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Merge branch 'JAL-3878_ws-overhaul-3' into with_ws_overhaul-3
[jalview.git]
/
src
/
jalview
/
datamodel
/
HiddenMarkovModel.java
2019-07-02
tva
JAL-2629 add simple jackhmmer functionality
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2019-06-28
tva
JAL-2629 add HMM Match Score colour scheme
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2019-06-10
tva
JAL-3297 pad gaps in alignment to ensure hmmalign runs
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2019-06-07
tva
JAL-3291 issue fixed, passing tests added
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2018-04-23
gmungoc
JAL-2956 save/restore HMMER profile to/from Jalview...
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2018-04-16
gmungoc
JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe...
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2018-04-09
Mungo Carstairs
JAL-2629 more error checking
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2018-03-30
gmungoc
JAL-2599 MapList from HMM nodes to consensus dataset...
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2018-02-27
gmungoc
JAL-2717 JAL-2668 fixes to HMMER colour scheme display...
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2018-02-26
gmungoc
JAL-2599 test coverage and bug fixes for 'minimal file...
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2018-02-23
gmungoc
JAL-2599 corrected case-insensitive symbol indexing
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2018-02-23
gmungoc
JAL-2599 parser and datamodel use primitive double...
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2018-02-22
gmungoc
JAL-2629 tidy tests, refactor hmmer node mapping slightly
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2018-02-22
gmungoc
JAL-2629 tidy unit tests, constants etc
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2017-08-29
osboxes
JAL-2629 fix incorrect mapping between HMM and columns...
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2017-08-25
TZVanaalten
JAL-2629 add multiple options for running hmmbuild...
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2017-08-25
TZVanaalten
JAL-2629 add adjustable parameters to hmmbuild
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2017-08-18
TZVanaalten
JAL-2668 add tests for HMMER commands, annotation and io
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2017-08-17
TZVanaalten
JAL-2629 add documentation to previous work
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2017-08-14
TZVanaalten
JAL-2629 fix incorrect gap insertions on HMM sequence
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2017-08-11
TZVanaalten
JAL-2599 HMMs can now be dropped onto the desktop
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2017-08-08
TZVanaalten
JAL-2599 fix for index issue on node lookup
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2017-08-04
TZVanaalten
JAL-2629 multiple HMMs can now be dropped onto an alignment
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2017-08-02
TZVanaalten
JAL-2599 fix for information annotation buttons
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2017-07-31
TZVanaalten
JAL-2629 add hmmalign command
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2017-07-27
TZVanaalten
JAL-2629 implement hmmbuild
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2017-07-27
TZVanaalten
JAL-2629 moved HMM storage location to placeholder...
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2017-07-26
TZVanaalten
JAL-2629 HMMs now map to reference annotation if exists
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2017-07-24
tzvanaalten
JAL-2616 add placeholder sequence for HMM, does not...
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2017-07-20
TZVanaalten
JAL-2599 small code improvements
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2017-07-18
TZVanaalten
JAL-2599 complete documentation for HMM and HMMFile...
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2017-07-18
TZVanaalten
JAL-2599 modified state transition probability storage
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2017-07-14
TZVanaalten
add partial button fix to annotation and statistics...
features/hmmer_statistics
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2017-07-11
TZVanaalten
complete Information Content annotation
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2017-06-29
TZVanaalten
add information content calculations
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2017-06-23
TZVanaalten
test HMMER colour scheme
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2017-06-23
TZVanaalten
add HMMER colour scheme
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2017-06-22
TZVanaalten
fully integrate HMMER3 file format into Jalview
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2017-06-20
TZVanaalten
restructure file exporter
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2017-06-15
TZVanaalten
add HMMFile class to read and write HMM files
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2017-06-09
TZVanaalten
Add HiddenMarkovModel class
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