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.fwd.hh |
| forward declaration for DP_Matrix class. | |
| 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 | |
