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

Example 26 with SingleFeatureQuery

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

the class IsoformMappingServiceTest method shouldNotValidateIncorrectAAVariantIsoform.

@Test
public void shouldNotValidateIncorrectAAVariantIsoform() throws Exception {
    FeatureQueryResult result = service.validateFeature(new SingleFeatureQuery("SCN11A-p.Met1158Pro", AnnotationCategory.VARIANT.getApiTypeName(), "NX_Q9UI33"));
    SingleFeatureQuery query = Mockito.mock(SingleFeatureQuery.class);
    when(query.getAccession()).thenReturn("NX_Q9UI33");
    when(query.getFeature()).thenReturn("SCN11A-p.Met1158Pro");
    assertIsoformFeatureNotValid((FeatureQueryFailure) result, new UnexpectedFeatureQueryAminoAcidException(query, 1158, new AminoAcidCode[] { AminoAcidCode.LEUCINE }, new AminoAcidCode[] { AminoAcidCode.METHIONINE }));
}

Example 27 with SingleFeatureQuery

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

the class IsoformMappingServiceTest method shouldNotMap1IsoformsContainingFirstAA.

@Test
public void shouldNotMap1IsoformsContainingFirstAA() throws Exception {
    SingleFeatureQuery query = new SingleFeatureQuery("TESPA1-p.Met1ext-5", AnnotationCategory.VARIANT.getApiTypeName(), "");
    FeatureQueryResult result = service.propagateFeature(query);
    assertIsoformFeatureValid(result, "NX_A2RU30-1", 1, 1, true);
    assertIsoformFeatureValid(result, "NX_A2RU30-2", null, null, false);
    assertIsoformFeatureValid(result, "NX_A2RU30-3", null, null, false);
}

Example 28 with SingleFeatureQuery

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

the class IsoformMappingServiceTest method shouldNotMapMet1_Arg406Deletion.

@Test
public void shouldNotMapMet1_Arg406Deletion() throws Exception {
    SingleFeatureQuery query = new SingleFeatureQuery("BARD1-p.Met1_Arg406del", AnnotationCategory.VARIANT.getApiTypeName(), "");
    FeatureQueryResult result = service.propagateFeature(query);
    assertIsoformFeatureValid(result, "NX_Q99728-1", 1, 406, 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 29 with SingleFeatureQuery

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

the class IsoformMappingServiceTest method shouldNotValidateInvalidVariantName.

@Test
public void shouldNotValidateInvalidVariantName() throws Exception {
    FeatureQueryResult result = service.validateFeature(new SingleFeatureQuery("SCN11A-z.Leu1158Pro", AnnotationCategory.VARIANT.getApiTypeName(), "NX_Q9UI33"));
    SingleFeatureQuery query = Mockito.mock(SingleFeatureQuery.class);
    when(query.getFeature()).thenReturn("SCN11A-z.Leu1158Pro");
    Assert.assertFalse(result.isSuccess());
    Assert.assertEquals("invalid feature format: SCN11A-z.Leu1158Pro", ((FeatureQueryFailureImpl) result).getError().getMessage());
    Assert.assertEquals(1, ((FeatureQueryFailureImpl) result).getError().getCauses().size());
    Assert.assertEquals("Cannot separate gene name from variation (missing '-p.')", ((FeatureQueryFailureImpl) result).getError().getCause(InvalidFeatureQueryFormatException.PARSE_ERROR_MESSAGE));
}

Example 30 with SingleFeatureQuery

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

the class IsoformMappingServiceTest method shouldPropagatePro358_Ser364delDeletion.

@Test
public void shouldPropagatePro358_Ser364delDeletion() throws Exception {
    SingleFeatureQuery query = new SingleFeatureQuery("BARD1-p.Pro358_Ser364del", AnnotationCategory.VARIANT.getApiTypeName(), "");
    FeatureQueryResult result = service.propagateFeature(query);
    assertIsoformFeatureValid(result, "NX_Q99728-1", 358, 364, true);
    assertIsoformFeatureValid(result, "NX_Q99728-2", 339, 345, true);
    assertIsoformFeatureValid(result, "NX_Q99728-3", 261, 267, true);
    assertIsoformFeatureValid(result, "NX_Q99728-4", null, null, false);
    assertIsoformFeatureValidOnMaster(result, "NX_Q99728-1", 1162, 1182);
    assertIsoformFeatureValidOnMaster(result, "NX_Q99728-2", 1162, 1182);
    assertIsoformFeatureValidOnMaster(result, "NX_Q99728-3", 1162, 1182);
    assertIsoformFeatureValidOnMaster(result, "NX_Q99728-4", null, null);
}