package jalview.gui;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;

import java.io.IOException;
import java.util.BitSet;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

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

/**
 * Unit tests for PopupMenu
 * 
 * @author gmcarstairs
 *
 */
public class PopupMenuTest
{
  // 4 sequences x 13 positions
  final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
          + "TIETHKEAELVG-\n"
          + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
          + "TIETHKEAELVG-\n"
          + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
          + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
          + "TIETHKEEELTA-\n";

  private static final int SEQ_ANN_COUNT = 10;

  private static final int AUTO_ANNS = 3;

  AlignmentI alignment;

  AlignmentPanel parentPanel;

  @Before
  public void setUp() throws IOException
  {
    AlignmentI al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
            AppletFormatAdapter.PASTE, "FASTA");
    AlignFrame af = new AlignFrame(al, 700, 500);
    parentPanel = new AlignmentPanel(af, af.getViewport());
    alignment = parentPanel.getAlignment();

    AlignmentAnnotation[] anns = new AlignmentAnnotation[SEQ_ANN_COUNT];
    for (int i = 0; i < anns.length; i++)
    {
      anns[i] = new AlignmentAnnotation("Label" + i, null, 0d);
      anns[i].setCalcId("CalcId" + i);
      anns[i].visible = true;
      alignment.addAnnotation(anns[i]);
    }
  }

  /**
   * Test method that determines visible graph groups.
   */
  @Test
  public void testGetVisibleGraphGroups()
  {
    AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
    /*
     * a bar graph group is not included
     */
    anns[0].graph = AlignmentAnnotation.BAR_GRAPH;
    anns[0].graphGroup = 1;
    anns[0].visible = true;

    /*
     * a line graph group is included as long as one of its members is visible
     */
    anns[1].graph = AlignmentAnnotation.LINE_GRAPH;
    anns[1].graphGroup = 5;
    anns[1].visible = false;
    anns[2].graph = AlignmentAnnotation.LINE_GRAPH;
    anns[2].graphGroup = 5;
    anns[2].visible = true;

    /*
     * a line graph group with no visible rows is not included
     */
    anns[3].graph = AlignmentAnnotation.LINE_GRAPH;
    anns[3].graphGroup = 3;
    anns[3].visible = false;

    // a visible line graph with no graph group is not included
    anns[4].graph = AlignmentAnnotation.LINE_GRAPH;
    anns[4].graphGroup = -1;
    anns[4].visible = true;

    BitSet result = PopupMenu.getVisibleLineGraphGroups(anns);
    assertTrue(result.get(5));
    assertFalse(result.get(0));
    assertFalse(result.get(1));
    assertFalse(result.get(2));
    assertFalse(result.get(3));
  }

  /**
   * Test a mixture of show/hidden annotations in/outside selection group.
   */
  @Test
  public void testGetAnnotationTypesForShowHide_forSelectionGroup()
  {
    Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
    Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
    AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
    BitSet visibleGraphGroups = new BitSet();
    selectSequences(0, 3);
    SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();

    /*
     * Configure annotation properties for test (offsetting for auto-calculated
     * rows).
     */
    // not in selection group (should be ignored):
    // hidden annotation Label4 not in selection group
    anns[AUTO_ANNS + 4].sequenceRef = seqs[2];
    anns[AUTO_ANNS + 4].visible = false;
    anns[AUTO_ANNS + 7].sequenceRef = seqs[1];
    anns[AUTO_ANNS + 7].visible = true;

    /*
     * in selection group, hidden:
     */
    anns[AUTO_ANNS + 2].sequenceRef = seqs[3]; // CalcId2/Label2
    anns[AUTO_ANNS + 2].visible = false;
    anns[AUTO_ANNS + 3].sequenceRef = seqs[3]; // CalcId3/Label2
    anns[AUTO_ANNS + 3].visible = false;
    anns[AUTO_ANNS + 3].label = "Label2";
    anns[AUTO_ANNS + 4].sequenceRef = seqs[3]; // CalcId2/Label3
    anns[AUTO_ANNS + 4].visible = false;
    anns[AUTO_ANNS + 4].label = "Label3";
    anns[AUTO_ANNS + 4].setCalcId("CalcId2");
    anns[AUTO_ANNS + 8].sequenceRef = seqs[0]; // CalcId9/Label9
    anns[AUTO_ANNS + 8].visible = false;
    anns[AUTO_ANNS + 8].label = "Label9";
    anns[AUTO_ANNS + 8].setCalcId("CalcId9");
    /*
     * in selection group, visible
     */
    anns[AUTO_ANNS + 6].sequenceRef = seqs[0]; // CalcId6/Label6
    anns[AUTO_ANNS + 6].visible = true;
    anns[AUTO_ANNS + 9].sequenceRef = seqs[3]; // CalcId9/Label9
    anns[AUTO_ANNS + 9].visible = true;

    PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes,
            visibleGraphGroups, anns, parentPanel.av.getSelectionGroup());

    // check results; note CalcId9/Label9 is both hidden and shown (for
    // different sequences) so should be in both
    // shown: CalcId6/Label6 and CalcId9/Label9
    assertEquals(2, shownTypes.size());
    assertEquals(1, shownTypes.get("CalcId6").size());
    assertEquals(1, shownTypes.get("CalcId6").get(0).size());
    assertEquals("Label6", shownTypes.get("CalcId6").get(0).get(0));
    assertEquals(1, shownTypes.get("CalcId9").size());
    assertEquals(1, shownTypes.get("CalcId9").get(0).size());
    assertEquals("Label9", shownTypes.get("CalcId9").get(0).get(0));

    // hidden: CalcId2/Label2, CalcId2/Label3, CalcId3/Label2, CalcId9/Label9
    assertEquals(3, hiddenTypes.size());
    assertEquals(2, hiddenTypes.get("CalcId2").size());
    assertEquals(1, hiddenTypes.get("CalcId2").get(0).size());
    assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));
    assertEquals(1, hiddenTypes.get("CalcId2").get(1).size());
    assertEquals("Label3", hiddenTypes.get("CalcId2").get(1).get(0));
    assertEquals(1, hiddenTypes.get("CalcId3").size());
    assertEquals(1, hiddenTypes.get("CalcId3").get(0).size());
    assertEquals("Label2", hiddenTypes.get("CalcId3").get(0).get(0));
    assertEquals(1, hiddenTypes.get("CalcId9").size());
    assertEquals(1, hiddenTypes.get("CalcId9").get(0).size());
    assertEquals("Label9", hiddenTypes.get("CalcId9").get(0).get(0));

    consoleDebug(shownTypes, hiddenTypes);
  }

  /**
   * This output is not part of the test but may help make sense of it...
   * 
   * @param shownTypes
   * @param hiddenTypes
   */
  protected void consoleDebug(Map<String, List<List<String>>> shownTypes,
          Map<String, List<List<String>>> hiddenTypes)
  {
    for (String calcId : shownTypes.keySet())
    {
      System.out.println("Visible annotation types for calcId=" + calcId);
      for (List<String> type : shownTypes.get(calcId))
      {
        System.out.println("   " + type);
      }
    }
    for (String calcId : hiddenTypes.keySet())
    {
      System.out.println("Hidden annotation types for calcId=" + calcId);
      for (List<String> type : hiddenTypes.get(calcId))
      {
        System.out.println("   " + type);
      }
    }
  }

  /**
   * Test case where there are 'grouped' annotations, visible and hidden, within
   * and without the selection group.
   */
  @Test
  public void testGetAnnotationTypesForShowHide_withGraphGroups()
  {
    final int GROUP_4 = 4;
    final int GROUP_5 = 5;
    final int GROUP_6 = 6;

    Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
    Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
    AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
    BitSet visibleGraphGroups = new BitSet();
    visibleGraphGroups.set(GROUP_4);
    visibleGraphGroups.set(GROUP_6);
    selectSequences(0, 3);
    SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();

    /*
     * Configure annotation properties for test (offsetting for auto-calculated
     * rows).
     */
    // annotations for selection group and graph group
    // hidden annotations Label2, Label3, in (hidden) group 5
    anns[AUTO_ANNS + 2].sequenceRef = seqs[3];
    anns[AUTO_ANNS + 2].visible = false;
    anns[AUTO_ANNS + 2].graph = AlignmentAnnotation.LINE_GRAPH;
    anns[AUTO_ANNS + 2].graphGroup = GROUP_5; // not a visible group
    anns[AUTO_ANNS + 3].sequenceRef = seqs[0];
    anns[AUTO_ANNS + 3].visible = false;
    anns[AUTO_ANNS + 3].graph = AlignmentAnnotation.LINE_GRAPH;
    anns[AUTO_ANNS + 3].graphGroup = GROUP_5;
    // need to ensure annotations have the same calcId as well
    anns[AUTO_ANNS + 3].setCalcId("CalcId2");

    // annotations Label1 (hidden), Label5 (visible) in group 6 (visible)
    anns[AUTO_ANNS + 1].sequenceRef = seqs[3];
    // being in a visible group should take precedence over this visibility
    anns[AUTO_ANNS + 1].visible = false;
    anns[AUTO_ANNS + 1].graph = AlignmentAnnotation.LINE_GRAPH;
    anns[AUTO_ANNS + 1].graphGroup = GROUP_6;
    anns[AUTO_ANNS + 5].sequenceRef = seqs[0];
    anns[AUTO_ANNS + 5].visible = true; // visibleGraphGroups overrides this
    anns[AUTO_ANNS + 5].graph = AlignmentAnnotation.LINE_GRAPH;
    anns[AUTO_ANNS + 5].graphGroup = GROUP_6;
    anns[AUTO_ANNS + 5].setCalcId("CalcId1");

    // annotations outwith selection group - should be ignored
    // hidden grouped annotations
    anns[AUTO_ANNS + 6].sequenceRef = seqs[2];
    anns[AUTO_ANNS + 6].visible = false;
    anns[AUTO_ANNS + 6].graph = AlignmentAnnotation.LINE_GRAPH;
    anns[AUTO_ANNS + 6].graphGroup = GROUP_4;
    anns[AUTO_ANNS + 8].sequenceRef = seqs[1];
    anns[AUTO_ANNS + 8].visible = false;
    anns[AUTO_ANNS + 8].graph = AlignmentAnnotation.LINE_GRAPH;
    anns[AUTO_ANNS + 8].graphGroup = GROUP_4;
    // visible grouped annotations Label7, Label9
    anns[AUTO_ANNS + 7].sequenceRef = seqs[2];
    anns[AUTO_ANNS + 7].visible = true;
    anns[AUTO_ANNS + 7].graph = AlignmentAnnotation.LINE_GRAPH;
    anns[AUTO_ANNS + 7].graphGroup = GROUP_4;
    anns[AUTO_ANNS + 9].sequenceRef = seqs[1];
    anns[AUTO_ANNS + 9].visible = true;
    anns[AUTO_ANNS + 9].graph = AlignmentAnnotation.LINE_GRAPH;
    anns[AUTO_ANNS + 9].graphGroup = GROUP_4;

    PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes,
            visibleGraphGroups, anns, parentPanel.av.getSelectionGroup());

    consoleDebug(shownTypes, hiddenTypes);

    // CalcId1 / Label1, Label5 (only) should be 'shown', as a compound type
    assertEquals(1, shownTypes.get("CalcId1").size());
    assertEquals(2, shownTypes.get("CalcId1").get(0).size());
    assertEquals("Label1", shownTypes.get("CalcId1").get(0).get(0));
    assertEquals("Label5", shownTypes.get("CalcId1").get(0).get(1));

    // CalcId2 / Label2, Label3 (only) should be 'hidden'
    assertEquals(1, hiddenTypes.get("CalcId2").size());
    assertEquals(2, hiddenTypes.get("CalcId2").get(0).size());
    assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));
    assertEquals("Label3", hiddenTypes.get("CalcId2").get(0).get(1));
  }

  /**
   * Add a sequence group to the alignment with the specified sequences (base 0)
   * in it
   * 
   * @param i
   * @param more
   */
  private void selectSequences(int... selected)
  {
    SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
    SequenceGroup sg = new SequenceGroup();
    for (int i : selected)
    {
      sg.addSequence(seqs[i], false);
    }
    parentPanel.av.setSelectionGroup(sg);
  }
}