package jalview.schemes;

import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;

/**
 * An HMM colour scheme that uses global ('Uniprot') background frequencies for
 * residues
 * 
 * @author tzvanaalten
 */
public class HmmerGlobalBackground extends HmmerColourScheme
{
  /*
   * The highest possible log ratio is when match emission probability in
   * the HMM model is 1, and background (for W) is 0.0109 giving
   * log(1/0.0109) = log(91.743) = 4.519
   */
  private static final float MAX_LOG_RATIO = 4.519f;

  /**
   * Constructor given a sequence collection
   * 
   * @param ac
   */
  public HmmerGlobalBackground(SequenceCollectionI ac)
  {
    super(ac.getHmmSequences());
    String alphabetType = getHmm() == null
            ? ResidueProperties.ALPHABET_AMINO
            : getHmm().getAlphabetType();
    setFrequencies(
            ResidueProperties.backgroundFrequencies.get(alphabetType));
  }

  /**
   * Default constructor (required by ColourSchemes.loadColourSchemes)
   */
  public HmmerGlobalBackground()
  {
  }

  @Override
  public String getSchemeName()
  {
    return JalviewColourScheme.HMMERU.toString();
  }

  @Override
  protected HmmerColourScheme newInstance(AnnotatedCollectionI ac)
  {
    return new HmmerGlobalBackground(ac);
  }

  @Override
  float getMaxInformationScore()
  {
    return MAX_LOG_RATIO;
  }

  /**
   * Answers a new colour scheme instance based on the HMM of the first sequence
   * in alignment that has an HMM
   */
  @Override
  public ColourSchemeI getInstance(AlignViewportI viewport,
          AnnotatedCollectionI ac)
  {
    return newInstance(ac);
  }

}