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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
2020-10-27 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
2020-09-23 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
2020-09-16 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
2020-08-17 Jim ProcterJAL-3675 report JAL-3702 as known defect commit | commitdiff | tree | snapshot
2020-08-17 Jim ProcterMerge branch 'patch/JAL-3561_JAL-3660_fileformatexport_... commit | commitdiff | tree | snapshot
2020-08-17 Jim ProcterJAL-3712 fix typos for rebuilding/updating getdown... commit | commitdiff | tree | snapshot
2020-08-17 Jim ProcterJAL-3490 JAL-3675 release notes, update Find dialog... commit | commitdiff | tree | snapshot
2020-08-17 Jim ProcterMerge branch 'patch/Release_2_11_1_Branch_patch_JAL... commit | commitdiff | tree | snapshot
2020-08-17 Jim ProcterJAL-3675 JAL-3597 release notes commit | commitdiff | tree | snapshot
2020-08-17 Jim ProcterMerge branch 'patch/JAL-3597_for_Release_2_11_1_Branch... commit | commitdiff | tree | snapshot
2020-08-14 Ben SoaresJAL-3676 More explicit tooltip about resetting log... commit | commitdiff | tree | snapshot
2020-08-13 Ben SoaresJAL-3597 Increased heap passmark to <= 45MB and report... commit | commitdiff | tree | snapshot
2020-08-13 gmungocJAL-3597 slight tidying of code and Javadoc, passmark... commit | commitdiff | tree | snapshot
2020-08-13 gmungocJAL-3597 additional references nulled, bug in test... commit | commitdiff | tree | snapshot
2020-08-13 Jim ProcterJAL-3675 brought forward patch to build.gradle for... commit | commitdiff | tree | snapshot
2020-08-13 Jim ProcterMerge branch 'releases/Release_2_11_1_Branch' of source... commit | commitdiff | tree | snapshot
2020-08-12 Ben SoaresJAL-3676 Removed BACKUPFILESPRESETENTRY logging for... commit | commitdiff | tree | snapshot
2020-08-12 Jim ProcterJAL-3675 added JAL-3576 as known defect (colocated... commit | commitdiff | tree | snapshot
2020-08-12 Ben SoaresJAL-3608 Changes from code review CR-JAL-236 commit | commitdiff | tree | snapshot
2020-08-11 Jim ProcterJAL-3675 fix issue attribution for JAL-3667 release... commit | commitdiff | tree | snapshot
2020-08-11 Jim ProcterJAL-3675 update release notes for JAL-3673 and tested... commit | commitdiff | tree | snapshot
2020-08-11 Jim ProcterJAL-3673 make sure font metrics are updated if dealing... commit | commitdiff | tree | snapshot
2020-08-11 Jim ProcterMerge branch 'bug/JAL-2983negativeSliderMin' into relea... commit | commitdiff | tree | snapshot
2020-08-11 gmungocJAL-3371 more fine-grained slider; set Param slider... commit | commitdiff | tree | snapshot
2020-08-10 gmungocJAL-3490 match count independent of contiguous matches... patch/Release_2_11_1_Branch_patch_JAL-3490 commit | commitdiff | tree | snapshot
2020-08-10 Jim ProcterJAL-3691 toUpperCase(Locale.ROOT) for all standard... commit | commitdiff | tree | snapshot
2020-08-10 Jim ProcterMerge branch 'releases/Release_2_11_1_Branch' into... commit | commitdiff | tree | snapshot
2020-08-10 Jim ProcterJAL-3628 JAL-3708 call Cache.initLogger() before using... commit | commitdiff | tree | snapshot
2020-08-05 Ben SoaresJAL-3691 Changed .toUppoerCase().startsWith(...) to... commit | commitdiff | tree | snapshot
2020-08-05 Jim ProcterJAL-3628 init log after loading testProps for each... commit | commitdiff | tree | snapshot
2020-08-05 Jim ProcterMerge branch 'patch/JAL-3692enaEndpointFlatfile' into... commit | commitdiff | tree | snapshot
2020-08-05 gmungocJAL-3692 unit test updated for ?gzip download endpoint URL patch/JAL-3692enaEndpointFlatfile commit | commitdiff | tree | snapshot
2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped... commit | commitdiff | tree | snapshot
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