DeUniqueSeqsCommand(string);
DeUniqueSeqsCommand();
~DeUniqueSeqsCommand() {}
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+
+ vector<string> setParameters();
+ string getCommandName() { return "deunique.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Deunique.seqs"; }
+ string getDescription() { return "reverse of the unique.seqs command, and creates a fasta file from a fasta and name file"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
string fastaFile, nameFile, outputDir;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
bool abort;
map<string, string> nameMap;