/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
 * Copyright (C) 2008 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.io;

import jalview.datamodel.*;

/**
 * Additional formatting methods used by the application in a number of places.
 * 
 * @author $author$
 * @version $Revision$
 */
public class FormatAdapter extends AppletFormatAdapter
{

  public String formatSequences(String format, SequenceI[] seqs,
          String[] omitHiddenColumns)
  {

    return formatSequences(format, replaceStrings(seqs, omitHiddenColumns));
  }

  /**
   * create sequences with each seuqence string replaced with the one given in
   * omitHiddenCOlumns
   * 
   * @param seqs
   * @param omitHiddenColumns
   * @return new sequences
   */
  public SequenceI[] replaceStrings(SequenceI[] seqs,
          String[] omitHiddenColumns)
  {
    if (omitHiddenColumns != null)
    {
      SequenceI[] tmp = new SequenceI[seqs.length];
      for (int i = 0; i < seqs.length; i++)
      {
        tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
                seqs[i].getStart(), seqs[i].getEnd());
        tmp[i].setDescription(seqs[i].getDescription());
      }
      seqs = tmp;
    }
    return seqs;
  }

  /**
   * Format a vector of sequences as a flat alignment file.
   * 
   * @param format
   *                Format string as givien in the AppletFormatAdaptor list
   *                (exact match to name of class implementing file io for that
   *                format)
   * @param seqs
   *                vector of sequences to write
   * 
   * @return String containing sequences in desired format
   */
  public String formatSequences(String format, SequenceI[] seqs)
  {

    try
    {
      AlignFile afile = null;

      if (format.equalsIgnoreCase("FASTA"))
      {
        afile = new FastaFile();
        afile.addJVSuffix(jalview.bin.Cache.getDefault("FASTA_JVSUFFIX",
                true));
      }
      else if (format.equalsIgnoreCase("MSF"))
      {
        afile = new MSFfile();
        afile.addJVSuffix(jalview.bin.Cache
                .getDefault("MSF_JVSUFFIX", true));
      }
      else if (format.equalsIgnoreCase("PileUp"))
      {
        afile = new PileUpfile();
        afile.addJVSuffix(jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX",
                true));
      }
      else if (format.equalsIgnoreCase("CLUSTAL"))
      {
        afile = new ClustalFile();
        afile.addJVSuffix(jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX",
                true));
      }
      else if (format.equalsIgnoreCase("BLC"))
      {
        afile = new BLCFile();
        afile.addJVSuffix(jalview.bin.Cache
                .getDefault("BLC_JVSUFFIX", true));
      }
      else if (format.equalsIgnoreCase("PIR"))
      {
        afile = new PIRFile();
        afile.addJVSuffix(jalview.bin.Cache
                .getDefault("PIR_JVSUFFIX", true));
      }
      else if (format.equalsIgnoreCase("PFAM"))
      {
        afile = new PfamFile();
        afile.addJVSuffix(jalview.bin.Cache.getDefault("PFAM_JVSUFFIX",
                true));
      }
      /*
       * amsa is not supported by this function - it requires an alignment
       * rather than a sequence vector else if (format.equalsIgnoreCase("AMSA")) {
       * afile = new AMSAFile(); afile.addJVSuffix(
       * jalview.bin.Cache.getDefault("AMSA_JVSUFFIX", true)); }
       */

      afile.setSeqs(seqs);

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

    return null;
  }

  public boolean getCacheSuffixDefault(String format)
  {
    if (isValidFormat(format))
      return jalview.bin.Cache.getDefault(format.toUpperCase()
              + "_JVSUFFIX", true);
    return false;
  }

  public String formatSequences(String format, AlignmentI alignment,
          String[] omitHidden, ColumnSelection colSel)
  {
    return formatSequences(format, alignment, omitHidden,
            getCacheSuffixDefault(format), colSel, null);
  }

  public String formatSequences(String format, AlignmentI alignment,
          String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp)
  {
    return formatSequences(format, alignment, omitHidden,
            getCacheSuffixDefault(format), colSel, sgp);
  }

  /**
   * hack function to replace seuqences with visible sequence strings before
   * generating a string of the alignment in the given format.
   * 
   * @param format
   * @param alignment
   * @param omitHidden
   *                sequence strings to write out in order of sequences in
   *                alignment
   * @param colSel
   *                defines hidden columns that are edited out of annotation
   * @return string representation of the alignment formatted as format
   */
  public String formatSequences(String format, AlignmentI alignment,
          String[] omitHidden, boolean suffix, ColumnSelection colSel)
  {
    return formatSequences(format, alignment, omitHidden, suffix, colSel,
            null);
  }

  public String formatSequences(String format, AlignmentI alignment,
          String[] omitHidden, boolean suffix, ColumnSelection colSel,
          jalview.datamodel.SequenceGroup selgp)
  {
    if (omitHidden != null)
    {
      // 
      Alignment alv = new Alignment(replaceStrings(alignment
              .getSequencesArray(), omitHidden));
      AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
      for (int i = 0; i < ala.length; i++)
      {
        AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
        if (selgp != null)
        {
          colSel.makeVisibleAnnotation(selgp.getStartRes(), selgp
                  .getEndRes(), na);
        }
        else
        {
          colSel.makeVisibleAnnotation(na);
        }
        alv.addAnnotation(na);
      }
      return this.formatSequences(format, alv, suffix);
    }
    return this.formatSequences(format, alignment, suffix);
  }
}