Examples with Annotation org.nextprot.api.core.domain.annotation.Annotation used on opensource projects

Example 11 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class ByAnnotationSubjectComparatorTest method compareAnnotationsFirstDefinedSubjectComponent.

@Test
public void compareAnnotationsFirstDefinedSubjectComponent() throws Exception {
    ByAnnotationSubjectComparator comparator = new ByAnnotationSubjectComparator(new HashMap<>());
    Annotation a1 = new Annotation();
    a1.setSubjectComponents(Collections.emptyList());
    int cmp = comparator.compare(a1, new Annotation());
    Assert.assertEquals(-1, cmp);
}

Example 12 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class ByAnnotationSubjectComparatorTest method compareAnnotationsCannotFindOneSubjectAnnot.

@Test(expected = NextProtException.class)
public void compareAnnotationsCannotFindOneSubjectAnnot() throws Exception {
    ByAnnotationSubjectComparator comparator = new ByAnnotationSubjectComparator(newHashMap(mockAnnotation(AnnotationCategory.VARIANT, "hash1")));
    Annotation a1 = new Annotation();
    a1.setSubjectComponents(Collections.singletonList("hash1"));
    Annotation a2 = new Annotation();
    a2.setSubjectComponents(Collections.singletonList("hash2"));
    int cmp = comparator.compare(a1, a2);
    Assert.assertEquals(0, cmp);
}

Example 13 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class AnnotationUtilsUnconfirmedPE1Test method createPeptideMappingAnnot.

private Annotation createPeptideMappingAnnot(int id, String pepname, Integer p1, Integer p2, boolean proteotypic) {
    Annotation a = new Annotation();
    a.setAnnotationCategory(AnnotationCategory.PEPTIDE_MAPPING);
    a.setAnnotationId(id);
    AnnotationProperty p = new AnnotationProperty();
    p.setName("is proteotypic");
    p.setValue(proteotypic ? "Y" : "N");
    a.addProperty(p);
    if (pepname != null) {
        p = new AnnotationProperty();
        p.setName("peptide name");
        p.setValue(pepname);
        a.addProperty(p);
    }
    AnnotationIsoformSpecificity spec1 = new AnnotationIsoformSpecificity();
    spec1.setIsoformAccession("NX_P10000-1");
    spec1.setFirstPosition(p1);
    spec1.setLastPosition(p2);
    AnnotationIsoformSpecificity spec2 = new AnnotationIsoformSpecificity();
    spec2.setIsoformAccession("NX_P10000-2");
    spec2.setFirstPosition(p1 == null ? null : p1 + 10);
    spec2.setLastPosition(p2 == null ? null : p2 + 10);
    List<AnnotationIsoformSpecificity> specs = new ArrayList<>();
    specs.add(spec1);
    specs.add(spec2);
    a.addTargetingIsoforms(specs);
    return a;
}

Example 14 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class InteractionServiceImpl method findInteractionsAsAnnotationsByEntry.

@Override
@Cacheable("interactions-as-annot")
public List<Annotation> findInteractionsAsAnnotationsByEntry(String entryName) {
    List<Annotation> annots = new ArrayList<>();
    List<Isoform> isoforms = this.isoService.findIsoformsByEntryName(entryName);
    List<Interaction> interactions = this.interactionDAO.findInteractionsByEntry(entryName);
    for (Interaction inter : interactions) {
        Annotation annot = BinaryInteraction2Annotation.transform(inter, entryName, isoforms, mainNamesService);
        annots.add(annot);
    }
    // returns a immutable list when the result is cacheable (this prevents modifying the cache, since the cache returns a reference) copy on read and copy on write is too much time consuming
    return new ImmutableList.Builder<Annotation>().addAll(annots).build();
}

Example 15 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class AnnotationBaseMerger method merge.

@Override
public Annotation merge(Annotation annotation1, Annotation annotation2) {
    Annotation dest = getDestAnnotation(annotation1, annotation2);
    Annotation source = getSourceAnnotation(annotation1, annotation2);
    updateDestEvidences(dest, source);
    updateDestAnnotationHash(dest, source);
    updateDestIsoformSpecificityName(dest, source);
    updateDestQualityQualifier(dest, source);
    updateDestBioObject(dest, source);
    return dest;
}