/*
* Copyright (c) 2007-2013 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* 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.
*/
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* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.renderer;
//~--- non-JDK imports --------------------------------------------------------
import org.broad.igv.Globals;
import org.broad.igv.PreferenceManager;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.track.RenderContext;
import org.broad.igv.track.Track;
import org.broad.igv.ui.FontManager;
import org.broad.igv.ui.UIConstants;
import org.broad.igv.ui.panel.FrameManager;
import java.awt.*;
import java.text.DecimalFormat;
import java.util.List;
/**
* @author jrobinso
*/
public abstract class XYPlotRenderer extends DataRenderer {
private double marginFraction = 0.2;
protected void drawDataPoint(Color graphColor, int dx, int pX, int baseY, int pY,
RenderContext context) {
context.getGraphic2DForColor(graphColor).fillRect(pX, pY, dx, 2);
}
/**
* Render the track in the given rectangle.
*
* @param track
* @param locusScores
* @param context
* @param arect
*/
public synchronized void renderScores(Track track, List<LocusScore> locusScores, RenderContext context, Rectangle arect) {
boolean showMissingData = PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SHOW_MISSING_DATA_KEY);
Graphics2D noDataGraphics = context.getGraphic2DForColor(UIConstants.NO_DATA_COLOR);
Graphics2D tickGraphics = context.getGraphic2DForColor(Color.BLACK);
Rectangle adjustedRect = calculateDrawingRect(arect);
double origin = context.getOrigin();
double locScale = context.getScale();
Color posColor = track.getColor();
Color negColor = track.getAltColor();
// Get the Y axis definition, consisting of minimum, maximum, and base value. Often
// the base value is == min value which is == 0.
DataRange dataRange = track.getDataRange();
float maxValue = dataRange.getMaximum();
float baseValue = dataRange.getBaseline();
float minValue = dataRange.getMinimum();
boolean isLog = dataRange.isLog();
if (isLog) {
minValue = (float) (minValue == 0 ? 0 : Math.log10(minValue));
maxValue = (float) Math.log10(maxValue);
}
// Calculate the Y scale factor.
double delta = (maxValue - minValue);
double yScaleFactor = adjustedRect.getHeight() / delta;
// Calculate the Y position in pixels of the base value. Clip to bounds of rectangle
double baseDelta = maxValue - baseValue;
int baseY = (int) (adjustedRect.getY() + baseDelta * yScaleFactor);
if (baseY < adjustedRect.y) {
baseY = adjustedRect.y;
} else if (baseY > adjustedRect.y + adjustedRect.height) {
baseY = adjustedRect.y + adjustedRect.height;
}
int lastPx = 0;
for (LocusScore score : locusScores) {
// 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((Math.max(1, score.getEnd() - score.getStart())) / locScale) + 1;
if ((pX + dx < 0)) {
continue;
} else if (pX > adjustedRect.getMaxX()) {
break;
}
float dataY = score.getScore();
if (isLog && dataY <= 0) {
continue;
}
if (!Float.isNaN(dataY)) {
// Compute the pixel y location. Clip to bounds of rectangle.
double dy = isLog ? Math.log10(dataY) - baseValue : (dataY - baseValue);
int pY = baseY - (int) (dy * yScaleFactor);
if (pY < adjustedRect.y) {
pY = adjustedRect.y;
} else if (pY > adjustedRect.y + adjustedRect.height) {
pY = adjustedRect.y + adjustedRect.height;
}
Color color = (dataY >= baseValue) ? posColor : negColor;
drawDataPoint(color, (int) dx, (int) pX, baseY, pY, context);
}
if (showMissingData) {
// Draw from lastPx + 1 to pX - 1;
int w = (int) pX - lastPx - 4;
if (w > 0) {
noDataGraphics.fillRect(lastPx + 2, (int) arect.getY(), w, (int) arect.getHeight());
}
}
if (!Float.isNaN(dataY)) {
lastPx = (int) pX + (int) dx;
}
}
if (showMissingData) {
int w = (int) arect.getMaxX() - lastPx - 4;
if (w > 0) {
noDataGraphics.fillRect(lastPx + 2, (int) arect.getY(), w, (int) arect.getHeight());
}
}
}
static DecimalFormat formatter = new DecimalFormat();
/**
* Method description
*
* @param track
* @param context
* @param arect
*/
@Override
public void renderAxis(Track track, RenderContext context, Rectangle arect) {
// For now disable axes for all chromosome view
if (context.getChr().equals(Globals.CHR_ALL)) {
return;
}
super.renderAxis(track, context, arect);
Rectangle drawingRect = calculateDrawingRect(arect);
PreferenceManager prefs = PreferenceManager.getInstance();
Color labelColor = prefs.getAsBoolean(PreferenceManager.CHART_COLOR_TRACK_NAME) ? track.getColor() : Color.black;
Graphics2D labelGraphics = context.getGraphic2DForColor(labelColor);
labelGraphics.setFont(FontManager.getFont(8));
if (prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TRACK_NAME)) {
// Only attempt if track height is > 25 pixels
if (arect.getHeight() > 25) {
Rectangle labelRect = new Rectangle(arect.x, arect.y + 10, arect.width, 10);
labelGraphics.setFont(FontManager.getFont(10));
GraphicUtils.drawCenteredText(track.getName(), labelRect, labelGraphics);
}
}
if (prefs.getAsBoolean(PreferenceManager.CHART_DRAW_Y_AXIS)) {
Rectangle axisRect = new Rectangle(arect.x, arect.y + 1, AXIS_AREA_WIDTH, arect.height);
DataRange axisDefinition = track.getDataRange();
float maxValue = axisDefinition.getMaximum();
float baseValue = axisDefinition.getBaseline();
float minValue = axisDefinition.getMinimum();
// Bottom (minimum tick mark)
int pY = computeYPixelValue(drawingRect, axisDefinition, minValue);
labelGraphics.drawLine(axisRect.x + AXIS_AREA_WIDTH - 10, pY, axisRect.x + AXIS_AREA_WIDTH - 5, pY);
GraphicUtils.drawRightJustifiedText(formatter.format(minValue), axisRect.x + AXIS_AREA_WIDTH - 15, pY, labelGraphics);
// Top (maximum tick mark)
int topPY = computeYPixelValue(drawingRect, axisDefinition, maxValue);
labelGraphics.drawLine(axisRect.x + AXIS_AREA_WIDTH - 10, topPY,
axisRect.x + AXIS_AREA_WIDTH - 5, topPY);
GraphicUtils.drawRightJustifiedText(formatter.format(maxValue),
axisRect.x + AXIS_AREA_WIDTH - 15, topPY + 4, labelGraphics);
// Connect top and bottom
labelGraphics.drawLine(axisRect.x + AXIS_AREA_WIDTH - 10, topPY,
axisRect.x + AXIS_AREA_WIDTH - 10, pY);
// Middle tick mark. Draw only if room
int midPY = computeYPixelValue(drawingRect, axisDefinition, baseValue);
if ((midPY < pY - 15) && (midPY > topPY + 15)) {
labelGraphics.drawLine(axisRect.x + AXIS_AREA_WIDTH - 10, midPY,
axisRect.x + AXIS_AREA_WIDTH - 5, midPY);
GraphicUtils.drawRightJustifiedText(formatter.format(baseValue),
axisRect.x + AXIS_AREA_WIDTH - 15, midPY + 4, labelGraphics);
}
} else if (!FrameManager.isExomeMode() && track.isShowDataRange() && arect.height > 20) {
drawScale(track.getDataRange(), context, arect);
}
}
@Override
public void renderBorder(Track track, RenderContext context, Rectangle arect) {
Rectangle adjustedRect = calculateDrawingRect(arect);
// Draw boundaries if there is room
if (adjustedRect.getHeight() >= 10) {
///TrackProperties pros = track.getProperties();
// midline
DataRange axisDefinition = track.getDataRange();
float maxValue = axisDefinition.getMaximum();
float baseValue = axisDefinition.getBaseline();
float minValue = axisDefinition.getMinimum();
double maxX = adjustedRect.getMaxX();
double x = adjustedRect.getX();
double y = adjustedRect.getY();
if ((baseValue > minValue) && (baseValue < maxValue)) {
int baseY = computeYPixelValue(adjustedRect, axisDefinition, baseValue);
getBaselineGraphics(context).drawLine((int) x, baseY, (int) maxX, baseY);
}
PreferenceManager prefs = PreferenceManager.getInstance();
Color altColor = track.getAltColor();
Color borderColor = (prefs.getAsBoolean(PreferenceManager.CHART_COLOR_BORDERS) && altColor != null && altColor.equals(track.getColor()) )
? track.getColor() : Color.lightGray;
Graphics2D borderGraphics = context.getGraphic2DForColor(borderColor);
// Draw the baseline -- todo, this is a wig track option?
double zeroValue = axisDefinition.getBaseline();
int zeroY = computeYPixelValue(adjustedRect, axisDefinition, zeroValue);
borderGraphics.drawLine(adjustedRect.x, zeroY, adjustedRect.x + adjustedRect.width, zeroY);
// Optionally draw "Y" line (UCSC track line option)
if (track.isDrawYLine()) {
Graphics2D yLineGraphics = context.getGraphic2DForColor(Color.gray);
int yLine = computeYPixelValue(adjustedRect, axisDefinition, track.getYLine());
GraphicUtils.drawDashedLine(borderGraphics, adjustedRect.x, yLine, adjustedRect.x + adjustedRect.width, yLine);
}
// If the chart has + and - numbers draw both borders or none. This
// needs documented somewhere.
boolean drawBorders = true;
if (minValue * maxValue < 0) {
drawBorders = prefs.getAsBoolean(PreferenceManager.CHART_DRAW_BOTTOM_BORDER) &&
prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TOP_BORDER);
}
if (drawBorders && prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TOP_BORDER)) {
borderGraphics.drawLine(adjustedRect.x, adjustedRect.y,
adjustedRect.x + adjustedRect.width, adjustedRect.y);
}
if (drawBorders && prefs.getAsBoolean(PreferenceManager.CHART_DRAW_BOTTOM_BORDER)) {
borderGraphics.drawLine(adjustedRect.x, adjustedRect.y + adjustedRect.height,
adjustedRect.x + adjustedRect.width,
adjustedRect.y + adjustedRect.height);
}
}
/*
(CHART_DRAW_TOP_BORDER));
prefs.setDrawBottomBorder(getBooleanPreference(CHART_DRAW_BOTTOM_BORDER));
prefs.setColorBorders(getBooleanPreference(CHART_COLOR_BORDERS));
prefs.setDrawAxis(getBooleanPreference(CHART_DRAW_Y_AXIS));
prefs.setDrawTrackName(getBooleanPreference(CHART_DRAW_TRACK_NAME));
prefs.setColorTrackName(getBooleanPreference(CHART_COLOR_TRACK_NAME));
prefs.setAutoscale(getBooleanPreference(CHART_AUTOSCALE));
prefs.setShowDataRange(getBooleanPreference(CHART_SHOW_DATA_RANGE));
*/
}
/**
* Get a graphics object for the baseline.
* TODO -- make the line style settable by the user
*
* @param context
* @return
*/
private static Graphics2D getBaselineGraphics(RenderContext context) {
Graphics2D baselineGraphics;
baselineGraphics = (Graphics2D) context.getGraphic2DForColor(Color.lightGray).create();
baselineGraphics.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
return baselineGraphics;
}
/**
* Method description
*
* @return
*/
public String getDisplayName() {
return "Scatter Plot";
}
protected int computeYPixelValue(Rectangle drawingRect, DataRange axisDefinition, double dataY) {
double maxValue = axisDefinition.getMaximum();
double minValue = axisDefinition.getMinimum();
double yScaleFactor = drawingRect.getHeight() / (maxValue - minValue);
// Compute the pixel y location. Clip to bounds of rectangle.
// The distince in pixels frmo the data value to the axis maximum
double delta = (maxValue - dataY) * yScaleFactor;
double pY = drawingRect.getY() + delta;
return (int) Math.max(drawingRect.getMinY(), Math.min(drawingRect.getMaxY(), pY));
}
protected Rectangle calculateDrawingRect(Rectangle arect) {
double buffer = Math.min(arect.getHeight() * marginFraction, 10);
Rectangle adjustedRect = new Rectangle(arect);
adjustedRect.y = (int) (arect.getY() + buffer);
adjustedRect.height = (int) (arect.height - (adjustedRect.y - arect.getY()));
return adjustedRect;
}
public void setMarginFraction(double marginFraction) {
this.marginFraction = marginFraction;
}
}