package jalview.gui;

import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AnnotationFilterParameter;
import jalview.datamodel.ColumnSelection;
import jalview.jbgui.FurtherActionPanel;
import jalview.jbgui.SearchPanel;
import jalview.jbgui.StructureFilterPanel;
import jalview.schemes.AnnotationColourGradient;
import jalview.util.MessageManager;

import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.util.Iterator;

import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.border.TitledBorder;

import net.miginfocom.swing.MigLayout;

@SuppressWarnings("serial")
public class AnnotationColumnChooser extends AnnotationRowFilter implements
        ItemListener
{

  private ColumnSelection oldColumnSelection;

  private JComboBox<String> annotations;

  JButton ok = new JButton();

  JButton cancel = new JButton();

  JPanel actionPanel = new JPanel();

  JPanel thresholdPanel = new JPanel();

  JPanel switchableViewsPanel = new JPanel(new CardLayout());

  CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
          .getLayout());

  JPanel noGraphFilterView = new JPanel();

  JPanel graphFilterView = new JPanel();

  JPanel annotationComboBoxPanel = new JPanel();

  StructureFilterPanel gStructureFilterPanel;

  StructureFilterPanel ngStructureFilterPanel;

  private StructureFilterPanel currentStructureFilterPanel;

  JLabel annotationLabel = new JLabel();

  BorderLayout borderLayout1 = new BorderLayout();

  private JComboBox<String> threshold = new JComboBox<String>();

  private SearchPanel currentSearchPanel;

  private SearchPanel gSearchPanel;

  private SearchPanel ngSearchPanel;

  private FurtherActionPanel currentFurtherActionPanel;

  private FurtherActionPanel gFurtherActionPanel;

  private FurtherActionPanel ngFurtherActionPanel;

  public static final int ACTION_OPTION_SELECT = 1;

  public static int ACTION_OPTION_HIDE = 2;

  public static String NO_GRAPH_VIEW = "0";

  public static String GRAPH_VIEW = "1";

  private int actionOption = ACTION_OPTION_SELECT;

  public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
  {
    super(av, ap);
    frame = new JInternalFrame();
    frame.setContentPane(this);
    frame.setLayer(JLayeredPane.PALETTE_LAYER);
    Desktop.addInternalFrame(frame,
            MessageManager.getString("label.select_by_annotation"), 520,
            215);

    addSliderChangeListener();
    addSliderMouseListeners();

    if (av.getAlignment().getAlignmentAnnotation() == null)
    {
      return;
    }
    setOldColumnSelection(av.getColumnSelection());
    adjusting = true;

    setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
    populateThresholdComboBox(threshold);

    // restore the Object state from the previous session if one exists
    if (av.getAnnotationColumnSelectionState() != null)
    {
      currentSearchPanel = av.getAnnotationColumnSelectionState()
              .getCurrentSearchPanel();
      currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
              .getCurrentStructureFilterPanel();
      annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
              .getAnnotations().getSelectedIndex());
      threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
              .getThreshold().getSelectedIndex());
      actionOption = av.getAnnotationColumnSelectionState()
              .getActionOption();

    }

    try
    {
      jbInit();
    } catch (Exception ex)
    {
    }
    adjusting = false;

    updateView();
    frame.invalidate();
    frame.pack();
  }

  public AnnotationColumnChooser()
  {
    try
    {
      jbInit();
    } catch (Exception ex)
    {
      ex.printStackTrace();
    }
  }

  private void jbInit() throws Exception
  {
    ok.setOpaque(false);
    ok.setText(MessageManager.getString("action.ok"));
    ok.addActionListener(new ActionListener()
    {
      @Override
      public void actionPerformed(ActionEvent e)
      {
        ok_actionPerformed(e);
      }
    });
    cancel.setOpaque(false);
    cancel.setText(MessageManager.getString("action.cancel"));
    cancel.addActionListener(new ActionListener()
    {
      @Override
      public void actionPerformed(ActionEvent e)
      {
        cancel_actionPerformed(e);
      }
    });

    getAnnotations().addItemListener(this);
    getThreshold().addActionListener(new ActionListener()
    {
      @Override
      public void actionPerformed(ActionEvent e)
      {
        threshold_actionPerformed(e);
      }
    });

    thresholdValue.addActionListener(new ActionListener()
    {
      @Override
      public void actionPerformed(ActionEvent e)
      {
        thresholdValue_actionPerformed(e);
      }
    });
    slider.setPaintLabels(false);
    slider.setPaintTicks(true);
    slider.setBackground(Color.white);
    slider.setEnabled(false);
    slider.setOpaque(false);
    slider.setPreferredSize(new Dimension(100, 32));
    thresholdValue.setEnabled(false);
    thresholdValue.setColumns(7);

    annotationLabel.setBackground(Color.white);
    annotationLabel.setFont(JvSwingUtils.getLabelFont());
    annotationLabel.setText("Select Annotation : ");

    thresholdPanel.setBorder(new TitledBorder("Threshold Filter"));
    thresholdPanel.setBackground(Color.white);
    thresholdPanel.setFont(JvSwingUtils.getLabelFont());
    thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));

    actionPanel.setBackground(Color.white);
    actionPanel.setFont(JvSwingUtils.getLabelFont());

    this.setLayout(borderLayout1);
    graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
    graphFilterView.setBackground(Color.white);

    noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
    noGraphFilterView.setBackground(Color.white);
    annotationComboBoxPanel.setBackground(Color.white);
    annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());

    gSearchPanel = new SearchPanel(this);
    ngSearchPanel = new SearchPanel(this);
    gFurtherActionPanel = new FurtherActionPanel(this);
    ngFurtherActionPanel = new FurtherActionPanel(this);
    gStructureFilterPanel = new StructureFilterPanel(this);
    ngStructureFilterPanel = new StructureFilterPanel(this);


    thresholdPanel.add(getThreshold());
    thresholdPanel.add(thresholdValue, "wrap");
    thresholdPanel.add(slider, "grow, span, wrap");

    actionPanel.add(ok);
    actionPanel.add(cancel);

    graphFilterView.add(gSearchPanel, "grow, span, wrap");
    graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
    graphFilterView.add(thresholdPanel, "grow, span, wrap");
    graphFilterView.add(gFurtherActionPanel);

    noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
    noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
    noGraphFilterView.add(ngFurtherActionPanel);

    annotationComboBoxPanel.add(getAnnotations());
    switchableViewsPanel.add(noGraphFilterView,
            AnnotationColumnChooser.NO_GRAPH_VIEW);
    switchableViewsPanel.add(graphFilterView,
            AnnotationColumnChooser.GRAPH_VIEW);

    this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
    this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
    this.add(actionPanel, java.awt.BorderLayout.SOUTH);

    selectedAnnotationChanged();
    this.validate();
  }

  @SuppressWarnings("unchecked")
  public void reset()
  {
    if (this.getOldColumnSelection() != null)
    {
      av.getColumnSelection().clear();

      if (av.getAnnotationColumnSelectionState() != null)
      {
        ColumnSelection oldSelection = av
                .getAnnotationColumnSelectionState()
                .getOldColumnSelection();
        if (oldSelection != null && oldSelection.getHiddenColumns() != null
                && !oldSelection.getHiddenColumns().isEmpty())
        {
          for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
                  .iterator(); itr.hasNext();)
          {
            int positions[] = itr.next();
            av.hideColumns(positions[0], positions[1]);
          }
        }
        av.setColumnSelection(oldSelection);
      }
      // ap.alignmentChanged();
      ap.paintAlignment(true);
    }

  }

  public void valueChanged(boolean updateAllAnnotation)
  {
    if (slider.isEnabled())
    {
      getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
      updateView();
      propagateSeqAssociatedThreshold(updateAllAnnotation,
              getCurrentAnnotation());
      ap.paintAlignment(false);
    }
  }

  public JComboBox<String> getThreshold()
  {
    return threshold;
  }

  public void setThreshold(JComboBox<String> threshold)
  {
    this.threshold = threshold;
  }

  public JComboBox<String> getAnnotations()
  {
    return annotations;
  }

  public void setAnnotations(JComboBox<String> annotations)
  {
    this.annotations = annotations;
  }

  @Override
  public void updateView()
  {
    // Check if combobox is still adjusting
    if (adjusting)
    {
      return;
    }

    AnnotationFilterParameter filterParams = new AnnotationFilterParameter();

    setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
            .getSelectedIndex()]]);

    int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
            .getSelectedIndex());

    slider.setEnabled(true);
    thresholdValue.setEnabled(true);

    if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
    {
      slider.setEnabled(false);
      thresholdValue.setEnabled(false);
      thresholdValue.setText("");
      // build filter params
    }
    else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
    {
      if (getCurrentAnnotation().threshold == null)
      {
        getCurrentAnnotation()
                .setThreshold(
                        new jalview.datamodel.GraphLine(
                                (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
                                "Threshold", Color.black));
      }

      adjusting = true;
      float range = getCurrentAnnotation().graphMax * 1000
              - getCurrentAnnotation().graphMin * 1000;

      slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
      slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
      slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
      thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
      slider.setMajorTickSpacing((int) (range / 10f));
      slider.setEnabled(true);
      thresholdValue.setEnabled(true);
      adjusting = false;

      // build filter params
      filterParams
              .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
      if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
      {

        if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
        {
          filterParams
                  .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
        }
        else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
        {
          filterParams
                  .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
        }
      }
    }

    if (currentStructureFilterPanel != null)
    {
      if (currentStructureFilterPanel.getAlphaHelix().isSelected())
      {
        filterParams.setFilterAlphaHelix(true);
      }
      if (currentStructureFilterPanel.getBetaStrand().isSelected())
      {
        filterParams.setFilterBetaSheet(true);
      }
      if (currentStructureFilterPanel.getTurn().isSelected())
      {
        filterParams.setFilterTurn(true);
      }
    }

    if (currentSearchPanel != null)
    {
      if (!currentSearchPanel.getSearchString().isEmpty())
      {
        currentSearchPanel.getDescription().setEnabled(true);
        currentSearchPanel.getDisplayName().setEnabled(true);
        filterParams.setRegexString(currentSearchPanel.getSearchString());
        if (currentSearchPanel.isDisplayNameChecked())
        {
          filterParams
                  .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
        }
        if (currentSearchPanel.isDescriptionChecked())
        {
          filterParams
                  .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
        }
      }
      else
      {
        currentSearchPanel.getDescription().setEnabled(false);
        currentSearchPanel.getDisplayName().setEnabled(false);
      }
    }

    filterAnnotations(getCurrentAnnotation().annotations, filterParams,
            av.getColumnSelection());

    av.showAllHiddenColumns();
    if (getActionOption() == ACTION_OPTION_HIDE)
    {
      av.hideSelectedColumns();
    }

    filterParams = null;
    av.setAnnotationColumnSelectionState(this);
    ap.paintAlignment(true);
  }

  public ColumnSelection getOldColumnSelection()
  {
    return oldColumnSelection;
  }

  public void setOldColumnSelection(ColumnSelection currentColumnSelection)
  {
    if (currentColumnSelection != null)
    {
      this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
    }
  }


  public void select_action(ActionEvent actionEvent)
  {
    JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
    if (radioButton.isSelected())
    {
      setActionOption(ACTION_OPTION_SELECT);
      updateView();
    }
  }

  public void hide_action(ActionEvent actionEvent)
  {
    JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
    if (radioButton.isSelected())
    {
      setActionOption(ACTION_OPTION_HIDE);
      updateView();
    }
  }


  @Override
  public void itemStateChanged(ItemEvent e)
  {
    selectedAnnotationChanged();
  }

  public void selectedAnnotationChanged()
  {
    String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
    if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
            .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
    {
      currentView = AnnotationColumnChooser.GRAPH_VIEW;
    }
    // else{
    // threshold.setSelectedIndex(AlignmentAnnotation.NO_GRAPH);
    // }
    
    gSearchPanel.syncState();
    gFurtherActionPanel.syncState();
    gFurtherActionPanel.syncState();
    gFurtherActionPanel.syncState();

    ngSearchPanel.syncState();
    ngFurtherActionPanel.syncState();
    ngStructureFilterPanel.syncState();
    ngFurtherActionPanel.syncState();

    switchableViewsLayout.show(switchableViewsPanel, currentView);
    updateView();
  }

  
  public FurtherActionPanel getCurrentFutherActionPanel()
  {
    return currentFurtherActionPanel;
  }

  public void setCurrentFutherActionPanel(
          FurtherActionPanel currentFutherActionPanel)
  {
    this.currentFurtherActionPanel = currentFutherActionPanel;
  }

  public SearchPanel getCurrentSearchPanel()
  {
    return currentSearchPanel;
  }

  public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
  {
    this.currentSearchPanel = currentSearchPanel;
  }

  public int getActionOption()
  {
    return actionOption;
  }

  public void setActionOption(int actionOption)
  {
    this.actionOption = actionOption;
  }

  public StructureFilterPanel getCurrentStructureFilterPanel()
  {
    return currentStructureFilterPanel;
  }

  public void setCurrentStructureFilterPanel(
          StructureFilterPanel currentStructureFilterPanel)
  {
    this.currentStructureFilterPanel = currentStructureFilterPanel;
  }

}