From d331d69d3a7b6515ff30171fb52a86708e909cf8 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 12 Sep 2012 12:03:26 +0100
Subject: [PATCH] look for /pseudogene as well as /pseudo qualifier
---
uk/ac/sanger/artemis/Entry.java | 19 ++++++++++---------
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/uk/ac/sanger/artemis/Entry.java b/uk/ac/sanger/artemis/Entry.java
index 8da8c0cc0..d71bb05ec 100644
--- a/uk/ac/sanger/artemis/Entry.java
+++ b/uk/ac/sanger/artemis/Entry.java
@@ -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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