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JAL-2629 add ability to add background frequencies to a HMM
[jalview.git] / src / jalview / datamodel /
2017-08-16 Jim ProcterJAL-2418 source formatting tree | commitdiff
2017-08-16 kiramtJAL-2665 Added hidden columns group selection - almost... tree | commitdiff
2017-08-16 kiramtJAL-2665 Added sequence group update event. tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 add insert sequence at method on alignment tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 fix incorrect gap insertions on HMM sequence tree | commitdiff
2017-08-11 TZVanaaltenJAL-2629 add ability to build a HMM from a group tree | commitdiff
2017-08-11 TZVanaaltenJAL-2599 HMMs can now be dropped onto the desktop tree | commitdiff
2017-08-10 TZVanaaltenJAL-2629 hmmalign now correctly creates a new frame tree | commitdiff
2017-08-09 gmungocJAL-2480 inline one method, improve comments tree | commitdiff
2017-08-08 TZVanaaltenJAL-2599 fix for index issue on node lookup tree | commitdiff
2017-08-04 TZVanaaltenJAL-2629 multiple HMMs can now be dropped onto an alignment tree | commitdiff
2017-08-02 TZVanaaltenJAL-2599 fix for information annotation buttons tree | commitdiff
2017-08-01 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-07-31 TZVanaaltenJAL-2629 add hmmalign command tree | commitdiff
2017-07-27 TZVanaaltenJAL-2629 implement hmmbuild tree | commitdiff
2017-07-27 TZVanaaltenJAL-2629 moved HMM storage location to placeholder... tree | commitdiff
2017-07-26 TZVanaaltenJAL-2629 HMMs now map to reference annotation if exists tree | commitdiff
2017-07-24 tzvanaaltenJAL-2616 add placeholder sequence for HMM, does not... tree | commitdiff
2017-07-24 gmungocspike branch updated from latest features/JAL-2446 tree | commitdiff
2017-07-22 kiramtMerge branch 'develop' into feature/JAL-2611 tree | commitdiff
2017-07-20 TZVanaaltenJAL-2599 small code improvements tree | commitdiff
2017-07-19 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-07-18 TZVanaaltenJAL-2599 complete documentation for HMM and HMMFile... tree | commitdiff
2017-07-18 TZVanaaltenJAL-2599 modified state transition probability storage tree | commitdiff
2017-07-14 TZVanaaltenadd partial button fix to annotation and statistics... features/hmmer_statistics tree | commitdiff
2017-07-13 kiramtJAL-2613 Unit tests and a fix. Phew. tree | commitdiff
2017-07-12 TZVanaaltentest HMM annotaTION tree | commitdiff
2017-07-11 TZVanaaltencomplete Information Content annotation tree | commitdiff
2017-07-05 gmungocJAL-147 additions to unit test, check for negative... tree | commitdiff
2017-07-05 gmungocJAL-147 prevent overview box move up over hidden first... tree | commitdiff
2017-06-30 gmungocJAL-2505 correct handling of change of feature type tree | commitdiff
2017-06-30 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-06-29 TZVanaaltenadd information content calculations tree | commitdiff
2017-06-29 TZVanaaltentransferred the storage position of the HMM to annotations tree | commitdiff
2017-06-29 kiramtJAL-2597 Fix and unit test bug/JAL-2597 tree | commitdiff
2017-06-27 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-06-24 gmungocMerge branch 'features/JAL-2446NCList' into spikes... tree | commitdiff
2017-06-24 gmungocJAL-2547 fix case of gap followed by enclosing contact... tree | commitdiff
2017-06-24 gmungocMerge branch 'features/JAL-2446NCList' into spikes... tree | commitdiff
2017-06-23 gmungocJAL-1858 handle hidden columns when computing region... tree | commitdiff
2017-06-23 TZVanaaltentest HMMER colour scheme tree | commitdiff
2017-06-23 TZVanaaltenadd HMMER colour scheme tree | commitdiff
2017-06-22 gmungocJAL-2481 JAL-2593 JAL-2526 further optimisation of... tree | commitdiff
2017-06-22 TZVanaaltenfully integrate HMMER3 file format into Jalview tree | commitdiff
2017-06-22 gmungocJAL-2480 simpler and safer test to avoid adding duplicates tree | commitdiff
2017-06-21 gmungocJAL-2480 tidy generic initialisations, SequenceFeatures... tree | commitdiff
2017-06-20 TZVanaaltenrestructure file exporter tree | commitdiff
2017-06-20 gmungocJAL-2526 don't retain lastColumnPosition from an invali... tree | commitdiff
2017-06-15 gmungocMerge branch 'bug/JAL-2386groupConservationColouring... tree | commitdiff
2017-06-15 TZVanaaltenadd HMMFile class to read and write HMM files tree | commitdiff
2017-06-15 TZVanaaltenUpdate HiddenMarkovModel class tree | commitdiff
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the... tree | commitdiff
2017-06-12 kiramtJAL-2591 Updates following code review tree | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch tree | commitdiff
2017-06-09 TZVanaaltenAdd HiddenMarkovModel class tree | commitdiff
2017-06-09 gmungocJAL-2480 tidy javadoc tree | commitdiff
2017-06-08 gmungocJAL-2526 correct boundary conditions for sequence left... tree | commitdiff
2017-06-08 gmungocJAL-2386 JAL-2570 use ResidueShader copy constructor... bug/JAL-2386groupConservationColouring tree | commitdiff
2017-06-08 kiramtJAL-2591 Refactor HiddenColumns to use ArrayList instea... tree | commitdiff
2017-06-08 kiramtJAL-2591 More HiddenColumns refactoring. Tests passing. tree | commitdiff
2017-06-08 gmungocJAL-2526 cache first/last residue column positions... tree | commitdiff
2017-06-08 gmungocJAL-2526 reuse findIndex result if start==end tree | commitdiff
2017-06-07 kiramtJAL-2591 Further refactoring (still incomplete) tree | commitdiff
2017-06-07 kiramtJAL-2591 More refactoring (incomplete) tree | commitdiff
2017-06-07 kiramtJAL-2591 Hidden columns regions can be output to string... tree | commitdiff
2017-06-07 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-06-07 kiramtJAL-2591 updated HiddenColumns::findHiddenRegionPositio... tree | commitdiff
2017-06-07 gmungocJAL-2386 ensure group conservation shading is applied... tree | commitdiff
2017-06-07 kiramtJAL-2591 simplifying hidden columns usage tree | commitdiff
2017-06-06 kiramtJAL-2591 Added readwrite locking on HiddenColumns tree | commitdiff
2017-06-06 gmungocJAL-2526 less stringent test for invalid cursor tree | commitdiff
2017-06-06 kiramtMerge remote-tracking branch 'origin/bug/JAL-2576'... tree | commitdiff
2017-06-05 Jim ProcterMerge branch 'bug/JAL-2576' into develop tree | commitdiff
2017-06-05 gmungocJAL-2505 comments updated tree | commitdiff
2017-06-05 gmungocJAL-2480 remove redundant method, further test coverage tree | commitdiff
2017-06-05 gmungocJAL-2505 explicit (and final) contactFeature property tree | commitdiff
2017-06-05 gmungocMerge branch 'features/JAL-2526sequenceCursor' into tree | commitdiff
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into tree | commitdiff
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor tree | commitdiff
2017-06-05 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-06-04 Jim ProcterJAL-2291 get bitset representing hidden columns tree | commitdiff
2017-06-04 Jim ProcterJAL-2291 method taking a BitSet for hiding columns tree | commitdiff
2017-06-04 Jim ProcterJAL-2291 bug fix - BitSet.set is [start,end+1) tree | commitdiff
2017-06-04 Jim ProcterJAL-2291 SequenceI.getInsertionsAsBits for convenient... tree | commitdiff
2017-06-02 gmungocJAL-2526 additional tests for findPosition with/without... tree | commitdiff
2017-06-02 kiramtJAL-2576 Proposed fix bug/JAL-2576 tree | commitdiff
2017-06-02 gmungocMerge branch 'features/JAL-2446NCList' into features... tree | commitdiff
2017-06-01 gmungocJAL-2526 additional calls to sequenceChanged() after... tree | commitdiff
2017-06-01 gmungocJAL-2526 zapCursor() renamed sequenceChanged() tree | commitdiff
2017-06-01 gmungocMerge branch 'features/JAL-2446NCList' into features... tree | commitdiff
2017-06-01 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn tree | commitdiff
2017-05-31 Jim ProcterMerge branch 'JAL-2571' into develop tree | commitdiff
2017-05-30 kiramtJAL-2571 Corrected alignment width/height checks to... tree | commitdiff
2017-05-30 gmungocMerge branch 'features/JAL-2446NCList' into features... tree | commitdiff
2017-05-30 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-30 gmungocJAL-2570 don't zap group colour scheme when mapping... tree | commitdiff
2017-05-30 gmungocJAL-2526 first draft of findIndex/findPosition with... tree | commitdiff
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2034contextchange' into develop tree | commitdiff
2017-05-29 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
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