#ifndef SEQUENCEALIGNMENT_H
#define SEQUENCEALIGNMENT_H

#include "alignedSequence.h"
#include "sequence.h"
#include "symbol.h"

#include <stdio.h>

// XXX: NEED A FEW TYPES OF ITERATORS

class SequenceAlignment {

 public:
  SequenceAlignment(int mL, int mSC);
  ~SequenceAlignment();

  int addSequence(AlignedSequence* sequence);
  AlignedSequence* getSequence(int i);
  Symbol* getSymbol(int i, int j);
  // XXX - NEED AN ASSOCIATED ALPHABET
  int getLength();
  int getSequenceCount();

 private:
  AlignedSequence** alignment;
  int length;
  int maxLength;
  int sequenceCount;
  int maxSequenceCount;

};

#endif