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[mothur.git] / unweighted.h

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+#ifndef UNWEIGHTED_H
+#define UNWEIGHTED_H
+
+
+/*
+ *  unweighted.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 2/9/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "treecalculator.h"
+#include "treemap.h"
+
+/***********************************************************************/
+
+class Unweighted : public TreeCalculator  {
+       
+       public:
+        Unweighted(bool r) : includeRoot(r) {};
+               ~Unweighted() {};
+               EstOutput getValues(Tree*, int, string);
+               EstOutput getValues(Tree*, string, string, 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;
+               map< vector<string>, set<int> > rootForGrouping;  //maps a grouping combo to the roots for that combo
+               bool includeRoot;
+               
+               EstOutput driver(Tree*, vector< vector<string> >, int, int, TreeMap*); 
+               EstOutput createProcesses(Tree*, vector< vector<string> >, TreeMap*);
+               EstOutput driver(Tree*, vector< vector<string> >, int, int, bool, TreeMap*); 
+               EstOutput createProcesses(Tree*, vector< vector<string> >, bool, TreeMap*);
+               int getRoot(Tree*, int, vector<string>);
+};
+
+/***********************************************************************/
+
+#endif