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

[mothur.git] / subsample.h

diff --git a/subsample.h b/subsample.h
index ef5c389a938820a61201d83629efc6b27c5237d8..feca37eddbfbf42cd4d7674adea5a18ceed3acee 100644 (file)
--- a/subsample.h
+++ b/subsample.h
@@ -25,8 +25,8 @@ class SubSample {
     
         vector<string> getSample(vector<SharedRAbundVector*>&, int); //returns the bin labels for the subsample, mothurOuts binlabels are preserved so you can run this multiple times. Overwrites original vector passed in, if you need to preserve it deep copy first.
         
-        Tree* getSample(Tree*, TreeMap*, map<string, string>, int); //creates new subsampled tree, destroys treemap so copy if needed.
-        Tree* getSample(Tree*, TreeMap*, map<string, string>, int, map<string, string>); //creates new subsampled tree, destroys treemap so copy if needed.
+        //Tree* getSample(Tree*, TreeMap*, map<string, string>, int); //creates new subsampled tree, destroys treemap so copy if needed.
+        Tree* getSample(Tree*, TreeMap*, TreeMap*, int, map<string, string>); //creates new subsampled tree. Uses first treemap to fill new treemap with sabsampled seqs. Sets groups of seqs not in subsample to "doNotIncludeMe".
     
     private:
     
@@ -35,6 +35,7 @@ class SubSample {
     
         vector<string> getSample(TreeMap*, vector<string>);
         vector<string> getSample(TreeMap*, int); //names of seqs to include in sample tree 
+        vector<string> getSample(TreeMap* tMap, int size, map<string, vector<string> >& sample); //sample maps group -> seqs in group. seqs not in sample are in doNotIncludeMe group
         map<string, string> deconvolute(map<string, string> wholeSet, vector<string>& subsampleWanted); //returns new nameMap containing only subsampled names, and removes redundants from subsampled wanted because it makes the new nameMap.