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JAL-2629 add adjustable parameters to hmmbuild
2017-08-25 TZVanaaltenJAL-2629 add adjustable parameters to hmmbuild
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2017-08-25 TZVanaaltenJAL-2629 adjust log parameter slightly and reduce granularity
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2017-08-25 TZVanaaltenJAL-2629 fix issue where Stockholm file would print...
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2017-08-25 TZVanaaltenJAL-2629 hmmsearch no longer throws an error if no...
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2017-08-25 TZVanaaltenJAL-2629 adjust parameter min and max to better suit...
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2017-08-25 TZVanaaltenJAL-2629 hmmsearch/build/align no longer run after...
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2017-08-25 TZVanaaltenJAL-2629 fix for NPE caused by incorrect initiation...
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2017-08-25 TZVanaaltenJAL-2629 hmmsearch now works for different databases
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2017-08-25 TZVanaaltenJAL-2629 add ability to add and select a DB for hmmsearch
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2017-08-25 TZVanaaltenJAL-2629 remove sequence and group HMMER options
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2017-08-25 TZVanaaltenJAL-2629 add basic parameter adjustment to hmmsearch...
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2017-08-23 tzvanaaltenJAL-2629 selected HMM is now a sequence, not a HMM
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2017-08-23 tzvanaaltenJAL-2629 fix for addHMMConsensus failing if no HMM...
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2017-08-23 tzvanaaltenJAL-2629 add logarithmic parameter for logarithmic...
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2017-08-22 TZVanaaltenJAL-2629 add hmmsearch class
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2017-08-21 TZVanaaltenMerge remote-tracking branch 'origin/releases/Release_2_10_2...
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2017-08-21 TZVanaaltenMerge remote-tracking branch 'origin/releases/Release_2_10_2...
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2017-08-21 TZVanaaltenJAL-2668 fix failing tests caused by HMMER-related...
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2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer
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2017-08-18 TZVanaaltenJAL-2668 add tests for HMMER commands, annotation and io
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2017-08-18 TZVanaaltenJAL-2668 HMMFile export method moved to print method
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2017-08-17 TZVanaaltenJAL-2599 move fillSymbol method to HMFile
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2017-08-17 TZVanaaltenJAL-2599 some slight renaming of variables and methods
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2017-08-17 TZVanaaltenJAL-2629 add documentation to previous work
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2017-08-16 TZVanaaltenJAL-2599 HMM annotation now shows consensus characters...
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2017-08-16 TZVanaaltenJAL-2599 fix background frequency storage and correct...
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2017-08-16 TZVanaaltenJAL-2629 fix for hmmbuild not loading a HMM onto the...
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2017-08-16 TZVanaaltenJAL-2629 add hmmbuild validation check which also gets...
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2017-08-15 TZVanaaltenJAL-2629 prevent hmmbuild from running if there are...
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2017-08-15 TZVanaaltenJAL-2629 configure file chooser to select either a...
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2017-08-15 TZVanaaltenJAL-2629 add checks for executing hmmer commands as...
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2017-08-15 TZVanaaltenJAL-2629 add HMMER version check
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2017-08-15 TZVanaaltenJAL-2629 selected HMM name now shown in HMMER menu
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2017-08-15 TZVanaaltenJAL-2629 exported HMMs are now named correctly
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2017-08-15 TZVanaaltenJAL-2629 fix uniquified sequence names appearing when...
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2017-08-15 TZVanaaltenJAL-2599 fix HMMER scheme not colouring inserts and...
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2017-08-15 TZVanaaltenJAL-2629 the HMMER tab is now disabled when HMMER is...
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2017-08-14 TZVanaaltenJAL-2629 remove annotation when exporting for hmmbuild
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2017-08-14 TZVanaaltenJAL-2629 remove gap padding, and now has option to...
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2017-08-14 TZVanaaltenJAL-2629 add insert sequence at method on alignment
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2017-08-14 TZVanaaltenJAL-2629 fix expected length error for hmmbuild by...
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2017-08-14 TZVanaaltenJAL-2629 add padding for .sto annotations to fix issues...
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2017-08-14 TZVanaaltenJAL-2629 remove redundant options from HMMER menu
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2017-08-14 TZVanaaltenJAL-2629 add validation for HMMER path
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2017-08-14 TZVanaaltenJAL-2629 fix incorrect gap insertions on HMM sequence
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2017-08-13 TZVanaaltenJAL-2629 fix issue where trim termini setting would...
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2017-08-13 TZVanaaltenJAL-2629 hmmalign can now be run from the sequence...
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2017-08-13 TZVanaaltenJAL-2629 add force alphabet type for HMMER commands
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2017-08-13 TZVanaaltenJAL-2629 fix issue where HMM sequences would be too...
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2017-08-13 TZVanaaltenJAL-2629 add HMMER tab in preferences menu
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2017-08-11 TZVanaaltenJAL-2629 delete unnecessary buffer files for hmmer...
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2017-08-11 TZVanaaltenJAL-2629 add ability to build a HMM from a group
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2017-08-11 TZVanaaltenJAL-2629 add ability to select HMMs
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2017-08-11 TZVanaaltenJAL-2599 HMMs can now be dropped onto the desktop
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2017-08-10 TZVanaaltenJAL-2629 hmmalign now correctly creates a new frame
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2017-08-09 TZVanaaltenJAL-2599 fix for issue where info annot would not display
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2017-08-09 TZVanaaltenJAL-2599 add uniref 50 hmm example
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2017-08-09 TZVanaaltenJAL-2629 buffers are now temporary files
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2017-08-09 TZVanaaltenJAL-2629 removed unnecessary exception throws from...
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2017-08-09 TZVanaaltenJAL-2629 disable AAFrequencyTest compilation error
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2017-08-08 TZVanaaltenJAL-2616 fix allowing clan sorting to work
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2017-08-08 TZVanaaltenJAL-2599 fix for index issue on node lookup
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2017-08-08 TZVanaaltenJAL-2629 add ability to select hmmer binaries folder
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2017-08-07 TZVanaaltenJAL-2629 fixed hmmalign failing due to differing sequence...
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2017-08-07 TZVanaaltenJAL-2629 current hmmer commands are now executed in...
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2017-08-04 TZVanaaltenJAL-2599 fixed information annotation buttons not working
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2017-08-04 TZVanaaltenJAL-2629 hmmbuild now runs on alignments of different...
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2017-08-04 TZVanaaltenJAL-2629 multiple HMMs can now be dropped onto an alignment
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2017-08-02 TZVanaaltenJAL-2599 fix for HMM logo not normalising correctly
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2017-08-02 TZVanaaltenJAL-2599 fix issue where parser exported map annotation...
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2017-08-02 TZVanaaltenJAL-2599 fix for information annotation buttons
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2017-07-31 TZVanaaltenJAL-2629 add hmmalign command
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2017-07-27 TZVanaaltenJAL-2629 implement hmmbuild
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2017-07-27 TZVanaaltenJAL-2629 moved HMM storage location to placeholder...
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2017-07-26 TZVanaaltenJAL-2629 HMMs now map to reference annotation if exists
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2017-07-25 TZVanaaltenJAL-2629 add non-functional HMMER menu
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2017-07-25 TZVanaaltenJAL-2616 add ability to perform random alignments within...
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2017-07-24 tzvanaaltenJAL-2616 add placeholder sequence for HMM, does not...
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2017-07-24 tzvanaaltenJAL-2616 add ability to change location of family and...
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2017-07-24 tzvanaaltenJAL-2599 add a couple of test files not included in...
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2017-07-24 tzvanaaltenJAL-2616 add test class and test files for analyser
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2017-07-24 tzvanaaltenJAL-2599 .hmm parser should now accept older .hmm files
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2017-07-21 TZVanaaltenJAL-2616 add ability to sort Pfam families and HMMs...
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2017-07-20 TZVanaaltenJAL-2616 remove statistical analysis from AlignFrame
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2017-07-20 TZVanaaltenJAL-2599 small code improvements
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2017-07-20 TZVanaaltenJAL-2616 add documentation for probability analyser
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2017-07-20 TZVanaaltenJAL-2616 add probability distribution analyser class
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2017-07-20 TZVanaaltenJAL-2599 add ability to process RNA HMMer files
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2017-07-18 TZVanaaltenJAL-2599 complete documentation for HMM and HMMFile...
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2017-07-18 TZVanaaltenJAL-2599 modified state transition probability storage
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2017-07-14 TZVanaaltenadd partial button fix to annotation and statistics...
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2017-07-12 TZVanaaltentest HMM annotaTION
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2017-07-11 TZVanaaltencomplete Information Content annotation
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2017-06-29 TZVanaaltenadd information content calculations
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2017-06-29 TZVanaaltentransferred the storage position of the HMM to annotations
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2017-06-23 TZVanaaltentest HMMER colour scheme
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2017-06-23 TZVanaaltenadd HMMER colour scheme
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2017-06-22 TZVanaaltenfully integrate HMMER3 file format into Jalview
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2017-06-20 TZVanaaltencreate method to test HMM model as string
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2017-06-20 TZVanaaltenrestructure file exporter
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