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