added mantel command

[mothur.git] / mantelcommand.h

diff --git a/mantelcommand.h b/mantelcommand.h
new file mode 100644 (file)
index 0000000..0646b29
--- /dev/null
+++ b/mantelcommand.h
@@ -0,0 +1,42 @@
+#ifndef MANTELCOMMAND_H
+#define MANTELCOMMAND_H
+
+/*
+ *  mantelcommand.h
+ *  mothur
+ *
+ *  Created by westcott on 2/9/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "linearalgebra.h"
+
+class MantelCommand : public Command {
+public:
+       MantelCommand(string);
+       MantelCommand();
+       ~MantelCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();
+       
+private:
+       
+       string phylipfile1, phylipfile2, outputDir, method;
+       bool abort;
+       int iters;
+       
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+};
+
+
+#endif
+
+
+