/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.plugin.mongovariant;
import org.broad.igv.renderer.GraphicUtils;
import org.broad.igv.track.RenderContext;
import org.broad.igv.ui.FontManager;
import org.broad.igv.variant.Variant;
import org.broad.igv.variant.VariantRenderer;
import org.broad.igv.variant.VariantTrack;
import org.broadinstitute.gatk.tools.walkers.na12878kb.core.TruthStatus;
import java.awt.*;
import java.awt.geom.Rectangle2D;
import java.util.HashMap;
/**
* User: jacob
* Date: 2013-Jan-28
*/
public class VariantReviewRenderer extends VariantRenderer {
private static HashMap<TruthStatus, String> symbolMap;
private static final String REVIEWED_STRING = "*";
private static Graphics2D stringGraphics;
private static final int FONT_SIZE = 10;
static{
symbolMap = new HashMap<TruthStatus, String>(4);
symbolMap.put(TruthStatus.TRUE_POSITIVE, "TP");
symbolMap.put(TruthStatus.FALSE_POSITIVE, "FP");
symbolMap.put(TruthStatus.UNKNOWN, "?");
symbolMap.put(TruthStatus.SUSPECT, "S");
}
public VariantReviewRenderer(VariantTrack track) {
super(track);
}
@Override
protected boolean defaultUseAlpha() {
return false;
}
@Override
public void renderSiteBand(Variant variant, Rectangle bandRectangle, int pixelX, int xWidth, RenderContext context) {
super.renderSiteBand(variant, bandRectangle, pixelX, xWidth, context);
if(variant instanceof MongoVCFVariant){
MongoVCFVariant mvc = (MongoVCFVariant) variant;
TruthStatus truthStatus = mvc.getTruthStatus();
int bandY = calculateBottomYSiteBand(bandRectangle);
int bandHeight = calculateBarHeightSiteBand(bandRectangle);
Graphics2D g = context.getGraphic2DForColor(Color.black);
g.setFont(FontManager.getFont(FONT_SIZE).deriveFont(Font.BOLD));
String symbol = symbolMap.get(truthStatus);
symbol = symbol != null ? symbol : "";
GraphicUtils.drawCenteredText(symbol, pixelX, bandY - bandHeight, xWidth, bandHeight, g, Color.white);
if(mvc.isReviewed()){
g = context.getGraphic2DForColor(Color.red);
g.setFont(FontManager.getFont(FONT_SIZE + 4).deriveFont(Font.BOLD));
FontMetrics fontMetrics = g.getFontMetrics();
Rectangle2D textBounds = fontMetrics.getStringBounds(REVIEWED_STRING, g);
g.drawString(REVIEWED_STRING, pixelX - (int) (textBounds.getWidth() / 2), bandY - bandHeight + (int) (textBounds.getHeight() / 2));
}
}
}
}