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jalview.git
2017-08-15
TZVanaalten
JAL-2629 the HMMER tab is now disabled when HMMER is...
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2017-08-14
TZVanaalten
JAL-2629 remove annotation when exporting for hmmbuild
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2017-08-14
TZVanaalten
JAL-2629 remove gap padding, and now has option to...
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2017-08-14
TZVanaalten
JAL-2629 add insert sequence at method on alignment
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2017-08-14
TZVanaalten
JAL-2629 fix expected length error for hmmbuild by...
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2017-08-14
TZVanaalten
JAL-2629 add padding for .sto annotations to fix issues...
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2017-08-14
TZVanaalten
JAL-2629 remove redundant options from HMMER menu
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2017-08-14
TZVanaalten
JAL-2629 add validation for HMMER path
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2017-08-14
TZVanaalten
JAL-2629 fix incorrect gap insertions on HMM sequence
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2017-08-13
TZVanaalten
JAL-2629 fix issue where trim termini setting would...
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2017-08-13
TZVanaalten
JAL-2629 hmmalign can now be run from the sequence...
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2017-08-13
TZVanaalten
JAL-2629 add force alphabet type for HMMER commands
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2017-08-13
TZVanaalten
JAL-2629 fix issue where HMM sequences would be too...
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2017-08-13
TZVanaalten
JAL-2629 add HMMER tab in preferences menu
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2017-08-11
TZVanaalten
JAL-2629 delete unnecessary buffer files for hmmer...
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2017-08-11
TZVanaalten
JAL-2629 add ability to build a HMM from a group
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2017-08-11
TZVanaalten
JAL-2629 add ability to select HMMs
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2017-08-11
TZVanaalten
JAL-2599 HMMs can now be dropped onto the desktop
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2017-08-10
TZVanaalten
JAL-2629 hmmalign now correctly creates a new frame
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2017-08-10
tzvanaalten
Merge branch 'features/hmmer' of https://source.jalview...
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2017-08-10
tzvanaalten
JAL-2629 fix files permission issue on Mac
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2017-08-09
TZVanaalten
JAL-2599 fix for issue where info annot would not display
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2017-08-09
tzvanaalten
JAL-2599 fix for issue where info annot would not display
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2017-08-09
TZVanaalten
JAL-2599 add uniref 50 hmm example
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2017-08-09
TZVanaalten
JAL-2629 buffers are now temporary files
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2017-08-09
TZVanaalten
JAL-2629 removed unnecessary exception throws from...
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2017-08-09
TZVanaalten
JAL-2629 disable AAFrequencyTest compilation error
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2017-08-08
TZVanaalten
JAL-2616 fix allowing clan sorting to work
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2017-08-08
TZVanaalten
JAL-2599 fix for index issue on node lookup
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2017-08-08
TZVanaalten
JAL-2629 add ability to select hmmer binaries folder
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2017-08-07
TZVanaalten
JAL-2629 fixed hmmalign failing due to differing sequen...
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2017-08-07
TZVanaalten
JAL-2629 current hmmer commands are now executed in...
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2017-08-04
TZVanaalten
JAL-2599 fixed information annotation buttons not working
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2017-08-04
TZVanaalten
JAL-2629 hmmbuild now runs on alignments of different...
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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 HMM logo not normalising correctly
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2017-08-02
TZVanaalten
JAL-2599 fix issue where parser exported map annotation...
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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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2017-07-25
TZVanaalten
JAL-2629 add non-functional HMMER menu
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2017-07-25
TZVanaalten
JAL-2616 add ability to perform random alignments withi...
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2017-07-24
tzvanaalten
JAL-2616 add placeholder sequence for HMM, does not...
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2017-07-24
tzvanaalten
JAL-2616 add ability to change location of family and...
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2017-07-24
tzvanaalten
JAL-2599 add a couple of test files not included in...
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2017-07-24
tzvanaalten
JAL-2616 add test class and test files for analyser
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2017-07-24
tzvanaalten
JAL-2599 .hmm parser should now accept older .hmm files
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2017-07-21
TZVanaalten
JAL-2616 add ability to sort Pfam families and HMMs...
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2017-07-20
TZVanaalten
JAL-2616 remove statistical analysis from AlignFrame
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2017-07-20
TZVanaalten
JAL-2599 small code improvements
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2017-07-20
TZVanaalten
JAL-2616 add documentation for probability analyser
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2017-07-20
TZVanaalten
JAL-2616 add probability distribution analyser class
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2017-07-20
TZVanaalten
JAL-2599 add ability to process RNA HMMer files
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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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2017-07-12
TZVanaalten
test HMM annotaTION
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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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2017-06-29
TZVanaalten
transferred the storage position of the HMM to annotations
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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
create method to test HMM model as string
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2017-06-20
TZVanaalten
restructure file exporter
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2017-06-15
TZVanaalten
add tests for HMMFile class
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2017-06-15
TZVanaalten
add HMMFile class to read and write HMM files
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2017-06-15
TZVanaalten
Update HiddenMarkovModel class
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2017-06-09
TZVanaalten
Add HiddenMarkovModel class
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2017-05-31
Jim Procter
Merge branch 'documentation/JAL-2418_release2102' into...
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2017-05-31
Jim Procter
JAL-2418 release notes for JAL-2547, JAL-2563, JAL...
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2017-05-31
Jim Procter
Merge branch 'JAL-2571' into develop
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2017-05-31
Jim Procter
Merge branch 'documentation/JAL-2418_release2102' into...
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2017-05-31
Jim Procter
JAL-2398 - updated groovy script for direct field modif...
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2017-05-31
Jim Procter
JAL-2418 JAL-2563 release notes
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2017-05-31
Jim Procter
JAL-2418 typo
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2017-05-31
Jim Procter
Merge branch 'develop' into documentation/JAL-2418_rele...
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2017-05-31
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
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2017-05-31
tcofoegbu
JAL-2375 fix unit test to reflect improvement
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2017-05-31
tcofoegbu
Fixed failing tests
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2017-05-31
tcofoegbu
JAL-2533 updated unit test to reflect improvement
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2017-05-31
gmungoc
JAL-2547 handle contact features 'around' a gap correctly
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2017-05-30
kiramt
JAL-2573 Fixes for alignment < viewport width, and...
JAL-2571
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2017-05-30
gmungoc
JAL-2547 tooltip/AmendFeatures on gap straddled by...
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2017-05-30
kiramt
JAL-2571 Corrected alignment width/height checks to...
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2017-05-30
gmungoc
JAL-2570 don't zap group colour scheme when mapping...
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2017-05-29
Jim Procter
Merge branch 'bug/JAL-2034contextchange' into develop
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2017-05-29
Jim Procter
JAL-2388 release notes
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2017-05-29
Jim Procter
Merge branch 'documentation/JAL-2418_release2102' into...
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2017-05-29
Jim Procter
JAL-2520 properly documented as a fixed bug in release...
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2017-05-29
Jim Procter
Merge branch 'documentation/JAL-2418_release2102' into...
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2017-05-29
Jim Procter
JAL-2465,JAL-2520,JAL-2533 release notes
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2017-05-29
Jim Procter
Merge branch 'features/JAL-2465_No-mapping_Jmol-structu...
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2017-05-29
Jim Procter
JAL-2533 update javadoc
features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url
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2017-05-29
Jim Procter
JAL-2465 fixed groups for JmolViewerTest.testStructureL...
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2017-05-29
Jim Procter
Merge branch 'bug/JAL-2536' into develop
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2017-05-29
Jim Procter
JAL-2536 tweak javadoc wording
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2017-05-29
Jim Procter
Merge branch 'documentation/JAL-2418_release2102' into...
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