added tree reader class to handle reading trees. Reworked the tree map to tree class...

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 0b61c6e5db4e2eb09638aa44d6b84ccbb07ce1c8..0660e8a181632ae09668d1484236276e5898ed39 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -22,6 +22,7 @@ public:
     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. 
@@ -39,11 +40,11 @@ public:
        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();     
-       int assembleTree(string);       
+       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.
@@ -54,6 +55,7 @@ private:
        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);
@@ -63,7 +65,8 @@ private:
        void randomBlengths();
        void randomLabels(vector<string>);
        //void randomLabels(string, string);
-       void printBranch(int, ostream&, string);  //recursively print out tree
+       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.