src/jalview/io/CountReader.java

   1 package jalview.io;
   2
   3 import jalview.bin.Jalview;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.ResidueCount;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.gui.AlignmentPanel;
   8 import jalview.gui.Desktop;
   9 import jalview.gui.JvOptionPane;
  10 import jalview.util.MessageManager;
  11
  12 import java.io.File;
  13 import java.io.IOException;
  14 import java.net.MalformedURLException;
  15
  16 import javax.swing.JFileChooser;
  17
  18 public class CountReader
  19 {
  20   public static ResidueCount getBackgroundFrequencies(AlignmentPanel ap, SequenceI seq) throws MalformedURLException, IOException
  21   {
  22     JFileChooser bkgdFreqChooser = new JFileChooser();
  23
  24     bkgdFreqChooser.showOpenDialog(ap);
  25
  26     File file = bkgdFreqChooser.getSelectedFile();
  27     if (file == null)
  28     {
  29       return null;
  30     }
  31
  32     IdentifyFile identifier = new IdentifyFile();
  33     FileFormatI format = null;
  34     try
  35     {
  36       format = identifier.identify(file.getPath(), DataSourceType.FILE);
  37     } catch (Exception e)
  38     {
  39
  40     }
  41
  42     if (format == null)
  43     {
  44       if (!Jalview.isHeadlessMode())
  45       {
  46         JvOptionPane.showInternalMessageDialog(Desktop.getInstance(),
  47                 MessageManager.getString("label.couldnt_read_data") + " in "
  48                         + file + "\n"
  49                         + AppletFormatAdapter.getSupportedFormats(),
  50                 MessageManager.getString("label.couldnt_read_data"),
  51                 JvOptionPane.WARNING_MESSAGE);
  52       }
  53     }
  54
  55     FileParse parser = new FileParse(file.getPath(), DataSourceType.FILE);
  56     AlignmentI al = new FormatAdapter().readFromFile(parser, format);
  57     parser.close();
  58
  59     ResidueCount counts = new ResidueCount(al.getSequences());
  60
  61     return counts;
  62   }
  63 }