X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=99cd68fa7f4b71dfeebffc90ad649a1f01c6564e;hb=2a7d1455e8cfe4f67a7173f3a7249762c5436217;hp=8b77d3ddbed48dddb5de57dfa44394118c7a1920;hpb=c76b65598a0b85183126bd764c83f354e9f490d1;p=mothur.git

diff --git a/tree.h b/tree.h
index 8b77d3d..99cd68f 100644
--- 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>);
@@ -36,11 +34,13 @@ public:
 	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;
@@ -49,14 +49,25 @@ 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);
+	
+	void addNamesToCounts();
 	void randomTopology();
 	void randomBlengths();
 	void randomLabels(vector<string>);
-	void randomLabels(string, string);
-	int findRoot();  //return index of root node
+	//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&);
+	string readLabel(ifstream&);
+	string readName(ifstream&);
+	string readBranchLength(ifstream&);
+	
+	MothurOut* m;
+	
 };
 
 #endif