How to use

getAliasClassType

method

in

uk.ac.ebi.intact.model.util.AnnotatedObjectUtils

  public static <A extends Alias> A newAliasInstanceFor(Class<? extends AnnotatedObject> aoClass) {
    Class<A> aliasClass = (Class<A>) AnnotatedObjectUtils.getAliasClassType(aoClass);
    return ClassUtils.newInstance(aliasClass);
  }
}

  public static <A extends Alias> A newAliasInstanceFor(Class<? extends AnnotatedObject> aoClass) {
    Class<A> aliasClass = (Class<A>) AnnotatedObjectUtils.getAliasClassType(aoClass);
    return ClassUtils.newInstance(aliasClass);
  }
}

  public static <A extends Alias> A newAliasInstanceFor(Class<? extends AnnotatedObject> aoClass) {
    Class<A> aliasClass = (Class<A>) AnnotatedObjectUtils.getAliasClassType(aoClass);
    return ClassUtils.newInstance(aliasClass);
  }
}

public CvObjectConverter(Institution institution, Class<C> intactCvClass, Class<T> psiCvClass) {
  super(institution);
  this.intactCvClass = intactCvClass;
  this.psiCvClass = psiCvClass;
  Class<?> aliasClass = AnnotatedObjectUtils.getAliasClassType(intactCvClass);
  Class<?> xrefClass = AnnotatedObjectUtils.getXrefClassType(intactCvClass);
  this.aliasConverter = new AliasConverter(institution, aliasClass);
  this.xrefConverter = new XrefConverter(institution, xrefClass);
}

public AbstractAnnotatedObjectConverter(Institution institution, Class<? extends A> intactClass, Class<T> psiClass) {
  super(institution);
  this.intactClass = intactClass;
  this.psiClass = psiClass;
  Class<?> aliasClass = AnnotatedObjectUtils.getAliasClassType(intactClass);
  Class<?> xrefClass = AnnotatedObjectUtils.getXrefClassType(intactClass);
  this.annotationConverter = new AnnotationConverter(institution);
  this.aliasConverter = new AliasConverter(institution, aliasClass);
  this.xrefConverter = new XrefConverter(institution, xrefClass);
}

public static void populateNames(Names names, AnnotatedObject<?, ?> annotatedObject) {
  String shortLabel = getShortLabelFromNames(names);
  if (names == null && (annotatedObject instanceof Experiment) ) {
    shortLabel = createExperimentTempShortLabel();
  }
  if ( ! ( annotatedObject instanceof Institution ) ) {
    if ( shortLabel != null ) {
      shortLabel = shortLabel.toLowerCase();
    }
  }
  annotatedObject.setShortLabel(shortLabel);
  if (names != null) {
    annotatedObject.setFullName(names.getFullName());
    Class<?> aliasClass = AnnotatedObjectUtils.getAliasClassType(annotatedObject.getClass());
    AliasConverter aliasConverter = new AliasConverter(getInstitution(annotatedObject), aliasClass);
    populateAliases(names.getAliases(), annotatedObject, aliasConverter);
  }
}

public static void populateNames(Names names, AnnotatedObject<?, ?> annotatedObject, AliasConverter aliasConverter) {
  String shortLabel = getShortLabelFromNames(names);
  if (names == null && (annotatedObject instanceof Experiment) ) {
    shortLabel = createExperimentTempShortLabel();
  }
  if ( ! ( annotatedObject instanceof Institution ) ) {
    if ( shortLabel != null ) {
      shortLabel = shortLabel.toLowerCase();
    }
  }
  annotatedObject.setShortLabel(shortLabel);
  if (names != null) {
    annotatedObject.setFullName(names.getFullName());
    if (aliasConverter == null){
      Class<?> aliasClass = AnnotatedObjectUtils.getAliasClassType(annotatedObject.getClass());
      aliasConverter = new AliasConverter(getInstitution(annotatedObject), aliasClass);
    }
    populateAliases(names.getAliases(), annotatedObject, aliasConverter);
  }
}

/**
 * Retrieves the aliases from an AnnotatedObject, initializing them if necessary.
 *
 * @param ao The annotated object instance with possibly non-initialized aliases
 * @return The returned aliases are ensured to be initialized
 * @since 2.4.0
 */
public static Collection<? extends Alias> ensureInitializedAliases(AnnotatedObject<?, ?> ao) {
  Collection<? extends Alias> aliases;
  if (IntactCore.isInitialized(ao.getAliases())) {
    aliases = ao.getAliases();
  } else {
    aliases = IntactContext.getCurrentInstance().getDaoFactory().getAliasDao(AnnotatedObjectUtils.getAliasClassType(ao.getClass()))
        .getByParentAc(ao.getAc());
  }
  return aliases;
}

/**
 * Retrieves the aliases from an AnnotatedObject, initializing them if necessary.
 *
 * @param ao The annotated object instance with possibly non-initialized aliases
 * @return The returned aliases are ensured to be initialized
 * @since 2.4.0
 */
public static Collection<? extends Alias> ensureInitializedAliases(AnnotatedObject<?, ?> ao) {
  Collection<? extends Alias> aliases;
  if (IntactCore.isInitialized(ao.getAliases())) {
    aliases = ao.getAliases();
  } else {
    aliases = IntactContext.getCurrentInstance().getDaoFactory().getAliasDao(AnnotatedObjectUtils.getAliasClassType(ao.getClass()))
        .getByParentAc(ao.getAc());
  }
  return aliases;
}

protected static void populateNames( AnnotatedObject<?, ?> annotatedObject, NamesContainer namesContainer ) {
  Names names = namesContainer.getNames();
  if ( names == null ) {
    names = new Names();
  }
  String shortLabel = annotatedObject.getShortLabel();
  String fullName = annotatedObject.getFullName();
  names.setShortLabel( shortLabel );
  names.setFullName( fullName );
  if ( !ConverterContext.getInstance().getInteractorConfig().isExcludeInteractorAliases() ) {
    AliasConverter aliasConverter = new AliasConverter( annotatedObject.getOwner(),
        AnnotatedObjectUtils.getAliasClassType( annotatedObject.getClass() ) );
    for ( Alias alias : IntactCore.ensureInitializedAliases(annotatedObject)) {
      names.getAliases().add( aliasConverter.intactToPsi( alias ) );
    }
  }
  namesContainer.setNames( names );
}