def makeReferencesPanel(self):
"""Make references selection panel."""
# init panel
ctrlPanel = mwx.bgrPanel(self, -1, images.lib["bgrControlbar"], size=(-1, mwx.CONTROLBAR_HEIGHT))
# make controls
references_label = wx.StaticText(ctrlPanel, -1, "References:")
references_label.SetFont(wx.SMALL_FONT)
choices = libs.references.keys()
choices.sort()
choices.insert(0, "Reference lists")
self.references_choice = wx.Choice(ctrlPanel, -1, choices=choices, size=(250, mwx.SMALL_CHOICE_HEIGHT))
self.references_choice.Select(0)
self.references_choice.Bind(wx.EVT_CHOICE, self.onReferencesSelected)
tolerance_label = wx.StaticText(ctrlPanel, -1, "Tolerance:")
tolerance_label.SetFont(wx.SMALL_FONT)
self.tolerance_value = wx.TextCtrl(
ctrlPanel,
-1,
str(config.calibration["tolerance"]),
size=(50, mwx.SMALL_TEXTCTRL_HEIGHT),
validator=mwx.validator("floatPos"),
)
self.tolerance_value.SetFont(wx.SMALL_FONT)
self.toleranceUnits_label = wx.StaticText(ctrlPanel, -1, config.calibration["units"])
self.toleranceUnits_label.SetFont(wx.SMALL_FONT)
self.statCalibration_check = wx.CheckBox(ctrlPanel, -1, "Statistical only")
self.statCalibration_check.SetFont(wx.SMALL_FONT)
self.statCalibration_check.Bind(wx.EVT_CHECKBOX, self.onStatCalibration)
self.makeReferencesList()
# pack controls
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(references_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.references_choice, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(tolerance_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.tolerance_value, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.toleranceUnits_label, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.statCalibration_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
controls = wx.BoxSizer(wx.VERTICAL)
controls.Add(sizer, 1, wx.EXPAND)
controls.Fit(ctrlPanel)
ctrlPanel.SetSizer(controls)
# pack main
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(ctrlPanel, 0, wx.EXPAND, 0)
mainSizer.Add(self.referencesList, 1, wx.EXPAND | wx.ALL, mwx.LISTCTRL_NO_SPACE)
return mainSizer
def makeGUI(self):
"""Make GUI elements."""
staticSizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, ""), wx.VERTICAL)
# make elements
threshold_label = wx.StaticText(self, -1, "Minimal value:")
self.threshold_value = wx.TextCtrl(self, -1, "", size=(150, -1), validator=mwx.validator('floatPos'))
self.threshold_value.Bind(wx.EVT_TEXT, self.onChange)
thresholdType_label = wx.StaticText(self, -1, "Threshold type:")
choices=['m/z', 'a.i.', 'Intensity', 'Relative Intensity', 's/n']
self.thresholdType_choice = wx.Choice(self, -1, choices=choices, size=(150, mwx.CHOICE_HEIGHT))
self.thresholdType_choice.Select(0)
cancel_butt = wx.Button(self, wx.ID_CANCEL, "Cancel")
delete_butt = wx.Button(self, wx.ID_OK, "Delete")
delete_butt.Bind(wx.EVT_BUTTON, self.onDelete)
delete_butt.SetDefault()
# pack elements
grid = wx.GridBagSizer(mwx.GRIDBAG_VSPACE, mwx.GRIDBAG_HSPACE)
grid.Add(threshold_label, (0,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.threshold_value, (0,1))
grid.Add(thresholdType_label, (1,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.thresholdType_choice, (1,1))
staticSizer.Add(grid, 0, wx.ALL, 5)
buttSizer = wx.BoxSizer(wx.HORIZONTAL)
buttSizer.Add(cancel_butt, 0, wx.RIGHT, 15)
buttSizer.Add(delete_butt, 0)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(staticSizer, 0, wx.CENTER|wx.ALL, mwx.PANEL_SPACE_MAIN)
mainSizer.Add(buttSizer, 0, wx.CENTER|wx.LEFT|wx.RIGHT|wx.BOTTOM, mwx.PANEL_SPACE_MAIN)
return mainSizer
def makeControlbar(self):
"""Make controlbar."""
# init toolbar
panel = mwx.bgrPanel(self, -1, images.lib["bgrControlbar"], size=(-1, mwx.CONTROLBAR_HEIGHT))
# make elements
self.collapse_butt = wx.BitmapButton(
panel, -1, images.lib["arrowsDown"], size=(mwx.TOOLBAR_TOOLSIZE), style=wx.BORDER_NONE
)
self.collapse_butt.Bind(wx.EVT_BUTTON, self.onCollapse)
fitTo_label = wx.StaticText(panel, -1, "Fit to:")
fitTo_label.SetFont(wx.SMALL_FONT)
self.fitToPeaklist_radio = wx.RadioButton(panel, -1, "Peak list", style=wx.RB_GROUP)
self.fitToPeaklist_radio.SetFont(wx.SMALL_FONT)
self.fitToSpectrum_radio = wx.RadioButton(panel, -1, "Spectrum")
self.fitToSpectrum_radio.SetFont(wx.SMALL_FONT)
self.fitToPeaklist_radio.SetValue(True)
if config.envelopeFit["fit"] == "spectrum":
self.fitToSpectrum_radio.SetValue(True)
fwhm_label = wx.StaticText(panel, -1, "Default FWHM:")
fwhm_label.SetFont(wx.SMALL_FONT)
self.fwhm_value = wx.TextCtrl(
panel,
-1,
str(config.envelopeFit["fwhm"]),
size=(50, mwx.SMALL_TEXTCTRL_HEIGHT),
validator=mwx.validator("floatPos"),
)
self.fwhm_value.SetFont(wx.SMALL_FONT)
self.forceFwhm_check = wx.CheckBox(panel, -1, "Force")
self.forceFwhm_check.SetFont(wx.SMALL_FONT)
self.forceFwhm_check.SetValue(config.envelopeFit["forceFwhm"])
relThreshold_label = wx.StaticText(panel, -1, "Rel. int. threshold:")
relThreshold_label.SetFont(wx.SMALL_FONT)
relThresholdUnits_label = wx.StaticText(panel, -1, "%")
relThresholdUnits_label.SetFont(wx.SMALL_FONT)
self.relThreshold_value = wx.TextCtrl(
panel,
-1,
str(config.envelopeFit["relThreshold"] * 100),
size=(50, mwx.SMALL_TEXTCTRL_HEIGHT),
validator=mwx.validator("floatPos"),
)
self.relThreshold_value.SetFont(wx.SMALL_FONT)
self.autoAlign_check = wx.CheckBox(panel, -1, "Auto align")
self.autoAlign_check.SetFont(wx.SMALL_FONT)
self.autoAlign_check.SetValue(config.envelopeFit["autoAlign"])
self.average_label = wx.StaticText(panel, -1, "", size=(100, -1))
self.average_label.SetFont(wx.SMALL_FONT)
self.updateAverageLabel()
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(self.collapse_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(10)
sizer.Add(fitTo_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.fitToPeaklist_radio, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.fitToSpectrum_radio, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(fwhm_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.fwhm_value, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.forceFwhm_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(relThreshold_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.relThreshold_value, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(relThresholdUnits_label, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.autoAlign_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.average_label, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
mainSizer.Fit(panel)
panel.SetSizer(mainSizer)
return panel
def makeIonseriesPanel(self):
"""Make controls for ionseries."""
# init panel
ctrlPanel = mwx.bgrPanel(self,
-1,
images.lib['bgrControlbar'],
size=(-1, mwx.CONTROLBAR_HEIGHT))
# make controls
ionseriesAgent_label = wx.StaticText(ctrlPanel, -1, "Agent:")
ionseriesAgent_label.SetFont(wx.SMALL_FONT)
self.ionseriesAgentFormula_value = wx.TextCtrl(
ctrlPanel,
-1,
config.massCalculator['ionseriesAgent'],
size=(60, mwx.SMALL_TEXTCTRL_HEIGHT))
self.ionseriesAgentFormula_value.SetFont(wx.SMALL_FONT)
self.ionseriesAgentFormula_value.Bind(wx.EVT_TEXT,
self.onCompoundChanged)
ionseriesAgentCharge_label = wx.StaticText(ctrlPanel, -1,
"Agent charge:")
ionseriesAgentCharge_label.SetFont(wx.SMALL_FONT)
self.ionseriesAgentCharge_value = wx.TextCtrl(
ctrlPanel,
-1,
str(config.massCalculator['ionseriesAgentCharge']),
size=(40, mwx.SMALL_TEXTCTRL_HEIGHT),
validator=mwx.validator('int'))
self.ionseriesAgentCharge_value.SetFont(wx.SMALL_FONT)
self.ionseriesAgentCharge_value.Bind(wx.EVT_TEXT,
self.onCompoundChanged)
ionseriesPolarity_label = wx.StaticText(ctrlPanel, -1, "Polarity:")
ionseriesPolarity_label.SetFont(wx.SMALL_FONT)
self.ionseriesPositive_radio = wx.RadioButton(ctrlPanel,
-1,
"Positive",
style=wx.RB_GROUP)
self.ionseriesPositive_radio.SetFont(wx.SMALL_FONT)
self.ionseriesPositive_radio.Bind(wx.EVT_RADIOBUTTON,
self.onCompoundChanged)
self.ionseriesNegative_radio = wx.RadioButton(ctrlPanel, -1,
"Negative")
self.ionseriesNegative_radio.SetFont(wx.SMALL_FONT)
self.ionseriesNegative_radio.Bind(wx.EVT_RADIOBUTTON,
self.onCompoundChanged)
if config.massCalculator['ionseriesPolarity'] == -1:
self.ionseriesNegative_radio.SetValue(True)
else:
self.ionseriesPositive_radio.SetValue(True)
# pack controls
controls = wx.BoxSizer(wx.HORIZONTAL)
controls.AddSpacer(mwx.CONTROLBAR_LSPACE)
controls.Add(ionseriesAgent_label, 0,
wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
controls.Add(self.ionseriesAgentFormula_value, 0,
wx.ALIGN_CENTER_VERTICAL)
controls.AddSpacer(20)
controls.Add(ionseriesAgentCharge_label, 0,
wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
controls.Add(self.ionseriesAgentCharge_value, 0,
wx.ALIGN_CENTER_VERTICAL)
controls.AddSpacer(20)
controls.Add(ionseriesPolarity_label, 0,
wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
controls.Add(self.ionseriesPositive_radio, 0,
wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
controls.Add(self.ionseriesNegative_radio, 0, wx.ALIGN_CENTER_VERTICAL)
controls.AddSpacer(mwx.CONTROLBAR_RSPACE)
controls.Fit(ctrlPanel)
ctrlPanel.SetSizer(controls)
# make ions list
self.makeIonsList()
# pack main
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(ctrlPanel, 0, wx.EXPAND)
mainSizer.Add(self.ionsList, 1, wx.EXPAND | wx.ALL,
mwx.LISTCTRL_NO_SPACE)
return mainSizer
def makeReferencesPanel(self):
"""Make references selection panel."""
# init panel
ctrlPanel = mwx.bgrPanel(self,
-1,
images.lib['bgrControlbar'],
size=(-1, mwx.CONTROLBAR_HEIGHT))
# make controls
references_label = wx.StaticText(ctrlPanel, -1, "References:")
references_label.SetFont(wx.SMALL_FONT)
choices = libs.references.keys()
choices.sort()
choices.insert(0, 'Reference lists')
self.references_choice = wx.Choice(ctrlPanel,
-1,
choices=choices,
size=(250, mwx.SMALL_CHOICE_HEIGHT))
self.references_choice.Select(0)
self.references_choice.Bind(wx.EVT_CHOICE, self.onReferencesSelected)
tolerance_label = wx.StaticText(ctrlPanel, -1, "Tolerance:")
tolerance_label.SetFont(wx.SMALL_FONT)
self.tolerance_value = wx.TextCtrl(
ctrlPanel,
-1,
str(config.calibration['tolerance']),
size=(50, mwx.SMALL_TEXTCTRL_HEIGHT),
validator=mwx.validator('floatPos'))
self.tolerance_value.SetFont(wx.SMALL_FONT)
self.toleranceUnits_label = wx.StaticText(ctrlPanel, -1,
config.calibration['units'])
self.toleranceUnits_label.SetFont(wx.SMALL_FONT)
self.statCalibration_check = wx.CheckBox(ctrlPanel, -1,
"Statistical only")
self.statCalibration_check.SetFont(wx.SMALL_FONT)
self.statCalibration_check.Bind(wx.EVT_CHECKBOX,
self.onStatCalibration)
self.makeReferencesList()
# pack controls
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(references_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.references_choice, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(tolerance_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.tolerance_value, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT,
5)
sizer.Add(self.toleranceUnits_label, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.statCalibration_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
controls = wx.BoxSizer(wx.VERTICAL)
controls.Add(sizer, 1, wx.EXPAND)
controls.Fit(ctrlPanel)
ctrlPanel.SetSizer(controls)
# pack main
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(ctrlPanel, 0, wx.EXPAND, 0)
mainSizer.Add(self.referencesList, 1, wx.EXPAND | wx.ALL,
mwx.LISTCTRL_NO_SPACE)
return mainSizer
def makeToolbar(self):
"""Make toolbar."""
# init toolbar
panel = mwx.bgrPanel(self, -1, images.lib['bgrToolbar'], size=(-1, mwx.TOOLBAR_HEIGHT))
# make elements
peakShape_label = wx.StaticText(panel, -1, "Peak shape:")
peakShape_label.SetFont(wx.SMALL_FONT)
self.peakShape_choice = wx.Choice(panel, -1, choices=['Symmetrical', 'Asymmetrical'], size=(125, mwx.CHOICE_HEIGHT))
self.peakShape_choice.Select(0)
if config.spectrumGenerator['peakShape'] == 'gausslorentzian':
self.peakShape_choice.Select(1)
fwhm_label = wx.StaticText(panel, -1, "Default FWHM:")
fwhm_label.SetFont(wx.SMALL_FONT)
self.fwhm_value = wx.TextCtrl(panel, -1, str(config.spectrumGenerator['fwhm']), size=(60, -1), validator=mwx.validator('floatPos'))
self.forceFwhm_check = wx.CheckBox(panel, -1, "Force")
self.forceFwhm_check.SetFont(wx.SMALL_FONT)
self.forceFwhm_check.SetValue(config.spectrumGenerator['forceFwhm'])
points_label = wx.StaticText(panel, -1, "Points/peak:")
points_label.SetFont(wx.SMALL_FONT)
self.points_value = wx.TextCtrl(panel, -1, str(config.spectrumGenerator['points']), size=(60, -1), validator=mwx.validator('intPos'))
noise_label = wx.StaticText(panel, -1, "Noise width:")
noise_label.SetFont(wx.SMALL_FONT)
self.noise_value = wx.TextCtrl(panel, -1, str(config.spectrumGenerator['noise']), size=(80, -1), validator=mwx.validator('floatPos'))
self.generate_butt = wx.Button(panel, -1, "Generate", size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.generate_butt.Bind(wx.EVT_BUTTON, self.onGenerate)
self.apply_butt = wx.Button(panel, -1, "Apply", size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.apply_butt.Bind(wx.EVT_BUTTON, self.onApply)
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(peakShape_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.peakShape_choice, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(fwhm_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.fwhm_value, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.forceFwhm_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(points_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.points_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(noise_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.noise_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.AddStretchSpacer()
sizer.Add(self.generate_butt, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 10)
sizer.Add(self.apply_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
panel.SetSizer(mainSizer)
mainSizer.Fit(panel)
return panel
def makeImagePanel(self):
"""Image export panel."""
panel = wx.Panel(self, -1)
# make elements
imageWidth_label = wx.StaticText(panel, -1, "Width:")
self.imageWidth_value = wx.TextCtrl(panel, -1, str(config.export['imageWidth']), size=(140, -1), validator=mwx.validator('floatPos'))
imageHeight_label = wx.StaticText(panel, -1, "Height:")
self.imageHeight_value = wx.TextCtrl(panel, -1, str(config.export['imageHeight']), size=(140, -1), validator=mwx.validator('floatPos'))
self.imageUnits_choice = wx.Choice(panel, -1, choices=['cm', 'in', 'px'], size=(60, mwx.CHOICE_HEIGHT))
self.imageUnits_choice.SetStringSelection(config.export['imageUnits'])
imageFormat_label = wx.StaticText(panel, -1, "Format:")
self.imageFormat_choice = wx.Choice(panel, -1, choices=['PNG', 'TIFF', 'JPEG'], size=(140, mwx.CHOICE_HEIGHT))
self.imageFormat_choice.SetStringSelection(config.export['imageFormat'])
imageResolution_label = wx.StaticText(panel, -1, "Resolution:")
imageResolutionUnits_label = wx.StaticText(panel, -1, "dpi")
choices = ['72', '150', '200', '300', '600']
self.imageResolution_choice = wx.Choice(panel, -1, choices=choices, size=(140, mwx.CHOICE_HEIGHT))
self.imageResolution_choice.Select(0)
if str(config.export['imageResolution']) in choices:
self.imageResolution_choice.Select(choices.index(str(config.export['imageResolution'])))
self.imageResolution_choice.Bind(wx.EVT_CHOICE, self.onImageResolutionChanged)
imageFontsScale_label = wx.StaticText(panel, -1, "Font scale:")
self.imageFontsScale_slider = wx.Slider(panel, -1, config.export['imageFontsScale'], 1, 10, size=(140, -1), style=mwx.SLIDER_STYLE)
self.imageFontsScale_slider.SetTickFreq(1,1)
imageDrawingsScale_label = wx.StaticText(panel, -1, "Line scale:")
self.imageDrawingsScale_slider = wx.Slider(panel, -1, config.export['imageDrawingsScale'], 1, 10, size=(140, -1), style=mwx.SLIDER_STYLE)
self.imageDrawingsScale_slider.SetTickFreq(1,1)
# pack elements
grid = wx.GridBagSizer(mwx.GRIDBAG_VSPACE, mwx.GRIDBAG_HSPACE)
grid.Add(imageWidth_label, (0,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.imageWidth_value, (0,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.imageUnits_choice, (0,2), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_LEFT)
grid.Add(imageHeight_label, (1,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.imageHeight_value, (1,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(imageResolution_label, (2,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.imageResolution_choice, (2,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(imageResolutionUnits_label, (2,2), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_LEFT)
grid.Add(imageFontsScale_label, (3,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.imageFontsScale_slider, (3,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(imageDrawingsScale_label, (4,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.imageDrawingsScale_slider, (4,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(imageFormat_label, (5,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.imageFormat_choice, (5,1), flag=wx.ALIGN_CENTER_VERTICAL)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(grid, 0, wx.ALIGN_CENTER|wx.ALL, mwx.PANEL_SPACE_MAIN)
# fit layout
mainSizer.Fit(panel)
panel.SetSizer(mainSizer)
return panel
def makeToolbar(self):
"""Make toolbar."""
# init toolbar
panel = mwx.bgrPanel(self, -1, images.lib['bgrToolbar'], size=(-1, mwx.TOOLBAR_HEIGHT))
# make elements
formula_label = wx.StaticText(panel, -1, "Formula:")
formula_label.SetFont(wx.SMALL_FONT)
self.formula_value = mwx.formulaCtrl(panel, -1, "", size=(220, -1))
charge_label = wx.StaticText(panel, -1, "Charge:")
charge_label.SetFont(wx.SMALL_FONT)
self.charge_value = wx.TextCtrl(panel, -1, str(config.envelopeFit['charge']), size=(35, -1), validator=mwx.validator('int'))
exchange_label = wx.StaticText(panel, -1, "Exchange:")
exchange_label.SetFont(wx.SMALL_FONT)
self.exchangeLoss_value = mwx.formulaCtrl(panel, -1, str(config.envelopeFit['loss']), size=(60, -1))
exchangeVs_label = wx.StaticText(panel, -1, " vs.")
exchangeVs_label.SetFont(wx.SMALL_FONT)
self.exchangeGain_value = mwx.formulaCtrl(panel, -1, str(config.envelopeFit['gain']), size=(60, -1))
scale_label = wx.StaticText(panel, -1, "Range:")
scale_label.SetFont(wx.SMALL_FONT)
scaleDash_label = wx.StaticText(panel, -1, "-")
scaleDash_label.SetFont(wx.SMALL_FONT)
self.scaleMin_value = wx.TextCtrl(panel, -1, str(config.envelopeFit['scaleMin']), size=(35, -1), validator=mwx.validator('intPos'))
self.scaleMax_value = wx.TextCtrl(panel, -1, str(config.envelopeFit['scaleMax']), size=(35, -1), validator=mwx.validator('intPos'))
self.calculate_butt = wx.Button(panel, -1, "Calculate", size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.calculate_butt.Bind(wx.EVT_BUTTON, self.onCalculate)
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(formula_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.formula_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(charge_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.charge_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(exchange_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.exchangeLoss_value, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(exchangeVs_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.exchangeGain_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(scale_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.scaleMin_value, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(scaleDash_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.scaleMax_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddStretchSpacer()
sizer.AddSpacer(20)
sizer.Add(self.calculate_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
mainSizer.Fit(panel)
panel.SetSizer(mainSizer)
return panel
def makeToolbar(self):
"""Make toolbar."""
# init toolbar
panel = mwx.bgrPanel(self,
-1,
images.lib['bgrToolbar'],
size=(-1, mwx.TOOLBAR_HEIGHT))
# make buttons
self.errors_butt = wx.BitmapButton(panel,
ID_matchErrors,
images.lib['matchErrorsOff'],
size=(mwx.TOOLBAR_TOOLSIZE),
style=wx.BORDER_NONE)
self.errors_butt.SetToolTip(wx.ToolTip("Error plot"))
self.errors_butt.Bind(wx.EVT_BUTTON, self.onToolSelected)
self.summary_butt = wx.BitmapButton(panel,
ID_matchSummary,
images.lib['matchSummaryOff'],
size=(mwx.TOOLBAR_TOOLSIZE),
style=wx.BORDER_NONE)
self.summary_butt.SetToolTip(wx.ToolTip("Match summary"))
self.summary_butt.Bind(wx.EVT_BUTTON, self.onToolSelected)
# make match fields
tolerance_label = wx.StaticText(panel, -1, "Tolerance:")
tolerance_label.SetFont(wx.SMALL_FONT)
self.tolerance_value = wx.TextCtrl(panel,
-1,
str(config.match['tolerance']),
size=(60, -1),
validator=mwx.validator('floatPos'))
self.unitsDa_radio = wx.RadioButton(panel, -1, "Da", style=wx.RB_GROUP)
self.unitsDa_radio.SetFont(wx.SMALL_FONT)
self.unitsDa_radio.SetValue(True)
self.unitsDa_radio.Bind(wx.EVT_RADIOBUTTON, self.onUnitsChanged)
self.unitsPpm_radio = wx.RadioButton(panel, -1, "ppm")
self.unitsPpm_radio.SetFont(wx.SMALL_FONT)
self.unitsPpm_radio.Bind(wx.EVT_RADIOBUTTON, self.onUnitsChanged)
self.unitsPpm_radio.SetValue((config.match['units'] == 'ppm'))
self.ignoreCharge_check = wx.CheckBox(panel, -1, "Ignore charge")
self.ignoreCharge_check.SetFont(wx.SMALL_FONT)
self.ignoreCharge_check.SetValue(config.match['ignoreCharge'])
if self.currentModule == 'massfilter':
self.ignoreCharge_check.Disable()
self.match_butt = wx.Button(panel,
-1,
"Match",
size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.match_butt.Bind(wx.EVT_BUTTON, self.onMatch)
self.calibrate_butt = wx.Button(panel,
-1,
"Calibrate",
size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.calibrate_butt.Bind(wx.EVT_BUTTON, self.onCalibrate)
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.TOOLBAR_LSPACE)
sizer.Add(self.errors_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.Add(self.summary_butt, 0, wx.ALIGN_CENTER_VERTICAL | wx.LEFT,
mwx.BUTTON_SIZE_CORRECTION)
sizer.AddSpacer(20)
sizer.Add(tolerance_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.tolerance_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(10)
sizer.Add(self.unitsDa_radio, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT,
5)
sizer.Add(self.unitsPpm_radio, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.ignoreCharge_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddStretchSpacer()
sizer.AddSpacer(20)
sizer.Add(self.match_butt, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 10)
sizer.Add(self.calibrate_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.TOOLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
panel.SetSizer(mainSizer)
mainSizer.Fit(panel)
return panel
def makeSpectrumPanel(self):
"""Spectrum info panel."""
panel = wx.Panel(self, -1)
# make elements
scanNumber_label = wx.StaticText(panel, -1, "Scan ID:")
self.scanNumber_value = wx.TextCtrl(panel, -1, "", size=(180, -1), validator=mwx.validator('intPos'))
self.scanNumber_value.Bind(wx.EVT_TEXT, self.onSave)
retentionTime_label = wx.StaticText(panel, -1, "Retention time:")
self.retentionTime_value = wx.TextCtrl(panel, -1, "", size=(180, -1), validator=mwx.validator('floatPos'))
self.retentionTime_value.Bind(wx.EVT_TEXT, self.onSave)
msLevel_label = wx.StaticText(panel, -1, "MS level:")
self.msLevel_value = wx.TextCtrl(panel, -1, "", size=(180, -1), validator=mwx.validator('intPos'))
self.msLevel_value.Bind(wx.EVT_TEXT, self.onSave)
precursorMZ_label = wx.StaticText(panel, -1, "Precursor m/z:")
self.precursorMZ_value = wx.TextCtrl(panel, -1, "", size=(180, -1), validator=mwx.validator('floatPos'))
self.precursorMZ_value.Bind(wx.EVT_TEXT, self.onSave)
precursorCharge_label = wx.StaticText(panel, -1, "Precursor charge:")
self.precursorCharge_value = wx.TextCtrl(panel, -1, "", size=(180, -1), validator=mwx.validator('int'))
self.precursorCharge_value.Bind(wx.EVT_TEXT, self.onSave)
polarity_label = wx.StaticText(panel, -1, "Polarity:")
self.polarity_choice = wx.Choice(panel, -1, choices=['Unknown', 'Positive', 'Negative'], size=(180, mwx.SMALL_CHOICE_HEIGHT))
self.polarity_choice.Bind(wx.EVT_CHOICE, self.onSave)
points_label = wx.StaticText(panel, -1, "Spectrum points:")
self.points_value = wx.TextCtrl(panel, -1, "", size=(180, -1))
self.points_value.Enable(False)
peaklist_label = wx.StaticText(panel, -1, "Peak list:")
self.peaklist_value = wx.TextCtrl(panel, -1, "", size=(180, -1))
self.peaklist_value.Enable(False)
# pack elements
grid = wx.GridBagSizer(mwx.GRIDBAG_VSPACE, mwx.GRIDBAG_HSPACE)
grid.Add(scanNumber_label, (0,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.scanNumber_value, (0,1))
grid.Add(retentionTime_label, (1,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.retentionTime_value, (1,1))
grid.Add(msLevel_label, (2,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.msLevel_value, (2,1))
grid.Add(precursorMZ_label, (3,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.precursorMZ_value, (3,1))
grid.Add(precursorCharge_label, (4,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.precursorCharge_value, (4,1))
grid.Add(polarity_label, (5,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.polarity_choice, (5,1))
grid.Add(points_label, (6,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.points_value, (6,1))
grid.Add(peaklist_label, (7,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
grid.Add(self.peaklist_value, (7,1))
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(grid, 0, wx.ALIGN_CENTER|wx.ALL, mwx.PANEL_SPACE_MAIN)
# fit layout
mainSizer.Fit(panel)
panel.SetSizer(mainSizer)
return panel
def makeEditor(self):
"""Make panel for peak editing."""
# init panel
panel = mwx.bgrPanel(self, -1, images.lib['bgrPeakEditor'])
# make elements
peakMz_label = wx.StaticText(panel, -1, "m/z:")
self.peakMz_value = wx.TextCtrl(panel, -1, '', size=(80, mwx.SMALL_TEXTCTRL_HEIGHT), validator=mwx.validator('floatPos'))
peakMz_label.SetFont(wx.SMALL_FONT)
self.peakMz_value.SetFont(wx.SMALL_FONT)
peakAi_label = wx.StaticText(panel, -1, "a.i.:")
self.peakAi_value = wx.TextCtrl(panel, -1, '', size=(80, mwx.SMALL_TEXTCTRL_HEIGHT), validator=mwx.validator('floatPos'))
peakAi_label.SetFont(wx.SMALL_FONT)
self.peakAi_value.SetFont(wx.SMALL_FONT)
peakBase_label = wx.StaticText(panel, -1, "base:")
self.peakBase_value = wx.TextCtrl(panel, -1, '', size=(80, mwx.SMALL_TEXTCTRL_HEIGHT), style=wx.TE_PROCESS_ENTER, validator=mwx.validator('floatPos'))
peakBase_label.SetFont(wx.SMALL_FONT)
self.peakBase_value.SetFont(wx.SMALL_FONT)
peakSN_label = wx.StaticText(panel, -1, "s/n:")
self.peakSN_value = wx.TextCtrl(panel, -1, '', size=(80, mwx.SMALL_TEXTCTRL_HEIGHT), validator=mwx.validator('floatPos'))
peakSN_label.SetFont(wx.SMALL_FONT)
self.peakSN_value.SetFont(wx.SMALL_FONT)
peakCharge_label = wx.StaticText(panel, -1, "charge:")
self.peakCharge_value = wx.TextCtrl(panel, -1, '', size=(80, mwx.SMALL_TEXTCTRL_HEIGHT), validator=mwx.validator('int'))
peakCharge_label.SetFont(wx.SMALL_FONT)
self.peakCharge_value.SetFont(wx.SMALL_FONT)
peakFwhm_label = wx.StaticText(panel, -1, "fwhm:")
self.peakFwhm_value = wx.TextCtrl(panel, -1, '', size=(80, mwx.SMALL_TEXTCTRL_HEIGHT), style=wx.TE_PROCESS_ENTER, validator=mwx.validator('floatPos'))
peakFwhm_label.SetFont(wx.SMALL_FONT)
self.peakFwhm_value.SetFont(wx.SMALL_FONT)
peakGroup_label = wx.StaticText(panel, -1, "group:")
self.peakGroup_value = wx.TextCtrl(panel, -1, '', size=(80, mwx.SMALL_TEXTCTRL_HEIGHT), style=wx.TE_PROCESS_ENTER)
peakGroup_label.SetFont(wx.SMALL_FONT)
self.peakGroup_value.SetFont(wx.SMALL_FONT)
self.peakMonoisotopic_check = wx.CheckBox(panel, -1, "monoisotopic")
self.peakMonoisotopic_check.SetValue(True)
self.peakMonoisotopic_check.SetFont(wx.SMALL_FONT)
self.peakAdd_butt = wx.Button(panel, -1, "Add", size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.peakAdd_butt.Bind(wx.EVT_BUTTON, self.onAddPeak)
self.peakReplace_butt = wx.Button(panel, -1, "Update", size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.peakReplace_butt.Bind(wx.EVT_BUTTON, self.onReplacePeak)
self.peakReplace_butt.Enable(False)
# pack elements
grid = wx.GridBagSizer(mwx.GRIDBAG_VSPACE, mwx.GRIDBAG_HSPACE)
grid.Add(peakMz_label, (0,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.peakMz_value, (0,1), flag=wx.EXPAND)
grid.Add(peakAi_label, (1,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.peakAi_value, (1,1), flag=wx.EXPAND)
grid.Add(peakBase_label, (2,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.peakBase_value, (2,1), flag=wx.EXPAND)
grid.Add(peakSN_label, (3,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.peakSN_value, (3,1), flag=wx.EXPAND)
grid.Add(peakCharge_label, (4,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.peakCharge_value, (4,1), flag=wx.EXPAND)
grid.Add(peakFwhm_label, (5,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.peakFwhm_value, (5,1), flag=wx.EXPAND)
grid.Add(peakGroup_label, (6,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.peakGroup_value, (6,1), flag=wx.EXPAND)
grid.Add(self.peakMonoisotopic_check, (7,1), flag=wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
grid.AddGrowableCol(1)
buttons = wx.BoxSizer(wx.HORIZONTAL)
buttons.Add(self.peakAdd_butt, 0, wx.RIGHT, 10)
buttons.Add(self.peakReplace_butt, 0)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(grid, 0, wx.EXPAND|wx.ALIGN_CENTER|wx.ALL, 10)
mainSizer.Add(buttons, 0, wx.ALIGN_CENTER|wx.RIGHT|wx.LEFT|wx.BOTTOM, 10)
# fit layout
mainSizer.Fit(panel)
panel.SetSizer(mainSizer)
return panel
def makeImagePanel(self):
"""Image export panel."""
panel = wx.Panel(self, -1)
# make elements
imageWidth_label = wx.StaticText(panel, -1, "Width:")
self.imageWidth_value = wx.TextCtrl(
panel,
-1,
str(config.export['imageWidth']),
size=(140, -1),
validator=mwx.validator('floatPos'))
imageHeight_label = wx.StaticText(panel, -1, "Height:")
self.imageHeight_value = wx.TextCtrl(
panel,
-1,
str(config.export['imageHeight']),
size=(140, -1),
validator=mwx.validator('floatPos'))
self.imageUnits_choice = wx.Choice(panel,
-1,
choices=['cm', 'in', 'px'],
size=(60, mwx.CHOICE_HEIGHT))
self.imageUnits_choice.SetStringSelection(config.export['imageUnits'])
imageFormat_label = wx.StaticText(panel, -1, "Format:")
self.imageFormat_choice = wx.Choice(panel,
-1,
choices=['PNG', 'TIFF', 'JPEG'],
size=(140, mwx.CHOICE_HEIGHT))
self.imageFormat_choice.SetStringSelection(
config.export['imageFormat'])
imageResolution_label = wx.StaticText(panel, -1, "Resolution:")
imageResolutionUnits_label = wx.StaticText(panel, -1, "dpi")
choices = ['72', '150', '200', '300', '600']
self.imageResolution_choice = wx.Choice(panel,
-1,
choices=choices,
size=(140, mwx.CHOICE_HEIGHT))
self.imageResolution_choice.Select(0)
if str(config.export['imageResolution']) in choices:
self.imageResolution_choice.Select(
choices.index(str(config.export['imageResolution'])))
self.imageResolution_choice.Bind(wx.EVT_CHOICE,
self.onImageResolutionChanged)
imageFontsScale_label = wx.StaticText(panel, -1, "Font scale:")
self.imageFontsScale_slider = wx.Slider(
panel,
-1,
config.export['imageFontsScale'],
1,
10,
size=(140, -1),
style=mwx.SLIDER_STYLE)
self.imageFontsScale_slider.SetTickFreq(1, 1)
imageDrawingsScale_label = wx.StaticText(panel, -1, "Line scale:")
self.imageDrawingsScale_slider = wx.Slider(
panel,
-1,
config.export['imageDrawingsScale'],
1,
10,
size=(140, -1),
style=mwx.SLIDER_STYLE)
self.imageDrawingsScale_slider.SetTickFreq(1, 1)
# pack elements
grid = wx.GridBagSizer(mwx.GRIDBAG_VSPACE, mwx.GRIDBAG_HSPACE)
grid.Add(imageWidth_label, (0, 0),
flag=wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
grid.Add(self.imageWidth_value, (0, 1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.imageUnits_choice, (0, 2),
flag=wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_LEFT)
grid.Add(imageHeight_label, (1, 0),
flag=wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
grid.Add(self.imageHeight_value, (1, 1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(imageResolution_label, (2, 0),
flag=wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
grid.Add(self.imageResolution_choice, (2, 1),
flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(imageResolutionUnits_label, (2, 2),
flag=wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_LEFT)
grid.Add(imageFontsScale_label, (3, 0),
flag=wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
grid.Add(self.imageFontsScale_slider, (3, 1),
flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(imageDrawingsScale_label, (4, 0),
flag=wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
grid.Add(self.imageDrawingsScale_slider, (4, 1),
flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(imageFormat_label, (5, 0),
flag=wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
grid.Add(self.imageFormat_choice, (5, 1),
flag=wx.ALIGN_CENTER_VERTICAL)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(grid, 0, wx.ALIGN_CENTER | wx.ALL, mwx.PANEL_SPACE_MAIN)
# fit layout
mainSizer.Fit(panel)
panel.SetSizer(mainSizer)
return panel
def makeIonseriesPanel(self):
"""Make controls for ionseries."""
# init panel
ctrlPanel = mwx.bgrPanel(self, -1, images.lib['bgrControlbar'], size=(-1, mwx.CONTROLBAR_HEIGHT))
# make controls
ionseriesAgent_label = wx.StaticText(ctrlPanel, -1, "Agent:")
ionseriesAgent_label.SetFont(wx.SMALL_FONT)
self.ionseriesAgentFormula_value = wx.TextCtrl(ctrlPanel, -1, config.massCalculator['ionseriesAgent'], size=(60, mwx.SMALL_TEXTCTRL_HEIGHT))
self.ionseriesAgentFormula_value.SetFont(wx.SMALL_FONT)
self.ionseriesAgentFormula_value.Bind(wx.EVT_TEXT, self.onCompoundChanged)
ionseriesAgentCharge_label = wx.StaticText(ctrlPanel, -1, "Agent charge:")
ionseriesAgentCharge_label.SetFont(wx.SMALL_FONT)
self.ionseriesAgentCharge_value = wx.TextCtrl(ctrlPanel, -1, str(config.massCalculator['ionseriesAgentCharge']), size=(40, mwx.SMALL_TEXTCTRL_HEIGHT), validator=mwx.validator('int'))
self.ionseriesAgentCharge_value.SetFont(wx.SMALL_FONT)
self.ionseriesAgentCharge_value.Bind(wx.EVT_TEXT, self.onCompoundChanged)
ionseriesPolarity_label = wx.StaticText(ctrlPanel, -1, "Polarity:")
ionseriesPolarity_label.SetFont(wx.SMALL_FONT)
self.ionseriesPositive_radio = wx.RadioButton(ctrlPanel, -1, "Positive", style=wx.RB_GROUP)
self.ionseriesPositive_radio.SetFont(wx.SMALL_FONT)
self.ionseriesPositive_radio.Bind(wx.EVT_RADIOBUTTON, self.onCompoundChanged)
self.ionseriesNegative_radio = wx.RadioButton(ctrlPanel, -1, "Negative")
self.ionseriesNegative_radio.SetFont(wx.SMALL_FONT)
self.ionseriesNegative_radio.Bind(wx.EVT_RADIOBUTTON, self.onCompoundChanged)
if config.massCalculator['ionseriesPolarity'] == -1:
self.ionseriesNegative_radio.SetValue(True)
else:
self.ionseriesPositive_radio.SetValue(True)
# pack controls
controls = wx.BoxSizer(wx.HORIZONTAL)
controls.AddSpacer(mwx.CONTROLBAR_LSPACE)
controls.Add(ionseriesAgent_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
controls.Add(self.ionseriesAgentFormula_value, 0, wx.ALIGN_CENTER_VERTICAL)
controls.AddSpacer(20)
controls.Add(ionseriesAgentCharge_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
controls.Add(self.ionseriesAgentCharge_value, 0, wx.ALIGN_CENTER_VERTICAL)
controls.AddSpacer(20)
controls.Add(ionseriesPolarity_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
controls.Add(self.ionseriesPositive_radio, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
controls.Add(self.ionseriesNegative_radio, 0, wx.ALIGN_CENTER_VERTICAL)
controls.AddSpacer(mwx.CONTROLBAR_RSPACE)
controls.Fit(ctrlPanel)
ctrlPanel.SetSizer(controls)
# make ions list
self.makeIonsList()
# pack main
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(ctrlPanel, 0, wx.EXPAND)
mainSizer.Add(self.ionsList, 1, wx.EXPAND|wx.ALL, mwx.LISTCTRL_NO_SPACE)
return mainSizer
def makeControlbar(self):
"""Make controlbar."""
# init toolbar
panel = mwx.bgrPanel(self,
-1,
images.lib['bgrControlbar'],
size=(-1, mwx.CONTROLBAR_HEIGHT))
# make elements
massType_label = wx.StaticText(panel, -1, "Mass:")
massType_label.SetFont(wx.SMALL_FONT)
self.massTypeMo_radio = wx.RadioButton(panel,
-1,
"Mo",
style=wx.RB_GROUP)
self.massTypeMo_radio.SetFont(wx.SMALL_FONT)
self.massTypeMo_radio.SetValue(True)
self.massTypeAv_radio = wx.RadioButton(panel, -1, "Av")
self.massTypeAv_radio.SetFont(wx.SMALL_FONT)
self.massTypeAv_radio.SetValue(config.compoundsSearch['massType'])
maxCharge_label = wx.StaticText(panel, -1, "Max charge:")
maxCharge_label.SetFont(wx.SMALL_FONT)
self.maxCharge_value = wx.TextCtrl(
panel,
-1,
str(config.compoundsSearch['maxCharge']),
size=(30, mwx.SMALL_TEXTCTRL_HEIGHT),
validator=mwx.validator('int'))
self.maxCharge_value.SetFont(wx.SMALL_FONT)
self.radicals_check = wx.CheckBox(panel, -1, "M*")
self.radicals_check.SetFont(wx.SMALL_FONT)
self.radicals_check.SetValue(config.compoundsSearch['radicals'])
adducts_label = wx.StaticText(panel, -1, "Adducts:")
adducts_label.SetFont(wx.SMALL_FONT)
self.adductNa_check = wx.CheckBox(panel, -1, "Na")
self.adductNa_check.SetFont(wx.SMALL_FONT)
self.adductNa_check.SetValue(
config.compoundsSearch['adducts'].count('Na'))
self.adductK_check = wx.CheckBox(panel, -1, "K")
self.adductK_check.SetFont(wx.SMALL_FONT)
self.adductK_check.SetValue(
config.compoundsSearch['adducts'].count('K'))
self.adductLi_check = wx.CheckBox(panel, -1, "Li")
self.adductLi_check.SetFont(wx.SMALL_FONT)
self.adductLi_check.SetValue(
config.compoundsSearch['adducts'].count('Li'))
self.adductNH4_check = wx.CheckBox(panel, -1, "NH4")
self.adductNH4_check.SetFont(wx.SMALL_FONT)
self.adductNH4_check.SetValue(
config.compoundsSearch['adducts'].count('NH4'))
self.adductH2O_check = wx.CheckBox(panel, -1, "-H2O")
self.adductH2O_check.SetFont(wx.SMALL_FONT)
self.adductH2O_check.SetValue(
config.compoundsSearch['adducts'].count('-H2O'))
self.adductACN_check = wx.CheckBox(panel, -1, "ACN")
self.adductACN_check.SetFont(wx.SMALL_FONT)
self.adductACN_check.SetValue(
config.compoundsSearch['adducts'].count('ACN'))
self.adductMeOH_check = wx.CheckBox(panel, -1, "MeOH")
self.adductMeOH_check.SetFont(wx.SMALL_FONT)
self.adductMeOH_check.SetValue(
config.compoundsSearch['adducts'].count('MeOH'))
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(massType_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.massTypeMo_radio, 0,
wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.massTypeAv_radio, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(maxCharge_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.maxCharge_value, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT,
5)
sizer.Add(self.radicals_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(adducts_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.adductNa_check, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT,
5)
sizer.Add(self.adductK_check, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT,
5)
sizer.Add(self.adductLi_check, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT,
5)
sizer.Add(self.adductNH4_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.adductH2O_check, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT,
5)
sizer.Add(self.adductACN_check, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT,
5)
sizer.Add(self.adductMeOH_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
mainSizer.Fit(panel)
panel.SetSizer(mainSizer)
return panel
def makeGUI(self):
"""Make GUI elements."""
labelBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, ""), wx.HORIZONTAL)
formulaBox = wx.StaticBoxSizer(wx.StaticBox(self, -1, ""), wx.HORIZONTAL)
# make elements
label_label = wx.StaticText(self, -1, "Label:", style=wx.ALIGN_RIGHT)
self.label_value = wx.TextCtrl(self, -1, '', size=(300,-1), style=wx.TE_PROCESS_ENTER)
self.label_value.Bind(wx.EVT_TEXT_ENTER, self.onOK)
formula_label = wx.StaticText(self, -1, "Formula:", style=wx.ALIGN_RIGHT)
self.formula_value = mwx.formulaCtrl(self, -1, '', size=(300,-1), style=wx.TE_PROCESS_ENTER)
self.formula_value.Bind(wx.EVT_TEXT, self.onFormula)
self.formula_value.Bind(wx.EVT_TEXT_ENTER, self.onOK)
theoreticalMZ_label = wx.StaticText(self, -1, "Theoretical m/z:", style=wx.ALIGN_RIGHT)
self.theoreticalMZ_value = wx.TextCtrl(self, -1, '', size=(120,-1), style=wx.TE_PROCESS_ENTER, validator=mwx.validator('float'))
self.theoreticalMZ_value.Bind(wx.EVT_TEXT_ENTER, self.onOK)
charge_label = wx.StaticText(self, -1, " z:")
self.charge_value = wx.TextCtrl(self, -1, '', size=(30,-1), style=wx.TE_PROCESS_ENTER, validator=mwx.validator('int'))
self.charge_value.Bind(wx.EVT_TEXT, self.onFormula)
self.charge_value.Bind(wx.EVT_TEXT_ENTER, self.onOK)
self.radical_check = wx.CheckBox(self, -1, "M*", size=(50,-1))
self.radical_check.Bind(wx.EVT_CHECKBOX, self.onMassType)
self.mzByUser_radio = wx.RadioButton(self, -1, "Manual", style=wx.RB_GROUP)
self.mzByUser_radio.SetFont(wx.SMALL_FONT)
self.mzByUser_radio.Bind(wx.EVT_RADIOBUTTON, self.onMassType)
self.mzByUser_radio.SetValue(True)
self.mzByFormulaMo_radio = wx.RadioButton(self, -1, "Mo")
self.mzByFormulaMo_radio.SetFont(wx.SMALL_FONT)
self.mzByFormulaMo_radio.Bind(wx.EVT_RADIOBUTTON, self.onMassType)
self.mzByFormulaAv_radio = wx.RadioButton(self, -1, "Av")
self.mzByFormulaAv_radio.SetFont(wx.SMALL_FONT)
self.mzByFormulaAv_radio.Bind(wx.EVT_RADIOBUTTON, self.onMassType)
buttons = self.makeButtons()
# pack elements
labelBox.Add(label_label, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
labelBox.Add(self.label_value, 1, wx.TOP|wx.RIGHT|wx.BOTTOM|wx.ALIGN_CENTER_VERTICAL, 10)
formulaGrid = wx.GridBagSizer(mwx.GRIDBAG_VSPACE, mwx.GRIDBAG_HSPACE)
formulaGrid.Add(formula_label, (0,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
formulaGrid.Add(self.formula_value, (0,1), (1,7), flag=wx.EXPAND)
formulaGrid.Add(theoreticalMZ_label, (1,0), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
formulaGrid.Add(self.theoreticalMZ_value, (1,1))
formulaGrid.Add(charge_label, (1,2), flag=wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
formulaGrid.Add(self.charge_value, (1,3))
formulaGrid.Add(self.radical_check, (1,4), flag=wx.ALIGN_CENTER_VERTICAL)
formulaGrid.Add(self.mzByUser_radio, (1,5), flag=wx.ALIGN_CENTER_VERTICAL)
formulaGrid.Add(self.mzByFormulaMo_radio, (1,6), flag=wx.ALIGN_CENTER_VERTICAL)
formulaGrid.Add(self.mzByFormulaAv_radio, (1,7), flag=wx.ALIGN_CENTER_VERTICAL)
formulaGrid.AddGrowableCol(1)
formulaBox.Add(formulaGrid, 1, wx.EXPAND|wx.ALL, 10)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(labelBox, 0, wx.EXPAND|wx.CENTER|wx.ALL, mwx.PANEL_SPACE_MAIN)
mainSizer.Add(formulaBox, 0, wx.EXPAND|wx.CENTER|wx.LEFT|wx.RIGHT|wx.BOTTOM, mwx.PANEL_SPACE_MAIN)
mainSizer.Add(buttons, 0, wx.CENTER|wx.LEFT|wx.RIGHT|wx.BOTTOM, mwx.PANEL_SPACE_MAIN)
return mainSizer
def makeToolbar(self):
"""Make toolbar."""
# init toolbar
panel = mwx.bgrPanel(self,
-1,
images.lib['bgrToolbarNoBorder'],
size=(-1, mwx.TOOLBAR_HEIGHT))
# make elements
compare_label = wx.StaticText(panel, -1, "Compare:")
compare_label.SetFont(wx.SMALL_FONT)
choices = [
'Peak Lists', 'Notations (measured)', 'Notations (theoretical)'
]
self.compare_choice = wx.Choice(panel,
-1,
choices=choices,
size=(180, mwx.SMALL_CHOICE_HEIGHT))
self.compare_choice.Bind(wx.EVT_CHOICE, self.onUpdatePeaklist)
self.compare_choice.Select(0)
if config.comparePeaklists['compare'] == 'measured':
self.compare_choice.Select(1)
elif config.comparePeaklists['compare'] == 'theoretical':
self.compare_choice.Select(2)
tolerance_label = wx.StaticText(panel, -1, "Tolerance:")
tolerance_label.SetFont(wx.SMALL_FONT)
self.tolerance_value = wx.TextCtrl(
panel,
-1,
str(config.comparePeaklists['tolerance']),
size=(60, -1),
style=wx.TE_PROCESS_ENTER,
validator=mwx.validator('floatPos'))
self.tolerance_value.Bind(wx.EVT_TEXT_ENTER, self.onCompare)
self.unitsDa_radio = wx.RadioButton(panel, -1, "Da", style=wx.RB_GROUP)
self.unitsDa_radio.SetFont(wx.SMALL_FONT)
self.unitsDa_radio.SetValue(True)
self.unitsPpm_radio = wx.RadioButton(panel, -1, "ppm")
self.unitsPpm_radio.SetFont(wx.SMALL_FONT)
self.unitsPpm_radio.SetValue(
(config.comparePeaklists['units'] == 'ppm'))
self.ignoreCharge_check = wx.CheckBox(panel, -1, "Ignore charge")
self.ignoreCharge_check.SetFont(wx.SMALL_FONT)
self.ignoreCharge_check.SetValue(
config.comparePeaklists['ignoreCharge'])
self.ratioCheck_check = wx.CheckBox(panel, -1, "Int. ratio:")
self.ratioCheck_check.SetFont(wx.SMALL_FONT)
self.ratioCheck_check.SetValue(config.comparePeaklists['ratioCheck'])
self.ratioCheck_check.Bind(wx.EVT_CHECKBOX, self.onRatioCheckChanged)
self.ratioDirection_choice = wx.Choice(panel,
-1,
choices=['Above', 'Below'],
size=(80,
mwx.SMALL_CHOICE_HEIGHT))
self.ratioDirection_choice.Select(0)
if config.comparePeaklists['ratioDirection'] == -1:
self.ratioDirection_choice.Select(1)
self.ratioThreshold_value = wx.TextCtrl(
panel,
-1,
str(config.comparePeaklists['ratioThreshold']),
size=(50, -1),
validator=mwx.validator('floatPos'))
self.compare_butt = wx.Button(panel,
-1,
"Compare",
size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.compare_butt.Bind(wx.EVT_BUTTON, self.onCompare)
self.onRatioCheckChanged()
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(compare_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.compare_choice, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(tolerance_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.tolerance_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(10)
sizer.Add(self.unitsDa_radio, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT,
5)
sizer.Add(self.unitsPpm_radio, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.ignoreCharge_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.ratioCheck_check, 0,
wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.ratioDirection_choice, 0,
wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 10)
sizer.Add(self.ratioThreshold_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddStretchSpacer()
sizer.AddSpacer(20)
sizer.Add(self.compare_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
panel.SetSizer(mainSizer)
mainSizer.Fit(panel)
return panel
def makeToolbar(self):
"""Make toolbar."""
# init toolbar
panel = mwx.bgrPanel(self, -1, images.lib["bgrToolbar"], size=(-1, mwx.TOOLBAR_HEIGHT))
# make elements
formula_label = wx.StaticText(panel, -1, "Formula:")
formula_label.SetFont(wx.SMALL_FONT)
self.formula_value = mwx.formulaCtrl(panel, -1, "", size=(220, -1))
charge_label = wx.StaticText(panel, -1, "Charge:")
charge_label.SetFont(wx.SMALL_FONT)
self.charge_value = wx.TextCtrl(
panel, -1, str(config.envelopeFit["charge"]), size=(35, -1), validator=mwx.validator("int")
)
exchange_label = wx.StaticText(panel, -1, "Exchange:")
exchange_label.SetFont(wx.SMALL_FONT)
self.exchangeLoss_value = mwx.formulaCtrl(panel, -1, str(config.envelopeFit["loss"]), size=(60, -1))
exchangeVs_label = wx.StaticText(panel, -1, " vs.")
exchangeVs_label.SetFont(wx.SMALL_FONT)
self.exchangeGain_value = mwx.formulaCtrl(panel, -1, str(config.envelopeFit["gain"]), size=(60, -1))
scale_label = wx.StaticText(panel, -1, "Range:")
scale_label.SetFont(wx.SMALL_FONT)
scaleDash_label = wx.StaticText(panel, -1, "-")
scaleDash_label.SetFont(wx.SMALL_FONT)
self.scaleMin_value = wx.TextCtrl(
panel, -1, str(config.envelopeFit["scaleMin"]), size=(35, -1), validator=mwx.validator("intPos")
)
self.scaleMax_value = wx.TextCtrl(
panel, -1, str(config.envelopeFit["scaleMax"]), size=(35, -1), validator=mwx.validator("intPos")
)
self.calculate_butt = wx.Button(panel, -1, "Calculate", size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.calculate_butt.Bind(wx.EVT_BUTTON, self.onCalculate)
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(formula_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.formula_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(charge_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.charge_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(exchange_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.exchangeLoss_value, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(exchangeVs_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.exchangeGain_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(scale_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.scaleMin_value, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(scaleDash_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.scaleMax_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddStretchSpacer()
sizer.AddSpacer(20)
sizer.Add(self.calculate_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
mainSizer.Fit(panel)
panel.SetSizer(mainSizer)
return panel
def makeToolbar(self):
"""Make toolbar."""
# init toolbar
panel = mwx.bgrPanel(self,
-1,
images.lib['bgrToolbarNoBorder'],
size=(-1, mwx.TOOLBAR_HEIGHT))
# make match fields
difference_label = wx.StaticText(panel, -1, "Difference:")
difference_label.SetFont(wx.SMALL_FONT)
self.difference_value = wx.TextCtrl(
panel,
-1,
'',
size=(100, -1),
style=wx.TE_PROCESS_ENTER,
validator=mwx.validator('floatPos'))
self.difference_value.Bind(wx.EVT_TEXT_ENTER, self.onSearch)
self.aminoacids_check = wx.CheckBox(panel, -1, "Amino acids")
self.aminoacids_check.SetFont(wx.SMALL_FONT)
self.aminoacids_check.SetValue(config.peakDifferences['aminoacids'])
self.dipeptides_check = wx.CheckBox(panel, -1, "Dipeptides")
self.dipeptides_check.SetFont(wx.SMALL_FONT)
self.dipeptides_check.SetValue(config.peakDifferences['dipeptides'])
massType_label = wx.StaticText(panel, -1, "Mass:")
massType_label.SetFont(wx.SMALL_FONT)
self.massTypeMo_radio = wx.RadioButton(panel,
-1,
"Mo",
style=wx.RB_GROUP)
self.massTypeMo_radio.SetFont(wx.SMALL_FONT)
self.massTypeMo_radio.SetValue(True)
self.massTypeAv_radio = wx.RadioButton(panel, -1, "Av")
self.massTypeAv_radio.SetFont(wx.SMALL_FONT)
self.massTypeAv_radio.SetValue(config.peakDifferences['massType'])
tolerance_label = wx.StaticText(panel, -1, "Tolerance:")
tolerance_label.SetFont(wx.SMALL_FONT)
self.tolerance_value = wx.TextCtrl(
panel,
-1,
str(config.peakDifferences['tolerance']),
size=(50, -1),
validator=mwx.validator('floatPos'))
toleranceUnits_label = wx.StaticText(panel, -1, "m/z")
toleranceUnits_label.SetFont(wx.SMALL_FONT)
self.consolidate_check = wx.CheckBox(panel, -1, "Hide umatched")
self.consolidate_check.SetFont(wx.SMALL_FONT)
self.consolidate_check.SetValue(config.peakDifferences['consolidate'])
self.search_butt = wx.Button(panel,
-1,
"Search",
size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.search_butt.Bind(wx.EVT_BUTTON, self.onSearch)
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(difference_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.difference_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.aminoacids_check, 0,
wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.dipeptides_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(massType_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.massTypeMo_radio, 0,
wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.massTypeAv_radio, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(tolerance_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(self.tolerance_value, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT,
5)
sizer.Add(toleranceUnits_label, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.consolidate_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddStretchSpacer()
sizer.AddSpacer(20)
sizer.Add(self.search_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
panel.SetSizer(mainSizer)
mainSizer.Fit(panel)
return panel
def makeToolbar(self):
"""Make toolbar."""
# init toolbar
panel = mwx.bgrPanel(self, -1, images.lib['bgrToolbarNoBorder'], size=(-1, mwx.TOOLBAR_HEIGHT))
# make elements
compare_label = wx.StaticText(panel, -1, "Compare:")
compare_label.SetFont(wx.SMALL_FONT)
choices = ['Peak Lists', 'Notations (measured)', 'Notations (theoretical)']
self.compare_choice = wx.Choice(panel, -1, choices=choices, size=(180, mwx.SMALL_CHOICE_HEIGHT))
self.compare_choice.Bind(wx.EVT_CHOICE, self.onUpdatePeaklist)
self.compare_choice.Select(0)
if config.comparePeaklists['compare'] == 'measured':
self.compare_choice.Select(1)
elif config.comparePeaklists['compare'] == 'theoretical':
self.compare_choice.Select(2)
tolerance_label = wx.StaticText(panel, -1, "Tolerance:")
tolerance_label.SetFont(wx.SMALL_FONT)
self.tolerance_value = wx.TextCtrl(panel, -1, str(config.comparePeaklists['tolerance']), size=(60, -1), style=wx.TE_PROCESS_ENTER, validator=mwx.validator('floatPos'))
self.tolerance_value.Bind(wx.EVT_TEXT_ENTER, self.onCompare)
self.unitsDa_radio = wx.RadioButton(panel, -1, "Da", style=wx.RB_GROUP)
self.unitsDa_radio.SetFont(wx.SMALL_FONT)
self.unitsDa_radio.SetValue(True)
self.unitsPpm_radio = wx.RadioButton(panel, -1, "ppm")
self.unitsPpm_radio.SetFont(wx.SMALL_FONT)
self.unitsPpm_radio.SetValue((config.comparePeaklists['units'] == 'ppm'))
self.ignoreCharge_check = wx.CheckBox(panel, -1, "Ignore charge")
self.ignoreCharge_check.SetFont(wx.SMALL_FONT)
self.ignoreCharge_check.SetValue(config.comparePeaklists['ignoreCharge'])
self.ratioCheck_check = wx.CheckBox(panel, -1, "Int. ratio:")
self.ratioCheck_check.SetFont(wx.SMALL_FONT)
self.ratioCheck_check.SetValue(config.comparePeaklists['ratioCheck'])
self.ratioCheck_check.Bind(wx.EVT_CHECKBOX, self.onRatioCheckChanged)
self.ratioDirection_choice = wx.Choice(panel, -1, choices=['Above', 'Below'], size=(80, mwx.SMALL_CHOICE_HEIGHT))
self.ratioDirection_choice.Select(0)
if config.comparePeaklists['ratioDirection'] == -1:
self.ratioDirection_choice.Select(1)
self.ratioThreshold_value = wx.TextCtrl(panel, -1, str(config.comparePeaklists['ratioThreshold']), size=(50, -1), validator=mwx.validator('floatPos'))
self.compare_butt = wx.Button(panel, -1, "Compare", size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.compare_butt.Bind(wx.EVT_BUTTON, self.onCompare)
self.onRatioCheckChanged()
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(compare_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.compare_choice, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(tolerance_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.tolerance_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(10)
sizer.Add(self.unitsDa_radio, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.unitsPpm_radio, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.ignoreCharge_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.ratioCheck_check, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.ratioDirection_choice, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 10)
sizer.Add(self.ratioThreshold_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddStretchSpacer()
sizer.AddSpacer(20)
sizer.Add(self.compare_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
panel.SetSizer(mainSizer)
mainSizer.Fit(panel)
return panel
def makeControlbar(self):
"""Make controlbar."""
# init toolbar
panel = mwx.bgrPanel(self, -1, images.lib['bgrControlbar'], size=(-1, mwx.CONTROLBAR_HEIGHT))
# make elements
self.collapse_butt = wx.BitmapButton(panel, -1, images.lib['arrowsDown'], size=(mwx.TOOLBAR_TOOLSIZE), style=wx.BORDER_NONE)
self.collapse_butt.Bind(wx.EVT_BUTTON, self.onCollapse)
fitTo_label = wx.StaticText(panel, -1, "Fit to:")
fitTo_label.SetFont(wx.SMALL_FONT)
self.fitToPeaklist_radio = wx.RadioButton(panel, -1, "Peak list", style=wx.RB_GROUP)
self.fitToPeaklist_radio.SetFont(wx.SMALL_FONT)
self.fitToSpectrum_radio = wx.RadioButton(panel, -1, "Spectrum")
self.fitToSpectrum_radio.SetFont(wx.SMALL_FONT)
self.fitToPeaklist_radio.SetValue(True)
if config.envelopeFit['fit'] == 'spectrum':
self.fitToSpectrum_radio.SetValue(True)
fwhm_label = wx.StaticText(panel, -1, "Default FWHM:")
fwhm_label.SetFont(wx.SMALL_FONT)
self.fwhm_value = wx.TextCtrl(panel, -1, str(config.envelopeFit['fwhm']), size=(50, mwx.SMALL_TEXTCTRL_HEIGHT), validator=mwx.validator('floatPos'))
self.fwhm_value.SetFont(wx.SMALL_FONT)
self.forceFwhm_check = wx.CheckBox(panel, -1, "Force")
self.forceFwhm_check.SetFont(wx.SMALL_FONT)
self.forceFwhm_check.SetValue(config.envelopeFit['forceFwhm'])
relThreshold_label = wx.StaticText(panel, -1, "Rel. int. threshold:")
relThreshold_label.SetFont(wx.SMALL_FONT)
relThresholdUnits_label = wx.StaticText(panel, -1, "%")
relThresholdUnits_label.SetFont(wx.SMALL_FONT)
self.relThreshold_value = wx.TextCtrl(panel, -1, str(config.envelopeFit['relThreshold']*100), size=(50, mwx.SMALL_TEXTCTRL_HEIGHT), validator=mwx.validator('floatPos'))
self.relThreshold_value.SetFont(wx.SMALL_FONT)
self.autoAlign_check = wx.CheckBox(panel, -1, "Auto align")
self.autoAlign_check.SetFont(wx.SMALL_FONT)
self.autoAlign_check.SetValue(config.envelopeFit['autoAlign'])
self.average_label = wx.StaticText(panel, -1, "", size=(100, -1))
self.average_label.SetFont(wx.SMALL_FONT)
self.updateAverageLabel()
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(self.collapse_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(10)
sizer.Add(fitTo_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.fitToPeaklist_radio, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.fitToSpectrum_radio, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(fwhm_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.fwhm_value, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.forceFwhm_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(relThreshold_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.relThreshold_value, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(relThresholdUnits_label, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.autoAlign_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.average_label, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
mainSizer.Fit(panel)
panel.SetSizer(mainSizer)
return panel
def makeControlbar(self):
"""Make controlbar."""
# init toolbar
panel = mwx.bgrPanel(self, -1, images.lib['bgrControlbar'], size=(-1, mwx.CONTROLBAR_HEIGHT))
# make elements
massType_label = wx.StaticText(panel, -1, "Mass:")
massType_label.SetFont(wx.SMALL_FONT)
self.massTypeMo_radio = wx.RadioButton(panel, -1, "Mo", style=wx.RB_GROUP)
self.massTypeMo_radio.SetFont(wx.SMALL_FONT)
self.massTypeMo_radio.SetValue(True)
self.massTypeAv_radio = wx.RadioButton(panel, -1, "Av")
self.massTypeAv_radio.SetFont(wx.SMALL_FONT)
self.massTypeAv_radio.SetValue(config.compoundsSearch['massType'])
maxCharge_label = wx.StaticText(panel, -1, "Max charge:")
maxCharge_label.SetFont(wx.SMALL_FONT)
self.maxCharge_value = wx.TextCtrl(panel, -1, str(config.compoundsSearch['maxCharge']), size=(30, mwx.SMALL_TEXTCTRL_HEIGHT), validator=mwx.validator('int'))
self.maxCharge_value.SetFont(wx.SMALL_FONT)
self.radicals_check = wx.CheckBox(panel, -1, "M*")
self.radicals_check.SetFont(wx.SMALL_FONT)
self.radicals_check.SetValue(config.compoundsSearch['radicals'])
adducts_label = wx.StaticText(panel, -1, "Adducts:")
adducts_label.SetFont(wx.SMALL_FONT)
self.adductNa_check = wx.CheckBox(panel, -1, "Na")
self.adductNa_check.SetFont(wx.SMALL_FONT)
self.adductNa_check.SetValue(config.compoundsSearch['adducts'].count('Na'))
self.adductK_check = wx.CheckBox(panel, -1, "K")
self.adductK_check.SetFont(wx.SMALL_FONT)
self.adductK_check.SetValue(config.compoundsSearch['adducts'].count('K'))
self.adductLi_check = wx.CheckBox(panel, -1, "Li")
self.adductLi_check.SetFont(wx.SMALL_FONT)
self.adductLi_check.SetValue(config.compoundsSearch['adducts'].count('Li'))
self.adductNH4_check = wx.CheckBox(panel, -1, "NH4")
self.adductNH4_check.SetFont(wx.SMALL_FONT)
self.adductNH4_check.SetValue(config.compoundsSearch['adducts'].count('NH4'))
self.adductH2O_check = wx.CheckBox(panel, -1, "-H2O")
self.adductH2O_check.SetFont(wx.SMALL_FONT)
self.adductH2O_check.SetValue(config.compoundsSearch['adducts'].count('-H2O'))
self.adductACN_check = wx.CheckBox(panel, -1, "ACN")
self.adductACN_check.SetFont(wx.SMALL_FONT)
self.adductACN_check.SetValue(config.compoundsSearch['adducts'].count('ACN'))
self.adductMeOH_check = wx.CheckBox(panel, -1, "MeOH")
self.adductMeOH_check.SetFont(wx.SMALL_FONT)
self.adductMeOH_check.SetValue(config.compoundsSearch['adducts'].count('MeOH'))
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(massType_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.massTypeMo_radio, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.massTypeAv_radio, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(maxCharge_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.maxCharge_value, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.radicals_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(adducts_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.adductNa_check, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.adductK_check, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.adductLi_check, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.adductNH4_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.adductH2O_check, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.adductACN_check, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.adductMeOH_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
mainSizer.Fit(panel)
panel.SetSizer(mainSizer)
return panel
def makeToolbar(self):
"""Make toolbar."""
# init toolbar
panel = mwx.bgrPanel(self, -1, images.lib['bgrToolbar'], size=(-1, mwx.TOOLBAR_HEIGHT))
# make elements
mass_label = wx.StaticText(panel, -1, "Mo. mass:")
mass_label.SetFont(wx.SMALL_FONT)
self.mass_value = wx.TextCtrl(panel, -1, "", size=(120, -1), style=wx.TE_PROCESS_ENTER, validator=mwx.validator('floatPos'))
self.mass_value.Bind(wx.EVT_TEXT_ENTER, self.onGenerate)
charge_label = wx.StaticText(panel, -1, "Charge:")
charge_label.SetFont(wx.SMALL_FONT)
self.charge_value = wx.TextCtrl(panel, -1, str(config.massToFormula['charge']), size=(40, -1), validator=mwx.validator('int'))
choices = ['M', 'M*', 'H+', 'Na+', 'K+', 'Li+', 'NH4+']
self.ionization_choice = wx.Choice(panel, -1, choices=choices, size=(80, mwx.SMALL_CHOICE_HEIGHT))
choices = ['', 'e', 'H', 'Na', 'K', 'Li', 'NH4']
if config.massToFormula['ionization'] in choices:
self.ionization_choice.Select(choices.index(config.massToFormula['ionization']))
tolerance_label = wx.StaticText(panel, -1, "Tolerance:")
tolerance_label.SetFont(wx.SMALL_FONT)
self.tolerance_value = wx.TextCtrl(panel, -1, str(config.massToFormula['tolerance']), size=(50, -1), validator=mwx.validator('floatPos'))
self.tolerance_value.Bind(wx.EVT_TEXT_ENTER, self.onGenerate)
self.unitsDa_radio = wx.RadioButton(panel, -1, "Da", style=wx.RB_GROUP)
self.unitsDa_radio.SetFont(wx.SMALL_FONT)
self.unitsDa_radio.SetValue(True)
self.unitsDa_radio.Bind(wx.EVT_RADIOBUTTON, self.onUnitsChanged)
self.unitsPpm_radio = wx.RadioButton(panel, -1, "ppm")
self.unitsPpm_radio.SetFont(wx.SMALL_FONT)
self.unitsPpm_radio.Bind(wx.EVT_RADIOBUTTON, self.onUnitsChanged)
self.unitsPpm_radio.SetValue((config.massToFormula['units'] == 'ppm'))
self.generate_butt = wx.Button(panel, -1, "Generate", size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.generate_butt.Bind(wx.EVT_BUTTON, self.onGenerate)
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(mass_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.mass_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(charge_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.charge_value, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 10)
sizer.Add(self.ionization_choice, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(tolerance_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.tolerance_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(10)
sizer.Add(self.unitsDa_radio, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.unitsPpm_radio, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddStretchSpacer()
sizer.AddSpacer(20)
sizer.Add(self.generate_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.TOOLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
panel.SetSizer(mainSizer)
mainSizer.Fit(panel)
return panel
def makeToolbar(self):
"""Make toolbar."""
# init toolbar
panel = mwx.bgrPanel(self, -1, images.lib['bgrToolbarNoBorder'], size=(-1, mwx.TOOLBAR_HEIGHT))
# make match fields
difference_label = wx.StaticText(panel, -1, "Difference:")
difference_label.SetFont(wx.SMALL_FONT)
self.difference_value = wx.TextCtrl(panel, -1, '', size=(100, -1), style=wx.TE_PROCESS_ENTER, validator=mwx.validator('floatPos'))
self.difference_value.Bind(wx.EVT_TEXT_ENTER, self.onSearch)
self.aminoacids_check = wx.CheckBox(panel, -1, "Amino acids")
self.aminoacids_check.SetFont(wx.SMALL_FONT)
self.aminoacids_check.SetValue(config.peakDifferences['aminoacids'])
self.dipeptides_check = wx.CheckBox(panel, -1, "Dipeptides")
self.dipeptides_check.SetFont(wx.SMALL_FONT)
self.dipeptides_check.SetValue(config.peakDifferences['dipeptides'])
massType_label = wx.StaticText(panel, -1, "Mass:")
massType_label.SetFont(wx.SMALL_FONT)
self.massTypeMo_radio = wx.RadioButton(panel, -1, "Mo", style=wx.RB_GROUP)
self.massTypeMo_radio.SetFont(wx.SMALL_FONT)
self.massTypeMo_radio.SetValue(True)
self.massTypeAv_radio = wx.RadioButton(panel, -1, "Av")
self.massTypeAv_radio.SetFont(wx.SMALL_FONT)
self.massTypeAv_radio.SetValue(config.peakDifferences['massType'])
tolerance_label = wx.StaticText(panel, -1, "Tolerance:")
tolerance_label.SetFont(wx.SMALL_FONT)
self.tolerance_value = wx.TextCtrl(panel, -1, str(config.peakDifferences['tolerance']), size=(50, -1), validator=mwx.validator('floatPos'))
toleranceUnits_label = wx.StaticText(panel, -1, "m/z")
toleranceUnits_label.SetFont(wx.SMALL_FONT)
self.consolidate_check = wx.CheckBox(panel, -1, "Hide umatched")
self.consolidate_check.SetFont(wx.SMALL_FONT)
self.consolidate_check.SetValue(config.peakDifferences['consolidate'])
self.search_butt = wx.Button(panel, -1, "Search", size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.search_butt.Bind(wx.EVT_BUTTON, self.onSearch)
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(difference_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.difference_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.aminoacids_check, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.dipeptides_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(massType_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.massTypeMo_radio, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.massTypeAv_radio, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(tolerance_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.tolerance_value, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(toleranceUnits_label, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.consolidate_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddStretchSpacer()
sizer.AddSpacer(20)
sizer.Add(self.search_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
panel.SetSizer(mainSizer)
mainSizer.Fit(panel)
return panel
def makeToolbar(self):
"""Make toolbar."""
# init toolbar
panel = mwx.bgrPanel(self, -1, images.lib['bgrToolbar'], size=(-1, mwx.TOOLBAR_HEIGHT))
# make buttons
self.errors_butt = wx.BitmapButton(panel, ID_matchErrors, images.lib['matchErrorsOff'], size=(mwx.TOOLBAR_TOOLSIZE), style=wx.BORDER_NONE)
self.errors_butt.SetToolTip(wx.ToolTip("Error plot"))
self.errors_butt.Bind(wx.EVT_BUTTON, self.onToolSelected)
self.summary_butt = wx.BitmapButton(panel, ID_matchSummary, images.lib['matchSummaryOff'], size=(mwx.TOOLBAR_TOOLSIZE), style=wx.BORDER_NONE)
self.summary_butt.SetToolTip(wx.ToolTip("Match summary"))
self.summary_butt.Bind(wx.EVT_BUTTON, self.onToolSelected)
# make match fields
tolerance_label = wx.StaticText(panel, -1, "Tolerance:")
tolerance_label.SetFont(wx.SMALL_FONT)
self.tolerance_value = wx.TextCtrl(panel, -1, str(config.match['tolerance']), size=(60, -1), validator=mwx.validator('floatPos'))
self.unitsDa_radio = wx.RadioButton(panel, -1, "Da", style=wx.RB_GROUP)
self.unitsDa_radio.SetFont(wx.SMALL_FONT)
self.unitsDa_radio.SetValue(True)
self.unitsDa_radio.Bind(wx.EVT_RADIOBUTTON, self.onUnitsChanged)
self.unitsPpm_radio = wx.RadioButton(panel, -1, "ppm")
self.unitsPpm_radio.SetFont(wx.SMALL_FONT)
self.unitsPpm_radio.Bind(wx.EVT_RADIOBUTTON, self.onUnitsChanged)
self.unitsPpm_radio.SetValue((config.match['units'] == 'ppm'))
self.ignoreCharge_check = wx.CheckBox(panel, -1, "Ignore charge")
self.ignoreCharge_check.SetFont(wx.SMALL_FONT)
self.ignoreCharge_check.SetValue(config.match['ignoreCharge'])
if self.currentModule == 'massfilter':
self.ignoreCharge_check.Disable()
self.match_butt = wx.Button(panel, -1, "Match", size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.match_butt.Bind(wx.EVT_BUTTON, self.onMatch)
self.calibrate_butt = wx.Button(panel, -1, "Calibrate", size=(-1, mwx.SMALL_BUTTON_HEIGHT))
self.calibrate_butt.Bind(wx.EVT_BUTTON, self.onCalibrate)
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.TOOLBAR_LSPACE)
sizer.Add(self.errors_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.Add(self.summary_butt, 0, wx.ALIGN_CENTER_VERTICAL|wx.LEFT, mwx.BUTTON_SIZE_CORRECTION)
sizer.AddSpacer(20)
sizer.Add(tolerance_label, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.tolerance_value, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(10)
sizer.Add(self.unitsDa_radio, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 5)
sizer.Add(self.unitsPpm_radio, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.ignoreCharge_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddStretchSpacer()
sizer.AddSpacer(20)
sizer.Add(self.match_butt, 0, wx.ALIGN_CENTER_VERTICAL|wx.RIGHT, 10)
sizer.Add(self.calibrate_butt, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.TOOLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
panel.SetSizer(mainSizer)
mainSizer.Fit(panel)
return panel
def makeControlbar(self):
"""Make controlbar."""
# init toolbar
panel = mwx.bgrPanel(self,
-1,
images.lib['bgrControlbar'],
size=(-1, mwx.CONTROLBAR_HEIGHT))
# make elements
relIntCutoff_label = wx.StaticText(panel, -1, "Int. threshold:")
relIntCutoff_label.SetFont(wx.SMALL_FONT)
relIntCutoffUnits_label = wx.StaticText(panel, -1, "%")
relIntCutoffUnits_label.SetFont(wx.SMALL_FONT)
self.relIntCutoff_value = wx.TextCtrl(
panel,
-1,
str(config.massDefectPlot['relIntCutoff'] * 100),
size=(50, mwx.SMALL_TEXTCTRL_HEIGHT),
validator=mwx.validator('floatPos'))
self.relIntCutoff_value.SetFont(wx.SMALL_FONT)
self.removeIsotopes_check = wx.CheckBox(panel, -1, "Remove isotopes")
self.removeIsotopes_check.SetFont(wx.SMALL_FONT)
self.removeIsotopes_check.SetValue(
config.massDefectPlot['removeIsotopes'])
self.ignoreCharge_check = wx.CheckBox(panel, -1, "Ignore charge")
self.ignoreCharge_check.SetFont(wx.SMALL_FONT)
self.ignoreCharge_check.SetValue(config.massDefectPlot['ignoreCharge'])
self.showNotations_check = wx.CheckBox(panel, -1,
"Highlight annotated")
self.showNotations_check.SetFont(wx.SMALL_FONT)
self.showNotations_check.SetValue(
config.massDefectPlot['showNotations'])
self.showNotations_check.Bind(wx.EVT_CHECKBOX, self.onShowNotations)
self.showAllDocuments_check = wx.CheckBox(panel, -1,
"Show all documents")
self.showAllDocuments_check.SetFont(wx.SMALL_FONT)
self.showAllDocuments_check.SetValue(False)
self.showAllDocuments_check.Bind(wx.EVT_CHECKBOX,
self.onShowAllDocuments)
# pack elements
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.AddSpacer(mwx.CONTROLBAR_LSPACE)
sizer.Add(relIntCutoff_label, 0, wx.ALIGN_CENTER_VERTICAL | wx.RIGHT,
5)
sizer.Add(self.relIntCutoff_value, 0,
wx.ALIGN_CENTER_VERTICAL | wx.RIGHT, 5)
sizer.Add(relIntCutoffUnits_label, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.removeIsotopes_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.ignoreCharge_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.showNotations_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(20)
sizer.Add(self.showAllDocuments_check, 0, wx.ALIGN_CENTER_VERTICAL)
sizer.AddSpacer(mwx.CONTROLBAR_RSPACE)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(sizer, 1, wx.EXPAND)
mainSizer.Fit(panel)
panel.SetSizer(mainSizer)
return panel
def makePMFPanel(self):
"""Make controls for search form panel."""
panel = wx.Panel(self, -1)
# make info elements
paramSearchTitle_label = wx.StaticText(panel, -1, "Title:")
self.paramTitle_value = wx.TextCtrl(panel, -1, "", size=(250, -1))
# make sequence elements
paramTaxonomy_label = wx.StaticText(panel, -1, "Taxonomy:")
self.paramTaxonomy_choice = wx.Choice(panel, -1, choices=[], size=(300, mwx.CHOICE_HEIGHT))
paramDatabase_label = wx.StaticText(panel, -1, "Database:")
self.paramDatabase_choice = wx.Choice(panel, -1, choices=[], size=(150, mwx.CHOICE_HEIGHT))
paramEnzyme_label = wx.StaticText(panel, -1, " Enzyme:")
self.paramEnzyme_choice = wx.Choice(panel, -1, choices=[], size=(130, mwx.CHOICE_HEIGHT))
paramMiscleavages_label = wx.StaticText(panel, -1, " Miscl.:")
self.paramMiscleavages_choice = wx.Choice(panel, -1, choices=['0','1','2','3','4'], size=(50, mwx.CHOICE_HEIGHT))
self.paramMiscleavages_choice.SetStringSelection(str(config.profound['miscleavages']))
# make modifications elements
self.paramFixedMods_label = wx.StaticText(panel, -1, "Complete modifications:")
self.paramFixedMods_listbox = wx.ListBox(panel, -1, size=(200, 100), choices=[], style=wx.LB_EXTENDED)
self.paramFixedMods_listbox.SetFont(wx.SMALL_FONT)
self.paramFixedMods_listbox.Bind(wx.EVT_LISTBOX, self.onModificationSelected)
self.paramVariableMods_label = wx.StaticText(panel, -1, "Partial modifications:")
self.paramVariableMods_listbox = wx.ListBox(panel, -1, size=(200, 100), choices=[], style=wx.LB_EXTENDED)
self.paramVariableMods_listbox.SetFont(wx.SMALL_FONT)
self.paramVariableMods_listbox.Bind(wx.EVT_LISTBOX, self.onModificationSelected)
# make masses elements
paramProteinMass_label = wx.StaticText(panel, -1, "Protein mass:")
self.paramProteinMassLow_value = wx.TextCtrl(panel, -1, "0", size=(50, -1), validator=mwx.validator('floatPos'))
self.paramProteinMassHigh_value = wx.TextCtrl(panel, -1, "300", size=(50, -1), validator=mwx.validator('floatPos'))
paramProteinMass_dash = wx.StaticText(panel, -1, "-")
paramProteinMassUnits_label = wx.StaticText(panel, -1, "kDa")
paramProteinPI_label = wx.StaticText(panel, -1, "Protein pI:")
self.paramProteinPILow_value = wx.TextCtrl(panel, -1, "0", size=(50, -1), validator=mwx.validator('floatPos'))
self.paramProteinPIHigh_value = wx.TextCtrl(panel, -1, "14", size=(50, -1), validator=mwx.validator('floatPos'))
paramProteinPI_dash = wx.StaticText(panel, -1, "-")
paramPeptideTol_label = wx.StaticText(panel, -1, "Peptide tolerance:")
self.paramPeptideTol_value = wx.TextCtrl(panel, -1, str(config.profound['peptideTol']), size=(50, -1), validator=mwx.validator('floatPos'))
self.paramPeptideTolUnits_choice = wx.Choice(panel, -1, choices=['Da','%','ppm'], size=(80, mwx.CHOICE_HEIGHT))
self.paramPeptideTolUnits_choice.SetStringSelection(config.profound['peptideTolUnits'])
paramMassType_label = wx.StaticText(panel, -1, "Mass type:")
self.paramMassType_choice = wx.Choice(panel, -1, choices=['Monoisotopic', 'Average'], size=(150, mwx.CHOICE_HEIGHT))
self.paramMassType_choice.SetStringSelection(config.profound['massType'])
paramCharge_label = wx.StaticText(panel, -1, "Charge:")
self.paramCharge_choice = wx.Choice(panel, -1, choices=['MH+','M'], size=(150, mwx.CHOICE_HEIGHT))
self.paramCharge_choice.SetStringSelection(config.profound['charge'])
# results elements
self.paramExpectation_radio = wx.RadioButton(panel, -1, "Expectation value:", style=wx.RB_GROUP)
self.paramExpectation_value = wx.TextCtrl(panel, -1, str(config.profound['expectation']), size=(60, -1), validator=mwx.validator('floatPos'))
if config.profound['ranking'] == 'expect':
self.paramExpectation_radio.SetValue(True)
self.paramZscore_radio = wx.RadioButton(panel, -1, "Z Score candidates:")
self.paramCandidates_value = wx.TextCtrl(panel, -1, str(config.profound['candidates']), size=(60, -1), validator=mwx.validator('floatPos'))
if config.profound['ranking'] == 'zscore':
self.paramZscore_radio.SetValue(True)
# pack elements
infoGrid = wx.GridBagSizer(mwx.GRIDBAG_VSPACE, mwx.GRIDBAG_HSPACE)
infoGrid.Add(paramSearchTitle_label, (0,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
infoGrid.Add(self.paramTitle_value, (0,1), flag=wx.EXPAND)
infoGrid.AddGrowableCol(1)
sequenceGrid = wx.GridBagSizer(mwx.GRIDBAG_VSPACE, mwx.GRIDBAG_HSPACE)
sequenceGrid.Add(paramTaxonomy_label, (0,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
sequenceGrid.Add(self.paramTaxonomy_choice, (0,1), (1,5), flag=wx.EXPAND)
sequenceGrid.Add(paramDatabase_label, (1,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
sequenceGrid.Add(self.paramDatabase_choice, (1,1), flag=wx.EXPAND)
sequenceGrid.Add(paramEnzyme_label, (1,2), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
sequenceGrid.Add(self.paramEnzyme_choice, (1,3), flag=wx.EXPAND)
sequenceGrid.Add(paramMiscleavages_label, (1,4), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
sequenceGrid.Add(self.paramMiscleavages_choice, (1,5))
sequenceGrid.AddGrowableCol(1)
sequenceGrid.AddGrowableCol(3)
modsGrid = wx.GridBagSizer(5, 20)
modsGrid.Add(self.paramFixedMods_label, (0,0), flag=wx.ALIGN_CENTER_VERTICAL)
modsGrid.Add(self.paramVariableMods_label, (0,1), flag=wx.ALIGN_CENTER_VERTICAL)
modsGrid.Add(self.paramFixedMods_listbox, (1,0), flag=wx.EXPAND)
modsGrid.Add(self.paramVariableMods_listbox, (1,1), flag=wx.EXPAND)
modsGrid.AddGrowableCol(0)
modsGrid.AddGrowableCol(1)
massesGrid = wx.GridBagSizer(mwx.GRIDBAG_VSPACE, mwx.GRIDBAG_HSPACE)
massesGrid.Add(paramProteinMass_label, (0,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(self.paramProteinMassLow_value, (0,1), flag=wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(paramProteinMass_dash, (0,2), flag=wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(self.paramProteinMassHigh_value, (0,3), flag=wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(paramProteinMassUnits_label, (0,4), flag=wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(paramProteinPI_label, (1,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(self.paramProteinPILow_value, (1,1), flag=wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(paramProteinPI_dash, (1,2), flag=wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(self.paramProteinPIHigh_value, (1,3), flag=wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(paramPeptideTol_label, (2,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(self.paramPeptideTol_value, (2,1), flag=wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(self.paramPeptideTolUnits_choice, (2,3), (1,2), flag=wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(paramMassType_label, (0,5), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(self.paramMassType_choice, (0,6), flag=wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(paramCharge_label, (1,5), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
massesGrid.Add(self.paramCharge_choice, (1,6), flag=wx.ALIGN_CENTER_VERTICAL)
massesGrid.AddGrowableCol(4)
resultsGrid = wx.GridBagSizer(mwx.GRIDBAG_VSPACE, mwx.GRIDBAG_HSPACE)
resultsGrid.Add(self.paramExpectation_radio, (0,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
resultsGrid.Add(self.paramExpectation_value, (0,1), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
resultsGrid.Add(self.paramZscore_radio, (0,3), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
resultsGrid.Add(self.paramCandidates_value, (0,4), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
resultsGrid.AddGrowableCol(2)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(infoGrid, 0, wx.EXPAND|wx.ALL, mwx.PANEL_SPACE_MAIN)
mainSizer.Add(wx.StaticLine(panel), 0, wx.EXPAND|wx.LEFT|wx.RIGHT, mwx.PANEL_SPACE_MAIN)
mainSizer.Add(sequenceGrid, 0, wx.EXPAND|wx.ALL, mwx.PANEL_SPACE_MAIN)
mainSizer.Add(wx.StaticLine(panel), 0, wx.EXPAND|wx.LEFT|wx.RIGHT, mwx.PANEL_SPACE_MAIN)
mainSizer.Add(modsGrid, 0, wx.EXPAND|wx.ALL, mwx.PANEL_SPACE_MAIN)
mainSizer.Add(wx.StaticLine(panel), 0, wx.EXPAND|wx.LEFT|wx.RIGHT, mwx.PANEL_SPACE_MAIN)
mainSizer.Add(massesGrid, 0, wx.EXPAND|wx.ALL, mwx.PANEL_SPACE_MAIN)
mainSizer.Add(wx.StaticLine(panel), 0, wx.EXPAND|wx.LEFT|wx.RIGHT, mwx.PANEL_SPACE_MAIN)
mainSizer.Add(resultsGrid, 0, wx.EXPAND|wx.ALL, mwx.PANEL_SPACE_MAIN)
# fit layout
mainSizer.Fit(panel)
panel.SetSizer(mainSizer)
return panel
