jalview.git
2017-08-13 TZVanaaltenJAL-2629 add force alphabet type for HMMER commands
2017-08-13 TZVanaaltenJAL-2629 fix issue where HMM sequences would be too...
2017-08-13 TZVanaaltenJAL-2629 add HMMER tab in preferences menu
2017-08-11 TZVanaaltenJAL-2629 delete unnecessary buffer files for hmmer...
2017-08-11 TZVanaaltenJAL-2629 add ability to build a HMM from a group
2017-08-11 TZVanaaltenJAL-2629 add ability to select HMMs
2017-08-11 TZVanaaltenJAL-2599 HMMs can now be dropped onto the desktop
2017-08-10 TZVanaaltenJAL-2629 hmmalign now correctly creates a new frame
2017-08-10 tzvanaaltenMerge branch 'features/hmmer' of https://source.jalview...
2017-08-10 tzvanaaltenJAL-2629 fix files permission issue on Mac
2017-08-09 TZVanaaltenJAL-2599 fix for issue where info annot would not display
2017-08-09 tzvanaaltenJAL-2599 fix for issue where info annot would not display
2017-08-09 TZVanaaltenJAL-2599 add uniref 50 hmm example
2017-08-09 TZVanaaltenJAL-2629 buffers are now temporary files
2017-08-09 TZVanaaltenJAL-2629 removed unnecessary exception throws from...
2017-08-09 TZVanaaltenJAL-2629 disable AAFrequencyTest compilation error
2017-08-08 TZVanaaltenJAL-2616 fix allowing clan sorting to work
2017-08-08 TZVanaaltenJAL-2599 fix for index issue on node lookup
2017-08-08 TZVanaaltenJAL-2629 add ability to select hmmer binaries folder
2017-08-07 TZVanaaltenJAL-2629 fixed hmmalign failing due to differing sequen...
2017-08-07 TZVanaaltenJAL-2629 current hmmer commands are now executed in...
2017-08-04 TZVanaaltenJAL-2599 fixed information annotation buttons not working
2017-08-04 TZVanaaltenJAL-2629 hmmbuild now runs on alignments of different...
2017-08-04 TZVanaaltenJAL-2629 multiple HMMs can now be dropped onto an alignment
2017-08-02 TZVanaaltenJAL-2599 fix for HMM logo not normalising correctly
2017-08-02 TZVanaaltenJAL-2599 fix issue where parser exported map annotation...
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
2017-07-25 TZVanaaltenJAL-2629 add non-functional HMMER menu
2017-07-25 TZVanaaltenJAL-2616 add ability to perform random alignments withi...
2017-07-24 tzvanaaltenJAL-2616 add placeholder sequence for HMM, does not...
2017-07-24 tzvanaaltenJAL-2616 add ability to change location of family and...
2017-07-24 tzvanaaltenJAL-2599 add a couple of test files not included in...
2017-07-24 tzvanaaltenJAL-2616 add test class and test files for analyser
2017-07-24 tzvanaaltenJAL-2599 .hmm parser should now accept older .hmm files
2017-07-21 TZVanaaltenJAL-2616 add ability to sort Pfam families and HMMs...
2017-07-20 TZVanaaltenJAL-2616 remove statistical analysis from AlignFrame
2017-07-20 TZVanaaltenJAL-2599 small code improvements
2017-07-20 TZVanaaltenJAL-2616 add documentation for probability analyser
2017-07-20 TZVanaaltenJAL-2616 add probability distribution analyser class
2017-07-20 TZVanaaltenJAL-2599 add ability to process RNA HMMer files
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
2017-07-12 TZVanaaltentest HMM annotaTION
2017-07-11 TZVanaaltencomplete Information Content annotation
2017-06-29 TZVanaaltenadd information content calculations
2017-06-29 TZVanaaltentransferred the storage position of the HMM to annotations
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 TZVanaaltencreate method to test HMM model as string
2017-06-20 TZVanaaltenrestructure file exporter
2017-06-15 TZVanaaltenadd tests for HMMFile class
2017-06-15 TZVanaaltenadd HMMFile class to read and write HMM files
2017-06-15 TZVanaaltenUpdate HiddenMarkovModel class
2017-06-09 TZVanaaltenAdd HiddenMarkovModel class
2017-05-31 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into...
2017-05-31 Jim ProcterJAL-2418 release notes for JAL-2547, JAL-2563, JAL...
2017-05-31 Jim ProcterMerge branch 'JAL-2571' into develop
2017-05-31 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into...
2017-05-31 Jim ProcterJAL-2398 - updated groovy script for direct field modif...
2017-05-31 Jim ProcterJAL-2418 JAL-2563 release notes
2017-05-31 Jim ProcterJAL-2418 typo
2017-05-31 Jim ProcterMerge branch 'develop' into documentation/JAL-2418_rele...
2017-05-31 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2017-05-31 tcofoegbuJAL-2375 fix unit test to reflect improvement
2017-05-31 tcofoegbuFixed failing tests
2017-05-31 tcofoegbuJAL-2533 updated unit test to reflect improvement
2017-05-31 gmungocJAL-2547 handle contact features 'around' a gap correctly
2017-05-30 kiramtJAL-2573 Fixes for alignment < viewport width, and... JAL-2571
2017-05-30 gmungocJAL-2547 tooltip/AmendFeatures on gap straddled by...
2017-05-30 kiramtJAL-2571 Corrected alignment width/height checks to...
2017-05-30 gmungocJAL-2570 don't zap group colour scheme when mapping...
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2034contextchange' into develop
2017-05-29 Jim ProcterJAL-2388 release notes
2017-05-29 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into...
2017-05-29 Jim ProcterJAL-2520 properly documented as a fixed bug in release...
2017-05-29 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into...
2017-05-29 Jim ProcterJAL-2465,JAL-2520,JAL-2533 release notes
2017-05-29 Jim ProcterMerge branch 'features/JAL-2465_No-mapping_Jmol-structu...
2017-05-29 Jim ProcterJAL-2533 update javadoc features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url
2017-05-29 Jim ProcterJAL-2465 fixed groups for JmolViewerTest.testStructureL...
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2536' into develop
2017-05-29 Jim ProcterJAL-2536 tweak javadoc wording
2017-05-29 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into...
2017-05-29 Jim ProcterJAL-2517 release notes
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2517cancelAppletColour' into...
2017-05-29 Jim Procterrelease notes
2017-05-29 Jim ProcterJAL-2418 updated JABAWS server in what’s new
2017-05-29 Jim ProcterJAL-2491 JAL-2526 JAL-2566 JAL-2563 JAL-2547 release...
2017-05-27 Jim ProcterMerge branch 'bug/JAL-2491' into develop
2017-05-27 Jim ProcterMerge branch 'bug/JAL-2547tooltipOnGap' into develop
2017-05-27 Jim ProcterMerge branch 'task/JAL-2562_SequenceI.findPosition...
2017-05-27 Jim ProcterJAL-2563 failing test to verify SetStatus returns posit... task/JAL-2562_SequenceI.findPosition
2017-05-27 Jim ProcterJAL-2563 test to verify SetStatus returns -1 so mouseOv...
2017-05-27 Jim ProcterMerge branch 'task/JAL-2562_SequenceI.findPosition...
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