content: package aliview.color;
  
  import java.awt.Color;
  import java.awt.Font;
  
  import aliview.AminoAcid;
  import aliview.NucleotideUtilities;
  import aliview.alignment.AAHistogram;
  import aliview.alignment.AliHistogram;
  import aliview.alignment.Alignment;
  
  public class DefaultColorScheme implements ColorScheme {
  
  	Color[] baseBackgroundColor;
  	Color[] baseForegroundColor;
  	Color[] baseSelectionBackgroundColor;
  	Color[] baseSelectionForegroundColor;
  	Color[] aminoAcidBackgroundColor;
  	Color[] aminoAcidForegroundColor;
  	Color[] aminoAcidSelectionBackgroundColor;
  	Color[] aminoAcidSelectionForegroundColor;
  	Color baseConsensusBackgroundColor;
  	Color aminoAcidConsensusBackgroundColor;
  
  
  	protected String colorSchemeName = "Default";
  
  	public String getName() {
  		return colorSchemeName;
  	}
  
  	public DefaultColorScheme() {
  
  		this.colorSchemeName = "Default";
  
  
  		baseForegroundColor = new Color[64];
  		baseForegroundColor[NucleotideUtilities.A] = new Color(1,128,1); //Color.green
  		baseForegroundColor[NucleotideUtilities.C] = new Color(1,1,255); //Color.blue
  		baseForegroundColor[NucleotideUtilities.G] = Color.black; 
  		baseForegroundColor[NucleotideUtilities.TU] = new Color(255,1,1); // Color.red
  		baseForegroundColor[NucleotideUtilities.R] = Color.magenta;
  		baseForegroundColor[NucleotideUtilities.Y] = Color.magenta;
  		baseForegroundColor[NucleotideUtilities.M] = Color.magenta;
  		baseForegroundColor[NucleotideUtilities.K] = Color.magenta;
  		baseForegroundColor[NucleotideUtilities.W] = Color.magenta;
  		baseForegroundColor[NucleotideUtilities.S] = Color.magenta;
  		baseForegroundColor[NucleotideUtilities.B] = Color.magenta; 
  		baseForegroundColor[NucleotideUtilities.D] = Color.magenta;
  		baseForegroundColor[NucleotideUtilities.H] = Color.magenta;
  		baseForegroundColor[NucleotideUtilities.V] = Color.magenta;
  		baseForegroundColor[NucleotideUtilities.N] =  Color.magenta;//new Color(180,200,250);
  		baseForegroundColor[NucleotideUtilities.GAP] = Color.LIGHT_GRAY.darker(); 
  		baseForegroundColor[NucleotideUtilities.UNKNOWN] = Color.cyan;
  
  		baseBackgroundColor = new Color[64];
  		baseBackgroundColor[NucleotideUtilities.A] = new Color(90,220,90); 
  		baseBackgroundColor[NucleotideUtilities.C] = new Color(100,100,250);
  		baseBackgroundColor[NucleotideUtilities.G] = new Color(90,90,90); 
  		baseBackgroundColor[NucleotideUtilities.TU] = new Color(245,130,130); 
  		baseBackgroundColor[NucleotideUtilities.R] = Color.white;
  		baseBackgroundColor[NucleotideUtilities.Y] = Color.white;
  		baseBackgroundColor[NucleotideUtilities.M] = Color.white;
  		baseBackgroundColor[NucleotideUtilities.K] = Color.white;
  		baseBackgroundColor[NucleotideUtilities.W] = Color.white;
  		baseBackgroundColor[NucleotideUtilities.S] = Color.white;
  		baseBackgroundColor[NucleotideUtilities.B] = Color.white; 
  		baseBackgroundColor[NucleotideUtilities.D] = Color.white;
  		baseBackgroundColor[NucleotideUtilities.H] = Color.white;
  		baseBackgroundColor[NucleotideUtilities.V] = Color.white;
  		baseBackgroundColor[NucleotideUtilities.N] = Color.white; 
  		baseBackgroundColor[NucleotideUtilities.GAP] = new Color(250,250,250);
  		baseBackgroundColor[NucleotideUtilities.UNKNOWN] = Color.white;
  
  		baseConsensusBackgroundColor =  new Color(240,240,240);
  
  		baseSelectionForegroundColor = new Color[64];
  		baseSelectionForegroundColor[NucleotideUtilities.A]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.A] );
  		baseSelectionForegroundColor[NucleotideUtilities.C]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.C] );
  		baseSelectionForegroundColor[NucleotideUtilities.G]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.G] );
  		baseSelectionForegroundColor[NucleotideUtilities.TU]      =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.TU]);
  		baseSelectionForegroundColor[NucleotideUtilities.R]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.R] );
  		baseSelectionForegroundColor[NucleotideUtilities.Y]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.Y] );
  		baseSelectionForegroundColor[NucleotideUtilities.M]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.M] );
  		baseSelectionForegroundColor[NucleotideUtilities.K]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.K] );
  		baseSelectionForegroundColor[NucleotideUtilities.W]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.W] );
  		baseSelectionForegroundColor[NucleotideUtilities.S]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.S] );
  		baseSelectionForegroundColor[NucleotideUtilities.B]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.B] );
  		baseSelectionForegroundColor[NucleotideUtilities.D]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.D] );
  		baseSelectionForegroundColor[NucleotideUtilities.H]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.H] );
  		baseSelectionForegroundColor[NucleotideUtilities.V]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.V] );
  		baseSelectionForegroundColor[NucleotideUtilities.N]       =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.N] );
  		baseSelectionForegroundColor[NucleotideUtilities.GAP]     =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.GAP]);
  		baseSelectionForegroundColor[NucleotideUtilities.UNKNOWN] =createSelectionForegroundColor(baseForegroundColor[NucleotideUtilities.UNKNOWN]);
  
  
  		baseSelectionBackgroundColor = new Color[64];	
  		baseSelectionBackgroundColor[NucleotideUtilities.A]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.A]);
  		baseSelectionBackgroundColor[NucleotideUtilities.C]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.C]);
  		baseSelectionBackgroundColor[NucleotideUtilities.G]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.G]);
  		baseSelectionBackgroundColor[NucleotideUtilities.TU]      =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.TU]);
  		baseSelectionBackgroundColor[NucleotideUtilities.R]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.R]);
  		baseSelectionBackgroundColor[NucleotideUtilities.Y]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.Y]);
  		baseSelectionBackgroundColor[NucleotideUtilities.M]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.M]);
  		baseSelectionBackgroundColor[NucleotideUtilities.K]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.K]);
  		baseSelectionBackgroundColor[NucleotideUtilities.W]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.W]);
  		baseSelectionBackgroundColor[NucleotideUtilities.S]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.S]);
  		baseSelectionBackgroundColor[NucleotideUtilities.B]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.B]);
  		baseSelectionBackgroundColor[NucleotideUtilities.D]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.D]);
  		baseSelectionBackgroundColor[NucleotideUtilities.H]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.H]);
  		baseSelectionBackgroundColor[NucleotideUtilities.V]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.V]);
  		baseSelectionBackgroundColor[NucleotideUtilities.N]       =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.N]);
  		baseSelectionBackgroundColor[NucleotideUtilities.GAP]     =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.GAP]);
  		baseSelectionBackgroundColor[NucleotideUtilities.UNKNOWN] =  createSelectionColor(baseBackgroundColor[NucleotideUtilities.UNKNOWN]);
  
  
  
  		/*
  		 * 
  		 * This is mesquite color-sceme
  		 * 
  		 */
  		/*
  		aminoAcidBackgroundColor = new Color[255];
  		aminoAcidBackgroundColor[AminoAcid.A.intVal] = new Color(0x82e9ff);
  		aminoAcidBackgroundColor[AminoAcid.C.intVal] = new Color(0xffabff);
  		aminoAcidBackgroundColor[AminoAcid.D.intVal] = new Color(0xaea876);
  		aminoAcidBackgroundColor[AminoAcid.E.intVal] = new Color(0x948f71);
  		aminoAcidBackgroundColor[AminoAcid.F.intVal] = new Color(0x94b6ff);
  		aminoAcidBackgroundColor[AminoAcid.G.intVal] = new Color(0xe306b0);
  		aminoAcidBackgroundColor[AminoAcid.H.intVal] = new Color(0xb914ff);
  		aminoAcidBackgroundColor[AminoAcid.I.intVal] = new Color(0x4f9bff);
  		aminoAcidBackgroundColor[AminoAcid.K.intVal] = new Color(0xa70de3);
  		aminoAcidBackgroundColor[AminoAcid.L.intVal] = new Color(0x0012b8);
  		aminoAcidBackgroundColor[AminoAcid.M.intVal] = new Color(0x5eb5b5);
  		aminoAcidBackgroundColor[AminoAcid.N.intVal] = new Color(0xff000c);
  		aminoAcidBackgroundColor[AminoAcid.P.intVal] = new Color(0x14b86e);
  		aminoAcidBackgroundColor[AminoAcid.Q.intVal] = new Color(0x810d0f);
  		aminoAcidBackgroundColor[AminoAcid.R.intVal] = new Color(0xa172b7);
  		aminoAcidBackgroundColor[AminoAcid.S.intVal] = new Color(0xffdf0a);
  		aminoAcidBackgroundColor[AminoAcid.T.intVal] = new Color(0x781b1e);
  		aminoAcidBackgroundColor[AminoAcid.V.intVal] = new Color(0x2ab528);
  		aminoAcidBackgroundColor[AminoAcid.W.intVal] = new Color(0x9bc186);
  		aminoAcidBackgroundColor[AminoAcid.Y.intVal] = new Color(0xea8f85);
  		aminoAcidBackgroundColor[AminoAcid.STOP.intVal] = Color.black;
  		aminoAcidBackgroundColor[AminoAcid.GAP.intVal] = Color.white;
  		aminoAcidBackgroundColor[AminoAcid.X.intVal] = Color.white;
  		 */
  
  		/*
  		 * 
  		 * This is seaview color-sceme (almost - but I put shades on same color)
  		 * 
  		 */
  		aminoAcidBackgroundColor = new Color[255];
  		aminoAcidBackgroundColor[AminoAcid.A.intVal] = new Color(0x276eb7);
  		aminoAcidBackgroundColor[AminoAcid.C.intVal] = new Color(0xe68080);
  		aminoAcidBackgroundColor[AminoAcid.D.intVal] = new Color(0xcc4dcc);
  		aminoAcidBackgroundColor[AminoAcid.E.intVal] = new Color(0x984097);
  		aminoAcidBackgroundColor[AminoAcid.F.intVal] = new Color(0x1980e6);
  		aminoAcidBackgroundColor[AminoAcid.G.intVal] = new Color(0xe6994d);
  		aminoAcidBackgroundColor[AminoAcid.H.intVal] = new Color(0x19b3b3);
  		aminoAcidBackgroundColor[AminoAcid.I.intVal] = new Color(0x4ea0f3);
  		aminoAcidBackgroundColor[AminoAcid.K.intVal] = new Color(0xe63319);
  		aminoAcidBackgroundColor[AminoAcid.L.intVal] = new Color(0x78a6d5);
  		aminoAcidBackgroundColor[AminoAcid.M.intVal] = new Color(0x0f549b);
  		aminoAcidBackgroundColor[AminoAcid.N.intVal] = new Color(0x19cc19);
  		aminoAcidBackgroundColor[AminoAcid.P.intVal] = new Color(0xcccc00);
  		aminoAcidBackgroundColor[AminoAcid.Q.intVal] = new Color(0x5ced5c);
  		aminoAcidBackgroundColor[AminoAcid.R.intVal] = new Color(0xf6442c);
  		aminoAcidBackgroundColor[AminoAcid.S.intVal] = new Color(0x029602);
  		aminoAcidBackgroundColor[AminoAcid.T.intVal] = new Color(0x45c945);
  		aminoAcidBackgroundColor[AminoAcid.V.intVal] = new Color(0x047df9);
  		aminoAcidBackgroundColor[AminoAcid.W.intVal] = new Color(0x0355a9);
  		aminoAcidBackgroundColor[AminoAcid.Y.intVal] = new Color(0x14c6c8);
  		aminoAcidBackgroundColor[AminoAcid.STOP.intVal] = Color.darkGray;
  		aminoAcidBackgroundColor[AminoAcid.GAP.intVal] = new Color(230,230,230);
  		//aminoAcidBackgroundColor[AminoAcid.GAP.intVal] = Color.white;
  		aminoAcidBackgroundColor[AminoAcid.X.intVal] = Color.white;
  
  		aminoAcidConsensusBackgroundColor = new Color(240,240,240);
  
  		aminoAcidForegroundColor = new Color[255];
  		aminoAcidForegroundColor[AminoAcid.A.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.C.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.D.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.E.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.F.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.G.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.H.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.I.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.K.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.L.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.M.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.N.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.P.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.Q.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.R.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.S.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.T.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.V.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.W.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.Y.intVal] = Color.BLACK;
  		aminoAcidForegroundColor[AminoAcid.STOP.intVal] = Color.CYAN;
  		aminoAcidForegroundColor[AminoAcid.GAP.intVal] = Color.DARK_GRAY;
  		aminoAcidForegroundColor[AminoAcid.X.intVal] = Color.CYAN;
  
  		aminoAcidSelectionBackgroundColor = new Color[255];
  		aminoAcidSelectionBackgroundColor[AminoAcid.A.intVal] = new Color(0x276eb7).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.C.intVal] = new Color(0xe68080).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.D.intVal] = new Color(0xcc4dcc).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.E.intVal] = new Color(0x984097).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.F.intVal] = new Color(0x1980e6).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.G.intVal] = new Color(0xe6994d).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.H.intVal] = new Color(0x19b3b3).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.I.intVal] = new Color(0x4ea0f3).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.K.intVal] = new Color(0xe63319).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.L.intVal] = new Color(0x78a6d5).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.M.intVal] = new Color(0x0f549b).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.N.intVal] = new Color(0x19cc19).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.P.intVal] = new Color(0xcccc00).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.Q.intVal] = new Color(0x5ced5c).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.R.intVal] = new Color(0xf6442c).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.S.intVal] = new Color(0x029602).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.T.intVal] = new Color(0x45c945).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.V.intVal] = new Color(0x047df9).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.W.intVal] = new Color(0x0355a9).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.Y.intVal] = new Color(0x14c6c8).brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.STOP.intVal] = Color.darkGray.brighter();
  		aminoAcidSelectionBackgroundColor[AminoAcid.GAP.intVal] = Color.lightGray;
  		aminoAcidSelectionBackgroundColor[AminoAcid.X.intVal] = Color.lightGray;
  
  		aminoAcidSelectionForegroundColor = new Color[255];
  		aminoAcidSelectionForegroundColor[AminoAcid.A.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.C.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.D.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.E.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.F.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.G.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.H.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.I.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.K.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.L.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.M.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.N.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.P.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.Q.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.R.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.S.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.T.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.V.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.W.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.Y.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.STOP.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.GAP.intVal] = Color.GRAY;
  		aminoAcidSelectionForegroundColor[AminoAcid.X.intVal] = Color.GRAY;
  	}
  
  	public static Color createSelectionColor(Color color) {
  		//return color.darker();
  
  		int r = Math.max(color.getRed() - 85, 0);
  		int g = Math.max(color.getGreen() - 85, 0);
  		int b = Math.max(color.getBlue() - 85, 0);
  		return new Color(r,g,b);
  
  	}
  
  	public static Color createSelectionForegroundColor(Color color) {
  		//	return color.darker();
  
  		int r = Math.min(color.getRed() + 150, 255);
  		int g = Math.min(color.getGreen() + 150, 255);
  		int b = Math.min(color.getBlue() + 150, 255);
  		return new Color(r,g,b); //color.brighter().brighter().brighter().brighter().brighter();//Color.white;//color.brighter(); //Color.white;//
  	}
  
  	public Color getBaseBackgroundColor(int baseValue) {
  		return baseBackgroundColor[baseValue];
  	}
  
  	public Color getBaseForegroundColor(int baseValue) {
  		return baseForegroundColor[baseValue];
  	}
  
  	public Color getBaseSelectionForegroundColor(int baseValue) {
  		return baseSelectionForegroundColor[baseValue];
  	}
  
  	public Color getBaseSelectionBackgroundColor(int baseValue) {
  		return baseSelectionBackgroundColor[baseValue];
  	}
  
  	public Color getAminoAcidBackgroundColor(AminoAcid acid) {
  		return aminoAcidBackgroundColor[acid.intVal];
  	}
  
  	public Color getAminoAcidForgroundColor(AminoAcid acid){
  		return aminoAcidForegroundColor[acid.intVal];
  	}
  
  	public Color getAminoAcidSelectionBackgroundColor(AminoAcid acid) {
  		return aminoAcidSelectionBackgroundColor[acid.intVal];
  	}
  
  	public Color getAminoAcidSelectionForegroundColor(AminoAcid acid) {
  		return aminoAcidSelectionForegroundColor[acid.intVal];
  	}
  
  	public Color getAminoAcidBackgroundColor(AminoAcid acid, int xPos, Alignment aliment) {
  		return getAminoAcidBackgroundColor(acid);
  	}
  
  	public Color getAminoAcidForgroundColor(AminoAcid acid, int xPos, Alignment aliment) {
  		return getAminoAcidForgroundColor(acid);
  	}
  
  	public Color getAminoAcidSelectionBackgroundColor(AminoAcid acid, int xPos, Alignment aliment) {
  		return getAminoAcidSelectionBackgroundColor(acid);
  	}
  
  	public Color getAminoAcidSelectionForegroundColor(AminoAcid acid, int xPos, Alignment aliment) {
  		return getAminoAcidSelectionForegroundColor(acid);
  	}
  
  	public Color getBaseConsensusBackgroundColor() {
  		return baseConsensusBackgroundColor;
  	}
  
  	public Color getAminoAcidConsensusBackgroundColor() {
  		return aminoAcidConsensusBackgroundColor;
  	}
  
  
  	public Color[] getALLCompundColors() {
  		// TODO Auto-generated method stub
  		return null;
  	}
  
  
  
  }
  