public:
RemoveSeqsCommand(string);
- ~RemoveSeqsCommand(){};
- int execute();
- void help();
+ RemoveSeqsCommand();
+ ~RemoveSeqsCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "remove.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
+ string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+
private:
set<string> names;
- string accnosfile, fastafile, namefile, groupfile, alignfile, listfile;
- bool abort;
+ string accnosfile, fastafile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
+ bool abort, dups;
+ vector<string> outputNames;
+ map<string, string> uniqueMap;
- void readFasta();
- void readName();
- void readGroup();
- void readAlign();
- void readAccnos();
- void readList();
+ int readFasta();
+ int readName();
+ int readGroup();
+ int readCount();
+ int readAlign();
+ int readList();
+ int readTax();
+ int readQual();
};