Examples with IsoformMappingService org.nextprot.api.isoform.mapper.service.IsoformMappingService used on opensource projects

Example 1 with IsoformMappingService

use of org.nextprot.api.isoform.mapper.service.IsoformMappingService 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);
}