8 * Created by Sarah Westcott on 1/22/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
14 #include "globaldata.hpp"
16 /* This class represents the treefile. */
20 Tree(); //to generate a tree from a file
23 void getCopy(Tree*); //makes tree a copy of the one passed in.
24 void assembleRandomTree();
25 void assembleRandomUnifracTree(vector<string>);
26 void assembleRandomUnifracTree(string, string);
27 void createNewickFile(string);
29 void setIndex(string, int);
30 int getNumNodes() { return numNodes; }
31 int getNumLeaves(){ return numLeaves; }
32 map<string, int> mergeUserGroups(int, vector<string>); //returns a map with a groupname and the number of times that group was seen in the children
35 void printForBoot(ostream&);
36 int findRoot(); //return index of root node
38 //this function takes the leaf info and populates the non leaf nodes
41 vector<Node> tree; //the first n nodes are the leaves, where n is the number of sequences.
43 GlobalData* globaldata;
44 int numNodes, numLeaves;
48 map<string, int>::iterator it, it2;
49 map<string, int> mergeGroups(int); //returns a map with a groupname and the number of times that group was seen in the children
51 map<string,int> mergeGcounts(int);
52 void randomTopology();
53 void randomBlengths();
54 void randomLabels(vector<string>);
55 void randomLabels(string, string);
56 void printBranch(int, ostream&, string); //recursively print out tree
57 void parseTreeFile(); //parses through tree file to find names of nodes and number of them
58 //this is required in case user has sequences in the names file that are
59 //not included in the tree.
60 //only takes names from the first tree in the tree file and assumes that all trees use the same names.
61 void readTreeString(ifstream&);