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