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NonOverlapRegions.h
/*
* Copyright (C) 2011 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
//////////////////////////////////////////////////////////////////////////
#ifndef __NONOVERLAP_REGIONS_H__
#define __NONOVERLAP_REGIONS_H__
#include <map>
#include <string>
#include <list>
#include <stdint.h>
/// This class contains a list of non-overlapping regions, just positions, not
/// including chromosomes (see NonOverlapRegions for chromosomes and positions).
/// When regions are added that overlap, it merges them. After adding regions,
/// you can check to see if a position is found in one of the regions. It is
/// designed to work fastest if you make calls in sequential order.
class NonOverlapRegionPos
{
public:
friend class NonOverlapRegionsTest;
NonOverlapRegionPos();
/// Copy constructor, does not copy, but initializes with an empty
/// region list.
NonOverlapRegionPos(const NonOverlapRegionPos& reg);
~NonOverlapRegionPos();
/// End position is not included in the region.
/// If this region overlaps another region(s), they will be merged into
/// one region.
void add(int32_t start, int32_t end);
/// Return whether or not the position was found within a region.
/// If it is found within the region, myRegionIter will point to the region
/// otherwise myRegionIter will point to the region after the position
/// or to the end if the position is after the last region.
bool inRegion(int32_t pos);
private:
// True if pos found in the region pointed to by myRegionIter or to
// the right of myRegionIter. If the position is found in a region,
// myRegionIter will point to the region containing the position.
// If the position is not found in a region, myRegionIter will point
// to the region after the position, or to the end if the position is
// after the last region.
bool findRight(int32_t pos);
// True if pos found in the region pointed to by myRegionIter or to
// the left of myRegionIter. If the position is found in a region,
// myRegionIter will point to the region containing the position.
// If the position is not found in a region, myRegionIter will point
// to the region after the position, or to the end if the position is
// after the last region.
bool findLeft(int32_t pos);
std::list< std::pair<int32_t, int32_t> > myRegions;
std::list< std::pair<int32_t, int32_t> >::iterator myRegionIter;
std::list< std::pair<int32_t, int32_t> >::iterator myTmpIter;
};
/// This class contains a list of non-overlapping regions. When regions are
/// added that overlap, it merges them. After adding regions, you can check
/// to see if a position is found in one of the regions. It is designed to
/// work fastest if you make calls in sequential order.
class NonOverlapRegions
{
public:
friend class NonOverlapRegionsTest;
NonOverlapRegions();
~NonOverlapRegions();
/// End position is not included in the region.
/// If this region overlaps another region(s), they will be merged into
/// one region.
void add(const char* chrom, int32_t start, int32_t end);
/// Return whether or not the position was found within a region.
/// If it is found within the region, myRegionIter will point to the region
/// otherwise myRegionIter will point to the region after the position
/// or to the end if the position is after the last region.
bool inRegion(const char* chrom, int32_t pos);
private:
// Copy Constructor - unimplimented.
NonOverlapRegions(const NonOverlapRegions& reg);
std::map<std::string, NonOverlapRegionPos> myRegions;
};
#endif
NonOverlapRegionPos::add
void add(int32_t start, int32_t end)
End position is not included in the region.
Definition NonOverlapRegions.cpp:75
NonOverlapRegionPos::inRegion
bool inRegion(int32_t pos)
Return whether or not the position was found within a region.
Definition NonOverlapRegions.cpp:155
NonOverlapRegions::inRegion
bool inRegion(const char *chrom, int32_t pos)
Return whether or not the position was found within a region.
Definition NonOverlapRegions.cpp:42
NonOverlapRegions::add
void add(const char *chrom, int32_t start, int32_t end)
End position is not included in the region.
Definition NonOverlapRegions.cpp:35