Skip to content
This repository
tree: 9c52c8b751
Fetching contributors…

Octocat-spinner-32-eaf2f5

Cannot retrieve contributors at this time

file 56 lines (45 sloc) 1.349 kb
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55
#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 getOutputFileNameTag(string, string);
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
Something went wrong with that request. Please try again.