Sequence();
Sequence(string, string);
Sequence(ifstream&);
+ Sequence(ifstream&, string&, bool);
Sequence(istringstream&);
- Sequence(const Sequence& se) : name(se.name), unaligned(se.unaligned), aligned(se.aligned), pairwise(se.pairwise), numBases(se.numBases), startPos(se.startPos), endPos(se.endPos),
- alignmentLength(se.alignmentLength), isAligned(se.isAligned), longHomoPolymer(se.longHomoPolymer), ambigBases(se.ambigBases) { m = MothurOut::getInstance(); }
-
//these constructors just set the unaligned string to save space
Sequence(string, string, string);
Sequence(ifstream&, string);
int getEndPos();
void padToPos(int);
void padFromPos(int);
+ int filterToPos(int); //any character before the pos is changed to . and aligned and unaligned strings changed
+ int filterFromPos(int); //any character after the pos is changed to . and aligned and unaligned strings changed
int getAlignLength();
int getAmbigBases();
void removeAmbigBases();
private:
MothurOut* m;
void initialize();
- string getSequenceString(ifstream&);
+ string getSequenceString(ifstream&, int&);
string getCommentString(ifstream&);
- string getSequenceString(istringstream&);
+ string getSequenceString(istringstream&, int&);
string getCommentString(istringstream&);
string name;
string unaligned;