+package jalview.util;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.fail;
+
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class DnaUtilsTest
+{
+ /**
+ * Tests for parsing an ENA/GenBank location specifier
+ *
+ * @see http://www.insdc.org/files/feature_table.html#3.4
+ */
+ @Test(groups = { "Functional" })
+ public void testParseLocation()
+ {
+ /*
+ * simple range
+ */
+ List<int[]> ranges = DnaUtils.parseLocation("12..78");
+ assertEquals(1, ranges.size());
+ assertEquals(12, ranges.get(0)[0]);
+ assertEquals(78, ranges.get(0)[1]);
+
+ /*
+ * join of simple ranges
+ */
+ ranges = DnaUtils.parseLocation("join(12..78,134..202,322..345)");
+ assertEquals(3, ranges.size());
+ assertEquals(12, ranges.get(0)[0]);
+ assertEquals(78, ranges.get(0)[1]);
+ assertEquals(134, ranges.get(1)[0]);
+ assertEquals(202, ranges.get(1)[1]);
+ assertEquals(322, ranges.get(2)[0]);
+ assertEquals(345, ranges.get(2)[1]);
+
+ /*
+ * complement of a simple range
+ */
+ ranges = DnaUtils.parseLocation("complement(34..126)");
+ assertEquals(1, ranges.size());
+ assertEquals(126, ranges.get(0)[0]);
+ assertEquals(34, ranges.get(0)[1]);
+
+ /*
+ * complement of a join
+ */
+ ranges = DnaUtils
+ .parseLocation("complement(join(2691..4571,4918..5163))");
+ assertEquals(2, ranges.size());
+ assertEquals(5163, ranges.get(0)[0]);
+ assertEquals(4918, ranges.get(0)[1]);
+ assertEquals(4571, ranges.get(1)[0]);
+ assertEquals(2691, ranges.get(1)[1]);
+
+ /*
+ * join of two complements
+ */
+ ranges = DnaUtils
+ .parseLocation("join(complement(4918..5163),complement(2691..4571))");
+ assertEquals(2, ranges.size());
+ assertEquals(5163, ranges.get(0)[0]);
+ assertEquals(4918, ranges.get(0)[1]);
+ assertEquals(4571, ranges.get(1)[0]);
+ assertEquals(2691, ranges.get(1)[1]);
+
+ /*
+ * join complement to non-complement
+ * @see http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation/ Transpliced Genes
+ */
+ ranges = DnaUtils
+ .parseLocation("join(complement(36618..36700),86988..87064)");
+ assertEquals(2, ranges.size());
+ assertEquals(36700, ranges.get(0)[0]);
+ assertEquals(36618, ranges.get(0)[1]);
+ assertEquals(86988, ranges.get(1)[0]);
+ assertEquals(87064, ranges.get(1)[1]);
+
+ /*
+ * valid things we don't yet handle
+ */
+ assertNull(DnaUtils.parseLocation("<34..126"));
+ assertNull(DnaUtils.parseLocation("34..>126"));
+ assertNull(DnaUtils.parseLocation("34.126"));
+ assertNull(DnaUtils.parseLocation("34^126"));
+
+ /*
+ * invalid things
+ */
+ assertNull(DnaUtils.parseLocation(""));
+ assertNull(DnaUtils.parseLocation("JOIN(1..2)"));
+ assertNull(DnaUtils.parseLocation("join(1..2"));
+ try
+ {
+ assertNull(DnaUtils.parseLocation(null));
+ fail("Expected exception");
+ } catch (NullPointerException e)
+ {
+ // expected
+ }
+ }
+
+}