pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb Maven / Gradle / Ivy
package pl.poznan.put.structure.formats;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import javax.annotation.Nullable;
import javax.annotation.ParametersAreNonnullByDefault;
import javax.annotation.concurrent.Immutable;
import javax.annotation.concurrent.NotThreadSafe;
import org.apache.commons.collections4.BidiMap;
import org.immutables.value.Generated;
import pl.poznan.put.pdb.PdbNamedResidueIdentifier;
import pl.poznan.put.structure.DotBracketSymbol;
/**
* Immutable implementation of {@link CombinedStrandFromPdb}.
*
* Use the builder to create immutable instances:
* {@code ImmutableCombinedStrandFromPdb.builder()}.
* Use the static factory method to create immutable instances:
* {@code ImmutableCombinedStrandFromPdb.of()}.
*/
@Generated(from = "CombinedStrandFromPdb", generator = "Immutables")
@SuppressWarnings({"all"})
@ParametersAreNonnullByDefault
@javax.annotation.processing.Generated("org.immutables.processor.ProxyProcessor")
@Immutable
public final class ImmutableCombinedStrandFromPdb
extends CombinedStrandFromPdb {
private final List combineStrands;
private final List inputStrands;
private final Map inputSymbolToResidue;
private ImmutableCombinedStrandFromPdb(
Iterable inputStrands,
Map inputSymbolToResidue) {
this.inputStrands = createUnmodifiableList(false, createSafeList(inputStrands, true, false));
this.inputSymbolToResidue = createUnmodifiableMap(true, false, inputSymbolToResidue);
this.combineStrands = Collections.emptyList();
}
private ImmutableCombinedStrandFromPdb(
List combineStrands,
List inputStrands,
Map inputSymbolToResidue) {
this.combineStrands = combineStrands;
this.inputStrands = inputStrands;
this.inputSymbolToResidue = inputSymbolToResidue;
}
/**
* Combines strands which share a base pair into a new dot-bracket instance and returns a list of
* those.
* @return The list of dot-bracket instances, each containing strands which only pair with each
* other.
*/
@Override
public List combineStrands() {
return combineStrands;
}
/**
*@return The list of input strands.
*/
@Override
protected List inputStrands() {
return inputStrands;
}
/**
*@return The mapping of dot-bracket symbols with corresponding PDB identifiers.
*/
@Override
protected Map inputSymbolToResidue() {
return inputSymbolToResidue;
}
/**
* Copy the current immutable object with elements that replace the content of {@link CombinedStrandFromPdb#combineStrands() combineStrands}.
* @param elements The elements to set
* @return A modified copy of {@code this} object
*/
public final ImmutableCombinedStrandFromPdb withCombineStrands(DotBracket... elements) {
List newValue = createUnmodifiableList(false, createSafeList(Arrays.asList(elements), true, false));
return new ImmutableCombinedStrandFromPdb(newValue, this.inputStrands, this.inputSymbolToResidue);
}
/**
* Copy the current immutable object with elements that replace the content of {@link CombinedStrandFromPdb#combineStrands() combineStrands}.
* A shallow reference equality check is used to prevent copying of the same value by returning {@code this}.
* @param elements An iterable of combineStrands elements to set
* @return A modified copy of {@code this} object
*/
public final ImmutableCombinedStrandFromPdb withCombineStrands(Iterable elements) {
if (this.combineStrands == elements) return this;
List newValue = createUnmodifiableList(false, createSafeList(elements, true, false));
return new ImmutableCombinedStrandFromPdb(newValue, this.inputStrands, this.inputSymbolToResidue);
}
/**
* Copy the current immutable object with elements that replace the content of {@link CombinedStrandFromPdb#inputStrands() inputStrands}.
* @param elements The elements to set
* @return A modified copy of {@code this} object
*/
public final ImmutableCombinedStrandFromPdb withInputStrands(Strand... elements) {
List newValue = createUnmodifiableList(false, createSafeList(Arrays.asList(elements), true, false));
return new ImmutableCombinedStrandFromPdb(this.combineStrands, newValue, this.inputSymbolToResidue);
}
/**
* Copy the current immutable object with elements that replace the content of {@link CombinedStrandFromPdb#inputStrands() inputStrands}.
* A shallow reference equality check is used to prevent copying of the same value by returning {@code this}.
* @param elements An iterable of inputStrands elements to set
* @return A modified copy of {@code this} object
*/
public final ImmutableCombinedStrandFromPdb withInputStrands(Iterable elements) {
if (this.inputStrands == elements) return this;
List newValue = createUnmodifiableList(false, createSafeList(elements, true, false));
return new ImmutableCombinedStrandFromPdb(this.combineStrands, newValue, this.inputSymbolToResidue);
}
/**
* Copy the current immutable object by replacing the {@link CombinedStrandFromPdb#inputSymbolToResidue() 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 {@code this}.
* @param entries The entries to be added to the inputSymbolToResidue map
* @return A modified copy of {@code this} object
*/
public final ImmutableCombinedStrandFromPdb withInputSymbolToResidue(Map entries) {
if (this.inputSymbolToResidue == entries) return this;
Map newValue = createUnmodifiableMap(true, false, entries);
return new ImmutableCombinedStrandFromPdb(this.combineStrands, this.inputStrands, newValue);
}
/**
* This instance is equal to all instances of {@code ImmutableCombinedStrandFromPdb} 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 ImmutableCombinedStrandFromPdb
&& equalTo((ImmutableCombinedStrandFromPdb) another);
}
private boolean equalTo(ImmutableCombinedStrandFromPdb another) {
return combineStrands.equals(another.combineStrands)
&& inputStrands.equals(another.inputStrands)
&& inputSymbolToResidue.equals(another.inputSymbolToResidue);
}
/**
* Computes a hash code from attributes: {@code combineStrands}, {@code inputStrands}, {@code inputSymbolToResidue}.
* @return hashCode value
*/
@Override
public int hashCode() {
int h = 5381;
h += (h << 5) + combineStrands.hashCode();
h += (h << 5) + inputStrands.hashCode();
h += (h << 5) + inputSymbolToResidue.hashCode();
return h;
}
/**
* Prints the immutable value {@code CombinedStrandFromPdb} with attribute values.
* @return A string representation of the value
*/
@Override
public String toString() {
return "CombinedStrandFromPdb{"
+ "combineStrands=" + combineStrands
+ ", inputStrands=" + inputStrands
+ ", inputSymbolToResidue=" + inputSymbolToResidue
+ "}";
}
private transient volatile long lazyInitBitmap;
private static final long SYMBOLS_LAZY_INIT_BIT = 0x1L;
private transient List symbols;
/**
* {@inheritDoc}
*
* Returns a lazily initialized value of the {@link CombinedStrandFromPdb#symbols() 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.
* @return A lazily initialized value of the {@code symbols} attribute
*/
@Override
public List symbols() {
if ((lazyInitBitmap & SYMBOLS_LAZY_INIT_BIT) == 0) {
synchronized (this) {
if ((lazyInitBitmap & SYMBOLS_LAZY_INIT_BIT) == 0) {
this.symbols = Objects.requireNonNull(super.symbols(), "symbols");
lazyInitBitmap |= SYMBOLS_LAZY_INIT_BIT;
}
}
}
return symbols;
}
private static final long STRANDS_LAZY_INIT_BIT = 0x2L;
private transient List strands;
/**
* {@inheritDoc}
*
* Returns a lazily initialized value of the {@link CombinedStrandFromPdb#strands() 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.
* @return A lazily initialized value of the {@code strands} attribute
*/
@Override
public List strands() {
if ((lazyInitBitmap & STRANDS_LAZY_INIT_BIT) == 0) {
synchronized (this) {
if ((lazyInitBitmap & STRANDS_LAZY_INIT_BIT) == 0) {
this.strands = Objects.requireNonNull(super.strands(), "strands");
lazyInitBitmap |= STRANDS_LAZY_INIT_BIT;
}
}
}
return strands;
}
private static final long PAIRS_LAZY_INIT_BIT = 0x4L;
private transient Map pairs;
/**
* {@inheritDoc}
*
* Returns a lazily initialized value of the {@link CombinedStrandFromPdb#pairs() 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.
* @return A lazily initialized value of the {@code pairs} attribute
*/
@Override
public Map pairs() {
if ((lazyInitBitmap & PAIRS_LAZY_INIT_BIT) == 0) {
synchronized (this) {
if ((lazyInitBitmap & PAIRS_LAZY_INIT_BIT) == 0) {
this.pairs = Objects.requireNonNull(super.pairs(), "pairs");
lazyInitBitmap |= PAIRS_LAZY_INIT_BIT;
}
}
}
return pairs;
}
private static final long SYMBOL_TO_RESIDUE_LAZY_INIT_BIT = 0x8L;
private transient Map symbolToResidue;
/**
* {@inheritDoc}
*
* Returns a lazily initialized value of the {@link CombinedStrandFromPdb#symbolToResidue() 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.
* @return A lazily initialized value of the {@code symbolToResidue} attribute
*/
@Override
protected Map symbolToResidue() {
if ((lazyInitBitmap & SYMBOL_TO_RESIDUE_LAZY_INIT_BIT) == 0) {
synchronized (this) {
if ((lazyInitBitmap & SYMBOL_TO_RESIDUE_LAZY_INIT_BIT) == 0) {
this.symbolToResidue = Objects.requireNonNull(super.symbolToResidue(), "symbolToResidue");
lazyInitBitmap |= SYMBOL_TO_RESIDUE_LAZY_INIT_BIT;
}
}
}
return symbolToResidue;
}
private static final long MAPPING_LAZY_INIT_BIT = 0x10L;
private transient BidiMap mapping;
/**
* {@inheritDoc}
*
* Returns a lazily initialized value of the {@link CombinedStrandFromPdb#mapping() 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.
* @return A lazily initialized value of the {@code mapping} attribute
*/
@Override
protected BidiMap mapping() {
if ((lazyInitBitmap & MAPPING_LAZY_INIT_BIT) == 0) {
synchronized (this) {
if ((lazyInitBitmap & MAPPING_LAZY_INIT_BIT) == 0) {
this.mapping = Objects.requireNonNull(super.mapping(), "mapping");
lazyInitBitmap |= MAPPING_LAZY_INIT_BIT;
}
}
}
return mapping;
}
/**
* Construct a new immutable {@code CombinedStrandFromPdb} instance.
* @param inputStrands The value for the {@code inputStrands} attribute
* @param inputSymbolToResidue The value for the {@code inputSymbolToResidue} attribute
* @return An immutable CombinedStrandFromPdb instance
*/
public static ImmutableCombinedStrandFromPdb of(List inputStrands, Map inputSymbolToResidue) {
return of((Iterable) inputStrands, inputSymbolToResidue);
}
/**
* Construct a new immutable {@code CombinedStrandFromPdb} instance.
* @param inputStrands The value for the {@code inputStrands} attribute
* @param inputSymbolToResidue The value for the {@code inputSymbolToResidue} attribute
* @return An immutable CombinedStrandFromPdb instance
*/
public static ImmutableCombinedStrandFromPdb of(Iterable inputStrands, Map inputSymbolToResidue) {
return new ImmutableCombinedStrandFromPdb(inputStrands, inputSymbolToResidue);
}
/**
* Creates an immutable copy of a {@link CombinedStrandFromPdb} 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 CombinedStrandFromPdb instance
*/
public static ImmutableCombinedStrandFromPdb copyOf(CombinedStrandFromPdb instance) {
if (instance instanceof ImmutableCombinedStrandFromPdb) {
return (ImmutableCombinedStrandFromPdb) instance;
}
return ImmutableCombinedStrandFromPdb.builder()
.from(instance)
.build();
}
/**
* Creates a builder for {@link ImmutableCombinedStrandFromPdb ImmutableCombinedStrandFromPdb}.
*
* ImmutableCombinedStrandFromPdb.builder()
* .addCombineStrands|addAllCombineStrands(pl.poznan.put.structure.formats.DotBracket) // {@link CombinedStrandFromPdb#combineStrands() combineStrands} elements
* .addInputStrands|addAllInputStrands(pl.poznan.put.structure.formats.Strand) // {@link CombinedStrandFromPdb#inputStrands() inputStrands} elements
* .putInputSymbolToResidue|putAllInputSymbolToResidue(pl.poznan.put.structure.DotBracketSymbol => pl.poznan.put.pdb.PdbNamedResidueIdentifier) // {@link CombinedStrandFromPdb#inputSymbolToResidue() inputSymbolToResidue} mappings
* .build();
*
* @return A new ImmutableCombinedStrandFromPdb builder
*/
public static ImmutableCombinedStrandFromPdb.Builder builder() {
return new ImmutableCombinedStrandFromPdb.Builder();
}
/**
* Builds instances of type {@link ImmutableCombinedStrandFromPdb ImmutableCombinedStrandFromPdb}.
* 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 = "CombinedStrandFromPdb", generator = "Immutables")
@NotThreadSafe
public static final class Builder {
private List combineStrands = new ArrayList();
private List inputStrands = new ArrayList();
private Map inputSymbolToResidue = new LinkedHashMap();
private Builder() {
}
/**
* Fill a builder with attribute values from the provided {@code pl.poznan.put.structure.formats.CombinedStrandFromPdb} instance.
* @param instance The instance from which to copy values
* @return {@code this} builder for use in a chained invocation
*/
public final Builder from(CombinedStrandFromPdb instance) {
Objects.requireNonNull(instance, "instance");
from((Object) instance);
return this;
}
/**
* Fill a builder with attribute values from the provided {@code pl.poznan.put.structure.formats.AbstractCombinedStrand} instance.
* @param instance The instance from which to copy values
* @return {@code this} builder for use in a chained invocation
*/
public final Builder from(AbstractCombinedStrand instance) {
Objects.requireNonNull(instance, "instance");
from((Object) instance);
return this;
}
/**
* Fill a builder with attribute values from the provided {@code pl.poznan.put.structure.formats.DotBracket} instance.
* @param instance The instance from which to copy values
* @return {@code this} builder for use in a chained invocation
*/
public final Builder from(DotBracket instance) {
Objects.requireNonNull(instance, "instance");
from((Object) instance);
return this;
}
private void from(Object object) {
long bits = 0;
if (object instanceof CombinedStrandFromPdb) {
CombinedStrandFromPdb instance = (CombinedStrandFromPdb) object;
putAllInputSymbolToResidue(instance.inputSymbolToResidue());
if ((bits & 0x1L) == 0) {
addAllInputStrands(instance.inputStrands());
bits |= 0x1L;
}
}
if (object instanceof AbstractCombinedStrand) {
AbstractCombinedStrand instance = (AbstractCombinedStrand) object;
if ((bits & 0x1L) == 0) {
addAllInputStrands(instance.inputStrands());
bits |= 0x1L;
}
}
if (object instanceof DotBracket) {
DotBracket instance = (DotBracket) object;
addAllCombineStrands(instance.combineStrands());
}
}
/**
* Adds one element to {@link CombinedStrandFromPdb#combineStrands() combineStrands} list.
* @param element A combineStrands element
* @return {@code this} builder for use in a chained invocation
*/
public final Builder addCombineStrands(DotBracket element) {
this.combineStrands.add(Objects.requireNonNull(element, "combineStrands element"));
return this;
}
/**
* Adds elements to {@link CombinedStrandFromPdb#combineStrands() combineStrands} list.
* @param elements An array of combineStrands elements
* @return {@code this} builder for use in a chained invocation
*/
public final Builder addCombineStrands(DotBracket... elements) {
for (DotBracket element : elements) {
this.combineStrands.add(Objects.requireNonNull(element, "combineStrands element"));
}
return this;
}
/**
* Sets or replaces all elements for {@link CombinedStrandFromPdb#combineStrands() combineStrands} list.
* @param elements An iterable of combineStrands elements
* @return {@code this} builder for use in a chained invocation
*/
public final Builder combineStrands(Iterable elements) {
this.combineStrands.clear();
return addAllCombineStrands(elements);
}
/**
* Adds elements to {@link CombinedStrandFromPdb#combineStrands() combineStrands} list.
* @param elements An iterable of combineStrands elements
* @return {@code this} builder for use in a chained invocation
*/
public final Builder addAllCombineStrands(Iterable elements) {
for (DotBracket element : elements) {
this.combineStrands.add(Objects.requireNonNull(element, "combineStrands element"));
}
return this;
}
/**
* Adds one element to {@link CombinedStrandFromPdb#inputStrands() inputStrands} list.
* @param element A inputStrands element
* @return {@code this} builder for use in a chained invocation
*/
public final Builder addInputStrands(Strand element) {
this.inputStrands.add(Objects.requireNonNull(element, "inputStrands element"));
return this;
}
/**
* Adds elements to {@link CombinedStrandFromPdb#inputStrands() inputStrands} list.
* @param elements An array of inputStrands elements
* @return {@code this} builder for use in a chained invocation
*/
public final Builder addInputStrands(Strand... elements) {
for (Strand element : elements) {
this.inputStrands.add(Objects.requireNonNull(element, "inputStrands element"));
}
return this;
}
/**
* Sets or replaces all elements for {@link CombinedStrandFromPdb#inputStrands() inputStrands} list.
* @param elements An iterable of inputStrands elements
* @return {@code this} builder for use in a chained invocation
*/
public final Builder inputStrands(Iterable elements) {
this.inputStrands.clear();
return addAllInputStrands(elements);
}
/**
* Adds elements to {@link CombinedStrandFromPdb#inputStrands() inputStrands} list.
* @param elements An iterable of inputStrands elements
* @return {@code this} builder for use in a chained invocation
*/
public final Builder addAllInputStrands(Iterable elements) {
for (Strand element : elements) {
this.inputStrands.add(Objects.requireNonNull(element, "inputStrands element"));
}
return this;
}
/**
* Put one entry to the {@link CombinedStrandFromPdb#inputSymbolToResidue() inputSymbolToResidue} map.
* @param key The key in the inputSymbolToResidue map
* @param value The associated value in the inputSymbolToResidue map
* @return {@code this} builder for use in a chained invocation
*/
public final Builder putInputSymbolToResidue(DotBracketSymbol key, PdbNamedResidueIdentifier value) {
this.inputSymbolToResidue.put(
Objects.requireNonNull(key, "inputSymbolToResidue key"),
Objects.requireNonNull(value, "inputSymbolToResidue value"));
return this;
}
/**
* Put one entry to the {@link CombinedStrandFromPdb#inputSymbolToResidue() inputSymbolToResidue} map. Nulls are not permitted
* @param entry The key and value entry
* @return {@code this} builder for use in a chained invocation
*/
public final Builder putInputSymbolToResidue(Map.Entry entry) {
DotBracketSymbol k = entry.getKey();
PdbNamedResidueIdentifier v = entry.getValue();
this.inputSymbolToResidue.put(
Objects.requireNonNull(k, "inputSymbolToResidue key"),
Objects.requireNonNull(v, "inputSymbolToResidue value"));
return this;
}
/**
* Sets or replaces all mappings from the specified map as entries for the {@link CombinedStrandFromPdb#inputSymbolToResidue() inputSymbolToResidue} map. Nulls are not permitted
* @param entries The entries that will be added to the inputSymbolToResidue map
* @return {@code this} builder for use in a chained invocation
*/
public final Builder inputSymbolToResidue(Map entries) {
this.inputSymbolToResidue.clear();
return putAllInputSymbolToResidue(entries);
}
/**
* Put all mappings from the specified map as entries to {@link CombinedStrandFromPdb#inputSymbolToResidue() inputSymbolToResidue} map. Nulls are not permitted
* @param entries The entries that will be added to the inputSymbolToResidue map
* @return {@code this} builder for use in a chained invocation
*/
public final Builder putAllInputSymbolToResidue(Map entries) {
for (Map.Entry e : entries.entrySet()) {
DotBracketSymbol k = e.getKey();
PdbNamedResidueIdentifier v = e.getValue();
this.inputSymbolToResidue.put(
Objects.requireNonNull(k, "inputSymbolToResidue key"),
Objects.requireNonNull(v, "inputSymbolToResidue value"));
}
return this;
}
/**
* Builds a new {@link ImmutableCombinedStrandFromPdb ImmutableCombinedStrandFromPdb}.
* @return An immutable instance of CombinedStrandFromPdb
* @throws java.lang.IllegalStateException if any required attributes are missing
*/
public ImmutableCombinedStrandFromPdb build() {
return new ImmutableCombinedStrandFromPdb(
createUnmodifiableList(true, combineStrands),
createUnmodifiableList(true, inputStrands),
createUnmodifiableMap(false, false, inputSymbolToResidue));
}
}
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);
}
}
}
private static Map createUnmodifiableMap(boolean checkNulls, boolean skipNulls, Map map) {
switch (map.size()) {
case 0: return Collections.emptyMap();
case 1: {
Map.Entry e = map.entrySet().iterator().next();
K k = e.getKey();
V v = e.getValue();
if (checkNulls) {
Objects.requireNonNull(k, "key");
Objects.requireNonNull(v, "value");
}
if (skipNulls && (k == null || v == null)) {
return Collections.emptyMap();
}
return Collections.singletonMap(k, v);
}
default: {
Map linkedMap = new LinkedHashMap<>(map.size());
if (skipNulls || checkNulls) {
for (Map.Entry e : map.entrySet()) {
K k = e.getKey();
V v = e.getValue();
if (skipNulls) {
if (k == null || v == null) continue;
} else if (checkNulls) {
Objects.requireNonNull(k, "key");
Objects.requireNonNull(v, "value");
}
linkedMap.put(k, v);
}
} else {
linkedMap.putAll(map);
}
return Collections.unmodifiableMap(linkedMap);
}
}
}
}