JAL-653 updating 'align as' tests to match latest tweaks to algorithm

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

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 8abc03e..b4b0e12 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -22,6 +22,9 @@ package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.io.AppletFormatAdapter;
@@ -29,7 +32,9 @@ import jalview.io.FormatAdapter;
 import jalview.util.MapList;
 
 import java.io.IOException;
+import java.util.Arrays;
 import java.util.Iterator;
+import java.util.List;
 
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
@@ -245,7 +250,7 @@ public class AlignmentTest
     ((Alignment) al1).alignAs(al2, false, true);
     assertEquals("ACG---GCUCCA------ACT", al1.getSequenceAt(0)
             .getSequenceAsString());
-    assertEquals("---CGT---TAACGA---AGT", al1.getSequenceAt(1)
+    assertEquals("---CGT---TAACGA---AGT---", al1.getSequenceAt(1)
             .getSequenceAsString());
   }
 
@@ -385,4 +390,107 @@ public class AlignmentTest
     assertEquals("c--CCGgg-TT--T------AA-A", al1.getSequenceAt(1)
             .getSequenceAsString());
   }
+
+  @Test(groups = "Functional")
+  public void testCopyConstructor() throws IOException
+  {
+    AlignmentI protein = loadAlignment(AA_SEQS_1, FormatAdapter.PASTE);
+    // create sequence and alignment datasets
+    protein.setDataset(null);
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
+    { acf });
+    protein.getDataset().setCodonFrames(acfList);
+    AlignmentI copy = new Alignment(protein);
+
+    /*
+     * copy has different aligned sequences but the same dataset sequences
+     */
+    assertFalse(copy.getSequenceAt(0) == protein.getSequenceAt(0));
+    assertFalse(copy.getSequenceAt(1) == protein.getSequenceAt(1));
+    assertSame(copy.getSequenceAt(0).getDatasetSequence(), protein
+            .getSequenceAt(0).getDatasetSequence());
+    assertSame(copy.getSequenceAt(1).getDatasetSequence(), protein
+            .getSequenceAt(1).getDatasetSequence());
+
+    // TODO should the copy constructor copy the dataset?
+    // or make a new one referring to the same dataset sequences??
+    assertNull(copy.getDataset());
+    // assertArrayEquals(copy.getDataset().getSequencesArray(), protein
+    // .getDataset().getSequencesArray());
+  }
+
+  /**
+   * Test behaviour of createDataset
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testCreateDatasetAlignment() throws IOException
+  {
+    AlignmentI protein = new FormatAdapter().readFile(AA_SEQS_1,
+            AppletFormatAdapter.PASTE, "FASTA");
+    /*
+     * create a dataset sequence on first sequence
+     * leave the second without one
+     */
+    protein.getSequenceAt(0).createDatasetSequence();
+    assertNotNull(protein.getSequenceAt(0).getDatasetSequence());
+    assertNull(protein.getSequenceAt(1).getDatasetSequence());
+
+    /*
+     * add a mapping to the alignment
+     */
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    protein.addCodonFrame(acf);
+    assertNull(protein.getDataset());
+    assertTrue(protein.getCodonFrames().contains(acf));
+
+    /*
+     * create the alignment dataset
+     * note this creates sequence datasets where missing
+     * as a side-effect (in this case, on seq2
+     */
+    // TODO promote this method to AlignmentI
+    ((Alignment) protein).createDatasetAlignment();
+
+    // TODO this method should return AlignmentI not Alignment !!
+    Alignment ds = protein.getDataset();
+
+    // side-effect: dataset created on second sequence
+    assertNotNull(protein.getSequenceAt(1).getDatasetSequence());
+    // dataset alignment has references to dataset sequences
+    assertEquals(ds.getSequenceAt(0), protein.getSequenceAt(0)
+            .getDatasetSequence());
+    assertEquals(ds.getSequenceAt(1), protein.getSequenceAt(1)
+            .getDatasetSequence());
+
+    // codon frames should have been moved to the dataset
+    // getCodonFrames() should delegate to the dataset:
+    assertTrue(protein.getCodonFrames().contains(acf));
+    // prove the codon frames are indeed on the dataset:
+    assertTrue(ds.getCodonFrames().contains(acf));
+  }
+
+  @Test(groups = "Functional")
+  public void testAddCodonFrame()
+  {
+    AlignmentI align = new Alignment(new SequenceI[] {});
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    align.addCodonFrame(acf);
+    assertEquals(1, align.getCodonFrames().size());
+    assertTrue(align.getCodonFrames().contains(acf));
+    // can't add the same object twice:
+    align.addCodonFrame(acf);
+    assertEquals(1, align.getCodonFrames().size());
+
+    // create dataset alignment - mappings move to dataset
+    ((Alignment) align).createDatasetAlignment();
+    assertSame(align.getCodonFrames(), align.getDataset().getCodonFrames());
+    assertEquals(1, align.getCodonFrames().size());
+
+    AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    align.addCodonFrame(acf2);
+    assertTrue(align.getDataset().getCodonFrames().contains(acf));
+  }
 }