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=",";
  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())
    {
      // 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());
  }
  
}