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;
}
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;
}
/**
* Use DefaultFeatureBaseComparator to know if two features are equals.
*
* @param feature1
* @param feature2
* @return true if the two features are equal
*/
public static boolean areEquals(Feature feature1, Feature feature2) {
if (feature1 == feature2) {
return true;
} else if (feature1 == null || feature2 == null) {
return false;
} else {
// first compare shortnames
String name1 = feature1.getShortName();
String name2 = feature2.getShortName();
if (name1 != null && name2 != null) {
if (!name1.equalsIgnoreCase(name2)) {
return false;
}
}
// then compares feature types
CvTerm type1 = feature1.getType();
CvTerm type2 = feature2.getType();
if (!DefaultCvTermComparator.areEquals(type1, type2)) {
return false;
}
// then compares feature role
CvTerm interactionEffect1 = feature1.getRole();
CvTerm interactionEffect2 = feature2.getRole();
if (!DefaultCvTermComparator.areEquals(interactionEffect1, interactionEffect2)) {
return false;
}
// then compares interpro
String interpro1 = feature1.getInterpro();
String interpro2 = feature2.getInterpro();
if (interpro1 != null && interpro2 != null) {
if (!interpro1.equals(interpro2)) {
return false;
}
}
// or compare identifiers
else if (!feature1.getIdentifiers().isEmpty() && !feature2.getIdentifiers().isEmpty()) {
if (!ComparatorUtils.findAtLeastOneMatchingIdentifier(
feature1.getIdentifiers(), feature2.getIdentifiers())) {
return false;
}
}
// then compares the ranges
Collection<Range> ranges1 = feature1.getRanges();
Collection<Range> ranges2 = feature2.getRanges();
return ComparatorUtils.areRangesEqual(ranges1, ranges2);
}
}