package jalview.structure;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;

import jalview.datamodel.AlignedCodonFrame;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;

import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.Set;

import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;

public class StructureSelectionManagerTest
{
  private StructureSelectionManager ssm;

  @BeforeClass(alwaysRun = true)
  public static void setUpBeforeClass() throws Exception
  {
    jalview.bin.Jalview.main(new String[] { "-props",
        "test/jalview/testProps.jvprops" });
  }

 @BeforeMethod(alwaysRun = true)
  public void setUp()
  {
    ssm = new StructureSelectionManager();
  }

  @Test(groups ={ "Functional" })
  public void testRegisterMapping()
  {
    AlignedCodonFrame acf1 = new AlignedCodonFrame();
    AlignedCodonFrame acf2 = new AlignedCodonFrame();

    ssm.registerMapping(acf1);
    assertEquals(1, ssm.seqmappings.size());
    assertTrue(ssm.seqmappings.contains(acf1));

    ssm.registerMapping(acf2);
    assertEquals(2, ssm.seqmappings.size());
    assertTrue(ssm.seqmappings.contains(acf1));
    assertTrue(ssm.seqmappings.contains(acf2));

    /*
     * Re-adding the first mapping does nothing
     */
    ssm.registerMapping(acf1);
    assertEquals(2, ssm.seqmappings.size());
    assertTrue(ssm.seqmappings.contains(acf1));
    assertTrue(ssm.seqmappings.contains(acf2));
  }

  @Test(groups ={ "Functional" })
  public void testRegisterMappings()
  {
    AlignedCodonFrame acf1 = new AlignedCodonFrame();
    AlignedCodonFrame acf2 = new AlignedCodonFrame();
    AlignedCodonFrame acf3 = new AlignedCodonFrame();

    Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
    set1.add(acf1);
    set1.add(acf2);
    Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
    set2.add(acf2);
    set2.add(acf3);

    /*
     * Add both sets twice; each mapping should be added once only
     */
    ssm.registerMappings(set1);
    ssm.registerMappings(set1);
    ssm.registerMappings(set2);
    ssm.registerMappings(set2);

    assertEquals(3, ssm.seqmappings.size());
    assertTrue(ssm.seqmappings.contains(acf1));
    assertTrue(ssm.seqmappings.contains(acf2));
    assertTrue(ssm.seqmappings.contains(acf3));
  }

  /**
   * Test that a mapping is not deregistered if an alignment holds a reference
   * to it
   */
  @Test(groups ={ "Functional" })
  public void testDeregisterMapping_withAlignmentReference()
  {
    Desktop d = Desktop.instance;
    assertNotNull(d);

    /*
     * alignment with reference to mappings
     */
    AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
            ">Seq1\nCAGT\n", FormatAdapter.PASTE);

    AlignedCodonFrame acf1 = new AlignedCodonFrame();
    AlignedCodonFrame acf2 = new AlignedCodonFrame();

    Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
    mappings.add(acf1);
    mappings.add(acf2);
    af1.getViewport().getAlignment().setCodonFrames(mappings);

    /*
     * Add one and remove it.
     */
    ssm.registerMapping(acf1);
    ssm.deregisterMapping(acf1);
    assertEquals(1, ssm.seqmappings.size());
    assertTrue(ssm.seqmappings.contains(acf1));
  }

  /**
   * Test that a mapping is deregistered if no alignment holds a reference to it
   */
  @Test(groups ={ "Functional" })
  public void testDeregisterMapping_withNoReference()
  {
    Desktop d = Desktop.instance;
    assertNotNull(d);
  
    /*
     * alignment with reference to mappings
     */
    AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
            ">Seq1\nCAGT\n", FormatAdapter.PASTE);
  
    AlignedCodonFrame acf1 = new AlignedCodonFrame();
    AlignedCodonFrame acf2 = new AlignedCodonFrame();
  
    Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
    mappings.add(acf2);
    af1.getViewport().getAlignment().setCodonFrames(mappings);
  
    /*
     * Add one and remove it.
     */
    ssm.registerMapping(acf1);
    assertEquals(1, ssm.seqmappings.size());
    assertTrue(ssm.seqmappings.contains(acf1));
    ssm.deregisterMapping(acf1);
    assertEquals(0, ssm.seqmappings.size());
  }

  /**
   * Test that a mapping is not deregistered when a second view is closed but
   * the first still holds a reference to the mapping
   */
  @Test(groups ={ "Functional" })
  public void testDeregisterMapping_onCloseView()
  {
    /*
     * alignment with reference to mappings
     */
    AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
            ">Seq1\nCAGT\n", FormatAdapter.PASTE);
  
    AlignedCodonFrame acf1 = new AlignedCodonFrame();
    AlignedCodonFrame acf2 = new AlignedCodonFrame();
  
    Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
    mappings.add(acf1);
    mappings.add(acf2);
    af1.getViewport().getAlignment().setCodonFrames(mappings);
    af1.newView_actionPerformed(null);

    /*
     * Verify that creating the alignment for the new View has registered the
     * mappings
     */
    ssm = StructureSelectionManager
            .getStructureSelectionManager(Desktop.instance);
    assertEquals(2, ssm.seqmappings.size());
    assertTrue(ssm.seqmappings.contains(acf1));
    assertTrue(ssm.seqmappings.contains(acf2));

    /*
     * Close the second view. Verify that mappings are not removed as the first
     * view still holds a reference to them.
     */
    af1.closeMenuItem_actionPerformed(false);
    assertEquals(2, ssm.seqmappings.size());
    assertTrue(ssm.seqmappings.contains(acf1));
    assertTrue(ssm.seqmappings.contains(acf2));
  }
}