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[mothur.git] / parselistscommand.h

diff --git a/parselistscommand.h b/parselistscommand.h
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+#ifndef PARSELISTCOMMAND_H
+#define PARSELISTCOMMAND_H
+/*
+ *  parselistcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 2/24/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "groupmap.h"
+#include "inputdata.h"
+#include "listvector.hpp"
+
+/***************************************************************************************/
+
+class ParseListCommand : public Command {
+       
+public:
+       ParseListCommand(string);
+       ParseListCommand();     
+       ~ParseListCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "parse.list";                          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Parse.list"; }
+       string getDescription()         { return "parses a list file by group"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       int parse(ListVector*);
+               
+       ListVector* list;
+       GroupMap* groupMap;
+       InputData* input;
+       
+       ofstream out;
+       string outputDir, listfile, groupfile, label;
+       set<string> labels;
+       bool abort, allLines;
+       vector<string> outputNames;
+       
+       map<string, ofstream*> filehandles;
+       map<string, ofstream*>::iterator it3;
+
+};
+
+/***************************************************************************************/
+
+#endif
+