public:
GetSeqsCommand(string);
- ~GetSeqsCommand(){};
- int execute();
- void help();
-
+ GetSeqsCommand();
+ ~GetSeqsCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "get.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
+ string getDescription() { return "gets sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+
private:
set<string> names;
vector<string> outputNames;
- string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
- bool abort;
+ string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+ bool abort, dups;
int readFasta();
int readName();
int readAccnos();
int readList();
int readTax();
+ int readQual();
+ int compareAccnos();
};