*
*/
+
+//Data Structure for a fasta file.
+
#include "mothur.h"
#include "mothurout.h"
Sequence();
Sequence(string, string);
Sequence(ifstream&);
+ Sequence(ifstream&, string&, bool);
Sequence(istringstream&);
-
//these constructors just set the unaligned string to save space
Sequence(string, string, string);
Sequence(ifstream&, string);
string getPairwise();
string getUnaligned();
string getInlineSeq();
+ int getNumNs();
int getNumBases();
int getStartPos();
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 getSequenceName(ifstream&);
+ string getSequenceName(istringstream&);
string name;
string unaligned;
string aligned;