-#ifndef CLUSTER_H
-#define CLUSTER_H
+#ifndef CLUSTERCLASSIC_H
+#define CLUSTERCLASSIC_H
-#include "mothur.h"
#include "mothurout.h"
#include "listvector.hpp"
-#include "globaldata.hpp"
#include "rabundvector.hpp"
+#include "nameassignment.hpp"
+#include "counttable.h"
/*
* clusterclassic.h
class ClusterClassic {
public:
- ClusterClassic(float, string);
+ ClusterClassic(float, string, bool);
int readPhylipFile(string, NameAssignment*);
+ int readPhylipFile(string, CountTable*);
void update(double&);
double getSmallDist() { return smallDist; }
int getNSeqs() { return nseqs; }
ListVector* getListVector() { return list; }
RAbundVector* getRAbundVector() { return rabund; }
- string getTag();
+ string getTag() { return tag; }
void setMapWanted(bool m);
map<string, int> getSeqtoBin() { return seq2Bin; }
struct colDist {
int col;
int row;
- double dist;
- colDist(int i, int r, double d) : row(r), col(i), dist(d) {}
+ float dist;
+ colDist(int r, int c, double d) : row(r), col(c), dist(d) {}
};
RAbundVector* rabund;
ListVector* list;
- vector< vector<double> > dMatrix;
- vector<colDist> rowSmallDists;
+ vector< vector<float> > dMatrix;
+ //vector<colDist> rowSmallDists;
int smallRow;
int smallCol, nseqs;
double smallDist;
- bool mapWanted;
- float cutoff;
+ bool mapWanted, sim;
+ double cutoff, aboveCutoff;
map<string, int> seq2Bin;
- string method;
+ string method, tag;
MothurOut* m;
- GlobalData* globaldata;
};
#endif