JAL-2388 unit test initialisation fix for running full suite

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

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 0d6c8ae..68933bd 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;
@@ -1137,4 +1138,126 @@ public class AlignmentTest
     assertSame(pep.getDatasetSequence(), cds.getDBRefs()[0].map.to);
   }
 
+  @Test(groups = { "Functional" })
+  public void testFindGroup()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI");
+    SequenceI seq2 = new Sequence("seq2", "---JKLMNO---");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 });
+
+    assertNull(a.findGroup(null, 0));
+    assertNull(a.findGroup(seq1, 1));
+    assertNull(a.findGroup(seq1, -1));
+
+    /*
+     * add a group consisting of just "DEF"
+     */
+    SequenceGroup sg1 = new SequenceGroup();
+    sg1.addSequence(seq1, false);
+    sg1.setStartRes(3);
+    sg1.setEndRes(5);
+    a.addGroup(sg1);
+
+    assertNull(a.findGroup(seq1, 2)); // position not in group
+    assertNull(a.findGroup(seq1, 6)); // position not in group
+    assertNull(a.findGroup(seq2, 5)); // sequence not in group
+    assertSame(a.findGroup(seq1, 3), sg1); // yes
+    assertSame(a.findGroup(seq1, 4), sg1);
+    assertSame(a.findGroup(seq1, 5), sg1);
+
+    /*
+     * 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);
+
+    assertNull(a.findGroup(seq1, 2)); // unchanged
+    assertSame(a.findGroup(seq1, 3), sg1); // unchanged
+    /*
+     * if a residue is in more than one group, method returns
+     * the first found (in order groups were added)
+     */
+    assertSame(a.findGroup(seq1, 4), sg1);
+    assertSame(a.findGroup(seq1, 5), sg1);
+
+    /*
+     * seq2 only belongs to the second group
+     */
+    assertSame(a.findGroup(seq2, 4), sg2);
+    assertSame(a.findGroup(seq2, 5), sg2);
+    assertSame(a.findGroup(seq2, 6), sg2);
+    assertSame(a.findGroup(seq2, 7), sg2);
+    assertNull(a.findGroup(seq2, 3));
+    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);
+  }
+
 }