fixed a bug in calculating the # of ambig bases

[mothur.git] / binsequencecommand.h

diff --git a/binsequencecommand.h b/binsequencecommand.h
index 25f52160e6c314e300e0abd6f303c378881cf2af..bc2f883fe5f3e232d935780f7660e5a53647b18b 100644 (file)
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -14,8 +14,9 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "listvector.hpp"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "fastamap.h"
+#include "groupmap.h"
 
 
 class GlobalData;
@@ -30,14 +31,16 @@ public:
 private:
        GlobalData* globaldata;
        ListVector* list;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        InputData* input;
        FastaMap* fasta;
-       string filename, fastafile, namesfile;
+       GroupMap* groupMap;
+       string filename, fastafile, namesfile, groupfile;
        ofstream out;
        ifstream in, inNames;
        
        void readNamesFile();
+       int process(ListVector*, int);
 };
 
 #endif