Uses of Interface
pl.poznan.put.structure.formats.DotBracket

Packages that use DotBracket

Package	Description
pl.poznan.put.structure.formats

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

Subinterfaces of DotBracket in pl.poznan.put.structure.formats

Modifier and Type	Interface	Description
interface	DotBracketFromPdb	A dot-bracket structure with correspondence to a 3D structure.
interface	Strand	A continuous segment of residues.

Classes in pl.poznan.put.structure.formats that implement DotBracket

Modifier and Type	Class	Description
class	AbstractCombinedStrand
class	CombinedStrand	A dot-bracket encoded structure made from combining one or more strands.
class	CombinedStrandFromPdb	A dot-bracket encoded structure made from combining one or more strands.
class	DefaultDotBracket	A default implementation of a dot-bracket.
class	DefaultDotBracketFromPdb	A default implementation of a dot-bracket structure which is mapped to data from 3D coordinates.
class	DefaultStrand	A default implementation of a strand.
final class	ImmutableCombinedStrand	Immutable implementation of CombinedStrand.
final class	ImmutableCombinedStrandFromPdb	Immutable implementation of CombinedStrandFromPdb.
final class	ImmutableDefaultDotBracket	Immutable implementation of DefaultDotBracket.
final class	ImmutableDefaultDotBracketFromPdb	Immutable implementation of DefaultDotBracketFromPdb.
final class	ImmutableDefaultStrand	Immutable implementation of DefaultStrand.
final class	ImmutableStrandView	Immutable implementation of StrandView.
class	StrandView	A strand which is defined as a fragment of a dot-bracket structure.

Methods in pl.poznan.put.structure.formats that return DotBracket

Modifier and Type	Method	Description
DotBracket	Converter.convert(BpSeq bpSeq)	Converts the secondary structure from BPSEQ to dot-bracket format.
final DotBracket	DefaultConverter.convert(BpSeq bpSeq)	Converts the secondary structure in BPSEQ format to dot-bracket.
static DotBracket	DefaultDotBracket.copyWithoutIsolatedBasePairs(DotBracket input)	Creates a copy of existing instance, but removes isolated base pairs from it.
static DotBracket	DefaultDotBracket.copyWithStrands(DotBracket input, Ct ct)	Creates a copy of existing instance and applies the information in CT format to divide strands accordingly.
DotBracket	ImmutableStrandView.parent()
abstract DotBracket	StrandView.parent()

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

Modifier and Type	Method	Description
List<DotBracket>	AbstractCombinedStrand.combineStrands()
final List<DotBracket>	CombinedStrand.combineStrands()
final List<DotBracket>	DefaultDotBracket.combineStrands()
final List<DotBracket>	DefaultDotBracketFromPdb.combineStrands()
List<DotBracket>	DotBracket.combineStrands()	Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.
List<DotBracket>	ImmutableDefaultStrand.combineStrands()	Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.
List<DotBracket>	ImmutableStrandView.combineStrands()	Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.

Methods in pl.poznan.put.structure.formats with parameters of type DotBracket

Modifier and Type	Method	Description
final ImmutableDefaultStrand.Builder	ImmutableDefaultStrand.Builder.addCombineStrands(DotBracket element)	Adds one element to combineStrands list.
final ImmutableDefaultStrand.Builder	ImmutableDefaultStrand.Builder.addCombineStrands(DotBracket... elements)	Adds elements to combineStrands list.
final ImmutableStrandView.Builder	ImmutableStrandView.Builder.addCombineStrands(DotBracket element)	Adds one element to combineStrands list.
final ImmutableStrandView.Builder	ImmutableStrandView.Builder.addCombineStrands(DotBracket... elements)	Adds elements to combineStrands list.
static DotBracket	DefaultDotBracket.copyWithoutIsolatedBasePairs(DotBracket input)	Creates a copy of existing instance, but removes isolated base pairs from it.
static DotBracket	DefaultDotBracket.copyWithStrands(DotBracket input, Ct ct)	Creates a copy of existing instance and applies the information in CT format to divide strands accordingly.
final ImmutableDefaultDotBracket.Builder	ImmutableDefaultDotBracket.Builder.from(DotBracket instance)	Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.DotBracket instance.
final ImmutableDefaultDotBracketFromPdb.Builder	ImmutableDefaultDotBracketFromPdb.Builder.from(DotBracket instance)	Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.DotBracket instance.
final ImmutableDefaultStrand.Builder	ImmutableDefaultStrand.Builder.from(DotBracket instance)	Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.DotBracket instance.
final ImmutableStrandView.Builder	ImmutableStrandView.Builder.from(DotBracket instance)	Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.DotBracket instance.
static BpSeq	BpSeq.fromDotBracket(DotBracket db)	Converts RNA secondary structure in dot-bracket format to BPSEQ format.
static Ct	Ct.fromDotBracket(DotBracket dotBracket)	Converts RNA secondary structure in dot-bracket format to CT format.
static ImmutableStrandView	ImmutableStrandView.of(String name, DotBracket parent, int begin, int end)	Construct a new immutable StrandView instance.
final ImmutableStrandView.Builder	ImmutableStrandView.Builder.parent(DotBracket parent)	Initializes the value for the parent attribute.
final ImmutableDefaultStrand	ImmutableDefaultStrand.withCombineStrands(DotBracket... elements)	Copy the current immutable object with elements that replace the content of combineStrands.
final ImmutableStrandView	ImmutableStrandView.withCombineStrands(DotBracket... elements)	Copy the current immutable object with elements that replace the content of combineStrands.
final ImmutableStrandView	ImmutableStrandView.withParent(DotBracket value)	Copy the current immutable object by setting a value for the parent attribute.

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

Modifier and Type	Method	Description
final ImmutableDefaultStrand.Builder	ImmutableDefaultStrand.Builder.addAllCombineStrands(Iterable<? extends DotBracket> elements)	Adds elements to combineStrands list.
final ImmutableStrandView.Builder	ImmutableStrandView.Builder.addAllCombineStrands(Iterable<? extends DotBracket> elements)	Adds elements to combineStrands list.
final ImmutableDefaultStrand.Builder	ImmutableDefaultStrand.Builder.combineStrands(Iterable<? extends DotBracket> elements)	Sets or replaces all elements for combineStrands list.
final ImmutableStrandView.Builder	ImmutableStrandView.Builder.combineStrands(Iterable<? extends DotBracket> elements)	Sets or replaces all elements for combineStrands list.
final ImmutableDefaultStrand	ImmutableDefaultStrand.withCombineStrands(Iterable<? extends DotBracket> elements)	Copy the current immutable object with elements that replace the content of combineStrands.
final ImmutableStrandView	ImmutableStrandView.withCombineStrands(Iterable<? extends DotBracket> elements)	Copy the current immutable object with elements that replace the content of combineStrands.