changed filename of pcacommand to pcoacommand

[mothur.git] / pcoacommand.h

diff --git a/pcoacommand.h b/pcoacommand.h
new file mode 100644 (file)
index 0000000..22f288a
--- /dev/null
+++ b/pcoacommand.h
@@ -0,0 +1,53 @@
+#ifndef PCACOMMAND_H
+#define PCACOMMAND_H
+
+/*
+ *  pcacommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 1/4/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+
+
+/*****************************************************************/
+class PCACommand : public Command {
+       
+public:
+       PCACommand(string);     
+       PCACommand();
+       ~PCACommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();  
+       void help();
+       
+private:
+
+       bool abort;
+       string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
+       float cutoff, precision;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+       
+       void get_comment(istream&, char, char);
+       int read_phylip(istream&, int, vector<string>&, vector<vector<double> >&);
+       void read(string, vector<string>&, vector<vector<double> >&);
+       double pythag(double, double);
+       void matrix_mult(vector<vector<double> >, vector<vector<double> >, vector<vector<double> >&);
+       void recenter(double, vector<vector<double> >, vector<vector<double> >&);
+       void tred2(vector<vector<double> >&, vector<double>&, vector<double>&);
+       void qtli(vector<double>&, vector<double>&, vector<vector<double> >&);
+       void output(string, vector<string>, vector<vector<double> >, vector<double>);
+       
+};
+       
+/*****************************************************************/
+       
+#endif
+