class Ccode : public Chimera {
public:
- Ccode(string, string);
+ Ccode(string, string, bool, string, int, int, string); //fasta, template, filter, mask, window, numWanted, outputDir
~Ccode();
int getChimeras(Sequence* query);
- void print(ostream&, ostream&);
- void printHeader(ostream&);
+ int print(ostream&, ostream&);
+
+ #ifdef USE_MPI
+ int print(MPI_File&, MPI_File&);
+ #endif
private:
Dist* distCalc;
DeCalculator* decalc;
- int iters;
+ int iters, window, numWanted;
string fastafile, mapInfo;
Sequence* querySeq;
int getDiff(string, string); //return number of mismatched bases, a gap to base is not counted as a mismatch
float getT(int);
float getF(int);
+
+ #ifdef USE_MPI
+ int printMapping(string&);
+ MPI_File outMap;
+ #endif
+
};
/***********************************************************/