added count file to get.oturep, pre.cluster, screen.seqs, tree.shared. made remove...

[mothur.git] / subsample.h

diff --git a/subsample.h b/subsample.h
index 09c7dcdf0901f8a229ee3c89633ca1186d03a7ef..55abed9adae227e72713a9b1ed083d5731dc3be2 100644 (file)
--- a/subsample.h
+++ b/subsample.h
@@ -11,6 +11,10 @@
 
 #include "mothurout.h"
 #include "sharedrabundvector.h"
+#include "treemap.h"
+#include "tree.h"
+#include "counttable.h"
+
 
 //subsampling overwrites the sharedRabunds.  If you need to reuse the original use the getSamplePreserve function.
 
@@ -22,12 +26,15 @@ 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*, CountTable*, CountTable*, int); //creates new subsampled tree. Uses first counttable to fill new counttable with sabsampled seqs. Sets groups of seqs not in subsample to "doNotIncludeMe".
+        int getSample(SAbundVector*&, int); //destroys sabundvector passed in, so copy it if you need it
     
     private:
     
         MothurOut* m;
         int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+         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.
+
 
 };