X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readcluster.h;h=a838dace17f35547421c03b0dfc8dcc6efdc2317;hb=078d7227da8dda9ae8620822fa32d51ec2706fc3;hp=9e62e92aea46e04120c0992e12414d70b6207bba;hpb=d2cbe389d0e42eccb6bbb888462fe17e22a487a8;p=mothur.git

diff --git a/readcluster.h b/readcluster.h
index 9e62e92..a838dac 100644
--- a/readcluster.h
+++ b/readcluster.h
@@ -13,7 +13,6 @@
 #include "mothur.h"
 #include "nameassignment.hpp"
 #include "listvector.hpp"
-#include "globaldata.hpp"
 
 
 /******************************************************/
@@ -21,24 +20,22 @@
 class ReadCluster {
 	
 public:
-	ReadCluster(string, float);
+	ReadCluster(string, float, string, bool);
 	~ReadCluster();
-	void read(NameAssignment*);
+	int read(NameAssignment*&);
 	string getOutputFile() { return OutPutFile; }
 	void setFormat(string f) { format = f;	}
 	ListVector* getListVector()		{	return list;	}
-	//NameAssignment* getNameMap()	{	return nameMap;	}
 	
 private:
-	GlobalData* globaldata;
-	string distFile;
+	string distFile, outputDir;
 	string OutPutFile, format;
 	ListVector* list;
 	float cutoff;
-	//NameAssignment* nameMap;
+	MothurOut* m;
+	bool sortWanted;
 	
-	void createHClusterFile();
-	void convertPhylip2Column(NameAssignment*);
+	int convertPhylip2Column(NameAssignment*&);
 };
 
 /******************************************************/