using namespace std;
-#include <string>
-#include <iostream>
-#include <vector>
#include "treenode.h"
#include "globaldata.hpp"
/* This class represents the treefile. */
-
-
class Tree {
public:
- Tree();
+ Tree(); //to generate a tree from a file
~Tree() {};
- Tree generateRandomTree();
+
+ void getCopy(Tree*); //makes tree a copy of the one passed in.
+ void assembleRandomTree();
+ void assembleRandomUnifracTree();
void createNewickFile();
int getIndex(string);
void setIndex(string, int);
int getNumNodes() { return numNodes; }
- int getNumLeaves(){ return numLeaves;}
+ int getNumLeaves(){ return numLeaves; }
+
+ //this function takes the leaf info and populates the non leaf nodes
+ void assembleTree();
+
vector<Node> tree; //the first n nodes are the leaves, where n is the number of sequences.
private:
GlobalData* globaldata;
- int findRoot(); //return index of root node
- void printBranch(int); //recursively print out tree
int numNodes, numLeaves;
ofstream out;
string filename;
+
+ map<string, int>::iterator it;
+ 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> Tree::mergeGcounts(int);
+ void randomTopology();
+ void randomBlengths();
+ void randomLabels();
+ int findRoot(); //return index of root node
+ void printBranch(int); //recursively print out tree
};
#endif