#include "maligner.h"
#include "slayer.h"
+
+
//***********************************************************************/
//This class was modeled after the chimeraSlayer written by the Broad Institute
/***********************************************************************/
public:
ChimeraSlayer(string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
+ ChimeraSlayer(string, string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
+
~ChimeraSlayer();
int getChimeras(Sequence*);
map<int, int> spotMap;
Database* databaseRight;
Database* databaseLeft;
+ map<string, vector<string> > nameMapRank; //sequence name to rank so you can construct a template of the abundant sequences if the user uses itself as template
vector<data_struct> chimeraResults;
string chimeraFlags, searchMethod, fastafile;
void printBlock(data_struct, string, ostream&);
string getBlock(data_struct, string);
+ int readNameFile(string);
+ vector<Sequence*> getTemplate(Sequence*);
};