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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/>
*/
#include "ScaffoldingEdge.h"
#include <iostream>
#include <sstream>
#include <string>
#include <assert.h>
using namespace std;
ScaffoldingEdge::ScaffoldingEdge(PathHandle leftContig,Strand leftStrand,PathHandle rightContig,Strand rightStrand,int gapSize,
int average1,int count1,int standardDeviation1,
int average2,int count2,int standardDeviation2){
m_gapSize=gapSize;
m_leftContig=leftContig;
m_leftStrand=leftStrand;
m_rightContig=rightContig;
m_rightStrand=rightStrand;
m_count1=count1;
m_average1=average1;
m_standardDeviation1=standardDeviation1;
m_count2=count2;
m_average2=average2;
m_standardDeviation2=standardDeviation2;
}
ScaffoldingEdge ScaffoldingEdge::getReverseEdge(){
char reverseLeft='F';
if(m_leftStrand=='F')
reverseLeft='R';
char reverseRight='F';
if(m_rightStrand=='F')
reverseRight='R';
ScaffoldingEdge e2(m_rightContig,reverseRight,m_leftContig,reverseLeft,m_gapSize,m_average2,m_count2,m_standardDeviation2,m_average1,m_count1,m_standardDeviation1);
return e2;
}
PathHandle ScaffoldingEdge::getLeftContig(){
return m_leftContig;
}
Strand ScaffoldingEdge::getLeftStrand(){
return m_leftStrand;
}
PathHandle ScaffoldingEdge::getRightContig(){
return m_rightContig;
}
Strand ScaffoldingEdge::getRightStrand(){
return m_rightStrand;
}
int ScaffoldingEdge::getAverage1(){
return m_average1;
}
int ScaffoldingEdge::getCount1(){
return m_count1;
}
int ScaffoldingEdge::getStandardDeviation1(){
return m_standardDeviation1;
}
int ScaffoldingEdge::getAverage2(){
return m_average2;
}
int ScaffoldingEdge::getCount2(){
return m_count2;
}
int ScaffoldingEdge::getStandardDeviation2(){
return m_standardDeviation2;
}
void ScaffoldingEdge::read(ifstream*f){
/*
version 1
contig-0 F contig-2000306 F 7414 2 0 7384 40 1 7444 37
version 2
contig-0 R contig-356000158 F 9012 2 0 3 9012 0 1 3 9012 0
*/
{
string token;
(*f)>>token;
string number=token.substr(7,token.length()-7);
stringstream aStream;
aStream << number;
aStream >> m_leftContig;
}
(*f) >> m_leftStrand;
{
string token;
(*f)>>token;
string number=token.substr(7,token.length()-7);
stringstream aStream;
aStream << number;
aStream >> m_rightContig;
}
(*f) >> m_rightStrand;
(*f) >> m_gapSize;
int dummy;
(*f) >> dummy; /* count */
(*f) >> dummy; /* index */
(*f) >> m_count1;
(*f) >> m_average1;
(*f) >> m_standardDeviation1;
(*f) >> dummy; /* index */
(*f) >> m_count2;
(*f) >> m_average2;
(*f) >> m_standardDeviation2;
}
ScaffoldingEdge::ScaffoldingEdge(){
}
int ScaffoldingEdge::getPriority()const {
return (m_count1+m_count2)/2;
}
bool ScaffoldingEdge::operator<(const ScaffoldingEdge&other)const{
return getPriority()<other.getPriority();
}
void ScaffoldingEdge::print(){
cout<<m_leftContig<<" "<<m_leftStrand<<" "<<m_rightContig<<" "<<m_rightStrand<<" gap= "<<m_gapSize<<" priority= "<<getPriority()<<endl;
}
Strand ScaffoldingEdge::getStrand(PathHandle name){
#ifdef CONFIG_ASSERT
assert(name==getLeftContig() || name==getRightContig());
#endif
if(name==getLeftContig())
return getLeftStrand();
else if(name==getRightContig())
return getRightStrand();
return 'x';
}
int ScaffoldingEdge::getSide(PathHandle name){
#ifdef CONFIG_ASSERT
assert(name==getLeftContig() || name==getRightContig());
#endif
if(name==getLeftContig())
return LEFT_SIDE;
else if(name==getRightContig())
return RIGHT_SIDE;
return -1;
}
int ScaffoldingEdge::getGapSize(){
return m_gapSize;
}
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