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hierarchichalalignmentformatapi
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hal
Rearrangement
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::Rearrangement
friend
counted_ptr< Rearrangement >
(defined in
hal::Rearrangement
)
hal::Rearrangement
friend
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::Rearrangement
pure virtual
getDeletedRange
() const =0
hal::Rearrangement
pure virtual
getDuplicatedRange
() const =0
hal::Rearrangement
pure virtual
getGapLengthThreshold
() const =0
hal::Rearrangement
pure virtual
getID
() const =0
hal::Rearrangement
pure virtual
getInsertedRange
() const =0
hal::Rearrangement
pure virtual
getLeftBreakpoint
() const =0
hal::Rearrangement
pure virtual
getLength
() const =0
hal::Rearrangement
pure virtual
getNThreshold
() const =0 (defined in
hal::Rearrangement
)
hal::Rearrangement
pure virtual
getNumContainedGapBases
() const =0
hal::Rearrangement
pure virtual
getNumContainedGaps
() const =0
hal::Rearrangement
pure virtual
getRightBreakpoint
() const =0
hal::Rearrangement
pure virtual
ID
enum name (defined in
hal::Rearrangement
)
hal::Rearrangement
identifyDeletionFromLeftBreakpoint
(TopSegmentIteratorConstPtr topSegment)=0
hal::Rearrangement
pure virtual
identifyFromLeftBreakpoint
(TopSegmentIteratorConstPtr topSegment)=0
hal::Rearrangement
pure virtual
identifyInsertionFromLeftBreakpoint
(TopSegmentIteratorConstPtr topSegment)=0
hal::Rearrangement
pure virtual
identifyNext
()=0
hal::Rearrangement
pure 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)=0
hal::Rearrangement
pure virtual
setGapLengthThreshold
(hal_size_t threshold)=0
hal::Rearrangement
pure virtual
setNThreshold
(double nThreshold)=0 (defined in
hal::Rearrangement
)
hal::Rearrangement
pure virtual
Translocation
enum value (defined in
hal::Rearrangement
)
hal::Rearrangement
Transposition
enum value (defined in
hal::Rearrangement
)
hal::Rearrangement
~Rearrangement
()=0
hal::Rearrangement
inline
protected
pure virtual
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