changes to blastdb to make filenames given to blast unique, changes to split.abund...

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index a076cef8eb30e3cda0efd8d74fcb680ae007cb24..99cd68fa7f4b71dfeebffc90ad649a1f01c6564e 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -37,7 +37,7 @@ public:
        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.
                
@@ -55,13 +55,18 @@ private:
        void randomTopology();
        void randomBlengths();
        void randomLabels(vector<string>);
-       void randomLabels(string, string);
+       //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&);
+       string readLabel(ifstream&);
+       string readName(ifstream&);
+       string readBranchLength(ifstream&);
+       
+       MothurOut* m;
        
 };