package jalview.gui;

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


public class Finder extends GFinder
{
  AlignViewport av;
  AlignmentPanel ap;
  JInternalFrame frame;
  String searchString;

  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 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 );
      frame.setClosed(true);
    }catch(Exception ex){ }

  }

  void doSearch(boolean findAll)
  {
    searchString = textfield.getText().toUpperCase();

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

    Sequence seq;
    String item;
    boolean found = false;

    /// is the searchString a residue number?
    try{
      int res = Integer.parseInt(searchString);
      found = true;

      if(av.getSelection().size()>0)
        seq = (Sequence)(av.getSelection().sequenceAt(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 ) );


      //av.getAlignment().getSequenceAt(seq).findPosition(res)
    }catch(NumberFormatException ex){}


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

      if(av.getSelection().size()>0 && !av.getSelection().contains(seq))
      {
        // if a selection has been made, only search within that selection
        seqIndex++;
        resIndex=0;
        continue;
      }

      item = seq.getSequence();

      for(int r = resIndex; r<item.length(); r++)
      {
       if(item.indexOf(searchString,r)>-1)
       {
         resIndex = item.indexOf(searchString,r);
         searchResults.add( Integer.toString(seqIndex) );
         searchResults.add( Integer.toString( resIndex) );
         searchResults.add( Integer.toString( (resIndex+searchString.length()-1) ) );
         if(!findAll)
         {
           // thats enough, break and display the result
           found = true;
           resIndex++;
           break;
         }
       }
      }
      if(!found)
      {
        seqIndex++;
        resIndex = 0;
      }
    }

    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());

    }
    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 );


  }

}