X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=0660e8a181632ae09668d1484236276e5898ed39;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=a5259552d8fa09f18d1e81b1776ef94f84724748;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git

diff --git a/tree.h b/tree.h
index a525955..0660e8a 100644
--- a/tree.h
+++ b/tree.h
@@ -11,20 +11,26 @@
  */
 
 #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(TreeMap*, vector< vector<double> >&); //create tree from sim matrix
 	~Tree();
 	
+    TreeMap* getTreeMap() { return tmap; }
 	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.
+    int getSubTree(Tree* originalToCopy, vector<string> seqToInclude, map<string, string> nameMap);  //used with (int, TreeMap) constructor. SeqsToInclude contains subsample wanted - assumes these are unique seqs and size of vector=numLeaves passed into constructor. nameMap is unique -> redundantList can be empty if no namesfile was provided. 
+    
 	void assembleRandomTree();
 	void assembleRandomUnifracTree(vector<string>);
 	void assembleRandomUnifracTree(string, string);
+    
 	void createNewickFile(string);
 	int getIndex(string);
 	void setIndex(string, int);
@@ -33,33 +39,44 @@ 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);
+    void print(ostream&, map<string, string>);
 	int findRoot();  //return index of root node
 	
 	//this function takes the leaf info and populates the non leaf nodes
-	void assembleTree();		
+	int assembleTree(map<string, 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;
 	
+    map<string, string> names;
 	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(map<string, string>);
 	void randomTopology();
 	void randomBlengths();
 	void randomLabels(vector<string>);
-	void randomLabels(string, string);
-	void printBranch(int, ostream&, string);  //recursively print out tree
+	//void randomLabels(string, string);
+	void printBranch(int, ostream&, map<string, string>);  //recursively print out tree
+    void printBranch(int, ostream&, string);
 	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&);
+	int readTreeString(ifstream&);
+	int populateNewTree(vector<Node>&, int, int&);
+	void printBranch(int, ostream&, string, vector<Node>&);
+		
+	MothurOut* m;
+		
 };
 
 #endif