ScoringScheme.hh File Reference

abstract base class for representing scoring schemes for alignments. More...

#include <core/sequence/ScoringScheme.fwd.hh>
#include <core/types.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <utility/io/izstream.fwd.hh>
#include <utility/file/FileName.fwd.hh>
#include <utility/VirtualBase.hh>
#include <string>

Classes
class	core::sequence::ScoringScheme

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

Detailed Description

abstract base class for representing scoring schemes for alignments.

ScoringScheme objects contain two scoring rules:

• a rule for comparing any character from a sequence to a gap character (usually liste as gap insertion and gap extension, or d and e)
• a rule for scoring two elements from a sequence (simply S) Generally the rule for scoring gaps is composed of a gap insertion and a gap extension parameter. It's important to note that alignments derived using the ScoringScheme and Aligner objects are only guaranteed to be optimal if every element of S is bigger than -2 * e.

  Author

  James Thompson