/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
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
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));
}
}
}
}