public class AdjacencyMatrix {
  private int INIT_SIZE = 1024;
  private int INCREMENT_SIZE = 512;
  private int[][] data = new int[INIT_SIZE][INIT_SIZE];
  private String[] labels = new String[INIT_SIZE];
  private int count = 0;
  
  public int size(){
    return count;
  }
  public void clear(){
    count = 0;
  }
  public int[] addNodes(String[] labels){
    int[] idx = new int[labels.length];
    for(int cnt=0;cnt<labels.length;cnt++){
      idx[cnt] = addNode(labels[cnt]);
    }
    return idx;
  }
  public int addNode(String label){
    int idx = indexOf(label);
    if(idx != -1){
      return idx;
    }
    if(count == labels.length){
      int old_length = data.length;
      int new_length = data.length+INCREMENT_SIZE;
      labels = expand(labels,new_length);
      data = (int[][])expand(data,new_length);
      for(int cnt=0;cnt<old_length;cnt++){
        data[cnt] = expand(data[cnt],new_length);
      }
      for(int cnt=old_length;cnt<data.length;cnt++){
        data[cnt] = new int[new_length];
      }
    }
    labels[count] = new String(label);
    count++;
    for(int row=0;row<count;row++){
      data[row][count-1] = 0;
    }
    for(int col=0;col<count-1;col++){
      data[count-1][col] = 0;
    }
    return count-1;
  }
  public int indexOf(String label){
    for(int cnt=0;cnt<count;cnt++){
      if(labels[cnt].equals(label)){
        return cnt;
      }
    }
    return -1;
  }
  public boolean deleteNode(String label){
    return deleteNode(indexOf(label));
  }
  public boolean deleteNode(int index){
    if(index == -1){
      return false;
    }
    for(int row=0;row<count;row++){
      if(row<index){
        arrayCopy(data[row],index+1,data[row],index,count-index-1);
      }else if(row>index){
        arrayCopy(data[row],0,data[row-1],0,index);
        arrayCopy(data[row],index+1,data[row-1],index,count-index-1);
      }
    }
    arrayCopy(labels,index+1,labels,index,count-index-1);
    count--;
    return true;
  }
  public boolean addEdge(String from,String to){
    return addEdge(from,to,true);
  }
  public boolean addEdge(String from,String to,boolean directed){
    return set(indexOf(from),indexOf(to),directed,1);
  }
  public boolean addEdge(int f_idx,int t_idx){
    return addEdge(f_idx,t_idx,true);
  }
  public boolean addEdge(int f_idx,int t_idx,boolean directed){
    return set(f_idx,t_idx,directed,1);
  }
  public boolean deleteEdge(String from,String to){
    return deleteEdge(from,to,true);
  }
  public boolean deleteEdge(String from,String to,boolean directed){
    return set(indexOf(from),indexOf(to),directed,0);
  }
  public boolean deleteEdge(int f_idx,int t_idx){
    return deleteEdge(f_idx,t_idx,true);
  }
  public boolean deleteEdge(int f_idx,int t_idx,boolean directed){
    return set(f_idx,t_idx,directed,0);
  }
  private boolean set(int f_idx,int t_idx,boolean directed,int value){
    if(f_idx<0 || f_idx>=count || t_idx<0 || t_idx>=count){
      return false;
    }
    data[f_idx][t_idx] = value;
    if(directed==false){
      data[t_idx][f_idx] = value;
    }
    return true;
  }
  public int get(int f_idx,int t_idx){
    if(f_idx<0 || f_idx>=count || t_idx<0 || t_idx>=count){
      return -1;
    }
    return data[f_idx][t_idx];
  }
  public String getNodeName(int index){
    if(index < 0 || index >= count){
      return null;
    }
    return labels[index];
  }
  double[] getRates(int[] seeds_indexes,int index){
    double[] rates = new double[2];
    for(int rcnt=0;rcnt<rates.length;rcnt++){
      for(int cnt=seeds_indexes[0];cnt<seeds_indexes[1];cnt++){
        rates[rcnt] += data[rcnt==0?index:cnt][rcnt==0?cnt:index];
      }
      rates[rcnt] /= (seeds_indexes[1]-seeds_indexes[0]);
    }
    return rates;
  }
  public String toString(){
    String ret = new String();
    for(int row=0;row<count;row++){
      for(int col=0;col<count;col++){
        ret += (col==0?"":",")+data[row][col];
      }
      ret += " ("+labels[row]+")\n";
    }
    return ret;
  }
}