X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;fp=tree.h;h=0660e8a181632ae09668d1484236276e5898ed39;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/tree.h b/tree.h
new file mode 100644
index 0000000..0660e8a
--- /dev/null
+++ b/tree.h
@@ -0,0 +1,82 @@
+#ifndef TREE_H
+#define TREE_H
+
+/*
+ *  tree.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 1/22/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "treenode.h"
+#include "treemap.h"
+/* This class represents the treefile. */
+
+class 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, 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);
+	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(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:
+	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&, 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.
+	int readTreeString(ifstream&);
+	int populateNewTree(vector<Node>&, int, int&);
+	void printBranch(int, ostream&, string, vector<Node>&);
+		
+	MothurOut* m;
+		
+};
+
+#endif