org.snpeff.svg.SvgBnd Maven / Gradle / Ivy

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

import org.snpeff.interval.VariantBnd;

/**
 * Create an SVG representation of a BND (translocation) variant
 *
 *
 * In a VCF file, there are four possible translocations (BND) entries:
 *
 * 				REF ALT Meaning
 * 	type 1:		s t[p[ piece extending to the right of p is joined after t
 * 	type 2:		s t]p] reverse comp piece extending left of p is joined after t
 * 	type 3:		s ]p]t piece extending to the left of p is joined before t
 * 	type 4:		s [p[t reverse comp piece extending right of p is joined before t
 *
 */
public class SvgBnd extends Svg {

	public static final int BND_CURL_SIZE = 50;

	VariantBnd varBnd;
	Svg svgTr1, svgTr2;

	public SvgBnd(VariantBnd varBnd, Svg svgTr1, Svg svgTr2) {
		super();
		this.varBnd = varBnd;
		this.svgTr1 = svgTr1;
		this.svgTr2 = svgTr2;
		lineStrokeWidth = 10;
		lineColor = "#ff00ff";
	}

	/**
	 * Create a 'bnd type 1'
	 */
	String bndType1() {
		StringBuilder sb = new StringBuilder();
		int pos1 = pos1();
		double x1 = svgTr1.pos2coord(pos1);
		double y1 = svgTr1.baseY + svgTr1.rectHeight / 2;

		int pos2 = pos2();
		double x2 = svgTr2.pos2coord(pos2);
		double y2 = svgTr2.baseY + svgTr2.rectHeight / 2;

		double d = lineStrokeWidth / 2;

		if (x1 < x2) {
			double x3 = (x1 + x2) / 2;
			sb.append(line(x1, y1, x3, y1));
			sb.append(line(x3, y1 - d, x3, y2 + d));
			sb.append(line(x2, y2, x3, y2));
		} else {
			double x1e = Math.min(sizeX, x1 + BND_CURL_SIZE);
			double x2e = Math.max(0, x2 - BND_CURL_SIZE);
			double ymid = (y1 + y2) / 2;
			sb.append(line(x1, y1, x1e, y1));
			sb.append(line(x1e, y1 - d, x1e, ymid + d));
			sb.append(line(x1e, ymid, x2e, ymid));
			sb.append(line(x2e, y2 + d, x2e, ymid - d));
			sb.append(line(x2, y2, x2e, y2));
		}

		return sb.toString();
	}

	/**
	 * Create a 'bnd type 2'
	 */
	String bndType2() {
		StringBuilder sb = new StringBuilder();
		int pos1 = pos1();
		double x1 = svgTr1.pos2coord(pos1);
		double y1 = svgTr1.baseY + svgTr1.rectHeight / 2;

		int pos2 = pos2();
		double x2 = svgTr2.pos2coord(pos2);
		double y2 = svgTr2.baseY + svgTr2.rectHeight / 2;

		double x3 = Math.min(sizeX, Math.max(x1, x2) + BND_CURL_SIZE);

		double d = lineStrokeWidth / 2;

		sb.append(line(x1, y1, x3, y1));
		sb.append(line(x3, y1 - d, x3, y2 + d));
		sb.append(line(x2, y2, x3, y2));
		return sb.toString();
	}

	/**
	 * Create a 'bnd type 3'
	 */
	String bndType3() {
		StringBuilder sb = new StringBuilder();
		int pos1 = pos1();
		double x1 = svgTr1.pos2coord(pos1);
		double y1 = svgTr1.baseY + svgTr1.rectHeight / 2;

		int pos2 = pos2();
		double x2 = svgTr2.pos2coord(pos2);
		double y2 = svgTr2.baseY + svgTr2.rectHeight / 2;

		double d = lineStrokeWidth / 2;

		if (x2 < x1) {
			double x3 = (x1 + x2) / 2;
			sb.append(line(x1, y1, x3, y1));
			sb.append(line(x3, y1 - d, x3, y2 + d));
			sb.append(line(x2, y2, x3, y2));
		} else {
			double x1e = Math.max(0, x1 - BND_CURL_SIZE);
			double x2e = Math.min(sizeX, x2 + BND_CURL_SIZE);
			double ymid = (y1 + y2) / 2;
			sb.append(line(x1, y1, x1e, y1));
			sb.append(line(x1e, y1 - d, x1e, ymid + d));
			sb.append(line(x1e, ymid, x2e, ymid));
			sb.append(line(x2e, y2 + d, x2e, ymid - d));
			sb.append(line(x2, y2, x2e, y2));
		}

		return sb.toString();
	}

	/**
	 * Create a 'bnd type 4'
	 */
	String bndType4() {
		StringBuilder sb = new StringBuilder();
		int pos1 = pos1();
		double x1 = svgTr1.pos2coord(pos1);
		double y1 = svgTr1.baseY + svgTr1.rectHeight / 2;

		int pos2 = pos2();
		double x2 = svgTr2.pos2coord(pos2);
		double y2 = svgTr2.baseY + svgTr2.rectHeight / 2;

		double x3 = Math.max(0, Math.min(x1, x2) - BND_CURL_SIZE);

		double d = lineStrokeWidth / 2;

		sb.append(line(x1, y1, x3, y1));
		sb.append(line(x3, y1 - d, x3, y2 + d));
		sb.append(line(x2, y2, x3, y2));
		return sb.toString();
	}

	int pos1() {
		return varBnd.getStart();
	}

	int pos2() {
		return varBnd.getEndPoint().getStart();
	}

	@Override
	public String toString() {
		if (!varBnd.isBefore()) {
			if (!varBnd.isLeft()) return bndType1();
			return bndType2();
		}

		if (varBnd.isLeft()) return bndType3();
		return bndType4();
	}

}