fixed summary.shared bug and set jumble default to 1.

[mothur.git] / treemap.h

diff --git a/treemap.h b/treemap.h
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+#ifndef TREEMAP_H
+#define TREEMAP_H
+/*
+ *  treemap.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 1/26/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include <Carbon/Carbon.h>
+#include <map>
+#include <string>
+#include <iostream>
+#include <fstream>
+#include "utilities.hpp"
+
+/* This class is used by the read.tree command to build the tree container. */
+
+struct GroupIndex {
+       string  groupname;
+       int             vectorIndex;
+};
+
+
+
+class TreeMap {
+public:
+       TreeMap(string);
+       ~TreeMap();
+       void readMap();
+       int getNumGroups();
+       int getNumSeqs();
+       void setIndex(string, int);  //sequencename, index
+       int getIndex(string);           //returns vector index of sequence
+       string getGroup(string);
+       vector<string> namesOfGroups;
+       vector<string> namesOfSeqs;
+       void print(ostream&);
+       
+private:
+       ifstream fileHandle;
+       string groupFileName;
+       int numGroups;
+       map<string, GroupIndex>::iterator it;
+       void setNamesOfGroups(string); 
+       map<string, GroupIndex> treemap; //sequence name and groupname
+};
+
+#endif
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