added template=self capability to chimers.slayer, worked on corr.axes and added accno...

[mothur.git] / pcacommand.h

diff --git a/pcacommand.h b/pcacommand.h
index 822be3b905b1a808e74c8b3b59272ca2431cf763..22f288a7e768a74c939781df1302e42b92124600 100644 (file)
--- 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> >);
        
 };