X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=tree.h;h=c8e8478edb8f313ab16d4dbeebf0a3d60a0a2698;hp=872283dc95cccd5ba8cc3ea7faef058048bc4418;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed

diff --git a/tree.h b/tree.h
index 872283d..c8e8478 100644
--- a/tree.h
+++ b/tree.h
@@ -10,38 +10,75 @@
  *
  */
 
-using namespace std;
-
-#include <string>
-#include <iostream>
-#include <vector>
 #include "treenode.h"
-#include "globaldata.hpp"
-
+#include "counttable.h"
 /* This class represents the treefile. */
 
-
-
 class Tree {
-	public: 
-		Tree();  
-		~Tree() {};
+public: 
+	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, CountTable*); 
+	Tree(CountTable*);		//to generate a tree from a file
+    Tree(CountTable*, vector< vector<double> >&); //create tree from sim matrix
+	~Tree();
+	
+    CountTable* getCountTable() { return ct; }
+	void getCopy(Tree*);  //makes tree a copy of the one passed in.
+    void getCopy(Tree* copy, bool); //makes a copy of the tree structure passed in, (just parents, children and br). Used with the Tree(TreeMap*) constructor. Assumes the tmap already has set seqs groups you want.  Used by subsample to reassign seqs you don't want included to group "doNotIncludeMe".
+	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);
+	int getNumNodes() { return numNodes; }
+	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);
+    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
+	int assembleTree();	
+	
+	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:
+	CountTable* ct;
+	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);
+    map<string, int> indexes; //maps seqName -> index in tree vector
+	
+	void addNamesToCounts(map<string, string>);
+	void randomTopology();
+	void randomBlengths();
+	void randomLabels(vector<string>);
+	//void randomLabels(string, string);
+	void printBranch(int, ostream&, map<string, string>);  //recursively print out tree
+    void printBranch(int, ostream&, string);
+	int 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>&);
 		
-		Tree generateRandomTree();
-		void createNewickFile();
-		int getIndex(string);
-		void setIndex(string, int);
-		int getNumNodes() { return numNodes; }
-		int getNumLeaves(){	return numLeaves;}
-		vector<Node> tree;		//the first n nodes are the leaves, where n is the number of sequences.
+	MothurOut* m;
 		
-	private:
-		GlobalData* globaldata;
-		int findRoot();  //return index of root node
-		void printBranch(int);  //recursively print out tree
-		int numNodes, numLeaves;
-		ofstream out;
-		string filename;
 };
 
 #endif