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[mothur.git] / catchallcommand.h

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+#ifndef CATCHALLCOMMAND_H
+#define CATCHALLCOMMAND_H
+
+/*
+ *  catchallcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 5/11/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "sabundvector.hpp"
+
+/* 
+ citation goes here
+ */ 
+
+/****************************************************************************/
+
+class CatchAllCommand : public Command {
+
+public:
+
+       CatchAllCommand(string);
+       CatchAllCommand();
+       ~CatchAllCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "catchall";                    }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "Bunge, J. (2011). Estimating the number of species with CatchAll. Forthcoming in Proceedings of the Pacific Symposium on Biocomputing 2011.\nhttp://www.northeastern.edu/catchall/index.html http://www.mothur.org/wiki/Catchall"; }
+       string getDescription()         { return "estimate number of species"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       string outputDir, sharedfile, sabundfile, format, path, savedOutputDir;
+       bool abort, allLines;
+       set<string> labels;
+       vector<string> outputNames;
+       vector<string> groups;
+       
+       string process(SAbundVector*, string);
+       int createSummaryFile(string, string, ofstream&); 
+       vector<string> parseSharedFile(string);
+       string combineSummmary(vector<string>&);
+};
+
+/****************************************************************************/
+
+#endif
+
+