added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 8b77d3ddbed48dddb5de57dfa44394118c7a1920..2d9d4f815f90bd889c10b886853ca415840060f5 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -10,20 +10,19 @@
  *
  */
 
-using namespace std;
-
 #include "treenode.h"
-#include "globaldata.hpp"
-
+#include "treemap.h"
 /* This class represents the treefile. */
 
 class Tree {
 public: 
-       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();
        
-       
        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.
        void assembleRandomTree();
        void assembleRandomUnifracTree(vector<string>);
        void assembleRandomUnifracTree(string, string);
@@ -35,28 +34,42 @@ public:
        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 printForBoot(ostream&);
+       void print(ostream&, string);
+       int findRoot();  //return index of root node
        
        //this function takes the leaf info and populates the non leaf nodes
-       void assembleTree();            
+       int assembleTree();     
+       int assembleTree(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:
-       GlobalData* globaldata;
+       TreeMap* tmap;
        int numNodes, numLeaves;
        ofstream out;
        string filename;
        
        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();
        void randomTopology();
        void randomBlengths();
        void randomLabels(vector<string>);
-       void randomLabels(string, string);
-       int findRoot();  //return index of root node
+       //void randomLabels(string, string);
        void printBranch(int, ostream&, string);  //recursively print out tree
+       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