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JAL-2909 update tests for stranded insert map and writeback of mapped read extent...
2018-03-01 kiramtJAL-2909 Updated tests
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2018-03-01 kiramtJAL-2909 fixed another insertions bug
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2018-02-28 kiramtJAL-2909 Fixed a bug in the insertions code
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2018-02-28 kiramtJAL-2909 Gaps at start of reads only from start of...
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2018-02-28 kiramtJAL-2909 Wire up coordinates dialog with bam file reader
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2018-02-27 kiramtJAL-2909 Tidy up bam file cigar code
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2018-02-26 kiramtJAL-2909 Bam file parsing with insertions, first pass
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2018-02-26 kiramtJAL-2909 Changes to htsjdk import control
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2018-02-26 kiramtJAL-2909 Cigar parsing tests
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2018-02-21 kiramtJAL-2909 Partial insertions
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2018-02-21 kiramtJAL-2778 Adjust cursor changes in overview panel
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2018-02-21 kiramtJAL-2778 Revert back to old synchronisation
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2018-02-20 kiramtJAL-2909 Modified classpath
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2018-02-20 kiramtJAL-2909 Insertions almost
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2018-02-19 kiramtJAL-2909 Read in a bam file - but strand/location unaware
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2018-02-19 kiramtJAL-2909 Removed buggy CIGAR parsing code which was...
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2018-02-06 kiramtMerge branch 'develop' into feature/JAL-2759
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2018-02-05 kiramtJAL-2759 Fix errant RangeElementsIterator (unit tests...
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2018-02-05 kiramtJAL-2759 Rename getBoundedStartIterator
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2018-02-05 kiramtJAL-2759 Changes to StartRegionIterator after review
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2018-02-05 kiramtJAL-2788 possible adjustments to sequence accesses
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2018-02-05 kiramtJAL-2778 Sequence width benchmark
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2018-02-01 kiramtJAL-2759 Added in JAL-2851 fix
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2018-02-01 kiramtJAL-2759 use right iterator for getVisibleColsIterator
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2018-01-31 kiramtJAL-2759 Rationalise VisibleColsIterator and HiddenColsIterator
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2018-01-31 kiramtJAL-2759 Generalised HiddenColsIterator naming
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2018-01-31 kiramtJAL-2759 test renaming
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2018-01-31 kiramtJAL-2759 minor refactor to hiding bitsets
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2018-01-30 kiramtJAL-2759 Add missing hiddenColumns empty check
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2018-01-30 kiramtJAL-2759 updateForDeletedRegion no longer needed
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2018-01-30 kiramtJAL-2759 Rationalising hidden cols cursor, and sorting...
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2018-01-30 kiramtJAL-2759 comment
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2018-01-30 kiramtJAL-2759 Additional tests and tweaks to numColumns...
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2018-01-30 kiramtJAL-2759 Keep numColumns up to date
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2018-01-29 kiramtJAL-2759 remove unneeded cast
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2018-01-29 kiramtMerge branch 'feature/JAL-2759' of https://source.jalview...
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2018-01-29 kiramtJAL-2759 Combine findRegionForColumn code in HiddenColumnsCursor
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2018-01-29 kiramtJAL-2759 numColumns reset
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2018-01-29 kiramtJAL-2759 remove redundant hiddenColumns.clear()
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2018-01-29 kiramtJAL-2759 Tidy
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2018-01-29 kiramtJAL-2759 make a new cursor instead of resetting, updated...
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2018-01-29 kiramtJAL-2759 Fix unintended type change
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2018-01-26 kiramtJAL-2778 try another way to draw sequences with reduced...
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2018-01-26 kiramtJAL-2778 tightened up use of resetAlignmentDims
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2018-01-25 kiramtJAL-2778 Tidy
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2018-01-25 kiramtJAL-2778 added JAL-2851 fix to avoid confusion
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2018-01-25 kiramtJAL-2778 Reinstate id width adjuster
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2018-01-22 kiramtJAL-2579 Moved locateVisibleStartOfSequence to Sequence...
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2018-01-22 kiramtJAL-2759 Various minor HiddenColumns updates after...
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2018-01-19 kiramtJAL-2759 Changes to getVisibleSequenceStrings after...
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2018-01-19 kiramtJAL-2759 Moved propagateInsertions out of HiddenColumns
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2018-01-19 kiramtJAL-2759 Update to getVisibleStartAndEndIndex after...
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2018-01-18 kiramtJAL-2759 change subtractVisibleColumns and removal...
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2018-01-18 kiramtJAL-2759 Updated test
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2018-01-18 kiramtJAL-2759 unit tests (incomplete)
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2018-01-16 kiramtJAL-2759 setup hideBitSet over range for hideInsertions
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2018-01-16 kiramtJAL-2759 Unit test for PopupMenu hideInsertions code
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2018-01-16 kiramtJAL-2759 Moved alignment annotation code out of HiddenColumns
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2018-01-16 kiramtJAL-2759 Replaced StringBuffer with StringBuilder;...
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2018-01-15 kiramtJAL-2759 More compact iterator usage; after review
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2018-01-15 kiramtJAL-2759 First pass instantiate hiddenColumns collection...
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2018-01-15 kiramtJAL-2759 getVisContigsIterator returns VisibleContigsIterator
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2018-01-15 kiramtJAL-2759 Rename hideInsertionsFor to hideList, after...
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2018-01-15 kiramtJAL-2759 Refactor of hideInsertionsFor after review
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2018-01-15 kiramtJAL-2759 Simplified HiddenColumns constructor after...
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2018-01-15 kiramtJAL-2759 Changed VisibleColsCollection constructor...
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2018-01-15 kiramtJAL-2759 Minor doc and naming changes
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2018-01-15 kiramtJAL-2759 Updated absoluteToVisibleColumn doc (prev...
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2018-01-15 kiramtJAL-2759 Rename findColumnPosition and adjustForHiddenColumn...
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2018-01-15 kiramtJAL-2759 Renamed BoundedHiddenColsIterator to HiddenColsIterator
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2018-01-15 kiramtJAL-2759 Comments and renaming for has(Many)HiddenColumns...
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2018-01-15 kiramtJAL-2759 Tidy up javadoc and naming in HiddenColumnsCursor...
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2018-01-15 kiramtJAL-2759 Updated HiddenColumnsTest::testIsVisible following...
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2018-01-15 kiramtJAL-2759 Update to getHiddenBoundaryRight + unit test...
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2018-01-15 kiramtJAL-2759 Updates following review
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2018-01-12 kiramtJAL-2886 trivial unit test fix
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2018-01-11 kiramtMerge remote-tracking branch 'origin/task/JAL-2662...
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2018-01-11 kiramtJAL-2662 Updated README
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2017-11-24 kiramtJAL-2759 update benchmark code
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2017-11-23 kiramtMerge branch 'develop' into bug/JAL-2851
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2017-11-23 kiramtJAL-2851 Fix merge error breaking vertical scrolling
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2017-11-22 kiramtJAL-2842 JAL-2759 change to SeqPanel moveCursor
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2017-11-22 kiramtJAL-2759 code tidy
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2017-11-22 kiramtJAL-2759 performance improvements to hideColumns
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2017-11-22 kiramtJAL-2759 performance tweaks
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2017-11-22 kiramtJAL-2759 HiddenColumns test polishing
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2017-11-21 kiramtJAL-2759 corrected old getVisibleBlocksIterator calls...
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2017-11-21 kiramtJAL-2759 Remove getVisibleBlocksIterator call
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2017-11-21 kiramtMerge branch 'develop' into feature/JAL-2759
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2017-11-21 kiramtJAL-2759 BoundedStartRegionIterator test
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2017-11-21 kiramtJAL-2759 unit tests for VisibleContigsIterator
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2017-11-20 kiramtJAL-2759 cursor option for BoundedStartRegionIterator
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2017-11-20 kiramtJAL-2759 reinstate change from develop (JAL-2636) somehow...
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2017-11-20 kiramtJAL-2759 rationalise visible contigs iteration
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2017-11-20 kiramtJAL-2759 improvements to speed up synchronisation;...
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2017-11-17 kiramtMerge branch 'develop' into bug/JAL-2837
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2017-11-17 kiramtMerge branch 'develop' into bug/JAL-2837
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2017-11-17 kiramtJAL-2759 Move isVisible to use cursor
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2017-11-17 kiramtJAL-2759 tidy
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2017-11-17 kiramtJAL-2759 Update tests
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