X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.h;h=eedfcf35c58d508cb37ebc41416ca0a3bfc7b1c8;hb=943d3038553f82378567d3b651969146716e5862;hp=089d1c102f38d66bfa0d83c2120dd3d3f1cd883e;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/pcacommand.h b/pcacommand.h
index 089d1c1..eedfcf3 100644
--- a/pcacommand.h
+++ b/pcacommand.h
@@ -3,14 +3,16 @@
 
 /*
  *  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 "linearalgebra.h"
+#include "globaldata.hpp"
 
 
 /*****************************************************************/
@@ -18,30 +20,33 @@ 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();
 	
 private:
-
-	bool abort;
-	string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
-	float cutoff, precision;
-	vector<string> outputNames;
+	GlobalData* globaldata;
 	
-	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>);
+	bool abort, metric;
+	string outputDir, mode, inputFile, label, groups;
+	vector<string> outputNames, Groups;
+	set<string> labels;
+	map<string, vector<string> > outputTypes;
+	LinearAlgebra linearCalc;
 	
-};
+	//vector< vector<double> > createMatrix(vector<SharedRAbundFloatVector*>);
+	int process(vector<SharedRAbundFloatVector*>&);
+	void output(string, vector<string>, vector<vector<double> >&, vector<double>);
 	
+};
+
 /*****************************************************************/
-	
+
 #endif
 
+