X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.h;h=482ecc3fecf678cca5853eb9c1160f005204a604;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=9b4a881cb181823a58fcfa9c7962ca561e394346;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/pcacommand.h b/pcacommand.h
index 9b4a881..482ecc3 100644
--- a/pcacommand.h
+++ b/pcacommand.h
@@ -25,9 +25,12 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "pca";					}
 	string getCommandCategory()		{ return "Hypothesis Testing";	}
-	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/Pca"; }
 	
+	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/Pca"; }
+	string getDescription()		{ return "pca"; }
+
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
@@ -42,7 +45,7 @@ private:
 	
 	//vector< vector<double> > createMatrix(vector<SharedRAbundFloatVector*>);
 	int process(vector<SharedRAbundFloatVector*>&);
-	void output(string, vector<string>, vector<vector<double> >&, vector<double>);
+	void output(string, string, vector<string>, vector<vector<double> >&, vector<double>);
 	
 };