1 #ifndef REMOVESEQSCOMMAND_H 2 #define REMOVESEQSCOMMAND_H 3 4 /* 5 * removeseqscommand.h 6 * Mothur 7 * 8 * Created by Sarah Westcott on 7/8/09. 9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved. 10 * 11 */ 12 13 #include "command.hpp" 14 15 class RemoveSeqsCommand : public Command { 16 17 public: 18 19 RemoveSeqsCommand(string); 20 RemoveSeqsCommand(string, string dupsFile, string dupsFileType, string output); ~RemoveSeqsCommand()21 ~RemoveSeqsCommand(){} 22 23 vector<string> setParameters(); getCommandName()24 string getCommandName() { return "remove.seqs"; } getCommandCategory()25 string getCommandCategory() { return "Sequence Processing"; } 26 27 string getHelpString(); 28 string getOutputPattern(string); getCitation()29 string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; } getDescription()30 string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport, contigsreport, quality or taxonomy file"; } 31 32 int execute(); help()33 void help() { m->mothurOut(getHelpString()); } 34 35 private: 36 set<string> names; 37 string accnosfile, fastafile, fastqfile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, format, contigsreportfile; 38 bool abort, dups; 39 vector<string> outputNames; 40 map<string, string> uniqueMap; 41 42 void readFasta(); 43 void readFastq(); 44 void readName(); 45 void readGroup(); 46 void readCount(); 47 void readAlign(); 48 void readContigs(); 49 void readList(); 50 void readTax(); 51 void readQual(); 52 53 }; 54 55 #endif 56 57