def __init__(self, chartFun, isTemporal = False):
self.isTemporal = isTemporal
JPanel()
#self.setBackground(Color.LIGHT_GRAY)
self.chartFun = chartFun
self.enableChartFun = False
self.setLayout(GridLayout(6,2))
self.add(JLabel('CPU Cores'))
nprocs = ManagementFactory.getOperatingSystemMXBean().getAvailableProcessors()
procvals = sorted(set([nprocs, 1, 2, 4, 8, 16, 32, 64, 128]))
cores = JComboBox(procvals)
cores.setSelectedIndex(procvals.index(nprocs))
cores.setMaximumSize(cores.getPreferredSize())
self.cores = cores
self.add(self.cores)
self.add(JLabel('# of sims (x1000) '))
numSims = JComboBox(
map(lambda x: str((10+x)*5), range(10)) +
map(lambda x: str(x*100), range(1,11))
)
numSims.setMaximumSize(numSims.getPreferredSize())
self.numSims = numSims
self.add(self.numSims)
if isTemporal:
self.add(JLabel('"Neutral" Ne'))
self.neutral = JCheckBox()
self.neutral.addActionListener(self)
self.add(self.neutral)
else:
self.add(JLabel('"Neutral" mean Fst'))
self.neutral = JCheckBox()
self.neutral.addActionListener(self)
self.add(self.neutral)
self.add(JLabel('Force mean Fst'))
self.force = JCheckBox()
self.force.addActionListener(self)
self.add(self.force)
self.add(JLabel('Confidence interval '))
ci = JComboBox(['0.95', '0.99', '0.995'])
ci.addItemListener(self)
ci.setMaximumSize(cores.getPreferredSize())
self.ci = ci
self.add(self.ci)
self.add(JLabel('False Disc. Rate'))
fdr = JFormattedTextField(
NumberFormat.getNumberInstance(Locale.US))
fdr.setValue(0.1)
fdr.addPropertyChangeListener(self)
self.add(fdr)
self.fdr = fdr
class CurveDialog(JDialog):
def __init__(self, cattrs):
#JDialog.__init__(self,"Curve Attribute Editor")
#("Curve Attribute Editor")
if cattrs == None or len(cattrs) == 0:
raise "No curve attributes specified"
self.attrs = cattrs
self.cpanel = EditCurveAttr(cattrs[0])
pane = self.getContentPane()
pane.setLayout(BorderLayout())
x = map(lambda x: x + 1, range(len(self.attrs)))
self.curveBox = JComboBox(x)
self.curveBox.setBorder(BorderFactory.createTitledBorder("Curve #"))
self.curveBox.setSelectedItem(0)
class CListener(ItemListener):
def __init__(self, cbox, cpanel, cattrs):
self.cbox = cbox
self.cpanel = cpanel
self.attrs = cattrs
def itemStateChanged(self, evt):
crvNo = self.cbox.getSelectedItem()
self.cpanel.update()
self.cpanel.setAttribute(self.attrs[crvNo - 1])
self.curveBox.addItemListener(
CListener(self.curveBox, self.cpanel, self.attrs))
okBtn = JButton("OK", actionPerformed=self.ok_action)
cancelBtn = JButton("Cancel", actionPerformed=self.cancel_action)
btnPanel = JPanel()
btnPanel.setLayout(GridLayout(1, 3))
btnPanel.add(self.curveBox)
btnPanel.add(okBtn)
btnPanel.add(cancelBtn)
pane.add(self.cpanel, BorderLayout.CENTER)
pane.add(btnPanel, BorderLayout.SOUTH)
self.setLocation(100, 100)
self.pack()
self.setVisible(1)
def ok_action(self, evt):
#crvNo = self.curveBox.getSelectedItem()
#print 'Setting attributes for ', crvNo
#print self.attrs[crvNo-1]
self.cpanel.update()
self.cancel_action(evt)
def cancel_action(self, evt):
self.dispose()
def __init__(self, chartFun, isTemporal = False):
self.isTemporal = isTemporal
JPanel()
#self.setBackground(Color.LIGHT_GRAY)
self.chartFun = chartFun
self.enableChartFun = False
self.setLayout(GridLayout(6,2))
self.add(JLabel('CPU Cores'))
cores = JComboBox(['1', '2', '4', '8', '16', '32', '64', '128'])
nprocs = ManagementFactory.getOperatingSystemMXBean().getAvailableProcessors()
pos = min([7, log(ceil(nprocs)) / log(2)])
cores.setSelectedIndex(int(pos))
cores.setMaximumSize(cores.getPreferredSize())
self.cores = cores
self.add(self.cores)
self.add(JLabel('# of sims (x1000) '))
numSims = JComboBox(
map(lambda x: str((10+x)*5), range(10)) +
map(lambda x: str(x*100), range(1,11))
)
numSims.setMaximumSize(numSims.getPreferredSize())
self.numSims = numSims
self.add(self.numSims)
if isTemporal:
self.add(JLabel('"Neutral" Ne'))
self.neutral = JCheckBox()
self.neutral.addActionListener(self)
self.add(self.neutral)
else:
self.add(JLabel('"Neutral" mean Fst'))
self.neutral = JCheckBox()
self.neutral.addActionListener(self)
self.add(self.neutral)
self.add(JLabel('Force mean Fst'))
self.force = JCheckBox()
self.force.addActionListener(self)
self.add(self.force)
self.add(JLabel('Confidence interval '))
ci = JComboBox(['0.95', '0.99', '0.995'])
ci.addItemListener(self)
ci.setMaximumSize(cores.getPreferredSize())
self.ci = ci
self.add(self.ci)
self.add(JLabel('False Disc. Rate'))
fdr = JFormattedTextField(
NumberFormat.getNumberInstance(Locale.US))
fdr.setValue(0.1)
fdr.addPropertyChangeListener(self)
self.add(fdr)
self.fdr = fdr
class CurveDialog(JDialog):
def __init__(self, cattrs):
#JDialog.__init__(self,"Curve Attribute Editor")
#("Curve Attribute Editor")
if cattrs == None or len(cattrs) == 0:
raise "No curve attributes specified"
self.attrs = cattrs
self.cpanel = EditCurveAttr(cattrs[0])
pane = self.getContentPane()
pane.setLayout(BorderLayout())
x = map(lambda x: x+1,range(len(self.attrs)))
self.curveBox = JComboBox(x)
self.curveBox.setBorder(BorderFactory.createTitledBorder("Curve #"))
self.curveBox.setSelectedItem(0)
class CListener(ItemListener):
def __init__(self,cbox,cpanel,cattrs):
self.cbox = cbox
self.cpanel = cpanel
self.attrs = cattrs
def itemStateChanged(self, evt):
crvNo = self.cbox.getSelectedItem()
self.cpanel.update()
self.cpanel.setAttribute(self.attrs[crvNo-1])
self.curveBox.addItemListener(CListener(self.curveBox, self.cpanel,self.attrs))
okBtn = JButton("OK",actionPerformed=self.ok_action)
cancelBtn = JButton("Cancel",actionPerformed=self.cancel_action)
btnPanel = JPanel()
btnPanel.setLayout(GridLayout(1,3))
btnPanel.add(self.curveBox)
btnPanel.add(okBtn)
btnPanel.add(cancelBtn)
pane.add(self.cpanel,BorderLayout.CENTER)
pane.add(btnPanel, BorderLayout.SOUTH)
self.setLocation(100,100)
self.pack()
self.setVisible(1)
def ok_action(self,evt):
#crvNo = self.curveBox.getSelectedItem()
#print 'Setting attributes for ', crvNo
#print self.attrs[crvNo-1]
self.cpanel.update()
self.cancel_action(evt)
def cancel_action(self,evt):
self.dispose()
class EmpiricalPanel(JPanel, PropertyChangeListener, ItemListener):
def propertyChange(self, evt):
if self.ignoreChanges:
return
change = False
if not self.isTemporal:
if evt.getSource() == self.fst and evt.getPropertyName() == "value":
new = float(evt.getNewValue())
old = float(evt.getOldValue())
if new > 0.99:
evt.getSource().setValue(old)
if new < -0.2:
evt.getSource().setValue(old)
elif new < 0.0:
self.systemPanel.force.setSelected(False)
self.systemPanel.force.setEnabled(False)
else:
self.systemPanel.force.setEnabled(True)
else:
if evt.getSource() == self.ne and evt.getPropertyName() == "value":
new = float(evt.getNewValue())
old = float(evt.getOldValue())
if new < 0:
evt.getSource().setValue(old)
if (
self.isDominant
and evt.getSource() in [self.theta, self.beta1, self.beta2, self.crit]
and evt.getPropertyName() == "value"
):
new = float(evt.getNewValue())
old = float(evt.getOldValue())
if new > 0.99 or new < -0.2:
evt.getSource().setValue(old)
if evt.getSource() == self.sampleSize and evt.getPropertyName() == "value":
change = True
new = int(evt.getNewValue())
old = int(evt.getOldValue())
if new > 50 and old > 4:
warn(
self,
"A sample size bigger than 50 is not expected to produce better results, while it slows the computation",
)
if new < 5 and (new != 0 and not self.isDominant):
evt.getSource().setValue(old)
if evt.getSource() == self.pops and evt.getPropertyName() == "value":
change = True
new = int(evt.getNewValue())
old = int(evt.getOldValue())
if new > 100:
error(self, "Maximum value for total populations is 100")
evt.getSource().setValue(100)
if new < self.knownPops:
error(
self,
"Expected total populations has to be at least the same as the number of populations under study.",
)
evt.getSource().setValue(self.knownPops)
if evt.getSource() == self.mut:
change = True
if not change:
return
if self.menuHandles["item5000"].isEnabled():
self.menuHandles["item5000"].setEnabled(False)
warn(self, "Changed parameter will require restarting simulations")
def itemStateChanged(self, evt):
self.propertyChange(evt)
def getTotalPops(self):
return self.pops.getValue()
def setTotalPops(self, numPops):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.pops.setValue(numPops)
self.ignoreChanges = ignoreChanges
def getFst(self):
return self.fst.getValue()
def setFst(self, fst):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.fst.setValue(fst)
self.ignoreChanges = ignoreChanges
def getNe(self):
return self.ne.getValue()
def setNe(self, ne):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.ne.setValue(ne)
self.ignoreChanges = ignoreChanges
def getTheta(self):
return self.theta.getValue()
def setTheta(self, theta):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.theta.setValue(theta)
self.ignoreChanges = ignoreChanges
def getBeta(self):
return (self.beta1.getValue(), self.beta2.getValue())
def setBeta(self, beta):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.beta1.setValue(beta[0])
self.beta2.setValue(beta[1])
self.ignoreChanges = ignoreChanges
def getCrit(self):
return self.crit.getValue()
def setCrit(self, crit):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.crit.setValue(crit)
self.ignoreChanges = ignoreChanges
def getSampleSize(self):
return self.sampleSize.getValue()
def setSampleSize(self, sampleSize):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.sampleSize.setValue(sampleSize)
self.ignoreChanges = ignoreChanges
def __init__(self, menuHandles, manager, isDominant, systemPanel, isTemporal=False):
self.systemPanel = systemPanel
self.knownPops = 0
self.ignoreChanges = True
JPanel()
self.menuHandles = menuHandles
self.isDominant = isDominant
self.isTemporal = isTemporal
if isDominant:
self.setLayout(GridLayout(8, 2))
else:
self.setLayout(GridLayout(5, 2))
if isTemporal:
self.add(JLabel("Ne"))
ne = JFormattedTextField(NumberFormat.getNumberInstance(Locale.US))
ne.addPropertyChangeListener(self)
self.ne = ne
self.add(ne)
else:
self.add(JLabel("Attempted Fst"))
fst = JFormattedTextField(NumberFormat.getNumberInstance(Locale.US))
fst.addPropertyChangeListener(self)
self.fst = fst
self.add(fst)
self.add(JLabel("Expected total pops"))
pops = JFormattedTextField(NumberFormat.getIntegerInstance(Locale.US))
pops.addPropertyChangeListener(self)
# self.pops = JComboBox(['1', '2', '4', '8', '12', '16'])
self.pops = pops
self.add(self.pops)
if not isDominant and not isTemporal:
self.add(JLabel("Mutation model"))
self.mut = JComboBox(["Infinite Alleles", "Stepwise"])
self.mut.addItemListener(self)
self.add(self.mut)
self.add(JLabel("Subsample size"))
sampleSize = JFormattedTextField(NumberFormat.getIntegerInstance(Locale.US))
sampleSize.addPropertyChangeListener(self)
self.sampleSize = sampleSize
self.add(self.sampleSize)
if isDominant:
self.add(JLabel("Theta"))
theta = JFormattedTextField(NumberFormat.getNumberInstance(Locale.US))
theta.addPropertyChangeListener(self)
self.theta = theta
self.add(theta)
theta.setValue(0.1)
self.add(JLabel("Beta-a"))
beta1 = JFormattedTextField(NumberFormat.getNumberInstance(Locale.US))
beta1.addPropertyChangeListener(self)
self.beta1 = beta1
self.add(beta1)
beta1.setValue(0.25)
self.add(JLabel("Beta-b"))
beta2 = JFormattedTextField(NumberFormat.getNumberInstance(Locale.US))
beta2.addPropertyChangeListener(self)
self.beta2 = beta2
self.add(beta2)
beta2.setValue(0.25)
self.add(JLabel("Critical frequency"))
crit = JFormattedTextField(NumberFormat.getNumberInstance(Locale.US))
crit.addPropertyChangeListener(self)
self.crit = crit
self.add(crit)
crit.setValue(0.99)
run = JButton("Run!")
run.addActionListener(manager)
run.setActionCommand("RunFDist")
self.run = run
self.add(run)
cancel = JButton("Stop")
cancel.addActionListener(manager)
cancel.setActionCommand("CancelFDist")
self.cancel = cancel
class EmpiricalPanel(JPanel, PropertyChangeListener, ItemListener):
def propertyChange(self, evt):
if self.ignoreChanges:
return
change = False
if not self.isTemporal:
if evt.getSource() == self.fst and evt.getPropertyName(
) == 'value':
new = float(evt.getNewValue())
old = float(evt.getOldValue())
if new > 0.99:
evt.getSource().setValue(old)
if new < -0.2:
evt.getSource().setValue(old)
elif new < 0.0:
self.systemPanel.force.setSelected(False)
self.systemPanel.force.setEnabled(False)
else:
self.systemPanel.force.setEnabled(True)
else:
if evt.getSource() == self.ne and evt.getPropertyName() == 'value':
new = int(evt.getNewValue())
old = int(evt.getOldValue())
if new < 0:
evt.getSource().setValue(old)
if self.isDominant and \
evt.getSource() in [self.theta, self.beta1, self.beta2, self.crit] and \
evt.getPropertyName() == 'value':
new = float(evt.getNewValue())
old = float(evt.getOldValue())
if new > 0.99 or new < -0.2:
evt.getSource().setValue(old)
# Subsample size
if evt.getSource() == self.sampleSize and evt.getPropertyName(
) == 'value':
change = True
new = int(evt.getNewValue())
old = int(evt.getOldValue())
if new > 50 and old > 4:
warn(
self,
'A sample size bigger than 50 is not expected to produce better results, '
+ 'while it slows the computation')
if new < 5 and (new != 0 and not self.isDominant):
evt.getSource().setValue(old)
if evt.getSource() == self.pops and evt.getPropertyName() == 'value':
change = True
new = int(evt.getNewValue())
old = int(evt.getOldValue())
if new > 100:
error(self, 'Maximum value for total populations is 100')
evt.getSource().setValue(100)
if new < self.knownPops:
error(
self,
'Expected total populations has to be at least the same as the number of populations under study.'
)
evt.getSource().setValue(self.knownPops)
if not self.isTemporal:
if evt.getSource() == self.mut:
change = True
if not change:
return
if self.menuHandles['item5000'].isEnabled():
self.menuHandles['item5000'].setEnabled(False)
warn(self, "Changed parameter will require restarting simulations")
def itemStateChanged(self, evt):
self.propertyChange(evt)
#
def getTotalPops(self):
return self.pops.getValue()
def setTotalPops(self, numPops):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.pops.setValue(numPops)
self.ignoreChanges = ignoreChanges
#
def getFst(self):
return self.fst.getValue()
def setFst(self, fst):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.fst.setValue(fst)
self.ignoreChanges = ignoreChanges
#
def getNe(self):
return self.ne.getValue()
def setNe(self, ne):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.ne.setValue(int(ne))
self.ignoreChanges = ignoreChanges
#
def getTheta(self):
return self.theta.getValue()
def setTheta(self, theta):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.theta.setValue(theta)
self.ignoreChanges = ignoreChanges
#
def getBeta(self):
return (self.beta1.getValue(), self.beta2.getValue())
def setBeta(self, beta):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.beta1.setValue(beta[0])
self.beta2.setValue(beta[1])
self.ignoreChanges = ignoreChanges
#
def getCrit(self):
return self.crit.getValue()
def setCrit(self, crit):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.crit.setValue(crit)
self.ignoreChanges = ignoreChanges
#
def getSampleSize(self):
return self.sampleSize.getValue()
def setSampleSize(self, sampleSize):
ignoreChanges = self.ignoreChanges
self.ignoreChanges = True
self.sampleSize.setValue(sampleSize)
self.ignoreChanges = ignoreChanges
def __init__(self,
menuHandles,
manager,
isDominant,
systemPanel,
isTemporal=False):
self.systemPanel = systemPanel
self.knownPops = 0
self.ignoreChanges = True
JPanel()
self.menuHandles = menuHandles
self.isDominant = isDominant
self.isTemporal = isTemporal
if isDominant:
self.setLayout(GridLayout(8, 2))
else:
self.setLayout(GridLayout(5, 2))
if isTemporal:
self.add(JLabel('Ne'))
ne = JFormattedTextField(NumberFormat.getNumberInstance(Locale.US))
ne.addPropertyChangeListener(self)
self.ne = ne
self.add(ne)
self.add(JLabel('Expected total samples'))
else:
self.add(JLabel('Attempted Fst'))
fst = JFormattedTextField(NumberFormat.getNumberInstance(
Locale.US))
fst.addPropertyChangeListener(self)
self.fst = fst
self.add(fst)
self.add(JLabel('Expected total pops'))
pops = JFormattedTextField(NumberFormat.getIntegerInstance(Locale.US))
pops.addPropertyChangeListener(self)
# self.pops = JComboBox(['1', '2', '4', '8', '12', '16'])
self.pops = pops
self.add(self.pops)
if not isDominant and not isTemporal:
self.add(JLabel('Mutation model'))
self.mut = JComboBox(['Infinite Alleles', 'Stepwise'])
self.mut.addItemListener(self)
self.add(self.mut)
else:
self.mut = None
self.add(JLabel('Subsample size'))
sampleSize = JFormattedTextField(
NumberFormat.getIntegerInstance(Locale.US))
sampleSize.addPropertyChangeListener(self)
self.sampleSize = sampleSize
self.add(self.sampleSize)
if isDominant:
self.add(JLabel('Theta'))
theta = JFormattedTextField(
NumberFormat.getNumberInstance(Locale.US))
theta.addPropertyChangeListener(self)
self.theta = theta
self.add(theta)
theta.setValue(0.1)
self.add(JLabel('Beta-a'))
beta1 = JFormattedTextField(
NumberFormat.getNumberInstance(Locale.US))
beta1.addPropertyChangeListener(self)
self.beta1 = beta1
self.add(beta1)
beta1.setValue(0.25)
self.add(JLabel('Beta-b'))
beta2 = JFormattedTextField(
NumberFormat.getNumberInstance(Locale.US))
beta2.addPropertyChangeListener(self)
self.beta2 = beta2
self.add(beta2)
beta2.setValue(0.25)
self.add(JLabel('Critical frequency'))
crit = JFormattedTextField(
NumberFormat.getNumberInstance(Locale.US))
crit.addPropertyChangeListener(self)
self.crit = crit
self.add(crit)
crit.setValue(0.99)
run = JButton('Run!')
run.addActionListener(manager)
run.setActionCommand('RunFDist')
self.run = run
self.add(run)
