forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / subsample.h

diff --git a/subsample.h b/subsample.h
index 09c7dcdf0901f8a229ee3c89633ca1186d03a7ef..feca37eddbfbf42cd4d7674adea5a18ceed3acee 100644 (file)
--- a/subsample.h
+++ b/subsample.h
@@ -11,6 +11,8 @@
 
 #include "mothurout.h"
 #include "sharedrabundvector.h"
+#include "treemap.h"
+#include "tree.h"
 
 //subsampling overwrites the sharedRabunds.  If you need to reuse the original use the getSamplePreserve function.
 
@@ -22,12 +24,20 @@ class SubSample {
         ~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*, 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:
     
         MothurOut* m;
         int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+    
+        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.
+
 
 };