Rosetta  2020.50
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sequence Directory Reference
Directory dependency graph for sequence:
src/core/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