X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=0b61c6e5db4e2eb09638aa44d6b84ccbb07ce1c8;hb=03dca3b32a903c3f29fbcf5b410b19d6ab6dae63;hp=0b316c3042f01cbb000a3aed975a778f8af5f9fc;hpb=1916dd65829d6bb5b8bef74eddc61ea38fccf63a;p=mothur.git

diff --git a/tree.h b/tree.h
index 0b316c3..0b61c6e 100644
--- a/tree.h
+++ b/tree.h
@@ -11,23 +11,25 @@
  */
 
 #include "treenode.h"
-#include "globaldata.hpp"
-
-class GlobalData;
+#include "treemap.h"
 /* This class represents the treefile. */
 
 class Tree {
 public: 
-	Tree(string); 
-	Tree(int); 
-	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();
 	
 	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);
@@ -47,7 +49,7 @@ public:
 	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;
@@ -56,7 +58,7 @@ private:
 	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();
+	void addNamesToCounts(map<string, string>);
 	void randomTopology();
 	void randomBlengths();
 	void randomLabels(vector<string>);