package jalview.schemes;

import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.ResidueCount;

import java.util.HashMap;
import java.util.Map;

/**
 * An HMM colour scheme that uses local (alignment or sub-group) background
 * frequencies for residues
 * 
 * @author tzvanaalten
 */
public class HmmerLocalBackground extends HmmerColourScheme
{
  float logTotalCount;

  /**
   * Constructor given a Hidden Markov Model
   * 
   * @param sg
   * 
   * @param markov
   */
  public HmmerLocalBackground(AnnotatedCollectionI sg,
          HiddenMarkovModel markov)
  {
    super(markov);
    countFrequencies(sg);
  }

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

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

  /**
   * Counts and stores the relative frequency of every residue in the alignment
   * 
   * @param sg
   */
  public void countFrequencies(AnnotatedCollectionI sg)
  {
    Map<Character, Float> freqs = new HashMap<>();
    ResidueCount counts = new ResidueCount(sg.getSequences());
    int total = counts.getTotalResidueCount(); // excludes gaps

    for (char symbol : counts.getSymbolCounts().symbols)
    {
      double freq = counts.getCount(symbol) / (double) total;
      freqs.put(symbol, (float) freq);
    }

    setFrequencies(freqs);

    logTotalCount = (float) Math.log(total);
  }

  @Override
  float getMaxInformationScore()
  {
    return logTotalCount;
  }

  @Override
  protected HmmerColourScheme newInstance(AnnotatedCollectionI ac,
          HiddenMarkovModel model)
  {
    return new HmmerLocalBackground(ac, model);
  }
}