X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.h;fp=pcoacommand.h;h=ea4d2b381e8c5b60a3d7006e51d128dda72081bb;hb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;hp=d923006bdb663bfd8a782a59738681f951eca79f;hpb=36a867cbd85d9c276d3c8d13f25a150bbbe2466b;p=mothur.git

diff --git a/pcoacommand.h b/pcoacommand.h
index d923006..ea4d2b3 100644
--- a/pcoacommand.h
+++ b/pcoacommand.h
@@ -20,20 +20,21 @@ 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);