X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;fp=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;h=483ce10c5284993e3b3f4925e064ccaff7b88e95;hb=d71500a42803f307500c16250b40f0fc31e74aad;hp=3f917105597d854bbad5faeac061e6d8205e0934;hpb=dac9672dba85c9bb2d7b7313e015d7561f252fe1;p=jalview.git

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 3f91710..483ce10 100644
--- 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;
@@ -120,4 +121,90 @@ public class SequenceTest
     assertSame(annotation2, anns[1]);
 
   }
+
+  /**
+   * Test the method that returns an array, indexed by sequence position, whose
+   * entries are the residue positions at the sequence position (or to the right
+   * if a gap)
+   */
+  @Test
+  public void testFindPositionMap()
+  {
+    /*
+     * Note: Javadoc for findPosition says it returns the residue position to
+     * the left of a gapped position; in fact it returns the position to the
+     * right. Also it returns a non-existent residue position for a gap beyond
+     * the sequence.
+     */
+    Sequence seq = new Sequence("TestSeq", "AB.C-D E.");
+    int[] map = seq.findPositionMap();
+    assertEquals(Arrays.toString(new int[]
+    { 1, 2, 3, 3, 4, 4, 5, 5, 6 }), Arrays.toString(map));
+  }
+
+  /**
+   * Test for getSubsequence
+   */
+  @Test
+  public void testGetSubsequence()
+  {
+    SequenceI seq = new Sequence("TestSeq", "ABCDEFG");
+    seq.createDatasetSequence();
+
+    // positions are base 0, end position is exclusive
+    SequenceI subseq = seq.getSubSequence(2, 4);
+
+    assertEquals("CD", subseq.getSequenceAsString());
+    // start/end are base 1 positions
+    assertEquals(3, subseq.getStart());
+    assertEquals(4, subseq.getEnd());
+    // subsequence shares the full dataset sequence
+    assertSame(seq.getDatasetSequence(), subseq.getDatasetSequence());
+  }
+
+  /**
+   * Test for deriveSequence applied to a sequence with a dataset
+   */
+  @Test
+  public void testDeriveSequence_existingDataset()
+  {
+    SequenceI seq = new Sequence("Seq1", "CD");
+    seq.setDatasetSequence(new Sequence("Seq1", "ABCDEF"));
+    seq.setStart(3);
+    seq.setEnd(4);
+    SequenceI derived = seq.deriveSequence();
+    assertEquals("CD", derived.getSequenceAsString());
+    assertSame(seq.getDatasetSequence(), derived.getDatasetSequence());
+  }
+
+  /**
+   * Test for deriveSequence applied to an ungapped sequence with no dataset
+   */
+  @Test
+  public void testDeriveSequence_noDatasetUngapped()
+  {
+    SequenceI seq = new Sequence("Seq1", "ABCDEF");
+    assertEquals(1, seq.getStart());
+    assertEquals(6, seq.getEnd());
+    SequenceI derived = seq.deriveSequence();
+    assertEquals("ABCDEF", derived.getSequenceAsString());
+    assertEquals("ABCDEF", derived.getDatasetSequence()
+            .getSequenceAsString());
+  }
+
+  /**
+   * Test for deriveSequence applied to a gapped sequence with no dataset
+   */
+  @Test
+  public void testDeriveSequence_noDatasetGapped()
+  {
+    SequenceI seq = new Sequence("Seq1", "AB-C.D EF");
+    assertEquals(1, seq.getStart());
+    assertEquals(6, seq.getEnd());
+    assertNull(seq.getDatasetSequence());
+    SequenceI derived = seq.deriveSequence();
+    assertEquals("AB-C.D EF", derived.getSequenceAsString());
+    assertEquals("ABCDEF", derived.getDatasetSequence()
+            .getSequenceAsString());
+  }
 }