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/*
Ray
Copyright (C) 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 _ScaffoldingEdge_h
#define _ScaffoldingEdge_h
#include <code/Mock/constants.h>
#include <code/SeedingData/PathHandle.h>
#include <RayPlatform/core/types.h>
#include <stdint.h>
#include <fstream>
using namespace std;
#define LEFT_SIDE 0
#define RIGHT_SIDE 1
class ScaffoldingEdge{
PathHandle m_leftContig;
PathHandle m_rightContig;
Strand m_leftStrand;
Strand m_rightStrand;
int m_gapSize;
int m_count1;
int m_average1;
int m_standardDeviation1;
int m_count2;
int m_average2;
int m_standardDeviation2;
public:
ScaffoldingEdge(PathHandle leftContig,Strand leftStrand,PathHandle rightContig,Strand rightStrand,int gapSize,
int average1,int count1,int standardDeviation1,
int average2,int count2,int standardDeviation2);
ScaffoldingEdge();
int getGapSize();
PathHandle getLeftContig();
Strand getLeftStrand();
PathHandle getRightContig();
Strand getRightStrand();
int getCount1();
int getAverage1();
int getStandardDeviation1();
int getCount2();
int getAverage2();
int getStandardDeviation2();
void read(ifstream*f);
int getPriority()const ;
bool operator<(const ScaffoldingEdge&other)const;
Strand getStrand(PathHandle name);
int getSide(PathHandle name);
ScaffoldingEdge getReverseEdge();
void print();
};
/*
bool operator<(const ScaffoldingEdge*a,const ScaffoldingEdge*b){
return (*a)<(*b);
}
*/
#endif
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