*
*/
+
+//Data Structure for a fasta file.
+
#include "mothur.h"
#include "mothurout.h"
Sequence(string, string);
Sequence(ifstream&);
Sequence(istringstream&);
-
//these constructors just set the unaligned string to save space
Sequence(string, string, string);
Sequence(ifstream&, string);
void setAligned(string);
void setLength();
void reverseComplement();
+ void trim(int);
string convert2ints();
string getName();
string getAligned();
string getPairwise();
string getUnaligned();
+ string getInlineSeq();
int getNumBases();
int getStartPos();
int getEndPos();
+ void padToPos(int);
+ void padFromPos(int);
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;