Merge commit

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

diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
new file mode 100644 (file)
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+++ b/test/jalview/datamodel/AlignedCodonFrameTest.java
@@ -0,0 +1,141 @@
+package jalview.datamodel;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import jalview.util.MapList;
+
+import java.util.Arrays;
+
+import org.junit.Test;
+
+public class AlignedCodonFrameTest
+{
+
+  /**
+   * Test the method that locates the first aligned sequence that has a mapping.
+   */
+  @Test
+  public void testFindAlignedSequence()
+  {
+    AlignmentI cdna = new Alignment(new SequenceI[]
+    {});
+    final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
+    seq1.createDatasetSequence();
+    cdna.addSequence(seq1);
+    final Sequence seq2 = new Sequence("Seq2", "-TA-GG-GG");
+    seq2.createDatasetSequence();
+    cdna.addSequence(seq2);
+
+    AlignmentI aa = new Alignment(new SequenceI[]
+    {});
+    final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+    aseq1.createDatasetSequence();
+    aa.addSequence(aseq1);
+    final Sequence aseq2 = new Sequence("Seq2", "-LY-");
+    aseq2.createDatasetSequence();
+    aa.addSequence(aseq2);
+
+    /*
+     * Mapping from first DNA sequence to second AA sequence.
+     */
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+
+    assertNull(acf.findAlignedSequence(seq1, aa));
+
+    MapList map = new MapList(new int[]
+    { 1, 6 }, new int[]
+    { 1, 2 }, 3, 1);
+    acf.addMap(seq1.getDatasetSequence(), aseq2.getDatasetSequence(), map);
+
+    /*
+     * DNA seq1 maps to AA seq2
+     */
+    assertEquals(aa.getSequenceAt(1),
+ acf.findAlignedSequence(cdna
+            .getSequenceAt(0).getDatasetSequence(), aa));
+
+    assertEquals(cdna.getSequenceAt(0),
+ acf.findAlignedSequence(aa
+            .getSequenceAt(1).getDatasetSequence(), cdna));
+  }
+
+  /**
+   * Test the method that locates the mapped codon for a protein position.
+   */
+    @Test
+  public void testGetMappedRegion()
+  {
+    // introns lower case, exons upper case
+    final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
+    seq1.createDatasetSequence();
+    final Sequence seq2 = new Sequence("Seq2", "-TA-gG-Gg-CG-a");
+    seq2.createDatasetSequence();
+
+    final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+    aseq1.createDatasetSequence();
+    final Sequence aseq2 = new Sequence("Seq2", "-LY-");
+    aseq2.createDatasetSequence();
+
+    /*
+     * First with no mappings
+     */
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+
+    assertNull(acf.getMappedRegion(seq1, aseq1, 1));
+
+    /*
+     * Set up the mappings for the exons (upper-case bases)
+     */
+    MapList map = new MapList(new int[]
+    { 2, 4, 6, 6, 8, 9 }, new int[]
+    { 1, 2 }, 3, 1);
+    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+    map = new MapList(new int[]
+    { 1, 2, 4, 5, 7, 8 }, new int[]
+    { 1, 2 }, 3, 1);
+    acf.addMap(seq2.getDatasetSequence(), aseq2.getDatasetSequence(), map);
+
+    assertEquals("[2, 4]",
+            Arrays.toString(acf.getMappedRegion(seq1, aseq1, 1)));
+    assertEquals("[6, 6, 8, 9]",
+            Arrays.toString(acf.getMappedRegion(seq1, aseq1, 2)));
+    assertEquals("[1, 2, 4, 4]",
+            Arrays.toString(acf.getMappedRegion(seq2, aseq2, 1)));
+    assertEquals("[5, 5, 7, 8]",
+            Arrays.toString(acf.getMappedRegion(seq2, aseq2, 2)));
+
+    /*
+     * No mapping from sequence 1 to sequence 2
+     */
+    assertNull(acf.getMappedRegion(seq1, aseq2, 1));
+  }
+
+  @Test
+  public void testGetMappedCodon()
+  {
+    final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
+    seq1.createDatasetSequence();
+    final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+    aseq1.createDatasetSequence();
+
+    /*
+     * First with no mappings
+     */
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+
+    assertNull(acf.getMappedCodon(seq1.getDatasetSequence(), 0));
+
+    /*
+     * Set up the mappings for the exons (upper-case bases)
+     */
+    MapList map = new MapList(new int[]
+    { 2, 4, 6, 6, 8, 9 }, new int[]
+    { 1, 2 }, 3, 1);
+    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+    
+    assertEquals("[G, T, A]", Arrays.toString(acf.getMappedCodon(
+            aseq1.getDatasetSequence(), 1)));
+    assertEquals("[C, T, T]", Arrays.toString(acf.getMappedCodon(
+            aseq1.getDatasetSequence(), 2)));
+  }
+}