deconvolute command

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
new file mode 100644 (file)
index 0000000..6b05704
--- /dev/null
+++ b/deconvolutecommand.h
@@ -0,0 +1,40 @@
+#ifndef DECONVOLUTECOMMAND_H
+#define DECONVOLUTECOMMAND_H
+/*
+ *  deconvolute.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 1/21/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#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
+       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();  
+       
+private:
+       GlobalData* globaldata;
+       FastaMap* fastamap;
+       ifstream in;
+       ofstream out;
+       string filename, outputFileName;
+
+};
+
+#endif
\ No newline at end of file