X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.h;fp=parsimony.h;h=7316d508dd52729c8ddec87c34a08c76586cd4d1;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/parsimony.h b/parsimony.h
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+#ifndef PARSIMONY_H
+#define PARSIMONY_H
+
+
+/*
+ *  parsimony.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 1/26/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "treecalculator.h"
+#include "treemap.h"
+
+/***********************************************************************/
+
+class Parsimony : public TreeCalculator  {
+	
+	public:
+		Parsimony() {};
+		~Parsimony() {};
+		EstOutput getValues(Tree*, int, string);
+		
+	private:
+		struct linePair {
+			int start;
+			int num;
+			linePair(int i, int j) : start(i), num(j) {}
+		};
+		vector<linePair> lines;
+	
+		EstOutput data;
+		int processors;
+		string outputDir;
+	
+		EstOutput driver(Tree*, vector< vector<string> >, int, int, TreeMap*); 
+		EstOutput createProcesses(Tree*, vector< vector<string> >, TreeMap*);
+};
+
+/***********************************************************************/
+
+#endif