X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterclassic.h;h=eaccb273b4980b297e1ad4d9f419d6494e37a120;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=37d9b1b44cd1e13aa4198f5bde7e16c46de14437;hpb=6cf9539162b0fb0b5c0b99673e999df3cd717c55;p=mothur.git

diff --git a/clusterclassic.h b/clusterclassic.h
index 37d9b1b..eaccb27 100644
--- 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;
-		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