/usr/share/mmass/gui/dlg_modifications_editor.py is in mmass 5.1.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# Copyright (C) 2005-2012 Martin Strohalm <www.mmass.org>
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# Complete text of GNU GPL can be found in the file LICENSE.TXT in the
# main directory of the program.
# -------------------------------------------------------------------------
# load libs
import wx
# load modules
import mwx
import config
import mspy
# MODIFICATIONS EDITOR
# --------------------
class dlgModificationsEditor(wx.Dialog):
"""Edit modifications library."""
def __init__(self, parent):
wx.Dialog.__init__(self, parent, -1, "Modifications Library", style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER)
self.itemsMap = []
# make GUI
sizer = self.makeGUI()
# fit layout
self.Layout()
sizer.Fit(self)
self.SetSizer(sizer)
self.SetMinSize(self.GetSize())
self.Centre()
# get used modifications
self.used = parent.getUsedModifications()
# show data
self.updateItemsList()
# ----
def makeGUI(self):
"""Make GUI elements."""
# make GUI elements
self.makeItemsList()
editor = self.makeItemEditor()
# pack elements
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self.itemsList, 1, wx.EXPAND|wx.TOP|wx.LEFT|wx.RIGHT, mwx.LISTCTRL_SPACE)
sizer.Add(editor, 0, wx.EXPAND|wx.CENTER|wx.ALL, mwx.PANEL_SPACE_MAIN)
return sizer
# ----
def makeItemsList(self):
"""Make list for items."""
# init list
self.itemsList = mwx.sortListCtrl(self, -1, size=(841, 250), style=mwx.LISTCTRL_STYLE_MULTI)
self.itemsList.SetFont(wx.SMALL_FONT)
self.itemsList.setAltColour(mwx.LISTCTRL_ALTCOLOUR)
# set events
self.itemsList.Bind(wx.EVT_LIST_ITEM_SELECTED, self.onItemSelected)
# make columns
self.itemsList.InsertColumn(0, "name", wx.LIST_FORMAT_LEFT)
self.itemsList.InsertColumn(1, "gain", wx.LIST_FORMAT_LEFT)
self.itemsList.InsertColumn(2, "loss", wx.LIST_FORMAT_LEFT)
self.itemsList.InsertColumn(3, "mo. mass", wx.LIST_FORMAT_RIGHT)
self.itemsList.InsertColumn(4, "av. mass", wx.LIST_FORMAT_RIGHT)
self.itemsList.InsertColumn(5, "amino", wx.LIST_FORMAT_LEFT)
self.itemsList.InsertColumn(6, "term", wx.LIST_FORMAT_CENTER)
self.itemsList.InsertColumn(7, "description", wx.LIST_FORMAT_LEFT)
# set column widths
for col, width in enumerate((110,100,60,90,90,100,50,220)):
self.itemsList.SetColumnWidth(col, width)
# ----
def makeItemEditor(self):
"""Make items editor."""
mainSizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, ""), wx.VERTICAL)
# make elements
itemName_label = wx.StaticText(self, -1, "Name:")
self.itemName_value = wx.TextCtrl(self, -1, "", size=(250, -1))
itemDescription_label = wx.StaticText(self, -1, "Description:")
self.itemDescription_value = wx.TextCtrl(self, -1, "", size=(250, -1))
itemAminoSpecifity_label = wx.StaticText(self, -1, "Amino specifity:")
self.itemAminoSpecifity_value = wx.TextCtrl(self, -1, "", size=(250, -1))
itemTermSpecifity_label = wx.StaticText(self, -1, "Terminal specifity:")
self.itemTermSpecifity_choice = wx.Choice(self, -1, choices=['None','N-terminus','C-terminus'], size=(250, mwx.CHOICE_HEIGHT))
self.itemTermSpecifity_choice.SetStringSelection('None')
itemGainFormula_label = wx.StaticText(self, -1, "Gain formula:")
self.itemGainFormula_value = mwx.formulaCtrl(self, -1, "", size=(150, -1))
self.itemGainFormula_value.Bind(wx.EVT_TEXT, self.onFormulaEdited)
itemLossFormula_label = wx.StaticText(self, -1, "Loss formula:")
self.itemLossFormula_value = mwx.formulaCtrl(self, -1, "", size=(150, -1))
self.itemLossFormula_value.Bind(wx.EVT_TEXT, self.onFormulaEdited)
itemMoMass_label = wx.StaticText(self, -1, "Mo. mass:")
self.itemMoMass_value = wx.TextCtrl(self, -1, "", size=(150, -1))
itemMoMass_label.Enable(False)
self.itemMoMass_value.Enable(False)
itemAvMass_label = wx.StaticText(self, -1, "Av. mass:")
self.itemAvMass_value = wx.TextCtrl(self, -1, "", size=(150, -1))
itemAvMass_label.Enable(False)
self.itemAvMass_value.Enable(False)
# buttons
add_butt = wx.Button(self, -1, "Add", size=(80,-1))
add_butt.Bind(wx.EVT_BUTTON, self.onAddItem)
delete_butt = wx.Button(self, -1, "Delete", size=(80,-1))
delete_butt.Bind(wx.EVT_BUTTON, self.onDeleteItem)
# pack elements
grid = wx.GridBagSizer(mwx.GRIDBAG_VSPACE, mwx.GRIDBAG_HSPACE)
grid.Add(itemName_label, (0,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemName_value, (0,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemDescription_label, (1,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemDescription_value, (1,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemAminoSpecifity_label, (2,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemAminoSpecifity_value, (2,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemTermSpecifity_label, (3,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemTermSpecifity_choice, (3,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemGainFormula_label, (0,3), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemGainFormula_value, (0,4), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemLossFormula_label, (1,3), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemLossFormula_value, (1,4), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemMoMass_label, (2,3), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemMoMass_value, (2,4), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemAvMass_label, (3,3), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemAvMass_value, (3,4), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(add_butt, (0,7), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(delete_butt, (1,7), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
mainSizer.Add(grid, 0, wx.ALIGN_CENTER|wx.ALL, 10)
return mainSizer
# ----
def onItemSelected(self, evt):
"""Update item editor with selected item."""
# get selected item
name = evt.GetText()
mod = mspy.modifications[name]
# update item editor
self.itemName_value.SetValue(name)
self.itemDescription_value.SetValue(mod.description)
self.itemAminoSpecifity_value.SetValue(mod.aminoSpecifity)
self.itemGainFormula_value.SetValue(mod.gainFormula)
self.itemLossFormula_value.SetValue(mod.lossFormula)
if mod.termSpecifity == 'C':
self.itemTermSpecifity_choice.SetStringSelection('C-terminus')
elif mod.termSpecifity == 'N':
self.itemTermSpecifity_choice.SetStringSelection('N-terminus')
else:
self.itemTermSpecifity_choice.SetStringSelection('None')
# ----
def onAddItem(self, evt):
"""Add/replace item."""
# get item data
itemData = self.getItemData()
if not itemData:
return
# check name
if itemData.name in mspy.modifications:
wx.Bell()
title = 'Modification with the same name already exists.\nDo you want to replace it?'
message = 'Old modification 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.modifications[itemData.name] = itemData
# update gui
self.updateItemsList()
self.clearEditor()
# ----
def onDeleteItem(self, evt):
"""Remove selected items."""
# delete?
title = 'Do you really want to delete selected modifications?'
message = 'Modification 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.modifications[name]
else:
wx.Bell()
dlg = mwx.dlgMessage(self, title='Modification "'+name+'" is currently applied\nand cannot be removed.', message='Remove the modification from all of your documents first.')
dlg.ShowModal()
dlg.Destroy()
# update gui
self.updateItemsList()
self.clearEditor()
# ----
def onFormulaEdited(self, evt):
"""Update formula mass while editing."""
evt.Skip()
wx.CallAfter(self.updateFormulaMass)
# ----
def updateItemsMap(self):
"""Update items map."""
self.itemsMap = []
# make map
for name, mod in sorted(mspy.modifications.items()):
self.itemsMap.append((
mod.name,
mod.gainFormula,
mod.lossFormula,
mod.mass[0],
mod.mass[1],
mod.aminoSpecifity,
mod.termSpecifity,
mod.description,
))
# ----
def updateItemsList(self):
"""Update items list."""
# clear previous data and set new
self.updateItemsMap()
self.itemsList.DeleteAllItems()
self.itemsList.setDataMap(self.itemsMap)
# check data
if not self.itemsMap:
return
# add new data
digits = '%0.' + `config.main['mzDigits']` + 'f'
for row, item in enumerate(self.itemsMap):
# format data
moMass = digits % (item[3])
avMass = digits % (item[4])
# add data
self.itemsList.InsertStringItem(row, item[0])
self.itemsList.SetStringItem(row, 1, item[1])
self.itemsList.SetStringItem(row, 2, item[2])
self.itemsList.SetStringItem(row, 3, str(moMass))
self.itemsList.SetStringItem(row, 4, str(avMass))
self.itemsList.SetStringItem(row, 5, item[5])
self.itemsList.SetStringItem(row, 6, item[6])
self.itemsList.SetStringItem(row, 7, item[7])
self.itemsList.SetItemData(row, row)
# sort
self.itemsList.sort()
# ----
def updateFormulaMass(self):
"""Update formula mass."""
# get formula
gain = self.itemGainFormula_value.GetValue()
loss = self.itemLossFormula_value.GetValue()
# show formula masses
try:
gain = mspy.compound(gain)
loss = mspy.compound(loss)
gainMass = gain.mass()
lossMass = loss.mass()
self.itemMoMass_value.SetValue(str(gainMass[0] - lossMass[0]))
self.itemAvMass_value.SetValue(str(gainMass[1] - lossMass[1]))
except:
wx.Bell()
self.itemMoMass_value.SetValue('')
self.itemAvMass_value.SetValue('')
# ----
def clearEditor(self):
"""Clear item editor."""
# update editor
self.itemName_value.SetValue('')
self.itemDescription_value.SetValue('')
self.itemAminoSpecifity_value.SetValue('')
self.itemGainFormula_value.SetValue('')
self.itemLossFormula_value.SetValue('')
self.itemMoMass_value.SetValue('')
self.itemAvMass_value.SetValue('')
self.itemTermSpecifity_choice.SetStringSelection('None')
# ----
def getItemData(self):
"""Get formated item data."""
# get data
name = self.itemName_value.GetValue()
description = self.itemDescription_value.GetValue()
aminoSpecifity = self.itemAminoSpecifity_value.GetValue()
termSpecifity = self.itemTermSpecifity_choice.GetStringSelection()
gainFormula = self.itemGainFormula_value.GetValue()
lossFormula = self.itemLossFormula_value.GetValue()
# term specifity
if termSpecifity == 'None':
termSpecifity = ''
elif termSpecifity == 'N-terminus':
termSpecifity = 'N'
elif termSpecifity == 'C-terminus':
termSpecifity = 'C'
# check values
if not name or (not gainFormula and not lossFormula):
wx.Bell()
return False
# make compound
try:
modification = mspy.modification(
name = name,
gainFormula = gainFormula,
lossFormula = lossFormula,
aminoSpecifity = aminoSpecifity,
termSpecifity = termSpecifity,
description = description
)
except:
wx.Bell()
return False
return modification
# ----
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