"""
app.py
AIGO is a python library for
the Analysis and Inter-comparison of Gene Ontology functional annotations.
see (http://code.google.com/p/aigo).
Created by Michael Defoin-Platel on 21/02/2010.
Copyright (c) 2010. All rights reserved.
AIGO 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.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
from pylab import *
import os
import wx
from ObjectListView import FastObjectListView, ColumnDefn
import pydoc
from PIL import Image as Image
from AIGO.gui import project, popups, grid, gui
from AIGO import allAspect
from AIGO.Statistics import registerStat
from AIGO.Plot import PlotFA, registerPlot
from AIGO.IO import IOType
def PNGtoBitmap(fileName, resize=None):
mypilimage = Image.open(fileName, "r")
if resize:
#mypilimage.resize(resize, , Image.ANTIALIAS)
mypilimage.thumbnail( resize, Image.ANTIALIAS)
mywximage = wx.EmptyImage(mypilimage.size[0],mypilimage.size[1])
mywximage.SetData(mypilimage.convert("RGB").tostring())
mywximage.SetAlphaData(mypilimage.convert("RGBA").tostring()[3::4])
return wx.BitmapFromImage(mywximage)
def setNewID(wid):
ID=wx.NewId()
wid.SetId(ID)
return ID
class AIGOApp(wx.PySimpleApp):
def OnInit(self, doSplash=False):
#-----------------------------------------------------
# IMAGES
#-----------------------------------------------------
import os
import AIGO.gui
self.guiDir=os.path.dirname(AIGO.gui.__file__)
self.AIGOBmp = PNGtoBitmap("%s/AIGO.png" % self.guiDir)
self.checkBmp = PNGtoBitmap("%s/check.png" % self.guiDir, resize=[17,13])
self.crossBmp = PNGtoBitmap("%s/cross.png" % self.guiDir, resize=[13,13])
self.icon = wx.EmptyIcon()
self.icon.CopyFromBitmap(self.AIGOBmp)
#-----------------------------------------------------
# SPLASH
#-----------------------------------------------------
if doSplash:
splashStyle = wx.SPLASH_CENTRE_ON_SCREEN | wx.SPLASH_TIMEOUT
splashDuration = 2000 # milliseconds
splash=wx.SplashScreen(self.AIGOBmp, splashStyle,splashDuration, None)
splash.Show(True)
self.popup = popups.Popup()
#-----------------------------------------------------
# FRAMES
#-----------------------------------------------------
#Create main frame
self.frame = gui.AIGOFrame(None, -1, "")
self.frame.Show(True)
self.SetTopWindow(self.frame)
self.frame.SetIcon(self.icon)
self.statusField=self.frame.statusbar.GetFields()
#Create new project frame
self.npFrame = gui.NewProjectFrame(self.frame, -1, "New Project")
self.npFrame.Show(False)
self.npFrame.SetIcon(self.icon)
#Create new functional annotation frame
self.FAFrame = gui.FAFrame(self.frame, -1, "Add Functional Annotation")
self.FAFrame.combo_box_FileType.Clear()
self.FAFrame.combo_box_FileType.AppendItems(sort(IOType.keys()))
self.FAFrame.Show(False)
self.FAFrame.SetIcon(self.icon)
#Create view annotation set frame
self.ViewFrame = gui.ViewFrame(self.frame, -1, "View gene product annotations")
self.ViewFrame.Show(False)
self.ViewFrame.SetIcon(self.icon)
#-----------------------------------------------------
# LIST FA
#-----------------------------------------------------
self.frame.notebook.list_FA.InsertColumn(0, "Status")
self.frame.notebook.list_FA.InsertColumn(1, "Name")
self.frame.notebook.list_FA.InsertColumn(2, "File", wx.LIST_FORMAT_RIGHT)
self.frame.notebook.list_FA.InsertColumn(3, "File Type")
self.frame.notebook.list_FA.SetColumnWidth(0, 100)
self.frame.notebook.list_FA.SetColumnWidth(1, 200)
self.frame.notebook.list_FA.SetColumnWidth(2, 400)
self.frame.notebook.list_FA.SetColumnWidth(3, 100)
#-----------------------------------------------------
# STATISTICS
#-----------------------------------------------------
self.workflow=list()
self.viewStat=dict()
for statistics in registerStat.getAll():
if hasattr(self.frame.notebook, 'checkbox_%s' % statistics):
self.viewStat[statistics]=True
self.workflow.append(statistics)
self.frame.notebook.button_Export.SetLabel("Export")
for statistics in self.viewStat:
bmp=getattr(self.frame.notebook, 'bitmap_%s' % statistics)
bmp.SetBitmap(self.crossBmp)
#-----------------------------------------------------
# COMPARE
#-----------------------------------------------------
self.frame.notebook.button_Update_Venn.SetLabel("Venn diagram")
self.frame.notebook.button_Update_FuncSim.SetLabel("Functional Similarity")
for name in ["FA1", "FA2"]:
lst=getattr(self.frame.notebook, 'combo_box_Compare_%s' % name)
lst.SetName(name)
compareColumns = [
ColumnDefn("Gene Product", "left", 300, valueGetter="gp", minimumWidth=40, maximumWidth=500),
ColumnDefn("Annotations in first FA", "right", 250, valueGetter="nb1", minimumWidth=40, maximumWidth=300),
ColumnDefn("Annotations in second FA", "right", 250, valueGetter="nb2", minimumWidth=40, maximumWidth=300),
ColumnDefn("Functional Similarity", "right", 200, valueGetter="funcSim", minimumWidth=40)
]
for aspect in allAspect:
bmp=getattr(self.frame.notebook, 'bitmap_%s' % aspect)
size=bmp.GetSize().Get()
bmp.SetBitmap(self.AIGOBmp)
btn=getattr(self.frame.notebook, 'button_Compare_%s' % aspect)
btn.SetLabel("View")
lst=getattr(self.frame.notebook, 'list_ctrl_Compare_%s' % aspect)
lst.SetName(aspect)
lst.SetColumns(compareColumns)
btn=getattr(self.frame.notebook, 'button_Compare_%s' % aspect)
btn.SetName(aspect)
#-----------------------------------------------------
# PLOT
#-----------------------------------------------------
#-----------------------------------------------------
# EVENTS
#-----------------------------------------------------
# Menu Events
#
#wx.EVT_MENU(self, gui.ID_BLURB, self.MenuBlurb)
#self.frame.SetAcceleratorTable(wx.AcceleratorTable([
# (wx.ACCEL_NORMAL, wx.WXK_F1, gui.ID_EXIT),
# (wx.ACCEL_NORMAL, wx.WXK_F2, gui.ID_BLURB),
# ]))
#Menu
wx.EVT_MENU(self, gui.MENU_NEW, self.MenuNew)
wx.EVT_MENU(self, gui.MENU_OPEN, self.MenuOpen)
wx.EVT_MENU(self, gui.MENU_SAVE, self.MenuSave)
wx.EVT_MENU(self, gui.MENU_QUIT, self.MenuQuit)
wx.EVT_MENU(self, gui.MENU_ABOUT, self.MenuAbout)
#New Project
wx.EVT_BUTTON(self, self.npFrame.button_DirectoryChoose.GetId(), self.OnNewProjectDirChoose)
wx.EVT_BUTTON(self, setNewID(self.npFrame.button_NewProjectOK), self.OnNewProjectOK)
wx.EVT_BUTTON(self, setNewID(self.npFrame.button_NewProjectCancel), self.OnNewProjectCancel)
#Data
wx.EVT_BUTTON(self, self.frame.notebook.button_RefSetChoose.GetId(), self.OnBrowseRefSet)
wx.EVT_BUTTON(self, setNewID(self.frame.notebook.button_RefSetLoad), self.OnLoadRefSet)
wx.EVT_BUTTON(self, self.frame.notebook.button_GOChoose.GetId(), self.OnBrowseGO)
wx.EVT_BUTTON(self, setNewID(self.frame.notebook.button_GOLoad), self.OnLoadGO)
#Add FA
wx.EVT_BUTTON(self, self.frame.notebook.button_AddFA.GetId(), self.OnAddFA)
wx.EVT_BUTTON(self, self.frame.notebook.button_RemoveFA.GetId(), self.OnRemoveFA)
wx.EVT_BUTTON(self, self.frame.notebook.button_LoadFA.GetId(), self.OnLoadFA)
wx.EVT_BUTTON(self, self.FAFrame.button_FileChoose.GetId(), self.OnFAFileChoose)
wx.EVT_BUTTON(self, setNewID(self.FAFrame.button_FAOK), self.OnFAOK)
wx.EVT_BUTTON(self, setNewID(self.FAFrame.button_FACancel), self.OnFACancel)
#Statistics
wx.EVT_BUTTON(self, self.frame.notebook.button_Apply.GetId(), self.OnStatApply)
for statistics in registerStat.getAll():
cb=self.frame.notebook.__dict__.get('checkbox_%s' % statistics, None)
if cb:
cb.SetName(statistics)
wx.EVT_CHECKBOX(self, cb.GetId(), self.OnStatCheck)
wx.EVT_BUTTON(self, setNewID(self.frame.notebook.button_Export), self.OnStatExport)
#Compare
wx.EVT_BUTTON(self, setNewID(self.frame.notebook.button_Update_Venn), self.OnUpdateVenn)
wx.EVT_BUTTON(self, setNewID(self.frame.notebook.button_Update_FuncSim), self.OnUpdateFuncSim)
wx.EVT_SIZE(self.ViewFrame, self.OnResizeView)
for name in ["FA1", "FA2"]:
lst=getattr(self.frame.notebook, 'combo_box_Compare_%s' % name)
wx.EVT_COMBOBOX(self, lst.GetId(), self.OnCompareStat)
for aspect in allAspect:
btn=getattr(self.frame.notebook, 'button_Compare_%s' % aspect)
wx.EVT_BUTTON(self, setNewID(btn), self.OnCompareView)
#lst=getattr(self.frame.notebook, 'list_ctrl_Compare_%s' % aspect)
#wx.EVT_LIST_COL_CLICK(self, setNewID(lst), self.OnCompareColClick)
#Plot
wx.EVT_COMBOBOX(self, self.frame.notebook.combo_PlotStat.GetId(), self.OnStatPlot)
return True
