changed random forest output filename

[mothur.git] / pcoacommand.h

diff --git a/pcoacommand.h b/pcoacommand.h
index c62b3d668c9a38287769476a598033544d9790a3..29957f1140e81517cc5a244a696eba7aaf1db49a 100644 (file)
--- a/pcoacommand.h
+++ b/pcoacommand.h
@@ -20,27 +20,28 @@ class PCOACommand : public Command {
 public:
        PCOACommand(string);    
        PCOACommand();
-       ~PCOACommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       ~PCOACommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "pcoa";                                        }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Pcoa"; }
+       string getDescription()         { return "pcoa"; }
+
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }
        
 private:
 
        bool abort, metric;
-       string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
-       float cutoff, precision;
+       string phylipfile, filename, fbase, outputDir;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        LinearAlgebra linearCalc;
        
        void get_comment(istream&, char, char);
-       int read_phylip(istream&, int, vector<string>&, vector<vector<double> >&);
-       void read(string, vector<string>&, vector<vector<double> >&);
-       void recenter(double, vector<vector<double> >, vector<vector<double> >&);
        void output(string, vector<string>, vector<vector<double> >&, vector<double>);
        
 };