added modify names parameter to set.dir

[mothur.git] / clusterclassic.h

diff --git a/clusterclassic.h b/clusterclassic.h
index 9a896f28df1a51d29978914e6922ce924b083e86..eaccb273b4980b297e1ad4d9f419d6494e37a120 100644 (file)
--- a/clusterclassic.h
+++ b/clusterclassic.h
@@ -1,12 +1,12 @@
-#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
@@ -21,14 +21,15 @@
 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;      }
 
@@ -42,25 +43,24 @@ private:
        struct colDist {
                int col;
                int row;
-               double dist;
+               float dist;
                colDist(int r, int c, double d) : row(r), col(c), dist(d) {}
        };
        
        RAbundVector* rabund;
        ListVector* list;
-       vector< vector<double> > dMatrix;       
+       vector< vector<float> > dMatrix;        
        //vector<colDist> rowSmallDists;
        
        int smallRow;
        int smallCol, nseqs;
        double smallDist;
-       bool mapWanted;
+       bool mapWanted, sim;
        double cutoff, aboveCutoff;
        map<string, int> seq2Bin;
-       string method;
+       string method, tag;
        
        MothurOut* m;
-       GlobalData* globaldata;
 };
 
 #endif