Package pl.poznan.put.structure.formats

Class ImmutableCombinedStrandFromPdb

java.lang.Object

pl.poznan.put.structure.formats.AbstractCombinedStrand

pl.poznan.put.structure.formats.CombinedStrandFromPdb

pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb

All Implemented Interfaces:

DotBracket, DotBracketFromPdb

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

Immutable implementation of CombinedStrandFromPdb.

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

Nested Class Summary

Nested Classes

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

Method Summary

Modifier and Type	Method	Description
static ImmutableCombinedStrandFromPdb.Builder	builder()	Creates a builder for ImmutableCombinedStrandFromPdb.
List<DotBracket>	combineStrands()	Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.
static ImmutableCombinedStrandFromPdb	copyOf(CombinedStrandFromPdb instance)	Creates an immutable copy of a CombinedStrandFromPdb value.
boolean	equals(Object another)	This instance is equal to all instances of ImmutableCombinedStrandFromPdb that have equal attribute values.
int	hashCode()	Computes a hash code from attributes: combineStrands, inputStrands, inputSymbolToResidue.
protected List<Strand>	inputStrands()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	inputSymbolToResidue()
protected org.apache.commons.collections4.BidiMap<DotBracketSymbol,PdbResidueIdentifier>	mapping()
static ImmutableCombinedStrandFromPdb	of(Iterable<? extends Strand> inputStrands, Map<? extends DotBracketSymbol,? extends PdbResidueIdentifier> inputSymbolToResidue)	Construct a new immutable CombinedStrandFromPdb instance.
static ImmutableCombinedStrandFromPdb	of(List<Strand> inputStrands, Map<DotBracketSymbol,PdbResidueIdentifier> inputSymbolToResidue)	Construct a new immutable CombinedStrandFromPdb instance.
Map<DotBracketSymbol,DotBracketSymbol>	pairs()
List<Strand>	strands()
List<DotBracketSymbol>	symbols()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	symbolToResidue()
String	toString()	Prints the immutable value CombinedStrandFromPdb with attribute values.
ImmutableCombinedStrandFromPdb	withCombineStrands(Iterable<? extends DotBracket> elements)	Copy the current immutable object with elements that replace the content of combineStrands.
ImmutableCombinedStrandFromPdb	withCombineStrands(DotBracket... elements)	Copy the current immutable object with elements that replace the content of combineStrands.
ImmutableCombinedStrandFromPdb	withInputStrands(Iterable<? extends Strand> elements)	Copy the current immutable object with elements that replace the content of inputStrands.
ImmutableCombinedStrandFromPdb	withInputStrands(Strand... elements)	Copy the current immutable object with elements that replace the content of inputStrands.
ImmutableCombinedStrandFromPdb	withInputSymbolToResidue(Map<? extends DotBracketSymbol,? extends PdbResidueIdentifier> entries)	Copy the current immutable object by replacing the inputSymbolToResidue map with the specified map.

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

combineStrands, contains, identifier, identifierSet, originalIndex, symbol

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, sequence, structure, structure, toStringWithStrands

Method Detail

combineStrands

public List<DotBracket> combineStrands()

Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.

Returns:

The list of dot-bracket instances, each containing strands which only pair with each other.

inputStrands

protected List<Strand> inputStrands()

Specified by:

inputStrands in class CombinedStrandFromPdb

Returns:

The list of input strands.

inputSymbolToResidue

protected Map<DotBracketSymbol,PdbResidueIdentifier> inputSymbolToResidue()

Specified by:

inputSymbolToResidue in class CombinedStrandFromPdb

Returns:

The mapping of dot-bracket symbols with corresponding PDB identifiers.

withCombineStrands

public final ImmutableCombinedStrandFromPdb withCombineStrands(DotBracket... elements)

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

Parameters:

elements - The elements to set

Returns:

A modified copy of this object

withCombineStrands

public final ImmutableCombinedStrandFromPdb withCombineStrands(Iterable<? extends DotBracket> elements)

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

Parameters:

elements - An iterable of combineStrands elements to set

Returns:

A modified copy of this object

withInputStrands

public final ImmutableCombinedStrandFromPdb withInputStrands(Strand... elements)

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

Parameters:

elements - The elements to set

Returns:

A modified copy of this object

withInputStrands

public final ImmutableCombinedStrandFromPdb withInputStrands(Iterable<? extends Strand> elements)

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

Parameters:

elements - An iterable of inputStrands elements to set

Returns:

A modified copy of this object

withInputSymbolToResidue

public final ImmutableCombinedStrandFromPdb withInputSymbolToResidue(Map<? extends DotBracketSymbol,? extends PdbResidueIdentifier> entries)

Copy the current immutable object by replacing the inputSymbolToResidue map with the specified map. Nulls are not permitted as keys or values. A shallow reference equality check is used to prevent copying of the same value by returning this.

Parameters:

entries - The entries to be added to the inputSymbolToResidue map

Returns:

A modified copy of this object

equals

public boolean equals(@Nullable
                      Object another)

This instance is equal to all instances of ImmutableCombinedStrandFromPdb 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: combineStrands, inputStrands, inputSymbolToResidue.

Overrides:

hashCode in class Object

Returns:

hashCode value

toString

public String toString()

Prints the immutable value CombinedStrandFromPdb with attribute values.

Overrides:

toString in class Object

Returns:

A string representation of the value

symbols

public List<DotBracketSymbol> symbols()

Returns a lazily initialized value of the symbols 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:

symbols in interface DotBracket

Overrides:

symbols in class CombinedStrandFromPdb

Returns:

A lazily initialized value of the symbols attribute

strands

public List<Strand> strands()

Returns a lazily initialized value of the strands 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:

strands in interface DotBracket

Overrides:

strands in class CombinedStrandFromPdb

Returns:

A lazily initialized value of the strands attribute

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 CombinedStrandFromPdb

Returns:

A lazily initialized value of the pairs 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 CombinedStrandFromPdb

Returns:

A lazily initialized value of the symbolToResidue attribute

mapping

protected org.apache.commons.collections4.BidiMap<DotBracketSymbol,PdbResidueIdentifier> mapping()

Returns a lazily initialized value of the mapping 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:

mapping in class CombinedStrandFromPdb

Returns:

A lazily initialized value of the mapping attribute

of

public static ImmutableCombinedStrandFromPdb of(List<Strand> inputStrands,
                                                Map<DotBracketSymbol,PdbResidueIdentifier> inputSymbolToResidue)

Construct a new immutable CombinedStrandFromPdb instance.

Parameters:

inputStrands - The value for the inputStrands attribute

inputSymbolToResidue - The value for the inputSymbolToResidue attribute

Returns:

An immutable CombinedStrandFromPdb instance

of

public static ImmutableCombinedStrandFromPdb of(Iterable<? extends Strand> inputStrands,
                                                Map<? extends DotBracketSymbol,? extends PdbResidueIdentifier> inputSymbolToResidue)

Construct a new immutable CombinedStrandFromPdb instance.

Parameters:

inputStrands - The value for the inputStrands attribute

inputSymbolToResidue - The value for the inputSymbolToResidue attribute

Returns:

An immutable CombinedStrandFromPdb instance

copyOf

public static ImmutableCombinedStrandFromPdb copyOf(CombinedStrandFromPdb instance)

Creates an immutable copy of a CombinedStrandFromPdb 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 CombinedStrandFromPdb instance

builder

public static ImmutableCombinedStrandFromPdb.Builder builder()

Creates a builder for ImmutableCombinedStrandFromPdb.

 ImmutableCombinedStrandFromPdb.builder()
    .addCombineStrands|addAllCombineStrands(pl.poznan.put.structure.formats.DotBracket) // combineStrands elements
    .addInputStrands|addAllInputStrands(pl.poznan.put.structure.formats.Strand) // inputStrands elements
    .putInputSymbolToResidue|putAllInputSymbolToResidue(pl.poznan.put.structure.DotBracketSymbol => pl.poznan.put.pdb.PdbResidueIdentifier) // inputSymbolToResidue mappings
    .build();
 

Returns:

A new ImmutableCombinedStrandFromPdb builder