class ChimeraCheckRDP : public Chimera {
public:
- ChimeraCheckRDP(string, string);
+ ChimeraCheckRDP(string, string, string, bool, int, int, string); //fasta, template, name, svg, increment, ksize, outputDir
~ChimeraCheckRDP();
- void getChimeras();
- void print(ostream&);
-
- void setCons(string){};
- void setQuantiles(string q) {};
+ int getChimeras(Sequence*);
+ Sequence print(ostream&, ostream&);
+ #ifdef USE_MPI
+ Sequence print(MPI_File&, MPI_File&);
+ #endif
private:
- vector<linePair*> lines;
- vector<Sequence*> querySeqs;
+ Sequence* querySeq;
AlignmentDB* templateDB;
Kmer* kmer;
-
- vector< vector<sim> > IS; //IS[0] is the vector of IS values for each window for querySeqs[0]
- float chimeraCutoff;
-
-
- //map<string, vector< map<int, int> > >:: iterator it;
- //map<int, int>::iterator it2;
-
- vector<Sequence> closest; //closest[0] is the closest overall seq to querySeqs[0].
-
- string fastafile, templateFile;
+ Sequence closest; //closest is the closest overall seq to query
+
+ vector<sim> IS; //IS is the vector of IS values for each window for query
+ string fastafile;
map<string, string> names;
+ string name;
+ bool svg;
+ int kmerSize, increment;
- vector<sim> findIS(int);
+ vector<sim> findIS();
int calcKmers(map<int, int>, map<int, int>);
- void getCutoff();
- void makeSVGpic(vector<sim>, int);
+ void makeSVGpic(vector<sim>);
void readName(string);
-
- void createProcessesIS();
-
};
-
/***********************************************************/
#endif