From b0dd34bcf5afde1de749155477c659f486b7c484 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 12 Mar 2013 11:25:48 +0000
Subject: [PATCH] cache cds_predicate
---
uk/ac/sanger/artemis/io/ValidateFeature.java | 21 ++++++++------------
1 file changed, 8 insertions(+), 13 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/ValidateFeature.java b/uk/ac/sanger/artemis/io/ValidateFeature.java
index 8846f5ddc..a46bb1bd8 100644
--- a/uk/ac/sanger/artemis/io/ValidateFeature.java
+++ b/uk/ac/sanger/artemis/io/ValidateFeature.java
@@ -58,13 +58,7 @@ import uk.ac.sanger.artemis.util.StringVector;
public class ValidateFeature
{
-
- // TODO - auto-fix boundary option
- // - auto-fix by extending to next stop codon if no valid stop codon
- // - if all validations pass then report as "PASS"
- // -
-
-
+
private static String[] geneModelParts;
//##sequence-region seqid start end
@@ -81,10 +75,12 @@ public class ValidateFeature
"GPI_anchor_cleavage_site", "GPI_anchored", "PlasmoAP_score" };
private EntryGroup entryGrp;
+ private FeaturePredicate cds_predicate;
public ValidateFeature(EntryGroup entryGrp)
{
this.entryGrp = entryGrp;
+ this.cds_predicate = null;
}
public static void testHeader(final String headerTxt)
@@ -340,11 +336,8 @@ public class ValidateFeature
if(!cds_predicate.testPredicate (f))
return false;
- final AminoAcidSequence amino_acids = f.getTranslation ();
- if(amino_acids.containsStopCodon ())
- return true;
- else
- return false;
+ final AminoAcidSequence aa = f.getTranslation ();
+ return aa.containsStopCodon ();
}
public boolean hasValidStop(final uk.ac.sanger.artemis.io.Feature feature)
@@ -361,7 +354,9 @@ public class ValidateFeature
private FeaturePredicate getCodingFeaturePredicate()
{
- final FeaturePredicate cds_predicate;
+ if(cds_predicate != null)
+ return cds_predicate;
+
if(entryGrp != null && GeneUtils.isDatabaseEntry( entryGrp ))
{
--
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