package jalview.io;

import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ResidueCount;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;

import java.io.File;
import java.io.IOException;
import java.net.MalformedURLException;

import javax.swing.JFileChooser;

public class CountReader
{
  public static ResidueCount getBackgroundFrequencies(AlignmentPanel ap, SequenceI seq) throws MalformedURLException, IOException
  {
    JFileChooser bkgdFreqChooser = new JFileChooser();
    
    bkgdFreqChooser.showOpenDialog(ap);
    
    File file = bkgdFreqChooser.getSelectedFile();
    if (file == null)
    {
      return null;
    }
    
    IdentifyFile identifier = new IdentifyFile();
    FileFormatI format = null;
    try
    {
      format = identifier.identify(file.getPath(), DataSourceType.FILE);
    } catch (Exception e)
    {

    }
    
    if (format == null)
    {
      if (!Jalview.isHeadlessMode())
      {
        JvOptionPane.showInternalMessageDialog(Desktop.getInstance(),
                MessageManager.getString("label.couldnt_read_data") + " in "
                        + file + "\n"
                        + AppletFormatAdapter.getSupportedFormats(),
                MessageManager.getString("label.couldnt_read_data"),
                JvOptionPane.WARNING_MESSAGE);
      }
    }

    FileParse parser = new FileParse(file.getPath(), DataSourceType.FILE);
    AlignmentI al = new FormatAdapter().readFromFile(parser, format);
    parser.close();
    
    ResidueCount counts = new ResidueCount(al.getSequences());
    
    return counts;
  }
}