halapi
hierarchichalalignmentformatapi
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hal::PositionCache Class Reference

#include <halPositionCache.h>

Public Types

typedef std::map< hal_index_t,
hal_index_t > 
IntervalSet
 

Public Member Functions

bool insert (hal_index_t pos)
 
bool find (hal_index_t pos) const
 
void clear ()
 
bool check () const
 
hal_size_t size () const
 
hal_size_t numIntervals () const
 
const IntervalSet * getIntervalSet ()
 

Protected Attributes

IntervalSet _set
 
hal_size_t _size
 
IntervalSet::iterator _prev
 

Detailed Description

keep track of bases by storing 2d intervals For example, if we want to flag positions in a genome that we have visited, this structure will be fairly efficient provided positions are clustered into intervals


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