package jalview.schemes;

import jalview.io.TCoffeeScoreFile;

import java.awt.Color;

/**
 * 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
	};


	byte[][] scoreMatrix = null;

	/**
	 * Initialize the color sheme based on the content of the T-Coffee score file 
	 * 
	 * @param scoreFile
	 */
	public TCoffeeColourScheme(TCoffeeScoreFile scoreFile) {

		scoreMatrix = scoreFile != null ? scoreFile.getScoresArray() : null;

	}

	@Override
	public Color findColour(char c, int j, int sequenceIndex) {

		if( scoreMatrix == null ) {
			return Color.white;
		}
		
		if( sequenceIndex<0  || sequenceIndex >= scoreMatrix.length ) {
			System.out.printf("Sequence index out of range for the T-Coffee color scheme. Index:  %s\n", sequenceIndex);
			return Color.white;
		}

		byte[] seqScores = scoreMatrix[sequenceIndex]; 
		if( j < 0 || j>= seqScores.length ) {
			System.out.printf("Residue index out of range for the T-Coffee color scheme. Sequence %s - residue: %s\n", sequenceIndex, j);
			return Color.white;
		}
		
		byte val = seqScores[j];
		return val >= 0 && val < colors.length ? colors[val] : Color.white;
	}
}