package jalview.ws.rest.params;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.ws.rest.AlignmentProcessor;
import jalview.ws.rest.InputType;
import jalview.ws.rest.NoValidInputDataException;
import jalview.ws.rest.RestJob;
import jalview.ws.rest.InputType.molType;

import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.Vector;

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

/**
 * Represents the partitions defined on the alignment as indices e.g. for a
 * partition (A,B,C),(D,E),(F) The indices would be 3,2,1. Note, the alignment
 * must be ordered so groups are contiguous before this input type can be used.
 * 
 * @author JimP
 * 
 */
public class SeqGroupIndexVector extends InputType implements
        AlignmentProcessor
{
  public SeqGroupIndexVector()
  {
    super(new Class[]
    { AlignmentI.class });
  }

  /**
   * separator for list of sequence Indices - default is ','
   */
  public String sep = ",";

  /**
   * min size of each partition
   */
  public int minsize = 1;

  molType type;

  /**
   * prepare the context alignment for this input
   * 
   * @param al
   *          - alignment to be processed
   * @return al or a new alignment with appropriate attributes/order for input
   */
  public AlignmentI prepareAlignment(AlignmentI al)
  {
    jalview.analysis.AlignmentSorter.sortByGroup(al);
    return al;
  }

  @Override
  public ContentBody formatForInput(RestJob rj)
          throws UnsupportedEncodingException, NoValidInputDataException
  {
    StringBuffer idvector = new StringBuffer();
    boolean list = false;
    AlignmentI al = rj.getAlignmentForInput(token, type);
    // assume that alignment is properly ordered so groups form consecutive
    // blocks
    ArrayList<int[]> gl = new ArrayList<int[]>();
    for (SequenceGroup sg : (Vector<SequenceGroup>) al.getGroups())
    {
      if (sg.getSize()<minsize)
      {
        throw new NoValidInputDataException("Group contains less than "+minsize+" sequences.");
      }
      // TODO: refactor to sequenceGroup for efficiency -
      // getAlignmentRowInterval(AlignmentI al)
      int[] se = null;
      for (SequenceI sq : sg.getSequencesInOrder(al))
      {
        int p = al.findIndex(sq);
        if (se == null)
        {
          se = new int[]
          { p, p };
        }
        else
        {
          if (p < se[0])
            se[0] = p;
          if (p > se[1])
            se[1] = p;
        }
      }
      if (se != null)
      {
        gl.add(se);
      }
    }
    int[][] vals = gl.toArray(new int[gl.size()][]);
    int[] srt = new int[gl.size()];
    for (int i = 0; i < vals.length; i++)
      srt[i] = vals[i][0];
    jalview.util.QuickSort.sort(srt, vals);
    list = false;
    int last = vals[0][0] - 1;
    for (int[] range : vals)
    {
      if (range[1] > last)
      {
        if (list)
        {
          idvector.append(sep);
        }
        idvector.append(range[1] - last);
        last = range[1];
        list = true;
      }
    }
    return new StringBody(idvector.toString());
  }

}