本文整理了Java中uk.ac.ebi.intact.model.Annotation.<init>()
方法的一些代码示例,展示了Annotation.<init>()
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.<init>()
方法的具体详情如下:
包路径:uk.ac.ebi.intact.model.Annotation
类名称:Annotation
方法名:<init>
[英]This constructor should not be used as it could result in objects with invalid state. It is here for object mapping purposes only and if possible will be made private.
[中]
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-readonly
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/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
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.core/intact-core
private void addUsedInClass(CvObject cv, CvTopic usedInClass, String classes) {
final Annotation hiddenAnnotation = new Annotation(usedInClass, classes);
cv.addAnnotation(hiddenAnnotation);
corePersister.saveOrUpdate(cv);
}
代码示例来源:origin: uk.ac.ebi.intact.core/intact-core-readonly
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.core/intact-core-readonly
private void addUsedInClass(CvObject cv, CvTopic usedInClass, String classes) {
final Annotation hiddenAnnotation = new Annotation(usedInClass, classes);
cv.addAnnotation(hiddenAnnotation);
corePersister.saveOrUpdate(cv);
}
代码示例来源:origin: uk.ac.ebi.intact.dataexchange/intact-cvutils
private void addObsoleteAnnotation( CvObject existingCv, String obsoleteMessage ) {
obsoleteTopic.addAnnotation( new Annotation( existingCv.getOwner(), obsoleteTopic, obsoleteMessage ) );
}
代码示例来源:origin: uk.ac.ebi.intact.core/intact-core
/**
* Adds the 'on-hold' to a publication.
*
* @param intactContext The IntactContext as accessing data is necessary
* @param publication the publication to hold
* @param reason the reason for the 'on-hold' status
* @since 2.5.0
*/
public static void markAsOnHold(IntactContext intactContext, Publication publication, String reason) {
CvTopic onholdTopic = intactContext.getDaoFactory().getCvObjectDao(CvTopic.class).getByShortLabel(CvTopic.ON_HOLD);
if (onholdTopic == null) throw new IllegalStateException("CvTopic on-hold was not found in the database");
Annotation annotation = new Annotation(onholdTopic, reason);
publication.addAnnotation(annotation);
}
代码示例来源:origin: uk.ac.ebi.intact.core/intact-core-readonly
/**
* Adds the 'on-hold' to a publication.
*
* @param intactContext The IntactContext as accessing data is necessary
* @param publication the publication to hold
* @param reason the reason for the 'on-hold' status
* @since 2.5.0
*/
public static void markAsOnHold(IntactContext intactContext, Publication publication, String reason) {
CvTopic onholdTopic = intactContext.getDaoFactory().getCvObjectDao(CvTopic.class).getByShortLabel(CvTopic.ON_HOLD);
if (onholdTopic == null) throw new IllegalStateException("CvTopic on-hold was not found in the database");
Annotation annotation = new Annotation(onholdTopic, reason);
publication.addAnnotation(annotation);
}
代码示例来源:origin: uk.ac.ebi.intact.dataexchange/intact-cvutils
protected Annotation toAnnotation( String cvTopic, String annotation ) {
Institution owner = IntactContext.getCurrentInstance().getInstitution();
CvTopic topic = getCvObjectByLabel( CvTopic.class, cvTopic );
if ( topic == null ) {
if ( CvTopic.URL.equalsIgnoreCase( cvTopic ) ) {
topic = CvObjectUtils.createCvObject( owner, CvTopic.class, CvTopic.URL_MI_REF, CvTopic.URL );
} else if ( CvTopic.SEARCH_URL.equalsIgnoreCase( cvTopic ) ) {
topic = CvObjectUtils.createCvObject( owner, CvTopic.class, CvTopic.SEARCH_URL_MI_REF, CvTopic.SEARCH_URL );
} else if ( CvTopic.XREF_VALIDATION_REGEXP.equalsIgnoreCase( cvTopic ) ) {
topic = CvObjectUtils.createCvObject( owner, CvTopic.class, CvTopic.XREF_VALIDATION_REGEXP_MI_REF, CvTopic.XREF_VALIDATION_REGEXP );
} else if ( CvTopic.COMMENT.equalsIgnoreCase( cvTopic ) ) {
topic = CvObjectUtils.createCvObject( owner, CvTopic.class, CvTopic.COMMENT_MI_REF, CvTopic.COMMENT );
} else if ( CvTopic.OBSOLETE.equalsIgnoreCase( cvTopic ) ) {
topic = CvObjectUtils.createCvObject( owner, CvTopic.class, CvTopic.OBSOLETE_MI_REF, CvTopic.OBSOLETE );
topic.setFullName( CvTopic.OBSOLETE );
} else {
log.error( "Unexpected topic found on annotation: " + cvTopic );
return null;
}
}
if ( log.isTraceEnabled() )
log.debug( "Returning from toAnnotation: owner: " + owner + " topic: " + topic + " annotation " + annotation );
return new Annotation( owner, topic, annotation );
}
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-readonly
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/intact-core
Annotation a = new Annotation( owner, topic, text );
代码示例来源:origin: uk.ac.ebi.intact.dbupdate/intact-datasets-update
/**
*
* @return a new Dataset annotation with the dataset value contained in the DatasetSelector of this object
*/
private Annotation createNewDataset() throws DatasetException {
CvTopic dataset = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getCvObjectDao( CvTopic.class ).getByPsiMiRef( CvTopic.DATASET_MI_REF );
if (dataset == null){
throw new DatasetException("The CVTopic " + CvTopic.DATASET_MI_REF + " : " + CvTopic.DATASET + "doesn't exist in the database.");
}
Annotation annotation = new Annotation(dataset, this.selector.getDatasetValueToAdd());
return annotation;
}
代码示例来源:origin: uk.ac.ebi.intact.dbupdate/intact-cv-update
public static Annotation hideTerm(CvObject c, String message){
DaoFactory factory = IntactContext.getCurrentInstance().getDaoFactory();
CvTopic topicFromDb = factory.getCvObjectDao(CvTopic.class).getByShortLabel(CvTopic.HIDDEN);
if (topicFromDb == null){
topicFromDb = CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvTopic.class, null, CvTopic.HIDDEN);
IntactContext.getCurrentInstance().getCorePersister().saveOrUpdate(topicFromDb);
}
Annotation newAnnotation = new Annotation(topicFromDb, message);
c.addAnnotation(newAnnotation);
return newAnnotation;
}
代码示例来源:origin: uk.ac.ebi.intact.dataexchange.psimi/intact-psixml-converters
public Annotation psiToIntact(Attribute psiObject) {
psiStartConversion(psiObject);
CvTopic cvTopic = new CvTopic(getInstitution(), psiObject.getName());
// all name Acs should be from psi mi controlled vocabularies
if (psiObject.getNameAc() != null) {
cvTopic.setIdentifier(psiObject.getNameAc());
psiMiPopulator.populateWithPsiMi(cvTopic, psiObject.getNameAc());
}
Annotation annotation = new Annotation(getInstitution(), cvTopic, psiObject.getValue());
psiEndConversion(psiObject);
return annotation;
}
代码示例来源:origin: uk.ac.ebi.intact.dataexchange/intact-cvutils
protected void updateCVsUsingAnnotationDataset(List<CvDagObject> allCvs, AnnotationInfoDataset annotationInfoDataset, CorePersister corePersister) {
for ( CvDagObject cvObject : allCvs ) {
final String identity = CvObjectUtils.getIdentity( cvObject );
if ( identity != null && annotationInfoDataset.containsCvAnnotation( identity ) ) {
AnnotationInfo annotInfo = annotationInfoDataset.getCvAnnotation( identity );
// check if the topic has already been processed
CvTopic topic = createdNonMiTopics.get(annotInfo.getTopicShortLabel());
// if not, try to get it from the database
if (topic == null) {
topic = IntactContext.getCurrentInstance().getDataContext().getDaoFactory()
.getCvObjectDao(CvTopic.class).getByShortLabel(CvTopic.class, annotInfo.getTopicShortLabel());
// if it is not in the database, create it and persist it.
if (topic == null) {
topic = CvObjectUtils.createCvObject( IntactContext.getCurrentInstance().getInstitution(),
CvTopic.class,
null,
annotInfo.getTopicShortLabel() );
corePersister.saveOrUpdate(topic);
}
// now it has been created
createdNonMiTopics.put(annotInfo.getTopicShortLabel(), topic);
}
// create the corresponding annotation
Annotation annotation = new Annotation( IntactContext.getCurrentInstance().getInstitution(), topic, annotInfo.getReason() );
addAnnotation( annotation, cvObject, annotInfo.isApplyToChildren() );
}
}
}
代码示例来源:origin: uk.ac.ebi.intact.core/intact-core-readonly
CvTopic cvAddress = new CvTopic("postaladdress");
Annotation annotation = new Annotation( cvAddress, address);
institution.addAnnotation(annotation);
代码示例来源:origin: uk.ac.ebi.intact.core/intact-core
CvTopic cvAddress = new CvTopic("postaladdress");
Annotation annotation = new Annotation( cvAddress, address);
institution.addAnnotation(annotation);
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