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JAL-3878 update branch from 2.12 merge from 2.11.2
[jalview.git]
/
src
/
jalview
/
datamodel
/
2017-09-28
kiramt
JAL-2647 more iterators
tree
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commitdiff
2017-09-28
gmungoc
JAL-1796 GeneLociI as distinguished DBRefEntry
tree
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commitdiff
2017-09-28
gmungoc
JAL-2744 simple Feature Details report from Popup menu
tree
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commitdiff
2017-09-27
kiramt
JAL-2674 Removing most calls to getHiddenColumnsCopy
tree
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commitdiff
2017-09-26
kiramt
JAL-2674 tidied up CigarArray
tree
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commitdiff
2017-09-26
kiramt
Merge remote-tracking branch 'origin/bug/JAL-2742'...
tree
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commitdiff
2017-09-26
kiramt
JAL-2742 fixed
tree
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commitdiff
2017-09-26
kiramt
JAL-2674 Changed CigarArray constructor to use HiddenCo...
tree
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commitdiff
2017-09-26
kiramt
JAL-2674 Changes to pasting
tree
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commitdiff
2017-09-26
kiramt
JAL-2674 HiddenColumns interface tidies
tree
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commitdiff
2017-09-26
kiramt
JAL-2647 Added iterators and associated tests and bench...
tree
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commitdiff
2017-09-26
gmungoc
JAL-2738 promote setGeneLoci to SequenceI!
tree
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commitdiff
2017-09-25
gmungoc
JAL-2738 getGeneLoci promoted to SequenceI
tree
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commitdiff
2017-09-25
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2017-09-25
gmungoc
JAL-2525 return no features if none matches ontology...
tree
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commitdiff
2017-09-22
gmungoc
JAL-2738 correct handling of reverse strand genes
tree
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commitdiff
2017-09-22
kiramt
JAL-2674 add bounds to findHiddenRegionPositions
tree
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commitdiff
2017-09-21
kiramt
JAL-2674 Rewrote propagateInsertions
tree
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commitdiff
2017-09-21
gmungoc
JAL-2738 GeneLoci holds mapping of sequence to chromosome
tree
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commitdiff
2017-09-20
kiramt
JAL-2674 fix up interface of locateVisibleBoundsOfSequence
tree
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commitdiff
2017-09-15
Jim Procter
Merge branch 'develop' into trial_merge/JAL-1950
tree
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commitdiff
2017-09-14
gmungoc
JAL-2541 save/Undo only 'diffs' for features with Cut...
tree
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commitdiff
2017-09-14
gmungoc
JAL-2541 length check in deleteChars (redoing lost...
tree
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commitdiff
2017-09-14
gmungoc
JAL-2541 working Cut/Undo with feature relocation
tree
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commitdiff
2017-09-14
gmungoc
JAL-2541 revised cut with features (work in progress)
tree
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commitdiff
2017-09-05
Jim Procter
Merge branch 'master' into portforward/JAL-2675_2102b1t...
tree
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commitdiff
2017-09-04
Jim Procter
JAL-2675 source license
tree
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commitdiff
2017-09-03
Jim Procter
Merge branch 'bug/JAL-2665-2.10.2b' into documentation...
bug/JAL-2673_mergewithproblem
tree
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commitdiff
2017-09-03
Jim Procter
Merge branch 'documentation/JAL-2675_release2102b1...
tree
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commitdiff
2017-09-03
Jim Procter
Merge branch 'feature/JAL-2527' into documentation...
tree
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commitdiff
2017-09-01
gmungoc
JAL-2488 remove finalize methods
tree
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commitdiff
2017-08-30
kiramt
Merge branch 'feature/JAL-2664' into feature/JAL-2527
tree
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commitdiff
2017-08-29
kiramt
JAL-2664 Updates following review
feature/JAL-2664
tree
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commitdiff
2017-08-29
osboxes
JAL-2629 fix incorrect mapping between HMM and columns...
tree
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commitdiff
2017-08-29
osboxes
JAL-2629 HMMs dropped on the alignment now map to the...
tree
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commitdiff
2017-08-28
tzvanaalten
JAL-2629 add option to set HMM Logo letter height to...
tree
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commitdiff
2017-08-28
kiramt
Merge remote-tracking branch 'origin/develop' into...
tree
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commitdiff
2017-08-28
kiramt
Merge remote-tracking branch 'origin/releases/Release_2...
tree
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commitdiff
2017-08-28
kiramt
JAL-2665 Changes for review comments; printing with...
bug/JAL-2665
tree
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commitdiff
2017-08-28
TZVanaalten
JAL-2629 HMMER alignment background colour scheme is...
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 add multiple options for running hmmbuild...
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 add adjustable parameters to hmmbuild
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 remove sequence and group HMMER options
tree
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commitdiff
2017-08-23
gmungoc
JAL-2682 non-regex sequence id parsing, and tests added
tree
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commitdiff
2017-08-22
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2017-08-21
Jim Procter
Merge branch 'develop' into trial_merge/JAL-1950
spike/JAL-1950_hmmer3client
tree
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commitdiff
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
tree
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commitdiff
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
2017-08-16
kiramt
JAL-2665 Added hidden columns group selection - almost...
tree
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commitdiff
2017-08-16
kiramt
JAL-2665 Added sequence group update event.
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
2017-08-09
gmungoc
JAL-2480 inline one method, improve comments
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
2017-08-01
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
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
2017-07-24
gmungoc
spike branch updated from latest features/JAL-2446
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
2017-07-19
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
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
2017-07-13
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
tree
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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
2017-06-30
gmungoc
JAL-2505 correct handling of change of feature type
tree
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commitdiff
2017-06-30
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
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
2017-06-29
kiramt
JAL-2597 Fix and unit test
bug/JAL-2597
tree
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commitdiff
2017-06-27
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-06-24
gmungoc
Merge branch 'features/JAL-2446NCList' into spikes...
tree
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commitdiff
2017-06-24
gmungoc
JAL-2547 fix case of gap followed by enclosing contact...
tree
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commitdiff
2017-06-24
gmungoc
Merge branch 'features/JAL-2446NCList' into spikes...
tree
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commitdiff
2017-06-23
gmungoc
JAL-1858 handle hidden columns when computing region...
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
gmungoc
JAL-2481 JAL-2593 JAL-2526 further optimisation of...
tree
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commitdiff
2017-06-22
TZVanaalten
fully integrate HMMER3 file format into Jalview
tree
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commitdiff
2017-06-22
gmungoc
JAL-2480 simpler and safer test to avoid adding duplicates
tree
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commitdiff
2017-06-21
gmungoc
JAL-2480 tidy generic initialisations, SequenceFeatures...
tree
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commitdiff
2017-06-20
TZVanaalten
restructure file exporter
tree
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commitdiff
2017-06-20
gmungoc
JAL-2526 don't retain lastColumnPosition from an invali...
tree
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commitdiff
2017-06-15
gmungoc
Merge branch 'bug/JAL-2386groupConservationColouring...
tree
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commitdiff
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