removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / pcoacommand.h

diff --git a/pcoacommand.h b/pcoacommand.h
index 02e562ec23f97d1fdbd0e6e18c949ae3ffc44c54..ea4d2b381e8c5b60a3d7006e51d128dda72081bb 100644 (file)
--- a/pcoacommand.h
+++ b/pcoacommand.h
@@ -20,24 +20,24 @@ 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(); 
+       
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }
        
 private:
 
        bool abort, metric;
        string phylipfile, filename, fbase, outputDir;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        LinearAlgebra linearCalc;
        
        void get_comment(istream&, char, char);
-       void recenter(double, vector<vector<double> >, vector<vector<double> >&);
        void output(string, vector<string>, vector<vector<double> >&, vector<double>);
        
 };