/usr/share/mmass/gui/dlg_monomers_editor.py is in mmass 5.5.0-5.
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) 2005-2013 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 re
import wx
# load modules
import mwx
import config
import mspy
# MONOMERS EDITOR
# ---------------
class dlgMonomersEditor(wx.Dialog):
"""Edit monomers library."""
def __init__(self, parent):
wx.Dialog.__init__(self, parent, -1, "Monomers 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 regular amino acids
self._aminoacids = []
for abbr in mspy.monomers:
if mspy.monomers[abbr].category == '_InternalAA':
self._aminoacids.append(abbr)
# get used monomers
self.used = parent.getUsedMonomers()
# 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=(871, 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, "abbr.", wx.LIST_FORMAT_LEFT)
self.itemsList.InsertColumn(1, "name", wx.LIST_FORMAT_LEFT)
self.itemsList.InsertColumn(2, "category", wx.LIST_FORMAT_LEFT)
self.itemsList.InsertColumn(3, "formula", wx.LIST_FORMAT_LEFT)
self.itemsList.InsertColumn(4, "mo. mass", wx.LIST_FORMAT_RIGHT)
self.itemsList.InsertColumn(5, "av. mass", wx.LIST_FORMAT_RIGHT)
self.itemsList.InsertColumn(6, "losses", wx.LIST_FORMAT_LEFT)
# set column widths
for col, width in enumerate((110,180,90,110,90,90,180)):
self.itemsList.SetColumnWidth(col, width)
# ----
def makeItemEditor(self):
"""Make items editor."""
mainSizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, ""), wx.VERTICAL)
# make elements
itemSearch_label = wx.StaticText(self, -1, "Search:")
self.itemSearch_value = wx.TextCtrl(self, -1, "", size=(200, -1), style=wx.TE_PROCESS_ENTER)
self.itemSearch_value.Bind(wx.EVT_TEXT, self.onSearch)
itemAbbr_label = wx.StaticText(self, -1, "Abbr.:")
self.itemAbbr_value = wx.TextCtrl(self, -1, "", size=(200, -1))
itemName_label = wx.StaticText(self, -1, "Name:")
self.itemName_value = wx.TextCtrl(self, -1, "", size=(200, -1))
itemCategory_label = wx.StaticText(self, -1, "Category:")
self.itemCategory_value = wx.TextCtrl(self, -1, "", size=(200, -1))
itemFormula_label = wx.StaticText(self, -1, "Formula:")
self.itemFormula_value = mwx.formulaCtrl(self, -1, "", size=(150, -1))
self.itemFormula_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)
itemLossMoMass_label = wx.StaticText(self, -1, "Mo. loss mass:")
self.itemLossMoMass_value = wx.TextCtrl(self, -1, "", size=(150, -1))
itemLossMoMass_label.Enable(False)
self.itemLossMoMass_value.Enable(False)
itemLosses_label = wx.StaticText(self, -1, "Losses:")
self.itemLosses_values = []
for x in range(4):
item = mwx.formulaCtrl(self, -1, "", size=(100, -1))
item.Bind(wx.EVT_TEXT, self.onLossFormula)
item.Bind(wx.EVT_SET_FOCUS, self.onLossFormula)
item.Bind(wx.EVT_KILL_FOCUS, self.onLossFormula)
self.itemLosses_values.append(item)
# 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(itemSearch_label, (0,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemSearch_value, (0,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemAbbr_label, (1,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemAbbr_value, (1,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemName_label, (2,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemName_value, (2,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemCategory_label, (3,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemCategory_value, (3,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemFormula_label, (0,3), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemFormula_value, (0,4), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemMoMass_label, (1,3), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemMoMass_value, (1,4), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemAvMass_label, (2,3), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemAvMass_value, (2,4), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemLossMoMass_label, (3,3), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemLossMoMass_value, (3,4), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemLosses_label, (0,6), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemLosses_values[0], (0,7), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemLosses_values[1], (1,7), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemLosses_values[2], (2,7), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemLosses_values[3], (3,7), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(add_butt, (0,10), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(delete_butt, (1,10), 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
abbr = evt.GetText()
monomer = mspy.monomers[abbr]
# update item editor
self.itemAbbr_value.SetValue(abbr)
self.itemName_value.SetValue(monomer.name)
self.itemCategory_value.SetValue(monomer.category)
self.itemFormula_value.SetValue(monomer.formula)
for x in range(4):
self.itemLosses_values[x].SetValue('')
if x < len(monomer.losses):
self.itemLosses_values[x].SetValue(monomer.losses[x])
# ----
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 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 onSearch(self, evt):
"""Search monomers library."""
# clear editor
self.clearEditor()
# update list
self.updateItemsList()
# ----
def onFormulaEdited(self, evt):
"""Update formula mass while editing."""
evt.Skip()
wx.CallAfter(self.updateFormulaMass)
# ----
def onLossFormula(self, evt):
"""Update loss formula mass while editing."""
evt.Skip()
wx.CallAfter(self.updateLossFormulaMass)
# ----
def updateItemsMap(self):
"""Update items map."""
self.itemsMap = []
# get search
search = self.itemSearch_value.GetValue().lower().split()
# make map
for abbr, monomer in sorted(mspy.monomers.items()):
# skip regular amino acids
if monomer.category == '_InternalAA':
continue
# skip by search filter
if search and not (
all(map(lambda x: x in monomer.abbr.lower(), search)) or
all(map(lambda x: x in monomer.name.lower(), search))
):
continue
# append monomer
self.itemsMap.append((
abbr,
monomer.name,
monomer.category,
monomer.formula,
monomer.mass[0],
monomer.mass[1],
', '.join(monomer.losses),
))
# ----
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[4])
avMass = digits % (item[5])
# 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, item[3])
self.itemsList.SetStringItem(row, 4, str(moMass))
self.itemsList.SetStringItem(row, 5, str(avMass))
self.itemsList.SetStringItem(row, 6, item[6])
self.itemsList.SetItemData(row, row)
# sort
self.itemsList.sort()
# ----
def updateFormulaMass(self):
"""Update formula mass."""
# get formula
formula = self.itemFormula_value.GetValue()
# show formula masses
try:
formula = mspy.compound(formula)
mass = formula.mass()
self.itemMoMass_value.SetValue(str(mass[0]))
self.itemAvMass_value.SetValue(str(mass[1]))
except:
self.itemMoMass_value.SetValue('')
self.itemAvMass_value.SetValue('')
# ----
def updateLossFormulaMass(self):
"""Update loss formula mass."""
# erase old value
self.itemLossMoMass_value.SetValue('')
# get current item
focus = self.FindFocus()
for x in range(4):
item = self.itemLosses_values[x]
# found focused item
if item is focus:
try:
formula = item.GetValue()
formula = mspy.compound(formula)
mass = formula.mass()
self.itemLossMoMass_value.SetValue(str(mass[0]))
except:
pass
# ----
def clearEditor(self):
"""Clear item editor."""
# update editor
self.itemAbbr_value.SetValue('')
self.itemName_value.SetValue('')
self.itemCategory_value.SetValue('')
self.itemFormula_value.SetValue('')
self.itemMoMass_value.SetValue('')
self.itemAvMass_value.SetValue('')
for x in range(4):
self.itemLosses_values[x].SetValue('')
# ----
def getItemData(self):
"""Get formated item data."""
# get data
abbr = self.itemAbbr_value.GetValue()
name = self.itemName_value.GetValue()
category = self.itemCategory_value.GetValue()
formula = self.itemFormula_value.GetValue()
losses = []
for item in self.itemLosses_values:
if item.GetValue():
losses.append(item.GetValue())
# check values
if not abbr or not formula or not re.match('^[A-Za-z0-9\-_]*$', abbr):
wx.Bell()
return False
# make monomer
try:
monomer = mspy.monomer(
abbr = abbr,
name = name,
formula = formula,
losses = losses,
category = category
)
except:
wx.Bell()
return False
return monomer
# ----
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