- private:
- GlobalData* globaldata;
- int findRoot(); //return index of root node
- void printBranch(int); //recursively print out tree
- int numNodes, numLeaves;
- ofstream out;
- string filename;
+private:
+ GlobalData* globaldata;
+ int numNodes, numLeaves;
+ ofstream out;
+ string filename;
+
+ map<string, int>::iterator it, it2;
+ map<string, int> mergeGroups(int); //returns a map with a groupname and the number of times that group was seen in the children
+ map<string,int> mergeGcounts(int);
+
+ void addNamesToCounts();
+ void randomTopology();
+ void randomBlengths();
+ void randomLabels(vector<string>);
+ //void randomLabels(string, string);
+ void printBranch(int, ostream&, string); //recursively print out tree
+ void parseTreeFile(); //parses through tree file to find names of nodes and number of them
+ //this is required in case user has sequences in the names file that are
+ //not included in the tree.
+ //only takes names from the first tree in the tree file and assumes that all trees use the same names.
+ int readTreeString(ifstream&);
+