SequencePainter.java

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.AminoAcidAndPosition;
import aliview.sequences.Sequence;

public abstract class SequencePainter implements Runnable{
	private static final Logger logger = Logger.getLogger(SequencePainter.class);
	
	private Sequence seq;
	private int seqYPos;
	private int clipPosY;
	private int xMinSeqPos;
	private int xMaxSeqPos;
	private double seqPerPix;
	private double charWidth;
	private double charHeight;
	private double highDPIScaleFactor;
	private RGBArray clipRGB;
	private AlignmentPane aliPane;
	private Alignment alignment;
	
	
	public SequencePainter(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();
		this.seq = seq;
		this.seqYPos = seqYPos;
		this.clipPosY = clipPosY;
		this.xMinSeqPos = xMinSeqPos;
		this.xMaxSeqPos = xMaxSeqPos;
		this.seqPerPix = seqPerPix;
		this.charWidth = charWidth;
		this.charHeight = charHeight;
		this.highDPIScaleFactor = highDPIScaleFactor;
		this.clipRGB = clipRGB;
		this.aliPane = aliPane;
		this.alignment = alignment;
	}

	public void run(){
		// TODO maybe check before that sequence not is null
		if(seq != null){
			drawSequence(seq, seqYPos, clipPosY, xMinSeqPos, xMaxSeqPos, seqPerPix, charWidth, charHeight, highDPIScaleFactor, clipRGB, aliPane, alignment);
		}
	}
	
	public void drawSequence(Sequence seq, int seqYPos, int clipPosY, int xMin, int xMax, double seqPerPix, double charWidth, double charHeight, double highDPIScaleFactor,
			                  RGBArray clipRGB, AlignmentPane aliPane, Alignment alignment){
		
		// Make sure not outside length of seq
			int seqLength = seq.getLength();
			int clipPosX = 0;
			for(int x = xMin; x < xMax && x >=0 ; x ++){
				int seqXPos = (int)((double)x * seqPerPix);
				if(seqXPos >=0 && seqXPos < seqLength){
					int pixelPosX = (int)(clipPosX*charWidth*highDPIScaleFactor);
					int pixelPosY = (int)(clipPosY*charHeight*highDPIScaleFactor);
					
					if(pixelPosX < clipRGB.getScanWidth() && pixelPosY < clipRGB.getHeight()){
						copyPixels(seq, clipRGB, seqXPos, seqYPos,pixelPosX, pixelPosY, aliPane, alignment);
					}
				}
				clipPosX ++;
		}
	}
	
	
	

	abstract void copyPixels(Sequence seq, RGBArray clipRGB, int seqXPos, int seqYPos, int pixelPosX, int pixelPosY, AlignmentPane aliPane, Alignment alignment);
	
	
}