X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=deconvolutecommand.h;h=e514bdae70f7e0b51854b40baacf44d2b0174c8a;hp=6b05704c693ec902f5ed4bae6e79233e99f5b1cd;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=67b6343929b6dbed97c4b26c3bb849725d573f6d

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 6b05704..e514bda 100644
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -9,32 +9,40 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
-#include "utilities.hpp"
 #include "fastamap.h"
-#include "globaldata.hpp"
+#include "counttable.h"
 
-/* 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();
+	~DeconvoluteCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "unique.seqs";		}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+    
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; }
+	string getDescription()		{ return "creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
-	FastaMap* fastamap;
-	ifstream in;
-	ofstream out;
-	string filename, outputFileName;
+	string inFastaName, oldNameMapFName, outputDir, countfile;
+	vector<string> outputNames;
 
+	bool abort;
 };
 
-#endif
\ No newline at end of file
+#endif