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

Example 16 with Isoform

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

the class StatementTransformationUtil method computeTargetIsoformsForProteoformAnnotation.

public static TargetIsoformSet computeTargetIsoformsForProteoformAnnotation(Statement proteoformStatement, IsoformMappingService isoformMappingService, List<Statement> subjectsForThisProteoform, boolean isIsoSpecific, String isoSpecificAccession, List<String> isoformAccessions) {
    List<String> isoformsToBeConsidered = new ArrayList<>();
    if (isIsoSpecific) {
        isoformsToBeConsidered.add(isoSpecificAccession);
    } else {
        isoformsToBeConsidered.addAll(isoformAccessions);
    }
    Set<TargetIsoformStatementPosition> result = new TreeSet<>();
    for (String isoformAccession : isoformsToBeConsidered) {
        String name = null;
        boolean allOk = true;
        for (Statement s : subjectsForThisProteoform) {
            TargetIsoformSet targetIsoforms = TargetIsoformSet.deSerializeFromJsonString(s.getValue(StatementField.TARGET_ISOFORMS));
            List<TargetIsoformStatementPosition> targetIsoformsFiltered = targetIsoforms.stream().filter(ti -> ti.getIsoformAccession().equals(isoformAccession)).collect(Collectors.toList());
            if (targetIsoformsFiltered.isEmpty()) {
                LOGGER.debug("(skip) Could not map to isoform " + isoformAccession);
                allOk = false;
                break;
            } else if (targetIsoformsFiltered.size() > 1) {
                throw new NextProtException("Something got wrong. Found more than one target isoform for same accession" + isoformAccession);
            }
            TargetIsoformStatementPosition tisp = targetIsoformsFiltered.iterator().next();
            if (name == null) {
                name = tisp.getName();
            } else {
                name += (" + " + tisp.getName());
            }
        }
        if (name != null && allOk) {
            if (isIsoSpecific) {
                result.add(new TargetIsoformStatementPosition(isoformAccession, IsoTargetSpecificity.SPECIFIC.name(), name));
            } else {
                result.add(new TargetIsoformStatementPosition(isoformAccession, IsoTargetSpecificity.UNKNOWN.name(), name));
            }
        }
    }
    return new TargetIsoformSet(result);
}

Example 17 with Isoform

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

the class SequenceVariantTest method mockIsoform.

public static Isoform mockIsoform(String accession, String name, boolean canonical, String sequence) {
    Isoform isoform = mockIsoform(accession, name, canonical);
    when(isoform.getSequence()).thenReturn(sequence);
    return isoform;
}

Example 18 with Isoform

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

the class SequenceVariantTest method testFormatIsoformSpecifiqueFeatureTypeIso.

@Test
public void testFormatIsoformSpecifiqueFeatureTypeIso() throws Exception {
    SequenceVariant variant = new SequenceVariant("SCN11A-p.Leu1158Pro");
    Isoform iso = mockIsoform("whatever", "Iso 1", true);
    Assert.assertEquals("iso1", variant.formatIsoformFeatureName(iso));
}

Example 19 with Isoform

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

the class SequenceVariantTest method testIsospecFeature.

@Test
public void testIsospecFeature() throws Exception {
    SequenceVariant variant = new SequenceVariant("WT1-p.Phe154Ser");
    Isoform isoform = mockIsoform("NX_P19544", "Iso 1", true);
    Assert.assertEquals("WT1-iso1-p.Phe154Ser", variant.formatIsoSpecificFeature(isoform, 154, 154));
}

Example 20 with Isoform

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

the class SequenceVariantTest method testFormatIsoformSpecifiqueFeatureTypeNonIso.

@Test
public void testFormatIsoformSpecifiqueFeatureTypeNonIso() throws Exception {
    SequenceVariant variant = new SequenceVariant("ABL1-p.Ser439Gly");
    Isoform iso = mockIsoform("whatever", "IA", true);
    Assert.assertEquals("isoIA", variant.formatIsoformFeatureName(iso));
}