*
*/
-using namespace std;
-
#include "treenode.h"
#include "globaldata.hpp"
+class GlobalData;
/* This class represents the treefile. */
class Tree {
Tree(); //to generate a tree from a file
~Tree();
-
void getCopy(Tree*); //makes tree a copy of the one passed in.
void assembleRandomTree();
void assembleRandomUnifracTree(vector<string>);
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
void printTree();
void print(ostream&);
+ void printForBoot(ostream&);
+ int findRoot(); //return index of root node
//this function takes the leaf info and populates the non leaf nodes
- void assembleTree();
+ int assembleTree();
vector<Node> tree; //the first n nodes are the leaves, where n is the number of sequences.
+
private:
GlobalData* globaldata;
int numNodes, numLeaves;
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);
- int findRoot(); //return index of root node
- void printBranch(int, ostream&); //recursively print out tree
+ //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&);
+ MothurOut* m;
+
};
#endif