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;

public class HMMERColourScheme extends ResidueColourScheme
{

  AnnotatedCollectionI alignment;

  HiddenMarkovModel hmm;
  
  boolean peptideSpecific;

  boolean nucleotideSpecific;

  public HMMERColourScheme(HiddenMarkovModel markov)
  {
    hmm = markov;
  }
  public HMMERColourScheme()
  {

  }

  @Override
  public Color findColour(char symbol, int position, SequenceI seq,
          String consensusResidue, float pid)
  {
    if (hmm ==null)
    {
      return Color.white;
    }
    return findColour(symbol, position);
  }

  public Color findColour(char symbol, int position)
  {

    if (Comparison.isGap(symbol))
    {
      return Color.white;
    }
    if (Character.isLowerCase(symbol))
    {
      return new Color(230, 0, 0);
    }
    Double prob;
    prob = hmm.getMatchEmissionProbability(position, symbol);
    double freq = 0;
    if ("amino".equals(hmm.getAlphabetType()))
    {
      if (!ResidueProperties.aminoBackgroundFrequencies.containsKey(symbol))
      {
        return Color.white;
      }
      freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
    }
    else if ("DNA".equals(hmm.getAlphabetType()))
    {
      if (!ResidueProperties.dnaBackgroundFrequencies.containsKey(symbol))
      {
        return Color.white;
      }
      freq = ResidueProperties.dnaBackgroundFrequencies.get(symbol);
    }
    else if ("RNA".equals(hmm.getAlphabetType()))
    {
      if (!ResidueProperties.rnaBackgroundFrequencies.containsKey(symbol))
      {
        return Color.white;
      }
      freq = ResidueProperties.rnaBackgroundFrequencies.get(symbol);
    }
    if (prob == 0)
    {
      return new Color(230, 0, 0);
    }
    Double value = Math.log(prob / freq);
    Color colour = null;
    if (value > 0)
    {

      colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
              Color.WHITE, 4.52f, Color.blue);
    }
    else if (value < 0)
    {
      return Color.ORANGE;

    }
    return colour;

  }
    





  @Override
  public void alignmentChanged(AnnotatedCollectionI collection,
          Map<SequenceI, SequenceCollectionI> hiddenReps)
  {
	  List<SequenceI> seqs = collection.getSequences();
	    for (SequenceI seq : seqs)
	    {
	      if (seq.getHMM() != null)
	      {
	        hmm = seq.getHMM();
	        break;
	      }
	    }

  }



  @Override
  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
  {
	  HiddenMarkovModel markov = null;
	    List<SequenceI> seqs = sg.getSequences();
	    for (SequenceI seq : seqs)
	    {
	      if (seq.getHMM() != null)
	      {
	        markov = seq.getHMM();
	        break;
	      }
	    }
	    HMMERColourScheme colour = new HMMERColourScheme(markov);
	    return colour;

  }

  @Override
  public boolean isApplicableTo(AnnotatedCollectionI ac)
  {
      return true;

  }

  @Override
  public String getSchemeName()
  {

    return JalviewColourScheme.HMMER.name();
  }

  @Override
  public boolean isSimple()
  {
    // TODO Auto-generated method stub
    return false;
  }

}