/*
 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 * 
 * This program 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 2
 * of the License, or (at your option) any later version.
 * 
 * This program 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 this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
package jalview.gui;

import java.util.*;

import java.awt.*;
import java.awt.event.*;
import javax.swing.*;

import jalview.datamodel.*;
import jalview.jbgui.*;

/**
 * DOCUMENT ME!
 * 
 * @author $author$
 * @version $Revision$
 */
public class Finder extends GFinder
{
  AlignViewport av;

  AlignmentPanel ap;

  JInternalFrame frame;

  int seqIndex = 0;

  int resIndex = -1;

  SearchResults searchResults;

  /**
   * Creates a new Finder object.
   * 
   * @param av
   *                DOCUMENT ME!
   * @param ap
   *                DOCUMENT ME!
   * @param f
   *                DOCUMENT ME!
   */
  public Finder()
  {
    frame = new JInternalFrame();
    frame.setContentPane(this);
    frame.setLayer(JLayeredPane.PALETTE_LAYER);
    Desktop.addInternalFrame(frame, "Find", 340, 110);

    textfield.requestFocus();
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *                DOCUMENT ME!
   */
  public void findNext_actionPerformed(ActionEvent e)
  {
    if (getFocusedViewport())
    {
      doSearch(false);
    }
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *                DOCUMENT ME!
   */
  public void findAll_actionPerformed(ActionEvent e)
  {
    if (getFocusedViewport())
    {
      resIndex = -1;
      seqIndex = 0;
      doSearch(true);
    }
  }

  /**
   * gets the topmost alignment window and sets av and ap accordingly
   * @return false if no alignment window was found
   */
  boolean getFocusedViewport()
  {
    // now checks further down the window stack to fix bug https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
    for (int f=0;f<frames.length; f++) {
      JInternalFrame frame = frames[f];
      if (frame != null && frame instanceof AlignFrame)
      {
        av = ((AlignFrame) frame).viewport;
        ap = ((AlignFrame) frame).alignPanel;
        return true;
      }
    }
    return false;
  }

  /**
   * DOCUMENT ME!
   * 
   * @param e
   *                DOCUMENT ME!
   */
  public void createNewGroup_actionPerformed(ActionEvent e)
  {
    SequenceI[] seqs = new SequenceI[searchResults.getSize()];
    SequenceFeature[] features = new SequenceFeature[searchResults
            .getSize()];

    for (int i = 0; i < searchResults.getSize(); i++)
    {
      seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();

      features[i] = new SequenceFeature(textfield.getText().trim(),
              "Search Results", null, searchResults.getResultStart(i),
              searchResults.getResultEnd(i), "Search Results");
    }

    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
            features, true, ap))
    {
      ap.alignFrame.showSeqFeatures.setSelected(true);
      av.setShowSequenceFeatures(true);
      ap.highlightSearchResults(null);
    }
  }

  /**
   * incrementally search the alignment
   * 
   * @param findAll
   *                true means find all results and raise a dialog box
   */
  void doSearch(boolean findAll)
  {
    createNewGroup.setEnabled(false);

    String searchString = textfield.getText().trim();

    if (searchString.length() < 1)
    {
      return;
    }
    // TODO: extend finder to match descriptions, features and annotation, and
    // other stuff
    // TODO: add switches to control what is searched - sequences, IDS,
    // descriptions, features
    jalview.analysis.Finder finder = new jalview.analysis.Finder(
            av.alignment, av.getSelectionGroup(), seqIndex, resIndex);
    finder.setCaseSensitive(caseSensitive.isSelected());
    finder.setFindAll(findAll);

    finder.find(searchString); // returns true if anything was actually found

    seqIndex = finder.getSeqIndex();
    resIndex = finder.getResIndex();

    searchResults = finder.getSearchResults(); // find(regex,
                                                // caseSensitive.isSelected(), )
    Vector idMatch = finder.getIdMatch();
    boolean haveResults=false;
    // set or reset the GUI
    if ((idMatch.size() > 0))
    {
      haveResults=true;
      ap.idPanel.highlightSearchResults(idMatch);
    } else {
      ap.idPanel.highlightSearchResults(null);
    }
    
    if (searchResults.getSize() > 0)
    {
      haveResults=true;
      createNewGroup.setEnabled(true);
    }
    else
    {
      searchResults = null;
    }

    // if allResults is null, this effectively switches displaySearch flag in
    // seqCanvas
    ap.highlightSearchResults(searchResults);
    // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
    // 'SelectRegion' selection
    if (!haveResults)
    {
      JOptionPane.showInternalMessageDialog(this, "Finished searching",
              null, JOptionPane.INFORMATION_MESSAGE);
      resIndex = -1;
      seqIndex = 0;
    }

    if (findAll)
    {
      String message = (idMatch.size()>0) ? ""+idMatch.size()+" IDs" : "";
      if (idMatch.size()>0 && searchResults.getSize()>0) {
        message += " and ";
      }
      message += searchResults.getSize() + " subsequence matches found.";
      JOptionPane.showInternalMessageDialog(this, message, null,
              JOptionPane.INFORMATION_MESSAGE);
      resIndex = -1;
      seqIndex = 0;
    }

  }
}