X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.h;h=02e562ec23f97d1fdbd0e6e18c949ae3ffc44c54;hb=662c0b60d65f79f672ab199300b7ee4975233465;hp=8bb7c1bdc586798b70fb3ec3f601bf13b5a16d9e;hpb=605ab6fa594317a38f0df7bb6797740c735b2348;p=mothur.git

diff --git a/pcoacommand.h b/pcoacommand.h
index 8bb7c1b..02e562e 100644
--- a/pcoacommand.h
+++ b/pcoacommand.h
@@ -31,19 +31,14 @@ public:
 private:
 
 	bool abort, metric;
-	string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
-	float cutoff, precision;
+	string phylipfile, filename, fbase, outputDir;
 	vector<string> outputNames;
 	map<string, vector<string> > outputTypes;
 	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> >&);
 	void recenter(double, vector<vector<double> >, vector<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> >&);
 	
 };