package jalview.gui;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertSame;

import org.junit.Before;
import org.junit.Test;

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;

public class AlignViewportTest
{

  AlignmentI al;
  AlignViewport testee;

  @Before
  public void setUp()
  {
    SequenceI seq1 = new Sequence("Seq1", "ABC");
    SequenceI seq2 = new Sequence("Seq2", "ABC");
    SequenceI seq3 = new Sequence("Seq3", "ABC");
    SequenceI[] seqs = new SequenceI[]
    { seq1, seq2, seq3 };
    al = new Alignment(seqs);
    al.setDataset(null);
    testee = new AlignViewport(al);
  }

  @Test
  public void testCollateForPdb()
  {
    /*
     * Set up sequence pdb ids
     */
    PDBEntry pdb1 = new PDBEntry("1ABC", "A", Type.PDB, "1ABC.pdb");
    PDBEntry pdb2 = new PDBEntry("2ABC", "A", Type.PDB, "2ABC.pdb");
    PDBEntry pdb3 = new PDBEntry("3ABC", "A", Type.PDB, "3ABC.pdb");

    /*
     * seq1 and seq3 refer to 1ABC, seq2 to 2ABC, none to 3ABC
     */
    al.getSequenceAt(0).getDatasetSequence()
            .addPDBId(
            new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
    al.getSequenceAt(2).getDatasetSequence()
            .addPDBId(
            new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
    al.getSequenceAt(1).getDatasetSequence()
            .addPDBId(
            new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
    /*
     * Add a second chain PDB xref to Seq2 - should not result in a duplicate in
     * the results
     */
    al.getSequenceAt(1).getDatasetSequence()
            .addPDBId(new PDBEntry("2ABC", "D", Type.PDB, "2ABC.pdb"));
    /*
     * Seq3 refers to 3abc - this does not match 3ABC (as the code stands)
     */
    al.getSequenceAt(2).getDatasetSequence()
            .addPDBId(new PDBEntry("3abc", "D", Type.PDB, "3ABC.pdb"));

    /*
     * run method under test
     */
    SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[]
    { pdb1, pdb2, pdb3 });

    // seq1 and seq3 refer to PDBEntry[0]
    assertEquals(2, seqs[0].length);
    assertSame(al.getSequenceAt(0), seqs[0][0]);
    assertSame(al.getSequenceAt(2), seqs[0][1]);

    // seq2 refers to PDBEntry[1]
    assertEquals(1, seqs[1].length);
    assertSame(al.getSequenceAt(1), seqs[1][0]);

    // no sequence refers to PDBEntry[2]
    assertEquals(0, seqs[2].length);
  }
}