1 #ifndef BINSEQCOMMAND_H
2 #define BINSEQCOMMAND_H
7 * Created by Sarah Westcott on 4/3/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 /* The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name. */
14 #include "command.hpp"
15 #include "inputdata.h"
16 #include "listvector.hpp"
24 class BinSeqCommand : public Command {
27 BinSeqCommand(string);
30 vector<string> getRequiredParameters();
31 vector<string> getValidParameters();
32 vector<string> getRequiredFiles();
33 map<string, vector<string> > getOutputFiles() { return outputTypes; }
38 GlobalData* globaldata;
45 set<string> labels; //holds labels to be used
46 string filename, fastafile, namesfile, groupfile, label, outputDir;
49 vector<string> outputNames;
50 map<string, vector<string> > outputTypes;
53 int process(ListVector*);