#include "mothurout.h"
#include "listvector.hpp"
#include "rabundvector.hpp"
#include "nameassignment.hpp"
#include "mothurout.h"
#include "listvector.hpp"
#include "rabundvector.hpp"
#include "nameassignment.hpp"
public:
ClusterClassic(float, string, bool);
int readPhylipFile(string, NameAssignment*);
public:
ClusterClassic(float, string, bool);
int readPhylipFile(string, NameAssignment*);
void update(double&);
double getSmallDist() { return smallDist; }
int getNSeqs() { return nseqs; }
ListVector* getListVector() { return list; }
RAbundVector* getRAbundVector() { return rabund; }
void update(double&);
double getSmallDist() { return smallDist; }
int getNSeqs() { return nseqs; }
ListVector* getListVector() { return list; }
RAbundVector* getRAbundVector() { return rabund; }
void setMapWanted(bool m);
map<string, int> getSeqtoBin() { return seq2Bin; }
void setMapWanted(bool m);
map<string, int> getSeqtoBin() { return seq2Bin; }
colDist(int r, int c, double d) : row(r), col(c), dist(d) {}
};
RAbundVector* rabund;
ListVector* list;
colDist(int r, int c, double d) : row(r), col(c), dist(d) {}
};
RAbundVector* rabund;
ListVector* list;
bool mapWanted, sim;
double cutoff, aboveCutoff;
map<string, int> seq2Bin;
bool mapWanted, sim;
double cutoff, aboveCutoff;
map<string, int> seq2Bin;