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JAL-2629 fix issue where HMM sequences would be too long
[jalview.git]
/
src
/
jalview
/
2017-08-13
TZVanaalten
JAL-2629 fix issue where HMM sequences would be too...
tree
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commitdiff
2017-08-13
TZVanaalten
JAL-2629 add HMMER tab in preferences menu
tree
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commitdiff
2017-08-11
TZVanaalten
JAL-2629 delete unnecessary buffer files for hmmer...
tree
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commitdiff
2017-08-11
TZVanaalten
JAL-2629 add ability to build a HMM from a group
tree
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commitdiff
2017-08-11
TZVanaalten
JAL-2629 add ability to select HMMs
tree
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commitdiff
2017-08-11
TZVanaalten
JAL-2599 HMMs can now be dropped onto the desktop
tree
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commitdiff
2017-08-10
TZVanaalten
JAL-2629 hmmalign now correctly creates a new frame
tree
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commitdiff
2017-08-10
tzvanaalten
Merge branch 'features/hmmer' of https://source.jalview...
tree
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commitdiff
2017-08-10
tzvanaalten
JAL-2629 fix files permission issue on Mac
tree
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commitdiff
2017-08-09
TZVanaalten
JAL-2599 fix for issue where info annot would not display
tree
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commitdiff
2017-08-09
tzvanaalten
JAL-2599 fix for issue where info annot would not display
tree
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commitdiff
2017-08-09
TZVanaalten
JAL-2629 buffers are now temporary files
tree
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commitdiff
2017-08-09
TZVanaalten
JAL-2629 removed unnecessary exception throws from...
tree
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commitdiff
2017-08-08
TZVanaalten
JAL-2616 fix allowing clan sorting to work
tree
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commitdiff
2017-08-08
TZVanaalten
JAL-2599 fix for index issue on node lookup
tree
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commitdiff
2017-08-08
TZVanaalten
JAL-2629 add ability to select hmmer binaries folder
tree
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commitdiff
2017-08-07
TZVanaalten
JAL-2629 fixed hmmalign failing due to differing sequen...
tree
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commitdiff
2017-08-07
TZVanaalten
JAL-2629 current hmmer commands are now executed in...
tree
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commitdiff
2017-08-04
TZVanaalten
JAL-2599 fixed information annotation buttons not working
tree
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commitdiff
2017-08-04
TZVanaalten
JAL-2629 hmmbuild now runs on alignments of different...
tree
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commitdiff
2017-08-04
TZVanaalten
JAL-2629 multiple HMMs can now be dropped onto an alignment
tree
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commitdiff
2017-08-02
TZVanaalten
JAL-2599 fix for HMM logo not normalising correctly
tree
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commitdiff
2017-08-02
TZVanaalten
JAL-2599 fix issue where parser exported map annotation...
tree
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commitdiff
2017-08-02
TZVanaalten
JAL-2599 fix for information annotation buttons
tree
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commitdiff
2017-07-31
TZVanaalten
JAL-2629 add hmmalign command
tree
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commitdiff
2017-07-27
TZVanaalten
JAL-2629 implement hmmbuild
tree
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commitdiff
2017-07-27
TZVanaalten
JAL-2629 moved HMM storage location to placeholder...
tree
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commitdiff
2017-07-26
TZVanaalten
JAL-2629 HMMs now map to reference annotation if exists
tree
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commitdiff
2017-07-25
TZVanaalten
JAL-2629 add non-functional HMMER menu
tree
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commitdiff
2017-07-25
TZVanaalten
JAL-2616 add ability to perform random alignments withi...
tree
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commitdiff
2017-07-24
tzvanaalten
JAL-2616 add placeholder sequence for HMM, does not...
tree
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commitdiff
2017-07-24
tzvanaalten
JAL-2616 add ability to change location of family and...
tree
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commitdiff
2017-07-24
tzvanaalten
JAL-2599 .hmm parser should now accept older .hmm files
tree
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commitdiff
2017-07-21
TZVanaalten
JAL-2616 add ability to sort Pfam families and HMMs...
tree
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commitdiff
2017-07-20
TZVanaalten
JAL-2616 remove statistical analysis from AlignFrame
tree
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commitdiff
2017-07-20
TZVanaalten
JAL-2599 small code improvements
tree
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commitdiff
2017-07-20
TZVanaalten
JAL-2616 add documentation for probability analyser
tree
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commitdiff
2017-07-20
TZVanaalten
JAL-2616 add probability distribution analyser class
tree
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commitdiff
2017-07-20
TZVanaalten
JAL-2599 add ability to process RNA HMMer files
tree
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commitdiff
2017-07-18
TZVanaalten
JAL-2599 complete documentation for HMM and HMMFile...
tree
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commitdiff
2017-07-18
TZVanaalten
JAL-2599 modified state transition probability storage
tree
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commitdiff
2017-07-14
TZVanaalten
add partial button fix to annotation and statistics...
features/hmmer_statistics
tree
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commitdiff
2017-07-12
TZVanaalten
test HMM annotaTION
tree
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commitdiff
2017-07-11
TZVanaalten
complete Information Content annotation
tree
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commitdiff
2017-06-29
TZVanaalten
add information content calculations
tree
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commitdiff
2017-06-29
TZVanaalten
transferred the storage position of the HMM to annotations
tree
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commitdiff
2017-06-23
TZVanaalten
test HMMER colour scheme
tree
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commitdiff
2017-06-23
TZVanaalten
add HMMER colour scheme
tree
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commitdiff
2017-06-22
TZVanaalten
fully integrate HMMER3 file format into Jalview
tree
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commitdiff
2017-06-20
TZVanaalten
restructure file exporter
tree
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commitdiff
2017-06-15
TZVanaalten
add HMMFile class to read and write HMM files
tree
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commitdiff
2017-06-15
TZVanaalten
Update HiddenMarkovModel class
tree
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commitdiff
2017-06-09
TZVanaalten
Add HiddenMarkovModel class
tree
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commitdiff
2017-05-31
Jim Procter
Merge branch 'JAL-2571' into develop
tree
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commitdiff
2017-05-31
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-05-31
tcofoegbu
Fixed failing tests
tree
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commitdiff
2017-05-31
gmungoc
JAL-2547 handle contact features 'around' a gap correctly
tree
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commitdiff
2017-05-30
kiramt
JAL-2573 Fixes for alignment < viewport width, and...
JAL-2571
tree
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commitdiff
2017-05-30
gmungoc
JAL-2547 tooltip/AmendFeatures on gap straddled by...
tree
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commitdiff
2017-05-30
kiramt
JAL-2571 Corrected alignment width/height checks to...
tree
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commitdiff
2017-05-30
gmungoc
JAL-2570 don't zap group colour scheme when mapping...
tree
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commitdiff
2017-05-29
Jim Procter
Merge branch 'bug/JAL-2034contextchange' into develop
tree
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commitdiff
2017-05-29
Jim Procter
Merge branch 'features/JAL-2465_No-mapping_Jmol-structu...
tree
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commitdiff
2017-05-29
Jim Procter
JAL-2533 update javadoc
features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url
tree
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commitdiff
2017-05-29
Jim Procter
Merge branch 'bug/JAL-2536' into develop
tree
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commitdiff
2017-05-29
Jim Procter
JAL-2536 tweak javadoc wording
tree
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commitdiff
2017-05-29
Jim Procter
Merge branch 'bug/JAL-2517cancelAppletColour' into...
tree
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commitdiff
2017-05-27
Jim Procter
Merge branch 'bug/JAL-2491' into develop
tree
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commitdiff
2017-05-27
Jim Procter
Merge branch 'bug/JAL-2547tooltipOnGap' into develop
tree
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commitdiff
2017-05-27
Jim Procter
JAL-2526 test and documentation for SeqPanel.setStatus...
tree
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commitdiff
2017-05-27
Jim Procter
JAL-2562 javadoc TODO
tree
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commitdiff
2017-05-26
kiramt
JAL-2491 Missed port to applet from JAL-1691
bug/JAL-2491
tree
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commitdiff
2017-05-26
tcofoegbu
JAL-2465 Improvement to re-instate storing recently...
tree
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commitdiff
2017-05-26
tcofoegbu
JAL-2465 fix to prevent files loaded from the system...
tree
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commitdiff
2017-05-25
kiramt
JAl-2034 Ported to applet
bug/JAL-2034contextchange
tree
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commitdiff
2017-05-25
kiramt
JAL-2034 don't update overview after click without...
tree
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commitdiff
2017-05-25
kiramt
Merge branch 'bug/JAL-2551' into bug/JAL-2034contextchange
tree
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commitdiff
2017-05-24
kiramt
JAL-2551 Fix to group colouring when group extent is...
bug/JAL-2551
tree
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commitdiff
2017-05-24
kiramt
JAL-2034 Added isDefined flag to SequenceGroup
tree
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commitdiff
2017-05-23
Jim Procter
JAL-2549 replace JABAWS 2.1 with 2.2 client and remove...
tree
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commitdiff
2017-05-23
gmungoc
JAL-2547 don't show features in tooltip over a gap
bug/JAL-2547tooltipOnGap
tree
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commitdiff
2017-05-22
gmungoc
JAL-2504 update the right feature colour when creating...
bug/JAL-2510amendFeatures
tree
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commitdiff
2017-05-22
gmungoc
JAL-2544 check feature overlaps selection region
tree
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commitdiff
2017-05-22
kiramt
Merge remote-tracking branch 'origin/bug/JAL-2256'...
tree
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commitdiff
2017-05-22
Jim Procter
JAL-2418 patch build - broken htsjdk import
tree
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commitdiff
2017-05-19
gmungoc
JAL-2526 removed redundant call to Sequence.findPosition()
tree
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commitdiff
2017-05-18
Jim Procter
JAL-2388 return empty hidden columns for fully visible...
tree
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commitdiff
2017-05-18
kiramt
JAL-2256 Corrected AllCols/Rows iterator behaviour...
bug/JAL-2256
tree
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commitdiff
2017-05-17
Jim Procter
Merge branch 'bug/JAL-2510amendFeatures' into develop
tree
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commitdiff
2017-05-17
Jim Procter
Merge branch 'features/JAL-2447experimentalFlag' into...
tree
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commitdiff
2017-05-17
gmungoc
JAL-2504 use (and update) defaults for new feature...
tree
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commitdiff
2017-05-17
gmungoc
Merge branch 'develop' into bug/JAL-2510amendFeatures
tree
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commitdiff
2017-05-16
kiramt
JAL-2536 Overview window sizing not subject to min...
bug/JAL-2536
tree
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commitdiff
2017-05-16
gmungoc
JAL-2517 restore complex colour scheme on Cancel in...
bug/JAL-2517cancelAppletColour
tree
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commitdiff
2017-05-16
gmungoc
JAL-2403 simplify instantiation / configuration of...
tree
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commitdiff
2017-05-16
kiramt
JAL-2522 Missed fix to applet
tree
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commitdiff
2017-05-16
kiramt
JAL-2388 Rationalised hashCode method in HiddenColumns
tree
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commitdiff
2017-05-16
kiramt
Merge branch 'develop' into bug/JAL-2491
tree
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commitdiff
2017-05-16
kiramt
JAL-2491 Better merge
tree
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commitdiff
2017-05-15
Jim Procter
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into...
tree
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commitdiff
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