Module _core_sequence_

Classes

ABEGO

ABEGOAP

ABEGOCAP

ABEGOManagerCAP

Aligner

AlignerFactoryAP

AlignerFactoryCAP

AnnotatedSequence

AnnotatedSequenceAP

AnnotatedSequenceCAP

Cell

CellAP

CellCAP

ChemicalShiftScoringScheme

ChemicalShiftScoringSchemeAP

ChemicalShiftScoringSchemeCAP

ChemicalShiftSequence

ChemicalShiftSequenceAP

ChemicalShiftSequenceCAP

ChemicalShiftSequenceCreator

ChemicalShiftSequenceCreatorAP

ChemicalShiftSequenceCreatorCAP

CompassScoringScheme

CompassScoringSchemeAP

CompassScoringSchemeCAP

CompositeScoringScheme

CompositeScoringSchemeAP

CompositeScoringSchemeCAP

CompositeSequence

CompositeSequenceAP

CompositeSequenceCAP

CompositeSequenceCreator

CompositeSequenceCreatorAP

CompositeSequenceCreatorCAP

DPScoringScheme

DPScoringSchemeAP

DPScoringSchemeCAP

DerivedSequenceMapping

DerivedSequenceMappingAP

DerivedSequenceMappingCAP

L1ScoringScheme

L1ScoringSchemeAP

L1ScoringSchemeCAP

Line

LineAP

LineCAP

MatrixScoringScheme

MatrixScoringSchemeAP

MatrixScoringSchemeCAP

PairScoringScheme

PairScoringSchemeAP

PairScoringSchemeCAP

ProfSimScoringScheme

ProfSimScoringSchemeAP

ProfSimScoringSchemeCAP

ScoringSchemeAP

ScoringSchemeCAP

ScoringSchemeFactory

ScoringSchemeFactoryAP

ScoringSchemeFactoryCAP

Sequence

SequenceAlignment

SequenceAlignmentAP

SequenceAlignmentCAP

SequenceAlignmentHasher

SequenceAlignmentHasherAP

SequenceAlignmentHasherCAP

SequenceCoupling

SequenceCouplingAP

SequenceCouplingCAP

SequenceCouplingCreator

SequenceCouplingCreatorAP

SequenceCouplingCreatorCAP

SequenceCreator

SequenceCreatorAP

SequenceCreatorCAP

SequenceFactory

SequenceFactoryAP

SequenceFactoryCAP

SequenceProfile

SequenceProfileAP

SequenceProfileCAP

SequenceProfileCreator

SequenceProfileCreatorAP

SequenceProfileCreatorCAP

SimpleScoringScheme

SimpleScoringSchemeAP

SimpleScoringSchemeCAP

SimpleSequenceCreator

SimpleSequenceCreatorAP

SimpleSequenceCreatorCAP

SingletonBase_T_core_sequence_SequenceFactory_T

SingletonBase_T_core_sequence_SequenceFactory_TAP

SingletonBase_T_core_sequence_SequenceFactory_TCAP

__CPP_Aligner__

__CPP_ChemicalShiftScoringScheme__

__CPP_ChemicalShiftSequenceCreator__

__CPP_ChemicalShiftSequence__

__CPP_CompassScoringScheme__

__CPP_CompositeScoringScheme__

__CPP_CompositeSequenceCreator__

__CPP_CompositeSequence__

__CPP_DPScoringScheme__

__CPP_L1ScoringScheme__

__CPP_MCAligner__

__CPP_MatrixScoringScheme__

__CPP_NWAligner__

__CPP_PairScoringScheme__

__CPP_ProfSimScoringScheme__

__CPP_SWAligner__

__CPP_ScoringScheme__

__CPP_SequenceCouplingCreator__

__CPP_SequenceCoupling__

__CPP_SequenceCreator__

__CPP_SequenceProfileCreator__

__CPP_SequenceProfile__

__CPP_Sequence__

__CPP_SimpleScoringScheme__

__CPP_SimpleSequenceCreator__

Functions

align_poses_naive

alignment_from_pose

alignment_into_pose

calpha_superimpose_with_mapping

get_maximum_scores

mapping_to_alignment

n_correctly_aligned_positions

read_alignment_file

read_all_alignments

read_aln

read_fasta_file

read_fasta_file_return_str

read_fasta_file_str

read_general_aln

read_general_aln_file

read_grishin_aln_file

seqs_from_cmd_lines

simple_mapping_from_file

steal_alignment

Variables

above

diagonal

end

left