X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=2d9d4f815f90bd889c10b886853ca415840060f5;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=23ddf5dd87ed6d901d8db793861e34cb92b43e2d;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/tree.h b/tree.h
index 23ddf5d..2d9d4f8 100644
--- a/tree.h
+++ b/tree.h
@@ -11,17 +11,18 @@
  */
 
 #include "treenode.h"
-#include "globaldata.hpp"
-
-class GlobalData;
+#include "treemap.h"
 /* This class represents the treefile. */
 
 class Tree {
 public: 
-	Tree();		//to generate a tree from a file
+	Tree(string);  //do not use tree generated by this constructor its just to extract the treenames, its a chicken before the egg thing that needs to be revisited.
+	Tree(int, TreeMap*); 
+	Tree(TreeMap*);		//to generate a tree from a file
 	~Tree();
 	
 	void getCopy(Tree*);  //makes tree a copy of the one passed in.
+	void getSubTree(Tree*, vector<string>);  //makes tree a that contains only the names passed in.
 	void assembleRandomTree();
 	void assembleRandomUnifracTree(vector<string>);
 	void assembleRandomUnifracTree(string, string);
@@ -33,16 +34,18 @@ 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&);
+	void print(ostream&, string);
 	int findRoot();  //return index of root node
 	
 	//this function takes the leaf info and populates the non leaf nodes
 	int assembleTree();	
+	int assembleTree(string);	
 	
 	vector<Node> tree;		//the first n nodes are the leaves, where n is the number of sequences.
-		
+	map< string, vector<int> > groupNodeInfo;	//maps group to indexes of leaf nodes with that group, different groups may contain same node because of names file.
+			
 private:
-	GlobalData* globaldata;
+	TreeMap* tmap;
 	int numNodes, numLeaves;
 	ofstream out;
 	string filename;
@@ -62,8 +65,11 @@ private:
 							//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&);
+	int populateNewTree(vector<Node>&, int, int&);
+	void printBranch(int, ostream&, string, vector<Node>&);
+		
 	MothurOut* m;
-	
+		
 };
 
 #endif