X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fdatamodel%2FSequenceGroupTest.java;h=6e1c2db41453dca5534e9c4b39c7018c85bf635c;hb=14985603cea28569e295ddabb219da8034f1c7b2;hp=243bd53cc51a11489f3e79463955a805975484a2;hpb=c630afc899fc32c40c7ad72ff25c15c647492f11;p=jalview.git

diff --git a/test/jalview/datamodel/SequenceGroupTest.java b/test/jalview/datamodel/SequenceGroupTest.java
index 243bd53..6e1c2db 100644
--- a/test/jalview/datamodel/SequenceGroupTest.java
+++ b/test/jalview/datamodel/SequenceGroupTest.java
@@ -10,11 +10,13 @@ import static org.testng.Assert.fail;
 
 import jalview.schemes.NucleotideColourScheme;
 
+import junit.extensions.PA;
+
 import org.testng.annotations.Test;
 
 public class SequenceGroupTest
 {
-  @Test
+  @Test(groups={"Functional"})
   public void testAddSequence()
   {
     SequenceGroup sg = new SequenceGroup();
@@ -42,7 +44,7 @@ public class SequenceGroupTest
     assertTrue(sg.getSequences().contains(seq3));
   }
 
-  @Test
+  @Test(groups={"Functional"})
   public void testAddOrRemove()
   {
     SequenceGroup sg = new SequenceGroup();
@@ -66,7 +68,7 @@ public class SequenceGroupTest
     assertFalse(sg.getSequences().contains(seq1));
   }
 
-  @Test
+  @Test(groups={"Functional"})
   public void testGetColourScheme()
   {
     SequenceGroup sg = new SequenceGroup();
@@ -81,7 +83,7 @@ public class SequenceGroupTest
     assertSame(scheme, sg.getColourScheme());
   }
 
-  @Test
+  @Test(groups={"Functional"})
   public void testSetContext()
   {
     SequenceGroup sg1 = new SequenceGroup();
@@ -111,5 +113,91 @@ public class SequenceGroupTest
       // expected
       assertNull(sg3.getContext());
     }
+
+    /*
+     * use PrivilegedAccessor to 'force' a SequenceGroup with
+     * a circular context reference
+     */
+    PA.setValue(sg2, "context", sg2);
+    try
+    {
+      sg3.setContext(sg2); // circular reference in sg2
+      fail("Expected exception");
+    } catch (IllegalArgumentException e)
+    {
+      // expected
+      assertNull(sg3.getContext());
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testContains()
+  {
+    /* 
+     * essentially the same tests as AlignmentI.findGroup 
+     * but from a particular group's perspective
+     */
+
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI");
+    SequenceI seq2 = new Sequence("seq2", "---JKLMNO---");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 });
+    /*
+     * add a group consisting of just "DEF"
+     */
+    SequenceGroup sg1 = new SequenceGroup();
+    sg1.addSequence(seq1, false);
+    sg1.setStartRes(3);
+    sg1.setEndRes(5);
+
+    /*
+     * test sequence membership
+     */
+    assertTrue(sg1.contains(seq1));
+    assertFalse(sg1.contains(seq2));
+
+    /*
+     * test sequence+position
+     */
+
+    assertFalse(sg1.contains(seq1, 2)); // position not in group
+    assertFalse(sg1.contains(seq1, 6)); // position not in group
+    assertFalse(sg1.contains(seq2, 5)); // sequence not in group
+    assertTrue(sg1.contains(seq1, 3)); // yes
+    assertTrue(sg1.contains(seq1, 4));
+    assertTrue(sg1.contains(seq1, 5));
+
+    /*
+     * add a group consisting of 
+     * EF--
+     * KLMN
+     */
+    SequenceGroup sg2 = new SequenceGroup();
+    sg2.addSequence(seq1, false);
+    sg2.addSequence(seq2, false);
+    sg2.setStartRes(4);
+    sg2.setEndRes(7);
+    a.addGroup(sg2);
+
+    /*
+     * if a residue is in more than one group, method returns
+     * the first found (in order groups were added)
+     */
+    assertTrue(sg2.contains(seq1, 4));
+    assertTrue(sg2.contains(seq1, 5));
+
+    /*
+     * seq2 only belongs to the second group
+     */
+    assertTrue(sg2.contains(seq2, 4));
+    assertTrue(sg2.contains(seq2, 5));
+    assertTrue(sg2.contains(seq2, 6));
+    assertTrue(sg2.contains(seq2, 7));
+    assertFalse(sg2.contains(seq2, 3));
+    assertFalse(sg2.contains(seq2, 8));
+    sg2.setEndRes(8);
+    assertTrue(sg2.contains(seq2, 8));
+    sg2.deleteSequence(seq2, false);
+    assertFalse(sg2.contains(seq2));
+
   }
 }