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