package jalview.ext.jmol;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;

import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.AppJmolBinding;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;

import java.util.HashMap;
import java.util.List;
import java.util.Map;

import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;

import junit.extensions.PA;

public class JalviewJmolBindingTest
{
  private AlignFrame af;

  @BeforeTest(alwaysRun = true)
  public void setup()
  {
    af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
            DataSourceType.FILE);
  }

  @Test(groups = "Functional")
  public void testBuildShowStructuresCommand()
  {
    AlignViewport av = af.getViewport();
    PDBEntry[] pdbs = new PDBEntry[] {};
    SequenceI seq1 = av.getAlignment().findSequenceMatch("FER1_SPIOL")[0];
    assertNotNull(seq1);
    SequenceI seq2 = av.getAlignment().findSequenceMatch("FER2_ARATH")[0];
    assertNotNull(seq2);
    StructureSelectionManager ssm = new StructureSelectionManager();
    SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
    AppJmolBinding testee = new AppJmolBinding(null, ssm, pdbs, seqs,
            null);

    /*
     * map FER1_SPIOL residues 51-100 to residues 1-50 (atoms 1-250) in 1A70
     * and residues 110-147 to structure residues 60-97
     * (in fact there is no gap, added here for test purposes)
     */
    HashMap<Integer, int[]> map = new HashMap<>();
    for (int pos = 51; pos <= 100; pos++)
    {
      map.put(pos, new int[] { pos - 50, 5 * (pos - 50) });
    }
    for (int pos = 110; pos <= 147; pos++)
    {
      map.put(pos, new int[] { pos - 50, 5 * (pos - 50) });
    }
    StructureMapping sm1 = new StructureMapping(seq1, "1a70.pdb", "1A70",
            "A", map, null);
    ssm.addStructureMapping(sm1);

    /*
     * map FER2_ARATH residues 53-148 to residues 2-97 in 4ZHO
     */
    map = new HashMap<>();
    for (int pos = 53; pos <= 148; pos++)
    {
      map.put(pos, new int[] { pos - 51, 5 * (pos - 51) });
    }
    StructureMapping sm2 = new StructureMapping(seq2, "4zho.pdb", "4ZHO",
            "B", map, null);
    ssm.addStructureMapping(sm2);

    /*
     * show everything
     */
    String cmd = testee.buildShowStructuresCommand(av, true);
    assertEquals(cmd, "display *; cartoon only; zoom 0");
    cmd = testee.buildShowStructuresCommand(av, false);
    assertEquals(cmd, "display *; cartoon only");

    /*
     * stub out modelFileNames - array index is Jmol
     * model number - 1
     */
    PA.setValue(testee, "modelFileNames",
            new String[]
            { "1a70.pdb", "4zho.pdb" });

    /*
     * stub out lookup map from pdb:chain to filename
     */
    Map<String, String> chainFiles = new HashMap<>();
    PA.setValue(testee, "chainFile", chainFiles);
    chainFiles.put("1A70:A", "1a70.pdb");
    chainFiles.put("1A70:B", "1a70.pdb");
    chainFiles.put("4ZHO:B", "4zho.pdb");
    chainFiles.put("4ZHO:C", "4zho.pdb");

    /*
     * show all except for selected chains to hide
     */
    List<String> chainsToHide = (List<String>) PA.getValue(testee,
            "chainsToHide");
    chainsToHide.add("1A70:B");
    chainsToHide.add("4ZHO:C");
    cmd = testee.buildShowStructuresCommand(av, true);
    assertEquals(cmd,
            "display *; hide add :B/1.1,:C/2.1; cartoon only; zoom 0");

    /*
     * show alignment only, no chains hidden
     */
    chainsToHide.clear();
    testee.setShowAlignmentOnly(true);
    cmd = testee.buildShowStructuresCommand(av, false);
    assertEquals(cmd,
            "hide *;display (1-50,60-97)&:A/1.1,2-97:B/2.1; select displayed; cartoon only");

    /*
     * now with a chain hidden
     */
    chainsToHide.add("4ZHO:C");
    cmd = testee.buildShowStructuresCommand(av, false);
    String expected = "hide *;display (1-50,60-97)&:A/1.1,2-97:B/2.1; select displayed; hide add :C/2.1; cartoon only";
    assertEquals(cmd, expected);

    /*
     * hide columns in the mapped region - should not change the command (yet)
     */
    int fromCol = seq1.findIndex(60); // structure residue 10
    int toCol = seq1.findIndex(70); // structure residue 20
    av.hideColumns(fromCol - 1, toCol - 1);
    cmd = testee.buildShowStructuresCommand(av, false);
    assertEquals(cmd, expected);

    /*
     * select 'hide hidden columns'
     * command should now exclude these in both mapped sequences
     */
    testee.setHideHiddenRegions(true);
    cmd = testee.buildShowStructuresCommand(av, false);
    expected = "hide *;display (1-9,21-50,60-97)&:A/1.1,(2-10,22-97)&:B/2.1; select displayed; hide add :C/2.1; cartoon only";
    assertEquals(cmd, expected);

    /*
     * deselect 'show alignment only'
     * hide hidden columns is now ignored
     */
    testee.setShowAlignmentOnly(false);
    cmd = testee.buildShowStructuresCommand(av, false);
    assertEquals(cmd, "display *; hide add :C/2.1; cartoon only");
  }
}