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JAL-4420 Allow preprocessing of arguments if they are all simply filenames (or URLs...
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
2023-11-03
James Procter
JAL-4090 JAL-1551 spotlessApply
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commitdiff
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
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diff to current
2023-07-07
James Procter
JAL-4221 update description when transferring annotatio...
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diff to current
2023-05-25
James Procter
JAL-2381 copy and paste sequence also copies contact...
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commitdiff
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diff to current
2023-05-19
James Procter
JAL-1551 spotlessApply
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commitdiff
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diff to current
2023-05-18
James Procter
JAL-4134 colour by annotation needs distinct annotation...
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commitdiff
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diff to current
2023-05-14
James Procter
JAL-2349 fix up tests for Java 11 compatibility and...
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diff to current
2022-10-17
Jim Procter
JAL-2349 JAL-3855 Integrate pAE retrieval in StructureF...
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diff to current
2022-10-15
Jim Procter
JAL-2349 reusable contact map holder for SequenceI...
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diff to current
2022-03-25
Jim Procter
JAL-3980 JAL-3979 TODOs
bug/JAL-3980_JAL-3981_tooltips_sequence_details
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commitdiff
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diff to current
2021-09-20
Jim Procter
JAL-3829 ensure nulls are not wildcards when retrieving...
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commitdiff
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diff to current
2021-09-17
Jim Procter
JAL-2226 new method to search for annotation matching...
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commitdiff
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diff to current
2020-03-30
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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diff to current
2020-02-27
Jim Procter
Merge branch 'bug/JAL-3296changeStartInvalidateCursor...
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diff to current
2019-10-08
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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commitdiff
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diff to current
2019-09-26
gmungoc
JAL-2481 remove code duplication left by merge
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commitdiff
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diff to current
2019-07-30
gmungoc
JAL-3198 more efficient Sequence.getDisplayId()
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commitdiff
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diff to current
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
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commitdiff
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diff to current
2019-06-10
gmungoc
JAL-3296 ensure sequence cursor reset when sequence...
bug/JAL-3296changeStartInvalidateCursor
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commitdiff
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diff to current
2019-06-07
gmungoc
JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
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commitdiff
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diff to current
2019-04-18
hansonr
minor code clean up
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diff to current
2019-03-13
gmungoc
Merge branch 'develop' into trialMerge
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commitdiff
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diff to current
2019-03-01
gmungoc
Merge branch 'feature/intervalStoreJ' into merge/JAL...
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commitdiff
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diff to current
2019-02-28
gmungoc
JAL-3140 confine intervalstore imports to jalview.datam...
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commitdiff
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diff to current
2019-02-04
hansonr
refactoring for DBMODList
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2019-01-26
hansonr
Platform.timecheck calls removed or commented out.
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commitdiff
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diff to current
2019-01-26
hansonr
removing cyclic call
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diff to current
2019-01-26
hansonr
Jalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
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2018-12-17
Jim Procter
Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures
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2018-11-29
gmungoc
JAL-3140 NCList now via IntervalStore library
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diff to current
2018-05-11
gmungoc
JAL-2986 corrected findIndex for out of range residue...
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commitdiff
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diff to current
2018-03-07
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
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commitdiff
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diff to current
2018-01-29
kiramt
JAL-2759 Fix unintended type change
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commitdiff
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2018-01-22
kiramt
JAL-2579 Moved locateVisibleStartOfSequence to Sequence...
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commitdiff
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diff to current
2018-01-19
kiramt
JAL-2759 Changes to getVisibleSequenceStrings after...
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commitdiff
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diff to current
2017-11-22
gmungoc
JAL-2069 spike updated with latest (FeatureTypeSettings)
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commitdiff
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diff to current
2017-11-22
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
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2017-11-21
kiramt
Merge branch 'develop' into feature/JAL-2759
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commitdiff
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diff to current
2017-11-16
Jim Procter
Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures
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commitdiff
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diff to current
2017-11-16
Jim Procter
Merge branch 'bug/JAL-2829deleteCharsWithGaps' into...
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commitdiff
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diff to current
2017-11-15
gmungoc
JAL-2835 spike updated with latest
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commitdiff
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diff to current
2017-11-13
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
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commitdiff
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diff to current
2017-11-13
gmungoc
JAL-2176 removed unused Sequence.index
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diff to current
2017-11-13
gmungoc
Merge branch 'bug/JAL-2829deleteCharsWithGaps' into
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diff to current
2017-11-10
gmungoc
JAL-2829 fixes and unit tests
bug/JAL-2829deleteCharsWithGaps
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2017-11-08
kiramt
Merge branch 'develop' into feature/JAL-2759
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2017-11-06
Jim Procter
Merge branch 'bug/JAL-2541cutRelocateFeatures' into...
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commitdiff
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diff to current
2017-10-27
gmungoc
JAL-1793 spike branch updated to latest
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commitdiff
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diff to current
2017-10-24
gmungoc
JAL-2738 tidy Javadoc, remove debug logging
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commitdiff
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diff to current
2017-10-24
gmungoc
JAL-2738 update spike branch with latest
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commitdiff
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diff to current
2017-10-24
gmungoc
Merge branch 'develop' into features/JAL-1793VCF; lambd...
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2017-10-23
Jim Procter
Merge branch 'bug/JAL-2682parseId' into develop
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commitdiff
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diff to current
2017-10-20
gmungoc
Push 1793 latest to spike branch
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commitdiff
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diff to current
2017-10-11
gmungoc
JAL-2772 check array bounds for sequence access
bug/JAL-2772pdbArrayBounds
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commitdiff
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diff to current
2017-10-10
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
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commitdiff
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2017-10-09
gmungoc
JAL-2480 use interface type for sequenceFeatureStore
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diff to current
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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commitdiff
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diff to current
2017-09-28
gmungoc
JAL-1796 GeneLociI as distinguished DBRefEntry
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commitdiff
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diff to current
2017-09-26
gmungoc
JAL-2738 promote setGeneLoci to SequenceI!
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commitdiff
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2017-09-25
gmungoc
JAL-2738 getGeneLoci promoted to SequenceI
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diff to current
2017-09-22
gmungoc
JAL-2738 correct handling of reverse strand genes
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commitdiff
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diff to current
2017-09-21
kiramt
JAL-2674 Rewrote propagateInsertions
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commitdiff
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diff to current
2017-09-21
gmungoc
JAL-2738 GeneLoci holds mapping of sequence to chromosome
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diff to current
2017-09-14
gmungoc
JAL-2541 length check in deleteChars (redoing lost...
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commitdiff
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diff to current
2017-09-14
gmungoc
JAL-2541 working Cut/Undo with feature relocation
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commitdiff
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diff to current
2017-09-14
gmungoc
JAL-2541 revised cut with features (work in progress)
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commitdiff
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diff to current
2017-08-23
gmungoc
JAL-2682 non-regex sequence id parsing, and tests added
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2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
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diff to current
2017-08-16
Jim Procter
JAL-2418 source formatting
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commitdiff
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diff to current
2017-06-24
gmungoc
JAL-2547 fix case of gap followed by enclosing contact...
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diff to current
2017-06-22
gmungoc
JAL-2481 JAL-2593 JAL-2526 further optimisation of...
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diff to current
2017-06-20
gmungoc
JAL-2526 don't retain lastColumnPosition from an invali...
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commitdiff
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diff to current
2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
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commitdiff
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diff to current
2017-06-09
gmungoc
JAL-2446 merged to spike branch
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diff to current
2017-06-08
gmungoc
JAL-2526 correct boundary conditions for sequence left...
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commitdiff
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diff to current
2017-06-08
gmungoc
JAL-2526 cache first/last residue column positions...
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commitdiff
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diff to current
2017-06-06
gmungoc
JAL-2526 less stringent test for invalid cursor
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commitdiff
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diff to current
2017-06-05
gmungoc
Merge branch 'features/JAL-2526sequenceCursor' into
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diff to current
2017-06-05
gmungoc
Merge branch 'features/JAL-2446NCList' into
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2017-06-05
gmungoc
Merge branch 'features/JAL-2446NCList' into
features/JAL-2526sequenceCursor
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diff to current
2017-06-05
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
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diff to current
2017-06-04
Jim Procter
JAL-2291 bug fix - BitSet.set is [start,end+1)
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diff to current
2017-06-04
Jim Procter
JAL-2291 SequenceI.getInsertionsAsBits for convenient...
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commitdiff
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diff to current
2017-06-02
gmungoc
JAL-2526 additional tests for findPosition with/without...
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commitdiff
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diff to current
2017-06-01
gmungoc
JAL-2526 additional calls to sequenceChanged() after...
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commitdiff
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diff to current
2017-06-01
gmungoc
JAL-2526 zapCursor() renamed sequenceChanged()
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diff to current
2017-06-01
gmungoc
JAL-2754 Sequence.findFeatures(fromCol, toCol)
features/JAL-2754findFeaturesByColumn
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commitdiff
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diff to current
2017-05-30
gmungoc
JAL-2526 first draft of findIndex/findPosition with...
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commitdiff
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diff to current
2017-05-29
gmungoc
JAL-2526 Sequence.findPositions to get residue position...
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commitdiff
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diff to current
2017-05-25
gmungoc
JAL-2557 removal of Sequence.sequenceFeatures
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commitdiff
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diff to current
2017-05-24
gmungoc
Merge branch 'bug/JAL-2541cutWithFeatures' into feature...
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commitdiff
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diff to current
2017-05-18
gmungoc
JAL-2541 fix to initSeqFrom (and minor code tidy);...
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commitdiff
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diff to current
2017-05-09
gmungoc
JAL-2480 include sequenceFeatureStore in createDatasetS...
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commitdiff
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diff to current
2017-04-27
gmungoc
JAL-2480 don't allow null type in SequenceFeature
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commitdiff
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diff to current
2017-04-26
gmungoc
JAL-2490 findFeaturesAtRes with performant feature...
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commitdiff
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diff to current
2017-04-19
gmungoc
JAL-2483 use SequenceFeatures to look up groups, types...
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commitdiff
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diff to current
2017-04-18
gmungoc
JAL-2480 SequenceFeaturesI encapsulates features api
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commitdiff
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diff to current
2017-04-17
gmungoc
JAL-2446 add call to SequenceFeatures.delete(); use...
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diff to current
2017-03-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-653_JAL-1766_htslib_refseqsupport
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diff to current
2017-03-20
gmungoc
JAL-2446 FeatureStore with NCList - work in progress
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