Uses of Interface
pl.poznan.put.structure.ClassifiedBasePair

Packages that use ClassifiedBasePair

Package	Description
pl.poznan.put.rna
pl.poznan.put.structure	Package contains classes useful in describing secondary structure (base pairs, helices, etc.)
pl.poznan.put.structure.formats

Uses of ClassifiedBasePair in pl.poznan.put.rna

Method parameters in pl.poznan.put.rna with type arguments of type ClassifiedBasePair

Modifier and Type	Method	Description
static PdbModel	ChainReorderer.reorderAtoms(PdbModel model, Collection<? extends ClassifiedBasePair> basePairs)	Reorders chains according to given canonical base pairs to keep connected chains together while minimizing the overall pseudoknot order.

Uses of ClassifiedBasePair in pl.poznan.put.structure

Classes in pl.poznan.put.structure that implement ClassifiedBasePair

Modifier and Type	Class	Description
class	AnalyzedBasePair	A pair of residues with metadata taken from analysis tool.
class	ImmutableAnalyzedBasePair	Immutable implementation of AnalyzedBasePair.
class	ImmutableQuantifiedBasePair	Immutable implementation of QuantifiedBasePair.
class	QuantifiedBasePair	A base pair which is classified and quantified with numerical parameters.

Methods in pl.poznan.put.structure that return ClassifiedBasePair

Modifier and Type	Method	Description
ClassifiedBasePair	AnalyzedBasePair.invert()
ClassifiedBasePair	ClassifiedBasePair.invert()
ClassifiedBasePair	QuantifiedBasePair.invert()

Methods in pl.poznan.put.structure that return types with arguments of type ClassifiedBasePair

Modifier and Type	Method	Description
static Collection<ClassifiedBasePair>	CanonicalStructureExtractor.basePairs(ResidueCollection residueCollection)

Methods in pl.poznan.put.structure with parameters of type ClassifiedBasePair

Modifier and Type	Method	Description
default int	ClassifiedBasePair.compareTo(ClassifiedBasePair t)
ImmutableAnalyzedBasePair.Builder	ImmutableAnalyzedBasePair.Builder.from(ClassifiedBasePair instance)	Fill a builder with attribute values from the provided pl.poznan.put.structure.ClassifiedBasePair instance.
ImmutableQuantifiedBasePair.Builder	ImmutableQuantifiedBasePair.Builder.from(ClassifiedBasePair instance)	Fill a builder with attribute values from the provided pl.poznan.put.structure.ClassifiedBasePair instance.

Uses of ClassifiedBasePair in pl.poznan.put.structure.formats

Methods in pl.poznan.put.structure.formats that return types with arguments of type ClassifiedBasePair

Modifier and Type	Method	Description
Collection<? extends ClassifiedBasePair>	ImmutableMultiLineDotBracket.basePairs()
abstract Collection<? extends ClassifiedBasePair>	MultiLineDotBracket.basePairs()
protected Collection<ClassifiedBasePair>	ImmutableMultiLineDotBracket.basePairs5to3()
protected Collection<ClassifiedBasePair>	MultiLineDotBracket.basePairs5to3()

Method parameters in pl.poznan.put.structure.formats with type arguments of type ClassifiedBasePair

Modifier and Type	Method	Description
ImmutableMultiLineDotBracket.Builder	ImmutableMultiLineDotBracket.Builder.basePairs(Collection<? extends ClassifiedBasePair> basePairs)	Initializes the value for the basePairs attribute.
List<DotBracketFromPdb>	CombinedStrandFromPdb.combineStrands(List<ClassifiedBasePair> unused)
List<DotBracketFromPdb>	DefaultDotBracketFromPdb.combineStrands(List<ClassifiedBasePair> nonCanonical)
List<DotBracketFromPdb>	DotBracketFromPdb.combineStrands(List<ClassifiedBasePair> nonCanonical)	Combines strands which are connected via canonical or non-canonical base pairs.
static BpSeq	BpSeq.fromBasePairs(List<PdbNamedResidueIdentifier> residues, Collection<? extends ClassifiedBasePair> basePairs)	Creates an instance of BPSEQ from a list of residue identifiers and a list of base pairs.
static ImmutableMultiLineDotBracket	ImmutableMultiLineDotBracket.of(String sequence, Collection<? extends ClassifiedBasePair> basePairs)	Construct a new immutable MultiLineDotBracket instance.
ImmutableMultiLineDotBracket	ImmutableMultiLineDotBracket.withBasePairs(Collection<? extends ClassifiedBasePair> value)	Copy the current immutable object by setting a value for the basePairs attribute.