge strictly contiguous ranges of mappings commit | commitdiff | tree | snapshot
2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMapped... commit | commitdiff | tree | snapshot
2020-10-22 gmungocJAL-3700 JAL-3763 create datasets for test sequences commit | commitdiff | tree | snapshot
2020-10-22 gmungocJAL-3763 failsafe check for null commit | commitdiff | tree | snapshot
2020-10-22 gmungocJAL-3763 refactored getCoveringMapping for virtual... commit | commitdiff | tree | snapshot
2020-10-22 gmungocJAL-3763 always make a new dataset sequence for CDS... commit | commitdiff | tree | snapshot
2020-10-22 gmungocJAL-3700 additions and corrections to unit tests commit | commitdiff | tree | snapshot
2020-10-21 Jim ProcterJAL-3766 release notes for JAL-3611 JAL-3765 commit | commitdiff | tree | snapshot
2020-10-21 Jim ProcterMerge branch 'releases/Release_2_11_1_Branch' of source... commit | commitdiff | tree | snapshot
2020-10-21 Jim ProcterMerge branch 'bug/JAL-3765_Find_bugs_in_21112' into... commit | commitdiff | tree | snapshot
2020-10-21 Jim ProcterJAL-3766 cut new patch release commit | commitdiff | tree | snapshot
2020-10-20 Jim ProcterJAL-3765 fix test bug/JAL-3765_Find_bugs_in_21112 commit | commitdiff | tree | snapshot
2020-10-20 Jim Procterfix for JAL-3765 commit | commitdiff | tree | snapshot
2020-10-19 Jim ProcterJAL-3765 simple test that findAll finds all matches... commit | commitdiff | tree | snapshot
2020-10-15 Ben SoaresJAL-3611 added quotation marks for appdir argument... commit | commitdiff | tree | snapshot
2020-09-29 Jim ProcterJAL-3760 fix tests for changed behaviour bug/JAL-3760_protsTreatedAsNucleotides commit | commitdiff | tree | snapshot
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