Examples with SingleFeatureQuery org.nextprot.api.isoform.mapper.domain.SingleFeatureQuery used on opensource projects

Example 31 with SingleFeatureQuery

use of org.nextprot.api.isoform.mapper.domain.SingleFeatureQuery in project nextprot-api by calipho-sib.

the class IsoformMappingServiceTest method shouldValidateInsertionVariantOnCanonicalIsoform.

@Test
public void shouldValidateInsertionVariantOnCanonicalIsoform() throws Exception {
    FeatureQueryResult result = service.validateFeature(new SingleFeatureQuery("MLH1-p.Lys722_Ala723insTyrLys", AnnotationCategory.VARIANT.getApiTypeName(), "NX_P40692"));
    assertIsoformFeatureValid(result, "NX_P40692-1", 722, 723, true);
}

Example 32 with SingleFeatureQuery

use of org.nextprot.api.isoform.mapper.domain.SingleFeatureQuery in project nextprot-api by calipho-sib.

the class IsoformMappingServiceTest method shouldNotValidateIncompatibleProteinAndGeneName.

@Test
public void shouldNotValidateIncompatibleProteinAndGeneName() throws Exception {
    FeatureQueryResult result = service.validateFeature(new SingleFeatureQuery("SCN11A-p.Leu1158Pro", AnnotationCategory.VARIANT.getApiTypeName(), "NX_P01308"));
    SingleFeatureQuery query = Mockito.mock(SingleFeatureQuery.class);
    when(query.getAccession()).thenReturn("NX_P01308");
    assertIsoformFeatureNotValid((FeatureQueryFailureImpl) result, new IncompatibleGeneAndProteinNameException(query, "SCN11A", Lists.newArrayList("INS")));
}

Example 33 with SingleFeatureQuery

use of org.nextprot.api.isoform.mapper.domain.SingleFeatureQuery in project nextprot-api by calipho-sib.

the class IsoformMappingServiceTest method shouldNotMapMet1_Asp94Deletion.

@Test
public void shouldNotMapMet1_Asp94Deletion() throws Exception {
    SingleFeatureQuery query = new SingleFeatureQuery("BARD1-p.Met1_Asp94del", AnnotationCategory.VARIANT.getApiTypeName(), "");
    FeatureQueryResult result = service.propagateFeature(query);
    assertIsoformFeatureValid(result, "NX_Q99728-1", 1, 94, true);
    assertIsoformFeatureValid(result, "NX_Q99728-2", null, null, false);
    assertIsoformFeatureValid(result, "NX_Q99728-3", null, null, false);
    assertIsoformFeatureValid(result, "NX_Q99728-4", 1, 94, true);
    assertIsoformFeatureValidOnMaster(result, "NX_Q99728-1", 1, 354);
    assertIsoformFeatureValidOnMaster(result, "NX_Q99728-4", 1, 354);
    assertIsoformFeatureValidOnMaster(result, "NX_Q99728-2", null, null);
    assertIsoformFeatureValidOnMaster(result, "NX_Q99728-3", null, null);
}

Example 34 with SingleFeatureQuery

use of org.nextprot.api.isoform.mapper.domain.SingleFeatureQuery in project nextprot-api by calipho-sib.

the class IsoformMappingServiceTest method shouldNotMapMet1_Arg424Deletion.

@Test
public void shouldNotMapMet1_Arg424Deletion() throws Exception {
    SingleFeatureQuery query = new SingleFeatureQuery("BARD1-p.Met1_Arg424del", AnnotationCategory.VARIANT.getApiTypeName(), "");
    FeatureQueryResult result = service.propagateFeature(query);
    assertIsoformFeatureValid(result, "NX_Q99728-1", 1, 424, true);
    assertIsoformFeatureValid(result, "NX_Q99728-2", null, null, false);
    assertIsoformFeatureValid(result, "NX_Q99728-3", null, null, false);
    assertIsoformFeatureValid(result, "NX_Q99728-4", null, null, false);
}

Example 35 with SingleFeatureQuery

use of org.nextprot.api.isoform.mapper.domain.SingleFeatureQuery in project nextprot-api by calipho-sib.

the class IsoformMappingServiceTest method shouldValidatePtmOnCanonicalIsoform.

@Test
public void shouldValidatePtmOnCanonicalIsoform() throws Exception {
    FeatureQueryResult result = service.validateFeature(new SingleFeatureQuery("BRCA1-P-Ser988", AnnotationCategory.GENERIC_PTM.getApiTypeName(), "NX_P38398"));
    assertIsoformFeatureValid(result, "NX_P38398-1", 988, 988, true);
}