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. */
22 Tree(); //to generate a tree from a file
25 void getCopy(Tree*); //makes tree a copy of the one passed in.
26 void assembleRandomTree();
27 void assembleRandomUnifracTree(vector<string>);
28 void assembleRandomUnifracTree(string, string);
29 void createNewickFile(string);
31 void setIndex(string, int);
32 int getNumNodes() { return numNodes; }
33 int getNumLeaves(){ return numLeaves; }
34 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
37 void printForBoot(ostream&);
38 int findRoot(); //return index of root node
40 //this function takes the leaf info and populates the non leaf nodes
43 vector<Node> tree; //the first n nodes are the leaves, where n is the number of sequences.
47 GlobalData* globaldata;
48 int numNodes, numLeaves;
52 map<string, int>::iterator it, it2;
53 map<string, int> mergeGroups(int); //returns a map with a groupname and the number of times that group was seen in the children
54 map<string,int> mergeGcounts(int);
56 void addNamesToCounts();
57 void randomTopology();
58 void randomBlengths();
59 void randomLabels(vector<string>);
60 //void randomLabels(string, string);
61 void printBranch(int, ostream&, string); //recursively print out tree
62 void parseTreeFile(); //parses through tree file to find names of nodes and number of them
63 //this is required in case user has sequences in the names file that are
64 //not included in the tree.
65 //only takes names from the first tree in the tree file and assumes that all trees use the same names.
66 int readTreeString(ifstream&);