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