package jalview.schemes;

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

import java.awt.Color;
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 new Color(255, 255, 255);
    }
    return findColour(symbol, position);
  }

  public Color findColour(char symbol, int position)
  {


    Double probability;
    probability = hmm.getMatchEmissionProbability(position, symbol);
    // Double redModifier = Math.pow(probability, 0.9);
    Double doubleGreenModifier;
    float greenModifier;
    if (probability < 0.5)
    {
      doubleGreenModifier = probability;
      greenModifier = doubleGreenModifier.floatValue();
    }
    else
    {
      doubleGreenModifier = Math.pow(probability, 1 / 1.9);
      greenModifier = doubleGreenModifier.floatValue();
    }
    // Double blueModifier = Math.pow(probability, 0.9);
    return new Color(1f, 1f - greenModifier, 0.f);

  }

  @Override
  public void alignmentChanged(AnnotatedCollectionI collection,
          Map<SequenceI, SequenceCollectionI> hiddenReps)
  {

    collection.setHMM(hmm);
  }

  @Override
  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
  {
    
    
    
    

    HMMERColourScheme markov = new HMMERColourScheme(sg.getHMM());
    return markov;
  }

  @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;
  }

}