From 733490fd53e92414b5ae46a12e69581196e3419b Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 13 Sep 2013 10:11:06 +0100
Subject: [PATCH] add getCDSFeatureByIdPrefix()
---
test/uk/ac/sanger/artemis/io/Utils.java | 33 +++++++++++++++++++++++++
1 file changed, 33 insertions(+)
diff --git a/test/uk/ac/sanger/artemis/io/Utils.java b/test/uk/ac/sanger/artemis/io/Utils.java
index ab840fef0..b7a10ef91 100644
--- a/test/uk/ac/sanger/artemis/io/Utils.java
+++ b/test/uk/ac/sanger/artemis/io/Utils.java
@@ -34,6 +34,8 @@ import uk.ac.sanger.artemis.SimpleEntryGroup;
import uk.ac.sanger.artemis.io.DocumentEntryFactory;
import uk.ac.sanger.artemis.io.Entry;
import uk.ac.sanger.artemis.io.EntryInformationException;
+import uk.ac.sanger.artemis.io.InvalidRelationException;
+import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.sequence.AminoAcidSequence;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
@@ -85,6 +87,37 @@ public class Utils
return null;
}
+ /**
+ * Get a CDS feature with the feature ID prefix
+ * @param featureName
+ * @param features
+ * @return
+ */
+ public static Feature getCDSFeatureByIdPrefix(
+ final String id,
+ final FeatureVector features)
+ {
+ try
+ {
+ for (int i=0; i<features.size(); i++)
+ {
+ Feature f = features.elementAt(i);
+ final Qualifier q = f.getQualifierByName("ID");
+ if (q != null)
+ {
+ final String thisId = q.getValues().get(0);
+ if (thisId.startsWith(id) && f.isCDS())
+ return f;
+ }
+ }
+ }
+ catch(InvalidRelationException e)
+ {
+ Assert.fail(e.getMessage());
+ }
+ return null;
+ }
+
/**
* Method to change the translation table being used
* @param n - genetic code table number
--
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