/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2006 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.appletgui;

import java.util.*;

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

import jalview.datamodel.*;
import java.awt.Rectangle;

public class Finder extends Panel implements ActionListener
{
  AlignViewport av;
  AlignmentPanel ap;
  Frame frame;

  SearchResults searchResults;

  int seqIndex = 0;
  int resIndex = 0;
  public Finder(final AlignmentPanel ap)
  {
    try
    {
      jbInit();
    }
    catch (Exception e)
    {
      e.printStackTrace();
    }

    this.av = ap.av;
    this.ap = ap;
    frame = new Frame();
    frame.add(this);
    jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120);
    frame.repaint();
    frame.addWindowListener(new WindowAdapter()
    {
      public void windowClosing(WindowEvent evt)
      {
        ap.highlightSearchResults(null);
      }
    });
  }

  public void actionPerformed(ActionEvent evt)
  {
    if (evt.getSource() == textfield)
      doSearch(false);

    else if (evt.getSource() == findNext)
      doSearch(false);

    else if (evt.getSource() == findAll)
    {
      resIndex = 0;
      seqIndex = 0;
      doSearch(true);
    }
    else if(evt.getSource() == createNewGroup)
      createNewGroup_actionPerformed();
  }


  public void createNewGroup_actionPerformed()
  {

    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);
    cap.ok.setLabel("Accept");
    Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);
    dialog.add(cap);

    cap.setText(textfield.getText());

    dialog.setBounds( frame.getLocation().x+frame.getSize().width+5,
                      frame.getLocation().y+20,300,100);
    dialog.show();


    String featureName = cap.getText().trim();
    if(featureName.length()<1)
      return;


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

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

        ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
            featureName, new Color(60,160,115));
        seq.addSequenceFeature(sf);
    }

    ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
    ap.alignFrame.sequenceFeatures.setState(true);
    av.showSequenceFeatures(true);
    ap.highlightSearchResults(null);
  }

  void doSearch(boolean findAll)
  {
    if(jalview.bin.JalviewLite.currentAlignFrame!=null)
    {
      ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel;
      av = ap.av;
    }
    createNewGroup.setEnabled(false);

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

    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.getSequenceAsString();
      if(!caseSensitive.getState())
        item = item.toUpperCase();

      if (selection != null && selection.getEndRes() < av.alignment.getWidth())
      {
        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.addElement(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.elementAt(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.addElement(av.alignment.getSequenceAt(id));
      }
    }

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

    if (searchResults.getSize() > 0)
    {
      createNewGroup.setEnabled(true);
    }
    else
    {
      searchResults = null;
      resIndex = 0;
      seqIndex = 0;
    }

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

    if (findAll)
    {
      String message = (searchResults==null?0 : searchResults.getSize()) + " matches found.";
      ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message);
    }

  }

  Label jLabel1 = new Label();
  protected TextField textfield = new TextField();
  protected Button findAll = new Button();
  protected Button findNext = new Button();
  Panel jPanel1 = new Panel();
  GridLayout gridLayout1 = new GridLayout();
  protected Button createNewGroup = new Button();
  Checkbox caseSensitive = new Checkbox();

  private void jbInit() throws Exception {
      jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
      jLabel1.setText("Find");
      jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
      this.setLayout(null);
      textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
      textfield.setText("");
      textfield.setBounds(new Rectangle(40, 27, 133, 21));
      textfield.addKeyListener(new java.awt.event.KeyAdapter() {
              public void keyTyped(KeyEvent e) {
                  textfield_keyTyped(e);
              }
          });
      textfield.addActionListener(this);
      findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
      findAll.setLabel("Find all");
      findAll.addActionListener(this);
      findNext.setEnabled(false);
      findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
      findNext.setLabel("Find Next");
      findNext.addActionListener(this);
      jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
      jPanel1.setLayout(gridLayout1);
      gridLayout1.setHgap(0);
      gridLayout1.setRows(3);
      gridLayout1.setVgap(2);
      createNewGroup.setEnabled(false);
      createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
      createNewGroup.setLabel("New Feature");
      createNewGroup.addActionListener(this);
    caseSensitive.setLabel("Match Case");
    caseSensitive.setBounds(new Rectangle(40, 49, 126, 23));
    jPanel1.add(findNext, null);
      jPanel1.add(findAll, null);
      jPanel1.add(createNewGroup, null);
    this.add(caseSensitive);
    this.add(textfield, null);
      this.add(jLabel1, null);
      this.add(jPanel1, null);
  }

  void textfield_keyTyped(KeyEvent e) {
      findNext.setEnabled(true);
  }

}