X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readcluster.h;h=a838dace17f35547421c03b0dfc8dcc6efdc2317;hb=ce8794490ab1d83adcdb2b92e0302a1e43e17adf;hp=c81b1dd1b9f1684f54c70d666e1b3868076c1802;hpb=72ebb6fa35b45b149812d47c2b1cb8acaca64659;p=mothur.git

diff --git a/readcluster.h b/readcluster.h
index c81b1dd..a838dac 100644
--- a/readcluster.h
+++ b/readcluster.h
@@ -20,21 +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;	}
 	
 private:
-	string distFile;
+	string distFile, outputDir;
 	string OutPutFile, format;
 	ListVector* list;
 	float cutoff;
+	MothurOut* m;
+	bool sortWanted;
 	
-	void createHClusterFile();
-	void convertPhylip2Column(NameAssignment*);
+	int convertPhylip2Column(NameAssignment*&);
 };
 
 /******************************************************/