test/jalview/analysis/GroupingTest.java

   1 package jalview.analysis;
   2
   3 import org.testng.annotations.Test;
   4 import org.testng.AssertJUnit;
   5 import jalview.datamodel.Alignment;
   6 import jalview.datamodel.AlignmentI;
   7 import jalview.datamodel.ColumnSelection;
   8 import jalview.datamodel.Sequence;
   9 import jalview.datamodel.SequenceGroup;
  10 import jalview.datamodel.SequenceI;
  11
  12 import java.util.ArrayList;
  13 import java.util.Arrays;
  14
  15 public class GroupingTest
  16 {
  17   Sequence s1 = new Sequence("s1", "AAAADDDDEEEE");
  18
  19   Sequence s2 = new Sequence("s2", "AAAADDDDEEEE");
  20
  21   Sequence s3 = new Sequence("s3", "ACAADDEDEEEE");
  22
  23   Sequence s4 = new Sequence("s4", "AAAADDEDEEEE");
  24
  25   Sequence s5 = new Sequence("s5", "AAAADDEDTTEE");
  26
  27   SequenceGroup sg1 = new SequenceGroup(Arrays.asList(new SequenceI[]
  28   { s1, s2 }), "Group1", null, false, false, false, 0, 5);
  29
  30   SequenceGroup sg2 = new SequenceGroup(Arrays.asList(new SequenceI[]
  31   { s3, s4, s5 }), "Group2", null, false, false, false, 0, 5);
  32
  33   AlignmentI alignment = new Alignment(new SequenceI[]
  34   { s1, s2, s3, s4, s5 });
  35
  36   int[] positions = new int[]
  37   { 1, 7, 9 };
  38
  39   @Test
  40   public void testMakeGroupsWithBoth()
  41   {
  42     ArrayList<String> str = new ArrayList<String>();
  43     for (SequenceI s : alignment.getSequences())
  44     {
  45       StringBuilder sb = new StringBuilder();
  46       for (int p : positions)
  47       {
  48         sb.append(s.getCharAt(p));
  49       }
  50       str.add(sb.toString());
  51     }
  52     SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
  53             alignment.getSequencesArray(),
  54             str.toArray(new String[str.size()]),
  55             Arrays.asList(new SequenceGroup[]
  56             { sg1, sg2 }));
  57     ColumnSelection cs = new ColumnSelection();
  58     for (int p : positions)
  59     {
  60       cs.addElement(p);
  61     }
  62     SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
  63             alignment.getSequencesArray(), cs,
  64             Arrays.asList(new SequenceGroup[]
  65             { sg1, sg2 }));
  66     AssertJUnit.assertEquals(seqgroupsString.length, seqgroupsColSel.length);
  67     for (int p = 0; p < seqgroupsString.length; p++)
  68     {
  69       AssertJUnit.assertEquals(seqgroupsString[p].getName(),
  70               seqgroupsColSel[p].getName());
  71       AssertJUnit.assertArrayEquals(
  72               seqgroupsString[p].getSequencesInOrder(alignment),
  73               seqgroupsColSel[p].getSequencesInOrder(alignment));
  74       if (seqgroupsString[p].getSequences().contains(s2))
  75       {
  76         AssertJUnit.assertTrue(seqgroupsString[p].getSize() == 2);
  77       }
  78     }
  79   }
  80
  81 }