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JAL-2611 reinstate missed merge - again!
[jalview.git]
/
src
/
jalview
/
datamodel
/
2017-07-22
kiramt
Merge branch 'develop' into feature/JAL-2611
tree
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commitdiff
2017-07-13
kiramt
JAL-2613 Unit tests and a fix. Phew.
tree
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commitdiff
2017-07-05
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
kiramt
JAL-2597 Fix and unit test
bug/JAL-2597
tree
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commitdiff
2017-06-15
gmungoc
Merge branch 'bug/JAL-2386groupConservationColouring...
tree
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commitdiff
2017-06-12
kiramt
JAL-2591 Updates following code review
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
tree
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commitdiff
2017-05-31
Jim Procter
Merge branch 'JAL-2571' into develop
tree
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commitdiff
2017-05-30
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
tree
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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
tree
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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
tree
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commitdiff
2017-03-15
kiramt
JAL-2388 Unit tests and tidies
tree
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commitdiff
2017-03-14
kiramt
JAL-2388 New hidden cols/seqs functions to support...
tree
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commitdiff
2017-03-10
kiramt
JAL-2437 Fixed reordering of sequences when hiding...
tree
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commitdiff
2017-03-07
kiramt
JAL-2388 Missed commit
tree
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commitdiff
2017-03-07
kiramt
Merge remote-tracking branch 'origin/develop' into...
tree
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commitdiff
2017-03-07
kiramt
JAL-2429 findColumnPosition returns 0 for cols in regio...
tree
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commitdiff
2017-03-07
kiramt
JAL-2429 Additional fix to ColumnSelection when hidden...
tree
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commitdiff
2017-03-03
kiramt
JAL-2429 Fix to ColumnSelection::findColumnPosition
tree
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commitdiff
2017-03-03
kiramt
JAL-2388 Initial removal of hidden cols/seqs out of...
tree
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commitdiff
2017-03-01
gmungoc
Merge branch 'features/JAL-2295setChimeraAttributes...
tree
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commitdiff
2017-02-23
gmungoc
JAL-2403 JAL-1483 changes to ScoreModelI hierarchy...
tree
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commitdiff
2017-02-21
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-02-20
gmungoc
JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix...
tree
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commitdiff
2017-02-20
Jim Procter
Merge branch 'features/JAL-2379pcaMemory' into develop
tree
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commitdiff
2017-02-15
Jim Procter
JAL-2374 new contains methods for seq and seq,apos
tree
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commitdiff
2017-02-15
Jim Procter
JAL-2374 javadoc - qualify that sequence argument to...
tree
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commitdiff
2017-02-14
gmungoc
Merge branch 'develop' into bug/JAL-2346annotationChoice
tree
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commitdiff
2017-02-13
gmungoc
JAL-1632 JAL-2416 load score matrices from file, as...
tree
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commitdiff
2017-02-13
gmungoc
JAL-1632 first cut of Tree chooser dialog and ScoreMode...
tree
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commitdiff
2017-02-09
gmungoc
Merge branch 'develop' into features/JAL-2379pcaMemory
features/JAL-2379pcaMemory
tree
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commitdiff
2017-02-09
gmungoc
JAL-2405 check for circular reference in SequenceGroup...
tree
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commitdiff
2017-01-27
gmungoc
JAL-2371 CollectionColourScheme renamed ResidueShader...
tree
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commitdiff
2017-01-27
gmungoc
JAL-2360 JAL-2371 updates from review CR-JAL-1
tree
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commitdiff
2017-01-26
gmungoc
Merge branch 'develop' into features/JAL-2379pcaMemory
tree
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commitdiff
2017-01-20
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-20
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
2017-01-19
gmungoc
JAL-2370 corrected applet mouse drag, refactored into...
tree
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commitdiff
2017-01-17
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2017-01-17
gmungoc
JAL-2370 fix bug when hiding a range including two...
tree
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commitdiff
2017-01-17
gmungoc
JAL-2379 use SparseMatrix for encoded sequences, tidy...
tree
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commitdiff
2017-01-09
gmungoc
JAL-2371 pull up isNucleotide to SequenceCollectionI
tree
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commitdiff
2017-01-06
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-06
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
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