org.monarchinitiative.phenol.annotations.formats.GeneIdentifiers Maven / Gradle / Ivy

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phenol-annotation contains the annotation functionality for ontologies
There is a newer version: 2.1.2
package org.monarchinitiative.phenol.annotations.formats;

import org.monarchinitiative.phenol.ontology.data.TermId;

import java.util.*;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import java.util.stream.StreamSupport;

public class GeneIdentifiers implements Iterable {
  // an interface candidate

  private final List geneIdentifiers;
  private volatile Map geneIdToSymbol = null;
  private volatile Map geneIdToGeneIdentifier = null;
  private volatile Map symbolToGeneIdentifier = null;

  public static GeneIdentifiers of(List geneIdentifiers) {
    return new GeneIdentifiers(geneIdentifiers);
  }

  private GeneIdentifiers(List geneIdentifiers) {
    this.geneIdentifiers = Objects.requireNonNull(geneIdentifiers, "Gene identifiers must not be null");
  }

  /**
   * @deprecated to be removed in v2.0.0, use {@link #stream()} or {@link #iterator()}.
   */
  @Deprecated(forRemoval = true)
  public List geneIdentifiers() {
    return geneIdentifiers;
  }

  /**
   * Get {@link GeneIdentifier} associated with the given gene ID.
   *
   * @param geneId A CURIE for the gene ID, such as NCBIGene:3949.
   * @return optional with the gene identifier or empty optional if the CURIE is not present.
   * @throws NullPointerException if the {@code symbol} is null.
   */
  public Optional geneIdById(TermId geneId) {
    if (geneIdToGeneIdentifier == null) {
      synchronized (this) {
        if (geneIdToGeneIdentifier == null) {
          geneIdToGeneIdentifier = geneIdentifiers.stream()
            .collect(Collectors.toUnmodifiableMap(GeneIdentifier::id, Function.identity()));
        }
      }
    }
    return Optional.ofNullable(geneIdToGeneIdentifier.get(geneId));
  }

  /**
   * @deprecated to be removed in v2.0.0, use {@link #geneIdById(TermId)}.
   */
  @Deprecated(forRemoval = true)
  public Map geneIdToSymbol() {
    if (geneIdToSymbol == null) {
      synchronized (this) {
        if (geneIdToSymbol == null) {
          geneIdToSymbol = geneIdentifiers.stream()
            .collect(Collectors.toUnmodifiableMap(GeneIdentifier::id, GeneIdentifier::symbol));
        }
      }
    }
    return geneIdToSymbol;
  }


  /**
   * Get {@link GeneIdentifier} associated with the given HGVS gene symbol.
   *
   * @param symbol gene symbol (e.g. SURF1).
   * @return optional with the gene identifier or empty optional if the symbol is not present.
   * @throws NullPointerException if the {@code symbol} is null.
   */
  public Optional geneIdBySymbol(String symbol) {
    if (symbolToGeneIdentifier == null) {
      synchronized (this) {
        if (symbolToGeneIdentifier == null) {
          symbolToGeneIdentifier = geneIdentifiers.stream()
            .collect(Collectors.toUnmodifiableMap(GeneIdentifier::symbol, Function.identity()));
        }
      }
    }
    return Optional.ofNullable(symbolToGeneIdentifier.get(symbol));
  }

  /**
   * @deprecated to be removed in v2.0.0, use {@link #geneIdBySymbol(String)}.
   */
  @Deprecated(forRemoval = true)
  public Map symbolToGeneIdentifier() {
    if (symbolToGeneIdentifier == null) {
      synchronized (this) {
        if (symbolToGeneIdentifier == null) {
          symbolToGeneIdentifier = geneIdentifiers.stream()
            .collect(Collectors.toUnmodifiableMap(GeneIdentifier::symbol, Function.identity()));
        }
      }
    }
    return symbolToGeneIdentifier;
  }

  @Override
  public Iterator iterator() {
    return geneIdentifiers.iterator();
  }

  public Stream stream() {
    return StreamSupport.stream(spliterator(), false);
  }

  public int size() {
    return geneIdentifiers.size();
  }
}