ACE/LightVertex.C at master · bmajoros/ACE · GitHub

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/****************************************************************
 LightVertex.C
 Copyright (C)2013 William H. Majoros (martiandna@gmail.com).
 This is OPEN SOURCE SOFTWARE governed by the Gnu General Public
 License (GPL) version 3, as described at www.opensource.org.
 ****************************************************************/
#include <iostream>
#include "LightVertex.H"
#include "LightEdge.H"
using namespace std;
using namespace BOOM;

LightVertex::LightVertex(const String &substrate,SignalType t,int begin,
			 int end,float score,Strand s,int ID)
  : type(t), begin(begin), end(end), score(score), strand(s), ID(ID),
    substrate(substrate), supported(false), annotated(false)
{
  // ctor
}


void LightVertex::addEdgeIn(LightEdge *e)
{
  if(e->getLeft()->getBegin()>begin) INTERNAL_ERROR;
  edgesIn.push_back(e);
}


void LightVertex::addEdgeOut(LightEdge *e)
{
  if(e->getRight()->getBegin()<begin) {
    cout<<*this<<endl;
    cout<<*e->getRight()<<endl;
    INTERNAL_ERROR;
  }
  edgesOut.push_back(e);
}


SignalType LightVertex::getType() const
{
  return type;
}


Interval LightVertex::getInterval() const
{
  return Interval(begin,end);
}


int LightVertex::distanceTo(const LightVertex &other) const
{
  return getInterval().distanceTo(other.getInterval());
}


int LightVertex::getBegin() const
{
  return begin;
}


int LightVertex::getEnd() const
{
  return end;
}


float LightVertex::getScore() const
{
  return score;
}


void LightVertex::setScore(float s)
{
  score=s;
}


Strand LightVertex::getStrand() const
{
  return strand;
}


Vector<LightEdge*> &LightVertex::getEdgesIn()
{
  return edgesIn;
}


Vector<LightEdge*> &LightVertex::getEdgesOut()
{
  return edgesOut;
}


void LightVertex::printOn(ostream &os,String vertexType)
{
  int supportString=supported ? 1 : 0;
  os<<substrate<<"\t"<<vertexType<<"\t"<<signalTypeToName(type)
    <<"\t"<<begin+1<<"\t"<<
    end<<"\t"<<score<<"\t"<<strand<<"\t.\tID="<<ID<<"; in="<<edgesIn.size()
    <<"; out="<<edgesOut.size()<<"; sup="<<supportString<<";";
}


int LightVertex::getID() const
{
  return ID;
}


ostream &operator<<(ostream &os,const LightVertex &v)
{
  v.printOn(os);
  return os;
}


bool LightVertex::isSupported() const
{
  return supported;
}


void LightVertex::setSupport(bool s)
{
  supported=s;
}


void LightVertex::setID(int id)
{
  ID=id;
}


void LightVertex::dropEdgeIn(LightEdge *e)
{
  int n=edgesIn.size();
  for(int i=0 ; i<n ; ++i)
    if(edgesIn[i]==e) {
      edgesIn.cut(i);
      break;
    }
}


void LightVertex::dropEdgeOut(LightEdge *e)
{
  int n=edgesOut.size();
  for(int i=0 ; i<n ; ++i)
    if(edgesOut[i]==e) {
      edgesOut.cut(i);
      break;
    }
}


bool LightVertex::operator==(const LightVertex &other) const
{
  return substrate==other.substrate &&
    strand==other.strand &&
    begin==other.begin &&
    end==other.end &&
    type==other.type;
}