#include "command.hpp"
#include "fastamap.h"
-#include "globaldata.hpp"
-/* The deconvolute command reads a fasta file, finds the duplicate sequences and outputs a names file
+/* The unique.seqs command reads a fasta file, finds the duplicate sequences and outputs a names file
containing 2 columns. The first being the groupname and the second the list of identical sequence names. */
-using namespace std;
class DeconvoluteCommand : public Command {
public:
- DeconvoluteCommand() {};
- ~DeconvoluteCommand() { delete fastamap; };
- int execute();
+ DeconvoluteCommand(string);
+ DeconvoluteCommand();
+ ~DeconvoluteCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "unique.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; }
+ string getDescription() { return "creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- GlobalData* globaldata;
- FastaMap* fastamap;
- ifstream in;
- ofstream out, outFasta;
- string filename, outputFileName, outFastafile;
+ string inFastaName, oldNameMapFName, outputDir;
+ vector<string> outputNames;
+ bool abort;
};
#endif