MatrixScoringScheme.hh File Reference

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

#include <core/types.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <core/sequence/ScoringScheme.hh>
#include <core/chemical/AA.hh>
#include <utility/io/izstream.fwd.hh>
#include <utility/file/FileName.fwd.hh>
#include <utility/vector1_bool.hh>

Classes
class	core::sequence::MatrixScoringScheme

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.

Simply based on comparing single characters from two protein sequences, along with affine gap penalties of the form penalty = A + Bk, where A represents the penalty for starting a gap, and B represents the penalty for extending a previously opened gap by k characters.

Author

James Thompson