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jalview.git
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
2021-02-10 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
2021-01-26 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
2020-09-29 Jim ProcterJAL-3760 refactor nucleotide proportion test to per... commit | commitdiff | tree | snapshot
2020-09-25 Ben SoaresJAL-3577 Removed default JALVIEW_VERSION from gradle... commit | commitdiff | tree | snapshot
2020-09-25 Jim ProcterJAL-3758 tweak what’s new for 2.11.1.2! Release_2_11_1_2 commit | commitdiff | tree | snapshot
2020-09-25 Jim ProcterJAL-3758 release Fri 25th Sep commit | commitdiff | tree | snapshot
2020-09-25 Jim ProcterMerge branch 'releases/Release_2_11_1_Branch' of source... commit | commitdiff | tree | snapshot
2020-09-24 Ben SoaresJAL-3577 Quick fix adding quotation marks for findPrope... commit | commitdiff | tree | snapshot
2020-09-24 Jim ProcterJAL-3758 2.11.1.2 patch release notes and version bump commit | commitdiff | tree | snapshot
2020-09-24 Jim ProcterJAL-3757 JAL-3689 use AppletFormat.checkProtocol to... commit | commitdiff | tree | snapshot
2020-09-23 Ben SoaresJAL-3757 JAL-3689 Fixed checks for URLs by adding check... commit | commitdiff | tree | snapshot
2020-09-23 Ben SoaresJAL-3633 ensure check both or https:// for urls commit | commitdiff | tree | snapshot
2020-09-23 Jim ProcterJAL-3748 not testing for sequence’s containment in... bug/JAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2 commit | commitdiff | tree | snapshot
2020-09-23 Jim ProcterJAL-3748 fix compilation error commit | commitdiff | tree | snapshot
2020-09-23 Jim ProcterJAL-3748 maximal test for JAL-3748 using covid19 CDS... commit | commitdiff | tree | snapshot
2020-09-23 Jim ProcterJAL-3748 more tests verifying reconstruction of Alignem... commit | commitdiff | tree | snapshot
2020-09-23 Jim ProcterJAL-3748 reusable assert to trace specific issues with... commit | commitdiff | tree | snapshot
2020-09-23 Jim ProcterJAL-3748 allow AlignedCodonFrame.covers to optionally... commit | commitdiff | tree | snapshot
2020-09-22 Jim ProcterJAL-3748 test data for SplitFrameTest commit | commitdiff | tree | snapshot
2020-09-22 Jim ProcterJAL-3748 don’t trash start/end on SequenceI reconstruct... commit | commitdiff | tree | snapshot
2020-09-22 Jim ProcterJAL-3748 simple test for SeqCigar preservation of start... commit | commitdiff | tree | snapshot
2020-09-22 Jim ProcterJAL-3748 additional asserts to verify start/end after... commit | commitdiff | tree | snapshot
2020-09-17 Jim ProcterJAL-3675 release notes for JAL-3750 JAL-3751 Release_2_11_1_1 commit | commitdiff | tree | snapshot
2020-09-17 Jim ProcterMerge branch 'patch/JAL-3750_JAL-3741_https_patch'... commit | commitdiff | tree | snapshot
2020-09-17 Jim ProcterJAL-3741 http to https (and jar to jvp for exampleFile... commit | commitdiff | tree | snapshot
2020-09-17 Jim ProcterJAL-3750 parse protocol before checking if argument... commit | commitdiff | tree | snapshot
2020-09-17 Jim ProcterJAL-3675 patch release date 17th September 2020 commit | commitdiff | tree | snapshot
2020-09-16 Jim ProcterJAL-3748 preserve sequence IDs from original alignment... commit | commitdiff | tree | snapshot
2020-09-16 Jim ProcterJAL-3748 recover complement alignment from complement... commit | commitdiff | tree | snapshot
2020-09-16 Jim ProcterJAL-3748 make findAlignedSequence require mapped from... commit | commitdiff | tree | snapshot
2020-09-16 Jim ProcterJAL-3748 pass a list to findAlignedSequence to return... commit | commitdiff | tree | snapshot
2020-09-16 Jim ProcterJAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq... commit | commitdiff | tree | snapshot
2020-09-16 Jim ProcterJAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true... commit | commitdiff | tree | snapshot
2020-09-16 Jim ProcterMerge branch 'failingTest/JAL-3748_reconstructCDSafterP... commit | commitdiff | tree | snapshot
2020-09-16 gmungocJAL-3700 fix for propagation of sort commands commit | commitdiff | tree | snapshot
2020-09-16 gmungocJAL-3700 check for 'covering' mapping when matching... commit | commitdiff | tree | snapshot
2020-09-16 Jim ProcterJAL-3748 store an AlignmentView for the complement... commit | commitdiff | tree | snapshot
2020-09-15 Jim ProcterJAL-3675 logged JAL-3748 as known defect commit | commitdiff | tree | snapshot
2020-09-15 Jim ProcterJAL-3765 JAL-3718 release notes commit | commitdiff | tree | snapshot
2020-09-15 Jim ProcterMerge branch 'patch/JAL-3718_fixed_getdown_patched_for_... commit | commitdiff | tree | snapshot
2020-09-15 Ben SoaresJAL-3718 Fixed getdown auto-update. This commit Getdown... commit | commitdiff | tree | snapshot
2020-09-15 Ben SoaresJAL-3718 force re-initialise of getdown.txt file when... commit | commitdiff | tree | snapshot
2020-09-15 Jim ProcterJAL-3675 typo in release notes :( commit | commitdiff | tree | snapshot
2020-09-15 Jim ProcterJAL-3675 update release date and release notes for... commit | commitdiff | tree | snapshot
2020-09-03 gmungocJAL-3648 resize annotation panel after dragging to... commit | commitdiff | tree | snapshot
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