line and label no longer persist between commands. Added phylip formated output...

[mothur.git] / binsequencecommand.h

diff --git a/binsequencecommand.h b/binsequencecommand.h
index 22847dce9b45604515c97fab55a2673813324ec2..bc2f883fe5f3e232d935780f7660e5a53647b18b 100644 (file)
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -9,12 +9,14 @@
  *
  */
 
+/* The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name. */
 
 #include "command.hpp"
 #include "inputdata.h"
 #include "listvector.hpp"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "fastamap.h"
+#include "groupmap.h"
 
 
 class GlobalData;
@@ -29,14 +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