Package pl.poznan.put.structure.formats

Class ImmutableDefaultDotBracketFromPdb

java.lang.Object

pl.poznan.put.structure.formats.DefaultDotBracketFromPdb

pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb

All Implemented Interfaces:

DotBracket, DotBracketFromPdb

@ParametersAreNonnullByDefault
@Generated("org.immutables.processor.ProxyProcessor")
@Immutable
public final class ImmutableDefaultDotBracketFromPdb
extends DefaultDotBracketFromPdb

Immutable implementation of DefaultDotBracketFromPdb.

Use the builder to create immutable instances: ImmutableDefaultDotBracketFromPdb.builder(). Use the static factory method to create immutable instances: ImmutableDefaultDotBracketFromPdb.of().

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ImmutableDefaultDotBracketFromPdb.Builder	Builds instances of type ImmutableDefaultDotBracketFromPdb.

Method Summary

Modifier and Type	Method	Description
static ImmutableDefaultDotBracketFromPdb.Builder	builder()	Creates a builder for ImmutableDefaultDotBracketFromPdb.
protected List<List<Strand>>	candidatesToCombine()
static ImmutableDefaultDotBracketFromPdb	copyOf(DefaultDotBracketFromPdb instance)	Creates an immutable copy of a DefaultDotBracketFromPdb value.
boolean	equals(Object another)	This instance is equal to all instances of ImmutableDefaultDotBracketFromPdb that have equal attribute values.
int	hashCode()	Computes a hash code from attributes: identifierSet, model, sequence, structure.
Set<PdbResidueIdentifier>	identifierSet()
PdbModel	model()
static ImmutableDefaultDotBracketFromPdb	of(String sequence, String structure, PdbModel model)	Construct a new immutable DefaultDotBracketFromPdb instance.
Map<DotBracketSymbol,DotBracketSymbol>	pairs()
protected Map<PdbResidueIdentifier,DotBracketSymbol>	residueToSymbol()
String	sequence()
List<Strand>	strands()
String	structure()
List<DotBracketSymbol>	symbols()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	symbolToResidue()
String	toString()	Prints the immutable value DefaultDotBracketFromPdb with attribute values.
ImmutableDefaultDotBracketFromPdb	withIdentifierSet(Iterable<? extends PdbResidueIdentifier> elements)	Copy the current immutable object with elements that replace the content of identifierSet.
ImmutableDefaultDotBracketFromPdb	withIdentifierSet(PdbResidueIdentifier... elements)	Copy the current immutable object with elements that replace the content of identifierSet.
ImmutableDefaultDotBracketFromPdb	withModel(PdbModel value)	Copy the current immutable object by setting a value for the model attribute.
ImmutableDefaultDotBracketFromPdb	withSequence(String value)	Copy the current immutable object by setting a value for the sequence attribute.
ImmutableDefaultDotBracketFromPdb	withStrands(Iterable<? extends Strand> elements)	Copy the current immutable object with elements that replace the content of strands.
ImmutableDefaultDotBracketFromPdb	withStrands(Strand... elements)	Copy the current immutable object with elements that replace the content of strands.
ImmutableDefaultDotBracketFromPdb	withStructure(String value)	Copy the current immutable object by setting a value for the structure attribute.

Methods inherited from class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb

combineStrands, combineStrands, contains, identifier, originalIndex, symbol, validate

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface pl.poznan.put.structure.formats.DotBracket

containsMissing, findStrand, length, missingInternal, missingTerminal, pseudoknotOrder, sequence, structure, symbols, toStringWithStrands

Method Detail

identifierSet

public Set<PdbResidueIdentifier> identifierSet()

Returns:

The set of residue identifiers used in this structure.

model

public PdbModel model()

Specified by:

model in class DefaultDotBracketFromPdb

Returns:

The value of the model attribute

strands

public List<Strand> strands()

Specified by:

strands in interface DotBracket

Overrides:

strands in class DefaultDotBracketFromPdb

Returns:

The value of the strands attribute

sequence

public String sequence()

Specified by:

sequence in interface DotBracket

Specified by:

sequence in class DefaultDotBracketFromPdb

Returns:

The value of the sequence attribute

structure

public String structure()

Specified by:

structure in interface DotBracket

Specified by:

structure in class DefaultDotBracketFromPdb

Returns:

The value of the structure attribute

withIdentifierSet

public final ImmutableDefaultDotBracketFromPdb withIdentifierSet(PdbResidueIdentifier... elements)

Copy the current immutable object with elements that replace the content of identifierSet.

Parameters:

elements - The elements to set

Returns:

A modified copy of this object

withIdentifierSet

public final ImmutableDefaultDotBracketFromPdb withIdentifierSet(Iterable<? extends PdbResidueIdentifier> elements)

Copy the current immutable object with elements that replace the content of identifierSet. A shallow reference equality check is used to prevent copying of the same value by returning this.

Parameters:

elements - An iterable of identifierSet elements to set

Returns:

A modified copy of this object

withModel

public final ImmutableDefaultDotBracketFromPdb withModel(PdbModel value)

Copy the current immutable object by setting a value for the model attribute. A shallow reference equality check is used to prevent copying of the same value by returning this.

Parameters:

value - A new value for model

Returns:

A modified copy of the this object

withStrands

public final ImmutableDefaultDotBracketFromPdb withStrands(Strand... elements)

Copy the current immutable object with elements that replace the content of strands.

Parameters:

elements - The elements to set

Returns:

A modified copy of this object

withStrands

public final ImmutableDefaultDotBracketFromPdb withStrands(Iterable<? extends Strand> elements)

Copy the current immutable object with elements that replace the content of strands. A shallow reference equality check is used to prevent copying of the same value by returning this.

Parameters:

elements - An iterable of strands elements to set

Returns:

A modified copy of this object

withSequence

public final ImmutableDefaultDotBracketFromPdb withSequence(String value)

Copy the current immutable object by setting a value for the sequence attribute. An equals check used to prevent copying of the same value by returning this.

Parameters:

value - A new value for sequence

Returns:

A modified copy of the this object

withStructure

public final ImmutableDefaultDotBracketFromPdb withStructure(String value)

Copy the current immutable object by setting a value for the structure attribute. An equals check used to prevent copying of the same value by returning this.

Parameters:

value - A new value for structure

Returns:

A modified copy of the this object

equals

public boolean equals(@Nullable
                      Object another)

This instance is equal to all instances of ImmutableDefaultDotBracketFromPdb that have equal attribute values.

Overrides:

equals in class Object

Returns:

true if this is equal to another instance

hashCode

public int hashCode()

Computes a hash code from attributes: identifierSet, model, sequence, structure.

Overrides:

hashCode in class Object

Returns:

hashCode value

toString

public String toString()

Prints the immutable value DefaultDotBracketFromPdb with attribute values.

Overrides:

toString in class Object

Returns:

A string representation of the value

pairs

public Map<DotBracketSymbol,DotBracketSymbol> pairs()

Returns a lazily initialized value of the pairs attribute. Initialized once and only once and stored for subsequent access with proper synchronization. In case of any exception or error thrown by the lazy value initializer, the result will not be memoised (i.e. remembered) and on next call computation will be attempted again.

Specified by:

pairs in interface DotBracket

Overrides:

pairs in class DefaultDotBracketFromPdb

Returns:

A lazily initialized value of the pairs attribute

residueToSymbol

protected Map<PdbResidueIdentifier,DotBracketSymbol> residueToSymbol()

Returns a lazily initialized value of the residueToSymbol attribute. Initialized once and only once and stored for subsequent access with proper synchronization. In case of any exception or error thrown by the lazy value initializer, the result will not be memoised (i.e. remembered) and on next call computation will be attempted again.

Overrides:

residueToSymbol in class DefaultDotBracketFromPdb

Returns:

A lazily initialized value of the residueToSymbol attribute

symbolToResidue

protected Map<DotBracketSymbol,PdbResidueIdentifier> symbolToResidue()

Returns a lazily initialized value of the symbolToResidue attribute. Initialized once and only once and stored for subsequent access with proper synchronization. In case of any exception or error thrown by the lazy value initializer, the result will not be memoised (i.e. remembered) and on next call computation will be attempted again.

Overrides:

symbolToResidue in class DefaultDotBracketFromPdb

Returns:

A lazily initialized value of the symbolToResidue attribute

of

public static ImmutableDefaultDotBracketFromPdb of(String sequence,
                                                   String structure,
                                                   PdbModel model)

Construct a new immutable DefaultDotBracketFromPdb instance.

Parameters:

sequence - The value for the sequence attribute

structure - The value for the structure attribute

model - The value for the model attribute

Returns:

An immutable DefaultDotBracketFromPdb instance

copyOf

public static ImmutableDefaultDotBracketFromPdb copyOf(DefaultDotBracketFromPdb instance)

Creates an immutable copy of a DefaultDotBracketFromPdb value. Uses accessors to get values to initialize the new immutable instance. If an instance is already immutable, it is returned as is.

Parameters:

instance - The instance to copy

Returns:

A copied immutable DefaultDotBracketFromPdb instance

builder

public static ImmutableDefaultDotBracketFromPdb.Builder builder()

Creates a builder for ImmutableDefaultDotBracketFromPdb.

 ImmutableDefaultDotBracketFromPdb.builder()
    .addIdentifierSet|addAllIdentifierSet(pl.poznan.put.pdb.PdbResidueIdentifier) // identifierSet elements
    .model(pl.poznan.put.pdb.analysis.PdbModel) // required model
    .addStrands|addAllStrands(pl.poznan.put.structure.formats.Strand) // strands elements
    .sequence(String) // required sequence
    .structure(String) // required structure
    .build();
 

Returns:

A new ImmutableDefaultDotBracketFromPdb builder

symbols

public List<DotBracketSymbol> symbols()

Specified by:

symbols in interface DotBracket

Returns:

The list of dot-bracket symbols.

candidatesToCombine

protected final List<List<Strand>> candidatesToCombine()