adding treeclimber and unifrac pieces

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 872283dc95cccd5ba8cc3ea7faef058048bc4418..2ef8b23e94d0ad3921456c75518294c464a7ec0a 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -15,33 +15,50 @@ using namespace std;
 #include <string>
 #include <iostream>
 #include <vector>
+#include <fstream>
+#include <iomanip>
+#include <sstream>
+#include <map>
+
 #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