#include "mothur.h"
#include "sequence.hpp"
-
+/***********************************************************************/
+struct data_struct {
+ float divr_qla_qrb;
+ float divr_qlb_qra;
+ float qla_qrb;
+ float qlb_qra;
+ float qla;
+ float qrb;
+ float ab;
+ float qa;
+ float qb;
+ float lab;
+ float rab;
+ float qra;
+ float qlb;
+ int winLStart;
+ int winLEnd;
+ int winRStart;
+ int winREnd;
+ Sequence querySeq;
+ Sequence parentA;
+ Sequence parentB;
+ float bsa;
+ float bsb;
+ float bsMax;
+ float chimeraMax;
+
+};
+/***********************************************************************/
+struct data_results {
+ vector<data_struct> results;
+ string flag;
+ map<int, int> spotMap;
+ Sequence trimQuery;
+
+ data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), spotMap(s), trimQuery(t) {}
+ data_results() {}
+};
+/***********************************************************************/
+//sorts lowest to highest first by bsMax, then if tie by chimeraMax
+inline bool compareDataStruct(data_struct left, data_struct right){
+ if (left.bsMax < right.bsMax) { return true; }
+ else if (left.bsMax == right.bsMax) {
+ return (left.chimeraMax < right.chimeraMax);
+ }else { return false; }
+}
/***********************************************************************/
struct Preference {
string name;
virtual void printHeader(ostream&){};
virtual int getChimeras(Sequence*){ return 0; }
virtual int getChimeras(){ return 0; }
- virtual int print(ostream&, ostream&){ return 0; }
+ virtual Sequence* print(ostream&, ostream&){ return NULL; }
+ virtual Sequence* print(ostream&, ostream&, data_results, data_results) { return NULL; }
+ virtual int print(ostream&, ostream&, string){ return 0; }
+ virtual data_results getResults() { data_results results; return results; }
#ifdef USE_MPI
- virtual int print(MPI_File&, MPI_File&){ return 0; }
+ virtual Sequence* print(MPI_File&, MPI_File&){ return 0; }
+ virtual Sequence* print(MPI_File&, MPI_File&, data_results, data_results){ return NULL; }
+ virtual int print(MPI_File&, MPI_File&, string){ return 0; }
#endif