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