#include "mothur.h"
#include "command.hpp"
-#include "filterseqscommand.h"
-#include "sequence.hpp"
-#include "sparsematrix.hpp"
-#include "dist.h"
-
-typedef list<PCell>::iterator MatData;
-typedef map<int, float> SeqMap; //maps sequence to all distance for that seqeunce
/***********************************************************/
int execute();
void help();
+
private:
- //Dist* distCalculator;
-
- struct Preference {
- string leftParent;
- string rightParent;
- float score;
-
- };
-
- Dist* distCalculator;
- bool abort;
- string method, fastafile;
- bool filter, correction;
- int processors, midpoint;
- FilterSeqsCommand* filterSeqs;
- vector<Sequence> seqs;
- vector<Preference> pref;
-
- int findAverageMidPoint();
- void readSeqs();
- void generatePreferences(SparseMatrix*, SparseMatrix*);
- int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
-
};