/*
* 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.feature.bionano;
import org.broad.igv.feature.IGVFeature;
import org.broad.igv.renderer.FeatureRenderer;
import org.broad.igv.track.RenderContext;
import org.broad.igv.track.Track;
import org.broad.igv.ui.FontManager;
import org.broad.igv.ui.IGV;
import java.awt.*;
import java.awt.geom.Arc2D;
import java.util.List;
/**
* Created by jrobinson on 9/17/15.
*/
public class SMAPRenderer extends FeatureRenderer {
static final int BLOCK_HEIGHT = 14;
@Override
public void render(List<IGVFeature> featureList, RenderContext context, Rectangle trackRectangle, Track track) {
double origin = context.getOrigin();
double locScale = context.getScale();
for (IGVFeature feature : featureList) {
// Note -- don't cast these to an int until the range is checked.
// could get an overflow.
double pixelStart = Math.max(trackRectangle.x, ((feature.getStart() - origin) / locScale));
double pixelEnd = Math.min(trackRectangle.x + trackRectangle.width, ((feature.getEnd() - origin) / locScale));
if (pixelEnd < trackRectangle.x) continue;
if (pixelStart > (trackRectangle.x + trackRectangle.width)) break;
Color color = feature.getColor();
if (color == null) {
color = track.getColor();
}
Graphics2D g = context.getGraphic2DForColor(color);
int y = trackRectangle.y + trackRectangle.height / 2;
if (feature instanceof SMAPPairedFeature) {
SMAPFeature feature1 = ((SMAPPairedFeature) feature).feature1;
SMAPFeature feature2 = ((SMAPPairedFeature) feature).feature2;
int x1 = (int) Math.max(trackRectangle.x, ((feature1.getEnd() - origin) / locScale));
int x2 = (int) Math.min(trackRectangle.x + trackRectangle.width, ((feature2.getStart() - origin) / locScale));
g.drawLine(x1, y, x2, y);
drawSMapFeature(g, trackRectangle, origin, locScale, y, feature1);
drawSMapFeature(g, trackRectangle, origin, locScale, y, feature2);
} else {
drawSMapFeature(g, trackRectangle, origin, locScale, y, feature);
}
}
}
public void drawSMapFeature(Graphics2D g, Rectangle trackRectangle, double origin, double locScale, int y, IGVFeature feature) {
double pixelStart = Math.max(trackRectangle.x, ((feature.getStart() - origin) / locScale));
double pixelEnd = Math.min(trackRectangle.x + trackRectangle.width, ((feature.getEnd() - origin) / locScale));
// If the any part of the feature fits in the
// Track rectangle draw it
if (pixelEnd >= trackRectangle.getX() && pixelStart <= trackRectangle.getMaxX()) {
// Set color used to draw the feature
int w = (int) (pixelEnd - pixelStart);
if (w < 3) {
w = 3;
pixelStart--;
}
g.fillRect((int) pixelStart, y - BLOCK_HEIGHT / 2, w, BLOCK_HEIGHT);
}
}
}