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[mothur.git] / binsequencecommand.h

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+#ifndef BINSEQCOMMAND_H
+#define BINSEQCOMMAND_H
+/*
+ *  binsequencecommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 4/3/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+/* The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name. */
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "listvector.hpp"
+#include "fastamap.h"
+#include "groupmap.h"
+
+class BinSeqCommand : public Command {
+       
+public:
+       BinSeqCommand(string);  
+       BinSeqCommand();
+       ~BinSeqCommand();
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "bin.seqs";                    }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
+       string getDescription()         { return "maps sequences to otus"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
+       
+private:
+       
+       ListVector* list;
+       InputData* input;
+       FastaMap* fasta;
+       GroupMap* groupMap;
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string filename, fastafile, listfile, namesfile, groupfile, label, outputDir;
+       ofstream out;
+       ifstream in, inNames;
+       vector<string> outputNames;
+       
+       void readNamesFile();
+       int process(ListVector*);
+};
+
+#endif