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;
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
{
// 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