X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.h;h=ea1738b9113f967af45f52e0978f4d48dcd1b23f;hb=1b4b18b3e6fa1436b7cc6dcb14c749ac1ae1bdd8;hp=22f288a7e768a74c939781df1302e42b92124600;hpb=4956d362c5bc6a47cf7a6290258f0e763e3a406e;p=mothur.git

diff --git a/pcoacommand.h b/pcoacommand.h
index 22f288a..ea1738b 100644
--- a/pcoacommand.h
+++ b/pcoacommand.h
@@ -1,8 +1,8 @@
-#ifndef PCACOMMAND_H
-#define PCACOMMAND_H
+#ifndef PCOACOMMAND_H
+#define PCOACOMMAND_H
 
 /*
- *  pcacommand.h
+ *  pcoacommand.h
  *  Mothur
  *
  *  Created by westcott on 1/4/10.
@@ -14,12 +14,12 @@
 
 
 /*****************************************************************/
-class PCACommand : public Command {
+class PCOACommand : public Command {
 	
 public:
-	PCACommand(string);	
-	PCACommand();
-	~PCACommand();
+	PCOACommand(string);	
+	PCOACommand();
+	~PCOACommand();
 	vector<string> getRequiredParameters();
 	vector<string> getValidParameters();
 	vector<string> getRequiredFiles();
@@ -29,7 +29,7 @@ public:
 	
 private:
 
-	bool abort;
+	bool abort, metric;
 	string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
 	float cutoff, precision;
 	vector<string> outputNames;
@@ -43,7 +43,9 @@ private:
 	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>);
+	void output(string, vector<string>, vector<vector<double> >&, vector<double>);
+	vector< vector<double> > calculateEuclidianDistance(vector<vector<double> >&, int);
+	double calcPearson(vector<vector<double> >&, vector<vector<double> >&);
 	
 };