/*
* Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
*
* 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.
*
* THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
* WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
* WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
* PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
* OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
* TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
* OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
* ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
* THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
* SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*/
/*
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*/
package org.broad.igv.renderer;
//~--- non-JDK imports --------------------------------------------------------
import org.broad.igv.data.rnai.RNAIGeneScore;
import org.broad.igv.data.rnai.RNAIHairpinValue;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.track.RenderContext;
import org.broad.igv.track.Track;
import java.awt.*;
import java.util.List;
/**
* @author jrobinso
*/
public class RNAiBarChartRenderer extends XYPlotRenderer {
/**
* Render the track in the given rectangle.
*
* @param track
* @param locusScores
* @param context
* @param trackRect
*/
@Override
public void renderScores(Track track, List<LocusScore> locusScores, RenderContext context,
Rectangle trackRect) {
// Experimental -- adjust the rectangle to maintain a buffer (space) between tracks. The
// settings (20% with 10 pixel maximum) should be adjustable.
double buffer = Math.min(trackRect.getHeight() * 0.2, 10);
Rectangle drawingRect = new Rectangle(trackRect);
drawingRect.y = (int) (trackRect.getY() + buffer);
drawingRect.height = (int) (trackRect.height - (drawingRect.y - trackRect.getY()));
// The starting location (origin) in bp (base pairs) of the current view
double origin = context.getOrigin();
// The locaction scale in bp / pixel of the current view
double locScale = context.getScale();
// The axis definition defines the scale of the y axis (minimum, base, and maximum values)
DataRange axisDefinition = track.getDataRange();
// Calculate the certical (Y) position in pixels of the base value.
int baseY = computeYPixelValue(drawingRect, axisDefinition, axisDefinition.getBaseline());
for (LocusScore score : locusScores) {
// We'll have to case this score to an RNAiGeneScore here for now. This is not
// particularly safe and should be redesigned to eliminate the need to cache.
RNAIGeneScore rnaiScore = (RNAIGeneScore) score;
// Note -- don't cast these to an int until the range is checked.
// could get an overflow.
double pX = ((score.getStart() - origin) / locScale);
double dx = Math.ceil((score.getEnd() - score.getStart()) / locScale) + 1;
// Don't bother drawing if the data is not in range
if ((pX + dx) >= 0 && (pX <= drawingRect.getMaxX())) {
float dataY = score.getScore();
// Draw the gene score
if (!Float.isNaN(dataY)) {
int pY = computeYPixelValue(drawingRect, axisDefinition, dataY);
drawDataPoint(new Color(57, 67, 201), (int) dx, (int) pX, baseY, pY,
context);
}
// Draw the hairpin values, if any
if (rnaiScore.getHairpinValues() != null) {
// my blue color new Color(195, 211, 237)
for (RNAIHairpinValue hValue : rnaiScore.getHairpinValues()) {
int scoreY = computeYPixelValue(drawingRect,
axisDefinition,
hValue.getScoreMean());
context.getGraphic2DForColor(new Color(95, 120, 200).brighter()).drawLine(
(int) pX, scoreY, ((int) pX + (int) dx) - 1, scoreY);
}
}
}
}
}
@Override
/**
* Render a data point, in this case as a bar.
*/
protected void drawDataPoint(Color graphColor, int dx, int pX, int baseY, int pY,
RenderContext context) {
if (pY > baseY) {
context.getGraphic2DForColor(graphColor).fillRect(pX, baseY, dx, pY - baseY);
} else {
context.getGraphic2DForColor(graphColor).fillRect(pX, pY, dx, baseY - pY);
}
// }
}
public String getDisplayName() {
return "RNAi BarChart";
}
}