JAL-845 further code/tests/refactoring

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 2a23104..3ccf88c 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -5,6 +5,7 @@ import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertSame;
 import static org.junit.Assert.assertTrue;
 
+import java.util.Arrays;
 import java.util.List;
 
 import org.junit.Before;
@@ -137,6 +138,38 @@ public class SequenceTest
     assertEquals(0, seq.getEnd()); // ??
   }
 
+  /**
+   * Tests for the method that returns an alignment column position (base 1) for
+   * a given sequence position (base 1).
+   */
+  @Test
+  public void testFindIndex()
+  {
+    SequenceI seq = new Sequence("test", "ABCDEF");
+    assertEquals(0, seq.findIndex(0));
+    assertEquals(1, seq.findIndex(1));
+    assertEquals(5, seq.findIndex(5));
+    assertEquals(6, seq.findIndex(6));
+    assertEquals(6, seq.findIndex(9));
+
+    seq = new Sequence("test", "-A--B-C-D-E-F--");
+    assertEquals(2, seq.findIndex(1));
+    assertEquals(5, seq.findIndex(2));
+    assertEquals(7, seq.findIndex(3));
+
+    // before start returns 0
+    assertEquals(0, seq.findIndex(0));
+    assertEquals(0, seq.findIndex(-1));
+
+    // beyond end returns last residue column
+    assertEquals(13, seq.findIndex(99));
+
+  }
+
+  /**
+   * Tests for the method that returns a dataset sequence position (base 1) for
+   * an aligned column position (base 0).
+   */
   @Test
   public void testFindPosition()
   {
@@ -202,4 +235,16 @@ public class SequenceTest
     
     // for static method see StringUtilsTest
   }
+
+  /**
+   * Test the method that returns an array of aligned sequence positions where
+   * the array index is the data sequence position (both base 0).
+   */
+  @Test
+  public void testGapMap()
+  {
+    SequenceI seq = new Sequence("test", "-A--B-CD-E--F-");
+    seq.createDatasetSequence();
+    assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(seq.gapMap()));
+  }
 }