8 * Created by Sarah Westcott on 1/22/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
15 /* This class represents the treefile. */
19 Tree(string); //do not use tree generated by this constructor its just to extract the treenames, its a chicken before the egg thing that needs to be revisited.
21 Tree(TreeMap*); //to generate a tree from a file
22 Tree(TreeMap*, vector< vector<double> >&); //create tree from sim matrix
25 TreeMap* getTreeMap() { return tmap; }
26 void getCopy(Tree*); //makes tree a copy of the one passed in.
27 void getSubTree(Tree*, vector<string>); //makes tree a that contains only the names passed in.
28 int getSubTree(Tree* originalToCopy, vector<string> seqToInclude, map<string, string> nameMap); //used with (int, TreeMap) constructor. SeqsToInclude contains subsample wanted - assumes these are unique seqs and size of vector=numLeaves passed into constructor. nameMap is unique -> redundantList can be empty if no namesfile was provided.
30 void assembleRandomTree();
31 void assembleRandomUnifracTree(vector<string>);
32 void assembleRandomUnifracTree(string, string);
34 void createNewickFile(string);
36 void setIndex(string, int);
37 int getNumNodes() { return numNodes; }
38 int getNumLeaves(){ return numLeaves; }
39 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
42 void print(ostream&, string);
43 void print(ostream&, map<string, string>);
44 int findRoot(); //return index of root node
46 //this function takes the leaf info and populates the non leaf nodes
47 int assembleTree(map<string, string>);
49 vector<Node> tree; //the first n nodes are the leaves, where n is the number of sequences.
50 map< string, vector<int> > groupNodeInfo; //maps group to indexes of leaf nodes with that group, different groups may contain same node because of names file.
54 int numNodes, numLeaves;
58 map<string, string> names;
59 map<string, int>::iterator it, it2;
60 map<string, int> mergeGroups(int); //returns a map with a groupname and the number of times that group was seen in the children
61 map<string,int> mergeGcounts(int);
63 void addNamesToCounts(map<string, string>);
64 void randomTopology();
65 void randomBlengths();
66 void randomLabels(vector<string>);
67 //void randomLabels(string, string);
68 void printBranch(int, ostream&, map<string, string>); //recursively print out tree
69 void printBranch(int, ostream&, string);
70 void parseTreeFile(); //parses through tree file to find names of nodes and number of them
71 //this is required in case user has sequences in the names file that are
72 //not included in the tree.
73 //only takes names from the first tree in the tree file and assumes that all trees use the same names.
74 int readTreeString(ifstream&);
75 int populateNewTree(vector<Node>&, int, int&);
76 void printBranch(int, ostream&, string, vector<Node>&);