X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=a5259552d8fa09f18d1e81b1776ef94f84724748;hb=cd37904452dc95b183ff313ff05720c562902487;hp=b0ae873a0b5ac0c5d364e4d6a9cdc3b5a6a877a7;hpb=5a3592c6478d5d786ec20e4bee71854ad92fdb8c;p=mothur.git

diff --git a/tree.h b/tree.h
index b0ae873..a525955 100644
--- a/tree.h
+++ b/tree.h
@@ -10,30 +10,31 @@
  *
  */
 
-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();
-	void assembleRandomUnifracTree();
+	void assembleRandomUnifracTree(vector<string>);
 	void assembleRandomUnifracTree(string, string);
 	void createNewickFile(string);
 	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
+	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 +49,17 @@ 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
+	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.
+	void readTreeString(ifstream&);
 };
 
 #endif