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Variant annotation and effect prediction package.
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package org.snpeff.svg;

import org.snpeff.interval.Cds;
import org.snpeff.interval.Exon;
import org.snpeff.interval.Gene;
import org.snpeff.interval.IntervalAndSubIntervals;
import org.snpeff.interval.Intron;
import org.snpeff.interval.Marker;
import org.snpeff.interval.Transcript;

/**
 * Create an SVG representation of a Marker
 */
public class Svg {

	public static final int DEFAULT_SIZE_X = 1000;
	public static final int DEFAULT_SIZE_Y = 1000;
	public static final int DEFAULT_BASE_Y = 10;

	public static final String LINE_COLOR_STROKE = "#000000";
	public static final int LINE_STROKE_WIDTH = 1;

	public static final String RECT_COLOR_FILL = "#FFFFFF";
	public static final String RECT_COLOR_STROKE = "#000000";
	public static final int RECT_HEIGHT = 20;
	public static final int RECT_STROKE_WIDTH = 1;

	public static final int TEXT_SIZE = 10;
	public static final String TEXT_STYLE = "font-family: Arial; font-size:" + TEXT_SIZE + ";";

	public static boolean debug = false;

	int baseY;
	int lineStrokeWidth;
	String lineColor;
	Marker m;
	int nextBaseY; // BaseY for next item
	int posStart, posEnd; // Chromosome positions
	int rectHeight;
	String rectColorFill;
	String rectColorStroke;
	double scaleX;
	int sizeX, sizeY; // Canvas size

	public static Svg factory(Marker m, Svg svg) {
		switch (m.getType()) {
		case EXON:
			return new SvgExon((Exon) m, svg);

		case CDS:
			return new SvgCds((Cds) m, svg);

		case INTRON:
			return new SvgIntron((Intron) m, svg);

		case GENE:
			return new SvgGene((Gene) m, svg);

		case TRANSCRIPT:
			return new SvgTranscript((Transcript) m, svg);

		default:
			return new Svg(m, svg);
		}
	}

	public Svg() {
		sizeX = DEFAULT_SIZE_X;
		sizeY = DEFAULT_SIZE_Y;
		baseY = DEFAULT_BASE_Y;

		lineStrokeWidth = LINE_STROKE_WIDTH;
		lineColor = LINE_COLOR_STROKE;

		rectColorFill = RECT_COLOR_FILL;
		rectColorStroke = RECT_COLOR_STROKE;
		rectHeight = RECT_HEIGHT;
	}

	public Svg(Marker m, Svg svg) {
		this();
		this.m = m;

		if (svg != null) {
			posStart = svg.posStart;
			posEnd = svg.posEnd;
			scaleX = svg.scaleX;
			baseY = svg.nextBaseY;
		} else setScaleX();

		nextBaseY = baseY + RECT_HEIGHT * 2;
	}

	public String close() {
		return "\n";
	}

	double end() {
		return (m.getEnd() - posStart) * scaleX;
	}

	public String hline(int y) {
		return line(start(), baseY + y, end(), baseY + y);
	}

	public String id() {
		double y = baseY - rectHeight / 2;
		return text(start(), y, m.getId());
	}

	String line(double x1, double y1, double x2, double y2) {
		String lineStyle = "stroke:" + lineColor //
				+ ";stroke-width:" + lineStrokeWidth //
		;

		return "\n";
	}

	@SuppressWarnings("rawtypes")
	public String marker() {
		StringBuilder sb = new StringBuilder();
		sb.append(rectangle());

		if (m instanceof IntervalAndSubIntervals) {
			IntervalAndSubIntervals msubs = (IntervalAndSubIntervals) m;
			for (Object o : msubs) {
				Marker sub = (Marker) o;
				Svg svg = factory(sub, this);
				sb.append("\t" + svg);
			}
		}

		return sb.toString();
	}

	public String markerId() {
		return marker() + id();
	}

	public String open() {
		return "