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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git]
/
src
/
jalview
/
datamodel
/ Alignment.java
2023-11-03
James Procter
JAL-4090 JAL-1551 spotlessApply
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2023-10-23
James Procter
Merge branch 'develop' into improvement/JAL-4124_dont_d...
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2023-09-26
James Procter
JAL-3858 JAL-4090 avoid NPE when given out of bound...
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2023-09-01
James Procter
JAL-4124 matrix is saved in dataset, with forward refer...
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2023-05-22
James Procter
JAL-1551 spotless
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commitdiff
2023-05-19
James Procter
JAL-1551 spotlessApply
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commitdiff
2023-05-19
James Procter
JAL-1551 spotlessApply
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commitdiff
2023-05-18
James Procter
JAL-4134 colour by annotation needs distinct annotation...
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commitdiff
2023-05-12
James Procter
JAL-2349 allow PAE or other contact matrices to hold...
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commitdiff
2023-03-20
James Procter
JAL-2349 fix off by one when resolving columns for...
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commitdiff
2023-02-27
James Procter
JAL-4134 allow tree groups to be stored/recovered on...
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commitdiff
2022-10-20
Jim Procter
JAL-2349 JAL-3855 off by one and daft return
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commitdiff
2022-10-20
Jim Procter
JAL-3855 JAL-2349 AlignmentI.getContactList takes care...
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commitdiff
2022-10-17
Jim Procter
JAL-2349 JAL-3855 Integrate pAE retrieval in StructureF...
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commitdiff
2022-10-15
Jim Procter
JAL-2349 reusable contact map holder for SequenceI...
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commitdiff
2022-06-10
Jim Procter
JAL-4027 getter for contact matrices on the Alignment.
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commitdiff
2022-06-10
Jim Procter
JAL-1551 formatting
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2022-06-10
Jim Procter
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...
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2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
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commitdiff
2021-08-18
Jim Procter
JAL-2349 allow contact map to be associated with a...
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commitdiff
2021-08-11
Jim Procter
Merge branch 'features/JAL-2349_matrixvis' into feature...
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2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
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2019-06-18
Jim Procter
Merge branch 'features/JAL-2349_matrixvis' into merge...
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2019-04-18
hansonr
minor code clean up
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commitdiff
2019-03-21
Ben Soares
JAL-3130 Replaced deprecated Class.newInstance() with...
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2019-03-13
gmungoc
Merge branch 'develop' into trialMerge
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2019-03-04
gmungoc
Merge branch 'bug/JAL-3072scrollThread' into merge...
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2019-03-04
gmungoc
Merge branch 'bug/JAL-3099alignmentVisibleWidth' into...
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2019-01-29
hansonr
iterators
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2018-11-28
gmungoc
JAL-3164 redraw complement overview on hide columns
bug/JAL-3164complementOverview
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2018-09-10
gmungoc
JAL-3099 new method AlignmentI.getVisibleWidth()
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2018-07-25
gmungoc
JAL-3074 don't scroll up/down on drag out of scale...
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2018-02-27
Jim Procter
Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104
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2018-02-21
Jim Procter
Merge branch 'bug/JAL-2778again' into releases/Release_...
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2018-02-21
kiramt
JAL-2778 Revert back to old synchronisation
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2018-02-06
kiramt
Merge branch 'develop' into feature/JAL-2759
feature/JAL-2759
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2018-02-05
Jim Procter
JAL-2780 JAL-2781 - patch and first test for AlignmentI...
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2018-02-05
kiramt
JAL-2788 possible adjustments to sequence accesses
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2018-01-26
kiramt
JAL-2778 try another way to draw sequences with reduced...
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2018-01-19
kiramt
JAL-2759 Moved propagateInsertions out of HiddenColumns
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2018-01-15
kiramt
JAL-2759 Rename hideInsertionsFor to hideList, after...
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2018-01-15
kiramt
JAL-2759 Refactor of hideInsertionsFor after review
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2017-11-22
gmungoc
JAL-2069 spike updated with latest (FeatureTypeSettings)
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2017-11-10
Jim Procter
JAL-2828 allow CalcId to match on String equivalence...
doc/JAL-2494_JAL-2828_mergefindAnnotation
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2017-11-10
Jim Procter
JAL-2828 refactored duplicate code for searching lists...
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2017-11-01
kiramt
JAL-2778 remove unnecessary code running in repaint
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2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
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2017-08-16
Jim Procter
JAL-2418 source formatting
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2017-07-24
gmungoc
spike branch updated from latest features/JAL-2446
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2017-06-27
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
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2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
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2017-06-09
gmungoc
JAL-2446 merged to spike branch
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2017-06-09
Jim Procter
Merge branch 'develop' into features/JAL-2349_matrixvis
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2017-06-07
kiramt
JAL-2591 More refactoring (incomplete)
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2017-06-02
kiramt
JAL-2576 Proposed fix
bug/JAL-2576
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2017-05-24
kiramt
JAL-2034 Added isDefined flag to SequenceGroup
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2017-05-05
kiramt
Merge remote-tracking branch 'origin/develop' into
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2017-04-27
Jim Procter
JAL-2494 fixed behaviour for null parameters in line...
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2017-04-27
Jim Procter
JAL-2494 javadoc for AnnotatedCollectionI.findAnnotations
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2017-04-24
kiramt
JAL-2388 Hidden cols separated from column selection...
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2017-03-31
gmungoc
JAL-2405 additional checks for circular reference in...
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2017-03-17
kiramt
JAL-2437 Synchronization corrections and unit tests
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2017-03-10
kiramt
JAL-2437 Fixed reordering of sequences when hiding...
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2017-03-07
kiramt
JAL-2388 Missed commit
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2017-03-03
kiramt
JAL-2388 Initial removal of hidden cols/seqs out of...
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2017-02-10
Jim Procter
Merge branch 'develop' into spike/matrix_annot
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2017-01-23
Jim Procter
JAL-2349 ContactMatrixI provided max/min getters
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2017-01-06
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
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2017-01-05
gmungoc
JAL-2374 fix popup out by one and multiple groups bugs
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2016-12-14
gmungoc
JAL-2360 added check for null annotations array
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commitdiff
2016-12-12
gmungoc
JAL-2360 simplify nucleotide flag, remove setter
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commitdiff
2016-12-04
Jim Procter
JAL-2348 JAL-2349 make contact maps non-editable so...
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commitdiff
2016-12-04
Jim Procter
JAL-2349 interfaces and logic for adding contact matric...
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2016-11-25
gmungoc
Merge branch 'develop' into trialMerge
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commitdiff
2016-10-28
Jim Procter
JAL-966 JAL-1738 JAL-345 interfaces for SearchResults...
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2016-10-25
Jim Procter
JAL-2089 patch broken merge to master for Release 2...
releases/Release_2_10_0_Branch
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commitdiff
2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
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commitdiff
2016-10-04
gmungoc
JAL-2232 JAL-2154 update dbrefs to newly created datase...
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2016-09-22
gmungoc
JAL-2216 finalize() refactored so not called programmat...
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commitdiff
2016-08-30
gmungoc
Merge branch 'develop' into features/filetypeEnum
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commitdiff
2016-08-22
Jim Procter
JAL-2154 always check dataset sequence for sequence...
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2016-08-19
Jim Procter
JAL-2154 refactor setSequenceAt to replaceSequenceAt...
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2016-08-07
Jim Procter
JAL-2154 add in missing class for createDatasetAlignmen...
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commitdiff
2016-08-04
Jim Procter
JAL-2154 make sure all sequences referenced via DBRefEn...
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2016-07-18
Jim Procter
JAL-2121 cleanup TODO
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2016-07-14
Jim Procter
JAL-1115 change implementation to avoid possibility...
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commitdiff
2016-07-14
Jim Procter
JAL-1270 test coverage TODO Alignment.append(AlignmentI)
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2016-07-12
Jim Procter
JAL-2110 javadoc and TODO re shortcomings of implementation
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2016-07-06
gmungoc
JAL-2110 ensuring mapped dbrefs between protein and cds
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2016-07-04
gmungoc
JAL-2110 unused method removed
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2016-06-20
Jim Procter
JAL-2110 copy alcodonframes only if copy constructor...
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2016-06-19
Jim Procter
JAL-2110 JAL-2131 JAL-1765 remove reference to jalview...
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commitdiff
2016-06-16
Jim Procter
JAL-2110 todo - select mappings involving sequences...
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2016-05-31
gmungoc
JAL-2023 adjustments to mappings added for split frame...
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2016-04-11
tcofoegbu
JAL-2054 Renamed getStartEnd in AlignFrame to getVisibl...
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2016-04-01
gmungoc
JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
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2015-12-22
gmungoc
JAL-653 realise virtual mappings and align when adding...
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2015-12-03
gmungoc
JAL-653 mappings always reside on the dataset alignment...
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2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
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