/*
 * 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 jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.io.AnnotationFile;
import jalview.io.FeaturesFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.util.MessageManager;

import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.FlowLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.FileWriter;
import java.io.PrintWriter;
import java.util.List;
import java.util.Map;

import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.JButton;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.SwingConstants;

/**
 * 
 * GUI dialog for exporting features or alignment annotations depending upon
 * which method is called.
 * 
 * @author AMW
 * 
 */
public class AnnotationExporter extends JPanel
{
  private JInternalFrame frame;

  private AlignmentPanel ap;

  /*
   * true if exporting features, false if exporting annotations
   */
  private boolean exportFeatures = true;

  private AlignmentAnnotation[] annotations;

  private boolean wholeView;

  public AnnotationExporter(AlignmentPanel panel)
  {
    this.ap = panel;
    try
    {
      jbInit();
    } catch (Exception ex)
    {
      ex.printStackTrace();
    }

    frame = new JInternalFrame();
    frame.setContentPane(this);
    frame.setLayer(JLayeredPane.PALETTE_LAYER);
    Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
            frame.getPreferredSize().height);
  }

  /**
   * Configures the diglog for options to export visible features
   */
  public void exportFeatures()
  {
    exportFeatures = true;
    CSVFormat.setVisible(false);
    frame.setTitle(MessageManager.getString("label.export_features"));
  }

  /**
   * Configures the dialog for options to export all visible annotations
   */
  public void exportAnnotations()
  {
    boolean showAnnotation = ap.av.isShowAnnotation();
    exportAnnotation(showAnnotation ? null
            : ap.av.getAlignment().getAlignmentAnnotation(), true);
  }

  /**
   * Configures the dialog for options to export the given annotation row
   * 
   * @param toExport
   */
  public void exportAnnotation(AlignmentAnnotation toExport)
  {
    exportAnnotation(new AlignmentAnnotation[] { toExport }, false);
  }

  private void exportAnnotation(AlignmentAnnotation[] toExport,
          boolean forWholeView)
  {
    wholeView = forWholeView;
    annotations = toExport;
    exportFeatures = false;
    GFFFormat.setVisible(false);
    CSVFormat.setVisible(true);
    frame.setTitle(MessageManager.getString("label.export_annotations"));
  }

  private void toFile_actionPerformed()
  {
    JalviewFileChooser chooser = new JalviewFileChooser(
            Cache.getProperty("LAST_DIRECTORY"));

    chooser.setFileView(new JalviewFileView());
    chooser.setDialogTitle(exportFeatures
            ? MessageManager.getString("label.save_features_to_file")
            : MessageManager.getString("label.save_annotation_to_file"));
    chooser.setToolTipText(MessageManager.getString("action.save"));

    int value = chooser.showSaveDialog(this);

    if (value == JalviewFileChooser.APPROVE_OPTION)
    {
      String text = getText();

      try
      {
        PrintWriter out = new PrintWriter(
                new FileWriter(chooser.getSelectedFile()));
        out.print(text);
        out.close();
      } catch (Exception ex)
      {
        ex.printStackTrace();
      }
    }

    close_actionPerformed();
  }

  /**
   * Answers the text to output for either Features (in GFF or Jalview format) or
   * Annotations (in CSV or Jalview format)
   * 
   * @return
   */
  private String getText()
  {
    return exportFeatures ? getFeaturesText() : getAnnotationsText();
  }

  /**
   * Returns the text contents for output of annotations in either CSV or Jalview
   * format
   * 
   * @return
   */
  private String getAnnotationsText()
  {
    String text;
    if (CSVFormat.isSelected())
    {
      text = new AnnotationFile().printCSVAnnotations(annotations);
    }
    else
    {
      if (wholeView)
      {
        text = new AnnotationFile().printAnnotationsForView(ap.av);
      }
      else
      {
        text = new AnnotationFile().printAnnotations(annotations, null,
                null);
      }
    }
    return text;
  }

  /**
   * Returns the text contents for output of features in either GFF or Jalview
   * format
   * 
   * @return
   */
  private String getFeaturesText()
  {
    String text;
    SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
    Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
            .getDisplayedFeatureCols();
    Map<String, FeatureMatcherSetI> featureFilters = ap.getFeatureRenderer()
            .getFeatureFilters();
    List<String> featureGroups = ap.getFeatureRenderer()
            .getDisplayedFeatureGroups();
    boolean includeNonPositional = ap.av.isShowNPFeats();

    FeaturesFile formatter = new FeaturesFile();
    if (GFFFormat.isSelected())
    {
      text = formatter.printGffFormat(sequences, featureColours,
              featureGroups, includeNonPositional);
    }
    else
    {
      text = formatter.printJalviewFormat(sequences, featureColours,
              featureFilters, featureGroups, includeNonPositional);
    }
    return text;
  }

  private void toTextbox_actionPerformed()
  {
    CutAndPasteTransfer cap = new CutAndPasteTransfer();

    try
    {
      String text = getText();
      cap.setText(text);
      Desktop.addInternalFrame(cap, (exportFeatures ? MessageManager
              .formatMessage("label.features_for_params", new String[]
              { ap.alignFrame.getTitle() })
              : MessageManager.formatMessage("label.annotations_for_params",
                      new String[]
                      { ap.alignFrame.getTitle() })),
              600, 500);
    } catch (OutOfMemoryError oom)
    {
      new OOMWarning((exportFeatures ? MessageManager.formatMessage(
              "label.generating_features_for_params", new String[]
              { ap.alignFrame.getTitle() })
              : MessageManager.formatMessage(
                      "label.generating_annotations_for_params",
                      new String[]
                      { ap.alignFrame.getTitle() })),
              oom);
      cap.dispose();
    }

    close_actionPerformed();
  }

  private void close_actionPerformed()
  {
    try
    {
      frame.setClosed(true);
    } catch (java.beans.PropertyVetoException ex)
    {
    }
  }

  private void jbInit() throws Exception
  {
    this.setLayout(new BorderLayout());

    toFile.setText(MessageManager.getString("label.to_file"));
    toFile.addActionListener(new ActionListener()
    {
      @Override
      public void actionPerformed(ActionEvent e)
      {
        toFile_actionPerformed();
      }
    });
    toTextbox.setText(MessageManager.getString("label.to_textbox"));
    toTextbox.addActionListener(new ActionListener()
    {
      @Override
      public void actionPerformed(ActionEvent e)
      {
        toTextbox_actionPerformed();
      }
    });
    close.setText(MessageManager.getString("action.close"));
    close.addActionListener(new ActionListener()
    {
      @Override
      public void actionPerformed(ActionEvent e)
      {
        close_actionPerformed();
      }
    });
    jalviewFormat.setOpaque(false);
    jalviewFormat.setSelected(true);
    jalviewFormat.setText("Jalview");
    GFFFormat.setOpaque(false);
    GFFFormat.setText("GFF");
    CSVFormat.setOpaque(false);
    CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
    jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
    jLabel1.setText(MessageManager.getString("action.format") + " ");
    this.setBackground(Color.white);
    jPanel3.setBorder(BorderFactory.createEtchedBorder());
    jPanel3.setOpaque(false);
    jPanel1.setOpaque(false);
    jPanel1.add(toFile);
    jPanel1.add(toTextbox);
    jPanel1.add(close);
    jPanel3.add(jLabel1);
    jPanel3.add(jalviewFormat);
    jPanel3.add(GFFFormat);
    jPanel3.add(CSVFormat);
    buttonGroup.add(jalviewFormat);
    buttonGroup.add(GFFFormat);
    buttonGroup.add(CSVFormat);
    this.add(jPanel3, BorderLayout.CENTER);
    this.add(jPanel1, BorderLayout.SOUTH);
  }

  JPanel jPanel1 = new JPanel();

  JButton toFile = new JButton();

  JButton toTextbox = new JButton();

  JButton close = new JButton();

  ButtonGroup buttonGroup = new ButtonGroup();

  JRadioButton jalviewFormat = new JRadioButton();

  JRadioButton GFFFormat = new JRadioButton();

  JRadioButton CSVFormat = new JRadioButton();

  JLabel jLabel1 = new JLabel();

  JPanel jPanel3 = new JPanel();

  FlowLayout flowLayout1 = new FlowLayout();
}