def onDeleteItem(self, evt):
"""Remove selected items."""
# delete?
title = 'Do you really want to delete selected monomers?'
message = 'Monomer definitions will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15),
(wx.ID_OK, "Delete", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# delete items
for i in self.itemsList.getSelected():
index = self.itemsList.GetItemData(i)
name = self.itemsMap[index][0]
if not name in self.used:
del mspy.monomers[name]
else:
wx.Bell()
dlg = mwx.dlgMessage(
self,
title='Monomer "' + name +
'" is currently used\nand cannot be removed.',
message=
'Remove the monomer from all of your documents first.')
dlg.ShowModal()
dlg.Destroy()
# update gui
self.updateItemsList()
self.clearEditor()
def onDeleteItem(self, evt):
"""Remove selected items."""
# delete?
title = 'Do you really want to delete selected monomers?'
message = 'Monomer definitions will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15), (wx.ID_OK, "Delete", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# delete items
for i in self.itemsList.getSelected():
index = self.itemsList.GetItemData(i)
name = self.itemsMap[index][0]
if not name in self.used:
del mspy.monomers[name]
else:
wx.Bell()
dlg = mwx.dlgMessage(self, title='Monomer "'+name+'" is currently used\nand cannot be removed.', message='Remove the monomer from all of your documents first.')
dlg.ShowModal()
dlg.Destroy()
# update gui
self.updateItemsList()
self.clearEditor()
def onAddItem(self, evt):
"""Add/replace item."""
# get item data
itemData = self.getItemData()
if not itemData:
return
# check regular amino acids
if itemData.abbr in self._aminoacids:
wx.Bell()
dlg = mwx.dlgMessage(self, title='Specified abbreviation is reserved!', message='Specified abbreviation is already used for regular amino acids\nwhich cannot be modified.')
dlg.ShowModal()
dlg.Destroy()
return
# check name
if itemData.abbr in mspy.monomers:
wx.Bell()
title = 'Monomer with the same abbreviation already exists.\nDo you want to replace it?'
message = 'Old monomer definition will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15), (wx.ID_OK, "Replace", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# add/replace item
mspy.monomers[itemData.abbr] = itemData
# update gui
self.updateItemsList()
self.clearEditor()
def onGenerate(self, evt=None):
"""Generate formulae."""
# check processing
if self.processing:
return
# clear previous data
self.currentFormulae = None
# get params
if not self.getParams():
self.updateFormulaeList()
wx.Bell()
return
# check mass limit
if not self.checkMassLimit():
wx.Bell()
message = "Neutral mass of your specified ion is too high (%.0f Da max)." % config.massToFormula['massLimit']
dlg = mwx.dlgMessage(self, title="Neutral mass is too high.", message=message)
dlg.ShowModal()
dlg.Destroy()
return
# show processing gauge
self.onProcessing(True)
self.generate_butt.Enable(False)
# do processing
self.processing = threading.Thread(target=self.runGenerator)
self.processing.start()
# pulse gauge while working
while self.processing and self.processing.isAlive():
self.gauge.pulse()
# update gui
self.updateFormulaeList()
# hide processing gauge
self.onProcessing(False)
self.generate_butt.Enable(True)
# show limit warning
if self.currentFormulae and len(self.currentFormulae) >= config.massToFormula['countLimit']:
wx.Bell()
dlg = mwx.dlgMessage(self, title="Maximum number of formulae reached.", message="The internal limit for number of formulae has been reached.\nPlease note that your formula could be missing.")
dlg.ShowModal()
dlg.Destroy()
def onDeleteItem(self, evt):
"""Remove selected items."""
# check group
if not self.group:
wx.Bell()
return
# delete?
title = 'Do you really want to delete selected references?'
message = 'Reference definitions will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15), (wx.ID_OK, "Delete", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# delete items
indexes = []
for i in self.itemsList.getSelected():
index = self.itemsList.GetItemData(i)
indexes.append(index)
# delete items
for i in sorted(indexes, reverse=True):
del libs.references[self.group][i]
# update gui
self.updateItemsList()
self.clearEditor()
def onDeleteGroup(self, evt):
"""Delete selected group."""
# check group
if not self.group:
wx.Bell()
return
# delete selected group
title = 'Do you really want to delete selected group?'
message = 'All references within the group will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15), (wx.ID_OK, "Delete", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# remove group
del libs.references[self.group]
# update gui
self.updateGroups()
self.groupName_choice.Select(0)
self.onGroupSelected()
def onAddGroup(self, evt):
"""Add new group."""
# get group name
dlg = dlgGroupName(self)
if dlg.ShowModal() == wx.ID_OK:
name = dlg.name
dlg.Destroy()
else:
dlg.Destroy()
return
# check group name
if name in libs.compounds:
wx.Bell()
dlg = mwx.dlgMessage(self, title='Group with the same name already exists.', message='Type a different name.')
dlg.ShowModal()
dlg.Destroy()
return
# add group
libs.references[name] = []
# update gui
self.updateGroups()
self.groupName_choice.SetStringSelection(name)
self.onGroupSelected()
def onDeleteItem(self, evt):
"""Remove selected items."""
# check group
if not self.group:
wx.Bell()
return
# delete?
title = "Do you really want to delete selected compounds?"
message = "Compound definitions will be lost."
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15), (wx.ID_OK, "Delete", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# delete items
for i in self.itemsList.getSelected():
index = self.itemsList.GetItemData(i)
name = self.itemsMap[index][0]
del libs.compounds[self.group][name]
# update gui
self.updateItemsList()
self.clearEditor()
def onAddItem(self, evt):
"""Add/replace item."""
# check group
if not self.group:
wx.Bell()
return
# get item data
itemData = self.getItemData()
if not itemData:
return
# check name
if itemData.name in libs.compounds[self.group]:
wx.Bell()
title = "Compound with the same name already exists.\nDo you want to replace it?"
message = "Old compound definition will be lost."
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15), (wx.ID_OK, "Replace", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# add/replace item
libs.compounds[self.group][itemData.name] = itemData
# update gui
self.updateItemsList()
self.clearEditor()
def onDeleteItem(self, evt):
"""Remove selected items."""
# check group
if not self.group:
wx.Bell()
return
# delete?
title = 'Do you really want to delete selected references?'
message = 'Reference definitions will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15),
(wx.ID_OK, "Delete", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# delete items
indexes = []
for i in self.itemsList.getSelected():
index = self.itemsList.GetItemData(i)
indexes.append(index)
# delete items
for i in sorted(indexes, reverse=True):
del libs.references[self.group][i]
# update gui
self.updateItemsList()
self.clearEditor()
def onAddItem(self, evt):
"""Add/replace item."""
# get item data
itemData = self.getItemData()
if not itemData:
return
# check name
name = self.itemName_value.GetValue()
if name in libs.mascot:
wx.Bell()
title = 'Server with the same name already exists.\nDo you want to replace it?'
message = 'Old server definition will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15),
(wx.ID_OK, "Replace", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# add/replace item
libs.mascot[name] = itemData
# update gui
self.updateItemsList()
self.clearEditor()
def onApply(self, evt):
"""Apply current profile to current document."""
# check data and document
if self.currentDocument == None or self.currentProfile == None:
wx.Bell()
return
# ask to owerwrite spectrum
if self.currentDocument.spectrum.hasprofile():
title = 'Do you really want to apply generated spectrum\nto current document?'
message = 'Original profile data will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15), (wx.ID_OK, "Apply", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# backup document
self.currentDocument.backup(('spectrum'))
# set profile to document
points = self.currentProfile.copy()
self.currentDocument.spectrum.setprofile(points)
# update document
self.parent.onDocumentChanged(items=('spectrum'))
def onRenameItem(self, evt):
"""Rename item."""
# check selection
if self.selectedItem == None:
wx.Bell()
return
# get item data
itemData = self.getItemData()
if not itemData:
return
# check name
if itemData[0] in libs.presets[itemData[1]]:
wx.Bell()
dlg = mwx.dlgMessage(self, title='Presets with the same name already exists.', message='Type a different name.')
dlg.ShowModal()
dlg.Destroy()
return
# rename item
oldName = self.itemsMap[self.selectedItem][0]
data = copy.deepcopy(libs.presets[itemData[1]][oldName])
libs.presets[itemData[1]][itemData[0]] = data
del libs.presets[itemData[1]][oldName]
# update gui
self.updateItemsList()
self.clearEditor()
def onDeleteItem(self, evt):
"""Remove selected items."""
# delete?
title = 'Do you really want to delete selected presets?'
message = 'Presets definitions will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15),
(wx.ID_OK, "Delete", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# delete items
for i in self.itemsList.getSelected():
index = self.itemsList.GetItemData(i)
name = self.itemsMap[index][0]
category = self.itemsMap[index][1]
del libs.presets[category][name]
# update gui
self.updateItemsList()
self.clearEditor()
def onAddItem(self, evt):
"""Add/replace item."""
# get item data
itemData = self.getItemData()
if not itemData:
return
# check name
if itemData.name in mspy.enzymes:
wx.Bell()
title = 'Enzyme with the same name already exists.\nDo you want to replace it?'
message = 'Old enzyme definition will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15), (wx.ID_OK, "Replace", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# add/replace item
mspy.enzymes[itemData.name] = itemData
# update gui
self.updateItemsList()
self.clearEditor()
def checkParams(self):
"""Check search parameters."""
errors = ''
# check taxonomy and database
if not config.profound['taxonomy']:
errors += '- Taxonomy must be selected.\n'
if not config.profound['database']:
errors += '- Database must be selected.\n'
if not config.profound['enzyme']:
errors += '- Enzyme must be selected.\n'
# check query
if not self.paramQuery_value.GetValue():
errors += '- Peak list is empty.\n'
# show warning if errors
if errors:
wx.Bell()
dlg = mwx.dlgMessage(self, title="You have the following errors in the search form.", message=errors)
dlg.ShowModal()
dlg.Destroy()
return False
else:
return True
def onDeleteGroup(self, evt):
"""Delete selected group."""
# check group
if not self.group:
wx.Bell()
return
# delete selected group
title = 'Do you really want to delete selected group?'
message = 'All compounds within the group will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15),
(wx.ID_OK, "Delete", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# remove group
del libs.compounds[self.group]
# update gui
self.updateGroups()
self.groupName_choice.Select(0)
self.onGroupSelected()
def onAddItem(self, evt):
"""Add/replace item."""
# check group
if not self.group:
wx.Bell()
return
# get item data
itemData = self.getItemData()
if not itemData:
return
# check name
if itemData.name in libs.compounds[self.group]:
wx.Bell()
title = 'Compound with the same name already exists.\nDo you want to replace it?'
message = 'Old compound definition will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15),
(wx.ID_OK, "Replace", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# add/replace item
libs.compounds[self.group][itemData.name] = itemData
# update gui
self.updateItemsList()
self.clearEditor()
def onRenameItem(self, evt):
"""Rename item."""
# check selection
if self.selectedItem == None:
wx.Bell()
return
# get item data
itemData = self.getItemData()
if not itemData:
return
# check name
if itemData[0] in libs.presets[itemData[1]]:
wx.Bell()
dlg = mwx.dlgMessage(
self,
title='Presets with the same name already exists.',
message='Type a different name.')
dlg.ShowModal()
dlg.Destroy()
return
# rename item
oldName = self.itemsMap[self.selectedItem][0]
data = copy.deepcopy(libs.presets[itemData[1]][oldName])
libs.presets[itemData[1]][itemData[0]] = data
del libs.presets[itemData[1]][oldName]
# update gui
self.updateItemsList()
self.clearEditor()
def onAddGroup(self, evt):
"""Add new group."""
# get group name
dlg = dlgGroupName(self)
if dlg.ShowModal() == wx.ID_OK:
name = dlg.name
dlg.Destroy()
else:
dlg.Destroy()
return
# check group name
if name in libs.compounds:
wx.Bell()
dlg = mwx.dlgMessage(
self,
title='Group with the same name already exists.',
message='Type a different name.')
dlg.ShowModal()
dlg.Destroy()
return
# add group
libs.compounds[name] = {}
# update gui
self.updateGroups()
self.groupName_choice.SetStringSelection(name)
self.onGroupSelected()
def onAddItem(self, evt):
"""Add/replace item."""
# get item data
itemData = self.getItemData()
if not itemData:
return
# check name
name = self.itemName_value.GetValue()
if name in libs.mascot:
wx.Bell()
title = 'Server with the same name already exists.\nDo you want to replace it?'
message = 'Old server definition will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15), (wx.ID_OK, "Replace", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# add/replace item
libs.mascot[name] = itemData
# update gui
self.updateItemsList()
self.clearEditor()
def onCalculate(self, evt):
"""Generate compounds ions."""
# check processing
if self.processing:
return
# clear recent
self.currentCompound = None
self.currentFit = None
# check document
if not self.currentDocument or not (self.currentDocument.spectrum.hasprofile() or self.currentDocument.spectrum.haspeaks()):
wx.Bell()
return
# get params
if not self.getParams():
self.updateAverageLabel()
self.updateSpectrumCanvas()
self.updateResultsList()
return
# show processing gauge
self.onProcessing(True)
self.calculate_butt.Enable(False)
# do processing
self.processing = threading.Thread(target=self.runEnvelopeFit)
self.processing.start()
# pulse gauge while working
while self.processing and self.processing.isAlive():
self.gauge.pulse()
# check error
error = False
if self.currentFit is False:
self.currentFit = None
error = True
# update gui
self.updateAverageLabel()
self.updateSpectrumCanvas()
self.updateResultsList()
# hide processing gauge
self.onProcessing(False)
self.calculate_butt.Enable(True)
# check errors
if error:
wx.Bell()
dlg = mwx.dlgMessage(self, title="No data to fit.", message="There are no data in relevant mass range. Please check\nspecified formula, charge and default FWHM.")
dlg.ShowModal()
dlg.Destroy()
def onAddItem(self, evt):
"""Add/replace item."""
# get item data
itemData = self.getItemData()
if not itemData:
return
# check regular amino acids
if itemData.abbr in self._aminoacids:
wx.Bell()
dlg = mwx.dlgMessage(
self,
title='Specified abbreviation is reserved!',
message=
'Specified abbreviation is already used for regular amino acids\nwhich cannot be modified.'
)
dlg.ShowModal()
dlg.Destroy()
return
# check name
if itemData.abbr in mspy.monomers:
wx.Bell()
title = 'Monomer with the same abbreviation already exists.\nDo you want to replace it?'
message = 'Old monomer definition will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15),
(wx.ID_OK, "Replace", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# add/replace item
mspy.monomers[itemData.abbr] = itemData
# update gui
self.updateItemsList()
self.clearEditor()
def onItemSearch(self, evt):
"""Make query and send formula to selected database."""
# get selected formula
selected = self.formulaeList.getSelected()
if selected:
index = self.formulaeList.GetItemData(selected[0])
formula = self.currentFormulae[index][0]
else:
wx.Bell()
return
# get selected server
if evt.GetId() == ID_massToFormulaSearchPubChem:
server = 'PubChem'
elif evt.GetId() == ID_massToFormulaSearchChemSpider:
server = 'ChemSpider'
elif evt.GetId() == ID_massToFormulaSearchMETLIN:
server = 'METLIN'
elif evt.GetId() == ID_massToFormulaSearchHMDB:
server = 'HMDB'
elif evt.GetId() == ID_massToFormulaSearchLipidMaps:
server = 'Lipid MAPS'
else:
wx.Bell()
return
# make search html
htmlData = self.makeSearchHTML(server, formula)
# run search
try:
path = os.path.join(tempfile.gettempdir(), 'mmass_formula_search.html')
htmlFile = file(path, 'w')
htmlFile.write(htmlData.encode("utf-8"))
htmlFile.close()
webbrowser.open('file://'+path, autoraise=1)
except:
wx.Bell()
dlg = mwx.dlgMessage(self, title='Unable to send data to '+server+' server.', message='Unknown error occured while creating the search page.')
dlg.ShowModal()
dlg.Destroy()
def onRenameGroup(self, evt):
"""Rename selected group."""
# check group
if not self.group:
wx.Bell()
return
# get group name
dlg = dlgGroupName(self, self.group)
if dlg.ShowModal() == wx.ID_OK:
name = dlg.name
dlg.Destroy()
else:
dlg.Destroy()
return
# check group name
if name == self.group:
return
if name in libs.compounds:
wx.Bell()
dlg = mwx.dlgMessage(
self,
title='Group with the same name already exists.',
message='Type a different name.')
dlg.ShowModal()
dlg.Destroy()
return
# rename group
data = copy.deepcopy(libs.compounds[self.group])
libs.compounds[name] = data
del libs.compounds[self.group]
# update gui
self.updateGroups()
self.groupName_choice.SetStringSelection(name)
self.onGroupSelected()
def onRenameGroup(self, evt):
"""Rename selected group."""
# check group
if not self.group:
wx.Bell()
return
# get group name
dlg = dlgGroupName(self, self.group)
if dlg.ShowModal() == wx.ID_OK:
name = dlg.name
dlg.Destroy()
else:
dlg.Destroy()
return
# check group name
if name == self.group:
return
if name in libs.compounds:
wx.Bell()
dlg = mwx.dlgMessage(
self, title="Group with the same name already exists.", message="Type a different name."
)
dlg.ShowModal()
dlg.Destroy()
return
# rename group
data = copy.deepcopy(libs.compounds[self.group])
libs.compounds[name] = data
del libs.compounds[self.group]
# update gui
self.updateGroups()
self.groupName_choice.SetStringSelection(name)
self.onGroupSelected()
def onDeleteItem(self, evt):
"""Remove selected items."""
# delete?
title = 'Do you really want to delete selected servers?'
message = 'Server definitions will be lost.'
buttons = [(wx.ID_CANCEL, "Cancel", 80, False, 15), (wx.ID_OK, "Delete", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
if dlg.ShowModal() != wx.ID_OK:
dlg.Destroy()
return
else:
dlg.Destroy()
# delete items
for i in self.itemsList.getSelected():
index = self.itemsList.GetItemData(i)
name = self.itemsMap[index][0]
del libs.mascot[name]
# update gui
self.updateItemsList()
self.clearEditor()
def onSearch(self, evt):
"""Make query and send data to ProFound."""
# get params
if not self.getParams():
return
# check params
if not self.checkParams():
return
# make temporary search file
htmlData = self.makeSearchHTML()
try:
path = os.path.join(tempfile.gettempdir(), 'mmass_profound_search.html')
htmlFile = file(path, 'w')
htmlFile.write(htmlData.encode("utf-8"))
htmlFile.close()
webbrowser.open('file://'+path, autoraise=1)
except:
wx.Bell()
dlg = mwx.dlgMessage(self, title='Unable to send data to ProFound server.', message='Unknown error occured while creating the search page.')
dlg.ShowModal()
dlg.Destroy()
def onImport(self, evt):
"""Import items from xml library."""
# show open file dialog
wildcard = "Library files|*.xml;*.XML"
dlg = wx.FileDialog(self, "Import Library", wildcard=wildcard, style=wx.FD_OPEN|wx.FD_FILE_MUST_EXIST)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
dlg.Destroy()
else:
dlg.Destroy()
return
# read data
importedItems = self.readLibraryXML(path)
if importedItems == False:
wx.Bell()
dlg = mwx.dlgMessage(self, title="Unrecognized library format.", message="Specified file is not a valid reference library.")
dlg.ShowModal()
dlg.Destroy()
return
elif importedItems == {}:
wx.Bell()
dlg = mwx.dlgMessage(self, title="No data to import.", message="Specified library contains no data.")
dlg.ShowModal()
dlg.Destroy()
return
# select groups to import
dlg = dlgSelectItemsToImport(self, importedItems)
if dlg.ShowModal() == wx.ID_OK:
selected = dlg.selected
dlg.Destroy()
else:
dlg.Destroy()
return
# check same items
selectAfter = 'Reference lists'
replaceAll = False
for item in selected:
if replaceAll or not item in libs.references:
libs.references[item] = importedItems[item]
selectAfter = item
else:
title = 'Group entitled "%s"\nis already in you library. Do you want to replace it?' % item
message = "All references within this group will be lost."
buttons = [(ID_dlgReplaceAll, "Replace All", 120, False, 40), (ID_dlgSkip, "Skip", 80, False, 15), (ID_dlgReplace, "Replace", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
ID = dlg.ShowModal()
if ID == ID_dlgSkip:
continue
elif ID == ID_dlgReplaceAll:
replaceAll = True
libs.references[item] = importedItems[item]
selectAfter = item
elif ID == ID_dlgReplace:
libs.references[item] = importedItems[item]
selectAfter = item
# update gui
self.updateGroups()
self.groupName_choice.SetStringSelection(selectAfter)
self.onGroupSelected()
def onCalculate(self, evt):
"""Generate compounds ions."""
# check processing
if self.processing:
return
# clear recent
self.currentCompound = None
self.currentFit = None
# check document
if not self.currentDocument or not (
self.currentDocument.spectrum.hasprofile() or self.currentDocument.spectrum.haspeaks()
):
wx.Bell()
return
# get params
if not self.getParams():
self.updateAverageLabel()
self.updateSpectrumCanvas()
self.updateResultsList()
return
# show processing gauge
self.onProcessing(True)
self.calculate_butt.Enable(False)
# do processing
self.processing = threading.Thread(target=self.runEnvelopeFit)
self.processing.start()
# pulse gauge while working
while self.processing and self.processing.isAlive():
self.gauge.pulse()
# check error
error = False
if self.currentFit is False:
self.currentFit = None
error = True
# update gui
self.updateAverageLabel()
self.updateSpectrumCanvas()
self.updateResultsList()
# hide processing gauge
self.onProcessing(False)
self.calculate_butt.Enable(True)
# check errors
if error:
wx.Bell()
dlg = mwx.dlgMessage(
self,
title="No data to fit.",
message="There are no data in relevant mass range. Please check\nspecified formula, charge and default FWHM.",
)
dlg.ShowModal()
dlg.Destroy()
def onImport(self, evt):
"""Import items from xml library."""
# show open file dialog
wildcard = "Library files|*.xml;*.XML"
dlg = wx.FileDialog(self,
"Import Library",
wildcard=wildcard,
style=wx.FD_OPEN | wx.FD_FILE_MUST_EXIST)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
dlg.Destroy()
else:
dlg.Destroy()
return
# read data
importedItems = self.readLibraryXML(path)
if importedItems == False:
wx.Bell()
dlg = mwx.dlgMessage(
self,
title="Unrecognized library format.",
message="Specified file is not a valid compounds library.")
dlg.ShowModal()
dlg.Destroy()
return
elif importedItems == {}:
wx.Bell()
dlg = mwx.dlgMessage(self,
title="No data to import.",
message="Specified library contains no data.")
dlg.ShowModal()
dlg.Destroy()
return
# select groups to import
dlg = dlgSelectItemsToImport(self, importedItems)
if dlg.ShowModal() == wx.ID_OK:
selected = dlg.selected
dlg.Destroy()
else:
dlg.Destroy()
return
# check same items
selectAfter = 'Compounds lists'
replaceAll = False
for item in selected:
if replaceAll or not item in libs.compounds:
libs.compounds[item] = importedItems[item]
selectAfter = item
else:
title = 'Group entitled "%s"\nis already in you library. Do you want to replace it?' % item
message = "All compounds within this group will be lost."
buttons = [(ID_dlgReplaceAll, "Replace All", 120, False, 40),
(ID_dlgSkip, "Skip", 80, False, 15),
(ID_dlgReplace, "Replace", 80, True, 0)]
dlg = mwx.dlgMessage(self, title, message, buttons)
ID = dlg.ShowModal()
if ID == ID_dlgSkip:
continue
elif ID == ID_dlgReplaceAll:
replaceAll = True
libs.compounds[item] = importedItems[item]
selectAfter = item
elif ID == ID_dlgReplace:
libs.compounds[item] = importedItems[item]
selectAfter = item
# update gui
self.updateGroups()
self.groupName_choice.SetStringSelection(selectAfter)
self.onGroupSelected()