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

Example 11 with SingleFeatureQuery

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

the class IsoformMappingServiceTest method shouldNotMapMet1_Lys170Deletion.

@Test
public void shouldNotMapMet1_Lys170Deletion() throws Exception {
    SingleFeatureQuery query = new SingleFeatureQuery("BARD1-p.Met1_Lys170del", AnnotationCategory.VARIANT.getApiTypeName(), "");
    FeatureQueryResult result = service.propagateFeature(query);
    assertIsoformFeatureValid(result, "NX_Q99728-1", 1, 170, 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 12 with SingleFeatureQuery

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

the class IsoformMappingServiceTest method shouldNotValidateInvalidPositionVariantIsoform.

@Test
public void shouldNotValidateInvalidPositionVariantIsoform() throws Exception {
    FeatureQueryResult result = service.validateFeature(new SingleFeatureQuery("SCN11A-p.Leu1158999Pro", AnnotationCategory.VARIANT.getApiTypeName(), "NX_Q9UI33"));
    SingleFeatureQuery query = Mockito.mock(SingleFeatureQuery.class);
    when(query.getAccession()).thenReturn("NX_Q9UI33");
    assertIsoformFeatureNotValid((FeatureQueryFailureImpl) result, new OutOfBoundSequencePositionException(query, 1158999));
}

Example 13 with SingleFeatureQuery

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

the class IsoformMappingService method handleMultipleQueries.

/**
 * Execute the given single feature query function to each feature query
 * @param multipleFeatureQuery multiple feature query
 * @param function the function that process a FeatureQuery and produces FeatureQueryResult
 * @return a map of results
 */
default Map<String, FeatureQueryResult> handleMultipleQueries(MultipleFeatureQuery multipleFeatureQuery, Function<SingleFeatureQuery, FeatureQueryResult> function) {
    Map<String, FeatureQueryResult> results = new HashMap<>(multipleFeatureQuery.getFeatureList().size() + multipleFeatureQuery.getFeatureMaps().size());
    multipleFeatureQuery.getFeatureList().stream().filter(feature -> !results.containsKey(feature)).forEach(feature -> results.put(feature, function.apply(new SingleFeatureQuery(feature, multipleFeatureQuery.getFeatureType(), multipleFeatureQuery.getAccession()))));
    multipleFeatureQuery.getFeatureMaps().stream().filter(featureQuery -> !results.containsKey(featureQuery.get("feature"))).forEach(featureQuery -> results.put(featureQuery.get("feature"), function.apply(new SingleFeatureQuery(featureQuery.get("feature"), multipleFeatureQuery.getFeatureType(), featureQuery.get("accession")))));
    return results;
}

Example 14 with SingleFeatureQuery

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

the class FeatureQueryExceptionTest method testInvalidFeatureQueryFormatException.

@Test
public void testInvalidFeatureQueryFormatException() throws FeatureQueryException {
    SingleFeatureQuery query = new SingleFeatureQuery("SCN11A-p.Leu1158Pro", AnnotationCategory.VARIANT.getApiTypeName(), "NX_P01308");
    InvalidFeatureQueryFormatException featureQueryException = new InvalidFeatureQueryFormatException(query, Mockito.mock(ParseException.class));
    Assert.assertEquals("invalid feature format: SCN11A-p.Leu1158Pro", featureQueryException.getReason().getMessage());
}

Example 15 with SingleFeatureQuery

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

the class FeatureQueryExceptionTest method testOutOfBoundSequencePositionException.

@Test
public void testOutOfBoundSequencePositionException() throws FeatureQueryException {
    SingleFeatureQuery query = new SingleFeatureQuery("SCN11A-p.Leu1158Pro", AnnotationCategory.VARIANT.getApiTypeName(), "NX_Q9UI33");
    OutOfBoundSequencePositionException featureQueryException = new OutOfBoundSequencePositionException(query, 23);
    Assert.assertEquals("out of bound sequence position: position 23 of NX_Q9UI33 sequence", featureQueryException.getReason().getMessage());
}