Sequence(ifstream&);
Sequence(istringstream&);
+ //these constructors just set the unaligned string to save space
+ Sequence(string, string, string);
+ Sequence(ifstream&, string);
+ Sequence(istringstream&, string);
+
void setName(string);
void setUnaligned(string);
void setPairwise(string);
int getEndPos();
int getAlignLength();
int getAmbigBases();
+ void removeAmbigBases();
int getLongHomoPolymer();
bool getIsAligned();
void printSequence(ostream&);
- int MPISend(int); //not working at the moment...
- int MPIRecv(int); //not working at the moment...
-
private:
MothurOut* m;
void initialize();