/*
* 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.jbgui.GFinder;
import jalview.datamodel.*;
import java.awt.event.*;
import javax.swing.*;
import javax.swing.event.*;
import java.util.*;
import java.awt.*;

public class Finder extends GFinder
{
  AlignViewport av;
  AlignmentPanel ap;
  JInternalFrame frame;
  SuperGroup searchGroup;
  Vector searchResults;

  int seqIndex = 0;
  int resIndex = 0;
  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();      }
       });
     }

     public void internalFrameClosing(InternalFrameEvent evt)
     {
       cancel_actionPerformed(null);
     }
});

  }

  public void textfield_actionPerformed(ActionEvent e)
  {
    doSearch(false);
  }

  public void findNext_actionPerformed(ActionEvent e)
  {
    doSearch(false);
  }

  public void findAll_actionPerformed(ActionEvent e)
  {
    resIndex=0;
    seqIndex=0;
    doSearch(true);
  }

  public void cancel_actionPerformed(ActionEvent e)
  {
    try{
      // if allResults is null, this effectively switches displaySearch flag in seqCanvas
      ap.highlightSearchResults( null );
      ap.idPanel.highlightSearchResults( null );
     // frame.setClosed(true);
    }catch(Exception ex){ }
  }


  public void createNewGroup_actionPerformed(ActionEvent e)
  {

   Color [] newColors = new Color[24];
   for(int i=0; i<24; i++)
     newColors[i] = new Color(60,160,115);

   jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
   String searchString = textfield.getText();

   searchGroup = new SuperGroup(searchString, ucs , true, true, false);


    for(int i=0; i<searchResults.size(); i+=3)
    {
      // its possible edits may have occurred since search was performed
      // account for this here

      SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );
      int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;
      int endRes = seq.findIndex(   Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;

      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes  );
      sg.addSequence(seq);
      av.alignment.addGroup(sg);
      searchGroup.addGroup( sg );

    }

    ap.av.alignment.addSuperGroup(searchGroup);
    ap.highlightSearchResults( null );
  }


  void doSearch(boolean findAll)
  {
    createNewGroup.setEnabled(false);

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

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

    searchResults = new Vector();
    int [] allResults = null;

    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().getSize()>0)
        seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));
      else
        seq = (Sequence)av.getAlignment().getSequenceAt(0);

      searchResults.add( Integer.toString( av.getAlignment().findIndex(seq) ) );
      searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
      searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );

    }catch(NumberFormatException ex){}
    ///////////////////////////////////////////////



    Color [] newColors = new Color[24];
    for(int i=0; i<24; i++)
      newColors[i] = new Color(60,160,115);

    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);

    searchGroup = new SuperGroup(searchString, ucs , true, true, false);

    int end = av.alignment.getHeight();

    SequenceGroup selection = av.getSelectionGroup();
    if(selection!=null)
     if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))
      selection = null;

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


      if(selection!=null && !selection.sequences.contains(seq))
      {
        seqIndex++;
        resIndex=0;
        continue;
      }

      item = seq.getSequence().toUpperCase();

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

      ///Shall we ignore gaps????
      StringBuffer noGaps = 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)))
         {
           noGaps.append(item.charAt(j));
           spaces.add(new Integer(insertCount));
         }
        else
           insertCount++;
      }



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

       if( regex.searchFrom( noGaps.toString(), r ) )
       {
         resIndex = regex.matchedFrom();
         if(selection!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<selection.getStartRes())
           continue;

         searchResults.add( Integer.toString( seqIndex) );

         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.addElement( sres+"" );
          searchResults.addElement( eres+"" );

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

         r=resIndex;
       }
      }
      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.size()==0 && idMatch.size()>0)
      ap.idPanel.highlightSearchResults( idMatch );


    if(searchResults.size()>0)
    {
      allResults = new int[searchResults.size()];
      for(int i=0; i<searchResults.size(); i++)
        allResults[i] = Integer.parseInt(searchResults.get(i).toString());

      createNewGroup.setEnabled(true);
    }
    else
    {
      JOptionPane.showInternalMessageDialog(this, "Finished searching", null, JOptionPane.INFORMATION_MESSAGE);
      resIndex=0;
      seqIndex=0;
    }

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

    if (findAll)
    {
      String message =  (searchResults.size()/3) + " matches found.";
      JOptionPane.showInternalMessageDialog(this, message, null,
                                            JOptionPane.INFORMATION_MESSAGE);
    }

  }

}