added checks for ^C to quit command instead of program

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 58f3a792e9fbb22547765d9d238ffcabc1a77a01..23ddf5dd87ed6d901d8db793861e34cb92b43e2d 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -10,11 +10,10 @@
  *
  */
 
-using namespace std;
-
 #include "treenode.h"
 #include "globaldata.hpp"
 
+class GlobalData;
 /* This class represents the treefile. */
 
 class Tree {
@@ -22,7 +21,6 @@ public:
        Tree();         //to generate a tree from a file
        ~Tree();
        
-       
        void getCopy(Tree*);  //makes tree a copy of the one passed in.
        void assembleRandomTree();
        void assembleRandomUnifracTree(vector<string>);
@@ -35,11 +33,14 @@ public:
        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();            
+       int assembleTree();     
        
        vector<Node> tree;              //the first n nodes are the leaves, where n is the number of sequences.
+               
 private:
        GlobalData* globaldata;
        int numNodes, numLeaves;
@@ -48,14 +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, ostream&);  //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