JAL-2629 JAL-2937 respect 'align automatically' option for HMMSearch
[jalview.git] / test /
2018-05-14 gmungocJAL-2711 removed unused and flaky utility method
2018-05-11 gmungocMerge branch 'develop' into features/mchmmer
2018-05-11 gmungocJAL-2986 additional asserts for SequenceCursor updates
2018-05-11 gmungocJAL-2986 failing test added
2018-05-08 gmungocMerge branch 'develop' into features/mchmmer
2018-05-07 gmungocJAL-2808 ensure test setUp/tearDown alwaysRun
2018-05-07 gmungocMerge branch 'releases/Release_2_10_4_Branch' into...
2018-04-25 Jim ProcterMerge branch 'features/JAL-2944_openStructuresInSelecte...
2018-04-24 gmungocJAL-2956 unit test
2018-04-23 gmungocJAL-2952 set negative TempFactor values as AlignmentAnn...
2018-04-20 gmungocJAL-591 OptionBox FlowLayout, tweaks to wrapping of...
2018-04-18 gmungocMerge branch 'develop' into features/mchmmer
2018-04-18 gmungocMerge branch 'releases/Release_2_10_4_Branch' into...
2018-04-18 gmungocJAL-2593 render 'duplicate' features if transparency...
2018-04-17 gmungocJAL-2629 choice of hmm profile now a parameter not...
2018-04-17 Mungo CarstairsJAL-2937 working Cygwin bash execution of hmmbuild...
2018-04-12 gmungocJAL-2223 don't add duplicate mappings to StructureSelec...
2018-04-12 gmungocJAL-2944 tidies for review comments
2018-04-06 Jim Procterfailing test for JAL-2223
2018-04-05 Jim ProcterJAL-2945 failing test for structure mapping
2018-04-05 Jim ProcterJAL-2945 formatting
2018-03-30 gmungocJAL-2599 MapList from HMM nodes to consensus dataset...
2018-03-30 gmungocJAL-2629 ensure hmm consensus sequence set on alignment...
2018-03-30 gmungocsmall tidy
2018-03-30 gmungocJAL-2938 revisions to implementation details
2018-03-30 gmungocJAL-2599 move utility method to MappingUtils
2018-03-30 gmungocJAL-2599 corrected test file name in unit test
2018-03-29 gmungocJAL-2907 test method renamed to match method name change
2018-03-29 gmungocJAL-2907 bug fix redone on HMMER branch
2018-03-28 gmungocJAL-1265 output all dbrefs in Stockholm (+tests) (...
2018-03-26 gmungocJAL-2939 pull up set/IsNormalise[HMM]SequenceLogo
2018-03-23 gmungocJAL-2938 extracted base class for Hmmer colour schems
2018-03-22 gmungocJAL-2929 unit test, tidy unused/unneeded fields/parameters
2018-03-21 Jim ProcterJAL-2754 reinstate PA import from bad conflict merge
2018-03-21 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-03-21 Jim ProcterJAL-2754 don’t use deprecated api for getting font...
2018-03-20 gmungocJAL-2629 InformationThread.findOrCreateAnnotation and...
2018-03-20 gmungocMerge branch 'develop' into features/mchmmer
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-03-16 gmungocMerge branch 'develop' into trialMerge
2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES
2018-03-08 gmungocMerge remote-tracking branch 'origin/releases/Release_2... merges/JAL-2906_update2_11_from_2_10_4
2018-03-08 gmungocJAL-2885 tests updated for code changes
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-03-07 gmungocJAL-2629 storage and lifecycle of alignment/group HMM...
2018-02-27 gmungocJAL-2668 method name change for clarity
2018-02-27 gmungocJAL-2717 JAL-2668 fixes to HMMER colour scheme display...
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104
2018-02-26 gmungocJAL-2599 test coverage and bug fixes for 'minimal file...
2018-02-23 gmungocJAL-2599 corrected case-insensitive symbol indexing
2018-02-23 Jim ProcterMerge branch 'features/JAL-2885UniprotHttps' into relea...
2018-02-23 gmungocJAL-2599 parser and datamodel use primitive double...
2018-02-22 gmungocJAL-2629 tidy tests, refactor hmmer node mapping slightly
2018-02-22 Jim ProcterMerge branch 'bug/JAL-2666' into releases/Release_2_10_...
2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc
2018-02-21 gmungocJAL-2629 simplifying method signatures in Hmmer command...
2018-02-20 gmungocJAL-2629 removed SequenceI.get/setLastPosition and...
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer
2018-02-20 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-20 gmungocJAL-2897 updated unit test for code change features/JAL-1793VCF
2018-02-13 Jim ProcterJAL-2780 scan all test IDs before testing and reporting... bugs/JAL-2780_JAL-2781_pdbnegativenums
2018-02-13 Jim ProcterJAL-2780 SequenceI.findFeatures takes column numbers...
2018-02-13 Jim ProcterJAL-2781 ensure Trim is disabled before test starts
2018-02-13 Jim ProcterJAL-2781 report exactly which residues do not receive...
2018-02-12 Jim ProcterJAL-2780 JAL-2781 extra column in mapping array
2018-02-12 Jim ProcterJAL-2904 JAL-2780 JAL-2781 update JmolCommandsTest...
2018-02-12 Jim ProcterJAL-2780 use value of ’UNASSIGNED’ constant in assert...
2018-02-12 Jim ProcterJAL-2904 replaced assert for (getEnd()-getStart()+1...
2018-02-11 Jim ProcterJAL-2781 fix test data for full length annotation
2018-02-09 gmungocJAL-2789 avoid using transcript (with no UTR) as CDS... bug/JAL-2666
2018-02-07 Jim ProcterJAL-2780 JAL-2781 run sequentially and ensure windows...
2018-02-07 Jim ProcterJAL-2780 JAL-2891 clear all windows always beforeTest...
2018-02-07 Jim ProcterJAL-2780 JAL-2781 first pass at failing test for incorr...
2018-02-07 Jim ProcterJAL-2780 JAL-2781 JAL-2902 refactored helper method...
2018-02-06 kiramtMerge branch 'develop' into feature/JAL-2759 feature/JAL-2759
2018-02-05 Jim ProcterJAL-2780 JAL-2781 (failing) test comparing location...
2018-02-05 Jim ProcterJAL-2780 JAL-2781 test AlignmentI.findAnnotations locat...
2018-02-05 Jim ProcterJAL-2780 JAL-2781 - patch and first test for AlignmentI...
2018-02-05 kiramtJAL-2759 Rename getBoundedStartIterator
2018-02-05 kiramtJAL-2759 Changes to StartRegionIterator after review
2018-02-05 gmungocJAL-2897 more informative description on synonymous...
2018-02-05 gmungocJAL-2897 more informative description on synonymous...
2018-02-05 gmungocMerge branch 'spikes/mungo' into trialMerge
2018-02-05 gmungocJAL-2897 more informative description on synonymous...
2018-01-31 kiramtJAL-2759 Rationalise VisibleColsIterator and HiddenCols...
2018-01-31 kiramtJAL-2759 test renaming
2018-01-31 kiramtJAL-2759 minor refactor to hiding bitsets
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and...
2018-01-30 gmungocJAL-2898 show 'stop_gained' variants on peptide sequences
2018-01-30 kiramtJAL-2759 Add missing hiddenColumns empty check
2018-01-30 kiramtJAL-2759 updateForDeletedRegion no longer needed
2018-01-30 gmungocJAL-2897 generate peptide variants for synonymous codon...
2018-01-30 kiramtJAL-2759 Rationalising hidden cols cursor, and sorting...
2018-01-30 kiramtJAL-2759 Additional tests and tweaks to numColumns...
2018-01-30 kiramtJAL-2759 Keep numColumns up to date
2018-01-29 kiramtMerge branch 'feature/JAL-2759' of https://source.jalvi...
2018-01-29 kiramtJAL-2759 Combine findRegionForColumn code in HiddenColu...
2018-01-29 gmungocJAL-1270 testPadGaps() added
2018-01-29 kiramtJAL-2759 make a new cursor instead of resetting, update...
2018-01-26 Jim ProcterMerge branch 'releases/Release_2_10_3_Branch' into...
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