#include "mothur.h"
#include "command.hpp"
-#include "filterseqscommand.h"
-#include "sequence.hpp"
-
-
/***********************************************************/
class ChimeraSeqsCommand : public Command {
public:
ChimeraSeqsCommand(string);
+ ChimeraSeqsCommand() {}
~ChimeraSeqsCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map< string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
+
private:
- //Dist* distCalculator;
-
- struct Preference {
- string leftParent;
- string rightParent;
- float score;
-
- };
-
-
- bool abort;
- string method, fastafile;
- bool filter, correction;
- int processors, midpoint;
- FilterSeqsCommand* filterSeqs;
- vector<Sequence> seqs;
- vector<Preference> pref;
-
- int findAverageMidPoint();
- void readSeqs();
-
+ vector<string> outputNames;
+ map< string, vector<string> > outputTypes;
};