class GenericTable(QtCore.QAbstractTableModel):
def __init__(self, data, headers, parent=None, *args):
QtCore.QAbstractTableModel.__init__(self, parent, *args)
self.arraydata = data
self.headerdata = headers
def rowCount(self, parent):
return len(self.arraydata)
def columnCount(self, parent):
if len(self.arraydata) > 0:
return len(self.arraydata[0])
else:
return -1
def data(self, index, role):
if not index.isValid():
return QtCore.QVariant()
elif role != QtCore.Qt.DisplayRole:
return QtCore.QVariant()
return QtCore.QVariant(self.arraydata[index.row()][index.column()])
def headerData(self, col, orientation, role):
if orientation == QtCore.Qt.Horizontal and role == QtCore.Qt.DisplayRole:
return QtCore.QVariant(self.headerdata[col])
return QtCore.QVariant()
def sort(self, Ncol, order):
'''
Sort table by given column number.
'''
if len(self.arraydata) == 0:
return
self.emit(QtCore.SIGNAL("layoutAboutToBeChanged()"))
dataIsNumeric = isNumber(self.arraydata[0][Ncol])
if dataIsNumeric:
self.arraydata = sorted(self.arraydata , key = operator.itemgetter(Ncol))
else:
self.arraydata = SortTableStrCol(self.arraydata, Ncol)
if order == QtCore.Qt.DescendingOrder:
self.arraydata.reverse()
self.emit(QtCore.SIGNAL("layoutChanged()"))
def save(self, filename):
fout = open(filename, 'w')
for header in self.headerdata:
fout.write(str(header) + '\t')
fout.write('\n')
for row in self.arraydata:
for item in row:
fout.write(str(item) + '\t')
fout.write('\n')
fout.close()
class GenericTable(QtCore.QAbstractTableModel):
def __init__(self, data, headers, parent=None, *args):
QtCore.QAbstractTableModel.__init__(self, parent, *args)
self.arraydata = data
self.headerdata = headers
def rowCount(self, parent):
return len(self.arraydata)
def columnCount(self, parent):
if len(self.arraydata) > 0:
return len(self.arraydata[0])
else:
return -1
def data(self, index, role):
if not index.isValid():
return QtCore.QVariant()
elif role != QtCore.Qt.DisplayRole:
return QtCore.QVariant()
return QtCore.QVariant(self.arraydata[index.row()][index.column()])
def headerData(self, col, orientation, role):
if orientation == QtCore.Qt.Horizontal and role == QtCore.Qt.DisplayRole:
return QtCore.QVariant(self.headerdata[col])
return QtCore.QVariant()
def sort(self, Ncol, order):
'''
Sort table by given column number.
'''
if len(self.arraydata) == 0:
return
self.emit(QtCore.SIGNAL("layoutAboutToBeChanged()"))
dataIsNumeric = isNumber(self.arraydata[0][Ncol])
if dataIsNumeric:
self.arraydata = SortTableNumericStrCol(self.arraydata, Ncol)
else:
self.arraydata = SortTableStrCol(self.arraydata, Ncol)
if order == QtCore.Qt.DescendingOrder:
self.arraydata.reverse()
self.emit(QtCore.SIGNAL("layoutChanged()"))
def save(self, filename):
fout = open(filename, 'w')
for header in self.headerdata:
fout.write(str(header) + '\t')
fout.write('\n')
for row in self.arraydata:
for item in row:
fout.write(str(item) + '\t')
fout.write('\n')
fout.close()
def saveSummaryTable(self, filename, statsTestResults, sampleName1,
sampleName2, coverage):
tableData = statsTestResults.tableData(True)
# update table summarizing statistical results
oneMinAlphaStr = str((1.0 - coverage))
tableHeadings = list(statsTestResults.profile.hierarchyHeadings)
tableHeadings += [sampleName1, sampleName2]
tableHeadings += ['Parent seq. 1', 'Parent seq. 2']
tableHeadings += ['Rel. freq. 1 (%)', 'Rel. freq. 2 (%)']
tableHeadings += ['p-values', 'p-values (corrected)']
tableHeadings += ['Effect size']
tableHeadings += [str(coverage * 100) + '% lower CI']
tableHeadings += [str(coverage * 100) + '% upper CI']
tableHeadings += ['Power (alpha = ' + oneMinAlphaStr + ')']
tableHeadings += [
'Equal sample size (alpha = ' + oneMinAlphaStr + '; power = 0.80)'
]
tableData = SortTableStrCol(tableData, 0)
fout = open(filename, 'w')
for heading in tableHeadings:
fout.write(heading + '\t')
fout.write('\n')
for row in tableData:
for entry in row:
fout.write(str(entry) + '\t')
fout.write('\n')
fout.close()
def sort(self, Ncol, order):
'''
Sort table by given column number.
'''
if len(self.arraydata) == 0:
return
self.emit(QtCore.SIGNAL("layoutAboutToBeChanged()"))
dataIsNumeric = isNumber(self.arraydata[0][Ncol])
if dataIsNumeric:
self.arraydata = sorted(self.arraydata , key = operator.itemgetter(Ncol))
else:
self.arraydata = SortTableStrCol(self.arraydata, Ncol)
if order == QtCore.Qt.DescendingOrder:
self.arraydata.reverse()
self.emit(QtCore.SIGNAL("layoutChanged()"))
def sort(self, Ncol, order):
'''
Sort table by given column number.
'''
if len(self.arraydata) == 0:
return
self.emit(QtCore.SIGNAL("layoutAboutToBeChanged()"))
dataIsNumeric = isNumber(self.arraydata[0][Ncol])
if dataIsNumeric:
self.arraydata = SortTableNumericStrCol(self.arraydata, Ncol)
else:
self.arraydata = SortTableStrCol(self.arraydata, Ncol)
if order == QtCore.Qt.DescendingOrder:
self.arraydata.reverse()
self.emit(QtCore.SIGNAL("layoutChanged()"))
def saveSummaryTable(self, filename, statsTestResults):
tableData, tableHeadings = statsTestResults.tableData(True)
tableData = SortTableStrCol(tableData, 0)
fout = open(filename, 'w')
for heading in tableHeadings:
fout.write(heading + '\t')
fout.write('\n')
for row in tableData:
for entry in row:
fout.write(str(entry) + '\t')
fout.write('\n')
fout.close()
