jFeature.setId( mFeature.getId() ); if ( mFeature.hasNames() ) { jFeature.setNames( namesConverter.toJaxb( mFeature.getNames() ) ); if ( mFeature.hasXref() ) { jFeature.setXref( xrefConverter.toJaxb( mFeature.getXref() ) ); if ( mFeature.hasFeatureType() ) { jFeature.setFeatureType( cvTypeConverter.toJaxb( mFeature.getFeatureType() ) ); if ( mFeature.hasFeatureDetectionMethod() ) { jFeature.setFeatureDetectionMethod( cvTypeConverter.toJaxb( mFeature.getFeatureDetectionMethod() ) ); if ( mFeature.getRanges() != null ) { if ( jFeature.getFeatureRangeList() == null ) { jFeature.setFeatureRangeList( new FeatureElementType.FeatureRangeList() ); for ( Range mRange : mFeature.getRanges() ) { jFeature.getFeatureRangeList().getFeatureRanges().add( rangeConverter.toJaxb( mRange ) ); if ( mFeature.hasExperiments() ) { if ( jFeature.getExperimentRefList() == null ) { jFeature.setExperimentRefList( new ExperimentRefListType() ); for ( ExperimentDescription mExperiment : mFeature.getExperiments() ) { jFeature.getExperimentRefList().getExperimentReves().add( mExperiment.getId() ); } else if ( mFeature.hasExperimentRefs() ) {
public static Feature createFeature(String name, FeatureType featureType, Collection<Range> ranges) { Feature feature = new Feature(); assignNextId(feature); feature.setNames(createNames(name, name)); feature.getRanges().addAll(ranges); feature.setFeatureType(featureType); return feature; }
private <T extends EntityFeature> T getFeature(Class<T> featureClass, Feature psiFeature) String entityFeatureUri = genUri(featureClass, psiFeature.getId()); T entityFeature = (T) bpModel.addNew(featureClass, entityFeatureUri); Set<SequenceInterval> featureLocations = getSequenceLocation(psiFeature.getRanges()); if (featureLocations != null) for (SequenceLocation featureLocation : featureLocations) if (psiFeature.hasNames()) term = getName(psiFeature.getNames()); UnificationXref uref = getPrimaryUnificationXref(psiFeature.getXref()); SequenceRegionVocabulary srv = findOrCreateControlledVocabulary(term, uref, SequenceRegionVocabulary.class); //can be null entityFeature.setFeatureLocationType(srv); if (psiFeature.hasFeatureType()) { psiFeature.getFeatureType(), SequenceModificationVocabulary.class); //can be null ((ModificationFeature)entityFeature).setModificationType(smv);
psidev.psi.mi.xml.model.Feature mFeature = new psidev.psi.mi.xml.model.Feature(); mFeature.setId( jFeature.getId() ); mFeature.setNames( namesConverter.fromJaxb( jFeature.getNames() ) ); mFeature.setXref( xrefConverter.fromJaxb( jFeature.getXref() ) ); mFeature.setFeatureType( cvTypeConverter.fromJaxb( jFeature.getFeatureType(), FeatureType.class ) ); mFeature.setFeatureDetectionMethod( cvTypeConverter.fromJaxb( jFeature.getFeatureDetectionMethod(), FeatureDetectionMethod.class ) ); mFeature.getAttributes().add( attributeConverter.fromJaxb( jAttribute ) ); mFeature.getRanges().add( rangeConverter.fromJaxb( jBaseLocation ) ); ExperimentDescription experimentDescription = experimentDAO.retreive( experimentId ); if ( experimentDescription == null ) { mFeature.getExperimentRefs().add( new ExperimentRef( experimentId ) ); } else { mFeature.getExperiments().add( experimentDescription );
IntactConverterUtils.populateNames(psiObject.getNames(), feature, aliasConverter); IntactConverterUtils.populateXref(psiObject.getXref(), feature, xrefConverter); IntactConverterUtils.populateAnnotations(psiObject, feature, getInstitution(), annotationConverter); if (psiObject.getFeatureType() != null) { CvFeatureType featureType = featureTypeConverter.psiToIntact(psiObject.getFeatureType()); feature.setCvFeatureType(featureType); FeatureDetectionMethod featureDetMethod = psiObject.getFeatureDetectionMethod(); if (featureDetMethod != null) { if (psiObject.getRanges().isEmpty()){ log.error("Feature without any ranges : " + feature.getShortLabel()); for (psidev.psi.mi.xml.model.Range psiRange : psiObject.getRanges()) { Range range = rangeConverter.psiToIntact(psiRange); feature.addRange(range);
String text = null; if (xmlFeature.getRanges() != null && !xmlFeature.getRanges().isEmpty()) { ranges = RangeUtils.toMitab(xmlFeature.getRanges()); if (xmlFeature.hasFeatureType()) { FeatureType featureType = xmlFeature.getFeatureType(); if (featureType.hasNames()) { String shortLabel = featureType.getNames().getShortLabel(); if (xmlFeature.hasNames()) { String shortLabel = xmlFeature.getNames().getShortLabel(); String fullName = xmlFeature.getNames().getFullName();
if (!features.isEmpty()) { for (Feature mitabFeature : features) { psidev.psi.mi.xml.model.Feature xmlfeature = new psidev.psi.mi.xml.model.Feature(); xmlfeature.setId(IdentifierGenerator.getInstance().nextId()); xmlfeature.setFeatureType(featureType); Attribute attribute = new Attribute("MI:0018", "caution", "Due to a limitation in the conversion form MITAB to XML," + " the real xref for the feature type can not be provided. However, you could use the name of the feature type."); xmlfeature.getAttributes().add(attribute); xmlfeature.getRanges().addAll(RangeUtils.fromMitab(mitabFeature.getRanges())); } catch (ConverterException e) { throw new XmlConversionException("The ranges could not be converted"); xmlfeature.getAttributes().add(attribute);
psiFeature.setFeatureDetectionMethod(featureMethod); psiFeature.setFeatureType(featureType); psiFeature.getRanges().add(psiRange);
if ( feature.hasExperimentRefs() ) { if( hasInteractionExperimentDescription && !parentInteraction.getExperiments().isEmpty() ) { for ( ExperimentRef eref : feature.getExperimentRefs()) { ExperimentDescription ed = findExperimentDescriptionInInteraction(eref, parentInteraction); feature.getExperiments().add( ed ); throw new PsimiXmlReaderException( "The feature ("+ feature.getId() +") defined in the participant (id="+ participant.getId() +") of the interaction (id="+ parentInteraction.getId()+") refers to experiment ref "+ eref.getRef() +"," + "however, this experiment isn't defined in this interaction." + feature.getExperimentRefs().clear(); for ( ExperimentRef eref : feature.getExperimentRefs()) { feature.getExperiments().add( ed ); feature.getExperimentRefs().clear();
if(exp==null || f.getExperiments().contains(exp) || f.getExperiments().isEmpty()) { EntityFeature feature = getFeature(ModificationFeature.class, f); if(feature != null) {
psidev.psi.mi.xml.model.Feature mFeature = new psidev.psi.mi.xml.model.Feature(); mFeature.setId( jFeature.getId() ); mFeature.setNames( namesConverter.fromJaxb( jFeature.getNames() ) ); mFeature.setXref( xrefConverter.fromJaxb( jFeature.getXref() ) ); mFeature.setFeatureType( cvTypeConverter.fromJaxb( jFeature.getFeatureType(), FeatureType.class ) ); mFeature.setFeatureDetectionMethod( cvTypeConverter.fromJaxb( jFeature.getFeatureDetectionMethod(), FeatureDetectionMethod.class ) ); mFeature.getAttributes().add( attributeConverter.fromJaxb( jAttribute ) ); mFeature.getRanges().add( rangeConverter.fromJaxb( jBaseLocation ) ); ExperimentDescription experimentDescription = experimentDAO.retreive( experimentId ); if ( experimentDescription == null ) { mFeature.getExperimentRefs().add( new ExperimentRef( experimentId ) ); } else { mFeature.getExperiments().add( experimentDescription );
jFeature.setId( mFeature.getId() ); if ( mFeature.hasNames() ) { jFeature.setNames( namesConverter.toJaxb( mFeature.getNames() ) ); if ( mFeature.hasXref() ) { jFeature.setXref( xrefConverter.toJaxb( mFeature.getXref() ) ); if ( mFeature.hasFeatureType() ) { jFeature.setFeatureType( cvTypeConverter.toJaxb( mFeature.getFeatureType() ) ); if ( mFeature.hasFeatureDetectionMethod() ) { jFeature.setFeatureDetectionMethod( cvTypeConverter.toJaxb( mFeature.getFeatureDetectionMethod() ) ); if ( mFeature.getRanges() != null ) { if ( jFeature.getFeatureRangeList() == null ) { jFeature.setFeatureRangeList( new psidev.psi.mi.xml254.jaxb.Feature.FeatureRangeList() ); for ( Range mRange : mFeature.getRanges() ) { jFeature.getFeatureRangeList().getFeatureRanges().add( rangeConverter.toJaxb( mRange ) ); if ( mFeature.hasExperiments() ) { if ( jFeature.getExperimentRefList() == null ) { jFeature.setExperimentRefList( new ExperimentRefList() ); for ( ExperimentDescription mExperiment : mFeature.getExperiments() ) { jFeature.getExperimentRefList().getExperimentReves().add( mExperiment.getId() ); } else if ( mFeature.hasExperimentRefs() ) {