From 5229f6f7c6bcaa94efebda83cede5d53b329f759 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 12 Sep 2012 14:15:36 +0100
Subject: [PATCH] add /pseudogene qualifier
---
uk/ac/sanger/artemis/components/variant/IOUtils.java | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 181640a9a..9d5f2c090 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -51,6 +51,7 @@ import uk.ac.sanger.artemis.Feature;
import uk.ac.sanger.artemis.FeatureEnumeration;
import uk.ac.sanger.artemis.FeatureKeyQualifierPredicate;
import uk.ac.sanger.artemis.FeaturePredicate;
+import uk.ac.sanger.artemis.FeaturePredicateConjunction;
import uk.ac.sanger.artemis.FeatureSegment;
import uk.ac.sanger.artemis.FeatureSegmentVector;
import uk.ac.sanger.artemis.FeatureVector;
@@ -156,9 +157,12 @@ class IOUtils
final List<String> vcfFiles,
final VCFview vcfView)
{
- // get all CDS features that do not have the /pseudo qualifier
+ // get all CDS features that do not have the /pseudo or /pseudogene qualifier
final FeatureVector features = getFeatures(
- new FeatureKeyQualifierPredicate(Key.CDS, "pseudo", false), vcfView.getEntryGroup());
+ new FeaturePredicateConjunction(
+ new FeatureKeyQualifierPredicate(Key.CDS, "pseudo", false),
+ new FeatureKeyQualifierPredicate(Key.CDS, "pseudogene", false),
+ FeaturePredicateConjunction.AND), vcfView.getEntryGroup());
String filterFiles = "";
for(int i=0; i<vcfFiles.size(); i++)
--
GitLab