fixed path redirect issue in shhh.flows. optimized the subsampling in unifrac commands

[mothur.git] / tree.h

diff --git a/tree.h b/tree.h
index 40ae14f8615651693985b8f7249c4098cde7f07b..03da5f6841d9f30cef2f946d6c9ecbc1d5c58cc0 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -24,7 +24,7 @@ public:
        
     TreeMap* getTreeMap() { return tmap; }
        void getCopy(Tree*);  //makes tree a copy of the one passed in.
-    void getCopy(Tree* copy, map<string, string>, vector<string>); //makes a copy of the tree passed in, but everyone who is not in the vector<string> has group set to doNotIncludeMe. Assumes the tmap already has these seqs group set to doNotIncludeMe.
+    void getCopy(Tree* copy, map<string, string>); //makes a copy of the tree structure passed in, (just parents, children and br). Used with the Tree(TreeMap*) constructor. Assumes the tmap already has set seqs groups you want.  Used by subsample to reassign seqs you don't want included to group "doNotIncludeMe".
        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.