added subsample and consensus parameters to unifrac.weighted command

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 2d9d4f815f90bd889c10b886853ca415840060f5..0b61c6e5db4e2eb09638aa44d6b84ccbb07ce1c8 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -19,13 +19,17 @@ 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();
        
        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. 
+    
        void assembleRandomTree();
        void assembleRandomUnifracTree(vector<string>);
        void assembleRandomUnifracTree(string, string);
+    
        void createNewickFile(string);
        int getIndex(string);
        void setIndex(string, int);
@@ -54,7 +58,7 @@ private:
        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 addNamesToCounts(map<string, string>);
        void randomTopology();
        void randomBlengths();
        void randomLabels(vector<string>);