JAL-2446 merged to spike branch

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

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 618bac5..d6e09fd 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -27,6 +27,7 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.analysis.AlignmentGenerator;
 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
@@ -611,6 +612,73 @@ public class AlignmentTest
     AlignmentAnnotation ann = iter.next();
     assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
     assertFalse(iter.hasNext());
+
+    // invalid id
+    anns = al.findAnnotation("CalcIdForD.melanogaster.?");
+    assertFalse(iter.hasNext());
+    anns = al.findAnnotation(null);
+    assertFalse(iter.hasNext());
+  }
+
+  /**
+   * Test method that returns annotations that match on reference sequence,
+   * label, or calcId.
+   */
+  @Test(groups = { "Functional" })
+  public void testFindAnnotations_bySeqLabelandorCalcId()
+  {
+    // TODO: finish testFindAnnotations_bySeqLabelandorCalcId test
+    /* Note - this is an incomplete test - need to check null or
+     * non-null [ matches, not matches ] behaviour for each of the three
+     * parameters..*/
+
+    // search for a single, unique calcId with wildcards on other params
+    Iterable<AlignmentAnnotation> anns = al.findAnnotations(null,
+            "CalcIdForD.melanogaster.2", null);
+    Iterator<AlignmentAnnotation> iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    AlignmentAnnotation ann = iter.next();
+    assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
+    assertFalse(iter.hasNext());
+
+    // save reference to test sequence reference parameter
+    SequenceI rseq = ann.sequenceRef;
+
+    // search for annotation associated with a single sequence
+    anns = al.findAnnotations(rseq, null, null);
+    iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    ann = iter.next();
+    assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
+    assertFalse(iter.hasNext());
+
+    // search for annotation with a non-existant calcId
+    anns = al.findAnnotations(null, "CalcIdForD.melanogaster.?", null);
+    iter = anns.iterator();
+    assertFalse(iter.hasNext());
+
+    // search for annotation with a particular label - expect three
+    anns = al.findAnnotations(null, null, "Secondary Structure");
+    iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    iter.next();
+    assertTrue(iter.hasNext());
+    iter.next();
+    assertTrue(iter.hasNext());
+    iter.next();
+    // third found.. so
+    assertFalse(iter.hasNext());
+
+    // null on all parameters == find all annotations
+    anns = al.findAnnotations(null, null, null);
+    iter = anns.iterator();
+    int n = al.getAlignmentAnnotation().length;
+    while (iter.hasNext())
+    {
+      n--;
+      iter.next();
+    }
+    assertTrue("Found " + n + " fewer annotations from search.", n == 0);
   }
 
   @Test(groups = { "Functional" })
@@ -1190,4 +1258,76 @@ public class AlignmentTest
     assertNull(a.findGroup(seq2, 8));
   }
 
+  @Test(groups = { "Functional" })
+  public void testDeleteSequenceByIndex()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+    // delete sequence 10, alignment reduced by 1
+    int height = a.getAbsoluteHeight();
+    a.deleteSequence(10);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+
+    // try to delete -ve index, nothing happens
+    a.deleteSequence(-1);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+
+    // try to delete beyond end of alignment, nothing happens
+    a.deleteSequence(14);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteSequenceBySeq()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+    // delete sequence 10, alignment reduced by 1
+    int height = a.getAbsoluteHeight();
+    SequenceI seq = a.getSequenceAt(10);
+    a.deleteSequence(seq);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+
+    // try to delete non-existent sequence, nothing happens
+    seq = new Sequence("cds", "GCCTCGGAT");
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteHiddenSequence()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+    // delete a sequence which is hidden, check it is NOT removed from hidden
+    // sequences
+    int height = a.getAbsoluteHeight();
+    SequenceI seq = a.getSequenceAt(2);
+    a.getHiddenSequences().hideSequence(seq);
+    assertEquals(a.getHiddenSequences().getSize(), 1);
+    a.deleteSequence(2);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+    assertEquals(a.getHiddenSequences().getSize(), 1);
+
+    // delete a sequence which is not hidden, check hiddenSequences are not
+    // affected
+    a.deleteSequence(10);
+    assertEquals(a.getAbsoluteHeight(), height - 2);
+    assertEquals(a.getHiddenSequences().getSize(), 1);
+  }
+
+  @Test(
+    groups = "Functional",
+    expectedExceptions = { IllegalArgumentException.class })
+  public void testSetDataset_selfReference()
+  {
+    SequenceI seq = new Sequence("a", "a");
+    AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+    alignment.setDataset(alignment);
+  }
 }