pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue Maven / Gradle / Ivy
package pl.poznan.put.pdb.analysis;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Objects;
import java.util.Set;
import javax.annotation.Nullable;
import javax.annotation.ParametersAreNonnullByDefault;
import javax.annotation.concurrent.Immutable;
import javax.annotation.concurrent.NotThreadSafe;
import org.immutables.value.Generated;
import pl.poznan.put.atom.AtomName;
import pl.poznan.put.pdb.PdbAtomLine;
import pl.poznan.put.pdb.PdbResidueIdentifier;
/**
* Immutable implementation of {@link DefaultPdbResidue}.
*
* Use the builder to create immutable instances:
* {@code ImmutableDefaultPdbResidue.builder()}.
* Use the static factory method to create immutable instances:
* {@code ImmutableDefaultPdbResidue.of()}.
*/
@Generated(from = "DefaultPdbResidue", generator = "Immutables")
@SuppressWarnings({"all"})
@ParametersAreNonnullByDefault
@javax.annotation.processing.Generated("org.immutables.processor.ProxyProcessor")
@Immutable
public final class ImmutableDefaultPdbResidue extends DefaultPdbResidue {
private final PdbResidueIdentifier identifier;
private final String standardResidueName;
private final String modifiedResidueName;
private final List atoms;
private ImmutableDefaultPdbResidue(
PdbResidueIdentifier identifier,
String standardResidueName,
String modifiedResidueName,
Iterable atoms) {
this.identifier = Objects.requireNonNull(identifier, "identifier");
this.standardResidueName = Objects.requireNonNull(standardResidueName, "standardResidueName");
this.modifiedResidueName = Objects.requireNonNull(modifiedResidueName, "modifiedResidueName");
this.atoms = createUnmodifiableList(false, createSafeList(atoms, true, false));
}
private ImmutableDefaultPdbResidue(
ImmutableDefaultPdbResidue original,
PdbResidueIdentifier identifier,
String standardResidueName,
String modifiedResidueName,
List atoms) {
this.identifier = identifier;
this.standardResidueName = standardResidueName;
this.modifiedResidueName = modifiedResidueName;
this.atoms = atoms;
}
/**
* @return The value of the {@code identifier} attribute
*/
@Override
public PdbResidueIdentifier identifier() {
return identifier;
}
/**
* @return The value of the {@code standardResidueName} attribute
*/
@Override
public String standardResidueName() {
return standardResidueName;
}
/**
* @return The value of the {@code modifiedResidueName} attribute
*/
@Override
public String modifiedResidueName() {
return modifiedResidueName;
}
/**
* @return The value of the {@code atoms} attribute
*/
@Override
public List atoms() {
return atoms;
}
/**
* Copy the current immutable object by setting a value for the {@link DefaultPdbResidue#identifier() identifier} attribute.
* A shallow reference equality check is used to prevent copying of the same value by returning {@code this}.
* @param value A new value for identifier
* @return A modified copy of the {@code this} object
*/
public final ImmutableDefaultPdbResidue withIdentifier(PdbResidueIdentifier value) {
if (this.identifier == value) return this;
PdbResidueIdentifier newValue = Objects.requireNonNull(value, "identifier");
return new ImmutableDefaultPdbResidue(this, newValue, this.standardResidueName, this.modifiedResidueName, this.atoms);
}
/**
* Copy the current immutable object by setting a value for the {@link DefaultPdbResidue#standardResidueName() standardResidueName} attribute.
* An equals check used to prevent copying of the same value by returning {@code this}.
* @param value A new value for standardResidueName
* @return A modified copy of the {@code this} object
*/
public final ImmutableDefaultPdbResidue withStandardResidueName(String value) {
String newValue = Objects.requireNonNull(value, "standardResidueName");
if (this.standardResidueName.equals(newValue)) return this;
return new ImmutableDefaultPdbResidue(this, this.identifier, newValue, this.modifiedResidueName, this.atoms);
}
/**
* Copy the current immutable object by setting a value for the {@link DefaultPdbResidue#modifiedResidueName() modifiedResidueName} attribute.
* An equals check used to prevent copying of the same value by returning {@code this}.
* @param value A new value for modifiedResidueName
* @return A modified copy of the {@code this} object
*/
public final ImmutableDefaultPdbResidue withModifiedResidueName(String value) {
String newValue = Objects.requireNonNull(value, "modifiedResidueName");
if (this.modifiedResidueName.equals(newValue)) return this;
return new ImmutableDefaultPdbResidue(this, this.identifier, this.standardResidueName, newValue, this.atoms);
}
/**
* Copy the current immutable object with elements that replace the content of {@link DefaultPdbResidue#atoms() atoms}.
* @param elements The elements to set
* @return A modified copy of {@code this} object
*/
public final ImmutableDefaultPdbResidue withAtoms(PdbAtomLine... elements) {
List newValue = createUnmodifiableList(false, createSafeList(Arrays.asList(elements), true, false));
return new ImmutableDefaultPdbResidue(this, this.identifier, this.standardResidueName, this.modifiedResidueName, newValue);
}
/**
* Copy the current immutable object with elements that replace the content of {@link DefaultPdbResidue#atoms() atoms}.
* A shallow reference equality check is used to prevent copying of the same value by returning {@code this}.
* @param elements An iterable of atoms elements to set
* @return A modified copy of {@code this} object
*/
public final ImmutableDefaultPdbResidue withAtoms(Iterable elements) {
if (this.atoms == elements) return this;
List newValue = createUnmodifiableList(false, createSafeList(elements, true, false));
return new ImmutableDefaultPdbResidue(this, this.identifier, this.standardResidueName, this.modifiedResidueName, newValue);
}
/**
* This instance is equal to all instances of {@code ImmutableDefaultPdbResidue} that have equal attribute values.
* @return {@code true} if {@code this} is equal to {@code another} instance
*/
@Override
public boolean equals(@Nullable Object another) {
if (this == another) return true;
return another instanceof ImmutableDefaultPdbResidue
&& equalTo((ImmutableDefaultPdbResidue) another);
}
private boolean equalTo(ImmutableDefaultPdbResidue another) {
return identifier.equals(another.identifier)
&& standardResidueName.equals(another.standardResidueName)
&& modifiedResidueName.equals(another.modifiedResidueName)
&& atoms.equals(another.atoms);
}
/**
* Computes a hash code from attributes: {@code identifier}, {@code standardResidueName}, {@code modifiedResidueName}, {@code atoms}.
* @return hashCode value
*/
@Override
public int hashCode() {
int h = 5381;
h += (h << 5) + identifier.hashCode();
h += (h << 5) + standardResidueName.hashCode();
h += (h << 5) + modifiedResidueName.hashCode();
h += (h << 5) + atoms.hashCode();
return h;
}
private transient volatile long lazyInitBitmap;
private static final long RESIDUE_INFORMATION_PROVIDER_LAZY_INIT_BIT = 0x1L;
private transient ResidueInformationProvider residueInformationProvider;
/**
* {@inheritDoc}
*
* Returns a lazily initialized value of the {@link DefaultPdbResidue#residueInformationProvider() residueInformationProvider} 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.
* @return A lazily initialized value of the {@code residueInformationProvider} attribute
*/
@Override
public ResidueInformationProvider residueInformationProvider() {
if ((lazyInitBitmap & RESIDUE_INFORMATION_PROVIDER_LAZY_INIT_BIT) == 0) {
synchronized (this) {
if ((lazyInitBitmap & RESIDUE_INFORMATION_PROVIDER_LAZY_INIT_BIT) == 0) {
this.residueInformationProvider = Objects.requireNonNull(super.residueInformationProvider(), "residueInformationProvider");
lazyInitBitmap |= RESIDUE_INFORMATION_PROVIDER_LAZY_INIT_BIT;
}
}
}
return residueInformationProvider;
}
private static final long ATOM_NAMES_LAZY_INIT_BIT = 0x2L;
private transient Set atomNames;
/**
* {@inheritDoc}
*
* Returns a lazily initialized value of the {@link DefaultPdbResidue#atomNames() atomNames} 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.
* @return A lazily initialized value of the {@code atomNames} attribute
*/
@Override
public Set atomNames() {
if ((lazyInitBitmap & ATOM_NAMES_LAZY_INIT_BIT) == 0) {
synchronized (this) {
if ((lazyInitBitmap & ATOM_NAMES_LAZY_INIT_BIT) == 0) {
this.atomNames = Objects.requireNonNull(super.atomNames(), "atomNames");
lazyInitBitmap |= ATOM_NAMES_LAZY_INIT_BIT;
}
}
}
return atomNames;
}
private static final long HAS_ALL_HEAVY_ATOMS_LAZY_INIT_BIT = 0x4L;
private transient boolean hasAllHeavyAtoms;
/**
* {@inheritDoc}
*
* Returns a lazily initialized value of the {@link DefaultPdbResidue#hasAllHeavyAtoms() hasAllHeavyAtoms} 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.
* @return A lazily initialized value of the {@code hasAllHeavyAtoms} attribute
*/
@Override
public boolean hasAllHeavyAtoms() {
if ((lazyInitBitmap & HAS_ALL_HEAVY_ATOMS_LAZY_INIT_BIT) == 0) {
synchronized (this) {
if ((lazyInitBitmap & HAS_ALL_HEAVY_ATOMS_LAZY_INIT_BIT) == 0) {
this.hasAllHeavyAtoms = super.hasAllHeavyAtoms();
lazyInitBitmap |= HAS_ALL_HEAVY_ATOMS_LAZY_INIT_BIT;
}
}
}
return hasAllHeavyAtoms;
}
/**
* Construct a new immutable {@code DefaultPdbResidue} instance.
* @param identifier The value for the {@code identifier} attribute
* @param standardResidueName The value for the {@code standardResidueName} attribute
* @param modifiedResidueName The value for the {@code modifiedResidueName} attribute
* @param atoms The value for the {@code atoms} attribute
* @return An immutable DefaultPdbResidue instance
*/
public static ImmutableDefaultPdbResidue of(PdbResidueIdentifier identifier, String standardResidueName, String modifiedResidueName, List atoms) {
return of(identifier, standardResidueName, modifiedResidueName, (Iterable) atoms);
}
/**
* Construct a new immutable {@code DefaultPdbResidue} instance.
* @param identifier The value for the {@code identifier} attribute
* @param standardResidueName The value for the {@code standardResidueName} attribute
* @param modifiedResidueName The value for the {@code modifiedResidueName} attribute
* @param atoms The value for the {@code atoms} attribute
* @return An immutable DefaultPdbResidue instance
*/
public static ImmutableDefaultPdbResidue of(PdbResidueIdentifier identifier, String standardResidueName, String modifiedResidueName, Iterable atoms) {
return new ImmutableDefaultPdbResidue(identifier, standardResidueName, modifiedResidueName, atoms);
}
/**
* Creates an immutable copy of a {@link DefaultPdbResidue} value.
* Uses accessors to get values to initialize the new immutable instance.
* If an instance is already immutable, it is returned as is.
* @param instance The instance to copy
* @return A copied immutable DefaultPdbResidue instance
*/
public static ImmutableDefaultPdbResidue copyOf(DefaultPdbResidue instance) {
if (instance instanceof ImmutableDefaultPdbResidue) {
return (ImmutableDefaultPdbResidue) instance;
}
return ImmutableDefaultPdbResidue.builder()
.from(instance)
.build();
}
/**
* Creates a builder for {@link ImmutableDefaultPdbResidue ImmutableDefaultPdbResidue}.
*
* ImmutableDefaultPdbResidue.builder()
* .identifier(pl.poznan.put.pdb.PdbResidueIdentifier) // required {@link DefaultPdbResidue#identifier() identifier}
* .standardResidueName(String) // required {@link DefaultPdbResidue#standardResidueName() standardResidueName}
* .modifiedResidueName(String) // required {@link DefaultPdbResidue#modifiedResidueName() modifiedResidueName}
* .addAtoms|addAllAtoms(pl.poznan.put.pdb.PdbAtomLine) // {@link DefaultPdbResidue#atoms() atoms} elements
* .build();
*
* @return A new ImmutableDefaultPdbResidue builder
*/
public static ImmutableDefaultPdbResidue.Builder builder() {
return new ImmutableDefaultPdbResidue.Builder();
}
/**
* Builds instances of type {@link ImmutableDefaultPdbResidue ImmutableDefaultPdbResidue}.
* Initialize attributes and then invoke the {@link #build()} method to create an
* immutable instance.
* {@code Builder} is not thread-safe and generally should not be stored in a field or collection,
* but instead used immediately to create instances.
*/
@Generated(from = "DefaultPdbResidue", generator = "Immutables")
@NotThreadSafe
public static final class Builder {
private static final long INIT_BIT_IDENTIFIER = 0x1L;
private static final long INIT_BIT_STANDARD_RESIDUE_NAME = 0x2L;
private static final long INIT_BIT_MODIFIED_RESIDUE_NAME = 0x4L;
private long initBits = 0x7L;
private @Nullable PdbResidueIdentifier identifier;
private @Nullable String standardResidueName;
private @Nullable String modifiedResidueName;
private List atoms = new ArrayList();
private Builder() {
}
/**
* Fill a builder with attribute values from the provided {@code pl.poznan.put.pdb.analysis.PdbResidue} instance.
* @param instance The instance from which to copy values
* @return {@code this} builder for use in a chained invocation
*/
public final Builder from(PdbResidue instance) {
Objects.requireNonNull(instance, "instance");
from((Object) instance);
return this;
}
/**
* Fill a builder with attribute values from the provided {@code pl.poznan.put.pdb.analysis.DefaultPdbResidue} instance.
* @param instance The instance from which to copy values
* @return {@code this} builder for use in a chained invocation
*/
public final Builder from(DefaultPdbResidue instance) {
Objects.requireNonNull(instance, "instance");
from((Object) instance);
return this;
}
private void from(Object object) {
long bits = 0;
if (object instanceof PdbResidue) {
PdbResidue instance = (PdbResidue) object;
if ((bits & 0x1L) == 0) {
standardResidueName(instance.standardResidueName());
bits |= 0x1L;
}
if ((bits & 0x2L) == 0) {
identifier(instance.identifier());
bits |= 0x2L;
}
if ((bits & 0x4L) == 0) {
modifiedResidueName(instance.modifiedResidueName());
bits |= 0x4L;
}
if ((bits & 0x8L) == 0) {
addAllAtoms(instance.atoms());
bits |= 0x8L;
}
}
if (object instanceof DefaultPdbResidue) {
DefaultPdbResidue instance = (DefaultPdbResidue) object;
if ((bits & 0x1L) == 0) {
standardResidueName(instance.standardResidueName());
bits |= 0x1L;
}
if ((bits & 0x2L) == 0) {
identifier(instance.identifier());
bits |= 0x2L;
}
if ((bits & 0x4L) == 0) {
modifiedResidueName(instance.modifiedResidueName());
bits |= 0x4L;
}
if ((bits & 0x8L) == 0) {
addAllAtoms(instance.atoms());
bits |= 0x8L;
}
}
}
/**
* Initializes the value for the {@link DefaultPdbResidue#identifier() identifier} attribute.
* @param identifier The value for identifier
* @return {@code this} builder for use in a chained invocation
*/
public final Builder identifier(PdbResidueIdentifier identifier) {
this.identifier = Objects.requireNonNull(identifier, "identifier");
initBits &= ~INIT_BIT_IDENTIFIER;
return this;
}
/**
* Initializes the value for the {@link DefaultPdbResidue#standardResidueName() standardResidueName} attribute.
* @param standardResidueName The value for standardResidueName
* @return {@code this} builder for use in a chained invocation
*/
public final Builder standardResidueName(String standardResidueName) {
this.standardResidueName = Objects.requireNonNull(standardResidueName, "standardResidueName");
initBits &= ~INIT_BIT_STANDARD_RESIDUE_NAME;
return this;
}
/**
* Initializes the value for the {@link DefaultPdbResidue#modifiedResidueName() modifiedResidueName} attribute.
* @param modifiedResidueName The value for modifiedResidueName
* @return {@code this} builder for use in a chained invocation
*/
public final Builder modifiedResidueName(String modifiedResidueName) {
this.modifiedResidueName = Objects.requireNonNull(modifiedResidueName, "modifiedResidueName");
initBits &= ~INIT_BIT_MODIFIED_RESIDUE_NAME;
return this;
}
/**
* Adds one element to {@link DefaultPdbResidue#atoms() atoms} list.
* @param element A atoms element
* @return {@code this} builder for use in a chained invocation
*/
public final Builder addAtoms(PdbAtomLine element) {
this.atoms.add(Objects.requireNonNull(element, "atoms element"));
return this;
}
/**
* Adds elements to {@link DefaultPdbResidue#atoms() atoms} list.
* @param elements An array of atoms elements
* @return {@code this} builder for use in a chained invocation
*/
public final Builder addAtoms(PdbAtomLine... elements) {
for (PdbAtomLine element : elements) {
this.atoms.add(Objects.requireNonNull(element, "atoms element"));
}
return this;
}
/**
* Sets or replaces all elements for {@link DefaultPdbResidue#atoms() atoms} list.
* @param elements An iterable of atoms elements
* @return {@code this} builder for use in a chained invocation
*/
public final Builder atoms(Iterable elements) {
this.atoms.clear();
return addAllAtoms(elements);
}
/**
* Adds elements to {@link DefaultPdbResidue#atoms() atoms} list.
* @param elements An iterable of atoms elements
* @return {@code this} builder for use in a chained invocation
*/
public final Builder addAllAtoms(Iterable elements) {
for (PdbAtomLine element : elements) {
this.atoms.add(Objects.requireNonNull(element, "atoms element"));
}
return this;
}
/**
* Builds a new {@link ImmutableDefaultPdbResidue ImmutableDefaultPdbResidue}.
* @return An immutable instance of DefaultPdbResidue
* @throws java.lang.IllegalStateException if any required attributes are missing
*/
public ImmutableDefaultPdbResidue build() {
if (initBits != 0) {
throw new IllegalStateException(formatRequiredAttributesMessage());
}
return new ImmutableDefaultPdbResidue(
null,
identifier,
standardResidueName,
modifiedResidueName,
createUnmodifiableList(true, atoms));
}
private String formatRequiredAttributesMessage() {
List attributes = new ArrayList<>();
if ((initBits & INIT_BIT_IDENTIFIER) != 0) attributes.add("identifier");
if ((initBits & INIT_BIT_STANDARD_RESIDUE_NAME) != 0) attributes.add("standardResidueName");
if ((initBits & INIT_BIT_MODIFIED_RESIDUE_NAME) != 0) attributes.add("modifiedResidueName");
return "Cannot build DefaultPdbResidue, some of required attributes are not set " + attributes;
}
}
private static List createSafeList(Iterable iterable, boolean checkNulls, boolean skipNulls) {
ArrayList list;
if (iterable instanceof Collection) {
int size = ((Collection) iterable).size();
if (size == 0) return Collections.emptyList();
list = new ArrayList<>();
} else {
list = new ArrayList<>();
}
for (T element : iterable) {
if (skipNulls && element == null) continue;
if (checkNulls) Objects.requireNonNull(element, "element");
list.add(element);
}
return list;
}
private static List createUnmodifiableList(boolean clone, List list) {
switch(list.size()) {
case 0: return Collections.emptyList();
case 1: return Collections.singletonList(list.get(0));
default:
if (clone) {
return Collections.unmodifiableList(new ArrayList<>(list));
} else {
if (list instanceof ArrayList) {
((ArrayList) list).trimToSize();
}
return Collections.unmodifiableList(list);
}
}
}
}