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

[mothur.git] / binsequencecommand.h

diff --git a/binsequencecommand.h b/binsequencecommand.h
index 1fb5664b0c018c4120881055014ec08a4e6d5559..5bdd401f9411e4abb21aa6a12284bfa98f4b5bda 100644 (file)
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -16,6 +16,7 @@
 #include "listvector.hpp"
 #include "fastamap.h"
 #include "groupmap.h"
+#include "counttable.h"
 
 class BinSeqCommand : public Command {
        
@@ -36,14 +37,14 @@ public:
        void help() { m->mothurOut(getHelpString()); }          
        
 private:
-       
+       CountTable ct;
        ListVector* list;
        InputData* input;
        FastaMap* fasta;
        GroupMap* groupMap;
        bool abort, allLines;
        set<string> labels; //holds labels to be used
-       string filename, fastafile, listfile, namesfile, groupfile, label, outputDir;
+       string filename, fastafile, listfile, namesfile, groupfile, countfile, label, outputDir;
        ofstream out;
        ifstream in, inNames;
        vector<string> outputNames;