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JAL-2629 add basic parameter adjustment to hmmsearch/align
[jalview.git] / src / jalview / datamodel /
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer tree | commitdiff
2017-08-18 TZVanaaltenJAL-2668 add tests for HMMER commands, annotation and io tree | commitdiff
2017-08-17 TZVanaaltenJAL-2599 some slight renaming of variables and methods tree | commitdiff
2017-08-17 TZVanaaltenJAL-2629 add documentation to previous work tree | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting 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
2017-08-08 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
2017-07-31 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
2017-07-22 kiramtMerge branch 'develop' into feature/JAL-2611 tree | commitdiff
2017-07-20 TZVanaaltenJAL-2599 small code improvements 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
2017-06-29 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
2017-06-23 TZVanaaltentest HMMER colour scheme tree | commitdiff
2017-06-23 TZVanaaltenadd HMMER colour scheme tree | commitdiff
2017-06-22 TZVanaaltenfully integrate HMMER3 file format into Jalview tree | commitdiff
2017-06-20 TZVanaaltenrestructure file exporter 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
2017-06-12 kiramtJAL-2591 Updates following code review tree | commitdiff
2017-06-09 TZVanaaltenAdd HiddenMarkovModel class 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
2017-06-07 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 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 kiramtMerge remote-tracking branch 'origin/bug/JAL-2576'... tree | commitdiff
2017-06-05 Jim ProcterMerge branch 'bug/JAL-2576' into develop tree | commitdiff
2017-06-04 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 kiramtJAL-2576 Proposed fix bug/JAL-2576 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 gmungocJAL-2570 don't zap group colour scheme when mapping... tree | commitdiff
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2034contextchange' into develop tree | commitdiff
2017-05-27 Jim ProcterJAL-2562 javadoc TODO tree | commitdiff
2017-05-24 kiramtJAL-2034 Added isDefined flag to SequenceGroup tree | commitdiff
2017-05-22 kiramtMerge remote-tracking branch 'origin/bug/JAL-2256'... tree | commitdiff
2017-05-22 Jim ProcterJAL-2418 patch build - broken htsjdk import tree | commitdiff
2017-05-18 Jim ProcterJAL-2388 return empty hidden columns for fully visible... tree | commitdiff
2017-05-18 kiramtJAL-2256 Corrected AllCols/Rows iterator behaviour... bug/JAL-2256 tree | commitdiff
2017-05-16 kiramtJAL-2388 Rationalised hashCode method in HiddenColumns tree | commitdiff
2017-05-12 Jim ProcterMerge branch 'features/JAL-2388OverviewWindow' into... tree | commitdiff
2017-05-11 Jim ProcterJAL-2507 test if an annotation is ‘whitespace’ tree | commitdiff
2017-05-11 Jim ProcterJAL-2507 Annotation.EMPTY_ANNOTATION - non-null whitesp... tree | commitdiff
2017-05-05 kiramtMerge remote-tracking branch tree | commitdiff
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges tree | commitdiff
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into tree | commitdiff
2017-05-03 Jim ProcterJAL-2503 AlignmentAnnotation.isQuantitative() test tree | commitdiff
2017-05-02 Jim ProcterMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-05-02 Jim ProcterMerge branch 'bug/JAL-2424getVisibleContigs' into develop tree | commitdiff
2017-04-28 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-04-27 Jim ProcterJAL-2494 fix: updated behaviour for SequenceGroup.findA... tree | commitdiff
2017-04-27 Jim ProcterJAL-2494 fixed behaviour for null parameters in line... tree | commitdiff
2017-04-27 Jim ProcterJAL-2494 javadoc for AnnotatedCollectionI.findAnnotations tree | commitdiff
2017-04-26 kiramtMerge remote-tracking branch 'origin/features/JAL-2388h... tree | commitdiff
2017-04-26 kiramtJAL-2388 last separation of hidden columns/col selection tree | commitdiff
2017-04-26 kiramtJAL-2388 Tidies and unit tests tree | commitdiff
2017-04-25 kiramtJAL-2388 Working hidden regions hide/show in desktop tree | commitdiff
2017-04-24 kiramtMerge remote-tracking branch tree | commitdiff
2017-04-24 kiramtJAL-2388 Finished split of hidden columns and selected... tree | commitdiff
2017-04-24 gmungocJAL-2424 final contig now an inclusive range bug/JAL-2424getVisibleContigs tree | commitdiff
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection... tree | commitdiff
2017-04-21 kiramtJAL-2388 Alignment col and row collections with iterators tree | commitdiff
2017-04-19 kiramtMerge remote-tracking branch 'origin/develop' into tree | commitdiff
2017-04-07 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-03-31 gmungocJAL-2405 additional checks for circular reference in... tree | commitdiff
2017-03-30 gmungocMerge branch 'develop' into bug/JAL-2346annotationChoice tree | commitdiff
2017-03-29 kiramtJAL-2388 New rendering code, extensions to support... tree | commitdiff
2017-03-29 kiramtJAL-2388 New iterators and tests tree | commitdiff
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-03-21 Jim ProcterMerge branch 'features/JAL-2388OverviewWindow' into... tree | commitdiff
2017-03-17 kiramtJAL-2437 Synchronization corrections and unit tests tree | commitdiff
2017-03-17 kiramtJAL-2388 Renamed column and row subtraction functions tree | commitdiff
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