tree.h

   1 #ifndef TREE_H
   2 #define TREE_H
   3
   4 /*
   5  *  tree.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 1/22/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 using namespace std;
  14
  15 #include <string>
  16 #include <iostream>
  17 #include <vector>
  18 #include "treenode.h"
  19 #include "globaldata.hpp"
  20
  21 /* This class represents the treefile. */
  22
  23
  24
  25 class Tree {
  26         public:
  27                 Tree();
  28                 ~Tree() {};
  29
  30                 Tree generateRandomTree();
  31                 void createNewickFile();
  32                 int getIndex(string);
  33                 void setIndex(string, int);
  34                 int getNumNodes() { return numNodes; }
  35                 int getNumLeaves(){     return numLeaves;}
  36                 vector<Node> tree;              //the first n nodes are the leaves, where n is the number of sequences.
  37
  38         private:
  39                 GlobalData* globaldata;
  40                 int findRoot();  //return index of root node
  41                 void printBranch(int);  //recursively print out tree
  42                 int numNodes, numLeaves;
  43                 ofstream out;
  44                 string filename;
  45 };
  46
  47
  48
  49
  50 #endif