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hierarchichalalignmentformatapi
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hal::Rearrangement Member List

This is the complete list of members for hal::Rearrangement, including all inherited members.

Complex enum value (defined in hal::Rearrangement)hal::Rearrangement
counted_ptr< const Rearrangement > (defined in hal::Rearrangement)hal::Rearrangementfriend
counted_ptr< Rearrangement > (defined in hal::Rearrangement)hal::Rearrangementfriend
Deletion enum value (defined in hal::Rearrangement)hal::Rearrangement
Duplication enum value (defined in hal::Rearrangement)hal::Rearrangement
Gap enum value (defined in hal::Rearrangement)hal::Rearrangement
getAtomic() const =0 (defined in hal::Rearrangement)hal::Rearrangementpure virtual
getDeletedRange() const =0hal::Rearrangementpure virtual
getDuplicatedRange() const =0hal::Rearrangementpure virtual
getGapLengthThreshold() const =0hal::Rearrangementpure virtual
getID() const =0hal::Rearrangementpure virtual
getInsertedRange() const =0hal::Rearrangementpure virtual
getLeftBreakpoint() const =0hal::Rearrangementpure virtual
getLength() const =0hal::Rearrangementpure virtual
getNThreshold() const =0 (defined in hal::Rearrangement)hal::Rearrangementpure virtual
getNumContainedGapBases() const =0hal::Rearrangementpure virtual
getNumContainedGaps() const =0hal::Rearrangementpure virtual
getRightBreakpoint() const =0hal::Rearrangementpure virtual
ID enum name (defined in hal::Rearrangement)hal::Rearrangement
identifyDeletionFromLeftBreakpoint(TopSegmentIteratorConstPtr topSegment)=0hal::Rearrangementpure virtual
identifyFromLeftBreakpoint(TopSegmentIteratorConstPtr topSegment)=0hal::Rearrangementpure virtual
identifyInsertionFromLeftBreakpoint(TopSegmentIteratorConstPtr topSegment)=0hal::Rearrangementpure virtual
identifyNext()=0hal::Rearrangementpure virtual
Insertion enum value (defined in hal::Rearrangement)hal::Rearrangement
Invalid enum value (defined in hal::Rearrangement)hal::Rearrangement
Inversion enum value (defined in hal::Rearrangement)hal::Rearrangement
Missing enum value (defined in hal::Rearrangement)hal::Rearrangement
Nothing enum value (defined in hal::Rearrangement)hal::Rearrangement
setAtomic(bool atomic)=0hal::Rearrangementpure virtual
setGapLengthThreshold(hal_size_t threshold)=0hal::Rearrangementpure virtual
setNThreshold(double nThreshold)=0 (defined in hal::Rearrangement)hal::Rearrangementpure virtual
Translocation enum value (defined in hal::Rearrangement)hal::Rearrangement
Transposition enum value (defined in hal::Rearrangement)hal::Rearrangement
~Rearrangement()=0hal::Rearrangementinlineprotectedpure virtual