X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.h;fp=pcoacommand.h;h=22f288a7e768a74c939781df1302e42b92124600;hb=4956d362c5bc6a47cf7a6290258f0e763e3a406e;hp=0000000000000000000000000000000000000000;hpb=5694c92fbf646fe01abc87bde2af59e14a9a56b6;p=mothur.git

diff --git a/pcoacommand.h b/pcoacommand.h
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--- /dev/null
+++ b/pcoacommand.h
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+#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
+