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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
2020-09-03 Jim ProcterJAL-3675 update release date and release notes for... commit | commitdiff | tree | snapshot
2020-09-03 Jim ProcterMerge branch 'improvement/JAL-3280_Migrate_the_VersionC... commit | commitdiff | tree | snapshot
2020-09-03 Jim ProcterJAL-3675 whats new, logging and release notes tidying... commit | commitdiff | tree | snapshot
2020-09-03 Jim ProcterJAL-3676 rework logging docs. commit | commitdiff | tree | snapshot
2020-09-03 Jim ProcterMerge branch 'bug/JAL-3718_Getdown_does_not_autoupdate_... commit | commitdiff | tree | snapshot
2020-09-03 Jim ProcterJAL-3676 remove mention of Castor commit | commitdiff | tree | snapshot
2020-09-03 Jim ProcterJAL-3675 tweak release notes for JAL-3667, JAL-3702 commit | commitdiff | tree | snapshot
2020-09-03 Jim ProcterJAL-3675 update sequence fetcher service documentation... commit | commitdiff | tree | snapshot
2020-09-02 Ben SoaresJAL-3280 Test for remote release build_properties file... commit | commitdiff | tree | snapshot
2020-09-01 Ben SoaresJAL-3280 fixes after CR-JAL-241. Now only checking... commit | commitdiff | tree | snapshot
2020-08-31 Ben SoaresJAL-3280 Pass appbase and appdir from getdown to jalvew... commit | commitdiff | tree | snapshot
2020-08-31 Jim ProcterJAL-3680 merged description of individual cursor key... commit | commitdiff | tree | snapshot
2020-08-31 Jim ProcterJAL-3732 - sequences can be moved up/down in cursor... commit | commitdiff | tree | snapshot
2020-08-28 Ben SoaresJAL-3676 adding Axis and Castor loggging properties... commit | commitdiff | tree | snapshot
2020-08-27 Ben SoaresJAL-3676 Documentation in Help for Java Console, Loggin... commit | commitdiff | tree | snapshot
2020-08-27 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into... merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch commit | commitdiff | tree | snapshot
2020-08-25 Jim Procterreport JAL-3127 as known defect (fix targeted for 2... commit | commitdiff | tree | snapshot
2020-08-25 Jim ProcterJAL-3671 hardwire log4j.root logger to INFO to supress... commit | commitdiff | tree | snapshot
2020-08-21 Jim ProcterJAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615... commit | commitdiff | tree | snapshot
2020-08-18 Ben SoaresJAL-3718 Added digestonly key to getdown.txt to copy... commit | commitdiff | tree | snapshot
2020-08-18 gmungocJAL-3692 parse multiline CDS location correctly commit | commitdiff | tree | snapshot
2020-08-18 Ben SoaresJAL-3676 Start of documentation in help pages logging... commit | commitdiff | tree | snapshot
2020-08-17 Jim ProcterJAL-3675 release notes for JAL-3691 commit | commitdiff | tree | snapshot
2020-08-17 Jim ProcterMerge branch 'patch/JAL-3691_No_score_models_available... commit | commitdiff | tree | snapshot
2020-08-17 Jim ProcterJAL-3675 JAL-3561 documented in release notes commit | commitdiff | tree | snapshot
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