* to set and get these values for the other classes where they are needed. *
*
*/
-using namespace std;
#include "mothur.h"
void setPairwise(string);
void setAligned(string);
void setLength();
+ void reverseComplement();
string convert2ints();
string getName();
string getAligned();
string getPairwise();
string getUnaligned();
- int getLength(); //the greater of the lengths of unaligned and aligned
- int getUnalignLength();
+ int getNumBases();
+ int getStartPos();
+ int getEndPos();
int getAlignLength();
+ int getAmbigBases();
+ int getLongHomoPolymer();
+ bool getIsAligned();
void printSequence(ostream&);
private:
+ void initialize();
string name;
string unaligned;
string aligned;
string pairwise;
- int length;
- int lengthAligned;
+ int numBases;
+ int alignmentLength;
+ bool isAligned;
+ int longHomoPolymer;
+ int ambigBases;
+ int startPos, endPos;
};
/**************************************************************************************************/