X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.h;h=9c8fd22d702f8a8b98ee12d682d6f880e5c1fb0e;hb=19b2ab858fcf2684213f741a0e7ac9c727f06362;hp=6b05704c693ec902f5ed4bae6e79233e99f5b1cd;hpb=67b6343929b6dbed97c4b26c3bb849725d573f6d;p=mothur.git

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 6b05704..9c8fd22 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, outputDir;
 
+	bool abort;
 };
 
-#endif
\ No newline at end of file
+#endif