JAL-3725 exclude stop codon from CDS-to-protein mapping

[jalview.git] / test / jalview / ws / dbsources / EmblXmlSourceTest.java

diff --git a/test/jalview/ws/dbsources/EmblXmlSourceTest.java b/test/jalview/ws/dbsources/EmblXmlSourceTest.java
index 5f288a8..51d50f5 100644 (file)
--- a/test/jalview/ws/dbsources/EmblXmlSourceTest.java
+++ b/test/jalview/ws/dbsources/EmblXmlSourceTest.java
@@ -26,6 +26,14 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.io.ByteArrayInputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -36,14 +44,6 @@ import jalview.xml.binding.embl.EntryType.Feature;
 import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
 import jalview.xml.binding.embl.XrefType;
 
-import java.io.ByteArrayInputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 public class EmblXmlSourceTest
 {
 
@@ -352,11 +352,12 @@ public class EmblXmlSourceTest
     // exact length match:
     assertSame(exons, EmblXmlSource.adjustForProteinLength(6, exons));
 
-    // match if we assume exons include stop codon not in protein:
-    assertSame(exons, EmblXmlSource.adjustForProteinLength(5, exons));
+    // truncate last exon by 3bp (e.g. stop codon)
+    int[] truncated = EmblXmlSource.adjustForProteinLength(5, exons);
+    assertEquals("[11, 15, 21, 25, 31, 35]", Arrays.toString(truncated));
 
     // truncate last exon by 6bp
-    int[] truncated = EmblXmlSource.adjustForProteinLength(4, exons);
+    truncated = EmblXmlSource.adjustForProteinLength(4, exons);
     assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
 
     // remove last exon and truncate preceding by 1bp