major change to the tree class to use the count table class instead of tree map....

[mothur.git] / subsample.h

diff --git a/subsample.h b/subsample.h
index b00f1a7141b49fb99a9683a58b96153c5986a6b7..55abed9adae227e72713a9b1ed083d5731dc3be2 100644 (file)
--- a/subsample.h
+++ b/subsample.h
@@ -13,6 +13,8 @@
 #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.
 
@@ -24,20 +26,14 @@ 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".
+        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*>&);
-    
-        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.
+         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.
 
 
 };