created mothurOut class to handle logfiles

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index d6a3b556f09ca251a2cbad64e07c0187dd50e6b4..04d9fb1fd3499cd87b5a8563b6e082fddb3d32dd 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -10,18 +10,16 @@
  *
  */
 
-using namespace std;
-
 #include "treenode.h"
 #include "globaldata.hpp"
 
+class GlobalData;
 /* This class represents the treefile. */
 
 class Tree {
 public: 
        Tree();         //to generate a tree from a file
-       ~Tree() {};
-       
+       ~Tree();
        
        void getCopy(Tree*);  //makes tree a copy of the one passed in.
        void assembleRandomTree();
@@ -34,11 +32,15 @@ public:
        int getNumLeaves(){     return numLeaves; }
        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();            
+       void assembleTree();    
        
        vector<Node> tree;              //the first n nodes are the leaves, where n is the number of sequences.
+               
 private:
        GlobalData* globaldata;
        int numNodes, numLeaves;
@@ -47,14 +49,21 @@ private:
        
        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);
        
-       map<string,int> Tree::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);  //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