added binary file operations to mothurout class. added comment to sequence class...

[mothur.git] / sracommand.h

diff --git a/sracommand.h b/sracommand.h
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+//
+//  sracommand.h
+//  Mothur
+//
+//  Created by SarahsWork on 10/28/13.
+//  Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#ifndef Mothur_sracommand_h
+#define Mothur_sracommand_h
+
+#include "command.hpp"
+
+
+/**************************************************************************************************/
+
+class SRACommand : public Command {
+public:
+    SRACommand(string);
+    SRACommand();
+    ~SRACommand(){}
+    
+    vector<string> setParameters();
+    string getCommandName()                    { return "sra";                 }
+    string getCommandCategory()                { return "Sequence Processing";         }
+    
+    string getOutputPattern(string);
+    
+       string getHelpString();
+    string getCitation() { return "http://www.mothur.org/wiki/sra"; }
+    string getDescription()            { return "create a Sequence Read Archive / SRA"; }
+    
+    int execute();
+    void help() { m->mothurOut(getHelpString()); }
+    
+private:
+    bool abort;
+    string sfffiles, fastqfiles, platform, outputDir;
+    vector<string> outputNames;
+};
+
+/**************************************************************************************************/
+
+
+
+#endif