/*
* 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.peaks;
import org.broad.igv.data.DataSource;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.renderer.BarChartRenderer;
import org.broad.igv.renderer.Renderer;
import org.broad.igv.track.RenderContext;
import org.broad.igv.track.Track;
import org.broad.igv.ui.color.ColorUtilities;
import java.awt.*;
import java.util.List;
/**
* @author jrobinso
* @date Apr 23, 2011
*/
public class PeakRenderer implements Renderer<LocusScore> {
BarChartRenderer chartRenderer = new BarChartRenderer();
public static final int SIGNAL_CHART_HEIGHT = 15;
public void render(List<LocusScore> peakList, RenderContext context, Rectangle rect, Track t) {
PeakTrack track = (PeakTrack) t;
final double locScale = context.getScale();
final double origin = context.getOrigin();
int lastPX = -1;
double pXMin = rect.getMinX();
double pXMax = rect.getMaxX();
Color fgColor = track.getColor();
Graphics2D borderGraphics = context.getGraphic2DForColor(Color.black);
String chr = context.getChr();
int contextStart = (int) context.getOrigin();
int contextEnd = (int) context.getEndLocation();
int zoom = context.getZoom();
if (PeakTrack.isShowPeaks()) {
int h = track.bandHeight;
int peakHeight = PeakTrack.isShowSignals() ? track.peakHeight : h;
for (LocusScore ls : peakList) {
Peak peak = (Peak) ls;
int start = peak.getStart();
int end = peak.getEnd();
int pX = (int) ((start - origin) / locScale);
int dX = (int) Math.max(2, (end - start) / locScale);
if (pX + dX < pXMin) continue;
if (pX > pXMax) break;
float score = peak.getCombinedScore();
if (PeakTrack.getColorOption() == PeakTrack.ColorOption.FOLD_CHANGE) {
score = peak.getDynamicScore();
}
int top = rect.y + 1;
if (PeakTrack.isShowSignals()) {
top += track.signalHeight;
}
if (PeakTrack.animate) {
int step = track.getTimeStep();
float[] timeScores = peak.getTimeScores();
int idx = Math.min(step, timeScores.length - 1);
score = timeScores[idx];
drawPeak(context, fgColor, pX, dX, top, peakHeight, score, PeakTrack.getColorOption());
} else {
if (track.getDisplayMode() == Track.DisplayMode.EXPANDED) {
float[] timeScores = peak.getTimeScores();
for (int i = 0; i < timeScores.length; i++) {
score = timeScores[i];
drawPeak(context, fgColor, pX, dX, top, peakHeight, score, PeakTrack.getColorOption());
top += h;
}
} else {
drawPeak(context, fgColor, pX, dX, top, peakHeight, score, PeakTrack.getColorOption());
// float[] timeScores = peak.getTimeScores();
// if (dX > 10 && timeScores.length > 1) {
// Graphics2D gLine = context.getGraphic2DForColor(Color.black);
// gLine.setRenderingHint(RenderingHints.KEY_ANTIALIASING,IGVPreferences.getInstance().getAntiAliasingHint());
// double deltaX = ((double) dX / (timeScores.length - 1));
// double scaleY = peakHeight / 200.0;
// int bottomY = top + peakHeight;
// int lastX = pX;
// int lastY = (bottomY - (int) (scaleY * timeScores[0]));
// for (int i = 1; i < timeScores.length; i++) {
// score = timeScores[i];
// int x = pX + (int) (i * deltaX);
// int y = Math.max(top + 2, (int) (bottomY - (int) (scaleY * timeScores[i])));
// gLine.drawLine(lastX, lastY, x, y);
// lastX = x;
// lastY = y;
//
// }
// }
}
}
}
}
if (PeakTrack.isShowSignals() && track.getSignalPath() != null) {
int h = track.bandHeight;
int signalHeight = PeakTrack.isShowPeaks() ? track.signalHeight : h;
if (PeakTrack.animate) {
int step = track.getTimeStep();
DataSource[] timeSignalSources = track.getTimeSignalSources();
int idx = Math.min(step, timeSignalSources.length - 1);
DataSource src = timeSignalSources[idx];
if (src != null) {
int top = rect.y + 2;List<LocusScore> timeSignals = src.getSummaryScoresForRange(chr, contextStart, contextEnd, zoom);
Rectangle timeSignalRect = new Rectangle(rect.x, top, rect.width, signalHeight - 1);
chartRenderer.render(timeSignals, context, timeSignalRect, track);
}
} else {
if (track.getDisplayMode() == Track.DisplayMode.EXPANDED) {
DataSource[] timeSignalSources = track.getTimeSignalSources();
if (timeSignalSources != null) {
int top = rect.y + 2;
for (int i = 0; i < timeSignalSources.length; i++) {
DataSource src = timeSignalSources[i];
if (src != null) {
List<LocusScore> timeSignals = src.getSummaryScoresForRange(chr, contextStart, contextEnd, zoom);
Rectangle timeSignalRect = new Rectangle(rect.x, top, rect.width, signalHeight - 1);
chartRenderer.render(timeSignals, context, timeSignalRect, track);
}
top += h;
}
}
} else {
final PeakTrack.WrappedDataSource signalSource = track.getSignalSource(chr, contextStart, contextEnd, zoom);
if (signalSource != null) {
List<LocusScore> signals = signalSource.getSummaryScoresForRange(chr, contextStart, contextEnd, zoom);
Rectangle signalRect = new Rectangle(rect.x, rect.y + 1, rect.width, signalHeight - 1);
chartRenderer.render(signals, context, signalRect, track);
}
}
}
}
if (track.getDisplayMode() == Track.DisplayMode.EXPANDED) {
borderGraphics.drawLine(rect.x, rect.y, rect.x + rect.width, rect.y);
borderGraphics.drawLine(rect.x, rect.y + rect.height, rect.x + rect.width, rect.y + rect.height);
}
}
private void drawPeak(RenderContext context, Color fgColor,
int pX, int dX, int top, int h, float score, PeakTrack.ColorOption option) {
Color c = getColor(fgColor, score, option);
Graphics2D g = context.getGraphic2DForColor(c);
g.fillRect(pX, top + 1, dX, h - 2);
}
private Color getColor(Color fgColor, float score, PeakTrack.ColorOption option) {
Color c = null;
float alpha = 1.0f;
if (option == PeakTrack.ColorOption.SCORE) {
// scale is 1 -> 100
int shadeStep = (int) (score / 10);
alpha = Math.max(0.2f, (Math.min(1.0f, shadeStep * 0.1f)));
} else if (option == PeakTrack.ColorOption.FOLD_CHANGE) {
// Scale is 1.58 -> 3.3 log2
if (Math.abs(score) < 1.58) {
alpha = 1f;
fgColor = Color.gray;
} else {
// vary alpha from .3 -> 1 over range 3.3 -> 1.58 in steps of 10
int shadeStep = (int) ((Math.abs(score) - 1.58) / (3.3 - 1.58) * 10);
alpha = Math.max(0.3f, (Math.min(1f, 0.3f + shadeStep * 0.1f)));
fgColor = (score < 0 ? Color.blue : Color.red);
}
}
c = ColorUtilities.getCompositeColor(fgColor, alpha);
//}
return c;
}
}