/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
 * Copyright (C) 2014 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.appletgui;

import jalview.datamodel.Alignment;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.IdentifyFile;
import jalview.io.TCoffeeScoreFile;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;

import java.awt.BorderLayout;
import java.awt.Button;
import java.awt.Dialog;
import java.awt.Font;
import java.awt.Frame;
import java.awt.Panel;
import java.awt.TextArea;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;

public class CutAndPasteTransfer extends Panel implements ActionListener,
        MouseListener
{
  boolean pdbImport = false;

  boolean treeImport = false;

  boolean annotationImport = false;

  Sequence seq;

  AlignFrame alignFrame;

  public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
  {
    try
    {
      jbInit();
    } catch (Exception e)
    {
      e.printStackTrace();
    }

    this.alignFrame = alignFrame;

    if (!forImport)
    {
      buttonPanel.setVisible(false);
    }
  }

  public String getText()
  {
    return textarea.getText();
  }

  public void setText(String text)
  {
    textarea.setText(text);
  }

  public void setPDBImport(Sequence seq)
  {
    this.seq = seq;
    accept.setLabel(MessageManager.getString("action.accept"));
    addSequences.setVisible(false);
    pdbImport = true;
  }

  public void setTreeImport()
  {
    treeImport = true;
    accept.setLabel(MessageManager.getString("action.accept"));
    addSequences.setVisible(false);
  }

  public void setAnnotationImport()
  {
    annotationImport = true;
    accept.setLabel(MessageManager.getString("action.accept"));
    addSequences.setVisible(false);
  }

  public void actionPerformed(ActionEvent evt)
  {
    if (evt.getSource() == accept)
    {
      ok(true);
    }
    else if (evt.getSource() == addSequences)
    {
      ok(false);
    }
    else if (evt.getSource() == cancel)
    {
      cancel();
    }
  }

  protected void ok(boolean newWindow)
  {
    String text = getText();
    int length = text.length();
    textarea.append("\n");
    if (textarea.getText().length() == length)
    {
      String warning = "\n\n#################################################\n"
              + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
              + "\nCAN'T INPUT FULL ALIGNMENT"
              + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
              + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
              + "\n#################################################\n";
      textarea.setText(text.substring(0, text.length() - warning.length())
              + warning);

      textarea.setCaretPosition(text.length());
    }

    if (pdbImport)
    {
      PDBEntry pdb = new PDBEntry();
      pdb.setFile(text);

      if (alignFrame.alignPanel.av.applet.jmolAvailable)
      {
        new jalview.appletgui.AppletJmol(pdb, new Sequence[]
        { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
      }
      else
      {
        new MCview.AppletPDBViewer(pdb, new Sequence[]
        { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
      }

    }
    else if (treeImport)
    {
      try
      {
        jalview.io.NewickFile fin = new jalview.io.NewickFile(
                textarea.getText(), "Paste");

        fin.parse();
        if (fin.getTree() != null)
        {
          alignFrame.loadTree(fin, "Pasted tree file");
        }

      } catch (Exception ex)
      {
        // TODO: JAL-1102 - should have a warning message in dialog, not simply
        // overwrite the broken input data with the exception
        textarea.setText(MessageManager.formatMessage(
                "label.could_not_parse_newick_file", new String[]
                { ex.getMessage() }));
        return;
      }
    }
    else if (annotationImport)
    {
      TCoffeeScoreFile tcf = null;
      try
      {
        tcf = new TCoffeeScoreFile(textarea.getText(),
                jalview.io.AppletFormatAdapter.PASTE);
        if (tcf.isValid())
        {
          if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
                  true))
          {
            alignFrame.tcoffeeColour.setEnabled(true);
            alignFrame.alignPanel.fontChanged();
            alignFrame.changeColour(new TCoffeeColourScheme(
                    alignFrame.viewport.getAlignment()));
            alignFrame.statusBar
                    .setText(MessageManager
                            .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
          }
          else
          {
            // file valid but didn't get added to alignment for some reason
            alignFrame.statusBar.setText(MessageManager.formatMessage(
                    "label.failed_add_tcoffee_scores",
                    new String[]
                    { (tcf.getWarningMessage() != null ? tcf
                            .getWarningMessage() : "") }));
          }
        }
        else
        {
          tcf = null;
        }
      } catch (Exception x)
      {
        tcf = null;
      }
      if (tcf == null)
      {
        if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
                textarea.getText(),
                jalview.io.AppletFormatAdapter.PASTE))
        {
          alignFrame.alignPanel.fontChanged();
          alignFrame.alignPanel.setScrollValues(0, 0);
          alignFrame.statusBar
                  .setText(MessageManager
                          .getString("label.successfully_pasted_annotation_to_alignment"));

        }
        else
        {
          if (!alignFrame.parseFeaturesFile(textarea.getText(),
                  jalview.io.AppletFormatAdapter.PASTE))
          {
            alignFrame.statusBar
                    .setText(MessageManager
                            .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
          }
        }
      }
    }
    else if (alignFrame != null)
    {
      Alignment al = null;

      String format = new IdentifyFile().Identify(text,
              AppletFormatAdapter.PASTE);
      try
      {
        al = new AppletFormatAdapter().readFile(text,
                AppletFormatAdapter.PASTE, format);
      } catch (java.io.IOException ex)
      {
        ex.printStackTrace();
      }

      if (al != null)
      {
        if (newWindow)
        {
          AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
                  "Cut & Paste input - " + format, false);
          af.statusBar
                  .setText(MessageManager
                          .getString("label.successfully_pasted_annotation_to_alignment"));
        }
        else
        {
          alignFrame.addSequences(al.getSequencesArray());
          alignFrame.statusBar.setText(MessageManager
                  .getString("label.successfully_pasted_alignment_file"));
        }
      }
    }
    // TODO: dialog should indicate if data was parsed correctly or not - see
    // JAL-1102
    if (this.getParent() instanceof Frame)
    {
      ((Frame) this.getParent()).setVisible(false);
    }
    else
    {
      ((Dialog) this.getParent()).setVisible(false);
    }
  }

  protected void cancel()
  {
    textarea.setText("");
    if (this.getParent() instanceof Frame)
    {
      ((Frame) this.getParent()).setVisible(false);
    }
    else
    {
      ((Dialog) this.getParent()).setVisible(false);
    }
  }

  protected TextArea textarea = new TextArea();

  Button accept = new Button("New Window");

  Button addSequences = new Button("Add to Current Alignment");

  Button cancel = new Button("Close");

  protected Panel buttonPanel = new Panel();

  BorderLayout borderLayout1 = new BorderLayout();

  private void jbInit() throws Exception
  {
    textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
    textarea.setText(MessageManager
            .getString("label.paste_your_alignment_file"));
    textarea.addMouseListener(this);
    this.setLayout(borderLayout1);
    accept.addActionListener(this);
    addSequences.addActionListener(this);
    cancel.addActionListener(this);
    this.add(buttonPanel, BorderLayout.SOUTH);
    buttonPanel.add(accept, null);
    buttonPanel.add(addSequences);
    buttonPanel.add(cancel, null);
    this.add(textarea, java.awt.BorderLayout.CENTER);
  }

  public void mousePressed(MouseEvent evt)
  {
    if (textarea.getText().startsWith(
            MessageManager.getString("label.paste_your")))
    {
      textarea.setText("");
    }
  }

  public void mouseReleased(MouseEvent evt)
  {
  }

  public void mouseClicked(MouseEvent evt)
  {
  }

  public void mouseEntered(MouseEvent evt)
  {
  }

  public void mouseExited(MouseEvent evt)
  {
  }
}