X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=tree.h;h=c8e8478edb8f313ab16d4dbeebf0a3d60a0a2698;hp=0660e8a181632ae09668d1484236276e5898ed39;hb=615301e57c25e241356a9c2380648d117709458d;hpb=f55cf350ca6643f8eb070d8336e1957699a3f109

diff --git a/tree.h b/tree.h
index 0660e8a..c8e8478 100644
--- a/tree.h
+++ b/tree.h
@@ -11,21 +11,22 @@
  */
 
 #include "treenode.h"
-#include "treemap.h"
+#include "counttable.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(int, CountTable*); 
+	Tree(CountTable*);		//to generate a tree from a file
+    Tree(CountTable*, vector< vector<double> >&); //create tree from sim matrix
 	~Tree();
 	
-    TreeMap* getTreeMap() { return tmap; }
+    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. 
+    //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>);
@@ -44,21 +45,22 @@ public:
 	int findRoot();  //return index of root node
 	
 	//this function takes the leaf info and populates the non leaf nodes
-	int assembleTree(map<string, string>);	
+	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:
-	TreeMap* tmap;
+	CountTable* ct;
 	int numNodes, numLeaves;
 	ofstream out;
 	string filename;
 	
-    map<string, string> names;
+    //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();
@@ -67,7 +69,7 @@ private:
 	//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
+	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.