mungo merge

[jalview.git] / test / jalview / ext / htsjdk / TestHtsContigDb.java

diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java
new file mode 100644 (file)
index 0000000..5e0f99a
--- /dev/null
+++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java
@@ -0,0 +1,32 @@
+/**
+ * 
+ */
+package jalview.ext.htsjdk;
+
+import jalview.datamodel.SequenceI;
+
+import java.io.File;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+/**
+ * @author jprocter
+ *
+ */
+public class TestHtsContigDb
+{
+  @Test
+  public final void testHTSReferenceSequence() throws Exception
+  {
+    HtsContigDb remmadb = new HtsContigDb("REEMADB", new File(
+            "test/jalview/ext/htsjdk/pgmb.fasta"));
+
+    Assert.assertTrue(remmadb.isValid());
+
+    SequenceI sq = remmadb.getSequenceProxy("Deminut");
+    Assert.assertNotNull(sq);
+    Assert.assertNotEquals(0, sq.getLength());
+  }
+
+}