X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=0b316c3042f01cbb000a3aed975a778f8af5f9fc;hb=1916dd65829d6bb5b8bef74eddc61ea38fccf63a;hp=733f3a082a87525dc1db339ccd5f983b9f2c4206;hpb=5318771152ee5b1a280b3dc50aedd887dd1da8a8;p=mothur.git

diff --git a/tree.h b/tree.h
index 733f3a0..0b316c3 100644
--- a/tree.h
+++ b/tree.h
@@ -10,22 +10,23 @@
  *
  */
 
-using namespace std;
-
 #include "treenode.h"
 #include "globaldata.hpp"
 
+class GlobalData;
 /* This class represents the treefile. */
 
 class Tree {
 public: 
+	Tree(string); 
+	Tree(int); 
 	Tree();		//to generate a tree from a file
-	~Tree() {};
-	
+	~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();
+	void assembleRandomUnifracTree(vector<string>);
 	void assembleRandomUnifracTree(string, string);
 	void createNewickFile(string);
 	int getIndex(string);
@@ -34,11 +35,17 @@ 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 print(ostream&, string);
+	int findRoot();  //return index of root node
 	
 	//this function takes the leaf info and populates the non leaf nodes
-	void assembleTree();		
+	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;
 	int numNodes, numLeaves;
@@ -47,15 +54,24 @@ 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();
-	void randomLabels(string, string);
-	int findRoot();  //return index of root node
-	void printBranch(int);  //recursively print out tree
-	void setGroups();
+	void randomLabels(vector<string>);
+	//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&);
+	int populateNewTree(vector<Node>&, int, int&);
+	void printBranch(int, ostream&, string, vector<Node>&);
+		
+	MothurOut* m;
+		
 };
 
 #endif