#include "decalc.h"
#include "chimera.h"
+#include "database.hpp"
/***********************************************************************/
//This class was modeled after the chimeraMaligner written by the Broad Institute
public:
- Maligner(vector<Sequence*>, int, int, int, float, int, int, string);
+ Maligner(vector<Sequence*>, int, int, int, float, int, int, string, Database*, Database*);
~Maligner() {};
string getResults(Sequence*, DeCalculator*);
string searchMethod;
float minDivR, percentIdenticalQueryChimera;
vector<results> outputResults;
+ vector<int> indexes; //stores index into template seqs of the refSeqs, so we can return the whole sequence rather than the trimmed and filtered one
map<int, int> spotMap;
+ Database* databaseLeft;
+ Database* databaseRight;
vector<Sequence*> minCoverageFilter(vector<Sequence*>); //removes top matches that do not have minimum coverage with query.
int computeChimeraPenalty();
float computePercentID(string, string);
string chimeraMaligner(int, DeCalculator*);
vector<Sequence*> getBlastSeqs(Sequence*, int);
+ vector<Sequence*> getKmerSeqs(Sequence*, int);
+ MothurOut* m;
};