def getValues(self):
"""Get the smoothing parameters (not limit).
Checks for valid input.
"""
# TODO(gns) - make alert boxes instead of printing to terminal
strings = self.listCtrl.getColumnStrings(1)
smoothing = utils.getBinaryReponse(strings[0])
if smoothing == 'Error':
smoothing = True
print 'Smoothing entry is not a binary value (using default - True)'
if utils.isNumber(strings[1]):
wlen = float(strings[1])
else:
wlen = 5
print 'Wlen entry is not a number (using default - %d)' % wlen
if utils.isNumber(strings[2]):
smoothes = int(strings[2])
else:
smoothes = 2
print 'Wlen entry is not a number (using default - %d)' % smoothes
if utils.isNumber(strings[3]):
poly = float(strings[3])
else:
poly = 1
print 'Polynomial entry is not a number (using default - %d)' % poly
return smoothing, wlen, smoothes, poly
def getValues(self):
"""Get the smoothing parameters (not limit).
Checks for valid input.
"""
# TODO(gns) - make alert boxes instead of printing to terminal
strings = self.listCtrl.getColumnStrings(1)
smoothing = utils.getBinaryReponse(strings[0])
if smoothing == 'Error':
smoothing = True
print 'Smoothing entry is not a binary value (using default - True)'
if utils.isNumber(strings[1]):
wlen = float(strings[1])
else:
wlen = 5
print 'Wlen entry is not a number (using default - %d)' %wlen
if utils.isNumber(strings[2]):
smoothes = int(strings[2])
else:
smoothes = 2
print 'Wlen entry is not a number (using default - %d)' %smoothes
if utils.isNumber(strings[3]):
poly = float(strings[3])
else:
poly = 1
print 'Polynomial entry is not a number (using default - %d)' %poly
return smoothing,wlen,smoothes,poly
def eventButtonSimulate(self,
event): # wxGlade: AtroposGui.<event_handler>
"""Simulate mass spectrum, display it and fill in the optimise ListCtrl with the
deconvolution results.
"""
# please wait dialog
bi = wx.BusyInfo("Simulating Spectrum...", self)
wx.Yield()
oneFwhm = 0
if self.checkboxSinglePeakFwhm.GetValue():
oneFwhm = utils.isNumber(self.textCtrlSinglePeakFwhm.GetValue())
if oneFwhm:
oneFwhm = float(self.textCtrlSinglePeakFwhm.GetValue())
else:
print 'Unrecognised value for single FWHM\nUsing default(10)'
oneFwhm = 10
self.settings.leastSquaresOptimisation(oneFwhm)
self.simulationCompleted = True
self.radioBoxDisplay.SetSelection(3)
self.listCtrlOptimise.calculatePercentageArea()
self.listCtrlOptimise.calculatePercentageIntensity()
# please wait dialog
bi.Destroy()
def setValues(self, values):
# TODO(gns) - do the comment
self.values = []
for value in values:
if utils.isNumber(value):
self.values.append(float(value))
else:
self.values.append(None)
def setValues(self,values):
# TODO(gns) - do the comment
self.values = []
for value in values:
if utils.isNumber(value):
self.values.append(float(value))
else:
self.values.append(None)
def getLimit(self):
"""Get the lower limit for peak finding. Value is given as a
percentage of base peak intensity.
"""
limit = self.listCtrlSmoothing.listCtrl.GetItem(4,1).GetText()
if utils.isNumber(limit):
return float(limit)
else:
print 'Limit value is not a number (using default - 0.0)'
return 0
def getLimit(self):
"""Get the lower limit for peak finding. Value is given as a
percentage of base peak intensity.
"""
limit = self.listCtrlSmoothing.listCtrl.GetItem(4, 1).GetText()
if utils.isNumber(limit):
return float(limit)
else:
print 'Limit value is not a number (using default - 0.0)'
return 0
def OnEndLabelEdit(self,event):
"""Function for editing the value labels for each of the
data files.
"""
val = event.GetText()
message = 'Only enter numerical values here'
if len(val):
if utils.isNumber(val):
self.listCtrl.SetItemText(event.GetIndex(),val)
self.updateUnitValues()
self.plotPanel.refresh_plot()
else:
gf.warningDialog(message)
event.Veto()
def eventAddPeak(self, event): # wxGlade: AtroposGui.<event_handler>
"""Add additional peaks to those automatically detected using first derivative."""
mz = self.textCtrlAddPeak.GetValue()
if utils.isNumber(mz):
self.settings.addPeakMz(float(mz))
limit = self.settings.getLimit()
self.msPanel.plotMsWithGpeaks(limit)
else:
dlg = wx.MessageDialog(self,
"Enter numerical m/z value!",
"Add Peak Error", wx.OK|wx.ICON_EXCLAMATION)
result = dlg.ShowModal()
dlg.Destroy()
def eventAddPeak(self, event): # wxGlade: AtroposGui.<event_handler>
"""Add additional peaks to those automatically detected using first derivative."""
mz = self.textCtrlAddPeak.GetValue()
if utils.isNumber(mz):
self.settings.addPeakMz(float(mz))
limit = self.settings.getLimit()
self.msPanel.plotMsWithGpeaks(limit)
else:
dlg = wx.MessageDialog(self, "Enter numerical m/z value!",
"Add Peak Error",
wx.OK | wx.ICON_EXCLAMATION)
result = dlg.ShowModal()
dlg.Destroy()
def setPeakMzsAndSpecies(self,peakIdsComplexString,name,column=-1):
"""Set the peak m/zs corresponding to the peak ids entered in the
ListCtrl. Also creates the Species() object and sets that.
:parameter peakIdsComplexString: String containing peak ids can include commas and hyphens e.g. '4-7,9'.
:parameter name: Species name
:parameter column: The column to write to. Use -1 to use currently selected column
"""
# get column to use
if column == -1:
self.getCurrentColumn()
# get and set mz values
peakIds = utils.getHyphenCommaList(peakIdsComplexString)
gPeaks = self.settings.msPanel.ms.getgPeaksFromIds(peakIds)
mzs = [ "%.2f" %gPeaks[k][0] for k in gPeaks.keys()]
mzString = ''
for i,v in enumerate(mzs):
if not i:
mzString = v
else:
mzString += ', '+v
self.listCtrl.SetStringItem(2,column,mzString)
# get Peak FWHM value
peakFwhm = self.listCtrl.GetItem(7,column).GetText()
if utils.isNumber(peakFwhm):
peakFwhm = float(peakFwhm)
else:
peakFwhm = 10
print 'Peak Fwhm not a number\nUsing 10 ...'
# set species
spOb = Species(name)
spOb.setSpecies(gPeaks, peakFwhm)
self.settings.msPanel.ms.addSpecies(spOb,allowReplace=1)
mass,error,zs = spOb.calculateMassAndCharges([float(mz) for mz in mzs])
self.listCtrl.SetStringItem(3,column,"{:,}".format(round(mass,2)))
self.listCtrl.SetStringItem(4,column,"{:,}".format(round(error,2)))
# display zs
if self.zsEmpty(column):
self.setZs(zs,column)
# put default calculated zs into ListCtrl
self.listCtrl.SetStringItem(8,column,str(spOb.charges)[1:-1])
# record current column
self.settings.setSpeciesColumn(column)
def OnEndLabelEdit(self, event):
"""Editing CCS value of a selected conformation entry in the ListCtrl.
"""
newVal = event.GetText()
i = event.GetIndex()
if utils.isNumber(newVal):
newVal = float(newVal)
self.conformations[i] = newVal
self.updateListCtrl()
self.plotPanel.refresh_plot()
else:
if not newVal == '':
message = 'Only enter a numerical value here!'
gf.warningDialog(message)
event.Veto()
else:
del self.conformations[i]
self.updateListCtrl()
def OnEndLabelEdit(self,event):
"""Editing CCS value of a selected conformation entry in the ListCtrl.
"""
newVal = event.GetText()
i = event.GetIndex()
if utils.isNumber(newVal):
newVal = float(newVal)
self.conformations[i] = newVal
self.updateListCtrl()
self.plotPanel.refresh_plot()
else:
if not newVal == '':
message = 'Only enter a numerical value here!'
gf.warningDialog(message)
event.Veto()
else:
del self.conformations[i]
self.updateListCtrl()
def checkFieldsValid(self):
"""Check if each of the plotting options contains a valid input.
:returns: valid,errors - Boolean, list of the names of values with errors
"""
valid = True
errors = []
smoothing = self.getSettingValue('Smoothing')
if not utils.isBinaryResponse(smoothing):
valid = False
errors.append('Smoothing')
aaxis = self.getSettingValue('Auto Axis')
if not utils.isBinaryResponse(aaxis):
valid = False
errors.append('Auto Axis')
colour = self.getSettingValue('Colour')
if not utils.isMplColour(colour):
valid = False
errors.append('Colour')
lw = self.getSettingValue('Line Width')
if not utils.isNumber(lw):
valid = False
errors.append('Line Width')
return valid, errors
def checkFieldsValid(self):
"""Check if each of the plotting options contains a valid input.
:returns: valid,errors - Boolean, list of the names of values with errors
"""
valid = True
errors = []
smoothing = self.getSettingValue('Smoothing')
if not utils.isBinaryResponse(smoothing):
valid = False
errors.append('Smoothing')
aaxis = self.getSettingValue('Auto Axis')
if not utils.isBinaryResponse(aaxis):
valid = False
errors.append('Auto Axis')
colour = self.getSettingValue('Colour')
if not utils.isMplColour(colour):
valid = False
errors.append('Colour')
lw = self.getSettingValue('Line Width')
if not utils.isNumber(lw):
valid = False
errors.append('Line Width')
return valid,errors
def eventButtonSimulate(self, event): # wxGlade: AtroposGui.<event_handler>
"""Simulate mass spectrum, display it and fill in the optimise ListCtrl with the
deconvolution results.
"""
# please wait dialog
bi = wx.BusyInfo("Simulating Spectrum...",self)
wx.Yield()
oneFwhm = 0
if self.checkboxSinglePeakFwhm.GetValue():
oneFwhm = utils.isNumber(self.textCtrlSinglePeakFwhm.GetValue())
if oneFwhm:
oneFwhm = float(self.textCtrlSinglePeakFwhm.GetValue())
else:
print 'Unrecognised value for single FWHM\nUsing default(10)'
oneFwhm = 10
self.settings.leastSquaresOptimisation(oneFwhm)
self.simulationCompleted = True
self.radioBoxDisplay.SetSelection(3)
self.listCtrlOptimise.calculatePercentageArea()
self.listCtrlOptimise.calculatePercentageIntensity()
# please wait dialog
bi.Destroy()
def setVmax(self, vmax):
"""The value used for the maximum color saturation value.
"""
if utils.isNumber(vmax):
self.vmax = float(vmax)
def setVmax(self,vmax):
"""The value used for the maximum color saturation value.
"""
if utils.isNumber(vmax):
self.vmax = float(vmax)
def OnEndLabelEdit(self,event):
"""Context specific function for deciding what to do when a cell
is edited depending on which row it belongs to.
"""
row = event.m_itemIndex
column = event.GetColumn()
#===========================================================================
# Species Name
#===========================================================================
if row == 0:
newName = event.GetText()
if not column in self.columnSpeciesNames:
# name not set before
self.columnSpeciesNames[column] = newName
else:
# name already set and changing it
spD = self.settings.msPanel.ms.species
spDsimulated = self.settings.msPanel.ms.simulatedSpecies
if not newName in spD:
oldName = self.columnSpeciesNames[column]
# TODO (gns) - this isn't doing enough
# The problem must be coming from elsewhere (trying to access
# species 'Default09' for example)
# The problem occured when I reloaded the figure, so look into what
# happens when that button is pushed
spD[newName] = spD.pop(oldName)
spD[newName].name = newName
try:
spDsimulated[newName] = spDsimulated.pop(oldName)
spDsimulated[newName].name = newName
except:
spDsimulated[newName] = Species(newName)
self.columnSpeciesNames[column] = newName
else:
print 'Provided species name is already in use'
#===========================================================================
# Peak finding
#===========================================================================
elif row == 1:
# get text and set m/zs
text = event.GetText()
# Add default name if none given
item = self.listCtrl.GetItem(0,column)
name = item.GetText()
if str(name) == '':
name = 'Default%02d' %column
self.listCtrl.SetStringItem(0,column,name)
self.columnSpeciesNames[column] = name
self.setPeakMzsAndSpecies(text,name, column)
#===========================================================================
# Entering mass
#===========================================================================
elif row == 3:
'''
use the mass to display theoretical charge states
only works on unassigned Species # TODO(gns) - why?
'''
charges = self.listCtrlAssigningSpecies.listCtrl.GetItem(5,column).GetText()
if charges == '': # TODO(gns) - why do the charges need to be blank?
# TODO(gns) - warning dialog to say "Enter charge states before simulating"
self.setManualMass(event.GetText())
else:
# Clear all the peak information
# open warning box saying "Enter charge states before simulating"
# Make sure that adding the charges recalculates the peak m/zs
# and sets them properly
event.Veto()
#===========================================================================
# Changing charges
#===========================================================================
elif row == 5:
event.Veto()
#===========================================================================
# Peak FWHM
#===========================================================================
elif row == 7:
# get current species name
item = self.listCtrl.GetItem(0,column)
name = item.GetText()
peakFwhm = event.GetText()
print peakFwhm, 'peakfwhm'
if utils.isNumber(peakFwhm):
peakFwhm = float(peakFwhm)
if name in self.settings.msPanel.ms.species.keys():
self.settings.msPanel.ms.species[name].peakFwhm = peakFwhm
else:
self.listCtrl.SetStringItem(row,column, "10")
event.Veto()
print 'Peak FWHM value not a number\nReverting to default (10)'
#===========================================================================
# Charges to simulate
#===========================================================================
elif row == 8:
# get current species name
item = self.listCtrl.GetItem(0,column)
name = item.GetText()
zstext = event.GetText()
zs = utils.getHyphenCommaList(zstext)
if zs:
#self.zsToSimulate[column] = zs
if name != '':
self.settings.msPanel.ms.species[name].charges = zs
else:
print 'Invalid list of charges: %s' %zstext
event.Veto()
