class ChimeraSlayer : public Chimera {
public:
- ChimeraSlayer(string);
+ ChimeraSlayer(string, bool, string);
~ChimeraSlayer();
int getChimeras(Sequence*);
- void print(ostream&);
+ int print(ostream&, ostream&);
void printHeader(ostream&);
+ int doPrep();
private:
Sequence* querySeq;
Maligner* maligner;
Slayer* slayer;
map<int, int> spotMap;
+ Database* databaseRight;
+ Database* databaseLeft;
vector<data_struct> chimeraResults;
- string chimeraFlags, searchMethod;
- string fastafile;
+ string chimeraFlags, searchMethod, fastafile;
+ bool realign;
void printBlock(data_struct, ostream&);
+
};
/************************************************************************/