halapi
hierarchichalalignmentformatapi
Public Member Functions | Static Public Attributes | Protected Attributes
hal::GenomeSegment Class Reference

#include <genomeSegment.h>

Inheritance diagram for hal::GenomeSegment:
hal::TopSegment

List of all members.

Public Member Functions

genidx_t getStart () const
genidx_t getLength () const
segidx_t getParseIdx () const
genidx_t getParseOffset () const

Static Public Attributes

static const segidx_t NullIndex

Protected Attributes

genidx_t _start
genidx_t _length
segidx_t _parseIdx
genidx_t _parseOffset

Detailed Description

Abstract base class for a DNA segment (interval in genome) Segments for now are glorified structs that hold the coordinates and little else. More useful interface will be at higher level


Member Function Documentation

genidx_t hal::GenomeSegment::getLength ( ) const

Get length of segment

segidx_t hal::GenomeSegment::getParseIdx ( ) const

Get index of leftmost segment overlapping in same genome

genidx_t hal::GenomeSegment::getParseOffset ( ) const

Get offset of above

genidx_t hal::GenomeSegment::getStart ( ) const

Get start coordinate in genome


Member Data Documentation

const segidx_t hal::GenomeSegment::NullIndex [static]

Null index value


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