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

Example 16 with Entry

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

the class IsoformMappingServiceImpl method validateFeature.

@Override
public BaseFeatureQueryResult validateFeature(SingleFeatureQuery query) {
    try {
        SequenceFeature sequenceFeature = SequenceFeatureBase.newFeature(query);
        if (Strings.isNullOrEmpty(query.getAccession()))
            query.setAccession(findAccessionFromGeneName(query, sequenceFeature.getGeneName()));
        Entry entry = entryBuilderService.build(EntryConfig.newConfig(query.getAccession()).withTargetIsoforms().withOverview());
        SequenceFeatureValidator validator = new SequenceFeatureValidator(entry, query);
        return validator.validate(sequenceFeature);
    } catch (FeatureQueryException e) {
        return new FeatureQueryFailureImpl(e);
    }
}

Example 17 with Entry

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

the class SequenceVariantTest method testGetIsoformCaseInsensitive.

@Test
public void testGetIsoformCaseInsensitive() throws Exception {
    SequenceVariant variant = new SequenceVariant("ABL1-isoib-p.Ser439Gly");
    Entry entry = mockEntry("NX_P00519", mockIsoform("NX_P00519-1", "IA", true), mockIsoform("NX_P00519-2", "IB", false));
    Assert.assertEquals("NX_P00519-2", variant.getIsoform(entry).getUniqueName());
}

Example 18 with Entry

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

the class SequenceVariantTest method testGetIsoformNonIso2.

@Test
public void testGetIsoformNonIso2() throws Exception {
    SequenceVariant variant = new SequenceVariant("INSR-isoShort-p.Arg113Pro");
    Entry entry = mockEntry("NX_P06213", mockIsoform("NX_P06213-1", "Long", true), mockIsoform("NX_P06213-2", "Short", false));
    Assert.assertEquals("NX_P06213-2", variant.getIsoform(entry).getUniqueName());
    Assert.assertEquals("Short", variant.getIsoformName());
}

Example 19 with Entry

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

the class SequenceVariantTest method testGetIsoformNonIso.

@Test
public void testGetIsoformNonIso() throws Exception {
    SequenceVariant variant = new SequenceVariant("INSR-isoshort-p.Arg113Pro");
    Entry entry = mockEntry("NX_P06213", mockIsoform("NX_P06213-1", "Long", true), mockIsoform("NX_P06213-2", "Short", false));
    Assert.assertEquals("NX_P06213-2", variant.getIsoform(entry).getUniqueName());
    Assert.assertEquals("short", variant.getIsoformName());
}

Example 20 with Entry

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

the class SequenceVariantTest method testGetIsoformIsoCanonical.

@Test
public void testGetIsoformIsoCanonical() throws Exception {
    SequenceVariant variant = new SequenceVariant("SCN11A-p.Leu1158Pro");
    Entry entry = mockEntry("NX_P06213", mockIsoform("NX_Q9UI33-1", "Iso 1", true), mockIsoform("NX_Q9UI33-2", "Iso 2", false), mockIsoform("NX_Q9UI33-3", "Iso 3", false));
    Assert.assertEquals("NX_Q9UI33-1", variant.getIsoform(entry).getUniqueName());
    Assert.assertNull(variant.getIsoformName());
}