sequence Directory Reference

Directory dependency graph for sequence:

Files
file	ABEGOManager.cc [code]
	class for ABEGO
file	ABEGOManager.fwd.hh [code]
file	ABEGOManager.hh [code]
	header file for class of ABEGO plus
file	Aligner.cc [code]
	class definition for a class that aligns two Sequence objects using dynamic programming algorithms.
file	Aligner.fwd.hh [code]
	forward declaration for Aligner class.
file	Aligner.hh [code]
	class definition for a class that aligns two Sequence objects using an dynamic programming and an arbitrary scoring scheme.
file	AlignerFactory.cc [code]
file	AlignerFactory.hh [code]
file	AnnotatedSequence.cc [code]
file	AnnotatedSequence.hh [code]
file	BasicSequenceCreators.cc [code]
file	BasicSequenceCreators.hh [code]
file	ChemicalShiftScoringScheme.cc [code]
	method implementations for ChemicalShiftScoringScheme class.
file	ChemicalShiftScoringScheme.hh [code]
file	ChemicalShiftSequence.cc [code]
file	ChemicalShiftSequence.fwd.hh [code]
	forward declaration for class ChemicalShiftSequence
file	ChemicalShiftSequence.hh [code]
	class definition for a sequence profile that represents each position in a sequence as a probability distribution over the allowed amino acids at that position.
file	CompassScoringScheme.cc [code]
	method implementations for CompassScoringScheme class.
file	CompassScoringScheme.hh [code]
	class definition for a profile-profile scoring scheme for comparing two sequence profiles using the Compass method, published by Sadreyev and Grishin.
file	CompositeScoringScheme.cc [code]
	class definition for a given scoring scheme for an alignment.
file	CompositeScoringScheme.fwd.hh [code]
	forward declaration for CompositeScoringScheme.fwd.hh
file	CompositeScoringScheme.hh [code]
	class definition for a given scoring scheme for an alignment.
file	CompositeSequence.cc [code]
file	CompositeSequence.fwd.hh [code]
	forward declaration for class CompositeSequence
file	CompositeSequence.hh [code]
	class definition for a sequence profile that represents each position in a sequence as a probability distribution over the allowed amino acids at that position.
file	DerivedSequenceMapping.cc [code]
file	DerivedSequenceMapping.fwd.hh [code]
file	DerivedSequenceMapping.hh [code]
file	DP_Matrix.cc [code]
file	DP_Matrix.hh [code]
	class for holding information on a dynamic programming matrix.
file	DPScoringScheme.cc [code]
	method implementations for DPScoringScheme class.
file	DPScoringScheme.hh [code]
	class definition for a profile-profile scoring scheme for comparing two sequence profiles using the DP city-block distance.
file	L1ScoringScheme.cc [code]
	method implementations for L1ScoringScheme class.
file	L1ScoringScheme.hh [code]
	class definition for a profile-profile scoring scheme for comparing two sequence profiles using the L1 city-block distance.
file	MatrixScoringScheme.cc [code]
	class definition for a given scoring scheme for an alignment.
file	MatrixScoringScheme.hh [code]
	class definition for a given scoring scheme for an alignment.
file	MCAligner.cc [code]
	class definition for a class that aligns two Sequence objects using a stochastic version of the Needleman-Wunsch algorithm.
file	MCAligner.hh [code]
	class definition for a class that aligns two Sequence objects using a the Needleman-Wunsch alignment algorithm.
file	NWAligner.cc [code]
	class definition for a class that aligns two Sequence objects using the Needleman-Wunsch alignment algorithm.
file	NWAligner.fwd.hh [code]
	forward declaration for NWAligner class.
file	NWAligner.hh [code]
	class definition for a class that aligns two Sequence objects using a the Needleman-Wunsch alignment algorithm.
file	PairScoringScheme.cc [code]
file	PairScoringScheme.fwd.hh [code]
	forward declaration for PairScoringScheme.fwd.hh
file	PairScoringScheme.hh [code]
	class definition for a given scoring scheme for an alignment.
file	ProfSimScoringScheme.cc [code]
file	ProfSimScoringScheme.hh [code]
	class definition for a given scoring scheme for an alignment.
file	ScoringScheme.cc [code]
	abstract base class for representing scoring schemes for alignments.
file	ScoringScheme.fwd.hh [code]
	forward declaration for ScoringScheme.fwd.hh
file	ScoringScheme.hh [code]
	abstract base class for representing scoring schemes for alignments.
file	ScoringSchemeFactory.cc [code]
	Factory for creating various types of ScoringSchemes for use in sequence alignment.
file	ScoringSchemeFactory.hh [code]
file	Sequence.cc [code]
	method definitions for Sequence class
file	Sequence.fwd.hh [code]
	forward declaration for Sequence class.
file	Sequence.hh [code]
	class definition for a sequence
file	SequenceAlignment.cc [code]
file	SequenceAlignment.fwd.hh [code]
	forward declaration for SequenceAlignment class.
file	SequenceAlignment.hh [code]
	class definition for a multiple sequence alignment
file	SequenceCoupling.cc [code]
file	SequenceCoupling.fwd.hh [code]
file	SequenceCoupling.hh [code]
	class definition for a sequence coupling profile that
file	SequenceCreator.cc [code]
file	SequenceCreator.fwd.hh [code]
file	SequenceCreator.hh [code]
	Base class for SequenceCreators for the Sequence load-time factory registration scheme.
file	SequenceFactory.cc [code]
	Factory for creating various types of sequences.
file	SequenceFactory.fwd.hh [code]
file	SequenceFactory.hh [code]
	Factory for creating various types of sequence.
file	SequenceProfile.cc [code]
	class definition for a given scoring scheme for an alignment.
file	SequenceProfile.fwd.hh [code]
	forward declaration for class SequenceProfile
file	SequenceProfile.hh [code]
	class definition for a sequence profile that represents each position in a sequence as a probability distribution over the allowed amino acids at that position.
file	SimpleScoringScheme.cc [code]
	class definition for a given scoring scheme for an alignment.
file	SimpleScoringScheme.hh [code]
	class definition for a given scoring scheme for an alignment.
file	SWAligner.cc [code]
file	SWAligner.fwd.hh [code]
	forward declaration for SWAligner class.
file	SWAligner.hh [code]
	class definition for a class that aligns two Sequence objects using a ScoringScheme object and the Smith-Waterman alignment algorithm.
file	util.cc [code]
	small bundle of utilities for dealing with sequences
file	util.hh [code]