MatrixScoringScheme.cc File Reference

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

#include <core/types.hh>
#include <basic/Tracer.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <core/sequence/ScoringScheme.hh>
#include <core/sequence/MatrixScoringScheme.hh>
#include <utility/exit.hh>
#include <utility/io/izstream.hh>
#include <utility/file/FileName.hh>
#include <core/chemical/AA.hh>
#include <basic/database/open.hh>
#include <iostream>
#include <string>
#include <utility/vector1.hh>

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::sequence

Variables
static basic::Tracer	core::sequence::tr ("core.sequence.MatrixScoringScheme")

Detailed Description

class definition for a given scoring scheme for an alignment.

Detailed: 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