/*
* 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.renderer;
import org.broad.igv.data.rnai.RNAIGeneScore;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.track.RenderContext;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackType;
import java.awt.*;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import static org.broad.igv.prefs.Constants.CHART_SHOW_ALL_HEATMAP;
/**
* @author jrobinso
*/
public class HeatmapRenderer extends DataRenderer {
public String getDisplayName() {
return "Heatmap";
}
/**
* Render the data track as a heat map.
* <p/>
* This method has gotten quite complicated, most of it from the option to join adjacent
* copy number segments.
*
* @param track
* @param scores
* @param context
* @param rect
*/
public void renderScores(Track track, List<LocusScore> scores, RenderContext context, Rectangle rect) {
ContinuousColorScale colorScale = track.getColorScale();
double origin = context.getOrigin();
double locScale = context.getScale();
Color bgColor = colorScale.getNoDataColor();
context.getGraphic2DForColor(bgColor).fill(rect);
boolean showAllFeatures = PreferencesManager.getPreferences().getAsBoolean(CHART_SHOW_ALL_HEATMAP);
double maxX = rect.getMaxX();
int minY = (int) rect.getMinY();
int height = (int) rect.getHeight();
int lastPEnd = 0;
int lastPStart = 0;
int lastW = 0;
for (LocusScore score : scores) {
if (lastPStart > maxX) {
break;
}
// Note -- don't cast these to an int until the range is checked,
// otherwise could get an overflow.
float fStart = (float) ((score.getStart() - origin) / locScale);
float fEnd = (float) ((score.getEnd() - origin) / locScale);
// float fw = fEnd - fStart;
int pStart = (int) fStart;
int pEnd = (int) fEnd;
int min;
if(showAllFeatures) {
min = 1;
} else {
min = Math.min(pStart - lastPEnd, 1);
}
int w = Math.max(min, pEnd - pStart);
float dataY = track.logScaleData(score.getScore());
Color graphColor = colorScale.getColor(dataY);
if ((pStart + w) >= 0 && (lastPStart <= maxX)) {
// Minimum width for DNA methylation
if(track.getTrackType() == TrackType.DNA_METHYLATION) {
if(w < 6) {
int pMid = (pStart + pEnd) / 2;
pStart = pMid - 3;
w = 6;
}
}
// This test handles the rather pathological case where the previous feature was 1 pixel wide, and
// the current feature overlaps it because of roundoff error when scaling.
else if (pStart < lastPEnd && w > 1 && lastW == 1) {
pStart++;
w--;
}
// TODo The instanceof test is very very ugly. Special RNAi treatment
// Refactor to generalize "confidence" for all datasets
if (!Float.isNaN(dataY)) {
if (score instanceof RNAIGeneScore) {
RNAIGeneScore rnaiScore = (RNAIGeneScore) score;
if (rnaiScore.getConfidence() < 2) {
graphColor = getLowConfColor(context.getZoom());
}
}
Graphics2D g2D = context.getGraphic2DForColor(graphColor);
if (pStart < maxX) {
// Clip at edges
int pLeft = Math.max(rect.x, pStart);
int pRight = Math.min(rect.x + rect.width, pStart + w);
int adjustedW = pRight - pLeft;
g2D.fillRect(pLeft, minY, adjustedW, height);
}
} // End special RNAi treagment
}
lastPStart = pStart;
lastPEnd = pStart + w;
lastW = w;
}
}
/**
* Return the color indicating a low confdence score as a function of zoom level. Currently
* this is only used with RNAi data.
*
* @param zoom
* @return
*/
private static Color getLowConfColor(int zoom) {
Color lowConfColor = lowConfColorCache.get(zoom);
if (lowConfColor == null) {
int value = 225 - Math.min(70, zoom * 10);
lowConfColor = new Color(value, value, value);
lowConfColorCache.put(zoom, lowConfColor);
}
return lowConfColor;
}
/**
* A cache for "low confidence color", which is a function of zoom level.
*/
static Map<Integer, Color> lowConfColorCache = new Hashtable();
}