X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pcacommand.h;h=482ecc3fecf678cca5853eb9c1160f005204a604;hp=089d1c102f38d66bfa0d83c2120dd3d3f1cd883e;hb=615301e57c25e241356a9c2380648d117709458d;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3

diff --git a/pcacommand.h b/pcacommand.h
index 089d1c1..482ecc3 100644
--- a/pcacommand.h
+++ b/pcacommand.h
@@ -3,45 +3,54 @@
 
 /*
  *  pcacommand.h
- *  Mothur
+ *  mothur
  *
- *  Created by westcott on 1/4/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
+ *  Created by westcott on 1/7/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
  *
  */
- 
-#include "command.hpp"
 
+#include "command.hpp"
+#include "linearalgebra.h"
+#include "sharedrabundfloatvector.h"
 
 /*****************************************************************/
 class PCACommand : public Command {
 	
 public:
 	PCACommand(string);	
-	~PCACommand();
-	int execute();	
-	void help();
+	PCACommand();
+	~PCACommand() {}
+	
+	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;
-	string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
-	float cutoff, precision;
-	vector<string> outputNames;
+	bool abort, metric;
+	string outputDir, mode, inputFile, label, groups, sharedfile, relabundfile;
+	vector<string> outputNames, Groups;
+	set<string> labels;
+	LinearAlgebra linearCalc;
 	
-	void get_comment(istream&, char, char);
-	int read_phylip(istream&, int, vector<string>&, vector<vector<double> >&);
-	void read(string, vector<string>&, vector<vector<double> >&);
-	double pythag(double, double);
-	void matrix_mult(vector<vector<double> >, vector<vector<double> >, vector<vector<double> >&);
-	void recenter(double, vector<vector<double> >, vector<vector<double> >&);
-	void tred2(vector<vector<double> >&, vector<double>&, vector<double>&);
-	void qtli(vector<double>&, vector<double>&, vector<vector<double> >&);
-	void output(string, vector<string>, vector<vector<double> >, vector<double>);
+	//vector< vector<double> > createMatrix(vector<SharedRAbundFloatVector*>);
+	int process(vector<SharedRAbundFloatVector*>&);
+	void output(string, string, vector<string>, vector<vector<double> >&, vector<double>);
 	
 };
-	
+
 /*****************************************************************/
-	
+
 #endif
 
+