#include "maligner.h"
#include "slayer.h"
+
+
//***********************************************************************/
//This class was modeled after the chimeraSlayer written by the Broad Institute
/***********************************************************************/
~ChimeraSlayer();
int getChimeras(Sequence*);
- Sequence* print(ostream&, ostream&);
- Sequence* print(ostream&, ostream&, data_results, data_results);
+ Sequence print(ostream&, ostream&);
+ Sequence print(ostream&, ostream&, data_results, data_results);
void printHeader(ostream&);
int doPrep();
data_results getResults() { return printResults; }
#ifdef USE_MPI
- Sequence* print(MPI_File&, MPI_File&);
- Sequence* print(MPI_File&, MPI_File&, data_results, data_results);
+ Sequence print(MPI_File&, MPI_File&);
+ Sequence print(MPI_File&, MPI_File&, data_results, data_results);
#endif
private:
- Sequence* querySeq;
+ Sequence querySeq;
Sequence trimQuery;
- DeCalculator* decalc;
+ DeCalculator decalc;
Database* databaseRight;
Database* databaseLeft;
map<string, int> priority; //for template=self, seqname, seqAligned, abundance
string getBlock(data_struct, string);
string getBlock(data_results, data_results, bool, bool, string);
//int readNameFile(string);
- vector<Sequence*> getTemplate(Sequence*, vector<Sequence*>&);
- vector<Sequence*> getRefSeqs(Sequence*, vector<Sequence*>&, vector<Sequence*>&);
- vector<Sequence*> getBlastSeqs(Sequence*, vector<Sequence*>&, int);
- vector<Sequence*> getKmerSeqs(Sequence*, vector<Sequence*>&, int);
+ vector<Sequence*> getTemplate(Sequence, vector<Sequence*>&);
+ vector<Sequence> getRefSeqs(Sequence, vector<Sequence*>&, vector<Sequence*>&);
+ vector<Sequence> getBlastSeqs(Sequence, vector<Sequence*>&, int);
+ vector<Sequence> getKmerSeqs(Sequence, vector<Sequence*>&, int);
};