X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pcacommand.h;h=482ecc3fecf678cca5853eb9c1160f005204a604;hp=cf4348ca92e393e9e6d46efd7da8f058bab7f422;hb=615301e57c25e241356a9c2380648d117709458d;hpb=37eac2026d91179acda0494c4dcca22f176551b9

diff --git a/pcacommand.h b/pcacommand.h
index cf4348c..482ecc3 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 {
@@ -21,27 +20,32 @@ 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() {}
 	
-private:
-	GlobalData* globaldata;
+	vector<string> setParameters();
+	string getCommandName()			{ return "pca";					}
+	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/Pca"; }
+	string getDescription()		{ return "pca"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
+	
+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*>);
+	//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>);
 	
 };