8 * Created by Sarah Westcott on 1/22/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
14 #include "globaldata.hpp"
17 /* This class represents the treefile. */
21 Tree(); //to generate a tree from a file
24 void getCopy(Tree*); //makes tree a copy of the one passed in.
25 void assembleRandomTree();
26 void assembleRandomUnifracTree(vector<string>);
27 void assembleRandomUnifracTree(string, string);
28 void createNewickFile(string);
30 void setIndex(string, int);
31 int getNumNodes() { return numNodes; }
32 int getNumLeaves(){ return numLeaves; }
33 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
36 void printForBoot(ostream&);
37 int findRoot(); //return index of root node
39 //this function takes the leaf info and populates the non leaf nodes
42 vector<Node> tree; //the first n nodes are the leaves, where n is the number of sequences.
45 GlobalData* globaldata;
46 int numNodes, numLeaves;
50 map<string, int>::iterator it, it2;
51 map<string, int> mergeGroups(int); //returns a map with a groupname and the number of times that group was seen in the children
52 map<string,int> mergeGcounts(int);
54 void addNamesToCounts();
55 void randomTopology();
56 void randomBlengths();
57 void randomLabels(vector<string>);
58 //void randomLabels(string, string);
59 void printBranch(int, ostream&, string); //recursively print out tree
60 void parseTreeFile(); //parses through tree file to find names of nodes and number of them
61 //this is required in case user has sequences in the names file that are
62 //not included in the tree.
63 //only takes names from the first tree in the tree file and assumes that all trees use the same names.
64 int readTreeString(ifstream&);