};
struct linePair {
- int start;
- int end;
- linePair(int i, int j) : start(i), end(j) {}
+ unsigned long int start;
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
linePair(){}
};
+
/***********************************************************************/
class Chimera {
public:
Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; }
- //Chimera(string) { m = MothurOut::getInstance(); }
- //Chimera(string, bool, string) { m = MothurOut::getInstance(); }
- //Chimera(string, string) { m = MothurOut::getInstance(); }
virtual ~Chimera(){ for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; } };
- //virtual void setFilter(bool f) { filter = f; }
- //virtual void setCorrection(bool c) { correction = c; }
- //virtual void setProcessors(int p) { processors = p; }
- //virtual void setWindow(int w) { window = w; }
- //virtual void setIncrement(int i) { increment = i; }
- //virtual void setNumWanted(int n) { numWanted = n; }
- //virtual void setKmerSize(int k) { kmerSize = k; }
- //virtual void setSVG(int s) { svg = s; }
- //virtual void setName(string n) { name = n; }
- //virtual void setMatch(int m) { match = m; }
- //virtual void setMisMatch(int m) { misMatch = m; }
- //virtual void setDivR(float d) { divR = d; }
- //virtual void setParents(int p) { parents = p; }
- //virtual void setMinSim(int s) { minSim = s; }
- //virtual void setMinCoverage(int c) { minCov = c; }
- //virtual void setMinBS(int b) { minBS = b; }
- //virtual void setMinSNP(int s) { minSNP = s; }
- //virtual void setIters(int i) { iters = i; }
virtual bool getUnaligned() { return unaligned; }
- //virtual void setTemplateFile(string t) { templateFileName = t; templateSeqs = readSeqs(t); }
virtual int getLength() { return length; }
-
- //virtual void setCons(string){};
- //virtual void setQuantiles(string){};
- //virtual int doPrep(){ return 0; }
virtual vector<Sequence*> readSeqs(string);
- //virtual vector< vector<float> > readQuantiles();
virtual void setMask(string);
virtual map<int, int> runFilter(Sequence*);
virtual string createFilter(vector<Sequence*>, float);
-
virtual void printHeader(ostream&){};
virtual int getChimeras(Sequence*){ return 0; }
virtual int getChimeras(){ return 0; }
- virtual int print(ostream&, ostream&){ return 0; }
+ virtual Sequence* print(ostream&, ostream&){ return NULL; }
+ virtual int print(ostream&, ostream&, string){ return 0; }
#ifdef USE_MPI
- virtual int print(MPI_File&, MPI_File&){ return 0; }
+ virtual Sequence* print(MPI_File&, MPI_File&){ return 0; }
+ virtual int print(MPI_File&, MPI_File&, string){ return 0; }
#endif
protected:
vector<Sequence*> templateSeqs;
- bool filter, unaligned; // correction, svg,
- int length; //processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters,
- //float divR;
- string seqMask, filterString, outputDir, templateFileName; //quanfile, name,
+ bool filter, unaligned;
+ int length;
+ string seqMask, filterString, outputDir, templateFileName;
Sequence* getSequence(string); //find sequence from name
MothurOut* m;
};