X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.h;h=635e53fe455ab05eacdb2a19e09837b30ef4c955;hb=163b300cfd7d4ca4e70c454be20f07b1d8346650;hp=b9b208493f2f6fea9a35055c448b65973ddc6a46;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index b9b2084..635e53f 100644
--- 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