uk.ac.ebi.intact.model.Annotation类的使用及代码示例

x33g5p2x  于2022-01-16 转载在 其他  
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本文整理了Java中uk.ac.ebi.intact.model.Annotation类的一些代码示例，展示了Annotation类的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。Annotation类的具体详情如下：
包路径：uk.ac.ebi.intact.model.Annotation
类名称：Annotation

Annotation介绍

[英]Funtional description of an object.
[中]对一个物体的功能描述。

代码示例

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

private Collection<String> convertAnnotToString(Collection<Annotation> annot){
  Collection<String> annotations = new ArrayList<String>(annot.size());
  for (Annotation a : annot){
     if (a.getCvTopic() == null){
       annotations.add(a.getAnnotationText() != null ? a.getAnnotationText() : "");
     }
    else {
       annotations.add(a.getCvTopic().getShortLabel() + (a.getAnnotationText() != null ? a.getAnnotationText() : ""));
     }
  }
  return annotations;
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

protected Annotation cloneAnnotation(Annotation annotation) throws IntactClonerException {
  if (annotation == null) return null;
  Annotation clone = new Annotation();
  clonerManager.addClone(annotation, clone);
  clone.setCvTopic(clone(annotation.getCvTopic()));
  clone.setAnnotationText(annotation.getAnnotationText());
  return clone;
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

@Deprecated
public Annotation( Institution owner, CvTopic topic ) {
  //super call sets creation time data
  super( );
  setCvTopic( topic );
  setOwner(owner);
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

public Annotation createAnnotation(String annotationText, CvTopic cvTopic) {
  Annotation annotation = new Annotation(institution, cvTopic);
  annotation.setAnnotationText(annotationText);
  return annotation;
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

public static boolean sameAnnotation( Annotation a1, Annotation a2 ) {
  if (a1.getAc() != null && a2.getAc() != null) {
    return a1.getAc().equals(a2.getAc());
  }
  if ( !same( a1.getAnnotationText(), a2.getAnnotationText() ) ) {
    return false;
  }
  if ( !CvObjectUtils.areEqual( a1.getCvTopic(), a2.getCvTopic() ) ) {
    return false;
  }
  return true;
}

代码示例来源：origin: uk.ac.ebi.intact.dataexchange/intact-cvutils

if (this.areEqual(annot.getCvTopic(),annotation.getCvTopic())) {
  if ( annot.getAnnotationText() != null
     && annot.getAnnotationText().equals( annotation.getAnnotationText() ) ) {
    containsAnnotation = true;
    break;
  } else{
    annot.setAnnotationText( annotation.getAnnotationText() );
    IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().update( annot );
    containsAnnotation = true;
  final CvTopic topic = annotation.getCvTopic();
  log.debug( "Added Annotation(" + topic.getShortLabel() + ", '" + annotation.getAnnotationText() +
        "') onto " + cvObject.getClass().getSimpleName() + "(" + cvObject.getShortLabel() +
        ")" );

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core-readonly

public static boolean isNegative(Interaction interaction) {
  Collection<Annotation> annotations = fetchAnnotations(interaction);
  for (Annotation annotation : annotations) {
    if (annotation.getCvTopic() != null && annotation.getCvTopic().getShortLabel().equals(CvTopic.NEGATIVE)) {
      return true;
    }
  }
  return false;
}

代码示例来源：origin: uk.ac.ebi.intact.util/data-conversion

annotation = new Annotation( institution, cvTopic );
    annotation.setAnnotationText( annotationTag.getText() );
    IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation );
for ( Iterator iterator3 = _annotations.iterator(); iterator3.hasNext() && annotation == null; ) {
  Annotation _annotation = (Annotation) iterator3.next();
  if ( authorConfidence.equals( _annotation.getCvTopic() ) ) {
    annotation = _annotation;
  annotation = new Annotation( institution, authorConfidence );
  annotation.setAnnotationText( confidence.getValue() );
  IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation );

代码示例来源：origin: uk.ac.ebi.intact.dataexchange/intact-cvutils

if ( CvTopic.OBSOLETE_MI_REF.equals( CvObjectUtils.getIdentity( annot.getCvTopic() ) ) ) {
  alreadyContainsObsolete = true;
  if ( CvTopic.OBSOLETE_MI_REF.equals( CvObjectUtils.getIdentity( annot.getCvTopic() ) ) ) {
    annotatedText = annot.getAnnotationText();
final Annotation annotation = new Annotation( existingCv.getOwner(), obsoleteTopic, annotatedText );
existingCv.addAnnotation( annotation );
stats.addUpdatedCv( existingCv );

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

private void markAsHidden(CvObject cv, CvTopic hidden) {
  final Annotation hiddenAnnotation = new Annotation(hidden, null);
  cv.addAnnotation(hiddenAnnotation);
  corePersister.saveOrUpdate(cv);
}

代码示例来源：origin: uk.ac.ebi.intact.bridges.coredep/intact-cdb

Annotation annotation = new Annotation( institution, topic );
annotation.setAnnotationText( text );
Annotation newAnnotation = new Annotation( institution, topic );
newAnnotation.setAnnotationText( text );
  String oldText = annotation.getAnnotationText();
  annotation.setAnnotationText( text );
String _text = annotation.getAnnotationText();
experiment.removeAnnotation( annotation );

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

@Transient
@Deprecated
/**
 * @deprecated now it is always stored as a simple annotation
 */
public String getPostalAddress() {
  Annotation annot = AnnotatedObjectUtils.findAnnotationByTopicMiOrLabel(this, "postaladdress");
  return annot != null ? annot.getAnnotationText() : null;
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core-readonly

private Annotation synchronizeAnnotation( Annotation annotation, AnnotatedObject parent ) {
  if (annotation.getAc() != null) {
    return IntactContext.getCurrentInstance().getDataContext().getDaoFactory()
        .getAnnotationDao().getByAc(annotation.getAc());
  }
  else {
  }
  annotation.setCvTopic( synchronize( annotation.getCvTopic() ) );
  if (annotation.getAc() == null && parent.getAc() != null) {
    annotatedObjectsToPersist.put(keyBuilder.keyForAnnotation(annotation, parent), annotation);
  }
  return annotation;
}

代码示例来源：origin: uk.ac.ebi.intact.dataexchange/intact-cvutils

@Override
  public void visitAnnotation( Annotation annotation ) {
    final CvTopic topic = annotation.getCvTopic();
    final String mi = topic.getIdentifier();
    if ( mi != null ) {
      final CvTopic oboTerm = ( CvTopic ) mi2cv.get( createCvKey( topic.getClass(), mi ) );
      if ( oboTerm == null ) {
        log.warn( "Could not find topic " + topic.getClass().getSimpleName() + "( " + topic.getShortLabel() + " ) by MI: " + mi );
      } else {
        annotation.setCvTopic( oboTerm );
      }
    }
  }
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-persister

CvTopic cvTopic = annotation.getCvTopic();
  cvTopic = (CvTopic) cvPersister.syncIfTransient(annotation.getCvTopic());
  annotation.setCvTopic(cvTopic);
annotation.setOwner(institutionPersister.syncIfTransient(annotation.getOwner()));

代码示例来源：origin: uk.ac.ebi.intact.dataexchange.psimi/intact-psixml-converters

if (CvTopic.NON_UNIPROT.equalsIgnoreCase(a.getCvTopic().getShortLabel())){
  hasNoUniprotUpdate = true;
Annotation noUniprot = new Annotation(noUniprotUpdate);
protein.addAnnotation(noUniprot);

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

protected void traverseAnnotation(Annotation annotation, IntactVisitor... visitors) {
  if (annotation == null) return;
  for (IntactVisitor visitor : visitors) {
    visitor.visitAnnotation(annotation);
  }
  // check if this element has been traversed already, to avoid cyclic recursion
  if (recursionChecker.isAlreadyTraversed(annotation)) {
    return;
  }
  traverse(annotation.getCvTopic(), visitors);
  traverse(annotation.getOwner(), visitors);
}

代码示例来源：origin: uk.ac.ebi.intact.dataexchange.psimi/intact-psixml-converters

public static void populateAnnotations(Collection<Attribute> attributesToConvert, Annotated annotated, Institution institution) {
  AnnotationConverter annotationConverter = new AnnotationConverter(institution);
  if (!attributesToConvert.isEmpty()) {
    for (Attribute attribute : attributesToConvert) {
      Annotation annotation = annotationConverter.psiToIntact(attribute);
      annotation.setOwner(institution);
      if (!annotated.getAnnotations().contains(annotation)) {
        annotated.getAnnotations().add(annotation);
      }
    }
  }
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

/**
 * Creates a valid Annotation instance. A valid instance must have at least
 * a non-null Institution specified. A side-effect of this constructor is to
 * set the <code>created</code> and <code>updated</code> fields of the instance
 * to the current time.
 *
 * @param topic Refers to the controlled vocabulary topic this Annotation relates
 *              to. This should be non-null.
 *
 * @throws NullPointerException thrown if no Institution specified.
 */
public Annotation( CvTopic topic ) {
  //super call sets creation time data
  super( );
  setCvTopic( topic );
}

代码示例来源：origin: uk.ac.ebi.intact.core/intact-core

if (areSameCvObject(annot.getCvTopic(), clonedAnnotation.getCvTopic())) {
  annot.setAnnotationText(clonedAnnotation.getAnnotationText());
  found = true;

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