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2017-08-25	TZVanaalten	JAL-2629 remove sequence and group HMMER options	commit \| commitdiff \| tree
2017-08-25	TZVanaalten	JAL-2629 add basic parameter adjustment to hmmsearch...	commit \| commitdiff \| tree
2017-08-23	tzvanaalten	JAL-2629 selected HMM is now a sequence, not a HMM	commit \| commitdiff \| tree
2017-08-23	tzvanaalten	JAL-2629 fix for addHMMConsensus failing if no HMM...	commit \| commitdiff \| tree
2017-08-23	tzvanaalten	JAL-2629 add logarithmic parameter for logarithmic...	commit \| commitdiff \| tree
2017-08-22	TZVanaalten	JAL-2629 add hmmsearch class	commit \| commitdiff \| tree
2017-08-21	TZVanaalten	Merge remote-tracking branch 'origin/releases/Release_2_10_2...	commit \| commitdiff \| tree
2017-08-21	TZVanaalten	Merge remote-tracking branch 'origin/releases/Release_2_10_2...	commit \| commitdiff \| tree
2017-08-21	TZVanaalten	JAL-2668 fix failing tests caused by HMMER-related...	commit \| commitdiff \| tree
2017-08-18	TZVanaalten	Merge branch 'develop' into features/hmmer	commit \| commitdiff \| tree
2017-08-18	TZVanaalten	JAL-2668 add tests for HMMER commands, annotation and io	commit \| commitdiff \| tree
2017-08-18	TZVanaalten	JAL-2668 HMMFile export method moved to print method	commit \| commitdiff \| tree
2017-08-17	TZVanaalten	JAL-2599 move fillSymbol method to HMFile	commit \| commitdiff \| tree
2017-08-17	TZVanaalten	JAL-2599 some slight renaming of variables and methods	commit \| commitdiff \| tree
2017-08-17	TZVanaalten	JAL-2629 add documentation to previous work	commit \| commitdiff \| tree
2017-08-16	TZVanaalten	JAL-2599 HMM annotation now shows consensus characters...	commit \| commitdiff \| tree
2017-08-16	TZVanaalten	JAL-2599 fix background frequency storage and correct...	commit \| commitdiff \| tree
2017-08-16	TZVanaalten	JAL-2629 fix for hmmbuild not loading a HMM onto the...	commit \| commitdiff \| tree
2017-08-16	TZVanaalten	JAL-2629 add hmmbuild validation check which also gets...	commit \| commitdiff \| tree
2017-08-15	TZVanaalten	JAL-2629 prevent hmmbuild from running if there are...	commit \| commitdiff \| tree
2017-08-15	TZVanaalten	JAL-2629 configure file chooser to select either a...	commit \| commitdiff \| tree
2017-08-15	TZVanaalten	JAL-2629 add checks for executing hmmer commands as...	commit \| commitdiff \| tree
2017-08-15	TZVanaalten	JAL-2629 add HMMER version check	commit \| commitdiff \| tree
2017-08-15	TZVanaalten	JAL-2629 selected HMM name now shown in HMMER menu	commit \| commitdiff \| tree
2017-08-15	TZVanaalten	JAL-2629 exported HMMs are now named correctly	commit \| commitdiff \| tree
2017-08-15	TZVanaalten	JAL-2629 fix uniquified sequence names appearing when...	commit \| commitdiff \| tree
2017-08-15	TZVanaalten	JAL-2599 fix HMMER scheme not colouring inserts and...	commit \| commitdiff \| tree
2017-08-15	TZVanaalten	JAL-2629 the HMMER tab is now disabled when HMMER is...	commit \| commitdiff \| tree
2017-08-14	TZVanaalten	JAL-2629 remove annotation when exporting for hmmbuild	commit \| commitdiff \| tree
2017-08-14	TZVanaalten	JAL-2629 remove gap padding, and now has option to...	commit \| commitdiff \| tree
2017-08-14	TZVanaalten	JAL-2629 add insert sequence at method on alignment	commit \| commitdiff \| tree
2017-08-14	TZVanaalten	JAL-2629 fix expected length error for hmmbuild by...	commit \| commitdiff \| tree
2017-08-14	TZVanaalten	JAL-2629 add padding for .sto annotations to fix issues...	commit \| commitdiff \| tree
2017-08-14	TZVanaalten	JAL-2629 remove redundant options from HMMER menu	commit \| commitdiff \| tree
2017-08-14	TZVanaalten	JAL-2629 add validation for HMMER path	commit \| commitdiff \| tree
2017-08-14	TZVanaalten	JAL-2629 fix incorrect gap insertions on HMM sequence	commit \| commitdiff \| tree
2017-08-13	TZVanaalten	JAL-2629 fix issue where trim termini setting would...	commit \| commitdiff \| tree
2017-08-13	TZVanaalten	JAL-2629 hmmalign can now be run from the sequence...	commit \| commitdiff \| tree
2017-08-13	TZVanaalten	JAL-2629 add force alphabet type for HMMER commands	commit \| commitdiff \| tree
2017-08-13	TZVanaalten	JAL-2629 fix issue where HMM sequences would be too...	commit \| commitdiff \| tree
2017-08-13	TZVanaalten	JAL-2629 add HMMER tab in preferences menu	commit \| commitdiff \| tree
2017-08-11	TZVanaalten	JAL-2629 delete unnecessary buffer files for hmmer...	commit \| commitdiff \| tree
2017-08-11	TZVanaalten	JAL-2629 add ability to build a HMM from a group	commit \| commitdiff \| tree
2017-08-11	TZVanaalten	JAL-2629 add ability to select HMMs	commit \| commitdiff \| tree
2017-08-11	TZVanaalten	JAL-2599 HMMs can now be dropped onto the desktop	commit \| commitdiff \| tree
2017-08-10	TZVanaalten	JAL-2629 hmmalign now correctly creates a new frame	commit \| commitdiff \| tree
2017-08-09	TZVanaalten	JAL-2599 fix for issue where info annot would not display	commit \| commitdiff \| tree
2017-08-09	TZVanaalten	JAL-2599 add uniref 50 hmm example	commit \| commitdiff \| tree
2017-08-09	TZVanaalten	JAL-2629 buffers are now temporary files	commit \| commitdiff \| tree
2017-08-09	TZVanaalten	JAL-2629 removed unnecessary exception throws from...	commit \| commitdiff \| tree
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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