def run(self):
frame = JFrame('cbEdit3',
size=(200, 125),
locationRelativeTo=None,
defaultCloseOperation=JFrame.EXIT_ON_CLOSE)
table = JTable(tm(), rowHeight=20)
table.setDefaultRenderer(JComboBox, cbRenderer())
table.setDefaultEditor(JComboBox, cbEditor())
frame.add(JScrollPane(table))
frame.setVisible(1)
def done(self):
table = JTable(methodTableModel(
self.data,
['Method', 'Description / Abstract'],
),
font=monoFont,
autoResizeMode=JTable.AUTO_RESIZE_LAST_COLUMN,
selectionMode=ListSelectionModel.SINGLE_SELECTION)
table.setDefaultRenderer(String, methRenderer())
table.getTableHeader().setReorderingAllowed(0)
self.tPanes.extend(self.getTableInfo(table))
self.splitPane.setBottomComponent(JScrollPane(table))
def run(self):
frame = JFrame(
'SpinEdit3',
size=(200, 106),
# size = ( 200, 116 ),
locationRelativeTo=None,
defaultCloseOperation=JFrame.EXIT_ON_CLOSE)
table = JTable(tm(), rowHeight=20)
# table = JTable( tm(), rowHeight = 25 )
table.setDefaultRenderer(JSpinner, sRenderer())
table.setDefaultEditor(JSpinner, editor())
frame.add(JScrollPane(table))
frame.setVisible(1)
def run(self):
frame = JFrame('SecConfigReport_03',
size=(300, 300),
locationRelativeTo=None,
defaultCloseOperation=JFrame.EXIT_ON_CLOSE)
data = []
text = AdminTask.generateSecConfigReport()
for line in text.splitlines()[2:]:
data.append([info.strip() for info in line[:-2].split(';')])
table = JTable(reportTableModel(
data,
';;;'.split(';'),
),
selectionMode=ListSelectionModel.SINGLE_SELECTION)
table.setDefaultRenderer(String, reportRenderer())
frame.add(JScrollPane(table))
frame.pack()
frame.setVisible(1)
def addTabs(self, container):
head = 'Row,Col,Cell'.split(',')
junk = 'False,True'.split(',')
data = [[0, 1], [0, 1]]
info = JTable( # Used to get default attributes
data,
head,
selectionMode=LSM.SINGLE_SELECTION)
bTable = JTable(booleanTM(self.settings(info), head))
bTable.setDefaultRenderer(Boolean, boolRenderer())
tab1 = JPanel()
tab1.add(JScrollPane(bTable))
info = JTable(data, head, selectionMode=LSM.SINGLE_INTERVAL_SELECTION)
bTable = JTable(booleanTM(self.settings(info), head))
bTable.setDefaultRenderer(Boolean, boolRenderer())
tab2 = JPanel()
tab2.add(JScrollPane(bTable))
info = JTable(data,
head,
selectionMode=LSM.MULTIPLE_INTERVAL_SELECTION)
bTable = JTable(booleanTM(self.settings(info), head))
bTable.setDefaultRenderer(Boolean, boolRenderer())
tab3 = JPanel()
tab3.add(JScrollPane(bTable))
tabs = JTabbedPane()
tabs.addTab('Single', tab1)
tabs.addTab('One Group', tab2)
tabs.addTab('Multi-Group', tab3)
container.add(tabs)
class SelPanel(JDialog, ActionListener):
def actionPerformed(self, event):
option = event.getActionCommand()
if option == 'Close':
self.dispose()
elif option == 'SCI':
chooser = JFileChooser()
returnVal = chooser.showSaveDialog(self)
if returnVal == JFileChooser.APPROVE_OPTION:
fileName = chooser.getSelectedFile().getPath()
f = open(fileName, 'w')
f.write("\t".join([
"Het", "Fst", "0.5(1-pval)quantile", "median",
"0.5(1+pval)quantile"
]) + "\n")
for line in self.confLines:
f.write('\t'.join(map(lambda x: str(x), line)) + "\n")
f.close()
elif option == 'SLL':
chooser = JFileChooser()
returnVal = chooser.showSaveDialog(self)
if returnVal == JFileChooser.APPROVE_OPTION:
fileName = chooser.getSelectedFile().getPath()
f = open(fileName, 'w')
f.write("\t".join(
["Locus", "Het", "Fst", "P(Simul Fst<sample Fst)"]) + "\n")
for i in range(self.data.size()):
line = self.data.elementAt(i)
lineList = [str(line.elementAt(0))]
lineList.append(str(line.elementAt(1)))
lineList.append(str(line.elementAt(2)))
lineList.append(str(line.elementAt(3)))
f.write("\t".join(lineList) + "\n")
f.close()
def getP(self, pvLine):
#there is a copy of this on Main
if self.isDominant:
p1 = pvLine[2]
p2 = pvLine[3]
p3 = pvLine[4]
p = p1 - 0.5 * (p1 + p2 - 1)
return p
else:
return pvLine[3]
def calcFalsePositives(self, pv, ci, fdr):
falses = []
pys = []
for i in range(len(pv)):
p = self.getP(pv[i])
py = 1 - 2 * abs(p - 0.5)
pys.append(py)
#if p > ci or p<1-ci:
# pys.append(py)
pys.append(0.0)
pys.sort()
rate = []
maxRank = 0
for i in range(len(pys)):
if pys[i] <= fdr * i / len(pys):
maxRank = i
#print maxRank
falseReports = []
for pvLine in pv:
p = self.getP(pvLine)
py = 1 - 2 * abs(p - 0.5)
if py in pys:
if pys.index(py) <= maxRank:
falseReports.append("Outlier")
else:
falseReports.append("--")
else:
falseReports.append("NA")
return falseReports
def initTable(self, lociNames, pv, ci, locusFst):
colNames = Vector()
colNames.add('Locus')
colNames.add('Het')
colNames.add('Fst')
colNames.add('P(simulated Fst < sample Fst)')
colNames.add('FDR')
data = Vector()
self.data = data
falses = self.calcFalsePositives(pv, ci, self.fdr)
currentPos = 0
for i in range(len(lociNames)):
line = Vector()
locus = lociNames[i]
line.add(locus)
if not locusFst[i]:
line.add("NA")
line.add("NA")
line.add("NA")
line.add("NA")
else:
line.add(str(pv[currentPos][0]))
line.add(str(pv[currentPos][1]))
line.add(str(self.getP(pv[currentPos])))
line.add(str(falses[currentPos]))
currentPos += 1
data.add(line)
self.table = JTable(data, colNames)
self.table.setDefaultRenderer(
Class.forName("java.lang.Object"),
ColorRenderer(data, ci, self.chart.neuColor, self.chart.balColor,
self.chart.posColor))
def __init__(self, frame, chart, lociNames, pv, ci, confLines, locusFst,
isDominant, fdr):
JDialog(frame)
self.chart = chart
self.frame = frame
self.confLines = confLines
self.isDominant = isDominant
self.fdr = fdr
pane = self.getRootPane().getContentPane()
pane.setLayout(BorderLayout())
self.initTable(lociNames, pv, ci, locusFst)
scrollPane = JScrollPane(self.table)
osName = System.getProperty('os.name').lower()
if not System.getProperty('java.specification.version')[-1] == '5':
self.table.setFillsViewportHeight(True)
pane.add(scrollPane, BorderLayout.CENTER)
buttonPane = JPanel()
sll = JButton('Save loci list')
sll.addActionListener(self)
sll.setActionCommand('SLL')
buttonPane.add(sll)
sci = JButton('Save confidence intervals')
sci.addActionListener(self)
sci.setActionCommand('SCI')
buttonPane.add(sci)
close = JButton('Close')
close.addActionListener(self)
close.setActionCommand('Close')
buttonPane.add(close)
pane.add(buttonPane, BorderLayout.PAGE_END)
self.pack()
class SelPanel(JDialog, ActionListener):
def actionPerformed(self, event):
option = event.getActionCommand()
if option == 'Close':
self.dispose()
elif option == 'SCI':
chooser = JFileChooser()
returnVal = chooser.showSaveDialog(self)
if returnVal == JFileChooser.APPROVE_OPTION:
fileName = chooser.getSelectedFile().getPath()
f = open(fileName, 'w')
f.write("\t".join(["Het", "Fst", "0.5(1-pval)quantile", "median", "0.5(1+pval)quantile"]) + "\n")
for line in self.confLines:
f.write('\t'.join(map(lambda x: str(x), line)) + "\n")
f.close()
elif option == 'SLL':
chooser = JFileChooser()
returnVal = chooser.showSaveDialog(self)
if returnVal == JFileChooser.APPROVE_OPTION:
fileName = chooser.getSelectedFile().getPath()
f = open(fileName, 'w')
f.write("\t".join(["Locus", "Het", "Fst", "P(Simul Fst<sample Fst)"]) + "\n")
for i in range(self.data.size()):
line = self.data.elementAt(i)
lineList = [str(line.elementAt(0))]
lineList.append(str(line.elementAt(1)))
lineList.append(str(line.elementAt(2)))
lineList.append(str(line.elementAt(3)))
f.write("\t".join(lineList) + "\n")
f.close()
def getP(self, pvLine):
#there is a copy of this on Main
if self.isDominant:
p1 = pvLine[2]
p2 = pvLine[3]
p3 = pvLine[4]
p = p1 - 0.5 * (p1+p2-1)
return p
else:
return pvLine[3]
def calcFalsePositives(self, pv, ci, fdr):
falses = []
pys = []
for i in range(len(pv)):
p = self.getP(pv[i])
py = 1-2*abs(p-0.5)
pys.append(py)
#if p > ci or p<1-ci:
# pys.append(py)
pys.append(0.0)
pys.sort()
rate = []
maxRank=0
for i in range(len(pys)):
if pys[i]<=fdr*i/len(pys):
maxRank = i
#print maxRank
falseReports = []
for pvLine in pv:
p = self.getP(pvLine)
py = 1-2*abs(p-0.5)
if py in pys:
if pys.index(py)<=maxRank:
falseReports.append("Outlier")
else:
falseReports.append("--")
else:
falseReports.append("NA")
return falseReports
def initTable(self, lociNames, pv, ci, locusFst):
colNames = Vector()
colNames.add('Locus')
colNames.add('Het')
colNames.add('Fst')
colNames.add('P(simulated Fst < sample Fst)')
colNames.add('FDR')
data = Vector()
self.data = data
falses = self.calcFalsePositives(pv, ci, self.fdr)
currentPos = 0
for i in range(len(lociNames)):
line = Vector()
locus = lociNames[i]
line.add(locus)
if not locusFst[i]:
line.add("NA")
line.add("NA")
line.add("NA")
line.add("NA")
else:
line.add(str(pv[currentPos][0]))
line.add(str(pv[currentPos][1]))
line.add(str(self.getP(pv[currentPos])))
line.add(str(falses[currentPos]))
currentPos += 1
data.add(line)
self.table = JTable(data, colNames)
self.table.setDefaultRenderer(Class.forName("java.lang.Object"),
ColorRenderer(data, ci, self.chart.neuColor,
self.chart.balColor, self.chart.posColor))
def __init__(self, frame, chart, lociNames, pv,
ci, confLines, locusFst, isDominant, fdr):
JDialog(frame)
self.chart = chart
self.frame = frame
self.confLines = confLines
self.isDominant = isDominant
self.fdr = fdr
pane = self.getRootPane().getContentPane()
pane.setLayout(BorderLayout())
self.initTable(lociNames, pv, ci, locusFst)
scrollPane = JScrollPane(self.table)
osName = System.getProperty('os.name').lower()
if not System.getProperty('java.specification.version')[-1] == '5':
self.table.setFillsViewportHeight(True)
pane.add(scrollPane, BorderLayout.CENTER)
buttonPane = JPanel()
sll = JButton('Save loci list')
sll.addActionListener(self)
sll.setActionCommand('SLL')
buttonPane.add(sll)
sci = JButton('Save confidence intervals')
sci.addActionListener(self)
sci.setActionCommand('SCI')
buttonPane.add(sci)
close = JButton('Close')
close.addActionListener(self)
close.setActionCommand('Close')
buttonPane.add(close)
pane.add(buttonPane, BorderLayout.PAGE_END)
self.pack()
