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

Example 61 with Annotation

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

the class IsoformPEFFHeaderBuilderTest method newIsoformPEFFHeaderBuilder.

private IsoformPEFFHeaderBuilder newIsoformPEFFHeaderBuilder(String isoName) {
    String entryAccession = isoformService.findEntryAccessionFromIsoformAccession(isoName);
    Isoform isoform = isoformService.findIsoform(isoName);
    List<Annotation> isoformAnnotations = annotationService.findAnnotations(entryAccession).stream().filter(annotation -> annotation.isSpecificForIsoform(isoName)).collect(Collectors.toList());
    Overview overview = overviewService.findOverviewByEntry(entryAccession);
    return new IsoformPEFFHeaderBuilder(isoform, isoformAnnotations, overview, terminologyService::findPsiModAccession, terminologyService::findPsiModName);
}

Example 62 with Annotation

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

the class AnnotationUtilsTest method shouldcomputeIsoformsDisplayedAsSpecificForBinaryInteractionCase2.

@Test
public void shouldcomputeIsoformsDisplayedAsSpecificForBinaryInteractionCase2() {
    // BinaryInteraction with 2 isoforms, 2 specific flag => should return 0 isoformDiplayed as specific
    int isoCount = 2;
    Map<String, AnnotationIsoformSpecificity> targetIsoformMap = new HashMap<>();
    AnnotationIsoformSpecificity spec1 = new AnnotationIsoformSpecificity();
    spec1.setIsoformAccession("iso1");
    spec1.setSpecificity("SPECIFIC");
    targetIsoformMap.put("iso1", spec1);
    AnnotationIsoformSpecificity spec2 = new AnnotationIsoformSpecificity();
    spec2.setIsoformAccession("iso2");
    spec2.setSpecificity("SPECIFIC");
    targetIsoformMap.put("iso2", spec2);
    Annotation annot = mock(Annotation.class);
    when(annot.getAPICategory()).thenReturn(AnnotationCategory.BINARY_INTERACTION);
    when(annot.getTargetingIsoformsMap()).thenReturn(targetIsoformMap);
    List<String> result = AnnotationUtils.computeIsoformsDisplayedAsSpecific(annot, isoCount);
    assertEquals(0, result.size());
}

Example 63 with Annotation

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

the class AnnotationUtilsTest method shouldNotReturnAnnotationIfOverlapsALittleBit.

@Test
public void shouldNotReturnAnnotationIfOverlapsALittleBit() {
    // This is used on the pepX logic, if you want to change the logic be careful (add a flag or change the method name for example), but keep the same logic for pepX
    String isoName = "iso-1";
    Annotation a1 = mock(Annotation.class);
    when(a1.isAnnotationPositionalForIsoform(isoName)).thenReturn(true);
    when(a1.getStartPositionForIsoform(isoName)).thenReturn(5);
    when(a1.getEndPositionForIsoform(isoName)).thenReturn(10);
    assertTrue(AnnotationUtils.filterAnnotationsBetweenPositions(10, 20, Arrays.asList(a1), isoName).isEmpty());
}

Example 64 with Annotation

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

the class AnnotationUtilsTest method shouldcomputeIsoformsDisplayedAsSpecificForBinaryInteractionCase1.

@Test
public void shouldcomputeIsoformsDisplayedAsSpecificForBinaryInteractionCase1() {
    // BinaryInteraction with 2 isoforms, 1 specific flag => should return 1 isoformDiplayed as specific
    int isoCount = 2;
    Map<String, AnnotationIsoformSpecificity> targetIsoformMap = new HashMap<>();
    AnnotationIsoformSpecificity spec1 = new AnnotationIsoformSpecificity();
    spec1.setIsoformAccession("iso1");
    spec1.setSpecificity("SPECIFIC");
    targetIsoformMap.put("iso1", spec1);
    AnnotationIsoformSpecificity spec2 = new AnnotationIsoformSpecificity();
    spec2.setIsoformAccession("iso2");
    spec2.setSpecificity("BY DEFAULT");
    targetIsoformMap.put("iso2", spec2);
    Annotation annot = mock(Annotation.class);
    when(annot.getAPICategory()).thenReturn(AnnotationCategory.BINARY_INTERACTION);
    when(annot.getTargetingIsoformsMap()).thenReturn(targetIsoformMap);
    List<String> result = AnnotationUtils.computeIsoformsDisplayedAsSpecific(annot, isoCount);
    assertEquals(1, result.size());
    assertEquals("iso1", result.get(0));
}

Example 65 with Annotation

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

the class AnnotationUtilsTest method shouldcomputeIsoformsDisplayedAsSpecificForBinaryInteractionCase4.

@Test
public void shouldcomputeIsoformsDisplayedAsSpecificForBinaryInteractionCase4() {
    // BinaryInteraction with 1 isoform, 0 specific flag => 0 isoformDiplayed as specific
    int isoCount = 1;
    Map<String, AnnotationIsoformSpecificity> targetIsoformMap = new HashMap<>();
    AnnotationIsoformSpecificity spec1 = new AnnotationIsoformSpecificity();
    spec1.setIsoformAccession("iso1");
    spec1.setSpecificity("BY DEFAULT");
    targetIsoformMap.put("iso1", spec1);
    Annotation annot = mock(Annotation.class);
    when(annot.getAPICategory()).thenReturn(AnnotationCategory.BINARY_INTERACTION);
    when(annot.getTargetingIsoformsMap()).thenReturn(targetIsoformMap);
    List<String> result = AnnotationUtils.computeIsoformsDisplayedAsSpecific(annot, isoCount);
    assertEquals(0, result.size());
}