fixed parsimony for groups

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 9dee24d2eec051428b9cbb977042a91195cca5f5..55d3c92aabca1083fd300896a813f41374eca860 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -12,43 +12,48 @@
 
 using namespace std;
 
-#include <string>
-#include <iostream>
-#include <vector>
-
-struct Node  {
-               string  name;
-               string  group;
-               float   branchLength;
-               Node*   parent;
-               Node*   lchild;
-               Node*   rchild;
-};             
-
+#include "treenode.h"
+#include "globaldata.hpp"
 
+/* This class represents the treefile. */
 
 class Tree {
        public: 
-               Tree();
-               ~Tree();
+               Tree();         //to generate a tree from a file
+               ~Tree() {};
                
-               Node* getParent(Node);
-               Node* getLChild(Node);
-               Node* getRChild(Node);
                
-               void setParent(Node);
-               void setLChild(Node);
-               void setRChild(Node);
+               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; }
+               map<string, int> mergeUserGroups(int);  //returns a map with a groupname and the number of times that group was seen in the children
                
+               //this function takes the leaf info and populates the non leaf nodes
+               void assembleTree();            
                
-               Tree generateRandomTree();
-               
-               vector<Node> leaves;            //gives you easy access to the leaves of the tree to generate the parsimony score
+               vector<Node> tree;              //the first n nodes are the leaves, where n is the number of sequences.
                
        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> Tree::mergeGcounts(int);
+               void randomTopology();
+               void randomBlengths();
+               void randomLabels();
+               int findRoot();  //return index of root node
+               void printBranch(int);  //recursively print out tree
+               void setGroups();
 };
 
-
-
-
-#endif
\ No newline at end of file
+#endif