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2017-08-17 TZVanaaltenJAL-2599 some slight renaming of variables and methods commit | commitdiff | tree | snapshot
2017-08-17 TZVanaaltenJAL-2629 add documentation to previous work commit | commitdiff | tree | snapshot
2017-08-16 TZVanaaltenJAL-2599 HMM annotation now shows consensus characters... commit | commitdiff | tree | snapshot
2017-08-16 TZVanaaltenJAL-2599 fix background frequency storage and correct... commit | commitdiff | tree | snapshot
2017-08-16 TZVanaaltenJAL-2629 fix for hmmbuild not loading a HMM onto the... commit | commitdiff | tree | snapshot
2017-08-16 TZVanaaltenJAL-2629 add hmmbuild validation check which also gets... commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 prevent hmmbuild from running if there are... commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 configure file chooser to select either a... commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 add checks for executing hmmer commands as... commit | commitdiff | tree | snapshot
2017-08-15 tzvanaaltenJAL-2629 fix file loading issues on Mac commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 add HMMER version check commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 selected HMM name now shown in HMMER menu commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 exported HMMs are now named correctly commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 fix uniquified sequence names appearing when... commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2599 fix HMMER scheme not colouring inserts and... commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 the HMMER tab is now disabled when HMMER is... commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 remove annotation when exporting for hmmbuild commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 remove gap padding, and now has option to... commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 add insert sequence at method on alignment commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 fix expected length error for hmmbuild by... commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 add padding for .sto annotations to fix issues... commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 remove redundant options from HMMER menu commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 add validation for HMMER path commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 fix incorrect gap insertions on HMM sequence commit | commitdiff | tree | snapshot
2017-08-13 TZVanaaltenJAL-2629 fix issue where trim termini setting would... commit | commitdiff | tree | snapshot
2017-08-13 TZVanaaltenJAL-2629 hmmalign can now be run from the sequence... commit | commitdiff | tree | snapshot
2017-08-13 TZVanaaltenJAL-2629 add force alphabet type for HMMER commands commit | commitdiff | tree | snapshot
2017-08-13 TZVanaaltenJAL-2629 fix issue where HMM sequences would be too... commit | commitdiff | tree | snapshot
2017-08-13 TZVanaaltenJAL-2629 add HMMER tab in preferences menu commit | commitdiff | tree | snapshot
2017-08-11 TZVanaaltenJAL-2629 delete unnecessary buffer files for hmmer... commit | commitdiff | tree | snapshot
2017-08-11 TZVanaaltenJAL-2629 add ability to build a HMM from a group commit | commitdiff | tree | snapshot
2017-08-11 TZVanaaltenJAL-2629 add ability to select HMMs commit | commitdiff | tree | snapshot
2017-08-11 TZVanaaltenJAL-2599 HMMs can now be dropped onto the desktop commit | commitdiff | tree | snapshot
2017-08-10 TZVanaaltenJAL-2629 hmmalign now correctly creates a new frame commit | commitdiff | tree | snapshot
2017-08-10 tzvanaaltenMerge branch 'features/hmmer' of https://source.jalview... commit | commitdiff | tree | snapshot
2017-08-10 tzvanaaltenJAL-2629 fix files permission issue on Mac commit | commitdiff | tree | snapshot
2017-08-09 TZVanaaltenJAL-2599 fix for issue where info annot would not display commit | commitdiff | tree | snapshot
2017-08-09 tzvanaaltenJAL-2599 fix for issue where info annot would not display commit | commitdiff | tree | snapshot
2017-08-09 TZVanaaltenJAL-2599 add uniref 50 hmm example commit | commitdiff | tree | snapshot
2017-08-09 TZVanaaltenJAL-2629 buffers are now temporary files commit | commitdiff | tree | snapshot
2017-08-09 TZVanaaltenJAL-2629 removed unnecessary exception throws from... commit | commitdiff | tree | snapshot
2017-08-09 TZVanaaltenJAL-2629 disable AAFrequencyTest compilation error commit | commitdiff | tree | snapshot
2017-08-08 TZVanaaltenJAL-2616 fix allowing clan sorting to work commit | commitdiff | tree | snapshot
2017-08-08 TZVanaaltenJAL-2599 fix for index issue on node lookup commit | commitdiff | tree | snapshot
2017-08-08 TZVanaaltenJAL-2629 add ability to select hmmer binaries folder commit | commitdiff | tree | snapshot
2017-08-07 TZVanaaltenJAL-2629 fixed hmmalign failing due to differing sequen... commit | commitdiff | tree | snapshot
2017-08-07 TZVanaaltenJAL-2629 current hmmer commands are now executed in... commit | commitdiff | tree | snapshot
2017-08-04 TZVanaaltenJAL-2599 fixed information annotation buttons not working commit | commitdiff | tree | snapshot
2017-08-04 TZVanaaltenJAL-2629 hmmbuild now runs on alignments of different... commit | commitdiff | tree | snapshot
2017-08-04 TZVanaaltenJAL-2629 multiple HMMs can now be dropped onto an alignment commit | commitdiff | tree | snapshot
2017-08-02 TZVanaaltenJAL-2599 fix for HMM logo not normalising correctly commit | commitdiff | tree | snapshot
2017-08-02 TZVanaaltenJAL-2599 fix issue where parser exported map annotation... commit | commitdiff | tree | snapshot
2017-08-02 TZVanaaltenJAL-2599 fix for information annotation buttons commit | commitdiff | tree | snapshot
2017-07-31 TZVanaaltenJAL-2629 add hmmalign command commit | commitdiff | tree | snapshot
2017-07-27 TZVanaaltenJAL-2629 implement hmmbuild commit | commitdiff | tree | snapshot
2017-07-27 TZVanaaltenJAL-2629 moved HMM storage location to placeholder... commit | commitdiff | tree | snapshot
2017-07-26 TZVanaaltenJAL-2629 HMMs now map to reference annotation if exists commit | commitdiff | tree | snapshot
2017-07-25 TZVanaaltenJAL-2629 add non-functional HMMER menu commit | commitdiff | tree | snapshot
2017-07-25 TZVanaaltenJAL-2616 add ability to perform random alignments withi... commit | commitdiff | tree | snapshot
2017-07-24 tzvanaaltenJAL-2616 add placeholder sequence for HMM, does not... commit | commitdiff | tree | snapshot
2017-07-24 tzvanaaltenJAL-2616 add ability to change location of family and... commit | commitdiff | tree | snapshot
2017-07-24 tzvanaaltenJAL-2599 add a couple of test files not included in... commit | commitdiff | tree | snapshot
2017-07-24 tzvanaaltenJAL-2616 add test class and test files for analyser commit | commitdiff | tree | snapshot
2017-07-24 tzvanaaltenJAL-2599 .hmm parser should now accept older .hmm files commit | commitdiff | tree | snapshot
2017-07-21 TZVanaaltenJAL-2616 add ability to sort Pfam families and HMMs... commit | commitdiff | tree | snapshot
2017-07-20 TZVanaaltenJAL-2616 remove statistical analysis from AlignFrame commit | commitdiff | tree | snapshot
2017-07-20 TZVanaaltenJAL-2599 small code improvements commit | commitdiff | tree | snapshot
2017-07-20 TZVanaaltenJAL-2616 add documentation for probability analyser commit | commitdiff | tree | snapshot
2017-07-20 TZVanaaltenJAL-2616 add probability distribution analyser class commit | commitdiff | tree | snapshot
2017-07-20 TZVanaaltenJAL-2599 add ability to process RNA HMMer files commit | commitdiff | tree | snapshot
2017-07-18 TZVanaaltenJAL-2599 complete documentation for HMM and HMMFile... commit | commitdiff | tree | snapshot
2017-07-18 TZVanaaltenJAL-2599 modified state transition probability storage commit | commitdiff | tree | snapshot
2017-07-14 TZVanaaltenadd partial button fix to annotation and statistics... features/hmmer_statistics commit | commitdiff | tree | snapshot
2017-07-12 TZVanaaltentest HMM annotaTION commit | commitdiff | tree | snapshot
2017-07-11 TZVanaaltencomplete Information Content annotation commit | commitdiff | tree | snapshot
2017-06-29 TZVanaaltenadd information content calculations commit | commitdiff | tree | snapshot
2017-06-29 TZVanaaltentransferred the storage position of the HMM to annotations commit | commitdiff | tree | snapshot
2017-06-23 TZVanaaltentest HMMER colour scheme commit | commitdiff | tree | snapshot
2017-06-23 TZVanaaltenadd HMMER colour scheme commit | commitdiff | tree | snapshot
2017-06-22 TZVanaaltenfully integrate HMMER3 file format into Jalview commit | commitdiff | tree | snapshot
2017-06-20 TZVanaaltencreate method to test HMM model as string commit | commitdiff | tree | snapshot
2017-06-20 TZVanaaltenrestructure file exporter commit | commitdiff | tree | snapshot
2017-06-15 TZVanaaltenadd tests for HMMFile class commit | commitdiff | tree | snapshot
2017-06-15 TZVanaaltenadd HMMFile class to read and write HMM files commit | commitdiff | tree | snapshot
2017-06-15 TZVanaaltenUpdate HiddenMarkovModel class commit | commitdiff | tree | snapshot
2017-06-09 TZVanaaltenAdd HiddenMarkovModel class commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into... commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterJAL-2418 release notes for JAL-2547, JAL-2563, JAL... commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterMerge branch 'JAL-2571' into develop commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into... commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterJAL-2398 - updated groovy script for direct field modif... commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterJAL-2418 JAL-2563 release notes commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterJAL-2418 typo commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterMerge branch 'develop' into documentation/JAL-2418_rele... commit | commitdiff | tree | snapshot
2017-05-31 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2017-05-31 tcofoegbuJAL-2375 fix unit test to reflect improvement commit | commitdiff | tree | snapshot
2017-05-31 tcofoegbuFixed failing tests commit | commitdiff | tree | snapshot
2017-05-31 tcofoegbuJAL-2533 updated unit test to reflect improvement commit | commitdiff | tree | snapshot
2017-05-31 gmungocJAL-2547 handle contact features 'around' a gap correctly commit | commitdiff | tree | snapshot
2017-05-30 kiramtJAL-2573 Fixes for alignment < viewport width, and... JAL-2571 commit | commitdiff | tree | snapshot
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