#define MAX_DEPTH 50
#define MAX_SYMBOLS 20
#define MAX_NODES 1000

#ifndef FSTREAM_H
#include <fstream.h>
#endif

#ifndef STDLIB_H
#include <stdlib.h>
#endif

#ifndef MATH_H
#include <math.h>
#endif


#include "strand.h"

#define TOP_H

struct Leaves
       { int Nodes,*Parent;
         Strand *Strands;
         double *Times;
         int *Number; };

class TreeTopology
      { 
        protected :
      
        struct Leaves *Tree;
        int Gaps,Conservatism;
        int *SiteIndex;
        int Depth,Length,MaxNodes,NumberOfSequences;
              
        public :
        
        TreeTopology(char *,char *);        
        virtual ~TreeTopology ();
    
        };