/*******************************************************************************
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.datamodel.SequenceI;
import jalview.ws.params.OptionI;
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.RestServiceDescription;
import jalview.ws.rest.InputType.molType;

import java.io.UnsupportedEncodingException;
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.StringBody;
import org.jmol.util.ArrayUtil;

/**
 * input a list of sequences separated by some separator 
 * @author JimP
 *
 */
public class SeqVector extends InputType {
  String sep;
  molType type;
  public SeqVector()
  {
    super(new Class[] { AlignmentI.class} );
  }

  @Override
  public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
  {
    StringBuffer idvector = new StringBuffer();
    boolean list=false;
    for (SequenceI seq:rj.getSequencesForInput(token, type))
    {
      if (list)
      {
        idvector.append(sep);
      }
      idvector.append(seq.getSequence());
    }
    return new StringBody(idvector.toString());
  }
  @Override
  public List<String> getURLEncodedParameter()
  {
    ArrayList<String> prms = new ArrayList<String>();
    super.addBaseParams(prms);
    prms.add("sep='"+ sep+"'");
    if (type!=null)
    {
      prms.add("type='"+type+"'");
    }
    return prms;
  }

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

  @Override
  public boolean configureProperty(String tok, String val,
          StringBuffer warnings)
  {

    if (tok.startsWith("sep"))
    {
      sep=val;
      return true;
    }
    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 Option("sep",
            "Separator character between elements of vector", true, ",",
            sep, Arrays.asList(new String[]
            { " ", ",", ";", "\t", "|" }), null));
    lst.add(createMolTypeOption("type", "Sequence type", false, type,
            molType.MIX));
    
    return lst;
  }

}