cgatools::util::FastRangeSet Class Reference

the class is designed to support a relatively small set of ranges and answer the questions:

• does a given range intersect one of the ranges in the FastRangeSet?
• is a given location contained by one of the ranges in the FastRangeSet?

More...

#include <RangeSet.hpp>

List of all members.

Classes
class	RangeSet
Public Types
typedef std::pair< uint32_t, uint32_t >	Range
typedef std::vector< RangeSet >	ChromosomeRanges
Public Member Functions
	FastRangeSet (const reference::CrrFile &ref)
bool	intersects (const reference::Range &inRange) const
	Returns true if there is a range in this set that overlaps the specified range.
bool	contains (const reference::Location &loc) const
	Returns true if any range of this set contains the given location.
void	add (const reference::Range &r)
void	add (const std::string &rangeStr)
	add a string range into the set
void	add (const StringVector &rangeStrSet)
void	addWholeReference (size_t extendRangeLength=0)
	Fills the range set to cover the whole reference.
const ChromosomeRanges &	getRanges () const
void	clear ()
bool	empty () const
void	regressionTest ()
Protected Attributes
const reference::CrrFile &	reference_
ChromosomeRanges	ranges_

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Detailed Description

the class is designed to support a relatively small set of ranges and answer the questions:

• does a given range intersect one of the ranges in the FastRangeSet?
• is a given location contained by one of the ranges in the FastRangeSet?

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Member Function Documentation

bool cgatools::util::FastRangeSet::intersects

(

const reference::Range &

inRange

)

const

Returns true if there is a range in this set that overlaps the specified range.

Zero-length overlap is allowed for empty ranges, therefore an empty range overlaps with itself. An empty range overlap includes begin of other range: [b,b) overlaps [a,b) and [b,c) and vise versa.

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

• RangeSet.hpp