package jalview.io;

import jalview.datamodel.*;
import java.util.Vector;
public class FormatAdapter
{

  public static Vector formats = new Vector();
  static{
    formats.addElement("FASTA");
    formats.addElement("MSF");
    formats.addElement("PileUp");
    formats.addElement("CLUSTAL");
    formats.addElement("BLC");
    formats.addElement("PIR");
    formats.addElement("PFAM");
  }

  public static SequenceI[] readFile(String inFile, String type, String format)
  {

    try
    {
      AlignFile afile = null;
      if (format.equals("FASTA"))
        afile = new FastaFile(inFile, type);
      else if (format.equals("MSF"))
        afile = new MSFfile(inFile, type);
      else if (format.equals("PileUp"))
              afile = new PileUpfile(inFile, type);
      else if (format.equals("CLUSTAL"))
        afile = new ClustalFile(inFile, type);
      else if (format.equals("BLC"))
        afile = new BLCFile(inFile, type);
      else if (format.equals("PIR"))
        afile = new PIRFile(inFile, type);
      else if (format.equals("PFAM"))
        afile = new PfamFile(inFile, type);

      return afile.getSeqsAsArray();
    }
    catch (Exception e)  {
    System.err.println("Failed to read alignment using the '"+format+"' reader.");
    e.printStackTrace();
    }

    return null;
  }


  public static String formatSequences(String format, Vector seqs)
  {
    SequenceI [] s = new SequenceI[seqs.size()];

    for (int i = 0; i < seqs.size(); i++)
      s[i] = (SequenceI) seqs.elementAt(i);

    try
    {
      AlignFile afile = null;
      if (format.equals("FASTA"))
        afile = new FastaFile();
      else if (format.equals("MSF"))
        afile = new MSFfile();
      else if (format.equals("PileUp"))
        afile = new PileUpfile();
      else if (format.equals("CLUSTAL"))
        afile = new ClustalFile();
      else if (format.equals("BLC"))
        afile = new BLCFile();
      else if (format.equals("PIR"))
        afile = new PIRFile();
      else if (format.equals("PFAM"))
        afile = new PfamFile();

      afile.setSeqs(s);
      return afile.print();
    }
    catch (Exception e)  {
      System.err.println("Failed to write alignment as a '"+format+"' file\n");
      e.printStackTrace();
    }

    return null;
  }
}