Examples with IsoformFeatureResult org.nextprot.api.isoform.mapper.domain.impl.SingleFeatureQuerySuccessImpl.IsoformFeatureResult used on opensource projects

Example 1 with IsoformFeatureResult

use of org.nextprot.api.isoform.mapper.domain.impl.SingleFeatureQuerySuccessImpl.IsoformFeatureResult in project nextprot-api by calipho-sib.

the class StatementTransformationUtil method mapVariationStatementToEntry.

/**
 * @param variationStatement
 *            Can be a variant or mutagenesis
 * @param result
 * @return
 */
static Statement mapVariationStatementToEntry(Statement variationStatement, FeatureQuerySuccess result) {
    String beginPositionOfCanonicalOrIsoSpec = null;
    String endPositionOfCanonicalOrIsoSpec = null;
    String masterBeginPosition = null;
    String masterEndPosition = null;
    String isoCanonical = null;
    TargetIsoformSet targetIsoforms = new TargetIsoformSet();
    for (IsoformFeatureResult isoformFeatureResult : result.getData().values()) {
        if (isoformFeatureResult.isMapped()) {
            targetIsoforms.add(new TargetIsoformStatementPosition(isoformFeatureResult.getIsoformAccession(), isoformFeatureResult.getBeginIsoformPosition(), // Target
            isoformFeatureResult.getEndIsoformPosition(), // Target
            IsoTargetSpecificity.UNKNOWN.name(), // propagated)
            isoformFeatureResult.getIsoSpecificFeature()));
            // canonical
            if (beginPositionOfCanonicalOrIsoSpec == null) {
                beginPositionOfCanonicalOrIsoSpec = String.valueOf(isoformFeatureResult.getBeginIsoformPosition());
            }
            if (endPositionOfCanonicalOrIsoSpec == null) {
                endPositionOfCanonicalOrIsoSpec = String.valueOf(isoformFeatureResult.getEndIsoformPosition());
            }
            // If possible use canonical
            if (isoformFeatureResult.isCanonical()) {
                if (isoCanonical != null) {
                    throw new NextProtException("Canonical position set already");
                }
                isoCanonical = isoformFeatureResult.getIsoformAccession();
                beginPositionOfCanonicalOrIsoSpec = String.valueOf(isoformFeatureResult.getBeginIsoformPosition());
                endPositionOfCanonicalOrIsoSpec = String.valueOf(isoformFeatureResult.getEndIsoformPosition());
            }
            if (masterBeginPosition == null) {
                masterBeginPosition = String.valueOf(isoformFeatureResult.getBeginMasterPosition());
            }
            if (masterEndPosition == null) {
                masterEndPosition = String.valueOf(isoformFeatureResult.getEndMasterPosition());
            }
            if (masterBeginPosition != null) {
                if (!masterBeginPosition.equals(String.valueOf(isoformFeatureResult.getBeginMasterPosition()))) {
                    throw new NextProtException("Begin master position " + masterBeginPosition + " does not match " + String.valueOf(isoformFeatureResult.getBeginMasterPosition() + " for different isoforms (" + result.getData().values().size() + ") for statement " + variationStatement.getStatementId()));
                }
            }
            if (masterEndPosition != null) {
                if (!masterEndPosition.equals(String.valueOf(isoformFeatureResult.getEndMasterPosition()))) {
                    throw new NextProtException("End master position does not match for different isoforms" + variationStatement.getStatementId());
                }
            }
        }
    }
    Statement rs = // Keep
    StatementBuilder.createNew().addMap(variationStatement).addField(StatementField.RAW_STATEMENT_ID, variationStatement.getStatementId()).addField(StatementField.LOCATION_BEGIN, beginPositionOfCanonicalOrIsoSpec).addField(StatementField.LOCATION_END, endPositionOfCanonicalOrIsoSpec).addField(StatementField.LOCATION_BEGIN_MASTER, masterBeginPosition).addField(StatementField.LOCATION_END_MASTER, masterEndPosition).addField(StatementField.ISOFORM_CANONICAL, isoCanonical).addField(StatementField.TARGET_ISOFORMS, targetIsoforms.serializeToJsonString()).buildWithAnnotationHash(AnnotationType.ENTRY);
    return rs;
}