/*******************************************************************************
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
 *
 * This file is part of Jalview.
 *
 * Jalview 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 3 of the License, or (at your option) any later version.
 *
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 *******************************************************************************/
package jalview.ws.rest.params;

import jalview.datamodel.AlignmentI;
import jalview.ws.params.OptionI;
import jalview.ws.params.simple.BooleanOption;
import jalview.ws.params.simple.Option;
import jalview.ws.rest.InputType;
import jalview.ws.rest.NoValidInputDataException;
import jalview.ws.rest.RestJob;
import jalview.ws.rest.InputType.molType;
import jalview.ws.rest.RestServiceDescription;

import java.io.BufferedOutputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import org.apache.http.entity.mime.content.ContentBody;
import org.apache.http.entity.mime.content.FileBody;
import org.apache.http.entity.mime.content.StringBody;

/**
 * format an alignment for input to rest service.
 * 
 * @author JimP
 * 
 */
public class Alignment extends InputType
{
  public Alignment()
  {
    super(new Class[]
    { AlignmentI.class });
  }

  String format = "FASTA";

  molType type;

  boolean jvsuffix = false;

  /**
   * input data as a file upload rather than inline content
   */
  public boolean writeAsFile=false;

  @Override
  public ContentBody formatForInput(RestJob rj)
          throws UnsupportedEncodingException, NoValidInputDataException
  {
    AlignmentI alignment = rj.getAlignmentForInput(token, type);
    if (writeAsFile)
    {
      try
      {
        File fa = File.createTempFile("jvmime", ".fa");
        PrintWriter pw = new PrintWriter(
                new OutputStreamWriter(new BufferedOutputStream(
                        new FileOutputStream(fa)), "UTF-8"));
        pw.append(new jalview.io.FormatAdapter().formatSequences(format,
                alignment, jvsuffix));
        pw.close();
        return new FileBody(fa, "text/plain");
      } catch (Exception ex)
      {
        throw new NoValidInputDataException(
                "Couldn't write out alignment to file.", ex);
      }
    }
    else
    {
      jalview.io.FormatAdapter fa = new jalview.io.FormatAdapter();
      fa.setNewlineString("\r\n");
      return new StringBody(
              (fa.formatSequences(format, alignment, jvsuffix)));
      // ,
      // "text/plain",Charset.forName("UTF-8"));
      // , "text/plain", Charset.forName("UTF-8"));
      // sb.getContentTypeParameters().put("filename", "alignment.fa");
    }
  }

  @Override
  public List<String> getURLEncodedParameter()
  {
    ArrayList<String> prms = new ArrayList<String>();
    prms.add("format='" + format + "'");
    if (type != null)
    {
      prms.add("type='" + type.toString() + "'");
    }
    if (jvsuffix)
    {
      prms.add("jvsuffix");
    }
    ;
    if (writeAsFile)
    {
      prms.add("writeasfile");
    }
    ;
    return prms;
  }

  @Override
  public String getURLtokenPrefix()
  {
    return "ALIGNMENT";
  }

  @Override
  public boolean configureProperty(String tok, String val,
          StringBuffer warnings)
  {
    if (tok.startsWith("jvsuffix"))
    {
      jvsuffix = true;
      return true;
    }
    if (tok.startsWith("writeasfile"))
    {
      writeAsFile = true;
      return true;
    }

    if (tok.startsWith("format"))
    {
      for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
      {
        if (val.equalsIgnoreCase(fmt))
        {
          format = fmt;
          return true;
        }
      }
      warnings.append("Invalid alignment format '" + val
              + "'. Must be one of (");
      for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
      {
        warnings.append(" " + fmt);
      }
      warnings.append(")\n");
    }
    if (tok.startsWith("type"))
    {
      try
      {
        type = molType.valueOf(val);
        return true;
      } catch (Exception x)
      {
        warnings.append("Invalid molecule type '" + val
                + "'. Must be one of (");
        for (molType v : molType.values())
        {
          warnings.append(" " + v);
        }
        warnings.append(")\n");
      }
    }
    return false;
  }
  @Override
  public List<OptionI> getOptions()
  {
    List<OptionI> lst = getBaseOptions();
    lst.add(new BooleanOption("jvsuffix","Append jalview style /start-end suffix to ID", false, false, jvsuffix, null));
    lst.add(new BooleanOption("writeasfile","Append jalview style /start-end suffix to ID", false, false, writeAsFile, null));
    
    lst.add(new Option("format",
            "Alignment upload format", true, "FASTA",
            format, Arrays.asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS), null));
    lst.add(createMolTypeOption("type", "Sequence type", false, type,
            null));
    
    return lst;
  }

}