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JAL-2629 add basic parameter adjustment to hmmsearch/align
[jalview.git]
/
src
/
jalview
/
datamodel
/
2017-08-18
TZVanaalten
Merge branch 'develop' into features/hmmer
tree
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commitdiff
2017-08-18
TZVanaalten
JAL-2668 add tests for HMMER commands, annotation and io
tree
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commitdiff
2017-08-17
TZVanaalten
JAL-2599 some slight renaming of variables and methods
tree
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commitdiff
2017-08-17
TZVanaalten
JAL-2629 add documentation to previous work
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
tree
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 add insert sequence at method on alignment
tree
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 fix incorrect gap insertions on HMM sequence
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-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
2017-08-08
TZVanaalten
JAL-2599 fix for index issue on node lookup
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 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
2017-07-24
tzvanaalten
JAL-2616 add placeholder sequence for HMM, does not...
tree
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commitdiff
2017-07-22
kiramt
Merge branch 'develop' into feature/JAL-2611
tree
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commitdiff
2017-07-20
TZVanaalten
JAL-2599 small code improvements
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
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commitdiff
2017-07-13
kiramt
JAL-2613 Unit tests and a fix. Phew.
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
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commitdiff
2017-07-05
gmungoc
JAL-147 additions to unit test, check for negative...
tree
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commitdiff
2017-07-05
gmungoc
JAL-147 prevent overview box move up over hidden first...
tree
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commitdiff
2017-06-29
TZVanaalten
add information content calculations
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commitdiff
2017-06-29
TZVanaalten
transferred the storage position of the HMM to annotations
tree
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commitdiff
2017-06-29
kiramt
JAL-2597 Fix and unit test
bug/JAL-2597
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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
gmungoc
Merge branch 'bug/JAL-2386groupConservationColouring...
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
2017-06-12
kiramt
JAL-2591 Updates following code review
tree
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commitdiff
2017-06-09
TZVanaalten
Add HiddenMarkovModel class
tree
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commitdiff
2017-06-08
gmungoc
JAL-2386 JAL-2570 use ResidueShader copy constructor...
bug/JAL-2386groupConservationColouring
tree
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commitdiff
2017-06-08
kiramt
JAL-2591 Refactor HiddenColumns to use ArrayList instea...
tree
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commitdiff
2017-06-08
kiramt
JAL-2591 More HiddenColumns refactoring. Tests passing.
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 Further refactoring (still incomplete)
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 More refactoring (incomplete)
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 Hidden columns regions can be output to string...
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 updated HiddenColumns::findHiddenRegionPositio...
tree
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commitdiff
2017-06-07
gmungoc
JAL-2386 ensure group conservation shading is applied...
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 simplifying hidden columns usage
tree
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commitdiff
2017-06-06
kiramt
JAL-2591 Added readwrite locking on HiddenColumns
tree
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commitdiff
2017-06-06
kiramt
Merge remote-tracking branch 'origin/bug/JAL-2576'...
tree
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commitdiff
2017-06-05
Jim Procter
Merge branch 'bug/JAL-2576' into develop
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2291 get bitset representing hidden columns
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2291 method taking a BitSet for hiding columns
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2291 bug fix - BitSet.set is [start,end+1)
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2291 SequenceI.getInsertionsAsBits for convenient...
tree
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commitdiff
2017-06-02
kiramt
JAL-2576 Proposed fix
bug/JAL-2576
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commitdiff
2017-05-31
Jim Procter
Merge branch 'JAL-2571' into develop
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
2017-05-27
Jim Procter
JAL-2562 javadoc TODO
tree
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commitdiff
2017-05-24
kiramt
JAL-2034 Added isDefined flag to SequenceGroup
tree
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commitdiff
2017-05-22
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
2017-05-18
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
2017-05-16
kiramt
JAL-2388 Rationalised hashCode method in HiddenColumns
tree
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commitdiff
2017-05-12
Jim Procter
Merge branch 'features/JAL-2388OverviewWindow' into...
tree
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commitdiff
2017-05-11
Jim Procter
JAL-2507 test if an annotation is ‘whitespace’
tree
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commitdiff
2017-05-11
Jim Procter
JAL-2507 Annotation.EMPTY_ANNOTATION - non-null whitesp...
tree
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commitdiff
2017-05-05
kiramt
Merge remote-tracking branch
tree
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commitdiff
2017-05-05
kiramt
Merge remote-tracking branch 'origin/develop' into
features/JAL-2388hiddencolumnschanges
tree
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commitdiff
2017-05-05
kiramt
Merge remote-tracking branch 'origin/develop' into
tree
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commitdiff
2017-05-03
Jim Procter
JAL-2503 AlignmentAnnotation.isQuantitative() test
tree
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commitdiff
2017-05-02
Jim Procter
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-05-02
Jim Procter
Merge branch 'bug/JAL-2424getVisibleContigs' into develop
tree
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commitdiff
2017-04-28
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-04-27
Jim Procter
JAL-2494 fix: updated behaviour for SequenceGroup.findA...
tree
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commitdiff
2017-04-27
Jim Procter
JAL-2494 fixed behaviour for null parameters in line...
tree
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commitdiff
2017-04-27
Jim Procter
JAL-2494 javadoc for AnnotatedCollectionI.findAnnotations
tree
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commitdiff
2017-04-26
kiramt
Merge remote-tracking branch 'origin/features/JAL-2388h...
tree
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commitdiff
2017-04-26
kiramt
JAL-2388 last separation of hidden columns/col selection
tree
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commitdiff
2017-04-26
kiramt
JAL-2388 Tidies and unit tests
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commitdiff
2017-04-25
kiramt
JAL-2388 Working hidden regions hide/show in desktop
tree
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commitdiff
2017-04-24
kiramt
Merge remote-tracking branch
tree
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commitdiff
2017-04-24
kiramt
JAL-2388 Finished split of hidden columns and selected...
tree
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commitdiff
2017-04-24
gmungoc
JAL-2424 final contig now an inclusive range
bug/JAL-2424getVisibleContigs
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commitdiff
2017-04-24
kiramt
JAL-2388 Hidden cols separated from column selection...
tree
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commitdiff
2017-04-21
kiramt
JAL-2388 Alignment col and row collections with iterators
tree
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commitdiff
2017-04-19
kiramt
Merge remote-tracking branch 'origin/develop' into
tree
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commitdiff
2017-04-07
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-03-31
gmungoc
JAL-2405 additional checks for circular reference in...
tree
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commitdiff
2017-03-30
gmungoc
Merge branch 'develop' into bug/JAL-2346annotationChoice
tree
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commitdiff
2017-03-29
kiramt
JAL-2388 New rendering code, extensions to support...
tree
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commitdiff
2017-03-29
kiramt
JAL-2388 New iterators and tests
tree
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commitdiff
2017-03-23
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-03-21
Jim Procter
Merge branch 'features/JAL-2388OverviewWindow' into...
tree
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commitdiff
2017-03-17
kiramt
JAL-2437 Synchronization corrections and unit tests
tree
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commitdiff
2017-03-17
kiramt
JAL-2388 Renamed column and row subtraction functions
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commitdiff
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