public static Feature createDefaultFeature(String name, CvTerm featureType, Collection<Range> ranges) { Feature feature = new DefaultFeature(name, null, featureType); if (ranges != null){ feature.getRanges().addAll(ranges); } return feature; }
public static Feature createDefaultFeature(String name, CvTerm featureType, Range range) { Feature feature = new DefaultFeature(name, null, featureType); if (range != null){ feature.getRanges().add(range); } return feature; }
if (feature.getRanges().isEmpty()){ getWriter().write(Range.UNDETERMINED_POSITION_SYMBOL); getWriter().write(Range.POSITION_SEPARATOR); Iterator<Range> rangeIterator = feature.getRanges().iterator(); while(rangeIterator.hasNext()){ getWriter().write(RangeUtils.convertRangeToString(rangeIterator.next()));
/*** * This method will copy properties of Feature source in Feature target and will override all the other properties of Target feature. * Only the participant is not copied * @param source * @param target */ public static void copyAndOverrideBasicFeaturesProperties(Feature source, Feature target){ if (source != null && target != null){ target.setShortName(source.getShortName()); target.setFullName(source.getFullName()); target.setType(source.getType()); target.setRole(source.getRole()); // copy collections target.getAliases().clear(); target.getAliases().addAll(source.getAliases()); target.getLinkedFeatures().clear(); target.getLinkedFeatures().addAll(source.getLinkedFeatures()); target.getAnnotations().clear(); target.getAnnotations().addAll(source.getAnnotations()); target.getIdentifiers().clear(); target.getIdentifiers().addAll(source.getIdentifiers()); target.getXrefs().clear(); target.getXrefs().addAll(source.getXrefs()); target.getRanges().clear(); target.getRanges().addAll(source.getRanges()); } } }
if (feature.getRanges().isEmpty()){ getWriter().write(Range.UNDETERMINED_POSITION_SYMBOL); getWriter().write(Range.POSITION_SEPARATOR); Iterator<Range> rangeIterator = feature.getRanges().iterator(); while(rangeIterator.hasNext()){ getWriter().write(RangeUtils.convertRangeToString(rangeIterator.next()));
if (feature.getRanges().isEmpty()){ getWriter().write(Range.UNDETERMINED_POSITION_SYMBOL); getWriter().write(Range.POSITION_SEPARATOR); Iterator<Range> rangeIterator = feature.getRanges().iterator(); while(rangeIterator.hasNext()){ getWriter().write(RangeUtils.convertRangeToString(rangeIterator.next()));
if (feature.getRanges().isEmpty()){ getWriter().write(Range.UNDETERMINED_POSITION_SYMBOL); getWriter().write(Range.POSITION_SEPARATOR); Iterator<Range> rangeIterator = feature.getRanges().iterator(); while(rangeIterator.hasNext()){ getWriter().write(RangeUtils.convertRangeToString(rangeIterator.next()));
/** * For each participants of the interaction, collect all respective feature types and feature range status and * check if the dependencies are correct. * * @param feature to check on. * @return a collection of validator messages. * if we fail to retreive the MI Ontology. */ public Collection<ValidatorMessage> check( Feature feature) throws ValidatorException { Collection<ValidatorMessage> messages = Collections.EMPTY_LIST; if (feature.getType() != null){ Collection<Range> featureRange = feature.getRanges(); CvTerm featureType = feature.getType(); messages = new ArrayList<ValidatorMessage>(); if (!feature.getRanges().isEmpty()){ for (Range r : featureRange){ // build a context in case of error MiContext context = RuleUtils.buildContext(feature, "feature"); context.addAssociatedContext(RuleUtils.buildContext(featureType, "feature type")); context.addAssociatedContext(RuleUtils.buildContext(r, "feature range")); CvTerm startStatus = r.getStart().getStatus(); CvTerm endStatus = r.getEnd().getStatus(); messages.addAll( mapping.check( featureType, startStatus, context, this ) ); messages.addAll( mapping.check( featureType, endStatus, context, this ) ); } } } return messages; }
List<Range> list1 = new ArrayList<Range>(feature.getRanges());
Collection<psidev.psi.mi.jami.model.Range> ranges = feature .getRanges();
if (!object.getRanges().isEmpty()){ MIJsonUtils.writeSeparator(writer); MIJsonUtils.writePropertyKey("sequenceData", writer); MIJsonUtils.writeOpenArray(writer); Iterator<Range> rangeIterator = object.getRanges().iterator(); while (rangeIterator.hasNext()){ getRangeWriter().write(rangeIterator.next(), object);
Collection<Range> ranges = feature.getRanges();