package jalview.schemes;

import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import jalview.util.ColorUtils;
import jalview.util.Comparison;

import java.awt.Color;
import java.util.List;
import java.util.Map;

/**
 * A colour scheme based on a selected Hidden Markov Model. The colour is
 * <ul>
 * <li>white for a gap</li>
 * <li>red for an insertion</li>
 * <li>orange for negative information content</li>
 * <li>white to blue for increasing information content</li>
 * </ul>
 * where information content is the log ratio
 * 
 * <pre>
 *   log(profile match emission probability / residue background probability>
 * </pre>
 * 
 * using global ('Uniprot') background frequencies for residues.
 * 
 * @author tzvanaalten
 *
 */
public class HMMERColourScheme extends ResidueColourScheme
{
  /*
   * 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;

  private static final Color REDDISH = new Color(230, 0, 0);

  HiddenMarkovModel hmm;

  /**
   * Constructor given a Hidden Markov Model
   * 
   * @param markov
   */
  public HMMERColourScheme(HiddenMarkovModel markov)
  {
    hmm = markov;
  }

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

  @Override
  public Color findColour(char symbol, int position, SequenceI seq,
          String consensusResidue, float pid)
  {
    return findColour(symbol, position);
  }

  /**
   * Returns the colour at a particular symbol at a column in the alignment:
   * <ul>
   * <li>white for a gap</li>
   * <li>red for an insertion</li>
   * <li>orange for negative information content</li>
   * <li>white to blue for increasing information content</li>
   * </ul>
   * 
   * @param symbol
   * @param column
   * @return
   */
  private Color findColour(char symbol, int column)
  {
    if (hmm == null || Comparison.isGap(symbol))
    {
      return Color.white;
    }
    if (Character.isLowerCase(symbol))
    {
      symbol = Character.toUpperCase(symbol);
    }

    double prob = hmm.getMatchEmissionProbability(column, symbol);
    Float freq = 0f;
    String alpha = hmm.getAlphabetType();
    if (!ResidueProperties.backgroundFrequencies.get(alpha)
            .containsKey(symbol))
    {
      return Color.WHITE;
    }
    else
    {
      freq = ResidueProperties.backgroundFrequencies.get(alpha).get(symbol);
    }
    if (prob == 0D)
    {
      return REDDISH;
    }
    double value = Math.log(prob / freq.floatValue());
    Color colour = null;
    if (value > 0)
    {
      colour = ColorUtils.getGraduatedColour((float) value, 0,
              Color.WHITE, MAX_LOG_RATIO, Color.blue);
    }
    else if (value < 0)
    {
      return Color.ORANGE;
    }
    return colour;
  }

  @Override
  public void alignmentChanged(AnnotatedCollectionI collection,
          Map<SequenceI, SequenceCollectionI> hiddenReps)
  {
    /*
     * ? no need to do anything if alignment is adjusted
     * since findColour() handles everything 
     */
  }

  /**
   * Answers a new colour scheme instance based on the HMM of the first sequence
   * in sg that has an HMM
   */
  @Override
  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
  {
    HiddenMarkovModel model = null;
    List<SequenceI> seqs = sg.getHMMConsensusSequences();
    if (!seqs.isEmpty())
    {
      model = seqs.get(0).getHMM();
    }
    HMMERColourScheme colour = new HMMERColourScheme(model);
    return colour;
  }

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

  @Override
  public boolean isSimple()
  {
    return false;
  }

  @Override
  public boolean isApplicableTo(AnnotatedCollectionI ac)
  {
    return !ac.getHMMConsensusSequences().isEmpty();
  }

}