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JAL-4136 Replace uses of isBlank with isEmpty
[jalview.git]
/
src
/
jalview
/
datamodel
/
2018-05-28
gmungoc
Merge remote-tracking branch 'origin/releases/Release_2...
tree
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commitdiff
2018-05-21
gmungoc
JAL-2920 use HGVS notation for protein variant feature
tree
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commitdiff
2018-05-11
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-05-11
gmungoc
JAL-2986 corrected findIndex for out of range residue...
tree
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commitdiff
2018-05-10
Jim Procter
Merge branch 'bug/JAL-2920_uniprotvariantfeature' into...
tree
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commitdiff
2018-05-10
Jim Procter
JAL-2920 simplified logic and added corner cases for...
tree
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commitdiff
2018-05-08
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-05-07
gmungoc
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-05-07
gmungoc
JAL-1767 unit test for save and restore PCA
features/JAL-1767pcaInProject
tree
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commitdiff
2018-05-07
Jim Procter
JAL-2906 apply GPLv3 license source
tree
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commitdiff
2018-05-04
gmungoc
JAL-1767 refactorings to enable faithful restore of...
tree
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commitdiff
2018-04-27
gmungoc
JAL-1767 refactoring and tidying of RotatableCanvas...
tree
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commitdiff
2018-04-26
gmungoc
JAL-2962 code tidying/documentation (non-functional...
tree
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commitdiff
2018-04-23
gmungoc
JAL-2956 save/restore HMMER profile to/from Jalview...
tree
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commitdiff
2018-04-23
gmungoc
JAL-2954 more efficient SearchResults.markColumns
tree
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commitdiff
2018-04-17
gmungoc
JAL-2629 choice of hmm profile now a parameter not...
tree
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commitdiff
2018-04-16
gmungoc
JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe...
tree
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commitdiff
2018-04-09
Mungo Carstairs
JAL-2629 more error checking
tree
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commitdiff
2018-03-30
gmungoc
JAL-2599 MapList from HMM nodes to consensus dataset...
tree
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commitdiff
2018-03-30
gmungoc
JAL-2939 field/method naming more consistent
tree
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commitdiff
2018-03-30
gmungoc
JAL-2941 'map hmm to RF' removed pending clarifications
tree
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commitdiff
2018-03-26
gmungoc
JAL-2939 always store Information profile
tree
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commitdiff
2018-03-20
gmungoc
JAL-2629 InformationThread.findOrCreateAnnotation and...
tree
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commitdiff
2018-03-20
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-03-16
gmungoc
Merge remote-tracking branch 'origin/releases/Release_2...
tree
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commitdiff
2018-03-16
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2018-03-14
gmungoc
JAL-2893 include ENSEMBLGENOMES as a 'roundtrip db...
tree
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commitdiff
2018-03-13
gmungoc
JAL-2839 addResult ignores duplicates
tree
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commitdiff
2018-03-09
gmungoc
JAL-2839 Finder refactoring prior to fixing the defect
tree
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commitdiff
2018-03-07
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-03-07
gmungoc
JAL-2925 handle empty annotation when copying group...
tree
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commitdiff
2018-03-07
gmungoc
JAL-2629 storage and lifecycle of alignment/group HMM...
tree
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commitdiff
2018-03-01
gmungoc
JAL-2629 revising hmmer annotation updating (wip)
tree
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commitdiff
2018-02-28
gmungoc
JAL-2629 some tidying of Hmmer commands (wip)
tree
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commitdiff
2018-02-27
gmungoc
JAL-2668 method name change for clarity
tree
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commitdiff
2018-02-27
gmungoc
JAL-2717 JAL-2668 fixes to HMMER colour scheme display...
tree
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commitdiff
2018-02-27
Jim Procter
Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104
tree
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commitdiff
2018-02-26
Jim Procter
JAL-2920 parse variation and original elements of the...
tree
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commitdiff
2018-02-26
gmungoc
JAL-2599 test coverage and bug fixes for 'minimal file...
tree
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commitdiff
2018-02-23
gmungoc
JAL-2599 corrected case-insensitive symbol indexing
tree
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commitdiff
2018-02-23
gmungoc
JAL-2599 parser and datamodel use primitive double...
tree
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commitdiff
2018-02-22
gmungoc
JAL-2629 tidy tests, refactor hmmer node mapping slightly
tree
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commitdiff
2018-02-22
gmungoc
JAL-2629 tidy unit tests, constants etc
tree
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commitdiff
2018-02-21
Jim Procter
Merge branch 'bug/JAL-2778again' into releases/Release_...
tree
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commitdiff
2018-02-21
kiramt
JAL-2778 Revert back to old synchronisation
tree
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commitdiff
2018-02-20
gmungoc
JAL-2629 removed SequenceI.get/setLastPosition and...
tree
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commitdiff
2018-02-20
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-02-20
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-02-06
kiramt
Merge branch 'develop' into feature/JAL-2759
feature/JAL-2759
tree
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commitdiff
2018-02-05
Jim Procter
JAL-2780 JAL-2781 - patch and first test for AlignmentI...
tree
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commitdiff
2018-02-05
kiramt
JAL-2759 Fix errant RangeElementsIterator (unit tests...
tree
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commitdiff
2018-02-05
kiramt
JAL-2759 Rename getBoundedStartIterator
tree
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commitdiff
2018-02-05
kiramt
JAL-2759 Changes to StartRegionIterator after review
tree
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commitdiff
2018-02-05
kiramt
JAL-2788 possible adjustments to sequence accesses
tree
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commitdiff
2018-02-01
kiramt
JAL-2759 use right iterator for getVisibleColsIterator
tree
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commitdiff
2018-01-31
kiramt
JAL-2759 Rationalise VisibleColsIterator and HiddenCols...
tree
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commitdiff
2018-01-31
kiramt
JAL-2759 Generalised HiddenColsIterator naming
tree
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commitdiff
2018-01-31
kiramt
JAL-2759 minor refactor to hiding bitsets
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 Add missing hiddenColumns empty check
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 updateForDeletedRegion no longer needed
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 Rationalising hidden cols cursor, and sorting...
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 comment
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 Additional tests and tweaks to numColumns...
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 Keep numColumns up to date
tree
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commitdiff
2018-01-29
kiramt
JAL-2759 Combine findRegionForColumn code in HiddenColu...
tree
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commitdiff
2018-01-29
kiramt
JAL-2759 numColumns reset
tree
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commitdiff
2018-01-29
kiramt
JAL-2759 remove redundant hiddenColumns.clear()
tree
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commitdiff
2018-01-29
kiramt
JAL-2759 Tidy
tree
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commitdiff
2018-01-29
kiramt
JAL-2759 make a new cursor instead of resetting, update...
tree
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commitdiff
2018-01-29
kiramt
JAL-2759 Fix unintended type change
tree
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commitdiff
2018-01-26
kiramt
JAL-2778 try another way to draw sequences with reduced...
tree
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commitdiff
2018-01-22
kiramt
JAL-2579 Moved locateVisibleStartOfSequence to Sequence...
tree
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commitdiff
2018-01-22
kiramt
JAL-2759 Various minor HiddenColumns updates after...
tree
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commitdiff
2018-01-19
kiramt
JAL-2759 Changes to getVisibleSequenceStrings after...
tree
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commitdiff
2018-01-19
kiramt
JAL-2759 Moved propagateInsertions out of HiddenColumns
tree
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commitdiff
2018-01-19
kiramt
JAL-2759 Update to getVisibleStartAndEndIndex after...
tree
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commitdiff
2018-01-18
kiramt
JAL-2759 change subtractVisibleColumns and removal...
tree
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commitdiff
2018-01-18
kiramt
JAL-2759 Updated test
tree
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commitdiff
2018-01-18
kiramt
JAL-2759 unit tests (incomplete)
tree
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commitdiff
2018-01-17
gmungoc
Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures
tree
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commitdiff
2018-01-16
kjvdheide
JAL-2750 startRes now directly assigned
tree
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commitdiff
2018-01-16
kiramt
JAL-2759 setup hideBitSet over range for hideInsertions
tree
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commitdiff
2018-01-16
kiramt
JAL-2759 Moved alignment annotation code out of HiddenC...
tree
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commitdiff
2018-01-16
kiramt
JAL-2759 Replaced StringBuffer with StringBuilder;...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 More compact iterator usage; after review
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 First pass instantiate hiddenColumns collectio...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 getVisContigsIterator returns VisibleContigsIt...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Rename hideInsertionsFor to hideList, after...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Refactor of hideInsertionsFor after review
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Simplified HiddenColumns constructor after...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Changed VisibleColsCollection constructor...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Minor doc and naming changes
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Updated absoluteToVisibleColumn doc (prev...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Rename findColumnPosition and adjustForHiddenC...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Renamed BoundedHiddenColsIterator to HiddenCol...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Comments and renaming for has(Many)HiddenColum...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Tidy up javadoc and naming in HiddenColumnsCur...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Update to getHiddenBoundaryRight + unit test...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Updates following review
tree
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commitdiff
2018-01-10
gmungoc
JAL-1793 update spike branch to latest
tree
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commitdiff
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