/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 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 jalview.datamodel.*;

import jalview.jbgui.*;

import java.awt.*;
import java.awt.event.*;

import java.util.*;

import javax.swing.*;
import javax.swing.event.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class Finder extends GFinder
{
    AlignViewport av;
    AlignmentPanel ap;
    JInternalFrame frame;
    int seqIndex = 0;
    int resIndex = 0;

    SearchResults searchResults;

    /**
     * Creates a new Finder object.
     *
     * @param av DOCUMENT ME!
     * @param ap DOCUMENT ME!
     * @param f DOCUMENT ME!
     */
    public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
    {
        this.av = av;
        this.ap = ap;
        frame = f;

        // all a big pain, but we need to wait until the frame is visible before the textfield can
        // obtain the focus/////////////////////////
        frame.addInternalFrameListener(new InternalFrameAdapter()
            {
                public void internalFrameOpened(InternalFrameEvent evt)
                {
                    SwingUtilities.invokeLater(new Runnable()
                        {
                            public void run()
                            {
                                textfield.requestFocus();
                            }
                        });
                }
            });
    }


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

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


    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void createNewGroup_actionPerformed(ActionEvent e)
    {
        JLabel label = new JLabel("Enter name of new sequence feature");
        JTextField textinput = new JTextField(textfield.getText());
        JPanel panel = new JPanel(new BorderLayout());
        panel.add(label, BorderLayout.NORTH);
        panel.add(textinput, BorderLayout.SOUTH);

         int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
            panel, "New Sequence Feature Name",
          JOptionPane.OK_CANCEL_OPTION );

         if(reply != JOptionPane.OK_OPTION)
           return;

        for (int i = 0; i < searchResults.getSize(); i ++ )
        {
            SequenceI seq = searchResults.getResultSequence(i);

            SequenceFeature sf = new SequenceFeature(textinput.getText(),
                "Search Results", null,
                searchResults.getResultStart(i),
               searchResults.getResultEnd(i),
               "Search Results");

            ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
                textinput.getText(), new Color(60,160,115),
                    "Search Results");

            seq.getDatasetSequence().addSequenceFeature(sf);
        }

        ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
        ap.alignFrame.showSeqFeatures.setSelected(true);
        av.setShowSequenceFeatures(true);
        ap.highlightSearchResults(null);
    }

    /**
     * DOCUMENT ME!
     *
     * @param findAll DOCUMENT ME!
     */
    void doSearch(boolean findAll)
    {
        createNewGroup.setEnabled(false);

        String searchString = textfield.getText().trim();
        if(!caseSensitive.isSelected())
          searchString = searchString.toUpperCase();

        if(searchString.length()<1)
          return;

        com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);

        searchResults = new SearchResults();

        Sequence seq;
        String item = null;
        boolean found = false;

        ////// is the searchString a residue number?
        try
        {
            int res = Integer.parseInt(searchString);
            found = true;
            if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)
            {
              seq = (Sequence) av.getAlignment().getSequenceAt(0);
            }
            else
            {
              seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
            }

            searchResults.addResult(seq, res, res);
        }
        catch (NumberFormatException ex)
        {
        }

        ///////////////////////////////////////////////

        int end = av.alignment.getHeight();

        SequenceGroup selection = av.getSelectionGroup();

        if (selection != null)
        {
            if ((selection.getSize(false) < 1) ||
                    ((selection.getEndRes() - selection.getStartRes()) < 2))
            {
                selection = null;
            }
        }

        while (!found && (seqIndex < end))
        {
            seq = (Sequence) av.alignment.getSequenceAt(seqIndex);

            if ((selection != null) && !selection.getSequences(false).contains(seq))
            {
                seqIndex++;
                resIndex = 0;

                continue;
            }

            item = seq.getSequence();
            if(!caseSensitive.isSelected())
              item = item.toUpperCase();

            if ((selection != null) &&
                    (selection.getEndRes() < av.alignment.getWidth()-1))
            {
                item = item.substring(0, selection.getEndRes() + 1);
            }

            ///Shall we ignore gaps????
            StringBuffer noGapsSB = new StringBuffer();
            int insertCount = 0;
            Vector spaces = new Vector();

            for (int j = 0; j < item.length(); j++)
            {
                if (!jalview.util.Comparison.isGap(item.charAt(j)))
                {
                    noGapsSB.append(item.charAt(j));
                    spaces.add(new Integer(insertCount));
                }
                else
                {
                    insertCount++;
                }
            }

            String noGaps = noGapsSB.toString();

            for (int r = resIndex; r < noGaps.length(); r++)
            {

                if (regex.searchFrom(noGaps, r))
                {
                    resIndex = regex.matchedFrom();

                    if ((selection != null) &&
                            ((resIndex +
                            Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))
                    {
                        continue;
                    }


                    int sres = seq.findPosition(resIndex +
                            Integer.parseInt(spaces.elementAt(resIndex)
                                                   .toString()));
                    int eres = seq.findPosition(regex.matchedTo() - 1 +
                            Integer.parseInt(spaces.elementAt(regex.matchedTo() -
                                    1).toString()));

                    searchResults.addResult(seq, sres, eres);

                    if (!findAll)
                    {
                        // thats enough, break and display the result
                        found = true;
                        resIndex++;

                        break;
                    }

                    r = resIndex;
                }
                else
                {
                  break;
                }
            }

            if (!found)
            {
                seqIndex++;
                resIndex = 0;
            }
        }

        Vector idMatch = new Vector();

        for (int id = 0; id < av.alignment.getHeight(); id++)
        {
            if (regex.search(av.alignment.getSequenceAt(id).getName()))
            {
                idMatch.add(av.alignment.getSequenceAt(id));
            }
        }

        if ((searchResults.getSize() == 0) && (idMatch.size() > 0))
        {
            ap.idPanel.highlightSearchResults(idMatch);
        }


        int resultSize = searchResults.getSize();

        if (searchResults.getSize() > 0)
          createNewGroup.setEnabled(true);
        else
          searchResults = null;

        // if allResults is null, this effectively switches displaySearch flag in seqCanvas
        ap.highlightSearchResults(searchResults);

        if(!findAll && resultSize==0)
        {
            JOptionPane.showInternalMessageDialog(this, "Finished searching",
                null, JOptionPane.INFORMATION_MESSAGE);
            resIndex = 0;
            seqIndex = 0;
        }

        if (findAll)
        {
          String message = resultSize + " matches found.";
          JOptionPane.showInternalMessageDialog(this, message, null,
                                                JOptionPane.INFORMATION_MESSAGE);
        }

    }
}