def __init__(self, width, height, range):
JPanel()
plot = MeterPlot(DefaultValueDataset(0))
self.plot = plot
self.setRange(range)
#plot.addInterval(MeterInterval("Normal", Range(0.0, 35.0),
# Color.lightGray, BasicStroke(2.0),
# Color(0, 255, 0, 64)))
#plot.addInterval(MeterInterval("Warning", Range(35.0, 50.0),
# Color.lightGray, BasicStroke(2.0), Color(255, 255, 0, 64)))
#plot.addInterval(MeterInterval("Critical", Range(50.0, 60.0),
# Color.lightGray, BasicStroke(2.0),
# Color(255, 0, 0, 128)))
plot.setNeedlePaint(Color.darkGray)
plot.setDialBackgroundPaint(Color.white)
plot.setDialOutlinePaint(Color.white)
plot.setDialShape(DialShape.CHORD)
plot.setMeterAngle(260)
plot.setTickLabelsVisible(True)
plot.setTickLabelFont(Font("Dialog", Font.BOLD, 10))
plot.setTickLabelPaint(Color.darkGray)
plot.setTickSize(5.0)
plot.setTickPaint(Color.lightGray)
plot.setValuePaint(Color.black)
plot.setValueFont(Font("Dialog", Font.BOLD, 14))
plot.setUnits("k sims")
chart = JFreeChart("Simulations computed",
JFreeChart.DEFAULT_TITLE_FONT, plot, False)
self.chart = chart
chart.setBackgroundPaint(Color.white)
cp = ChartPanel(chart)
cp.setPreferredSize(Dimension(width, height))
self.add(cp)
def __init__(self, width, height, range):
JPanel()
plot = MeterPlot(DefaultValueDataset(0))
self.plot = plot
self.setRange(range)
#plot.addInterval(MeterInterval("Normal", Range(0.0, 35.0),
# Color.lightGray, BasicStroke(2.0),
# Color(0, 255, 0, 64)))
#plot.addInterval(MeterInterval("Warning", Range(35.0, 50.0),
# Color.lightGray, BasicStroke(2.0), Color(255, 255, 0, 64)))
#plot.addInterval(MeterInterval("Critical", Range(50.0, 60.0),
# Color.lightGray, BasicStroke(2.0),
# Color(255, 0, 0, 128)))
plot.setNeedlePaint(Color.darkGray)
plot.setDialBackgroundPaint(Color.white)
plot.setDialOutlinePaint(Color.white)
plot.setDialShape(DialShape.CHORD)
plot.setMeterAngle(260)
plot.setTickLabelsVisible(True)
plot.setTickLabelFont(Font("Dialog", Font.BOLD, 10));
plot.setTickLabelPaint(Color.darkGray)
plot.setTickSize(5.0)
plot.setTickPaint(Color.lightGray)
plot.setValuePaint(Color.black)
plot.setValueFont(Font("Dialog", Font.BOLD, 14));
plot.setUnits("k sims")
chart = JFreeChart("Simulations computed",
JFreeChart.DEFAULT_TITLE_FONT, plot, False)
self.chart = chart
chart.setBackgroundPaint(Color.white)
cp = ChartPanel(chart)
cp.setPreferredSize(Dimension(width, height))
self.add(cp)
def __init__(self, width, height, isTemporal=False):
JPanel()
self.isTemporal = isTemporal
self.minY = 0.0 # -0.05
self.minX = 0.0 # -0.02
self.maxX = 0.5 # 0.52
self.maxY = 1.0
self.drawCI = False
if isTemporal:
self.title = "Fgt/Hs"
else:
self.title = "Fst/He"
self.labelSelected = True
self.labelNeutral = False
self.posColor = Color.RED
self.neuColor = Color.LIGHT_GRAY
self.balColor = Color.YELLOW
self.markerColor = Color.BLUE
self.exportX = width
self.exportY = height
self.chart = self._createEmptyChart()
self.chart.setAntiAlias(True)
self.resetData()
self.cp = ChartPanel(self.chart)
self.cp.setDisplayToolTips(True)
self.cp.setPreferredSize(Dimension(width, height))
self.add(self.cp)
def __init__(self, width, height, isTemporal=False):
JPanel()
self.isTemporal = isTemporal
self.minY = 0.0 # -0.05
self.minX = 0.0 # -0.02
self.maxX = 0.5 # 0.52
self.maxY = 1.0
self.drawCI = False
if isTemporal:
self.title = "Fgt/Hs"
else:
self.title = "Fst/He"
self.labelSelected = True
self.labelNeutral = False
self.posColor = Color.RED
self.neuColor = Color.LIGHT_GRAY
self.balColor = Color.YELLOW
self.markerColor = Color.BLUE
self.exportX = width
self.exportY = height
self.chart = self._createEmptyChart()
self.chart.setAntiAlias(False)
self.resetData()
self.cp = ChartPanel(self.chart)
self.cp.setDisplayToolTips(True)
self.cp.setPreferredSize(Dimension(width, height))
self.add(self.cp)
def generatePlotPanel(self, plotTitle, listData, showLegend, showTooltip):
"""
1) Create a PieDataset
2) Create a PieChart (or Create a PiePlot and put it in a JFreeChart)
3) Put the PieChart in a ChartPanel
"""
# Get a dictionary of value occurence in the list {value1:count, value2:count...}
dataDico = Counter(listData)
#print dataDico # value: counts OK
# Create a Pie dataset from the dicoData
pieDataset = DefaultPieDataset()
for key, value in dataDico.items():
#print key, value
pieDataset.setValue(key, value)
# Create an instance of JFreeChart
urls = False
chart = ChartFactory.createPieChart(plotTitle, pieDataset, showLegend, showTooltip, urls)
# Alternative way
#piePlot = PiePlot(pieDataset)
#chart = JFreeChart(plotTitle, piePlot)
return ChartPanel(chart)
def plot(self):
chart = self.createChart()
plot = chart.getXYPlot()
if self.logx:
logx = LogarithmicAxis("Log("+xlabel()+")")
plot.setDomainAxis(logx)
if self.logy:
logy = LogarithmicAxis("Log("+ylabel()+")")
plot.setRangeAxis(logy)
chartPanel = ChartPanel(chart)
chartPanel.setPreferredSize(java.awt.Dimension(self._size[0], self._size[1]))
self.setContentPane(chartPanel)
self.pack()
self.setVisible(True)
def __init__(self, automations):
# Create the frame
frame = JFrame("Automation Viewer")
frame.setSize(500, 300)
frame.setLayout(BorderLayout())
series = AutomationSeries
# Finalize the window
frame.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE)
frame.setVisible(True)
# Create an XY dataset
dataset = XYSeriesCollection()
for autoname in automations:
automation = ModbusPal.getAutomation(autoname)
series = AutomationSeries(automation)
dataset.addSeries(series)
frame.addWindowListener(series)
# Create chart
chart = ChartFactory.createXYLineChart("Automation Viewer",
"Time (seconds)", "Value",
dataset,
PlotOrientation.VERTICAL,
Boolean.TRUE, Boolean.TRUE,
Boolean.FALSE)
panel = ChartPanel(chart)
# Add chart to panel
frame.add(panel, BorderLayout.CENTER)
def plot(self):
chart = self.createChart()
plot = chart.getXYPlot()
if self.logx:
logx = LogarithmicAxis("Log(" + xlabel() + ")")
plot.setDomainAxis(logx)
if self.logy:
logy = LogarithmicAxis("Log(" + ylabel() + ")")
plot.setRangeAxis(logy)
chartPanel = ChartPanel(chart)
chartPanel.setPreferredSize(
java.awt.Dimension(self._size[0], self._size[1]))
self.setContentPane(chartPanel)
self.pack()
self.setVisible(True)
def show(self, size=(500, 500)):
panel = ChartPanel(self.chart)
def onclose(e):
e.getWindow().dispose()
self.dispose()
frame = swing.JFrame(windowClosing=onclose)
frame.setContentPane(panel)
frame.size = size
frame.visible = True
self.frame = frame
def __init__(self):
""" generated source for method __init__ """
super(ConfigurableDetailPanel, self).__init__(GridBagLayout())
model = DefaultTableModel()
model.addColumn("Step")
model.addColumn("My Move")
model.addColumn("Time spent")
model.addColumn("Out of time?")
self.moveTable = JZebraTable(model)
self.moveTable.setShowHorizontalLines(True)
self.moveTable.setShowVerticalLines(True)
sidePanel = JPanel()
self.memUsage = TimeSeries("Used Memory")
self.memTotal = TimeSeries("Total Memory")
self.memUsage.setMaximumItemCount(36000)
self.memTotal.setMaximumItemCount(36000)
memory = TimeSeriesCollection()
memory.addSeries(self.memUsage)
memory.addSeries(self.memTotal)
memChart = ChartFactory.createTimeSeriesChart(None, None, "Megabytes", memory, True, True, False)
memChart.setBackgroundPaint(getBackground())
memChartPanel = ChartPanel(memChart)
memChartPanel.setPreferredSize(Dimension(500, 175))
sidePanel.add(memChartPanel)
self.counters = HashSet()
self.countersCollection = TimeSeriesCollection()
counterChart = ChartFactory.createTimeSeriesChart(None, None, None, self.countersCollection, True, True, False)
counterChart.getXYPlot().setRangeAxis(LogarithmicAxis("Count per 100ms"))
counterChart.getXYPlot().getRangeAxis().setAutoRangeMinimumSize(1.0)
counterChart.setBackgroundPaint(getBackground())
counterChartPanel = ChartPanel(counterChart)
counterChartPanel.setPreferredSize(Dimension(500, 175))
sidePanel.add(counterChartPanel)
self.scoreCountersCollection = TimeSeriesCollection()
scoreCounterChart = ChartFactory.createTimeSeriesChart(None, None, "Score", self.scoreCountersCollection, True, True, False)
scoreCounterChart.getXYPlot().getRangeAxis().setRange(0, 100)
scoreCounterChart.setBackgroundPaint(getBackground())
scoreCounterChartPanel = ChartPanel(scoreCounterChart)
scoreCounterChartPanel.setPreferredSize(Dimension(500, 175))
sidePanel.add(scoreCounterChartPanel)
self.add(JScrollPane(self.moveTable, ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED, ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED), GridBagConstraints(0, 0, 1, 2, 1.0, 1.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, Insets(0, 0, 0, 0), 0, 0))
self.add(sidePanel, GridBagConstraints(1, 0, 1, 1, 1.0, 1.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, Insets(0, 0, 0, 0), 0, 0))
self.add(JButton(resetButtonMethod()), GridBagConstraints(1, 1, 1, 1, 0.0, 0.0, GridBagConstraints.SOUTHEAST, GridBagConstraints.NONE, Insets(0, 0, 0, 0), 0, 0))
def plot(geoms, size=(500, 500)):
"""
Plots a set of geometry objects into a xy grid.
*geom* is a `list` of geometry objects to plot. *size* is the resulting
size of the rendered plot.
"""
if not isinstance(geoms, list):
geoms = [geoms]
gd = GeometryDataset(geoms)
plot = gd.createPlot()
chart = JFreeChart(plot)
panel = ChartPanel(chart)
frame = swing.JFrame()
frame.setContentPane(panel)
frame.size = size
frame.visible = True
def renderHistogram(values,
n_bins,
min_max=None,
title="Histogram",
color=Color.red,
show=True,
setThemeFn=setTheme):
""" values: a list or array of numeric values.
n_bins: the number of bins to use.
min_max: defaults to None, a tuple with the minimum and maximum value.
title: defaults to "Histogram", must be not None.
show: defaults to True, showing the histogram in a new window.
setThemeFn: defaults to setTheme, can be None or another function that takes a chart
as argument and sets rendering colors etc.
Returns a tuple of the JFreeChart instance and the window JFrame, if shown.
"""
hd = HistogramDataset()
hd.setType(HistogramType.RELATIVE_FREQUENCY)
print min_max
if min_max:
hd.addSeries(title, values, n_bins, min_max[0], min_max[1])
else:
hd.addSeries(title, values, n_bins)
chart = ChartFactory.createHistogram(title, "", "", hd,
PlotOrientation.VERTICAL, False,
False, False)
# Adjust series color
chart.getXYPlot().getRendererForDataset(hd).setSeriesPaint(0, color)
#
if setThemeFn:
setThemeFn(chart)
frame = None
if show:
frame = JFrame(title)
frame.getContentPane().add(ChartPanel(chart))
frame.pack()
frame.setVisible(True)
return chart, frame
def generatePlotPanel(self, plotTitle, listData):
"""
1) Create a CategoryDataset
2) Create a BarChart (or Create a BarPlot and put it in a JFreeChart)
3) Put the BarChart in a ChartPanel
"""
# Get a dictionary of value occurence in the list {value1:count, value2:count...}
dataDico = Counter(listData)
#print dataDico # value: counts OK
# Create a Pie dataset from the dicoData
dataset = DefaultCategoryDataset()
for key, value in dataDico.items():
#print key, value
dataset.setValue(value, key, "")
# Create an instance of JFreeChart
chart = ChartFactory.createBarChart(plotTitle, "Categories", "Count", dataset)
# Alternative way
#piePlot = PiePlot(pieDataset)
#chart = JFreeChart(plotTitle, piePlot)
return ChartPanel(chart)
def plot(geoms, size=(500,500)):
"""
Plots a set of geometry objects into a xy grid.
*geom* is a `list` of geometry objects to plot. *size* is the resulting
size of the rendered plot.
"""
if not isinstance(geoms, list):
geoms = [geoms]
data = GeometryDataset(geoms)
r = GeometryRenderer()
#r.setFillPolygons(True)
plot = XYPlot(data, data.getDomain(), data.getRange(), r);
chart = JFreeChart(plot)
panel = ChartPanel(chart)
frame = swing.JFrame()
frame.setContentPane(panel)
frame.size = size
frame.visible = True
class Chart(JPanel):
def _createEmptyChart(self, dataset=None):
if self.isTemporal:
hText = "Hs"
fText = "Fgt"
else:
hText = "He"
fText = "Fst"
chart = ChartFactory.createXYLineChart(
self.title, # chart title
hText, # x axis label
fText, # y axis label
dataset, # data
PlotOrientation.VERTICAL,
True, # include legend
True, # tooltips
False # urls
)
chart.setBackgroundPaint(Color.white)
# get a reference to the plot for further customisation...
# change the auto tick unit selection to integer units only...
#rangeAxis = plot.getRangeAxis()
#rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits())
self.confArea = None
return chart
def setSelLoci(self, pv, allLoci, selLoci):
self.pv = pv
self.allLoci = allLoci
self.selLoci = selLoci
self.drawLabels()
def drawLabels(self):
if not hasattr(self, 'pv'): return
plot = self.chart.getPlot()
plot.clearAnnotations()
red = 0
for i in range(len(self.valMarkers)):
if not self.valMarkers[i]:
red += 1
continue
if self.allLoci[i] in self.selLoci:
if not self.labelSelected: continue
else:
if not self.labelNeutral: continue
x = self.pv[i - red][0]
y = self.pv[i - red][1]
locus = self.allLoci[i]
note = XYTextAnnotation(locus, x + 0.002, y + 0.002)
note.setTextAnchor(TextAnchor.BOTTOM_LEFT)
plot.addAnnotation(note)
def setMarkers(self, markers):
self.markers = XYSeries("Markers")
self.maxX = 0.0
self.maxY = 0.0
self.minY = -0.05
self.out = []
self.valMarkers = markers
for marker in markers:
if not marker:
continue
if marker[0] < 2 and marker[0] > self.maxX:
self.maxX = marker[0]
if marker[1] < 2 and marker[1] > self.maxY:
self.maxY = marker[1]
if marker[1] > -2 and marker[1] < self.minY:
self.minY = marker[1]
#self.markers.add(marker[0], max([0.0, marker[1]]))
self.markers.add(marker[0], marker[1])
self.maxX = max([0.501, self.maxX + 0.001])
self.maxX = min([1, self.maxX])
self.maxY += 0.05
self.minY -= 0.05
def setTop(self, markers):
#setBottom has to be done before, as setMarkers
self.top = YIntervalSeries("Candidate neutral")
self.limit = YIntervalSeries("Candidate positive selection")
if len(markers) > 1:
#if self.maxY > markers[0][1]:
# self.limit.add(0.0, markers[0][1], markers[0][0], markers[0][1])
#else: #It does not really matter
# self.limit.add(0.0, -1, 1.1, 1.1)
self.limit.add(0.0, markers[0][1], markers[0][1], 1.1)
for i in range(len(markers)):
self.top.add(markers[i][0], self.bottomList[i][1],
self.bottomList[i][1], markers[i][1])
if self.maxY > markers[i][1]:
self.limit.add(markers[i][0], markers[i][1], markers[i][1],
1.1)
else: #It does not really matter
self.limit.add(markers[i][0], markers[i][1], markers[i][1],
1.1)
#if markers[i][0] > self.maxX: break
#We do this at the end to fill the whole graphic
def setBottom(self, markers):
#print markers
self.bottomList = map(lambda (x, y): (x, y),
markers) #legacy, can remove...
self.bottom = YIntervalSeries("Candidate balancing selection")
if len(markers) > 0:
self.bottom.add(0.0, -1.0, -1.0, self.bottomList[0][1])
for marker in self.bottomList:
self.bottom.add(marker[0], -1.0, -1.0, marker[1])
#if marker[0] > self.maxX: break
#We do this at the end to fill the whole graphic
def updateChartDataset(self, drawLabels=True):
dataset = XYSeriesCollection()
#self._calculateConfArea()
#dataset.addSeries(self.confArea)
dataset.addSeries(self.markers)
plot = self.chart.getPlot()
rangeAxis = plot.getRangeAxis()
domainAxis = plot.getDomainAxis()
rangeAxis.setRange(self.minY, self.maxY) #change
domainAxis.setRange(self.minX, self.maxX)
#plot.setBackgroundPaint(Color.lightGray);
#plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
#plot.setDomainGridlinePaint(Color.white);
#plot.setRangeGridlinePaint(Color.white);
markerRenderer = XYLineAndShapeRenderer(False, True)
#print self.markerColor
markerRenderer.setSeriesPaint(0, self.markerColor)
markerRenderer.setSeriesShape(0, Ellipse2D.Double(-3, -3, 6, 6))
#markerRenderer.setToolTipGenerator(FDistToolTipGenerator(self.pointNames))
plot.setRenderer(0, markerRenderer)
plot.setDataset(0, dataset)
dataset = XYSeriesCollection()
if self.drawCI:
dataset = YIntervalSeriesCollection()
CIRenderer = DeviationRenderer(True, False)
# CIRenderer.setOutline(True)
# CIRenderer.setRoundXCoordinates(True)
dataset.addSeries(self.bottom)
dataset.addSeries(self.top)
dataset.addSeries(self.limit)
CIRenderer.setSeriesFillPaint(0, self.balColor)
CIRenderer.setSeriesFillPaint(1, self.neuColor)
CIRenderer.setSeriesFillPaint(2, self.posColor)
CIRenderer.setSeriesPaint(0, self.balColor)
CIRenderer.setSeriesPaint(1, self.neuColor)
CIRenderer.setSeriesPaint(2, self.posColor)
plot.setDataset(1, dataset)
plot.setRenderer(1, CIRenderer)
plot.setDataset(1, dataset)
if drawLabels:
self.drawLabels()
def resetData(self, justAnnots=False):
if not justAnnots:
self.markers = XYSeries("Markers")
self.drawCI = False
self.chart.getPlot().clearAnnotations()
if hasattr(self, 'pv'):
del (self.pv)
self.updateChartDataset()
def save(self, parent, format):
chooser = JFileChooser()
# filter = FileNameExtensionFilter(
# format + " files",
# array([format, format.lower()], String))
# chooser.setFileFilter(filter);
returnVal = chooser.showSaveDialog(parent)
if returnVal == JFileChooser.APPROVE_OPTION:
fileName = chooser.getSelectedFile().getPath()
if not fileName.upper().endswith('.' + format):
fileName += '.' + format.lower()
file = File(fileName)
else:
return
if format == 'PNG':
ChartUtils.saveChartAsPNG(file, self.chart, self.exportX,
self.exportY)
elif format == 'SVG':
domImpl = GenericDOMImplementation.getDOMImplementation()
doc = domImpl.createDocument(None, "svg", None)
svgGen = SVGGraphics2D(doc)
svgGen.getGeneratorContext().setPrecision(6)
self.chart.draw(
svgGen, Rectangle2D.Double(0, 0, self.exportX, self.exportY),
None)
out = OutputStreamWriter(FileOutputStream(file), "UTF-8")
svgGen.stream(out, True) #True is for useCSS
out.close()
elif format == 'PDF':
mapper = DefaultFontMapper()
pageSize = Rectangle(self.exportX, self.exportY)
doc = TextDocument(pageSize, 50, 50, 50, 50)
out = BufferedOutputStream(FileOutputStream(file))
writer = PdfWriter.getInstance(doc, out)
doc.open()
cb = writer.getDirectContent()
tp = cb.createTemplate(self.exportX, self.exportY)
g2 = tp.createGraphics(self.exportX, self.exportY, mapper)
r2D = Rectangle2D.Double(0, 0, self.exportX, self.exportY)
self.chart.draw(g2, r2D)
g2.dispose()
cb.addTemplate(tp, 0, 0)
doc.close()
#out.close()
def __init__(self, width, height, isTemporal=False):
JPanel()
self.isTemporal = isTemporal
self.minY = 0.0 # -0.05
self.minX = 0.0 # -0.02
self.maxX = 0.5 # 0.52
self.maxY = 1.0
self.drawCI = False
if isTemporal:
self.title = "Fgt/Hs"
else:
self.title = "Fst/He"
self.labelSelected = True
self.labelNeutral = False
self.posColor = Color.RED
self.neuColor = Color.LIGHT_GRAY
self.balColor = Color.YELLOW
self.markerColor = Color.BLUE
self.exportX = width
self.exportY = height
self.chart = self._createEmptyChart()
self.chart.setAntiAlias(True)
self.resetData()
self.cp = ChartPanel(self.chart)
self.cp.setDisplayToolTips(True)
self.cp.setPreferredSize(Dimension(width, height))
self.add(self.cp)
from ij import IJ
from org.jfree.chart import ChartFactory, ChartPanel
from org.jfree.data.statistics import HistogramDataset, HistogramType
from javax.swing import JFrame
from java.awt import Color
imp = IJ.getImage()
pixels = imp.getProcessor().convertToFloat().getPixels()
# Data and parameter of the histogram
values = list(pixels)
n_bins = 256 # number of histogram bins
# Construct the histogram from the pixel data
hist = HistogramDataset()
hist.setType(HistogramType.RELATIVE_FREQUENCY)
hist.addSeries("my data", values, n_bins)
# Create a JFreeChart histogram
chart = ChartFactory.createHistogram("My histogram", "the bins", "counts", hist)
# Adjust series color
chart.getXYPlot().getRendererForDataset(hist).setSeriesPaint(0, Color.blue)
# Show the histogram in an interactive window
# where the right-click menu enables saving to PNG or SVG, and adjusting properties
frame = JFrame("Histogram window")
frame.getContentPane().add(ChartPanel(chart))
frame.pack()
frame.setVisible(True)
class Chart(JPanel):
def _createEmptyChart(self, dataset = None):
chart = ChartFactory.createXYLineChart(
self.title, # chart title
"He", # x axis label
"Fst", # y axis label
dataset, # data
PlotOrientation.VERTICAL,
True, # include legend
True, # tooltips
False # urls
)
chart.setBackgroundPaint(Color.white)
# get a reference to the plot for further customisation...
# change the auto tick unit selection to integer units only...
#rangeAxis = plot.getRangeAxis()
#rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits())
self.confArea = None
return chart
def setSelLoci(self, pv, allLoci, selLoci):
self.pv = pv
self.allLoci = allLoci
self.selLoci = selLoci
self.drawLabels()
def drawLabels(self):
if not hasattr(self, 'pv'): return
plot = self.chart.getPlot()
plot.clearAnnotations()
red = 0
for i in range(len(self.valMarkers)):
if not self.valMarkers[i]:
red += 1
continue
if self.allLoci[i] in self.selLoci:
if not self.labelSelected: continue
else:
if not self.labelNeutral: continue
x = self.pv[i-red][0]
y = self.pv[i-red][1]
locus = self.allLoci[i]
note = XYTextAnnotation(locus, x + 0.002, y + 0.002)
note.setTextAnchor(TextAnchor.BOTTOM_LEFT)
plot.addAnnotation(note)
def setMarkers(self, markers):
self.markers = XYSeries("Markers")
self.maxX = 0.0
self.maxY = 0.0
self.minY = -0.05
self.out = []
self.valMarkers = markers
for marker in markers:
if not marker:
continue
if marker[0]<2 and marker[0] > self.maxX:
self.maxX = marker[0]
if marker[1]<2 and marker[1] > self.maxY:
self.maxY = marker[1]
if marker[1]>-2 and marker[1] < self.minY:
self.minY = marker[1]
#self.markers.add(marker[0], max([0.0, marker[1]]))
self.markers.add(marker[0], marker[1])
self.maxX += 0.1
self.maxX = min([1, self.maxX])
self.maxY += 0.05
self.minY -= 0.05
def setTop(self, markers):
#setBottom has to be done before, as setMarkers
self.top = YIntervalSeries("Candidate neutral")
self.limit = YIntervalSeries("Candidate positive selection")
if len(markers) > 1:
#if self.maxY > markers[0][1]:
# self.limit.add(0.0, markers[0][1], markers[0][0], markers[0][1])
#else: #It does not really matter
# self.limit.add(0.0, -1, 1.1, 1.1)
self.limit.add(0.0, markers[0][1], markers[0][1], 1.1)
for i in range(len(markers)):
self.top.add(markers[i][0], self.bottomList[i][1],self.bottomList[i][1],
markers[i][1] )
if self.maxY > markers[i][1]:
self.limit.add(markers[i][0], markers[i][1],markers[i][1],
1.1)
else: #It does not really matter
self.limit.add(markers[i][0], markers[i][1],markers[i][1], 1.1)
#if markers[i][0] > self.maxX: break
#We do this at the end to fill the whole graphic
def setBottom(self, markers):
#print markers
self.bottomList = map (
lambda (x,y): (x,y),
markers) #legacy, can remove...
self.bottom = YIntervalSeries("Candidate balancing selection")
if len(markers) > 0:
self.bottom.add(0.0, -1.0, -1.0, self.bottomList[0][1])
for marker in self.bottomList:
self.bottom.add(marker[0], -1.0, -1.0, marker[1])
#if marker[0] > self.maxX: break
#We do this at the end to fill the whole graphic
def updateChartDataset(self, drawLabels=True):
dataset = XYSeriesCollection()
#self._calculateConfArea()
#dataset.addSeries(self.confArea)
dataset.addSeries(self.markers)
plot = self.chart.getPlot()
rangeAxis = plot.getRangeAxis()
domainAxis = plot.getDomainAxis()
rangeAxis.setRange(self.minY, self.maxY) #change
domainAxis.setRange(0.0, self.maxX)
#plot.setBackgroundPaint(Color.lightGray);
#plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
#plot.setDomainGridlinePaint(Color.white);
#plot.setRangeGridlinePaint(Color.white);
markerRenderer = XYLineAndShapeRenderer(False, True)
#print self.markerColor
markerRenderer.setSeriesPaint(0, self.markerColor)
markerRenderer.setSeriesShape(0, Ellipse2D.Double(-3, -3, 6, 6))
#markerRenderer.setToolTipGenerator(FDistToolTipGenerator(self.pointNames))
plot.setRenderer(0, markerRenderer)
plot.setDataset(0, dataset)
dataset = XYSeriesCollection()
if self.drawCI:
dataset = YIntervalSeriesCollection()
CIRenderer = DeviationRenderer(True, False)
#CIRenderer.setOutline(True)
#CIRenderer.setRoundXCoordinates(True)
dataset.addSeries(self.bottom)
dataset.addSeries(self.top)
dataset.addSeries(self.limit)
CIRenderer.setSeriesFillPaint(0, self.balColor)
CIRenderer.setSeriesFillPaint(1, self.neuColor)
CIRenderer.setSeriesFillPaint(2, self.posColor)
CIRenderer.setSeriesPaint(0, self.balColor)
CIRenderer.setSeriesPaint(1, self.neuColor)
CIRenderer.setSeriesPaint(2, self.posColor)
plot.setDataset(1, dataset)
plot.setRenderer(1, CIRenderer)
plot.setDataset(1, dataset)
if drawLabels: self.drawLabels()
def resetData(self, justAnnots = False):
if not justAnnots:
self.markers = XYSeries("Markers")
self.drawCI = False
self.chart.getPlot().clearAnnotations()
if hasattr(self, 'pv'):
del(self.pv)
self.updateChartDataset()
def save(self, parent, format):
chooser = JFileChooser()
#filter = FileNameExtensionFilter(
# format + " files",
# array([format, format.lower()], String))
#chooser.setFileFilter(filter);
returnVal = chooser.showSaveDialog(parent)
if returnVal == JFileChooser.APPROVE_OPTION:
fileName = chooser.getSelectedFile().getPath()
if not fileName.upper().endswith('.' + format):
fileName += '.' + format.lower()
file = File(fileName)
else:
return
if format == 'PNG':
ChartUtilities.saveChartAsPNG(file, self.chart, self.exportX, self.exportY)
elif format == 'SVG':
domImpl = GenericDOMImplementation.getDOMImplementation()
doc = domImpl.createDocument(None, "svg", None)
svgGen = SVGGraphics2D(doc)
svgGen.getGeneratorContext().setPrecision(6)
self.chart.draw(svgGen,
Rectangle2D.Double(0, 0, self.exportX, self.exportY), None)
out = OutputStreamWriter(FileOutputStream(file), "UTF-8")
svgGen.stream(out, True) #True is for useCSS
out.close()
elif format == 'PDF':
mapper = DefaultFontMapper()
pageSize = Rectangle(self.exportX, self.exportY)
doc = TextDocument(pageSize, 50, 50, 50, 50)
out = BufferedOutputStream(FileOutputStream(file))
writer = PdfWriter.getInstance(doc, out)
doc.open()
cb = writer.getDirectContent()
tp = cb.createTemplate(self.exportX, self.exportY)
g2 = tp.createGraphics(self.exportX, self.exportY, mapper)
r2D = Rectangle2D.Double(0, 0, self.exportX, self.exportY)
self.chart.draw(g2, r2D)
g2.dispose()
cb.addTemplate(tp, 0, 0)
doc.close()
#out.close()
def __init__(self, width, height):
JPanel()
self.minY = -0.05
self.maxX = 1.0
self.maxY = 1.0
self.drawCI = False
self.title = "Fst/He"
self.labelSelected = True
self.labelNeutral = False
self.posColor = Color.RED
self.neuColor = Color.LIGHT_GRAY
self.balColor = Color.YELLOW
self.markerColor = Color.BLUE
self.exportX = width
self.exportY = height
self.chart = self._createEmptyChart()
self.chart.setAntiAlias(False)
self.resetData()
self.cp = ChartPanel(self.chart)
self.cp.setDisplayToolTips(True)
self.cp.setPreferredSize(Dimension(width, height))
self.add(self.cp)
def __init__(self,chart): chartPanel = ChartPanel(chart) chartPanel.setPreferredSize(Dimension(800,600)) chartPanel.setMouseZoomable(True,False) self.setContentPane(chartPanel)