def __init__(self, parent=None, rawfile=None, conffile=None):
self.parent = parent
if not self.parent:
Frame.__init__(self)
self.main = self.master
else:
self.main = Toplevel()
self.master = self.main
self.main.title('DNATool Desktop')
self.main.protocol('WM_DELETE_WINDOW', self.quit)
self.defaultprefs = {
'rememberwindowsize': 0,
'orientation': 'horizontal',
'alignmenttool': 'clustal',
'clustalpath': 'clustalw'
}
self.defaultopts = [
('rememberwindowsize', 'checkbutton', 1, 'Remember window size'),
('orientation', 'menu', ('horizontal', 'vertical'),
'Default sideframe orientation'),
('alignmenttool', 'menu', ('clustal', 'muscle', 'needle'),
'External alignment tool'),
('clustalpath', 'entry', '', 'Path to Clustal')
]
self.loadPrefs()
self.setGeometry()
self.P = Project()
self.primerdb = PrimerDatabase()
self.setupApps()
self.setupGUI()
self.sidepane.selectpage('PrimerDB')
return
def __init__(self, parent=None, rawfile=None, conffile=None):
self.parent=parent
if not self.parent:
Frame.__init__(self)
self.main=self.master
else:
self.main=Toplevel()
self.master=self.main
self.main.title('DNATool Desktop')
self.main.protocol('WM_DELETE_WINDOW',self.quit)
self.defaultprefs = {'rememberwindowsize':0,'orientation':'horizontal',
'alignmenttool':'clustal','clustalpath':'clustalw'}
self.defaultopts = [('rememberwindowsize','checkbutton',1,'Remember window size'),
('orientation','menu',('horizontal','vertical'),
'Default sideframe orientation'),
('alignmenttool','menu',('clustal','muscle','needle'),
'External alignment tool'),
('clustalpath','entry','','Path to Clustal')]
self.loadPrefs()
self.setGeometry()
self.P = Project()
self.primerdb = PrimerDatabase()
self.setupApps()
self.setupGUI()
self.sidepane.selectpage('PrimerDB')
return
class App(Frame, GUI_help):
"""Data pipe GUI for importing and fitting of raw data.
This class uses ekin provided an automated pipeline for fitting
raw text data files and propagating errors.
Uses a config file to store the pipeline settings"""
def __init__(self, parent=None, rawfile=None, conffile=None):
self.parent = parent
if not self.parent:
Frame.__init__(self)
self.main = self.master
else:
self.main = Toplevel()
self.master = self.main
self.main.title('DNATool Desktop')
self.main.protocol('WM_DELETE_WINDOW', self.quit)
self.defaultprefs = {
'rememberwindowsize': 0,
'orientation': 'horizontal',
'alignmenttool': 'clustal',
'clustalpath': 'clustalw'
}
self.defaultopts = [
('rememberwindowsize', 'checkbutton', 1, 'Remember window size'),
('orientation', 'menu', ('horizontal', 'vertical'),
'Default sideframe orientation'),
('alignmenttool', 'menu', ('clustal', 'muscle', 'needle'),
'External alignment tool'),
('clustalpath', 'entry', '', 'Path to Clustal')
]
self.loadPrefs()
self.setGeometry()
self.P = Project()
self.primerdb = PrimerDatabase()
self.setupApps()
self.setupGUI()
self.sidepane.selectpage('PrimerDB')
return
def setGeometry(self):
if self.rememberwindowsize == 1 and self.preferences.has_key(
'lastwindowsize'):
lastwindowsize = self.preferences.get('lastwindowsize')
self.winsize = lastwindowsize
#self.w = int(lastwindowsize.split('x')[0])
else:
self.winsize = self.getBestGeometry()
self.main.geometry(self.winsize)
return
def getBestGeometry(self):
"""Calculate optimal geometry from screen size"""
ws = self.main.winfo_screenwidth()
hs = self.main.winfo_screenheight()
self.w = w = ws / 1.3
h = 500
x = (ws / 2) - (w / 2)
y = (hs / 2) - (h / 2)
g = '%dx%d+%d+%d' % (w, h, x, y)
return g
def saveGeometry(self):
"""Save current geometry before quitting"""
g = self.main.geometry()
self.preferences.set('lastwindowsize', g)
return
def setupApps(self):
"""Creates a dict of classes so that GUI frames like primer design
can be dynamically added without explicit methods for each"""
self.apps = {
'Primer Design': PrimerDesignGUI,
'ORF Overview': ORFOverview,
'Sequence Analysis': SequenceAnalysis,
'Sequence Alignment Tool': SequenceAlignmentTool,
'Restriction Digest Summary': RestrictionDigestSummary,
'Blast Interface': BlastInterface,
'NotePad': TextEditor
}
return
def loadPrefs(self):
"""Load prefs from a preferences instance"""
self.preferences = Preferences('DNATool2', {})
temp = {}
for key in self.defaultprefs:
if not key in self.preferences.prefs:
self.preferences.set(key, self.defaultprefs[key])
temp[key] = self.preferences.get(key)
self.applyPrefs(temp)
return
def savePrefs(self):
"""Save prefs to a preferences instance"""
self.applyPrefs(self.prefsdialog.getValues())
self.preferences = Preferences('DNATool2', {})
for key in self.defaultprefs:
self.preferences.set(key, self.__dict__[key])
return
def applyPrefs(self, prefs=None):
"""Apply prefs from a given dict"""
if prefs == None: prefs = self.defaultprefs
for key in prefs:
self.__dict__[key] = prefs[key]
return
def setupGUI(self):
"""Do GUI elements"""
self.visibleapps = {}
#bottom panel
bottom = Frame(self.main, height=50)
bottom.pack(side=BOTTOM, fill=BOTH, pady=1)
#status bar
sb = self.addStatusBar(bottom)
tb = self.addWindowToolBar(bottom)
tb.pack(side=LEFT, anchor='e', expand=1)
self.m = PanedWindow(self.main,
orient=self.orientation,
sashwidth=2,
showhandle=True)
self.m.pack(side=TOP, fill=BOTH, pady=2, expand=1)
sc = self.sc = SequenceCanvas(self.m,
parentapp=self,
width=900,
height=800)
sc.pack(side=TOP, fill=BOTH, pady=2)
self.m.add(sc)
self.m.paneconfigure(sc, sticky='news', min=200)
self.createMenuBar()
self.createToolBar()
self.createSidePane()
if self.orientation == 'vertical':
self.m.paneconfigure(self.sidepane, min=200)
self.createPrimerDBGUI()
self.createChildFrame(name='NotePad')
return
def createMenuBar(self):
"""Create the menu bar for the application. """
self.menu = Menu(self.main)
self.file_menu = {
'01Open Project': {
'cmd': self.openProject
},
'02Open Sequence': {
'cmd': self.openSequence
},
'05Quit': {
'cmd': self.quit
}
}
self.file_menu = self.create_pulldown(self.menu, self.file_menu)
self.menu.add_cascade(label='File', menu=self.file_menu['var'])
self.edit_menu = {
'01Undo': {
'cmd': self.undo
},
'02Copy': {
'cmd': self.copy
},
'03Select All': {
'cmd': self.sc.selectAll
},
'04Configure Restriction Enzymes': {
'cmd': self.restrictionEnzymesDialog
}
}
self.edit_menu = self.create_pulldown(self.menu, self.edit_menu)
self.menu.add_cascade(label='Edit', menu=self.edit_menu['var'])
self.primer_menu = {'01Primer DB': {'cmd': self.createPrimerDBGUI}}
self.primer_menu = self.create_pulldown(self.menu, self.primer_menu)
self.menu.add_cascade(label='Primer Tools',
menu=self.primer_menu['var'])
self.seqanal_menu = {'01x': {'cmd': self.openSequence}}
self.seqanal_menu = self.create_pulldown(self.menu, self.seqanal_menu)
self.menu.add_cascade(label='Sequence Analysis',
menu=self.seqanal_menu['var'])
self.view_menu = Menu(self.menu)
self.menu.add_cascade(label='Tools', menu=self.view_menu)
self.appsvars = {}
for i in self.apps.keys():
self.appsvars[i] = IntVar()
def func(args):
def new():
self.toggleApps(args)
return new
self.view_menu.add_checkbutton(label=i,
onvalue=True,
offvalue=False,
command=func(i),
variable=self.appsvars[i])
self.help_menu = {
'01Online Help': {
'cmd': self.help
},
'02About': {
'cmd': self.about
},
}
self.help_menu = self.create_pulldown(self.menu, self.help_menu)
self.menu.add_cascade(label='Help', menu=self.help_menu['var'])
self.main.config(menu=self.menu)
return
def createSidePane(self, width=200):
"""Side panel for various dialogs is tabbed notebook that can hold multiple
dialogs at once """
self.closeSidePane()
self.sidepane = Frame(self.m, bd=1, relief=RAISED)
self.sidepane = Pmw.NoteBook(self.m)
self.sidepane.component('hull').configure(relief='sunken',
borderwidth=1)
self.m.paneconfigure(self.sidepane, width=width, sticky='news')
self.m.add(self.sidepane)
self.sidepane.setnaturalsize()
return self.sidepane
def closeSidePane(self):
"""Destroy sidepine"""
if hasattr(self, 'sidepane'):
self.m.forget(self.sidepane)
self.sidepane.destroy()
return
def createChildFrame(self, sidepane=True, width=400, name=None):
"""Create a child frame in sidepane notebook or as toplevel"""
geometry = '600x400+500+250'
if sidepane == True:
cframe = self.sidepane.add(name)
self.sidepane.tab(name).configure(font='fixed 8', anchor='w')
self.sidepane.selectpage(name)
else:
cframe = Toplevel()
if name == None:
title = 'default'
else:
title = name
cframe.title(title)
self.__dict__[name] = cframe
#if name is a pre-defined app we load fetch the class
if self.apps.has_key(name):
cls = self.apps[name]
inst = cls(cframe, parentapp=self)
inst.pack(fill=BOTH, expand=1)
self.appsvars[name].set(1)
if hasattr(inst, 'geometry'):
geometry = inst.geometry
if sidepane == False:
cframe.geometry(geometry)
#bind frame close
def func(evt):
if hasattr(self, name):
del self.__dict__[name]
if name in self.appsvars:
self.appsvars[name].set(0)
cframe.bind("<Destroy>", func)
return cframe
def closeChildFrame(self):
"""Close sidepane frame"""
name = self.sidepane.getcurselection()
self.sidepane.delete(name)
return
def detachChildFrame(self):
"""Since we cannot actually detach frames in Tkinter, we
remove the frame in the sidepane make a new toplevel window"""
name = self.sidepane.getcurselection()
self.sidepane.delete(name)
if name == 'PrimerDB':
fr = self.createPrimerDBGUI(sidepane=False)
else:
fr = self.createChildFrame(sidepane=False, name=name)
return fr
def toggleApps(self, name):
"""Remove or add apps from view"""
print name
if self.appsvars[name].get() == 1:
if not hasattr(self, name):
fr = self.createChildFrame(sidepane=True, name=name)
else:
if hasattr(self, name):
if name in self.sidepane.pagenames():
self.sidepane.delete(name)
else:
self.__dict__[name].destroy()
del self.__dict__[name]
return
def createToolBar(self):
"""Toolbar"""
self.toolbar = ToolBar(self.main, self)
self.toolbar.pack(side=TOP, fill=X, pady=1, before=self.m)
img = Images.openproject()
hlptxt = "Open Project from file"
self.toolbar.addButton('Open Project', self.openProject, img, hlptxt)
img = Images.saveproject()
hlptxt = "Save Project"
self.toolbar.addButton('Save Project', self.openProject, img, hlptxt)
img = Images.undo()
hlptxt = "Undo"
self.toolbar.addButton('Save Project', self.openProject, img, hlptxt)
img = Images.zoomout()
hlptxt = "Zoom Out"
self.toolbar.addButton('Save Project', self.sc.zoomOut, img, hlptxt)
img = Images.zoomin()
hlptxt = "Zoom In"
self.toolbar.addButton('Save Project', self.sc.zoomIn, img, hlptxt)
img = Images.windowprefs()
hlptxt = "Seqeuence display preferences"
self.toolbar.addButton('Seqeuence display preferences',
self.sc.showPrefs, img, hlptxt)
img = Images.prefs()
hlptxt = "Preferences"
self.toolbar.addButton('Preferences', self.globalPrefsDialog, img,
hlptxt)
return
def addWindowToolBar(self, parent):
"""Toolbar for changing frame views"""
toolbar = ToolBar(parent, self)
img = Images.closeframe()
hlptxt = "Close current sideframe"
toolbar.addButton('tile vertical', self.closeChildFrame, img, hlptxt)
img = Images.detachframe()
hlptxt = "Detach current sideframe as seperate window"
toolbar.addButton('tile vertical', self.detachChildFrame, img, hlptxt)
img = Images.tilevertical()
hlptxt = "Tile frames vertically"
toolbar.addButton('x', self.tileVertical, img, hlptxt)
img = Images.tilehorizontal()
hlptxt = "Tile frames horizontally"
toolbar.addButton('tile horizontal', self.tileHorizontal, img, hlptxt)
return toolbar
def addStatusBar(self, parent):
fr = Frame(parent, width=100)
Label(fr, text='status stuff').pack()
fr.pack(fill=X, side=LEFT, anchor='w')
return
def removeAll(self):
"""Remove all widgets"""
for w in self.main.children.values():
w.destroy()
return
def tileHorizontal(self):
"""Re-arrange paned widgets horizontally"""
if self.orientation == 'horizontal':
return
self.removeAll()
self.orientation = 'horizontal'
self.setupGUI()
return
def tileVertical(self):
"""Re-arrange paned widgets vertically"""
if self.orientation == 'vertical':
return
self.removeAll()
self.orientation = 'vertical'
self.setupGUI()
return
def openSequence(self):
"""Load a sequence"""
seq = Sequence()
self.sc.loadSequence(seq)
return
def openProject(self, filename=None):
"""Load a project"""
if filename == None:
filename = Dialogs.openFilename(parent=self, ext='dtp')
if not filename:
return
self.P.load(filename)
#open sequence
seq = self.P.DNAseq
#print self.P.used_enzymes, self.P.cut_pos
self.sc.project = self.P
self.sc.update()
#update primer db
self.primerdb = PrimerDatabase(self.P.data['primer_dict'])
self.pdbwin.database = self.primerdb
self.pdbwin.update()
return
def copy(self):
self.sc.copySequence()
return
def undo(self):
return
def createPrimerDBGUI(self, sidepane=True):
"""We create this individually to avoid confusion"""
if hasattr(self, 'PrimerDB'):
self.PrimerDB.lift()
return
fr = self.createChildFrame(name='PrimerDB', sidepane=sidepane)
self.pdbwin = PrimerDBGUI(fr, database=self.primerdb)
self.pdbwin.update()
self.pdbwin.pack(fill=BOTH, expand=1)
#bind window closing so it's automatically recreated in the sidepane
if sidepane == False:
def func(evt):
self.createPrimerDBGUI()
self.pdbwin.bind("<Destroy>", func)
return fr
def applyRestrSiteSettings(self):
if hasattr(self, 'restrsitedialog'):
vals = self.restrsitedialog.getValues()
self.sc.update()
return
def restrictionEnzymesDialog(self, sidepane=True):
defaults = {
'uniquesitesonly': 1,
'showonlyenzymescutmax': 50,
'ignorecutpos': 1,
'minlengthrecseq': 5,
'excludepromiscuous': 1
}
options = [('uniquesitesonly', 'checkbutton', 1,
'Show unique sites only'),
('showonlyenzymescutmax', 'scale', (1, 100),
'Show only enzymes that cut max'),
('ignorecutpos', 'checkbutton', 1,
'Ignore cut position when finding isoschiziomers'),
('minlengthrecseq', 'scale', (1, 10),
'Min length of recognition sequence'),
('excludepromiscuous', 'checkbutton', 1,
'Exclude promiscuous enzymes')]
geometry = '400x250+500+250'
fr = self.createChildFrame(name='Configure Restriction Enzymes',
sidepane=sidepane)
self.restrsitedialog = Dialogs.GenericDialog(fr, options, defaults)
defaults = {
'uniquesitesonly': 1,
'showonlyenzymescutmax': 50,
'ignorecutpos': 1,
'minlengthrecseq': 5,
'excludepromiscuous': 1
}
self.restrsitedialog.pack(fill=BOTH, expand=1)
return
def applySettings(self):
self.applyPrefs(self.prefsdialog.getValues())
#self.removeAll()
#self.setupGUI()
#self.globalPrefsDialog()
return
def globalPrefsDialog(self, sidepane=True):
curr = {}
for key in self.defaultprefs:
curr[key] = self.__dict__[key]
fr = self.createChildFrame(name='Global settings', sidepane=sidepane)
self.prefsdialog = Dialogs.PrefsDialog(fr, self, self.defaultopts,
curr, self.applySettings)
self.prefsdialog.pack(fill=BOTH, expand=1)
return
def help(self):
import webbrowser
link = 'http://code.google.com/p/peat/wiki/DNAtool'
webbrowser.open(link, autoraise=1)
return
def about(self):
win = Toplevel()
win.geometry('+500+350')
win.title('About DNATool')
win.maxsize(width=400, height=400)
logo = Images.logo()
label = Label(win, image=logo)
label.image = logo
label.pack(fill=BOTH, padx=4, pady=4)
text = """DNATool App, Version 2
is a python desktop application for DNA sequence manipulation.
Released under GPL v3
(C) Copyright 2012- Damien Farrell """
text = text.replace('\t', '')
text = ' '.join(text.split())
Label(win, text=text, wraplength=400).pack(fill=Y, side=TOP, pady=4)
return
def quit(self):
if self.rememberwindowsize == 1:
self.saveGeometry()
self.main.destroy()
if not self.parent:
sys.exit()
return
class App(Frame, GUI_help):
"""Data pipe GUI for importing and fitting of raw data.
This class uses ekin provided an automated pipeline for fitting
raw text data files and propagating errors.
Uses a config file to store the pipeline settings"""
def __init__(self, parent=None, rawfile=None, conffile=None):
self.parent=parent
if not self.parent:
Frame.__init__(self)
self.main=self.master
else:
self.main=Toplevel()
self.master=self.main
self.main.title('DNATool Desktop')
self.main.protocol('WM_DELETE_WINDOW',self.quit)
self.defaultprefs = {'rememberwindowsize':0,'orientation':'horizontal',
'alignmenttool':'clustal','clustalpath':'clustalw'}
self.defaultopts = [('rememberwindowsize','checkbutton',1,'Remember window size'),
('orientation','menu',('horizontal','vertical'),
'Default sideframe orientation'),
('alignmenttool','menu',('clustal','muscle','needle'),
'External alignment tool'),
('clustalpath','entry','','Path to Clustal')]
self.loadPrefs()
self.setGeometry()
self.P = Project()
self.primerdb = PrimerDatabase()
self.setupApps()
self.setupGUI()
self.sidepane.selectpage('PrimerDB')
return
def setGeometry(self):
if self.rememberwindowsize == 1 and self.preferences.has_key('lastwindowsize'):
lastwindowsize = self.preferences.get('lastwindowsize')
self.winsize = lastwindowsize
#self.w = int(lastwindowsize.split('x')[0])
else:
self.winsize = self.getBestGeometry()
self.main.geometry(self.winsize)
return
def getBestGeometry(self):
"""Calculate optimal geometry from screen size"""
ws = self.main.winfo_screenwidth()
hs = self.main.winfo_screenheight()
self.w=w=ws/1.3; h=500
x = (ws/2)-(w/2); y = (hs/2)-(h/2)
g = '%dx%d+%d+%d' % (w,h,x,y)
return g
def saveGeometry(self):
"""Save current geometry before quitting"""
g = self.main.geometry()
self.preferences.set('lastwindowsize', g)
return
def setupApps(self):
"""Creates a dict of classes so that GUI frames like primer design
can be dynamically added without explicit methods for each"""
self.apps = {'Primer Design': PrimerDesignGUI,
'ORF Overview': ORFOverview,
'Sequence Analysis': SequenceAnalysis,
'Sequence Alignment Tool': SequenceAlignmentTool,
'Restriction Digest Summary': RestrictionDigestSummary,
'Blast Interface':BlastInterface,
'NotePad': TextEditor}
return
def loadPrefs(self):
"""Load prefs from a preferences instance"""
self.preferences = Preferences('DNATool2',{})
temp = {}
for key in self.defaultprefs:
if not key in self.preferences.prefs:
self.preferences.set(key, self.defaultprefs[key])
temp[key] = self.preferences.get(key)
self.applyPrefs(temp)
return
def savePrefs(self):
"""Save prefs to a preferences instance"""
self.applyPrefs(self.prefsdialog.getValues())
self.preferences = Preferences('DNATool2',{})
for key in self.defaultprefs:
self.preferences.set(key, self.__dict__[key])
return
def applyPrefs(self, prefs=None):
"""Apply prefs from a given dict"""
if prefs == None: prefs=self.defaultprefs
for key in prefs:
self.__dict__[key] = prefs[key]
return
def setupGUI(self):
"""Do GUI elements"""
self.visibleapps = {}
#bottom panel
bottom = Frame(self.main,height=50)
bottom.pack(side=BOTTOM,fill=BOTH,pady=1)
#status bar
sb = self.addStatusBar(bottom)
tb = self.addWindowToolBar(bottom)
tb.pack(side=LEFT,anchor='e',expand=1)
self.m = PanedWindow(self.main,
orient=self.orientation,
sashwidth=2,
showhandle=True)
self.m.pack(side=TOP,fill=BOTH,pady=2,expand=1)
sc = self.sc = SequenceCanvas(self.m,parentapp=self,
width=900,height=800)
sc.pack(side=TOP,fill=BOTH,pady=2)
self.m.add(sc)
self.m.paneconfigure(sc,sticky='news',min=200)
self.createMenuBar()
self.createToolBar()
self.createSidePane()
if self.orientation == 'vertical':
self.m.paneconfigure(self.sidepane,
min=200)
self.createPrimerDBGUI()
self.createChildFrame(name='NotePad')
return
def createMenuBar(self):
"""Create the menu bar for the application. """
self.menu=Menu(self.main)
self.file_menu={'01Open Project':{'cmd':self.openProject},
'02Open Sequence':{'cmd':self.openSequence},
'05Quit':{'cmd':self.quit}}
self.file_menu=self.create_pulldown(self.menu,self.file_menu)
self.menu.add_cascade(label='File',menu=self.file_menu['var'])
self.edit_menu={'01Undo':{'cmd':self.undo},
'02Copy':{'cmd':self.copy},
'03Select All':{'cmd':self.sc.selectAll},
'04Configure Restriction Enzymes':{'cmd':self.restrictionEnzymesDialog}}
self.edit_menu=self.create_pulldown(self.menu,self.edit_menu)
self.menu.add_cascade(label='Edit',menu=self.edit_menu['var'])
self.primer_menu={'01Primer DB':{'cmd':self.createPrimerDBGUI}}
self.primer_menu=self.create_pulldown(self.menu,self.primer_menu)
self.menu.add_cascade(label='Primer Tools',menu=self.primer_menu['var'])
self.seqanal_menu={'01x':{'cmd':self.openSequence}}
self.seqanal_menu=self.create_pulldown(self.menu,self.seqanal_menu)
self.menu.add_cascade(label='Sequence Analysis',menu=self.seqanal_menu['var'])
self.view_menu=Menu(self.menu)
self.menu.add_cascade(label='Tools',menu=self.view_menu)
self.appsvars = {}
for i in self.apps.keys():
self.appsvars[i] = IntVar()
def func(args):
def new():
self.toggleApps(args)
return new
self.view_menu.add_checkbutton(label=i, onvalue=True,
offvalue=False,
command=func(i),
variable=self.appsvars[i])
self.help_menu={ '01Online Help':{'cmd': self.help},
'02About':{'cmd': self.about},}
self.help_menu=self.create_pulldown(self.menu,self.help_menu)
self.menu.add_cascade(label='Help',menu=self.help_menu['var'])
self.main.config(menu=self.menu)
return
def createSidePane(self, width=200):
"""Side panel for various dialogs is tabbed notebook that can hold multiple
dialogs at once """
self.closeSidePane()
self.sidepane = Frame(self.m,
bd=1,relief=RAISED)
self.sidepane = Pmw.NoteBook(self.m)
self.sidepane.component('hull').configure(relief='sunken',
borderwidth=1)
self.m.paneconfigure(self.sidepane,
width=width,
sticky='news')
self.m.add(self.sidepane)
self.sidepane.setnaturalsize()
return self.sidepane
def closeSidePane(self):
"""Destroy sidepine"""
if hasattr(self, 'sidepane'):
self.m.forget(self.sidepane)
self.sidepane.destroy()
return
def createChildFrame(self, sidepane=True, width=400, name=None):
"""Create a child frame in sidepane notebook or as toplevel"""
geometry = '600x400+500+250'
if sidepane == True:
cframe = self.sidepane.add(name)
self.sidepane.tab(name).configure(font='fixed 8',anchor='w')
self.sidepane.selectpage(name)
else:
cframe = Toplevel()
if name == None:
title = 'default'
else:
title = name
cframe.title(title)
self.__dict__[name] = cframe
#if name is a pre-defined app we load fetch the class
if self.apps.has_key(name):
cls = self.apps[name]
inst = cls(cframe, parentapp=self)
inst.pack(fill=BOTH,expand=1)
self.appsvars[name].set(1)
if hasattr(inst, 'geometry'):
geometry = inst.geometry
if sidepane == False:
cframe.geometry(geometry)
#bind frame close
def func(evt):
if hasattr(self, name):
del self.__dict__[name]
if name in self.appsvars:
self.appsvars[name].set(0)
cframe.bind("<Destroy>", func)
return cframe
def closeChildFrame(self):
"""Close sidepane frame"""
name = self.sidepane.getcurselection()
self.sidepane.delete(name)
return
def detachChildFrame(self):
"""Since we cannot actually detach frames in Tkinter, we
remove the frame in the sidepane make a new toplevel window"""
name = self.sidepane.getcurselection()
self.sidepane.delete(name)
if name == 'PrimerDB':
fr = self.createPrimerDBGUI(sidepane=False)
else:
fr = self.createChildFrame(sidepane=False, name=name)
return fr
def toggleApps(self, name):
"""Remove or add apps from view"""
print name
if self.appsvars[name].get() == 1:
if not hasattr(self, name):
fr = self.createChildFrame(sidepane=True, name=name)
else:
if hasattr(self, name):
if name in self.sidepane.pagenames():
self.sidepane.delete(name)
else:
self.__dict__[name].destroy()
del self.__dict__[name]
return
def createToolBar(self):
"""Toolbar"""
self.toolbar = ToolBar(self.main, self)
self.toolbar.pack(side=TOP,fill=X,pady=1,before=self.m)
img = Images.openproject()
hlptxt="Open Project from file"
self.toolbar.addButton('Open Project', self.openProject, img, hlptxt)
img = Images.saveproject()
hlptxt="Save Project"
self.toolbar.addButton('Save Project', self.openProject, img, hlptxt)
img = Images.undo()
hlptxt="Undo"
self.toolbar.addButton('Save Project', self.openProject, img, hlptxt)
img = Images.zoomout()
hlptxt="Zoom Out"
self.toolbar.addButton('Save Project', self.sc.zoomOut, img, hlptxt)
img = Images.zoomin()
hlptxt="Zoom In"
self.toolbar.addButton('Save Project', self.sc.zoomIn, img, hlptxt)
img = Images.windowprefs()
hlptxt="Seqeuence display preferences"
self.toolbar.addButton('Seqeuence display preferences', self.sc.showPrefs,
img, hlptxt)
img = Images.prefs()
hlptxt="Preferences"
self.toolbar.addButton('Preferences', self.globalPrefsDialog, img, hlptxt)
return
def addWindowToolBar(self, parent):
"""Toolbar for changing frame views"""
toolbar = ToolBar(parent, self)
img = Images.closeframe()
hlptxt="Close current sideframe"
toolbar.addButton('tile vertical', self.closeChildFrame, img, hlptxt)
img = Images.detachframe()
hlptxt="Detach current sideframe as seperate window"
toolbar.addButton('tile vertical', self.detachChildFrame, img, hlptxt)
img = Images.tilevertical()
hlptxt="Tile frames vertically"
toolbar.addButton('x', self.tileVertical, img, hlptxt)
img = Images.tilehorizontal()
hlptxt="Tile frames horizontally"
toolbar.addButton('tile horizontal', self.tileHorizontal, img, hlptxt)
return toolbar
def addStatusBar(self, parent):
fr = Frame(parent, width=100)
Label(fr,text='status stuff').pack()
fr.pack(fill=X,side=LEFT,anchor='w')
return
def removeAll(self):
"""Remove all widgets"""
for w in self.main.children.values():
w.destroy()
return
def tileHorizontal(self):
"""Re-arrange paned widgets horizontally"""
if self.orientation == 'horizontal':
return
self.removeAll()
self.orientation = 'horizontal'
self.setupGUI()
return
def tileVertical(self):
"""Re-arrange paned widgets vertically"""
if self.orientation == 'vertical':
return
self.removeAll()
self.orientation = 'vertical'
self.setupGUI()
return
def openSequence(self):
"""Load a sequence"""
seq = Sequence()
self.sc.loadSequence(seq)
return
def openProject(self, filename=None):
"""Load a project"""
if filename == None:
filename = Dialogs.openFilename(parent=self, ext='dtp')
if not filename:
return
self.P.load(filename)
#open sequence
seq = self.P.DNAseq
#print self.P.used_enzymes, self.P.cut_pos
self.sc.project = self.P
self.sc.update()
#update primer db
self.primerdb = PrimerDatabase(self.P.data['primer_dict'])
self.pdbwin.database = self.primerdb
self.pdbwin.update()
return
def copy(self):
self.sc.copySequence()
return
def undo(self):
return
def createPrimerDBGUI(self, sidepane=True):
"""We create this individually to avoid confusion"""
if hasattr(self, 'PrimerDB'):
self.PrimerDB.lift()
return
fr = self.createChildFrame(name='PrimerDB',sidepane=sidepane)
self.pdbwin = PrimerDBGUI(fr, database=self.primerdb)
self.pdbwin.update()
self.pdbwin.pack(fill=BOTH,expand=1)
#bind window closing so it's automatically recreated in the sidepane
if sidepane == False:
def func(evt):
self.createPrimerDBGUI()
self.pdbwin.bind("<Destroy>", func)
return fr
def applyRestrSiteSettings(self):
if hasattr(self, 'restrsitedialog'):
vals = self.restrsitedialog.getValues()
self.sc.update()
return
def restrictionEnzymesDialog(self, sidepane=True):
defaults = {'uniquesitesonly':1,'showonlyenzymescutmax':50,
'ignorecutpos':1,'minlengthrecseq':5,'excludepromiscuous':1}
options = [('uniquesitesonly','checkbutton',1,'Show unique sites only'),
('showonlyenzymescutmax','scale',(1,100),'Show only enzymes that cut max'),
('ignorecutpos','checkbutton',1,'Ignore cut position when finding isoschiziomers'),
('minlengthrecseq','scale',(1,10),'Min length of recognition sequence'),
('excludepromiscuous','checkbutton',1,'Exclude promiscuous enzymes')]
geometry = '400x250+500+250'
fr = self.createChildFrame(name='Configure Restriction Enzymes',sidepane=sidepane)
self.restrsitedialog = Dialogs.GenericDialog(fr, options, defaults)
defaults = {'uniquesitesonly':1,'showonlyenzymescutmax':50,
'ignorecutpos':1,'minlengthrecseq':5,'excludepromiscuous':1}
self.restrsitedialog.pack(fill=BOTH,expand=1)
return
def applySettings(self):
self.applyPrefs(self.prefsdialog.getValues())
#self.removeAll()
#self.setupGUI()
#self.globalPrefsDialog()
return
def globalPrefsDialog(self, sidepane=True):
curr = {}
for key in self.defaultprefs:
curr[key] = self.__dict__[key]
fr = self.createChildFrame(name='Global settings', sidepane=sidepane)
self.prefsdialog = Dialogs.PrefsDialog(fr, self, self.defaultopts,
curr, self.applySettings)
self.prefsdialog.pack(fill=BOTH,expand=1)
return
def help(self):
import webbrowser
link='http://code.google.com/p/peat/wiki/DNAtool'
webbrowser.open(link,autoraise=1)
return
def about(self):
win=Toplevel()
win.geometry('+500+350')
win.title('About DNATool')
win.maxsize(width=400,height=400)
logo = Images.logo()
label = Label(win,image=logo)
label.image = logo
label.pack(fill=BOTH,padx=4,pady=4)
text="""DNATool App, Version 2
is a python desktop application for DNA sequence manipulation.
Released under GPL v3
(C) Copyright 2012- Damien Farrell """
text=text.replace('\t','')
text= ' '.join(text.split())
Label(win,text=text,wraplength=400).pack(fill=Y,side=TOP,pady=4)
return
def quit(self):
if self.rememberwindowsize == 1:
self.saveGeometry()
self.main.destroy()
if not self.parent:
sys.exit()
return
