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[]
  29   { s1, s2 }), "Group1", null, false, false, false, 0, 5);
  30
  31   SequenceGroup sg2 = new SequenceGroup(Arrays.asList(new SequenceI[]
  32   { s3, s4, s5 }), "Group2", null, false, false, false, 0, 5);
  33
  34   AlignmentI alignment = new Alignment(new SequenceI[]
  35   { s1, s2, s3, s4, s5 });
  36
  37   int[] positions = new int[]
  38   { 1, 7, 9 };
  39
  40   @Test(groups ={ "Functional" })
  41   public void testMakeGroupsWithBoth()
  42   {
  43     ArrayList<String> str = new ArrayList<String>();
  44     for (SequenceI s : alignment.getSequences())
  45     {
  46       StringBuilder sb = new StringBuilder();
  47       for (int p : positions)
  48       {
  49         sb.append(s.getCharAt(p));
  50       }
  51       str.add(sb.toString());
  52     }
  53     SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
  54             alignment.getSequencesArray(),
  55             str.toArray(new String[str.size()]),
  56             Arrays.asList(new SequenceGroup[]
  57             { sg1, sg2 }));
  58     ColumnSelection cs = new ColumnSelection();
  59     for (int p : positions)
  60     {
  61       cs.addElement(p);
  62     }
  63     SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
  64             alignment.getSequencesArray(), cs,
  65             Arrays.asList(new SequenceGroup[]
  66             { sg1, sg2 }));
  67     AssertJUnit.assertEquals(seqgroupsString.length, seqgroupsColSel.length);
  68     for (int p = 0; p < seqgroupsString.length; p++)
  69     {
  70       AssertJUnit.assertEquals(seqgroupsString[p].getName(),
  71               seqgroupsColSel[p].getName());
  72       AssertJUnit.assertArrayEquals(
  73               seqgroupsString[p].getSequencesInOrder(alignment),
  74               seqgroupsColSel[p].getSequencesInOrder(alignment));
  75       if (seqgroupsString[p].getSequences().contains(s2))
  76       {
  77         AssertJUnit.assertTrue(seqgroupsString[p].getSize() == 2);
  78       }
  79     }
  80   }
  81
  82 }