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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 _ReadAnnotation
#define _ReadAnnotation
#include <code/SequencesLoader/ReadHandle.h>
#include <code/Mock/common_functions.h>
#include <fstream>
using namespace std;
/*
* implemented as linked lists, read annotations give
* information about read index in the graph.
* The read paths are restored using read annotations.
* \author Sébastien Boisvert
*/
class ReadAnnotation{
ReadAnnotation*m_next;
uint32_t m_readIndex;
uint16_t m_rank; // should be Rank
uint16_t m_positionOnStrand;
Strand m_strand;
bool m_lower;
public:
void constructor(int a,int b,int positionOnStrand,char c,bool lower);
bool isLower();
int getRank()const;
int getReadIndex()const;
int getPositionOnStrand()const;
Strand getStrand()const;
ReadAnnotation*getNext()const;
void setNext(ReadAnnotation*a);
ReadHandle getUniqueId() const;
void read(istream*f,bool isLower);
void write(ostream*f);
} ATTRIBUTE_PACKED;
#endif
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