added heatmap.sim command and changed heatmap to heatmap.bin

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 733f3a082a87525dc1db339ccd5f983b9f2c4206..4f77e50578bad8c234ae4711adf69a612175b088 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -10,8 +10,6 @@
  *
  */
 
-using namespace std;
-
 #include "treenode.h"
 #include "globaldata.hpp"
 
@@ -20,12 +18,12 @@ using namespace std;
 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();
-       void assembleRandomUnifracTree();
+       void assembleRandomUnifracTree(vector<string>);
        void assembleRandomUnifracTree(string, string);
        void createNewickFile(string);
        int getIndex(string);
@@ -34,6 +32,9 @@ 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();            
@@ -48,14 +49,12 @@ 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> Tree::mergeGcounts(int);
+       map<string,int> mergeGcounts(int);
        void randomTopology();
        void randomBlengths();
-       void randomLabels();
+       void randomLabels(vector<string>);
        void randomLabels(string, string);
-       int findRoot();  //return index of root node
-       void printBranch(int);  //recursively print out tree
-       void setGroups();
+       void printBranch(int, ostream&, string);  //recursively print out tree
 };
 
 #endif