Merge branch 'JAL-3878_ws-overhaul-3' into with_ws_overhaul-3
[jalview.git] / src / jalview / datamodel / HiddenMarkovModel.java
2019-07-02 tvaJAL-2629 add simple jackhmmer functionality
2019-06-28 tvaJAL-2629 add HMM Match Score colour scheme
2019-06-10 tvaJAL-3297 pad gaps in alignment to ensure hmmalign runs
2019-06-07 tvaJAL-3291 issue fixed, passing tests added
2018-04-23 gmungocJAL-2956 save/restore HMMER profile to/from Jalview...
2018-04-16 gmungocJAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe...
2018-04-09 Mungo CarstairsJAL-2629 more error checking
2018-03-30 gmungocJAL-2599 MapList from HMM nodes to consensus dataset...
2018-02-27 gmungocJAL-2717 JAL-2668 fixes to HMMER colour scheme display...
2018-02-26 gmungocJAL-2599 test coverage and bug fixes for 'minimal file...
2018-02-23 gmungocJAL-2599 corrected case-insensitive symbol indexing
2018-02-23 gmungocJAL-2599 parser and datamodel use primitive double...
2018-02-22 gmungocJAL-2629 tidy tests, refactor hmmer node mapping slightly
2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc
2017-08-29 osboxesJAL-2629 fix incorrect mapping between HMM and columns...
2017-08-25 TZVanaaltenJAL-2629 add multiple options for running hmmbuild...
2017-08-25 TZVanaaltenJAL-2629 add adjustable parameters to hmmbuild
2017-08-18 TZVanaaltenJAL-2668 add tests for HMMER commands, annotation and io
2017-08-17 TZVanaaltenJAL-2629 add documentation to previous work
2017-08-14 TZVanaaltenJAL-2629 fix incorrect gap insertions on HMM sequence
2017-08-11 TZVanaaltenJAL-2599 HMMs can now be dropped onto the desktop
2017-08-08 TZVanaaltenJAL-2599 fix for index issue on node lookup
2017-08-04 TZVanaaltenJAL-2629 multiple HMMs can now be dropped onto an alignment
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
2017-07-24 tzvanaaltenJAL-2616 add placeholder sequence for HMM, does not...
2017-07-20 TZVanaaltenJAL-2599 small code improvements
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
2017-07-11 TZVanaaltencomplete Information Content annotation
2017-06-29 TZVanaaltenadd information content calculations
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 TZVanaaltenrestructure file exporter
2017-06-15 TZVanaaltenadd HMMFile class to read and write HMM files
2017-06-09 TZVanaaltenAdd HiddenMarkovModel class