test/jalview/analysis/GroupingTest.java

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