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

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
index b924775cf5b30436c1783714a758281cf072c32f..45e377c3cbe1ac1ad735cd9c4f47d4c4c37c30a5 100644 (file)
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -13,6 +13,7 @@
 #include "command.hpp"
 #include "listvector.hpp"
 #include "inputdata.h"
+#include "counttable.h"
 
 
 class ClassifyOtuCommand : public Command {
@@ -34,10 +35,11 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
 
 private:
-
+    GroupMap* groupMap;
+    CountTable* ct;
        ListVector* list;
        InputData* input;
-       string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
+       string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis, countfile;
        bool abort, allLines, probs;
        int cutoff;
        set<string> labels; //holds labels to be used