package jalview.analysis;

import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;

import java.util.Arrays;
import java.util.Comparator;

/**
 * A helper class to sort all annotations associated with an alignment in
 * various ways.
 * 
 * @author gmcarstairs
 *
 */
public class AnnotationSorter
{

  private final AlignmentI alignment;

  public AnnotationSorter(AlignmentI alignmentI)
  {
    this.alignment = alignmentI;
  }

  /**
   * Default comparator sorts as follows by annotation type within sequence
   * order:
   * <ul>
   * <li>annotations with a reference to a sequence in the alignment are sorted
   * on sequence ordering</li>
   * <li>other annotations go 'at the end', with their mutual order unchanged</li>
   * <li>within the same sequence ref, sort by label (non-case-sensitive)</li>
   * </ul>
   */
  private final Comparator<? super AlignmentAnnotation> bySequenceAndType = new Comparator<AlignmentAnnotation>()
  {
    @Override
    public int compare(AlignmentAnnotation o1, AlignmentAnnotation o2)
    {
      if (o1 == null && o2 == null)
      {
        return 0;
      }
      if (o1 == null)
      {
        return -1;
      }
      if (o2 == null)
      {
        return 1;
      }

      /*
       * Ignore label (keep existing ordering) for
       * Conservation/Quality/Consensus etc
       */
      if (o1.sequenceRef == null && o2.sequenceRef == null)
      {
        return 0;
      }
      int sequenceOrder = compareSequences(o1, o2);
      return sequenceOrder == 0 ? compareLabels(o1, o2) : sequenceOrder;
    }
  };

  /**
   * This comparator sorts as follows by sequence order within annotation type
   * <ul>
   * <li>annotations with a reference to a sequence in the alignment are sorted
   * on label (non-case-sensitive)</li>
   * <li>other annotations go 'at the end', with their mutual order unchanged</li>
   * <li>within the same label, sort by order of the related sequences</li>
   * </ul>
   */
  private final Comparator<? super AlignmentAnnotation> byTypeAndSequence = new Comparator<AlignmentAnnotation>()
  {
    @Override
    public int compare(AlignmentAnnotation o1, AlignmentAnnotation o2)
    {
      if (o1 == null && o2 == null)
      {
        return 0;
      }
      if (o1 == null)
      {
        return -1;
      }
      if (o2 == null)
      {
        return 1;
      }

      /*
       * Ignore label (keep existing ordering) for
       * Conservation/Quality/Consensus etc
       */
      if (o1.sequenceRef == null && o2.sequenceRef == null)
      {
        return 0;
      }

      /*
       * Sort non-sequence-related after sequence-related.
       */
      if (o1.sequenceRef == null)
      {
        return 1;
      }
      if (o2.sequenceRef == null)
      {
        return -1;
      }
      int labelOrder = compareLabels(o1, o2);
      return labelOrder == 0 ? compareSequences(o1, o2) : labelOrder;
    }
  };

  /**
   * Sort by annotation type (label), within sequence order.
   * Non-sequence-related annotations sort to the end.
   * 
   * @param alignmentAnnotations
   */
  public void sortBySequenceAndType(
          AlignmentAnnotation[] alignmentAnnotations)
  {
    if (alignmentAnnotations != null)
    {
      synchronized (alignmentAnnotations)
      {
        Arrays.sort(alignmentAnnotations, bySequenceAndType);
      }
    }
  }

  /**
   * Sort by sequence order within annotation type (label). Non-sequence-related
   * annotations sort to the end.
   * 
   * @param alignmentAnnotations
   */
  public void sortByTypeAndSequence(
          AlignmentAnnotation[] alignmentAnnotations)
  {
    if (alignmentAnnotations != null)
    {
      synchronized (alignmentAnnotations)
      {
        Arrays.sort(alignmentAnnotations, byTypeAndSequence);
      }
    }
  }

  /**
   * Non-case-sensitive comparison of annotation labels. Returns zero if either
   * argument is null.
   * 
   * @param o1
   * @param o2
   * @return
   */
  private int compareLabels(AlignmentAnnotation o1, AlignmentAnnotation o2)
  {
    if (o1 == null || o2 == null)
    {
      return 0;
    }
    String label1 = o1.label;
    String label2 = o2.label;
    if (label1 == null && label2 == null)
    {
      return 0;
    }
    if (label1 == null)
    {
      return -1;
    }
    if (label2 == null)
    {
      return 1;
    }
    return label1.toUpperCase().compareTo(label2.toUpperCase());
  }

  /**
   * Comparison based on position of associated sequence (if any) in the
   * alignment. Returns zero if either argument is null.
   * 
   * @param o1
   * @param o2
   * @return
   */
  private int compareSequences(AlignmentAnnotation o1,
          AlignmentAnnotation o2)
  {
    SequenceI seq1 = o1.sequenceRef;
    SequenceI seq2 = o2.sequenceRef;
    if (seq1 == null && seq2 == null)
    {
      return 0;
    }
    if (seq1 == null)
    {
      return 1;
    }
    if (seq2 == null)
    {
      return -1;
    }
    // get sequence index - but note -1 means 'at end' so needs special handling
    int index1 = AlignmentUtils.getSequenceIndex(alignment, seq1);
    int index2 = AlignmentUtils.getSequenceIndex(alignment, seq2);
    if (index1 == index2)
    {
      return 0;
    }
    if (index1 == -1)
    {
      return -1;
    }
    if (index2 == -1)
    {
      return 1;
    }
    return Integer.compare(index1, index2);
  }
}