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ScaffoldLink.cpp
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ScaffoldLink.cpp
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//-----------------------------------------------
// Copyright 2010 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// ScaffoldLink - Data structure representing
// an inferred relationship between two scaffold
// components
//
#include "ScaffoldLink.h"
ScaffoldLink::ScaffoldLink(const std::string& id,
EdgeDir dir,
EdgeComp comp,
int dist,
double sd,
int np,
int sl,
ScaffoldLinkType slt) : endpointID(id),
distance(dist),
stdDev(sd),
numPairs(np),
seqLen(sl),
type(slt)
{
edgeData.setDir(dir);
edgeData.setComp(comp);
}
int ScaffoldLink::getEndpoint() const
{
assert(seqLen > 0);
return distance + seqLen;
}
//
EdgeDir ScaffoldLink::getDir() const
{
return edgeData.getDir();
}
// Return the direction of the twin edge
EdgeDir ScaffoldLink::getTwinDir() const
{
return (getComp() == EC_SAME) ? !getDir() : getDir();
}
//
EdgeComp ScaffoldLink::getComp() const
{
return edgeData.getComp();
}
//
char ScaffoldLink::getTypeCode() const
{
switch(type)
{
case SLT_DISTANCEEST:
return 'D';
case SLT_REFERENCE:
return 'R';
case SLT_INFERRED:
return 'I';
default:
return 'N';
}
}
//
ScaffoldLinkType ScaffoldLink::getType(char tc)
{
switch(tc)
{
case 'D':
return SLT_DISTANCEEST;
case 'R':
return SLT_REFERENCE;
case 'I':
return SLT_INFERRED;
default:
return SLT_NOTYPE;
}
}
//
void ScaffoldLink::parse(const std::string& text)
{
StringVector fields = split(text, ',');
assert(fields.size() == 6);
endpointID = fields[0];
std::stringstream d_parser(fields[1]);
d_parser >> distance;
std::stringstream sd_parser(fields[2]);
sd_parser >> stdDev;
std::stringstream dir_parser(fields[3]);
int dir;
dir_parser >> dir;
std::stringstream comp_parser(fields[4]);
int comp;
comp_parser >> comp;
std::stringstream type_parser(fields[5]);
char tc;
type_parser >> tc;
edgeData.setDir((EdgeDir)dir);
edgeData.setComp((EdgeComp)comp);
type = getType(tc);
}
//
std::ostream& operator<<(std::ostream& out, const ScaffoldLink& link)
{
out << link.endpointID << "," << link.distance << "," << link.stdDev << ","
<< link.edgeData.getDir() << "," << link.edgeData.getComp() << "," << link.getTypeCode();
return out;
}