adao.persist( a );
/** * Search in IntAct for an Annotation having the a specific type and annotationText. * * @param annotationTag the description of the Annotation we are looking for. * * @return the found Annotation or null if not found. * * @throws IntactException */ private static Annotation searchIntactAnnotation( final AnnotationTag annotationTag ) throws IntactException { Annotation annotation = null; final String text = annotationTag.getText(); Collection annotations = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().getByTextLike(text); for ( Iterator iterator = annotations.iterator(); iterator.hasNext() && annotation == null; ) { Annotation anAnnotation = (Annotation) iterator.next(); if ( annotationTag.getType().equals( anAnnotation.getCvTopic().getShortLabel() ) ) { annotation = anAnnotation; } } return annotation; }
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation ); Collection _annotations = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().getByTextLike(confidence.getValue()); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation );
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation ); Collection _annotations = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().getByDescriptionLike(confidence.getValue()); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation );
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation ); Collection _annotations = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().getByDescriptionLike(confidence.getValue()); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation );
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation ); proteinType.addAnnotation( annotation ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().update( (ProteinImpl)protein );
/** * Search in IntAct for an Annotation having the a specific type and annotationText. * * @param annotationTag the description of the Annotation we are looking for. * * @return the found Annotation or null if not found. * * @throws IntactException */ private static Annotation searchIntactAnnotation( final AnnotationTag annotationTag ) throws IntactException { Annotation annotation = null; final String text = annotationTag.getText(); Collection annotations = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().getByTextLike(text); for ( Iterator iterator = annotations.iterator(); iterator.hasNext() && annotation == null; ) { Annotation anAnnotation = (Annotation) iterator.next(); if ( annotationTag.getType().equals( anAnnotation.getCvTopic().getShortLabel() ) ) { annotation = anAnnotation; } } return annotation; }
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation ); proteinType.addAnnotation( annotation ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().update( (ProteinImpl)protein );
/** * Search in IntAct for an Annotation having the a specific type and annotationText. * * @param annotationTag the description of the Annotation we are looking for. * * @return the found Annotation or null if not found. * * @throws IntactException */ private static Annotation searchIntactAnnotation( final AnnotationTag annotationTag ) throws IntactException { final String text = annotationTag.getText(); Collection annotations = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().getByTextLike(text); Annotation annotation = null; if ( annotations != null ) { for ( Iterator iterator = annotations.iterator(); iterator.hasNext() && annotation == null; ) { Annotation anAnnotation = (Annotation) iterator.next(); if ( annotationTag.getType().equals( anAnnotation.getCvTopic().getShortLabel() ) ) { annotation = anAnnotation; } } } return annotation; } }
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation ); proteinType.addAnnotation( annotation ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().update( (ProteinImpl)protein );
/** * Search in IntAct for an Annotation having the a specific type and annotationText. * * @param annotationTag the description of the Annotation we are looking for. * * @return the found Annotation or null if not found. * * @throws IntactException */ private static Annotation searchIntactAnnotation( final AnnotationTag annotationTag ) throws IntactException { final String text = annotationTag.getText(); Collection annotations = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().getByTextLike(text); Annotation annotation = null; if ( annotations != null ) { for ( Iterator iterator = annotations.iterator(); iterator.hasNext() && annotation == null; ) { Annotation anAnnotation = (Annotation) iterator.next(); if ( annotationTag.getType().equals( anAnnotation.getCvTopic().getShortLabel() ) ) { annotation = anAnnotation; } } } return annotation; } }
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation );
/** * Search in IntAct for an Annotation having the a specific type and annotationText. * * @param annotationTag the description of the Annotation we are looking for. * * @return the found Annotation or null if not found. * * @throws IntactException */ private static Annotation searchIntactAnnotation( final AnnotationTag annotationTag ) throws IntactException { Annotation annotation = null; final String text = annotationTag.getText(); Collection annotations = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().getByTextLike(text); for ( Iterator iterator = annotations.iterator(); iterator.hasNext() && annotation == null; ) { Annotation anAnnotation = (Annotation) iterator.next(); if ( annotationTag.getType().equals( anAnnotation.getCvTopic().getShortLabel() ) ) { annotation = anAnnotation; } } return annotation; }
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation );
/** * Search in IntAct for an Annotation having the a specific type and annotationText. * * @param annotationTag the description of the Annotation we are looking for. * * @return the found Annotation or null if not found. * * @throws IntactException */ private static Annotation searchIntactAnnotation( final AnnotationTag annotationTag ) throws IntactException { final String text = annotationTag.getText(); Collection annotations = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().getByTextLike(text); Annotation annotation = null; if ( annotations != null ) { for ( Iterator iterator = annotations.iterator(); iterator.hasNext() && annotation == null; ) { Annotation anAnnotation = (Annotation) iterator.next(); if ( annotationTag.getType().equals( anAnnotation.getCvTopic().getShortLabel() ) ) { annotation = anAnnotation; } } } return annotation; } }
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation );