/usr/share/mmass/gui/dlg_enzymes_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 re
import wx
# load modules
import mwx
import config
import mspy
# ENZYMES EDITOR
# --------------
class dlgEnzymesEditor(wx.Dialog):
"""Edit enzymes library."""
def __init__(self, parent):
wx.Dialog.__init__(self, parent, -1, "Enzymes 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()
# 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=(741, 200), 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, "expression", wx.LIST_FORMAT_LEFT)
self.itemsList.InsertColumn(2, "c-term", wx.LIST_FORMAT_LEFT)
self.itemsList.InsertColumn(3, "n-term", wx.LIST_FORMAT_LEFT)
self.itemsList.InsertColumn(4, "mods before", wx.LIST_FORMAT_CENTER)
self.itemsList.InsertColumn(5, "mods after", wx.LIST_FORMAT_CENTER)
# set column widths
for col, width in enumerate((130,130,130,130,100,100)):
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=(200, -1))
itemExpression_label = wx.StaticText(self, -1, "Expression:")
self.itemExpression_value = wx.TextCtrl(self, -1, "", size=(200, -1))
itemCTerm_label = wx.StaticText(self, -1, "C-term formula:")
self.itemCTerm_value = mwx.formulaCtrl(self, -1, "", size=(200, -1))
itemNTerm_label = wx.StaticText(self, -1, "N-term formula:")
self.itemNTerm_value = mwx.formulaCtrl(self, -1, "", size=(200, -1))
self.itemModsBefore_check = wx.CheckBox(self, -1, "Allow modification before cut")
self.itemModsAfter_check = wx.CheckBox(self, -1, "Allow modification after cut")
# 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(itemExpression_label, (1,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemExpression_value, (1,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemCTerm_label, (2,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemCTerm_value, (2,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(itemNTerm_label, (3,0), flag=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemNTerm_value, (3,1), flag=wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemModsBefore_check, (0,3), flag=wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
grid.Add(self.itemModsAfter_check, (1,3), flag=wx.ALIGN_LEFT|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()
enzyme = mspy.enzymes[name]
# update item editor
self.itemName_value.SetValue(name)
self.itemExpression_value.SetValue(enzyme.expression)
self.itemCTerm_value.SetValue(enzyme.cTermFormula)
self.itemNTerm_value.SetValue(enzyme.nTermFormula)
self.itemModsBefore_check.SetValue(enzyme.modsBefore)
self.itemModsAfter_check.SetValue(enzyme.modsAfter)
# ----
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 onDeleteItem(self, evt):
"""Remove selected items."""
# delete?
title = 'Do you really want to delete selected enzymes?'
message = 'Enzyme 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 mspy.enzymes[name]
# update gui
self.updateItemsList()
self.clearEditor()
# ----
def updateItemsMap(self):
"""Update items map."""
self.itemsMap = []
# make map
for name, enzyme in sorted(mspy.enzymes.items()):
self.itemsMap.append((
enzyme.name,
enzyme.expression,
enzyme.cTermFormula,
enzyme.nTermFormula,
enzyme.modsBefore,
enzyme.modsAfter,
))
# ----
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
for row, item in enumerate(self.itemsMap):
# format data
modsBefore = 'not allowed'
if item[4]:
modsBefore = 'allowed'
modsAfter = 'not allowed'
if item[5]:
modsAfter = 'allowed'
# 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, modsBefore)
self.itemsList.SetStringItem(row, 5, modsAfter)
self.itemsList.SetItemData(row, row)
# sort
self.itemsList.sort()
# ----
def clearEditor(self):
"""Clear item editor."""
# update editor
self.itemName_value.SetValue('')
self.itemExpression_value.SetValue('')
self.itemCTerm_value.SetValue('')
self.itemNTerm_value.SetValue('')
self.itemModsBefore_check.SetValue(False)
self.itemModsAfter_check.SetValue(False)
# ----
def getItemData(self):
"""Get formated item data."""
# get data
name = self.itemName_value.GetValue()
expression = self.itemExpression_value.GetValue()
cTermFormula = self.itemCTerm_value.GetValue()
nTermFormula = self.itemNTerm_value.GetValue()
modsBefore = int(self.itemModsBefore_check.GetValue())
modsAfter = int(self.itemModsAfter_check.GetValue())
# check values
if not name or not expression or not cTermFormula or not nTermFormula:
wx.Bell()
return False
# make enzyme
try:
expr = re.compile(expression)
enzyme = mspy.enzyme(
name = name,
expression = expression,
cTermFormula = cTermFormula,
nTermFormula = nTermFormula,
modsBefore = modsBefore,
modsAfter = modsAfter
)
except:
wx.Bell()
return False
return enzyme
# ----
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