Revert to previous commit

[mothur.git] / getsabundcommand.h

diff --git a/getsabundcommand.h b/getsabundcommand.h
new file mode 100644 (file)
index 0000000..5be00df
--- /dev/null
+++ b/getsabundcommand.h
@@ -0,0 +1,47 @@
+#ifndef GETSABUNDCOMMAND_H
+#define GETSABUNDCOMMAND_H
+
+/*
+ *  getsabundcommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 6/2/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "sabundvector.hpp"
+
+class GetSAbundCommand : public Command {
+public:
+       GetSAbundCommand(string);
+       GetSAbundCommand();
+       ~GetSAbundCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.sabund";                          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.sabund"; }
+       string getDescription()         { return "creates a sabund file"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       string filename, format, inputfile, listfile, rabundfile, outputDir;
+       ofstream out;
+       InputData* input;
+       SAbundVector* sabund;
+       vector<string> outputNames;
+
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string label;
+
+};
+
+#endif