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Commit d331d69d authored by tcarver's avatar tcarver
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look for /pseudogene as well as /pseudo qualifier

parent add6859f
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......@@ -949,25 +949,24 @@ public class Entry implements FeatureChangeListener, Selectable
**/
public FeatureVector checkFeatureStartCodons()
{
// get all the CDS features that do not have a /pseudo qualifier
final FeatureKeyQualifierPredicate predicate =
new FeatureKeyQualifierPredicate(Key.CDS, "pseudo", false);
// get all the CDS features that do not have a /pseudo or /pseudogene qualifier
final FeaturePredicateConjunction predicate = new FeaturePredicateConjunction(
new FeatureKeyQualifierPredicate(Key.CDS, "pseudo", false),
new FeatureKeyQualifierPredicate(Key.CDS, "pseudogene", false),
FeaturePredicateConjunction.AND);
final FeatureVector non_embl_features = new FeatureVector();
final FeatureEnumeration feature_enum = features();
while(feature_enum.hasMoreFeatures())
{
final Feature current_feature = feature_enum.nextFeature();
if(predicate.testPredicate(current_feature))
{
if(!current_feature.hasValidStartCodon())
non_embl_features.add(current_feature);
}
}
return non_embl_features;
}
......@@ -978,9 +977,11 @@ public class Entry implements FeatureChangeListener, Selectable
**/
public FeatureVector checkFeatureStopCodons()
{
// get all the CDS features that do not have a /pseudo qualifier
final FeatureKeyQualifierPredicate predicate =
new FeatureKeyQualifierPredicate(Key.CDS, "pseudo", false);
// get all the CDS features that do not have a /pseudo or /pseudogene qualifier
final FeaturePredicateConjunction predicate = new FeaturePredicateConjunction(
new FeatureKeyQualifierPredicate(Key.CDS, "pseudo", false),
new FeatureKeyQualifierPredicate(Key.CDS, "pseudogene", false),
FeaturePredicateConjunction.AND);
final FeatureVector non_embl_features = new FeatureVector();
......
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