X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readcluster.h;h=7ea579c2fc1a250bba3500f7d6dc59d3ebed26f8;hp=d578a0fe76b025d03431446cf74f426814bc9c46;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0

diff --git a/readcluster.h b/readcluster.h
index d578a0f..7ea579c 100644
--- a/readcluster.h
+++ b/readcluster.h
@@ -13,7 +13,7 @@
 #include "mothur.h"
 #include "nameassignment.hpp"
 #include "listvector.hpp"
-#include "globaldata.hpp"
+#include "counttable.h"
 
 
 /******************************************************/
@@ -21,22 +21,24 @@
 class ReadCluster {
 	
 public:
-	ReadCluster(string, float);
+	ReadCluster(string, float, string, bool);
 	~ReadCluster();
-	void read(NameAssignment*);
+	int read(NameAssignment*&);
+    int read(CountTable*&);
 	string getOutputFile() { return OutPutFile; }
 	void setFormat(string f) { format = f;	}
 	ListVector* getListVector()		{	return list;	}
 	
 private:
-	GlobalData* globaldata;
-	string distFile;
+	string distFile, outputDir;
 	string OutPutFile, format;
 	ListVector* list;
 	float cutoff;
 	MothurOut* m;
+	bool sortWanted;
 	
-	void convertPhylip2Column(NameAssignment*);
+	int convertPhylip2Column(NameAssignment*&);
+    int convertPhylip2Column(CountTable*&);
 };
 
 /******************************************************/