package jalview.schemes;

import jalview.analysis.SequenceIdMatcher;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.io.TCoffeeScoreFile;

import java.awt.Color;
import java.util.ArrayList;
import java.util.IdentityHashMap;
import java.util.TreeMap;

/**
 * Defines the color score for T-Coffee MSA 
 * <p>
 * See http://tcoffee.org
 * 
 * 
 * @author Paolo Di Tommaso
 *
 */
public class TCoffeeColourScheme extends ResidueColourScheme {

	static final Color[] colors = {
		new Color( 102, 102, 255 ),	// #6666FF
		new Color( 0, 255, 0),		// #00FF00
		new Color( 102, 255, 0),	// #66FF00
		new Color( 204, 255, 0),	// #CCFF00
		new Color( 255, 255, 0),	// #FFFF00
		new Color( 255, 204, 0),	// #FFCC00
		new Color( 255, 153, 0),	// #FF9900
		new Color( 255, 102, 0),	// #FF6600
		new Color( 255, 51, 0), 	// #FF3300
		new Color( 255, 34, 0)		// #FF2000
	};


	IdentityHashMap<SequenceI, Color[]> seqMap;
	/**
	 * the color scheme needs to look at the alignment to get and cache T-COFFEE scores 
	 * 
	 * @param alignment - annotated sequences to be searched
	 */
	public TCoffeeColourScheme(AnnotatedCollectionI alignment) {
	  alignmentChanged(alignment);
	}
	@Override public void alignmentChanged(AnnotatedCollectionI alignment)
	{
          // assume only one set of TCOFFEE scores - but could have more than one potentially.
          ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
          // Search alignment to get all tcoffee annotation and pick one set of annotation to use to colour seqs.
          seqMap = new IdentityHashMap<SequenceI, Color[]>();
          int w=0;
          for (AlignmentAnnotation al:alignment.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
          {
            if (al.sequenceRef!=null && !al.belowAlignment)
            {
              annots.add(al);
              if (w<al.annotations.length)
              {
                w=al.annotations.length;
              }
              Color[] scores=new Color[al.annotations.length];
              int i=0;
              for (Annotation an:al.annotations)
              {
                scores[i++]=(an!=null) ? an.colour : Color.white;
              }
              seqMap.put(al.sequenceRef, scores);
            }
          }
    // TODO: compute average colour for each symbol type in each column - gives
    // a second order colourscheme for colouring a sequence logo derived from
    // the alignment (colour reflects quality of alignment for each residue
    // class)
	}
	@Override
	public Color findColour(char c, int j, SequenceI seq) {
          Color[] cols;

	  if( seqMap==null || (cols=seqMap.get(seq))==null) {
//      see above TODO about computing a colour for each residue in each column:	    cc = _rcols[i][indexFor[c]];
	    return Color.white;
	  }
	  
	  if( j < 0 || j>= cols.length ) {
	    return Color.white;
	  }
	  return cols[j];
	}
}