X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=tree.h;h=c8e8478edb8f313ab16d4dbeebf0a3d60a0a2698;hp=b0ae873a0b5ac0c5d364e4d6a9cdc3b5a6a877a7;hb=615301e57c25e241356a9c2380648d117709458d;hpb=5a3592c6478d5d786ec20e4bee71854ad92fdb8c

diff --git a/tree.h b/tree.h
index b0ae873..c8e8478 100644
--- a/tree.h
+++ b/tree.h
@@ -10,52 +10,75 @@
  *
  */
 
-using namespace std;
-
 #include "treenode.h"
-#include "globaldata.hpp"
-
+#include "counttable.h"
 /* This class represents the treefile. */
 
 class Tree {
 public: 
-	Tree();		//to generate a tree from a file
-	~Tree() {};
-	
+	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();
+	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);  //returns a map with a groupname and the number of times that group was seen in the children
+	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
-	void assembleTree();		
+	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:
-	GlobalData* globaldata;
+	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
 	
-	map<string,int> Tree::mergeGcounts(int);
+	void addNamesToCounts(map<string, string>);
 	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&, 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>&);
+		
+	MothurOut* m;
+		
 };
 
 #endif