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[mothur.git] / phylotypecommand.h

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+#ifndef PHYLOTYPECOMMAND_H
+#define PHYLOTYPECOMMAND_H
+
+
+/*
+ *  phylotypecommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/20/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "taxonomyequalizer.h"
+#include "command.hpp"
+
+/*************************************************************************/
+
+class PhylotypeCommand : public Command {
+       
+public:
+       PhylotypeCommand(string);       
+       PhylotypeCommand();
+       ~PhylotypeCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "phylotype";           }
+       string getCommandCategory()             { return "Clustering";          }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
+       string getDescription()         { return "cluster your sequences into OTUs based on their classifications"; }
+
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }
+       
+private:
+       bool abort, allLines;
+       string taxonomyFileName, label, outputDir, namefile;
+       set<string> labels; //holds labels to be used
+       int cutoff;
+       map<string, string> namemap;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+       
+       map<int, int> currentNodes;
+       map<int, int> parentNodes;
+       map<int, int>::iterator itCurrent;
+       
+       int readNamesFile();
+
+};
+
+
+/*************************************************************************/
+
+
+#endif
+
+
+