X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.h;h=64235841a9a29b651ea4f1fe2b64e2125876bc43;hb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;hp=eedfcf35c58d508cb37ebc41416ca0a3bfc7b1c8;hpb=943d3038553f82378567d3b651969146716e5862;p=mothur.git

diff --git a/pcacommand.h b/pcacommand.h
index eedfcf3..6423584 100644
--- a/pcacommand.h
+++ b/pcacommand.h
@@ -12,8 +12,7 @@
 
 #include "command.hpp"
 #include "linearalgebra.h"
-#include "globaldata.hpp"
-
+#include "sharedrabundfloatvector.h"
 
 /*****************************************************************/
 class PCACommand : public Command {
@@ -21,22 +20,26 @@ class PCACommand : 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();
+	~PCACommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "pca";					}
+	string getCommandCategory()		{ return "Hypothesis Testing";	}
+	string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	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()); }	
 	
-private:
-	GlobalData* globaldata;
 	
+private:
+
 	bool abort, metric;
-	string outputDir, mode, inputFile, label, groups;
+	string outputDir, mode, inputFile, label, groups, sharedfile, relabundfile;
 	vector<string> outputNames, Groups;
 	set<string> labels;
-	map<string, vector<string> > outputTypes;
 	LinearAlgebra linearCalc;
 	
 	//vector< vector<double> > createMatrix(vector<SharedRAbundFloatVector*>);