*
*/
+/* The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name. */
#include "command.hpp"
#include "inputdata.h"
#include "listvector.hpp"
-#include "readmatrix.hpp"
#include "fastamap.h"
-
-
-class GlobalData;
+#include "groupmap.h"
+#include "counttable.h"
class BinSeqCommand : public Command {
public:
- BinSeqCommand();
+ BinSeqCommand(string);
+ BinSeqCommand();
~BinSeqCommand();
- int execute();
+
+ vector<string> setParameters();
+ string getCommandName() { return "bin.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
+ string getDescription() { return "maps sequences to otus"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
+ CountTable ct;
ListVector* list;
- ReadMatrix* read;
InputData* input;
FastaMap* fasta;
- string filename, fastafile, namesfile;
+ GroupMap* groupMap;
+ bool abort, allLines;
+ set<string> labels; //holds labels to be used
+ string filename, fastafile, listfile, namesfile, groupfile, countfile, label, outputDir;
ofstream out;
ifstream in, inNames;
+ vector<string> outputNames;
void readNamesFile();
+ int process(ListVector*);
};
#endif