changed random forest output filename

[mothur.git] / pcoacommand.h

diff --git a/pcoacommand.h b/pcoacommand.h
index 22f288a7e768a74c939781df1302e42b92124600..29957f1140e81517cc5a244a696eba7aaf1db49a 100644 (file)
--- a/pcoacommand.h
+++ b/pcoacommand.h
@@ -1,8 +1,8 @@
-#ifndef PCACOMMAND_H
-#define PCACOMMAND_H
+#ifndef PCOACOMMAND_H
+#define PCOACOMMAND_H
 
 /*
- *  pcacommand.h
+ *  pcoacommand.h
  *  Mothur
  *
  *  Created by westcott on 1/4/10.
@@ -11,39 +11,38 @@
  */
  
 #include "command.hpp"
+#include "linearalgebra.h"
 
 
 /*****************************************************************/
-class PCACommand : public Command {
+class PCOACommand : 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();
+       PCOACommand(string);    
+       PCOACommand();
+       ~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;
-       string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
-       float cutoff, precision;
+       bool abort, metric;
+       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> >&);
-       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 output(string, vector<string>, vector<vector<double> >&, vector<double>);
        
 };