X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.h;h=22f288a7e768a74c939781df1302e42b92124600;hb=e99751591aa21705e58edda87383457b9738dd9e;hp=143e83dda8efbfb2bbd3548e0c02f47920433f26;hpb=d5bf2c1354d0811a33394d918b15620606560d58;p=mothur.git

diff --git a/pcacommand.h b/pcacommand.h
index 143e83d..22f288a 100644
--- a/pcacommand.h
+++ b/pcacommand.h
@@ -18,19 +18,25 @@ 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;
+	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
 	
 	void get_comment(istream&, char, char);
-	void read_mega(istream&, vector<string>&, vector<vector<double> >&);
-	void read_phylip(istream&, 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> >&);
@@ -38,7 +44,6 @@ private:
 	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> >);
 	
 };