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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/>
*/
#include "ReadAnnotation.h"
#include <code/Mock/common_functions.h>
#include <assert.h>
#include <stdlib.h>
void ReadAnnotation::constructor(int rank,int readIndex,int positionOnStrand,char c,bool lower){
m_lower=lower;
m_rank=rank;
m_positionOnStrand=positionOnStrand;
m_readIndex=readIndex;
m_next=NULL; // xor on the next.
m_strand=c;
}
int ReadAnnotation::getPositionOnStrand()const{
return m_positionOnStrand;
}
char ReadAnnotation::getStrand()const{
return m_strand;
}
int ReadAnnotation::getRank()const{
return m_rank;
}
int ReadAnnotation::getReadIndex()const{
return m_readIndex;
}
void ReadAnnotation::setNext(ReadAnnotation*a){
m_next=a;
}
ReadAnnotation*ReadAnnotation::getNext()const{
return m_next;
}
ReadHandle ReadAnnotation::getUniqueId()const{
PathHandle handle = getPathUniqueId(m_rank,m_readIndex);
return handle.getValue();
}
bool ReadAnnotation::isLower(){
return m_lower;
}
void ReadAnnotation::write(ostream*f){
int rank=getRank();
int readIndex=getReadIndex();
int positionOnStrand=getPositionOnStrand();
char strand=getStrand();
f->write((char*)&rank,sizeof(int));
f->write((char*)&readIndex,sizeof(int));
f->write((char*)&positionOnStrand,sizeof(int));
f->write((char*)&strand,sizeof(char));
}
void ReadAnnotation::read(istream*f,bool isLower){
int rank=0;
int readIndex=0;
int positionOnStrand=0;
char strand=0;
f->read((char*)&rank,sizeof(int));
f->read((char*)&readIndex,sizeof(int));
f->read((char*)&positionOnStrand,sizeof(int));
f->read((char*)&strand,sizeof(char));
constructor(rank,readIndex,positionOnStrand,strand,isLower);
}
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