JAL-845 applet colour by tree; translate as cDNA; pull up history list

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

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 2a23104..1ef1d07 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;
@@ -12,7 +13,7 @@ import org.junit.Test;
 
 public class SequenceTest
 {
-  Sequence seq;
+  SequenceI seq;
 
   @Before
   public void setUp()
@@ -20,6 +21,21 @@ public class SequenceTest
     seq = new Sequence("FER1", "AKPNGVL");
   }
   @Test
+  public void testInsertGapsAndGapmaps()
+  {
+    SequenceI aseq = seq.deriveSequence();
+    aseq.insertCharAt(2, 3, '-');
+    aseq.insertCharAt(6, 3, '-');
+    assertEquals("Gap insertions not correct", "AK---P---NGVL",
+            aseq.getSequenceAsString());
+    List<int[]> gapInt = aseq.getInsertions();
+    assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]);
+    assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
+    assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
+    assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
+  }
+
+  @Test
   public void testGetAnnotation()
   {
     // initial state returns null not an empty array
@@ -94,7 +110,7 @@ public class SequenceTest
   @Test
   public void testAddAlignmentAnnotation()
   {
-    assertNull(seq.annotation);
+    assertNull(seq.getAnnotation());
     final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
             "b", 2d);
     assertNull(annotation.sequenceRef);
@@ -137,6 +153,38 @@ 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 +250,64 @@ 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()));
+  }
+
+  /**
+   * Test the method that gets sequence features, either from the sequence or
+   * its dataset.
+   */
+  @Test
+  public void testGetSequenceFeatures()
+  {
+    SequenceI seq = new Sequence("test", "GATCAT");
+    seq.createDatasetSequence();
+
+    assertNull(seq.getSequenceFeatures());
+
+    /*
+     * SequenceFeature on sequence
+     */
+    SequenceFeature sf = new SequenceFeature();
+    seq.addSequenceFeature(sf);
+    SequenceFeature[] sfs = seq.getSequenceFeatures();
+    assertEquals(1, sfs.length);
+    assertSame(sf, sfs[0]);
+
+    /*
+     * SequenceFeature on sequence and dataset sequence; returns that on
+     * sequence
+     */
+    SequenceFeature sf2 = new SequenceFeature();
+    seq.getDatasetSequence().addSequenceFeature(sf2);
+    sfs = seq.getSequenceFeatures();
+    assertEquals(1, sfs.length);
+    assertSame(sf, sfs[0]);
+
+    /*
+     * SequenceFeature on dataset sequence only
+     */
+    seq.setSequenceFeatures(null);
+    sfs = seq.getSequenceFeatures();
+    assertEquals(1, sfs.length);
+    assertSame(sf2, sfs[0]);
+
+    /*
+     * Corrupt case - no SequenceFeature, dataset's dataset is the original
+     * sequence. Test shows no infinite loop results.
+     */
+    seq.getDatasetSequence().setSequenceFeatures(null);
+    seq.getDatasetSequence().setDatasetSequence(seq); // loop!
+    assertNull(seq.getSequenceFeatures());
+  }
 }