jalview.git
2020-10-29 Jim ProcterJAL-3766 what’s new and release notes for 2.11.1.3 Release_2_11_1_3
2020-10-29 Jim ProcterJAL-3759 fix compilation error for test
2020-10-29 Jim ProcterJAL-3766 release notes for JAL-3759
2020-10-29 Jim Procter JAL-3759 exclude hidden columns when processing...
2020-10-29 Jim ProcterMerge branch 'documentation/JAL-3766_relnotes' into...
2020-10-29 Jim ProcterJAL-3766 release notes for JAL-3765 JAL-3763 JAL-3760...
2020-10-29 Jim ProcterMerge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11...
2020-10-29 Ben SoaresJAL-3248 Fixed path typos in building.md/html and corre...
2020-10-29 gmungocJAL-3700 mapped sequence group includes short (or all... patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3
2020-10-28 Jim ProcterJAL-3725 fix tests for EMBLFlatFile parser when mapping...
2020-10-28 Jim ProcterJAL-3725 patch EMBL flat file to exclude stop codon...
2020-10-28 gmungocJAL-3725 restrict mapped virtual feature location to...
2020-10-28 gmungocJAL-3725 helper methods for computing mapped feature...
2020-10-28 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping
2020-10-28 Jim ProcterMerge branch 'bug/JAL-3760_protsTreatedAsNucleotides...
2020-10-28 Ben SoaresJAL-3248 Added step to create the eclipse files before...
2020-10-27 Jim ProcterJAL-3768 noticed failure of test when run as part of...
2020-10-27 Jim ProcterJAL-3700 JAL-3748 JAL-3763 don’t add stop codon via...
2020-10-27 Jim Procterupdate test for JAL-3763 redact shared DS sequences...
2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests
2020-10-22 gmungocJAL-3751 only merge strictly contiguous ranges of mappings
2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMapped...
2020-10-22 gmungocJAL-3700 JAL-3763 create datasets for test sequences
2020-10-22 gmungocJAL-3763 failsafe check for null
2020-10-22 gmungocJAL-3763 refactored getCoveringMapping for virtual...
2020-10-22 gmungocJAL-3763 always make a new dataset sequence for CDS...
2020-10-22 gmungocJAL-3700 additions and corrections to unit tests
2020-10-21 Jim ProcterJAL-3766 release notes for JAL-3611 JAL-3765
2020-10-21 Jim ProcterMerge branch 'releases/Release_2_11_1_Branch' of source...
2020-10-21 Jim ProcterMerge branch 'bug/JAL-3765_Find_bugs_in_21112' into...
2020-10-21 Jim ProcterJAL-3766 cut new patch release
2020-10-20 Jim ProcterJAL-3765 fix test bug/JAL-3765_Find_bugs_in_21112
2020-10-20 Jim Procterfix for JAL-3765
2020-10-19 Jim ProcterJAL-3765 simple test that findAll finds all matches...
2020-10-15 Ben SoaresJAL-3611 added quotation marks for appdir argument...
2020-09-29 Jim ProcterJAL-3760 fix tests for changed behaviour bug/JAL-3760_protsTreatedAsNucleotides
2020-09-29 Jim ProcterJAL-3760 refactor nucleotide proportion test to per...
2020-09-25 Ben SoaresJAL-3577 Removed default JALVIEW_VERSION from gradle...
2020-09-25 Jim ProcterJAL-3758 tweak what’s new for 2.11.1.2! Release_2_11_1_2
2020-09-25 Jim ProcterJAL-3758 release Fri 25th Sep
2020-09-25 Jim ProcterMerge branch 'releases/Release_2_11_1_Branch' of source...
2020-09-24 Ben SoaresJAL-3577 Quick fix adding quotation marks for findPrope...
2020-09-24 Jim ProcterJAL-3758 2.11.1.2 patch release notes and version bump
2020-09-24 Jim ProcterJAL-3757 JAL-3689 use AppletFormat.checkProtocol to...
2020-09-23 Ben SoaresJAL-3757 JAL-3689 Fixed checks for URLs by adding check...
2020-09-23 Ben SoaresJAL-3633 ensure check both or https:// for urls
2020-09-23 Jim ProcterJAL-3748 not testing for sequence’s containment in... bug/JAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2
2020-09-23 Jim ProcterJAL-3748 fix compilation error
2020-09-23 Jim ProcterJAL-3748 maximal test for JAL-3748 using covid19 CDS...
2020-09-23 Jim ProcterJAL-3748 more tests verifying reconstruction of Alignem...
2020-09-23 Jim ProcterJAL-3748 reusable assert to trace specific issues with...
2020-09-23 Jim ProcterJAL-3748 allow AlignedCodonFrame.covers to optionally...
2020-09-22 Jim ProcterJAL-3748 test data for SplitFrameTest
2020-09-22 Jim ProcterJAL-3748 don’t trash start/end on SequenceI reconstruct...
2020-09-22 Jim ProcterJAL-3748 simple test for SeqCigar preservation of start...
2020-09-22 Jim ProcterJAL-3748 additional asserts to verify start/end after...
2020-09-17 Jim ProcterJAL-3675 release notes for JAL-3750 JAL-3751 Release_2_11_1_1
2020-09-17 Jim ProcterMerge branch 'patch/JAL-3750_JAL-3741_https_patch'...
2020-09-17 Jim ProcterJAL-3741 http to https (and jar to jvp for exampleFile...
2020-09-17 Jim ProcterJAL-3750 parse protocol before checking if argument...
2020-09-17 Jim ProcterJAL-3675 patch release date 17th September 2020
2020-09-16 Jim ProcterJAL-3748 preserve sequence IDs from original alignment...
2020-09-16 Jim ProcterJAL-3748 recover complement alignment from complement...
2020-09-16 Jim ProcterJAL-3748 make findAlignedSequence require mapped from...
2020-09-16 Jim ProcterJAL-3748 pass a list to findAlignedSequence to return...
2020-09-16 Jim ProcterJAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq...
2020-09-16 Jim ProcterJAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true...
2020-09-16 Jim ProcterMerge branch 'failingTest/JAL-3748_reconstructCDSafterP...
2020-09-16 gmungocJAL-3700 fix for propagation of sort commands
2020-09-16 gmungocJAL-3700 check for 'covering' mapping when matching...
2020-09-16 Jim ProcterJAL-3748 store an AlignmentView for the complement...
2020-09-15 Jim ProcterJAL-3675 logged JAL-3748 as known defect
2020-09-15 Jim ProcterJAL-3765 JAL-3718 release notes
2020-09-15 Jim ProcterMerge branch 'patch/JAL-3718_fixed_getdown_patched_for_...
2020-09-15 Ben SoaresJAL-3718 Fixed getdown auto-update. This commit Getdown...
2020-09-15 Ben SoaresJAL-3718 force re-initialise of getdown.txt file when...
2020-09-15 Jim ProcterJAL-3675 typo in release notes :(
2020-09-15 Jim ProcterJAL-3675 update release date and release notes for...
2020-09-03 gmungocJAL-3648 resize annotation panel after dragging to...
2020-09-03 Jim ProcterJAL-3675 update release date and release notes for...
2020-09-03 Jim ProcterMerge branch 'improvement/JAL-3280_Migrate_the_VersionC...
2020-09-03 Jim ProcterJAL-3675 whats new, logging and release notes tidying...
2020-09-03 Jim ProcterJAL-3676 rework logging docs.
2020-09-03 Jim ProcterMerge branch 'bug/JAL-3718_Getdown_does_not_autoupdate_...
2020-09-03 Jim ProcterJAL-3676 remove mention of Castor
2020-09-03 Jim ProcterJAL-3675 tweak release notes for JAL-3667, JAL-3702
2020-09-03 Jim ProcterJAL-3675 update sequence fetcher service documentation...
2020-09-02 Ben SoaresJAL-3280 Test for remote release build_properties file... improvement/JAL-3280_Migrate_the_VersionChecker_service_to_build_properties
2020-09-01 Ben SoaresJAL-3280 fixes after CR-JAL-241. Now only checking...
2020-08-31 Ben SoaresJAL-3280 Pass appbase and appdir from getdown to jalvew...
2020-08-31 Jim ProcterJAL-3680 merged description of individual cursor key...
2020-08-31 Jim ProcterJAL-3732 - sequences can be moved up/down in cursor...
2020-08-28 Ben SoaresJAL-3676 adding Axis and Castor loggging properties...
2020-08-27 Ben SoaresJAL-3676 Documentation in Help for Java Console, Loggin...
2020-08-27 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into... merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch
2020-08-25 Jim Procterreport JAL-3127 as known defect (fix targeted for 2...
2020-08-25 Jim ProcterJAL-3671 hardwire log4j.root logger to INFO to supress...
2020-08-21 Jim ProcterJAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615...
2020-08-18 Ben SoaresJAL-3718 Added digestonly key to getdown.txt to copy...
2020-08-18 gmungocJAL-3692 parse multiline CDS location correctly
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