test/jalview/analysis/GroupingTest.java

   1 package jalview.analysis;
   2
   3 import static org.junit.Assert.fail;
   4 import jalview.datamodel.Alignment;
   5 import jalview.datamodel.AlignmentI;
   6 import jalview.datamodel.ColumnSelection;
   7 import jalview.datamodel.Sequence;
   8 import jalview.datamodel.SequenceGroup;
   9 import jalview.datamodel.SequenceI;
  10
  11 import java.util.ArrayList;
  12 import java.util.Arrays;
  13
  14 import org.junit.Assert;
  15 import org.junit.Test;
  16
  17 public class GroupingTest
  18 {
  19   Sequence s1 = new Sequence("s1", "AAAADDDDEEEE");
  20
  21   Sequence s2 = new Sequence("s2", "AAAADDDDEEEE");
  22
  23   Sequence s3 = new Sequence("s3", "ACAADDEDEEEE");
  24
  25   Sequence s4 = new Sequence("s4", "AAAADDEDEEEE");
  26
  27   Sequence s5 = new Sequence("s5", "AAAADDEDTTEE");
  28
  29   SequenceGroup sg1 = new SequenceGroup(Arrays.asList(new SequenceI[]
  30   { s1, s2 }), "Group1", null, false, false, false, 0, 5);
  31
  32   SequenceGroup sg2 = new SequenceGroup(Arrays.asList(new SequenceI[]
  33   { s3, s4, s5 }), "Group2", null, false, false, false, 0, 5);
  34
  35   AlignmentI alignment = new Alignment(new SequenceI[]
  36   { s1, s2, s3, s4, s5 });
  37
  38   int[] positions = new int[]
  39   { 1, 7, 9 };
  40
  41   @Test
  42   public void testMakeGroupsWithBoth()
  43   {
  44     ArrayList<String> str = new ArrayList<String>();
  45     for (SequenceI s : alignment.getSequences())
  46     {
  47       StringBuilder sb = new StringBuilder();
  48       for (int p : positions)
  49       {
  50         sb.append(s.getCharAt(p));
  51       }
  52       str.add(sb.toString());
  53     }
  54     SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
  55             alignment.getSequencesArray(),
  56             str.toArray(new String[str.size()]),
  57             Arrays.asList(new SequenceGroup[]
  58             { sg1, sg2 }));
  59     ColumnSelection cs = new ColumnSelection();
  60     for (int p : positions)
  61     {
  62       cs.addElement(p);
  63     }
  64     SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
  65             alignment.getSequencesArray(), cs,
  66             Arrays.asList(new SequenceGroup[]
  67             { sg1, sg2 }));
  68     Assert.assertEquals(seqgroupsString.length, seqgroupsColSel.length);
  69     for (int p = 0; p < seqgroupsString.length; p++)
  70     {
  71       Assert.assertEquals(seqgroupsString[p].getName(),
  72               seqgroupsColSel[p].getName());
  73       Assert.assertArrayEquals(
  74               seqgroupsString[p].getSequencesInOrder(alignment),
  75               seqgroupsColSel[p].getSequencesInOrder(alignment));
  76       if (seqgroupsString[p].getSequences().contains(s2))
  77       {
  78         Assert.assertTrue(seqgroupsString[p].getSize() == 2);
  79       }
  80     }
  81   }
  82
  83   @Test
  84   public void testMakeGroupsFromCols()
  85   {
  86     fail("Not yet implemented"); // TODO
  87   }
  88
  89 }