sequence Directory Reference

Directory dependency graph for sequence:

Files
file	ABEGOManager.cc
	class for ABEGO
file	ABEGOManager.fwd.hh
file	ABEGOManager.hh
	header file for class of ABEGO plus
file	Aligner.cc
	class definition for a class that aligns two Sequence objects using dynamic programming algorithms.
file	Aligner.fwd.hh
	forward declaration for Aligner class.
file	Aligner.hh
	class definition for a class that aligns two Sequence objects using an dynamic programming and an arbitrary scoring scheme.
file	AlignerFactory.cc
file	AlignerFactory.hh
file	AnnotatedSequence.cc
file	AnnotatedSequence.hh
file	BasicSequenceCreators.cc
file	BasicSequenceCreators.hh
file	Blosum62Map.hh
	Creates a std::unordered_map that maps a char pair of name1s to their BLOSUM62 score.
file	ChemicalShiftScoringScheme.cc
	method implementations for ChemicalShiftScoringScheme class.
file	ChemicalShiftScoringScheme.hh
file	ChemicalShiftSequence.cc
file	ChemicalShiftSequence.fwd.hh
	forward declaration for class ChemicalShiftSequence
file	ChemicalShiftSequence.hh
	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
	method implementations for CompassScoringScheme class.
file	CompassScoringScheme.hh
	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
	class definition for a given scoring scheme for an alignment.
file	CompositeScoringScheme.fwd.hh
	forward declaration for CompositeScoringScheme.fwd.hh
file	CompositeScoringScheme.hh
	class definition for a given scoring scheme for an alignment.
file	CompositeSequence.cc
file	CompositeSequence.fwd.hh
	forward declaration for class CompositeSequence
file	CompositeSequence.hh
	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
file	DerivedSequenceMapping.fwd.hh
file	DerivedSequenceMapping.hh
file	DP_Matrix.cc
file	DP_Matrix.hh
	class for holding information on a dynamic programming matrix.
file	DPScoringScheme.cc
	method implementations for DPScoringScheme class.
file	DPScoringScheme.hh
	class definition for a profile-profile scoring scheme for comparing two sequence profiles using the DP city-block distance.
file	L1ScoringScheme.cc
	method implementations for L1ScoringScheme class.
file	L1ScoringScheme.hh
	class definition for a profile-profile scoring scheme for comparing two sequence profiles using the L1 city-block distance.
file	MatrixScoringScheme.cc
	class definition for a given scoring scheme for an alignment.
file	MatrixScoringScheme.hh
	class definition for a given scoring scheme for an alignment.
file	MCAligner.cc
	class definition for a class that aligns two Sequence objects using a stochastic version of the Needleman-Wunsch algorithm.
file	MCAligner.hh
	class definition for a class that aligns two Sequence objects using a the Needleman-Wunsch alignment algorithm.
file	NWAligner.cc
	class definition for a class that aligns two Sequence objects using the Needleman-Wunsch alignment algorithm.
file	NWAligner.fwd.hh
	forward declaration for NWAligner class.
file	NWAligner.hh
	class definition for a class that aligns two Sequence objects using a the Needleman-Wunsch alignment algorithm.
file	PairScoringScheme.cc
file	PairScoringScheme.fwd.hh
	forward declaration for PairScoringScheme.fwd.hh
file	PairScoringScheme.hh
	class definition for a given scoring scheme for an alignment.
file	ProfSimScoringScheme.cc
file	ProfSimScoringScheme.hh
	class definition for a given scoring scheme for an alignment.
file	ScoringScheme.cc
	abstract base class for representing scoring schemes for alignments.
file	ScoringScheme.fwd.hh
	forward declaration for ScoringScheme.fwd.hh
file	ScoringScheme.hh
	abstract base class for representing scoring schemes for alignments.
file	ScoringSchemeFactory.cc
	Factory for creating various types of ScoringSchemes for use in sequence alignment.
file	ScoringSchemeFactory.hh
file	Sequence.cc
	method definitions for Sequence class
file	Sequence.fwd.hh
	forward declaration for Sequence class.
file	Sequence.hh
	class definition for a sequence
file	sequence_motif.cc
file	sequence_motif.hh
file	SequenceAlignment.cc
file	SequenceAlignment.fwd.hh
	forward declaration for SequenceAlignment class.
file	SequenceAlignment.hh
	class definition for a multiple sequence alignment
file	SequenceCoupling.cc
file	SequenceCoupling.fwd.hh
file	SequenceCoupling.hh
	class definition for a sequence coupling profile that
file	SequenceCreator.cc
file	SequenceCreator.fwd.hh
file	SequenceCreator.hh
	Base class for SequenceCreators for the Sequence load-time factory registration scheme.
file	SequenceFactory.cc
	Factory for creating various types of sequences.
file	SequenceFactory.fwd.hh
file	SequenceFactory.hh
	Factory for creating various types of sequence.
file	SequenceProfile.cc
	class definition for a given scoring scheme for an alignment.
file	SequenceProfile.fwd.hh
	forward declaration for class SequenceProfile
file	SequenceProfile.hh
	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
	class definition for a given scoring scheme for an alignment.
file	SimpleScoringScheme.hh
	class definition for a given scoring scheme for an alignment.
file	SSManager.cc
	class for converting SS to int. For use with the ss hashed fragment database
file	SSManager.fwd.hh
file	SSManager.hh
file	SWAligner.cc
file	SWAligner.fwd.hh
	forward declaration for SWAligner class.
file	SWAligner.hh
	class definition for a class that aligns two Sequence objects using a ScoringScheme object and the Smith-Waterman alignment algorithm.
file	util.cc
	Utilities for working with sequence motifs.
file	util.hh
	small bundle of utilities for dealing with sequences