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 "treenode.h"
  16 #include "globaldata.hpp"
  17
  18 /* This class represents the treefile. */
  19
  20 class Tree {
  21         public:
  22                 Tree();         //to generate a tree from a file
  23                 ~Tree() {};
  24
  25
  26                 void getCopy(Tree*);  //makes tree a copy of the one passed in.
  27                 void assembleRandomTree();
  28                 void assembleRandomUnifracTree();
  29                 void createNewickFile();
  30                 int getIndex(string);
  31                 void setIndex(string, int);
  32                 int getNumNodes() { return numNodes; }
  33                 int getNumLeaves(){     return numLeaves; }
  34
  35                 //this function takes the leaf info and populates the non leaf nodes
  36                 void assembleTree();
  37
  38                 vector<Node> tree;              //the first n nodes are the leaves, where n is the number of sequences.
  39
  40         private:
  41                 GlobalData* globaldata;
  42                 int numNodes, numLeaves;
  43                 ofstream out;
  44                 string filename;
  45
  46                 map<string, int>::iterator it;
  47                 map<string, int> mergeGroups(int);  //returns a map with a groupname and the number of times that group was seen in the children
  48                 map<string,int> Tree::mergeGcounts(int);
  49                 void randomTopology();
  50                 void randomBlengths();
  51                 void randomLabels();
  52                 int findRoot();  //return index of root node
  53                 void printBranch(int);  //recursively print out tree
  54                 void setGroups();
  55 };
  56
  57 #endif