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hal::MappedSegment Class Referenceabstract

`#include <halMappedSegment.h>`

Inheritance diagram for hal::MappedSegment:

## Classes

struct | EqualTo
struct | Less
struct | LessSource

## Public Member Functions

virtual SlicedSegmentConstPtr | getSource () const =0
virtual bool | lessThan (const MappedSegmentConstPtr &other) const =0
virtual bool | lessThanBySource (const MappedSegmentConstPtr &other) const =0
virtual bool | equals (const MappedSegmentConstPtr &other) const =0
virtual void | flip () const =0
virtual void | fullReverse () const =0
virtual MappedSegmentConstPtr | copy () const =0
virtual bool | canMergeRightWith (const MappedSegmentConstPtr &next, const std::set< hal_index_t > *cutSet=NULL, const std::set< hal_index_t > *sourceCutSet=NULL) const =0
virtual void | print (std::ostream &os) const =0
Public Member Functions inherited from hal::SlicedSegment
virtual void | toReverse () const =0
virtual void | toReverseInPlace () const =0
virtual hal_offset_t | getStartOffset () const =0
virtual hal_offset_t | getEndOffset () const =0
virtual void | slice (hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0
virtual bool | getReversed () const =0
Public Member Functions inherited from hal::Segment
virtual void | setArrayIndex (Genome *genome, hal_index_t arrayIndex)=0
virtual void | setArrayIndex (const Genome *genome, hal_index_t arrayIndex) const =0
virtual const Genome * | getGenome () const =0
virtual Genome * | getGenome ()=0
virtual const Sequence * | getSequence () const =0
virtual Sequence * | getSequence ()=0
virtual hal_index_t | getStartPosition () const =0
virtual hal_index_t | getEndPosition () const =0
virtual hal_size_t | getLength () const =0
virtual void | getString (std::string &outString) const =0
virtual void | setCoordinates (hal_index_t startPos, hal_size_t length)=0
virtual hal_index_t | getArrayIndex () const =0
virtual bool | leftOf (hal_index_t genomePos) const =0
virtual bool | rightOf (hal_index_t genomePos) const =0
virtual bool | overlaps (hal_index_t genomePos) const =0
virtual bool | isFirst () const =0
virtual bool | isLast () const =0
virtual bool | isMissingData (double nThreshold) const =0
virtual bool | isTop () const =0
virtual hal_size_t | getMappedSegments (std::set< MappedSegmentConstPtr > &outSegments, const Genome *tgtGenome, const std::set< const Genome * > *genomesOnPath=NULL, bool doDupes=true, hal_size_t minLength=0) const =0

## Friends

class | counted_ptr< MappedSegment >
class | counted_ptr< const MappedSegment >

## Detailed Description

Interface for a mapped segement. A mapped segment keeps track of a homologous region in another genome (from which it was mapped). Mapped segments are used to keep pairwise alignment fragments across the tree as an alternative to the column iterator.

## Member Function Documentation

virtual bool hal::MappedSegment::canMergeRightWith | ( | const MappedSegmentConstPtr & | next,
|  | const std::set< hal_index_t > * | cutSet = `NULL`,
|  | const std::set< hal_index_t > * | sourceCutSet = `NULL`
| ) |  | const

pure virtual

Test if mapped segment can be merged to the right with input segment. will return false if the right coordinate of this is in either (optional) cutSet.

virtual MappedSegmentConstPtr hal::MappedSegment::copy | ( |  | ) | const

pure virtual

Return of a copy of the mapped segment

virtual bool hal::MappedSegment::equals | ( | const MappedSegmentConstPtr & | other | ) | const

pure virtual

Comparison used to determine uniqueness in lists. Tests lessThan in both directions. Note that equality is the same regardless of whether or not we use the source segment as our primary index.

virtual void hal::MappedSegment::flip | ( |  | ) | const

pure virtual

Flip the mapping direction. This segment becomes the source, and the source becomes this.

virtual void hal::MappedSegment::fullReverse | ( |  | ) | const

pure virtual

Reverse both segments. Also swap their start and end offsets. Note that toReverse() does not reverse the source segment.

virtual SlicedSegmentConstPtr hal::MappedSegment::getSource | ( |  | ) | const

pure virtual

Get the original segment from which this segment was mapped

virtual bool hal::MappedSegment::lessThan | ( | const MappedSegmentConstPtr & | other | ) | const

pure virtual

Comparison used to store in stl sets and maps. We sort based on the coordinate of the mapped segemnt's (target) interval as the primary index and the target genome as the secondary index.

virtual bool hal::MappedSegment::lessThanBySource | ( | const MappedSegmentConstPtr & | other | ) | const

pure virtual

Comparison used to store in STL containers. We sort based on the coordinate of the Source genome interval as the primary index and the target genome as the secondary index.

virtual void hal::MappedSegment::print | ( | std::ostream & | os | ) | const

pure virtual

Print contents of segment

Implements hal::Segment.

The documentation for this class was generated from the following file:

- inc/halMappedSegment.h