/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.gui;

import static jalview.util.UrlConstants.DB_ACCESSION;
import static jalview.util.UrlConstants.SEQUENCE_ID;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;

import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.util.MessageManager;

import java.awt.Component;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JPopupMenu;
import javax.swing.JSeparator;

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

public class PopupMenuTest
{

  @BeforeClass(alwaysRun = true)
  public void setUpJvOptionPane()
  {
    JvOptionPane.setInteractiveMode(false);
    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  }

  // 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";

  AlignmentI alignment;

  AlignmentPanel parentPanel;

  PopupMenu testee = null;

  @BeforeMethod(alwaysRun = true)
  public void setUp() throws IOException
  {
    alignment = new FormatAdapter().readFile(TEST_DATA,
            DataSourceType.PASTE, FileFormat.Fasta);
    AlignFrame af = new AlignFrame(alignment, 700, 500);
    parentPanel = new AlignmentPanel(af, af.getViewport());
    testee = new PopupMenu(parentPanel, null, null);
    int i = 0;
    for (SequenceI seq : alignment.getSequences())
    {
      final AlignmentAnnotation annotation = new AlignmentAnnotation(
              "label" + i, "desc" + i, i);
      annotation.setCalcId("calcId" + i);
      seq.addAlignmentAnnotation(annotation);
      annotation.setSequenceRef(seq);
    }
  }

  @Test(groups = { "Functional" })
  public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
  {
    JMenuItem menu = new JMenuItem();
    List<SequenceI> seqs = new ArrayList<SequenceI>();
    testee.configureReferenceAnnotationsMenu(menu, seqs);
    assertFalse(menu.isEnabled());
    // now try null list
    menu.setEnabled(true);
    testee.configureReferenceAnnotationsMenu(menu, null);
    assertFalse(menu.isEnabled());
  }

  /**
   * Test building the 'add reference annotations' menu for the case where there
   * are no reference annotations to add to the alignment. The menu item should
   * be disabled.
   */
  @Test(groups = { "Functional" })
  public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
  {
    JMenuItem menu = new JMenuItem();

    /*
     * Initial state is that sequences have annotations, and have dataset
     * sequences, but the dataset sequences have no annotations. Hence nothing
     * to add.
     */
    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();

    testee.configureReferenceAnnotationsMenu(menu, seqs);
    assertFalse(menu.isEnabled());
  }

  /**
   * Test building the 'add reference annotations' menu for the case where all
   * reference annotations are already on the alignment. The menu item should be
   * disabled.
   */
  @Test(groups = { "Functional" })
  public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
  {
    JMenuItem menu = new JMenuItem();
    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();

    // make up new annotations and add to dataset sequences, sequences and
    // alignment
    attachReferenceAnnotations(seqs, true, true);

    testee.configureReferenceAnnotationsMenu(menu, seqs);
    assertFalse(menu.isEnabled());
  }

  /**
   * Test building the 'add reference annotations' menu for the case where
   * several reference annotations are on the dataset but not on the sequences.
   * The menu item should be enabled, and acquire a tooltip which lists the
   * annotation sources (calcIds) and type (labels).
   */
  @Test(groups = { "Functional" })
  public void testConfigureReferenceAnnotationsMenu()
  {
    JMenuItem menu = new JMenuItem();
    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();

    // make up new annotations and add to dataset sequences
    attachReferenceAnnotations(seqs, false, false);

    testee.configureReferenceAnnotationsMenu(menu, seqs);
    assertTrue(menu.isEnabled());
    String s = MessageManager.getString("label.add_annotations_for");
    String expected = "<html><style> p.ttip {width: 350; text-align: justify; word-wrap: break-word;}</style><p class=\"ttip\">"
            + s + "<br/>Jmol/secondary structure<br/>PDB/Temp</p></html>";
    assertEquals(expected, menu.getToolTipText());
  }

  /**
   * Test building the 'add reference annotations' menu for the case where
   * several reference annotations are on the dataset and the sequences but not
   * on the alignment. The menu item should be enabled, and acquire a tooltip
   * which lists the annotation sources (calcIds) and type (labels).
   */
  @Test(groups = { "Functional" })
  public void testConfigureReferenceAnnotationsMenu_notOnAlignment()
  {
    JMenuItem menu = new JMenuItem();
    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();

    // make up new annotations and add to dataset sequences and sequences
    attachReferenceAnnotations(seqs, true, false);

    testee.configureReferenceAnnotationsMenu(menu, seqs);
    assertTrue(menu.isEnabled());
    String s = MessageManager.getString("label.add_annotations_for");
    String expected = "<html><style> p.ttip {width: 350; text-align: justify; word-wrap: break-word;}</style><p class=\"ttip\">"
            + s + "<br/>Jmol/secondary structure<br/>PDB/Temp</p></html>";
    assertEquals(expected, menu.getToolTipText());
  }

  /**
   * Generate annotations and add to dataset sequences and (optionally)
   * sequences and/or alignment
   * 
   * @param seqs
   * @param addToSequence
   * @param addToAlignment
   */
  private void attachReferenceAnnotations(List<SequenceI> seqs,
          boolean addToSequence, boolean addToAlignment)
  {
    // PDB.secondary structure on Sequence0
    AlignmentAnnotation annotation = new AlignmentAnnotation(
            "secondary structure", "", 0);
    annotation.setCalcId("PDB");
    seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
    if (addToSequence)
    {
      seqs.get(0).addAlignmentAnnotation(annotation);
    }
    if (addToAlignment)
    {
      this.alignment.addAnnotation(annotation);
    }

    // PDB.Temp on Sequence1
    annotation = new AlignmentAnnotation("Temp", "", 0);
    annotation.setCalcId("PDB");
    seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
    if (addToSequence)
    {
      seqs.get(1).addAlignmentAnnotation(annotation);
    }
    if (addToAlignment)
    {
      this.alignment.addAnnotation(annotation);
    }

    // JMOL.secondary structure on Sequence0
    annotation = new AlignmentAnnotation("secondary structure", "", 0);
    annotation.setCalcId("Jmol");
    seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
    if (addToSequence)
    {
      seqs.get(0).addAlignmentAnnotation(annotation);
    }
    if (addToAlignment)
    {
      this.alignment.addAnnotation(annotation);
    }
  }

  /**
   * Test building the 'add reference annotations' menu for the case where there
   * are two alignment views:
   * <ul>
   * <li>in one view, reference annotations have been added (are on the
   * datasets, sequences and alignment)</li>
   * <li>in the current view, reference annotations are on the dataset and
   * sequence, but not the alignment</li>
   * </ul>
   * The menu item should be enabled, and acquire a tooltip which lists the
   * annotation sources (calcIds) and type (labels).
   */
  @Test(groups = { "Functional" })
  public void testConfigureReferenceAnnotationsMenu_twoViews()
  {
  }

  /**
   * Test for building menu options including 'show' and 'hide' annotation
   * types.
   */
  @Test(groups = { "Functional" })
  public void testBuildAnnotationTypesMenus()
  {
    JMenu showMenu = new JMenu();
    JMenu hideMenu = new JMenu();
    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();

    // make up new annotations and add to sequences and to the alignment

    // PDB.secondary structure on Sequence0
    AlignmentAnnotation annotation = new AlignmentAnnotation(
            "secondary structure", "", new Annotation[] {});
    annotation.setCalcId("PDB");
    annotation.visible = true;
    seqs.get(0).addAlignmentAnnotation(annotation);
    parentPanel.getAlignment().addAnnotation(annotation);

    // JMOL.secondary structure on Sequence0 - hidden
    annotation = new AlignmentAnnotation("secondary structure", "",
            new Annotation[] {});
    annotation.setCalcId("JMOL");
    annotation.visible = false;
    seqs.get(0).addAlignmentAnnotation(annotation);
    parentPanel.getAlignment().addAnnotation(annotation);

    // Jpred.SSP on Sequence0 - hidden
    annotation = new AlignmentAnnotation("SSP", "", new Annotation[] {});
    annotation.setCalcId("JPred");
    annotation.visible = false;
    seqs.get(0).addAlignmentAnnotation(annotation);
    parentPanel.getAlignment().addAnnotation(annotation);

    // PDB.Temp on Sequence1
    annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
    annotation.setCalcId("PDB");
    annotation.visible = true;
    seqs.get(1).addAlignmentAnnotation(annotation);
    parentPanel.getAlignment().addAnnotation(annotation);

    /*
     * Expect menu options to show "secondary structure" and "SSP", and to hide
     * "secondary structure" and "Temp". Tooltip should be calcId.
     */
    testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);

    assertTrue(showMenu.isEnabled());
    assertTrue(hideMenu.isEnabled());

    Component[] showOptions = showMenu.getMenuComponents();
    Component[] hideOptions = hideMenu.getMenuComponents();

    assertEquals(4, showOptions.length); // includes 'All' and separator
    assertEquals(4, hideOptions.length);
    String all = MessageManager.getString("label.all");
    assertEquals(all, ((JMenuItem) showOptions[0]).getText());
    assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
    assertEquals(JSeparator.HORIZONTAL,
            ((JSeparator) showOptions[1]).getOrientation());
    assertEquals("secondary structure",
            ((JMenuItem) showOptions[2]).getText());
    assertEquals("JMOL", ((JMenuItem) showOptions[2]).getToolTipText());
    assertEquals("SSP", ((JMenuItem) showOptions[3]).getText());
    assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText());

    assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
    assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
    assertEquals(JSeparator.HORIZONTAL,
            ((JSeparator) hideOptions[1]).getOrientation());
    assertEquals("secondary structure",
            ((JMenuItem) hideOptions[2]).getText());
    assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
    assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
    assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
  }

  /**
   * Test for building menu options with only 'hide' annotation types enabled.
   */
  @Test(groups = { "Functional" })
  public void testBuildAnnotationTypesMenus_showDisabled()
  {
    JMenu showMenu = new JMenu();
    JMenu hideMenu = new JMenu();
    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();

    // make up new annotations and add to sequences and to the alignment

    // PDB.secondary structure on Sequence0
    AlignmentAnnotation annotation = new AlignmentAnnotation(
            "secondary structure", "", new Annotation[] {});
    annotation.setCalcId("PDB");
    annotation.visible = true;
    seqs.get(0).addAlignmentAnnotation(annotation);
    parentPanel.getAlignment().addAnnotation(annotation);

    // PDB.Temp on Sequence1
    annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
    annotation.setCalcId("PDB");
    annotation.visible = true;
    seqs.get(1).addAlignmentAnnotation(annotation);
    parentPanel.getAlignment().addAnnotation(annotation);

    /*
     * Expect menu options to hide "secondary structure" and "Temp". Tooltip
     * should be calcId. 'Show' menu should be disabled.
     */
    testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);

    assertFalse(showMenu.isEnabled());
    assertTrue(hideMenu.isEnabled());

    Component[] showOptions = showMenu.getMenuComponents();
    Component[] hideOptions = hideMenu.getMenuComponents();

    assertEquals(2, showOptions.length); // includes 'All' and separator
    assertEquals(4, hideOptions.length);
    String all = MessageManager.getString("label.all");
    assertEquals(all, ((JMenuItem) showOptions[0]).getText());
    assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
    assertEquals(JSeparator.HORIZONTAL,
            ((JSeparator) showOptions[1]).getOrientation());

    assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
    assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
    assertEquals(JSeparator.HORIZONTAL,
            ((JSeparator) hideOptions[1]).getOrientation());
    assertEquals("secondary structure",
            ((JMenuItem) hideOptions[2]).getText());
    assertEquals("PDB", ((JMenuItem) hideOptions[2]).getToolTipText());
    assertEquals("Temp", ((JMenuItem) hideOptions[3]).getText());
    assertEquals("PDB", ((JMenuItem) hideOptions[3]).getToolTipText());
  }

  /**
   * Test for building menu options with only 'show' annotation types enabled.
   */
  @Test(groups = { "Functional" })
  public void testBuildAnnotationTypesMenus_hideDisabled()
  {
    JMenu showMenu = new JMenu();
    JMenu hideMenu = new JMenu();
    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();

    // make up new annotations and add to sequences and to the alignment

    // PDB.secondary structure on Sequence0
    AlignmentAnnotation annotation = new AlignmentAnnotation(
            "secondary structure", "", new Annotation[] {});
    annotation.setCalcId("PDB");
    annotation.visible = false;
    seqs.get(0).addAlignmentAnnotation(annotation);
    parentPanel.getAlignment().addAnnotation(annotation);

    // PDB.Temp on Sequence1
    annotation = new AlignmentAnnotation("Temp", "", new Annotation[] {});
    annotation.setCalcId("PDB2");
    annotation.visible = false;
    seqs.get(1).addAlignmentAnnotation(annotation);
    parentPanel.getAlignment().addAnnotation(annotation);

    /*
     * Expect menu options to show "secondary structure" and "Temp". Tooltip
     * should be calcId. 'hide' menu should be disabled.
     */
    testee.buildAnnotationTypesMenus(showMenu, hideMenu, seqs);

    assertTrue(showMenu.isEnabled());
    assertFalse(hideMenu.isEnabled());

    Component[] showOptions = showMenu.getMenuComponents();
    Component[] hideOptions = hideMenu.getMenuComponents();

    assertEquals(4, showOptions.length); // includes 'All' and separator
    assertEquals(2, hideOptions.length);
    String all = MessageManager.getString("label.all");
    assertEquals(all, ((JMenuItem) showOptions[0]).getText());
    assertTrue(showOptions[1] instanceof JPopupMenu.Separator);
    assertEquals(JSeparator.HORIZONTAL,
            ((JSeparator) showOptions[1]).getOrientation());
    assertEquals("secondary structure",
            ((JMenuItem) showOptions[2]).getText());
    assertEquals("PDB", ((JMenuItem) showOptions[2]).getToolTipText());
    assertEquals("Temp", ((JMenuItem) showOptions[3]).getText());
    assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText());

    assertEquals(all, ((JMenuItem) hideOptions[0]).getText());
    assertTrue(hideOptions[1] instanceof JPopupMenu.Separator);
    assertEquals(JSeparator.HORIZONTAL,
            ((JSeparator) hideOptions[1]).getOrientation());
  }

  /**
   * Test for adding feature links
   */
  @Test(groups = { "Functional" })
  public void testAddFeatureLinks()
  {
    // sequences from the alignment
    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();

    // create list of links and list of DBRefs
    List<String> links = new ArrayList<String>();
    List<DBRefEntry> refs = new ArrayList<DBRefEntry>();

    // links as might be added into Preferences | Connections dialog
    links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
            + SEQUENCE_ID + "$");
    links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
            + "$");
    links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
            + DB_ACCESSION + "$");
    // Gene3D entry tests for case (in)sensitivity
    links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
            + DB_ACCESSION + "$&mode=protein");

    // make seq0 dbrefs
    refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
    refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041"));
    refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058"));
    refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675"));
    
    // make seq1 dbrefs
    refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
    refs.add(new DBRefEntry("GENE3D", "1", "3.10.20.30"));

    // add all the dbrefs to the sequences: Uniprot 1 each, Interpro all 3 to
    // seq0, Gene3D to seq1
    seqs.get(0).addDBRef(refs.get(0));

    seqs.get(0).addDBRef(refs.get(1));
    seqs.get(0).addDBRef(refs.get(2));
    seqs.get(0).addDBRef(refs.get(3));
    
    seqs.get(1).addDBRef(refs.get(4));
    seqs.get(1).addDBRef(refs.get(5));
    
    // get the Popup Menu for first sequence
    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0), links);
    Component[] seqItems = testee.sequenceMenu.getMenuComponents();
    JMenu linkMenu = (JMenu) seqItems[6];
    Component[] linkItems = linkMenu.getMenuComponents();
    
    // check the number of links are the expected number
    assertEquals(5, linkItems.length);

    // first entry is EMBL-EBI which just uses sequence id not accession id?
    assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());

    // sequence id for each link should match corresponding DB accession id
    for (int i = 1; i < 4; i++)
    {
      assertEquals(refs.get(i - 1).getSource(), ((JMenuItem) linkItems[i])
              .getText().split("\\|")[0]);
      assertEquals(refs.get(i - 1).getAccessionId(),
              ((JMenuItem) linkItems[i])
              .getText().split("\\|")[1]);
    }

    // get the Popup Menu for second sequence
    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(1), links);
    seqItems = testee.sequenceMenu.getMenuComponents();
    linkMenu = (JMenu) seqItems[6];
    linkItems = linkMenu.getMenuComponents();
    
    // check the number of links are the expected number
    assertEquals(3, linkItems.length);

    // first entry is EMBL-EBI which just uses sequence id not accession id?
    assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText());

    // sequence id for each link should match corresponding DB accession id
    for (int i = 1; i < 3; i++)
    {
      assertEquals(refs.get(i + 3).getSource(), ((JMenuItem) linkItems[i])
              .getText().split("\\|")[0].toUpperCase());
      assertEquals(refs.get(i + 3).getAccessionId(),
              ((JMenuItem) linkItems[i]).getText().split("\\|")[1]);
    }

    // if there are no valid links the Links submenu is disabled
    List<String> nomatchlinks = new ArrayList<String>();
    nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$"
            + DB_ACCESSION + "$");

    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0),
            nomatchlinks);
    seqItems = testee.sequenceMenu.getMenuComponents();
    linkMenu = (JMenu) seqItems[6];
    assertFalse(linkMenu.isEnabled());

  }
}