added hcluster command and fixed some bugs, namely one with smart distancing.

[mothur.git] / readcluster.h

diff --git a/readcluster.h b/readcluster.h
new file mode 100644 (file)
index 0000000..c81b1dd
--- /dev/null
+++ b/readcluster.h
@@ -0,0 +1,43 @@
+#ifndef READCLUSTER_H
+#define READCLUSTER_H
+/*
+ *  readcluster.h
+ *  Mothur
+ *
+ *  Created by westcott on 10/28/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "mothur.h"
+#include "nameassignment.hpp"
+#include "listvector.hpp"
+
+
+/******************************************************/
+
+class ReadCluster {
+       
+public:
+       ReadCluster(string, float);
+       ~ReadCluster();
+       void read(NameAssignment*);
+       string getOutputFile() { return OutPutFile; }
+       void setFormat(string f) { format = f;  }
+       ListVector* getListVector()             {       return list;    }
+       
+private:
+       string distFile;
+       string OutPutFile, format;
+       ListVector* list;
+       float cutoff;
+       
+       void createHClusterFile();
+       void convertPhylip2Column(NameAssignment*);
+};
+
+/******************************************************/
+
+#endif
+