package jalview.analysis;

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;

import java.util.ArrayList;
import java.util.Arrays;

import org.testng.AssertJUnit;
import org.testng.annotations.Test;

public class GroupingTest
{
  Sequence s1 = new Sequence("s1", "AAAADDDDEEEE");

  Sequence s2 = new Sequence("s2", "AAAADDDDEEEE");

  Sequence s3 = new Sequence("s3", "ACAADDEDEEEE");

  Sequence s4 = new Sequence("s4", "AAAADDEDEEEE");

  Sequence s5 = new Sequence("s5", "AAAADDEDTTEE");

  SequenceGroup sg1 = new SequenceGroup(Arrays.asList(new SequenceI[]
  { s1, s2 }), "Group1", null, false, false, false, 0, 5);

  SequenceGroup sg2 = new SequenceGroup(Arrays.asList(new SequenceI[]
  { s3, s4, s5 }), "Group2", null, false, false, false, 0, 5);

  AlignmentI alignment = new Alignment(new SequenceI[]
  { s1, s2, s3, s4, s5 });

  int[] positions = new int[]
  { 1, 7, 9 };

  @Test(groups ={ "Functional" })
  public void testMakeGroupsWithBoth()
  {
    ArrayList<String> str = new ArrayList<String>();
    for (SequenceI s : alignment.getSequences())
    {
      StringBuilder sb = new StringBuilder();
      for (int p : positions)
      {
        sb.append(s.getCharAt(p));
      }
      str.add(sb.toString());
    }
    SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
            alignment.getSequencesArray(),
            str.toArray(new String[str.size()]),
            Arrays.asList(new SequenceGroup[]
            { sg1, sg2 }));
    ColumnSelection cs = new ColumnSelection();
    for (int p : positions)
    {
      cs.addElement(p);
    }
    SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
            alignment.getSequencesArray(), cs,
            Arrays.asList(new SequenceGroup[]
            { sg1, sg2 }));
    AssertJUnit.assertEquals(seqgroupsString.length, seqgroupsColSel.length);
    for (int p = 0; p < seqgroupsString.length; p++)
    {
      AssertJUnit.assertEquals(seqgroupsString[p].getName(),
              seqgroupsColSel[p].getName());
      AssertJUnit.assertArrayEquals(
              seqgroupsString[p].getSequencesInOrder(alignment),
              seqgroupsColSel[p].getSequencesInOrder(alignment));
      if (seqgroupsString[p].getSequences().contains(s2))
      {
        AssertJUnit.assertTrue(seqgroupsString[p].getSize() == 2);
      }
    }
  }

}