JAL-2114 parser + tests for GenBank location descriptors

[jalview.git] / test / jalview / util / DnaUtilsTest.java

diff --git a/test/jalview/util/DnaUtilsTest.java b/test/jalview/util/DnaUtilsTest.java
new file mode 100644 (file)
index 0000000..af76885
--- /dev/null
+++ b/test/jalview/util/DnaUtilsTest.java
@@ -0,0 +1,107 @@
+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
+    }
+  }
+
+}