class myRenderer( DefaultTableCellRenderer ) :
#---------------------------------------------------------------------------
# Name: __init__()
# Role: Constructor - instantiate the JFormattedTextField to be used
#---------------------------------------------------------------------------
def __init__( self ) :
nf = NumberFormat.getInstance()
nf.setMinimumFractionDigits( 2 )
nf.setMaximumFractionDigits( 2 )
self.result = JFormattedTextField(
nf,
horizontalAlignment = JTextField.RIGHT
)
#---------------------------------------------------------------------------
# Name: getTableCellRendererComponent()
# Role: Return the component containing the rendered value
# Note: Called frequently, don't create a new component each time
#---------------------------------------------------------------------------
def getTableCellRendererComponent(
self,
table, # JTable - table containing value
value, # Object - value being rendered
isSelected, # boolean - Is value selected?
hasFocus, # boolean - Does this cell have focus?
rowIndex, # int - Row # (0..N)
vColIndex # int - Col # (0..N)
) :
self.result.setValue( value )
return self.result
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
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
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
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)
