Rosetta Core  2014.35
Classes | Namespaces
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/pointer/ReferenceCount.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.

Detailed: 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