package jalview.analysis;


/**
 * A data bean to hold the result of computing a profile for a column of an
 * alignment
 * 
 * @author gmcarstairs
 *
 */
public class Profile
{
  /*
   * counts of keys (chars)
   */
  private ResidueCount counts;

  /*
   * the number of sequences in the profile
   */
  private int height;

  /*
   * the number of non-gapped sequences in the profile
   */
  private int gapped;

  /*
   * the highest count for any residue in the profile
   */
  private int maxCount;

  /*
   * the residue (e.g. K) or residues (e.g. KQW) with the
   * highest count in the profile
   */
  private String modalResidue;

  /**
   * Constructor which allows derived data to be stored without having to store
   * the full profile
   * 
   * @param seqCount
   *          the number of sequences in the profile
   * @param gaps
   *          the number of gapped sequences
   * @param max
   *          the highest count for any residue
   * @param modalres
   *          the residue (or concatenated residues) with the highest count
   */
  public Profile(int seqCount, int gaps, int max, String modalRes)
  {
    this.height = seqCount;
    this.gapped = gaps;
    this.maxCount = max;
    this.modalResidue = modalRes;
  }

  /**
   * Set the full profile of counts
   * 
   * @param residueCounts
   */
  public void setCounts(ResidueCount residueCounts)
  {
    this.counts = residueCounts;
  }

  /**
   * Returns the percentage identity of the profile, i.e. the highest proportion
   * of conserved (equal) symbols. The percentage is as a fraction of all
   * sequences, or only ungapped sequences if flag ignoreGaps is set true.
   * 
   * @param ignoreGaps
   * @return
   */
  public float getPercentageIdentity(boolean ignoreGaps)
  {
    if (height == 0)
    {
      return 0f;
    }
    float pid = 0f;
    if (ignoreGaps && gapped < height)
    {
      pid = (maxCount * 100f) / (height - gapped);
    }
    else
    {
      pid = (maxCount * 100f) / height;
    }
    return pid;
  }

  /**
   * Returns the full symbol counts for this profile
   * 
   * @return
   */
  public ResidueCount getCounts()
  {
    return counts;
  }

  /**
   * Returns the number of sequences in the profile
   * 
   * @return
   */
  public int getHeight()
  {
    return height;
  }

  /**
   * Returns the number of sequences in the profile which had a gap character
   * (or were too short to be included in this column's profile)
   * 
   * @return
   */
  public int getGapped()
  {
    return gapped;
  }

  /**
   * Returns the highest count for any symbol(s) in the profile
   * 
   * @return
   */
  public int getMaxCount()
  {
    return maxCount;
  }

  /**
   * Returns the symbol (or concatenated symbols) which have the highest count
   * in the profile, or an empty string if there were no symbols counted
   * 
   * @return
   */
  public String getModalResidue()
  {
    return modalResidue;
  }

  /**
   * Answers the number of non-gapped sequences in the profile
   * 
   * @return
   */
  public int getNonGapped()
  {
    return height - gapped;
  }
}