package jalview.schemes;

import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.ResidueCount;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;

import java.util.HashMap;
import java.util.List;
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 sequence collection
   * 
   * @param ac
   */
  public HmmerLocalBackground(AnnotatedCollectionI ac)
  {
    super(ac.getHmmSequences());
    countFrequencies(ac);
  }

  /**
   * 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
   * (apart from any HMM consensus sequences)
   * 
   * @param sc
   */
  public void countFrequencies(SequenceCollectionI sc)
  {
    // TODO or total counts in Consensus Profile (how do we get at it?)?
    Map<Character, Float> freqs = new HashMap<>();

    /*
     * count symbols, excluding any HMM consensus sequences
     */
    ResidueCount counts = new ResidueCount();
    List<SequenceI> seqs = sc.getSequences();
    for (SequenceI seq : seqs)
    {
      if (!seq.hasHMMProfile())
      {
        for (char c : seq.getSequence())
        {
          counts.add(c);
        }
      }
    }
    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)
  {
    return new HmmerLocalBackground(ac);
  }
}