content: package aliview.gui.pane;
  
  import org.apache.log4j.Logger;
  
  import aliview.AminoAcid;
  import aliview.NucleotideUtilities;
  import aliview.alignment.Alignment;
  import aliview.alignment.NucleotideHistogram;
  import aliview.sequences.Sequence;
  
  public class SequencePainterNucleotideTranslatedShowNucAndAcid extends SequencePainter {
  
  	private static final Logger logger = Logger.getLogger(SequencePainterNucleotideTranslatedShowNucAndAcid.class);
  
  	public SequencePainterNucleotideTranslatedShowNucAndAcid(Sequence seq,
  			int seqYPos, int clipPosY, int xMinSeqPos, int xMaxSeqPos,
  			double seqPerPix, double charWidth, double charHeight,
  			double highDPIScaleFactor, RGBArray clipRGB, AlignmentPane aliPane,
  			Alignment alignment) {
  		super(seq, seqYPos, clipPosY, xMinSeqPos, xMaxSeqPos, seqPerPix, charWidth,
  				charHeight, highDPIScaleFactor, clipRGB, aliPane, alignment);
  		// TODO Auto-generated constructor stub
  	}
  
  
  
  
  
  	@Override
  	protected void copyPixels(Sequence seq, RGBArray clipArray, int seqXPos, int seqYPos, int pixelPosX, int pixelPosY, AlignmentPane aliPane, Alignment alignment){
  
  		byte residue = seq.getBaseAtPos(seqXPos);
  		AminoAcid acid = seq.getTranslatedAminoAcidAtNucleotidePos(seqXPos);
  		// A small hack
  		if(residue == 0){
  			residue = ' ';
  		}
  
  
  		// adjust colors if selected and temp selection
  		// We have to calculate within this way - because rect.contains(Point) is always returning false on a 0-width or 0 height Rectangle
  		boolean isPointWithinSelectionRect = false;
  		if(alignment.getTempSelection() != null){
  			if(seqXPos <= alignment.getTempSelection().getMaxX() && seqXPos >= alignment.getTempSelection().getMinX() && seqYPos <= alignment.getTempSelection().getMaxY() && seqYPos >= alignment.getTempSelection().getMinY()){
  				isPointWithinSelectionRect = true;
  			}
  		}
  		boolean isSelected = false;
  		if(seq.isBaseSelected(seqXPos) || (alignment.getTempSelection() != null && isPointWithinSelectionRect)){
  			isSelected = true;
  		}
  
  		boolean isSecondPos = false;
  		if(seq.isCodonSecondPos(seqXPos)){
  			isSecondPos = true;
  		}
  
  		TranslationCharPixelsContainer pixContainerToUse = aliPane.charPixTranslationAndNucDefault;
  		if(! aliPane.isDrawAminoAcidCode()){
  			if(isSecondPos){
  				if(isSelected){
  					pixContainerToUse = aliPane.charPixTranslationAndNucSelected;
  				}else{
  					pixContainerToUse = aliPane.charPixTranslationAndNucDefault;
  				}
  			}else{
  				if(isSelected){
  					pixContainerToUse = aliPane.charPixTranslationAndNucSelectedNoAALetter;
  				}else{
  					pixContainerToUse = aliPane.charPixTranslationAndNucDefaultNoAALetter;
  				}	
  			}
  		}else{
  			if(isSecondPos){
  				if(isSelected){
  					pixContainerToUse = aliPane.charPixTranslationAndNucDominantNucSelected;
  				}else{
  					pixContainerToUse = aliPane.charPixTranslationAndNucDominantNuc;
  				}
  			}else{
  				if(isSelected){
  					pixContainerToUse = aliPane.charPixTranslationAndNucDominantNucNoAALetterSelected;
  				}else{
  					pixContainerToUse = aliPane.charPixTranslationAndNucDominantNucNoAALetter;
  				}	
  			}
  		}
  
  		RGBArray newPiece = pixContainerToUse.getRGBArray(acid, residue);
  
  
  		try {
  			ImageUtils.insertRGBArrayAt(pixelPosX, pixelPosY, newPiece, clipArray);
  		} catch (Exception e) {
  			logger.info("clipX" + pixelPosX);
  			logger.info("clipY" + pixelPosY);
  		}
  	}
  
  }
  