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/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
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, version 3 of the License.
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 have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#ifndef _VirtualKmerColor_h
#define _VirtualKmerColor_h
#include <code/Mock/constants.h>
#include <stdint.h>
#include <vector>
#include <set>
using namespace std;
/** a physical color contains its namespace **/
typedef uint64_t PhysicalKmerColor;
/**
* An implementation of a virtual color type.
* A virtual color can be translated to a set of physical colors.
*
* This class utilises the Flyweight design pattern.
*
* \author: Sébastien Boisvert
*/
class VirtualKmerColor{
/**
* half the number of k-mers using this virtual color
*/
LargeCount m_references;
/**
* the list of physical colors
*/
set<PhysicalKmerColor> m_colors;
uint64_t m_hash;
public:
VirtualKmerColor();
void addPhysicalColor(PhysicalKmerColor color);
void addPhysicalColors(set<PhysicalKmerColor>*color);
void incrementReferences();
void decrementReferences();
LargeCount getNumberOfReferences();
set<PhysicalKmerColor>*getPhysicalColors();
bool hasPhysicalColor(PhysicalKmerColor color);
bool hasPhysicalColors(set<PhysicalKmerColor>*colors);
void setHash(uint64_t hash);
uint64_t getCachedHashValue();
int getNumberOfPhysicalColors();
void clear();
bool virtualColorHasAllPhysicalColorsOf(VirtualKmerColor*a,PhysicalKmerColor color);
void copyPhysicalColors(VirtualKmerColor*a);
};
#endif
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