This is v.1.4.0

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index b9b208493f2f6fea9a35055c448b65973ddc6a46..635e53fe455ab05eacdb2a19e09837b30ef4c955 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -9,32 +9,25 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
-#include "utilities.hpp"
 #include "fastamap.h"
-#include "globaldata.hpp"
 
-/* The deconvolute command reads a fasta file, finds the duplicate sequences and outputs a names file
+/* The unique.seqs command reads a fasta file, finds the duplicate sequences and outputs a names file
        containing 2 columns.  The first being the groupname and the second the list of identical sequence names. */ 
 
-using namespace std;
 
 class DeconvoluteCommand : public Command {
 
 public:
-       DeconvoluteCommand() {};        
-       ~DeconvoluteCommand() { delete fastamap; };
-       int execute();  
+       DeconvoluteCommand(string);     
+       ~DeconvoluteCommand() { };
+       int execute();
+       void help();    
        
 private:
-       GlobalData* globaldata;
-       FastaMap* fastamap;
-       ifstream in;
-       ofstream out;
-       string filename, outputFileName;
+       string inFastaName, oldNameMapFName;
 
+       bool abort;
 };
 
 #endif