broke up globaldata and moved error checking and help into commands

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 4f77e50578bad8c234ae4711adf69a612175b088..b6d5ea807a38801a872daf96b23557d53a241f4e 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -20,7 +20,6 @@ public:
        Tree();         //to generate a tree from a file
        ~Tree();
        
-       
        void getCopy(Tree*);  //makes tree a copy of the one passed in.
        void assembleRandomTree();
        void assembleRandomUnifracTree(vector<string>);
@@ -55,6 +54,11 @@ private:
        void randomLabels(vector<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.
+       void readTreeString(ifstream&);
 };
 
 #endif