added phylo.diversity command. added hard parameter to cluster, hcluster and read...

[mothur.git] / phylodiversitycommand.h

diff --git a/phylodiversitycommand.h b/phylodiversitycommand.h
new file mode 100644 (file)
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+++ b/phylodiversitycommand.h
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+#ifndef PHYLODIVERSITYCOMMAND_H
+#define PHYLODIVERSITYCOMMAND_H
+
+/*
+ *  phylodiversitycommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 4/30/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "treemap.h"
+#include "globaldata.hpp"
+
+class PhyloDiversityCommand : public Command {
+       
+       public:
+               PhyloDiversityCommand(string);
+               ~PhyloDiversityCommand();
+               int execute();  
+               void help();
+       
+       private:
+               GlobalData* globaldata;
+       
+               int iters, freq;  
+               bool abort, rarefy;
+               string groups, outputDir;
+               vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
+               
+               void printData(vector<int>&, vector< vector<float> >&, string);
+};
+
+#endif
+