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/*
Ray
Copyright (C) 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 "ContigSearchEntry.h"
ContigSearchEntry::ContigSearchEntry(PathHandle name,int length,int mode,double mean,int coloredKmers){
m_name=name;
m_length=length;
m_modeCoverage=mode;
m_meanCoverage=mean;
m_coloredKmers=coloredKmers;
}
PathHandle ContigSearchEntry::getName(){
return m_name;
}
int ContigSearchEntry::getLength(){
return m_length;
}
int ContigSearchEntry::getMode(){
return m_modeCoverage;
}
double ContigSearchEntry::getMean(){
return m_meanCoverage;
}
int ContigSearchEntry::getTotal(){
// the repeated k-mers are considered once
return getMode()*getLength();
}
void ContigSearchEntry::write(ofstream*file,LargeCount total,int kmerLength){
double ratio=getTotal();
// be careful with those 0s
if(total!=0)
ratio/=total;
(*file)<<"contig-"<<getName()<<" "<<kmerLength;
(*file)<<" "<<getLength();
(*file)<<" "<<m_coloredKmers;
double ratioColored=m_coloredKmers;
if(getLength()!=0){
ratioColored/=getLength();
}
(*file)<<" "<<ratioColored;
(*file)<<" "<<getMode();
//(*file)<<" "<<getMean();
(*file)<<" "<<getTotal()<<" ";
(*file)<<total<<" "<<ratio<<endl;
}
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