+++ /dev/null
-#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