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2017-08-09	TZVanaalten	JAL-2629 disable AAFrequencyTest compilation error	commit \| commitdiff \| tree
2017-08-08	TZVanaalten	JAL-2616 fix allowing clan sorting to work	commit \| commitdiff \| tree
2017-08-08	TZVanaalten	JAL-2599 fix for index issue on node lookup	commit \| commitdiff \| tree
2017-08-08	TZVanaalten	JAL-2629 add ability to select hmmer binaries folder	commit \| commitdiff \| tree
2017-08-07	TZVanaalten	JAL-2629 fixed hmmalign failing due to differing sequence...	commit \| commitdiff \| tree
2017-08-07	TZVanaalten	JAL-2629 current hmmer commands are now executed in...	commit \| commitdiff \| tree
2017-08-04	TZVanaalten	JAL-2599 fixed information annotation buttons not working	commit \| commitdiff \| tree
2017-08-04	TZVanaalten	JAL-2629 hmmbuild now runs on alignments of different...	commit \| commitdiff \| tree
2017-08-04	TZVanaalten	JAL-2629 multiple HMMs can now be dropped onto an alignment	commit \| commitdiff \| tree
2017-08-02	TZVanaalten	JAL-2599 fix for HMM logo not normalising correctly	commit \| commitdiff \| tree
2017-08-02	TZVanaalten	JAL-2599 fix issue where parser exported map annotation...	commit \| commitdiff \| tree
2017-08-02	TZVanaalten	JAL-2599 fix for information annotation buttons	commit \| commitdiff \| tree
2017-07-31	TZVanaalten	JAL-2629 add hmmalign command	commit \| commitdiff \| tree
2017-07-27	TZVanaalten	JAL-2629 implement hmmbuild	commit \| commitdiff \| tree
2017-07-27	TZVanaalten	JAL-2629 moved HMM storage location to placeholder...	commit \| commitdiff \| tree
2017-07-26	TZVanaalten	JAL-2629 HMMs now map to reference annotation if exists	commit \| commitdiff \| tree
2017-07-25	TZVanaalten	JAL-2629 add non-functional HMMER menu	commit \| commitdiff \| tree
2017-07-25	TZVanaalten	JAL-2616 add ability to perform random alignments within...	commit \| commitdiff \| tree
2017-07-24	tzvanaalten	JAL-2616 add placeholder sequence for HMM, does not...	commit \| commitdiff \| tree
2017-07-24	tzvanaalten	JAL-2616 add ability to change location of family and...	commit \| commitdiff \| tree
2017-07-24	tzvanaalten	JAL-2599 add a couple of test files not included in...	commit \| commitdiff \| tree
2017-07-24	tzvanaalten	JAL-2616 add test class and test files for analyser	commit \| commitdiff \| tree
2017-07-24	tzvanaalten	JAL-2599 .hmm parser should now accept older .hmm files	commit \| commitdiff \| tree
2017-07-21	TZVanaalten	JAL-2616 add ability to sort Pfam families and HMMs...	commit \| commitdiff \| tree
2017-07-20	TZVanaalten	JAL-2616 remove statistical analysis from AlignFrame	commit \| commitdiff \| tree
2017-07-20	TZVanaalten	JAL-2599 small code improvements	commit \| commitdiff \| tree
2017-07-20	TZVanaalten	JAL-2616 add documentation for probability analyser	commit \| commitdiff \| tree
2017-07-20	TZVanaalten	JAL-2616 add probability distribution analyser class	commit \| commitdiff \| tree
2017-07-20	TZVanaalten	JAL-2599 add ability to process RNA HMMer files	commit \| commitdiff \| tree
2017-07-18	TZVanaalten	JAL-2599 complete documentation for HMM and HMMFile...	commit \| commitdiff \| tree
2017-07-18	TZVanaalten	JAL-2599 modified state transition probability storage	commit \| commitdiff \| tree
2017-07-14	TZVanaalten	add partial button fix to annotation and statistics...	commit \| commitdiff \| tree
2017-07-12	TZVanaalten	test HMM annotaTION	commit \| commitdiff \| tree
2017-07-11	TZVanaalten	complete Information Content annotation	commit \| commitdiff \| tree
2017-06-29	TZVanaalten	add information content calculations	commit \| commitdiff \| tree
2017-06-29	TZVanaalten	transferred the storage position of the HMM to annotations	commit \| commitdiff \| tree
2017-06-23	TZVanaalten	test HMMER colour scheme	commit \| commitdiff \| tree
2017-06-23	TZVanaalten	add HMMER colour scheme	commit \| commitdiff \| tree
2017-06-22	TZVanaalten	fully integrate HMMER3 file format into Jalview	commit \| commitdiff \| tree
2017-06-20	TZVanaalten	create method to test HMM model as string	commit \| commitdiff \| tree
2017-06-20	TZVanaalten	restructure file exporter	commit \| commitdiff \| tree
2017-06-15	TZVanaalten	add tests for HMMFile class	commit \| commitdiff \| tree
2017-06-15	TZVanaalten	add HMMFile class to read and write HMM files	commit \| commitdiff \| tree
2017-06-15	TZVanaalten	Update HiddenMarkovModel class	commit \| commitdiff \| tree
2017-06-09	TZVanaalten	Add HiddenMarkovModel class	commit \| commitdiff \| tree

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