/**
* Returns the content size for the title. This will reflect the fact that a text title positioned
* on the left or right of a chart will be rotated 90 degrees.
*
* @param g2 the graphics device.
* @param widthRange the width range.
* @param heightRange the height range.
* @return The content size.
*/
protected Size2D arrangeRR(Graphics2D g2, Range widthRange, Range heightRange) {
RectangleEdge position = getPosition();
if (position == RectangleEdge.TOP || position == RectangleEdge.BOTTOM) {
float maxWidth = (float) widthRange.getUpperBound();
// determine the space required for the axis
AxisSpace space =
this.axis.reserveSpace(
g2, null, new Rectangle2D.Double(0, 0, maxWidth, 100), RectangleEdge.BOTTOM, null);
return new Size2D(
maxWidth, this.stripWidth + this.axisOffset + space.getTop() + space.getBottom());
} else if (position == RectangleEdge.LEFT || position == RectangleEdge.RIGHT) {
float maxHeight = (float) heightRange.getUpperBound();
AxisSpace space =
this.axis.reserveSpace(
g2, null, new Rectangle2D.Double(0, 0, 100, maxHeight), RectangleEdge.RIGHT, null);
return new Size2D(
this.stripWidth + this.axisOffset + space.getLeft() + space.getRight(), maxHeight);
} else {
throw new RuntimeException("Unrecognised position.");
}
}
/** Replaces the dataset and checks that the data range is as expected. */
public void testReplaceDataset() {
// create a dataset...
Number[][] data =
new Integer[][] {
{new Integer(-30), new Integer(-20)},
{new Integer(-10), new Integer(10)},
{new Integer(20), new Integer(30)}
};
CategoryDataset newData = DatasetUtilities.createCategoryDataset("S", "C", data);
LocalListener l = new LocalListener();
this.chart.addChangeListener(l);
this.chart.getCategoryPlot().setDataset(newData);
assertEquals(true, l.flag);
ValueAxis axis = this.chart.getCategoryPlot().getRangeAxis();
Range range = axis.getRange();
assertTrue(
"Expecting the lower bound of the range to be around -30: " + range.getLowerBound(),
range.getLowerBound() <= -30);
assertTrue(
"Expecting the upper bound of the range to be around 30: " + range.getUpperBound(),
range.getUpperBound() >= 30);
}
/**
* Shifts the range by the specified amount.
*
* @param base the base range (<code>null</code> not permitted).
* @param delta the shift amount.
* @param allowZeroCrossing a flag that determines whether or not the bounds of the range are
* allowed to cross zero after adjustment.
* @return A new range.
*/
public static Range shift(Range base, double delta, boolean allowZeroCrossing) {
ParamChecks.nullNotPermitted(base, "base");
if (allowZeroCrossing) {
return new Range(base.getLowerBound() + delta, base.getUpperBound() + delta);
} else {
return new Range(
shiftWithNoZeroCrossing(base.getLowerBound(), delta),
shiftWithNoZeroCrossing(base.getUpperBound(), delta));
}
}
/**
* Combines two ranges. This method has a special handling for Double.NaN.
*
* @param range1 the first range (<code>null</code> permitted).
* @param range2 the second range (<code>null</code> permitted).
* @return A new range (possibly <code>null</code>).
* @since 1.0.15
*/
public static Range combineIgnoringNaN(Range range1, Range range2) {
if (range1 == null) {
return range2;
}
if (range2 == null) {
return range1;
}
double l = min(range1.getLowerBound(), range2.getLowerBound());
double u = max(range1.getUpperBound(), range2.getUpperBound());
return new Range(l, u);
}
/**
* Returns a range that includes all the values in the specified <code>range</code> AND the
* specified <code>value</code>.
*
* @param range the range (<code>null</code> permitted).
* @param value the value that must be included.
* @return A range.
* @since 1.0.1
*/
public static Range expandToInclude(Range range, double value) {
if (range == null) {
return new Range(value, value);
}
if (value < range.getLowerBound()) {
return new Range(value, range.getUpperBound());
} else if (value > range.getUpperBound()) {
return new Range(range.getLowerBound(), value);
} else {
return range;
}
}
private Range trimToContentHeight(Range r) {
if (r == null) {
return null;
}
double lowerBound = 0.0;
double upperBound = Double.POSITIVE_INFINITY;
if (r.getLowerBound() > 0.0) {
lowerBound = trimToContentHeight(r.getLowerBound());
}
if (r.getUpperBound() < Double.POSITIVE_INFINITY) {
upperBound = trimToContentHeight(r.getUpperBound());
}
return new Range(lowerBound, upperBound);
}
/**
* Converts a data value to a coordinate in Java2D space, assuming that the axis runs along one
* edge of the specified plotArea. Note that it is possible for the coordinate to fall outside the
* plotArea.
*
* @param value the data value.
* @param plotArea the area for plotting the data.
* @param edge the axis location.
* @return The Java2D coordinate.
*/
@Override
public double valueToJava2D(double value, Rectangle2D plotArea, RectangleEdge edge) {
Range range = getRange();
double axisMin = switchedLog10(range.getLowerBound());
double axisMax = switchedLog10(range.getUpperBound());
double min = 0.0;
double max = 0.0;
if (RectangleEdge.isTopOrBottom(edge)) {
min = plotArea.getMinX();
max = plotArea.getMaxX();
} else if (RectangleEdge.isLeftOrRight(edge)) {
min = plotArea.getMaxY();
max = plotArea.getMinY();
}
value = switchedLog10(value);
if (isInverted()) {
return max - (((value - axisMin) / (axisMax - axisMin)) * (max - min));
} else {
return min + (((value - axisMin) / (axisMax - axisMin)) * (max - min));
}
}
/**
* Scales the range by the specified factor.
*
* @param base the base range (<code>null</code> not permitted).
* @param factor the scaling factor (must be non-negative).
* @return A new range.
* @since 1.0.9
*/
public static Range scale(Range base, double factor) {
ParamChecks.nullNotPermitted(base, "base");
if (factor < 0) {
throw new IllegalArgumentException("Negative 'factor' argument.");
}
return new Range(base.getLowerBound() * factor, base.getUpperBound() * factor);
}
/**
* Converts a coordinate from Java 2D space to data space.
*
* @param java2DValue the coordinate in Java2D space.
* @param dataArea the data area.
* @param edge the edge.
* @return The data value.
*/
public double java2DToValue(double java2DValue, Rectangle2D dataArea, RectangleEdge edge) {
Range range = getRange();
double vmax = range.getUpperBound();
double vp = getCycleBound();
double jmin = 0.0;
double jmax = 0.0;
if (RectangleEdge.isTopOrBottom(edge)) {
jmin = dataArea.getMinX();
jmax = dataArea.getMaxX();
} else if (RectangleEdge.isLeftOrRight(edge)) {
jmin = dataArea.getMaxY();
jmax = dataArea.getMinY();
}
if (isInverted()) {
double jbreak = jmax - (vmax - vp) * (jmax - jmin) / this.period;
if (java2DValue >= jbreak) {
return vp + (jmax - java2DValue) * this.period / (jmax - jmin);
} else {
return vp - (java2DValue - jmin) * this.period / (jmax - jmin);
}
} else {
double jbreak = (vmax - vp) * (jmax - jmin) / this.period + jmin;
if (java2DValue <= jbreak) {
return vp + (java2DValue - jmin) * this.period / (jmax - jmin);
} else {
return vp - (jmax - java2DValue) * this.period / (jmax - jmin);
}
}
}
/**
* Converts a coordinate in Java2D space to the corresponding data value, assuming that the axis
* runs along one edge of the specified plotArea.
*
* @param java2DValue the coordinate in Java2D space.
* @param plotArea the area in which the data is plotted.
* @param edge the axis location.
* @return The data value.
*/
@Override
public double java2DToValue(double java2DValue, Rectangle2D plotArea, RectangleEdge edge) {
Range range = getRange();
double axisMin = switchedLog10(range.getLowerBound());
double axisMax = switchedLog10(range.getUpperBound());
double plotMin = 0.0;
double plotMax = 0.0;
if (RectangleEdge.isTopOrBottom(edge)) {
plotMin = plotArea.getX();
plotMax = plotArea.getMaxX();
} else if (RectangleEdge.isLeftOrRight(edge)) {
plotMin = plotArea.getMaxY();
plotMax = plotArea.getMinY();
}
if (isInverted()) {
return switchedPow10(
axisMax - ((java2DValue - plotMin) / (plotMax - plotMin)) * (axisMax - axisMin));
} else {
return switchedPow10(
axisMin + ((java2DValue - plotMin) / (plotMax - plotMin)) * (axisMax - axisMin));
}
}
/** Rescales the axis to ensure that all data is visible. */
@Override
protected void autoAdjustRange() {
Plot plot = getPlot();
if (plot == null) {
return; // no plot, no data
}
if (plot instanceof ValueAxisPlot) {
ValueAxisPlot vap = (ValueAxisPlot) plot;
Range r = vap.getDataRange(this);
if (r == null) {
r = getDefaultAutoRange();
}
long upper = Math.round(r.getUpperBound());
long lower = Math.round(r.getLowerBound());
this.first =
createInstance(
this.autoRangeTimePeriodClass, new Date(lower), this.timeZone, this.locale);
this.last =
createInstance(
this.autoRangeTimePeriodClass, new Date(upper), this.timeZone, this.locale);
setRange(r, false, false);
}
}
/**
* Sets a new axis range. The period is extended to fit the range size, if necessary.
*
* @param range the range.
* @param turnOffAutoRange switch off the auto range.
* @param notify notify?
* @see org.jfree.chart.axis.ValueAxis#setRange(Range, boolean, boolean)
*/
public void setRange(Range range, boolean turnOffAutoRange, boolean notify) {
double size = range.getUpperBound() - range.getLowerBound();
if (size > this.period) {
this.period = size;
}
super.setRange(range, turnOffAutoRange, notify);
}
protected int calculateVisibleTickCount() {
double unit = getTickUnit().getSize();
Range range = getRange();
return (int)
((Math.floor(range.getUpperBound() / unit) - Math.ceil(range.getLowerBound() / unit))
+ NormalizedMatrixSeries.DEFAULT_SCALE_FACTOR);
}
/**
* Returns the maximum x-value in the dataset.
*
* @param includeInterval a flag that determines whether or not the x-interval is taken into
* account.
* @return The maximum value.
*/
public double getDomainUpperBound(boolean includeInterval) {
double result = Double.NaN;
Range r = getDomainBounds(includeInterval);
if (r != null) {
result = r.getUpperBound();
}
return result;
}
/**
* Returns the content size for the title. This will reflect the fact that a text title positioned
* on the left or right of a chart will be rotated 90 degrees.
*
* @param g2 the graphics device.
* @param widthRange the width range.
* @param heightRange the height range.
* @return The content size.
*/
protected Size2D arrangeRR(Graphics2D g2, Range widthRange, Range heightRange) {
RectangleEdge position = getPosition();
if (position == RectangleEdge.TOP || position == RectangleEdge.BOTTOM) {
float maxWidth = (float) widthRange.getUpperBound();
g2.setFont(this.font);
this.content =
TextUtilities.createTextBlock(
this.text,
this.font,
this.paint,
maxWidth,
this.maximumLinesToDisplay,
new G2TextMeasurer(g2));
this.content.setLineAlignment(this.textAlignment);
Size2D contentSize = this.content.calculateDimensions(g2);
if (this.expandToFitSpace) {
return new Size2D(maxWidth, contentSize.getHeight());
} else {
return contentSize;
}
} else if (position == RectangleEdge.LEFT || position == RectangleEdge.RIGHT) {
float maxWidth = (float) heightRange.getUpperBound();
g2.setFont(this.font);
this.content =
TextUtilities.createTextBlock(
this.text,
this.font,
this.paint,
maxWidth,
this.maximumLinesToDisplay,
new G2TextMeasurer(g2));
this.content.setLineAlignment(this.textAlignment);
Size2D contentSize = this.content.calculateDimensions(g2);
// transpose the dimensions, because the title is rotated
if (this.expandToFitSpace) {
return new Size2D(contentSize.getHeight(), maxWidth);
} else {
return new Size2D(contentSize.height, contentSize.width);
}
} else {
throw new RuntimeException("Unrecognised exception.");
}
}
/**
* Returns the lower and upper bounds (range) of the x-values in the specified dataset.
*
* @param dataset the dataset (<code>null</code> permitted).
* @return The range (<code>null</code> if the dataset is <code>null</code> or empty).
* @see #findRangeBounds(XYDataset)
*/
public Range findDomainBounds(XYDataset dataset) {
if (dataset == null) {
return null;
}
Range r = DatasetUtilities.findDomainBounds(dataset, false);
if (r == null) {
return null;
}
return new Range(
r.getLowerBound() + this.xOffset, r.getUpperBound() + this.blockWidth + this.xOffset);
}
/**
* Creates a new range by adding margins to an existing range.
*
* @param range the range (<code>null</code> not permitted).
* @param lowerMargin the lower margin (expressed as a percentage of the range length).
* @param upperMargin the upper margin (expressed as a percentage of the range length).
* @return The expanded range.
*/
public static Range expand(Range range, double lowerMargin, double upperMargin) {
ParamChecks.nullNotPermitted(range, "range");
double length = range.getLength();
double lower = range.getLowerBound() - length * lowerMargin;
double upper = range.getUpperBound() + length * upperMargin;
if (lower > upper) {
lower = lower / 2.0 + upper / 2.0;
upper = lower;
}
return new Range(lower, upper);
}
/**
* Returns the range of values the renderer requires to display all the items from the specified
* dataset.
*
* @param dataset the dataset (<code>null</code> permitted).
* @return The range (<code>null</code> if the dataset is <code>null</code> or empty).
*/
public Range findRangeBounds(XYDataset dataset) {
if (dataset == null) {
return null;
}
Range r = DatasetUtilities.findRangeBounds(dataset, false);
if (r == null) {
return null;
}
double offset = 0; // TODO getSeriesShape(n).getBounds().height / 2;
return new Range(r.getLowerBound() + offset, r.getUpperBound() + offset);
}
/** A test for bug 3072674. */
@Test
public void test3072674() {
DefaultStatisticalCategoryDataset dataset = new DefaultStatisticalCategoryDataset();
dataset.add(1.0, Double.NaN, "R1", "C1");
assertEquals(1.0, dataset.getRangeLowerBound(true), EPSILON);
assertEquals(1.0, dataset.getRangeUpperBound(true), EPSILON);
Range r = dataset.getRangeBounds(true);
assertEquals(1.0, r.getLowerBound(), EPSILON);
assertEquals(1.0, r.getUpperBound(), EPSILON);
}
/**
* Sets the range for the axis, if requested, sends an {@link AxisChangeEvent} to all registered
* listeners. As a side-effect, the auto-range flag is set to <code>false</code> (optional).
*
* @param range the range (<code>null</code> not permitted).
* @param turnOffAutoRange a flag that controls whether or not the auto range is turned off.
* @param notify a flag that controls whether or not listeners are notified.
*/
public void setRange(Range range, boolean turnOffAutoRange, boolean notify) {
long upper = Math.round(range.getUpperBound());
long lower = Math.round(range.getLowerBound());
this.first =
createInstance(this.autoRangeTimePeriodClass, new Date(lower), this.timeZone, this.locale);
this.last =
createInstance(this.autoRangeTimePeriodClass, new Date(upper), this.timeZone, this.locale);
super.setRange(
new Range(this.first.getFirstMillisecond(), this.last.getLastMillisecond() + 1.0),
turnOffAutoRange,
notify);
}
/**
* Returns the range of the values in the dataset's domain, including or excluding the interval
* around each x-value as specified.
*
* @param includeInterval a flag that determines whether or not the x-interval should be taken
* into account.
* @return The range.
*/
@Override
public Range getDomainBounds(boolean includeInterval) {
// first get the range without the interval, then expand it for the
// interval width
Range range = DatasetUtilities.findDomainBounds(this.dataset, false);
if (includeInterval && range != null) {
double lowerAdj = getIntervalWidth() * getIntervalPositionFactor();
double upperAdj = getIntervalWidth() - lowerAdj;
range = new Range(range.getLowerBound() - lowerAdj, range.getUpperBound() + upperAdj);
}
return range;
}
/**
* Returns the range of values the renderer requires to display all the items from the specified
* dataset.
*
* @param dataset the dataset (<code>null</code> permitted).
* @return The range (<code>null</code> if the dataset is <code>null</code> or empty).
* @see #findDomainBounds(XYDataset)
*/
public Range findRangeBounds(XYDataset dataset) {
if (dataset != null) {
Range r = DatasetUtilities.findRangeBounds(dataset, false);
if (r == null) {
return null;
} else {
return new Range(
r.getLowerBound() + this.yOffset, r.getUpperBound() + this.blockHeight + this.yOffset);
}
} else {
return null;
}
}
/** Replaces the dataset and checks that it has changed as expected. */
public void testReplaceDataset() {
// create a dataset...
XYSeries series1 = new XYSeries("Series 1");
series1.add(10.0, 10.0);
series1.add(20.0, 20.0);
series1.add(30.0, 30.0);
XYDataset dataset = new XYSeriesCollection(series1);
LocalListener l = new LocalListener();
this.chart.addChangeListener(l);
XYPlot plot = (XYPlot) this.chart.getPlot();
plot.setDataset(dataset);
assertEquals(true, l.flag);
ValueAxis axis = plot.getRangeAxis();
Range range = axis.getRange();
assertTrue(
"Expecting the lower bound of the range to be around 10: " + range.getLowerBound(),
range.getLowerBound() <= 10);
assertTrue(
"Expecting the upper bound of the range to be around 30: " + range.getUpperBound(),
range.getUpperBound() >= 30);
}
/** Returns a peak list with the top peaks defined by the parameter "threshold" */
PeakList getTopThresholdPeakList(int threshold) {
PeakList selectedPeakList = (PeakList) peakListSelector.getSelectedItem();
if (selectedPeakList == null) return null;
SimplePeakList newList =
new SimplePeakList(selectedPeakList.getName(), selectedPeakList.getRawDataFiles());
Vector<PeakListRow> peakRows = new Vector<PeakListRow>();
Range<Double> mzRange = selectedPeakList.getRowsMZRange();
Range<Double> rtRange = selectedPeakList.getRowsRTRange();
PeakThresholdMode selectedPeakOption = (PeakThresholdMode) thresholdCombo.getSelectedItem();
if (selectedPeakOption == PeakThresholdMode.TOP_PEAKS_AREA) {
XYPlot xyPlot = masterFrame.getPlot().getXYPlot();
org.jfree.data.Range yAxis = xyPlot.getRangeAxis().getRange();
org.jfree.data.Range xAxis = xyPlot.getDomainAxis().getRange();
rtRange = Range.closed(xAxis.getLowerBound(), xAxis.getUpperBound());
mzRange = Range.closed(yAxis.getLowerBound(), yAxis.getUpperBound());
}
for (PeakListRow peakRow : selectedPeakList.getRows()) {
if (mzRange.contains(peakRow.getAverageMZ()) && rtRange.contains(peakRow.getAverageRT())) {
peakRows.add(peakRow);
}
}
Collections.sort(
peakRows, new PeakListRowSorter(SortingProperty.Intensity, SortingDirection.Descending));
if (threshold > peakRows.size()) threshold = peakRows.size();
for (int i = 0; i < threshold; i++) {
newList.addRow(peakRows.elementAt(i));
}
return newList;
}
public double java2DToValue(double java2DValue, Rectangle2D area, RectangleEdge edge) {
Range range = getRange();
double axisMin = range.getLowerBound();
double axisMax = range.getUpperBound();
double min = 0.0d;
double max = 0.0d;
if (RectangleEdge.isTopOrBottom(edge)) {
min = area.getX();
max = area.getMaxX();
} else if (RectangleEdge.isLeftOrRight(edge)) {
min = area.getMaxY();
max = area.getY();
}
if (isInverted()) {
return axisMax - (((java2DValue - min) / (max - min)) * (axisMax - axisMin));
}
return (((java2DValue - min) / (max - min)) * (axisMax - axisMin)) + axisMin;
}
private void handleAxisRangeControlChanges(
PropertyChangeEvent evt,
AxisRangeControl axisRangeControl,
ValueAxis valueAxis,
Range computedAutoRange) {
final String propertyName = evt.getPropertyName();
switch (propertyName) {
case AxisRangeControl.PROPERTY_NAME_AUTO_MIN_MAX:
if (axisRangeControl.isAutoMinMax()) {
final double min = computedAutoRange.getLowerBound();
final double max = computedAutoRange.getUpperBound();
axisRangeControl.adjustComponents(min, max, 3);
}
break;
case AxisRangeControl.PROPERTY_NAME_MIN:
valueAxis.setLowerBound(axisRangeControl.getMin());
break;
case AxisRangeControl.PROPERTY_NAME_MAX:
valueAxis.setUpperBound(axisRangeControl.getMax());
break;
}
}
/**
* Translates a value from data space to Java 2D space.
*
* @param value the data value.
* @param dataArea the data area.
* @param edge the edge.
* @return The Java 2D value.
*/
public double valueToJava2D(double value, Rectangle2D dataArea, RectangleEdge edge) {
Range range = getRange();
double vmin = range.getLowerBound();
double vmax = range.getUpperBound();
double vp = getCycleBound();
if ((value < vmin) || (value > vmax)) {
return Double.NaN;
}
double jmin = 0.0;
double jmax = 0.0;
if (RectangleEdge.isTopOrBottom(edge)) {
jmin = dataArea.getMinX();
jmax = dataArea.getMaxX();
} else if (RectangleEdge.isLeftOrRight(edge)) {
jmax = dataArea.getMinY();
jmin = dataArea.getMaxY();
}
if (isInverted()) {
if (value == vp) {
return this.boundMappedToLastCycle ? jmin : jmax;
} else if (value > vp) {
return jmax - (value - vp) * (jmax - jmin) / this.period;
} else {
return jmin + (vp - value) * (jmax - jmin) / this.period;
}
} else {
if (value == vp) {
return this.boundMappedToLastCycle ? jmax : jmin;
} else if (value >= vp) {
return jmin + (value - vp) * (jmax - jmin) / this.period;
} else {
return jmax - (vp - value) * (jmax - jmin) / this.period;
}
}
}
protected double estimateMaximumTickLabelWidth(Graphics2D g2, TickUnit unit) {
RectangleInsets tickLabelInsets = getTickLabelInsets();
double result = tickLabelInsets.getLeft() + tickLabelInsets.getRight();
if (isVerticalTickLabels()) {
FontRenderContext frc = g2.getFontRenderContext();
return result + ((double) getTickLabelFont().getLineMetrics("0", frc).getHeight());
}
String lowerStr;
String upperStr;
FontMetrics fm = g2.getFontMetrics(getTickLabelFont());
Range range = getRange();
double lower = range.getLowerBound();
double upper = range.getUpperBound();
NumberFormat formatter = getNumberFormatOverride();
if (formatter != null) {
lowerStr = formatter.format(lower);
upperStr = formatter.format(upper);
} else {
lowerStr = unit.valueToString(lower);
upperStr = unit.valueToString(upper);
}
return result + Math.max((double) fm.stringWidth(lowerStr), (double) fm.stringWidth(upperStr));
}
/**
* Constructs a new range that is based on another {@link Range}. The other range does not have to
* be a {@link DateRange}. If it is not, the upper and lower bounds are evaluated as milliseconds
* since midnight GMT, 1-Jan-1970.
*
* @param other the other range (<code>null</code> not permitted).
*/
public DateRange(Range other) {
this(other.getLowerBound(), other.getUpperBound());
}
/**
* Returns <code>true</code> if the range intersects with the specified range, and <code>false
* </code> otherwise.
*
* @param range another range (<code>null</code> not permitted).
* @return A boolean.
* @since 1.0.9
*/
public boolean intersects(Range range) {
return intersects(range.getLowerBound(), range.getUpperBound());
}