X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.h;h=22f288a7e768a74c939781df1302e42b92124600;hb=134a9c1275862a6b3ea10a2c0f11965c0a535854;hp=822be3b905b1a808e74c8b3b59272ca2431cf763;hpb=f27b66ce6415eb14c434f9850019c7cf140e023e;p=mothur.git

diff --git a/pcacommand.h b/pcacommand.h
index 822be3b..22f288a 100644
--- a/pcacommand.h
+++ b/pcacommand.h
@@ -18,28 +18,32 @@ 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;
+	string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
 	float cutoff, precision;
-	int matrix;
+	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
 	
 	void get_comment(istream&, char, char);
-	void read_mega(istream&, int, vector<string>&, vector<vector<double> >&);
-	void read_phylip(istream&, int, vector<string>&, vector<vector<double> >&);
-	void read(string, int, vector<string>&, vector<vector<double> >&);
+	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>);
-	void print_matrix(vector<vector<double> >);
 	
 };