void buildCreature(position p,lattice phen,genome gen,int maxNodes)
{
  constructPhenome(p,phen,gen,maxNodes);
  if(useMirror)
    mirror(phen);
    
  buildNeurons(phen);
  buildMuscles(phen);
}
void constructPhenome(position p,lattice phen,genome gen,int maxNodes)
{
  float cellDistance=18;  
  position curPos=new position(p);
  phen.addNode(curPos,gen.strain[0]);
  constructChild(phen,phen.nodes[0],curPos,maxNodes);
}


void constructChild(lattice phen,cell curCell,position curPos,int maxNodes)
{
  if(curCell.g.repeat>0)
  {
    int r=curCell.g.repeat;
      if(curCell.g.id==0&&curCell.g.repeat>0)
        r++;
    position repeatPos=new position(curPos.displace(curCell.g.heading,17));
    constructRepeat(phen,curCell,repeatPos,r,maxNodes);
  }

  if(curCell.g.child!=null&&phen.nodes.length<maxNodes)
  {
    gene newGene=new gene(curCell.g.child);
    position childPos=new position(curPos.displace(curCell.g.child.heading,17));
    phen.addNode(childPos,newGene);
    int cellID=phen.nodes.length-1;
    constructChild(phen,phen.nodes[cellID],childPos,maxNodes);  
  }
  
  return;
}

void constructRepeat(lattice phen,cell curCell,position curPos,int repeat,int maxNodes)
{  
  repeat--;  
  if(repeat>0)
  {
    phen.addNode(curPos,curCell.g);
    constructRepeat(phen,curCell,curPos.displace(curCell.g.heading,17),repeat,maxNodes);
  }  

  if(curCell.g.child!=null&&phen.nodes.length<maxNodes&&repeat>0)
  {
    gene newGene=new gene(curCell.g.child);
    position childPos=new position(curPos.displace(curCell.g.child.heading,17));
    phen.addNode(childPos,newGene);
    int cellID=phen.nodes.length-1;
    constructChild(phen,phen.nodes[cellID],childPos,maxNodes);  
  }  
  return;
}


void mirror(lattice phen)
{
  int numNodes=phen.nodes.length;
  for(int i=1;i<numNodes;i++)
  {
    position curPos=phen.nodes[i].p;
    gene curGene=phen.nodes[i].g;
    float distance=phen.nodes[i].x()-(width/2);
    position opPos=new position(width/2-distance,curPos.y);
    phen.addNode(opPos,curGene);
  }
}

void buildNeurons(lattice phen)
{
  int numNodes=phen.nodes.length;
//  println("------------------");
  for(int i=0;i<numNodes;i++)
  {
    if(phen.nodes[i].isNeuron)
    {
      int outNum=phen.nodes[i].c.output.length;
      int inNum=phen.nodes[i].c.input.length;
//      int total=outNum+inNum;
//      println("Neuon "+i+" has output to "+total+" connections.");
      for(int out=0;out<outNum;out++)
      {
        int id=phen.nodes[i].c.output[out];
//        if(phen.nodes[id].isNeuron)
          phen.nodes[i].n.addOutput(phen.nodes[id].n);
//        println("connecting "+i+" to "+id);
      }
      for(int in=0;in<inNum;in++)
      {
        int id=phen.nodes[i].c.input[in];
//        if(phen.nodes[id].isNeuron)        
          phen.nodes[i].n.addOutput(phen.nodes[id].n);
//        println("connecting "+i+" to "+id);        
      }      
    }
  }
}

void buildMuscles(lattice phen)
{
  int numNodes=phen.nodes.length;
  for(int i=0;i<numNodes;i++)
  {
    cell node=phen.nodes[i];
    int totalLength=node.c.output.length;
    node.c.m=new muscle[totalLength];
    for(int im=0;im<node.c.output.length;im++)
    {
      node.c.m[im]=new muscle(node.c.distanceOut[im]);    
    }  
  }
}