SimpleScoringScheme.cc File Reference

class definition for a given scoring scheme for an alignment. More...

#include <core/types.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SimpleScoringScheme.hh>
#include <utility/exit.hh>

Namespaces
	core
	A class for reading in the atom type properties.
	core::sequence

Detailed Description

class definition for a given scoring scheme for an alignment.

Scoring scheme based on comparing single characters from two sequences with three types of score:

• score for a match (characters are equal)
• score for a mismatch (characters are not equal)
• affine gap penalties of the form penalty = A + Bk

  Author

  James Thompson