def build_widgets(self):
"Build the various widgets that will be used in the program."
# Create processing frame widgets.
self.processing_frame = LabelFrame(self, text='Processing Mode:')
self.mode_var = StringVar(self, 'encode')
self.decode_button = Radiobutton(self.processing_frame,
text='Decode Cipher-Text',
command=self.handle_radiobuttons,
value='decode',
variable=self.mode_var)
self.encode_button = Radiobutton(self.processing_frame,
text='Encode Plain-Text',
command=self.handle_radiobuttons,
value='encode',
variable=self.mode_var)
self.freeze_var = BooleanVar(self, False)
self.freeze_button = Checkbutton(self.processing_frame,
text='Freeze Key & Primer',
command=self.handle_checkbutton,
offvalue=False,
onvalue=True,
variable=self.freeze_var)
# Create encoding frame widgets.
self.encoding_frame = LabelFrame(self, text='Encoding Options:')
self.chain_size_label = Label(self.encoding_frame, text='Chain Size:')
self.chain_size_entry = Entry(self.encoding_frame)
self.plain_text_label = Label(self.encoding_frame, text='Plain-Text:')
self.plain_text_entry = Entry(self.encoding_frame)
# Create input frame widgets.
self.input_frame = LabelFrame(self, text='Input Area:')
self.input_text = ScrolledText(self.input_frame, **self.TEXT)
# Create output frame widgets.
self.output_frame = LabelFrame(self, text='Output Area:')
self.output_text = ScrolledText(self.output_frame, **self.TEXT)
def __init__(self, parent, name):
LabelFrame.__init__(self, parent, text=name)
self.height = 100
self.width = 100
self.amount = IntVar()
self.scheduled = IntVar()
self.canvas = Canvas(self,
bg='#FFF8B8',
height=self.height,
width=self.width,
relief=SUNKEN)
self.canvas.pack()
self.img = Picture(self.canvas,
name,
self.height,
relief=None,
borderwidth=0,
highlightthickness=0)
x = int((self.width - self.img.width) / 2)
y = int((self.height - self.img.height) / 2)
self.img.place(x=x, y=y)
self.lblA = Label(self.canvas,
textvariable=self.amount,
bg='#FFF8B8',
font=("Verdana", 16))
self.lblS = Label(self.canvas,
textvariable=self.scheduled,
bg='#FFF8B8',
font=("Verdana", 16))
d = 3
y = self.height - d
self.lblA.place(x=d, y=y, anchor='sw')
self.lblS.place(x=self.width - d, y=y, anchor='se')
def __init__(self, win, tabs):
super().__init__(tabs)
self.win = win
self.tabs = tabs
self.tabs.add(self, text="Stats")
self.stats: StatsCollection = None
self.selection: StatsCollection = None
self._body = Frame(self)
self._body.grid(row=0, column=0, sticky=EW, padx=PAD_X, pady=PAD_Y)
# Load
self._load_stats = LoadStatsFrame(self._body, self.set_stats)
self._load_stats.grid(row=0, column=0, padx=PAD_X, pady=PAD_Y, sticky=EW)
# Summary
self._summary = LabelFrame(self._body, text=" Records ")
self._summary.grid(row=1, column=0, sticky=EW)
self._all_counters = CountersFrame(self._summary, text=" All ")
self._all_counters.grid(row=0, column=0, padx=2 * PAD_X, pady=2 * PAD_Y, sticky=EW)
self._selection_counters = CountersFrame(self._summary, text=" Selection ")
self._selection_counters.grid(column=1, row=0, padx=2 * PAD_X, pady=2 * PAD_Y, sticky=EW)
# Filter
self._filters = FilterSelectionFrame(self._body, self.get_all, self.get_selection, self.set_selection)
self._filters.grid(row=2, column=0, sticky=EW)
# Reports
self._reports = ReportsFrame(self._body, self.get_selection)
self._reports.grid(row=3, column=0, sticky=EW)
def on_create_frame_down_lf(self, frame_name, col, row, colpad, rowpad):
self.graph_down = LabelFrame(master=self.master, text=frame_name)
self.graph_down.grid(column=col,
row=row,
padx=colpad,
pady=rowpad,
sticky='SE')
def add_file_info_box(self, mainframe, name, labeldict, btncallback, fvar):
"""
Create and add a infobox containing the info about a loaded
savegame.
"""
title = {'source':'Copy face from source file:',
'target':'To target file:'}
frame = LabelFrame(mainframe, text=title[name])
frame.pack(anchor=N, fill=X, expand=1, side=TOP, padx=0, pady=0)
frame.columnconfigure(1, weight=1)
btn = Button(frame, text='Browse', command=btncallback)
btn.grid(column=0, row=0, padx=2, pady=2)
field = Entry(frame, width=50, textvariable=fvar)
field.grid(column=1, row=0, columnspan=2, padx=2, pady=2, sticky=W+E)
l = ('name','gender','level','race','location','save number','playing time')
for n, (i, j) in enumerate([(x.capitalize()+':', x) for x in l]):
Label(frame, text=i, state=DISABLED).grid(column=0, row=n+1, padx=4,
pady=3, sticky=E)
labeldict[j] = StringVar()
Label(frame, textvariable=labeldict[j]).grid(column=1, row=n+1,
padx=4, pady=3, sticky=W)
self.screenshot[name] = Label(frame)
self.screenshot[name].grid(column=2, row=1, rowspan=len(l),
padx=4, pady=4)
def settings():
global settings_popup
try: settings_popup.destroy()
except: pass
settings_styles = Style()
settings_styles.configure(
"SettingsLabelframe.TLabelframe.Label", font=("Verdana", 18, "normal"))
settings_styles.configure(
"SettingsLabelframe.TLabelframe.Label", foreground=COLORS['TEXTCOLOR'])
settings_popup = Toplevel()
settings_popup.title("Settings")
settings_popup.transient(root)
settings_popup.resizable(False, False)
other_frame = LabelFrame(settings_popup, text="Settings", style="SettingsLabelframe.TLabelframe")
basefreq_lbl = Label(other_frame, text="Octave")
basefreq_om = OptionMenu(other_frame, OPTIONS['BASE_FREQ'], BASE_FREQS[-1], *BASE_FREQS)
basefreq_lbl.grid(row=0, column=0, padx=5)
basefreq_om.grid(row=0, column=1, padx=5)
other_frame.pack(padx=15, pady=15, ipadx=5, ipady=5)
settings_popup.mainloop()
class MyContainerLabeled(object):
def __init__(self, parent, name, del_name, label, x, y, width, height):
self.container = LabelFrame(parent,
text=label,
width=width,
height=height)
parent.children[name] = parent.children.pop(del_name)
self.container.place(x=x, y=y)
self.buf_access = self.collect_access()
def collect_access(self):
result = {}
for obj in self.container.children.values():
result[obj] = obj["state"]
return result
def add_objects(self, objects):
self.objects += objects
def disable_all(self):
for obj in self.objects:
obj.object.configure(state="disabled")
def enable_all(self):
for obj in self.objects:
obj.object.configure(state="normal")
def restore_state_all(self):
for obj in self.objects:
obj.object.configure(state=obj.buf_state)
def popup_window(self, text, filename):
top = Toplevel()
info = LabelFrame(top, text=text) #"Group Information")
info_text = Text(
info,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold", "11"))
def savefunc():
self.writepaste(filename, info_text)
def loadfunc():
self.readpaste(filename, info_text)
info_save_button = Button(info, text="Save", command=savefunc)
info_load_button = Button(info, text="Load", command=loadfunc)
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
info_load_button.grid(row=5, column=5, padx=10, pady=5)
info_save_button.grid(row=5, column=6, padx=10, pady=5)
info_text.grid(row=1,
rowspan=3,
column=1,
columnspan=7,
padx=5,
pady=5)
info.grid(row=7, column=0, columnspan=6, sticky=W, padx=20, pady=10)
top.focus_force()
def __init__(self, parent, source):
LabelFrame.__init__(self, parent, text="Tasklist")
self.parent = parent
self.getData = source
self.text = Text(self)
self.text.pack()
self.parent.after(1000, self.update)
def __init__(self, parent, source):
LabelFrame.__init__(self, parent, text="Orders")
self.parent = parent
# self.frame=Frame(self,width=550,height=400)
# self.frame.pack(expand=None, fill=Y)
self.getData = source
self.parent.after(1000, self.update)
self.orders = {}
def __init__(self, parent, name, del_name, label, x, y, width, height):
self.container = LabelFrame(parent,
text=label,
width=width,
height=height)
parent.children[name] = parent.children.pop(del_name)
self.container.place(x=x, y=y)
self.buf_access = self.collect_access()
def memory_frame(self):
self.frame_memory = LabelFrame(self.ventana,
width=250,
height=220,
text="Recent requests",
labelanchor='n',
relief='ridge')
self.frame_memory.place(x=780, y=130 + self.despy)
def __init__(self,parent): LabelFrame.__init__(self,parent,text="Calculate",borderwidth=5) self.startCalculationB = Button(self,text="Start calculation",width=20) self.startCalculationB.grid(row=0,column=0,padx=10,pady=5) self.endCalculationB = Button(self,text="Cancel calculation",width=20) self.endCalculationB.grid(row=1,column=0,padx=10,pady=5) self.calculationPB = Progressbar(self, mode="indeterminate",length=128) self.calculationPB.grid(row=2,column=0,padx=10,pady=5)
def showMainValues():
global tkroot
global labels
global mframe
global values
from tkinter import Tk, N, W
from tkinter.ttk import LabelFrame, Label
# first run, set up the thingy
print("Setting up Main Values...")
init_parse(getMainValues, _parse_main_values_xml, values)
sleep(0.5)
print("Setting up Advanced Values...")
init_parse(getAdvancedValues, _parse_adv_values_xml, values)
print("initializing tkinter interface...")
tkroot = Tk()
mframe = LabelFrame(tkroot, text="Main Frame")
labels = {}
for group in values:
lframe = LabelFrame(mframe, text=group)
labels[group] = OrderedDict()
labels[group]['frame'] = lframe
for param, pv in values[group].items():
labels[group][param] = {}
plabel = Label(lframe, text=param)
vlabel = Label(lframe, text=pv)
labels[group][param]['plabel'] = plabel
labels[group][param]['vlabel'] = vlabel
mframe.grid()
for i, group in enumerate(labels):
for param in labels[group]:
if param == 'frame':
labels[group][param].grid(column=i, row=0, sticky=N)
else:
labels[group][param]['plabel'].grid(sticky=W)
labels[group][param]['vlabel'].grid(sticky=W)
tkroot.grid()
print('setting up polling intervals')
tkroot.after(500, poll_main_values)
tkroot.after(750, poll_adv_values)
print('Ready')
tkroot.mainloop()
print("afterloop")
def _build_state_display(self, position):
state_field = LabelFrame(self,
text=s.language.cards,
relief=RAISED,
width=self.master.width - 31)
state_slots_per_row = int((self.master.width - 31) / 32)
state_slot_height = 24 + (
(int(len(self._current_player.states) / state_slots_per_row) + 1) *
32)
if self._current_player.states:
for index, state in enumerate(self._current_player.states):
if state not in self._main_window.engine.nemKartyaStatusz:
if state in self._main_window.engine.eventszotar.keys():
origin = self._main_window.engine.eventszotar
prefix = "event"
else:
origin = self._main_window.engine.kincsszotar
prefix = "treasure"
icon = f"{prefix}_{self._main_window.engine.eventszotar[state].kep}_i"
icon = icon[(icon.find('_') + 1):]
button = Button(
state_field,
image=Gallery.get(icon),
command=lambda s=state: origin[s].megjelenik(1))
button.grid(row=int(index / state_slots_per_row),
column=index % state_slots_per_row)
state_field.config(height=state_slot_height)
if state_field.winfo_children():
state_field.grid(row=position, column=0)
state_field.grid_propagate(False)
def serverpanel(server):
''' Draws the top panel with the server information '''
serverpanel = LabelFrame(win, text = "Server Details")
serverpanel.grid(column = 0, row = 0, padx = 5, pady = 5, sticky = W+E)
Label(serverpanel, text = "Server Name: ").grid(column = 0, row = 0, sticky = W)
Label(serverpanel, text = "Server Type: ").grid(column = 0, row = 1, sticky = W)
Label(serverpanel, text = "Load Balancer Status: ").grid(column = 0, row = 2, sticky = W)
Label(serverpanel, textvariable = snv).grid(column = 1, row = 0, sticky = W)
Label(serverpanel, textvariable = stv ).grid(column = 1, row = 1, sticky = W)
Label(serverpanel, textvariable = lbv).grid(column = 1, row = 2, sticky = W)
serverstatus(server)
def __init__(self, master):
Frame.__init__(self, master)
self._main_window = self.master.master
self._land_land_roll = False
self._heading = Frame(self)
self._inventory_display = Frame(self)
self._die_field = Frame(self)
self._score_field = LabelFrame(self)
self._turn_order = Frame(self)
self.die = None
if self._main_window.is_game_in_progress.get():
self._load_content()
class StatsTabFrame(Frame):
def __init__(self, win, tabs):
super().__init__(tabs)
self.win = win
self.tabs = tabs
self.tabs.add(self, text="Stats")
self.stats: StatsCollection = None
self.selection: StatsCollection = None
self._body = Frame(self)
self._body.grid(row=0, column=0, sticky=EW, padx=PAD_X, pady=PAD_Y)
# Load
self._load_stats = LoadStatsFrame(self._body, self.set_stats)
self._load_stats.grid(row=0, column=0, padx=PAD_X, pady=PAD_Y, sticky=EW)
# Summary
self._summary = LabelFrame(self._body, text=" Records ")
self._summary.grid(row=1, column=0, sticky=EW)
self._all_counters = CountersFrame(self._summary, text=" All ")
self._all_counters.grid(row=0, column=0, padx=2 * PAD_X, pady=2 * PAD_Y, sticky=EW)
self._selection_counters = CountersFrame(self._summary, text=" Selection ")
self._selection_counters.grid(column=1, row=0, padx=2 * PAD_X, pady=2 * PAD_Y, sticky=EW)
# Filter
self._filters = FilterSelectionFrame(self._body, self.get_all, self.get_selection, self.set_selection)
self._filters.grid(row=2, column=0, sticky=EW)
# Reports
self._reports = ReportsFrame(self._body, self.get_selection)
self._reports.grid(row=3, column=0, sticky=EW)
def get_all(self) -> StatsCollection:
return self.stats
def get_selection(self) -> StatsCollection:
return self.selection
def set_stats(self, stats: StatsCollection):
self.stats = stats
self._all_counters.set_stats(stats.get_counters())
self._filters.set_countries(stats.unique_countries)
self.set_selection(stats)
def set_selection(self, stats: StatsCollection):
self.selection = stats
self._selection_counters.set_stats(stats.get_counters())
self._filters.set_tournaments(stats.unique_tournaments)
def __init__(self, parent, label_text, add_headers, params,
category_type, *args, **kw):
LabelFrame.__init__(self, parent, text=label_text, *args, **kw)
self.parent = parent
self.frame_with_boxes = None
self.canvas = None
self.options = dict()
self.nb_entries = 0
self.add_headers = add_headers
self.category_objects = dict()
self.params = params
self.category_type = category_type
self.create_widgets()
def buttonpanel():
''' Draws the panel with the buttons at the bottom '''
butpanel = LabelFrame(win, text = "")
butpanel.grid(column = 0, row = 2, padx = 5, pady = 5, sticky = W+E)
Button(butpanel, text = "Stop Services", command = onStop).grid(column = 0, row = 0)
Button(butpanel, text = "Start Services", command = onStart).grid(column = 1, row = 0)
Button(butpanel, text = "Refresh List", command = onStatus).grid(column = 2, row = 0)
if server.lbalanced.upper() == "YES":
# lbutpanel = LabelFrame(win, text = "")
# lbutpanel.grid(column = 0, row = 3, padx = 5, pady = 5, sticky = W+E)
Button(butpanel, text = "Stop Load Balancer", command = lbStop).grid(column = 0, row = 1)
Button(butpanel, text = "Start Load Balancer", command = lbStart).grid(column = 1, row = 1)
def __init__(self, parent, label_text, add_headers, params, category_type,
*args, **kw):
LabelFrame.__init__(self, parent, text=label_text, *args, **kw)
self.parent = parent
self.frame_with_boxes = None
self.canvas = None
self.options = dict()
self.nb_entries = 0
self.add_headers = add_headers
self.category_objects = dict()
self.params = params
self.category_type = category_type
self.create_widgets()
def on_create_labelframe(self, frame_name, col, row, colpad, rowpad, pos):
"""
Erstellung eines oberen Bezeichner fuer ein Element und Positionierung des Elements in einem Frame
:param frame_name: Titel oben auf ein Objekt
:param col: Spalten
:param row: ZEile
:param colpad: Innenabstand in der Spaltenrichtung
:param rowpad: Innenabstand in der Zeilenrichtung
:param pos: Plazierung in einem Frame ('N':Nord, 'S':Sued, 'W':West, usw.)
:return:
"""
self.lf = LabelFrame(master=self.master, text=frame_name)
self.lf.grid(column=col, row=row, padx=colpad, pady=rowpad, sticky=pos)
def body(self, szulo):
self._projekt_valaszto = Valaszto("megnevezés", self._projektek(),
self)
self._projekt_valaszto.set_callback(self._projekt_megjelenit)
self._projekt_valaszto.pack(ipadx=2, ipady=2)
megnevezes = LabelFrame(self, text="projekt neve")
self._projekt_urlap = ProjektUrlap(megnevezes)
self._projekt_urlap.pack(ipadx=2, ipady=2)
self._projekt_megjelenit(1)
megnevezes.pack(fill=X, padx=2, pady=2)
return self._projekt_valaszto.valaszto
def __init__(self, parent):
LabelFrame.__init__(self,
parent,
text="Results",
width=825,
height=485)
# Terrible kludgy hack to force the app to stay the right size
# Need to work out how to remove
self.grid_propagate(False)
self.resultsDict = None
self.modelType = None
self.currentSegment = 0
# Stats frame
self.statsFrame = StatsFrame(self, self.padX, self.padY)
self.statsFrame.calculate_B.bind("<Button-1>", self._parametersChanged)
self.statsFrame.reset_B.bind("<Button-1>", self._parametersReset)
def onComboBoxSelect(e):
self.currentSegment = e.widget.current()
self._updateDisplay(True)
self.statsFrame.expSeg_CB.bind("<<ComboboxSelected>>",
onComboBoxSelect)
# Error frame
self.errorSurfaceFrame = ErrorSurfaceFrame(self)
self.errorSurfaceFrame.errorSurfaceB.bind("<Button-1>",
self._displayErrorSurface)
# Graph notebook
self.errorSurfaceSeperator = Separator(self, orient=tkinter.HORIZONTAL)
self.graphNotebook = ImprovedNotebook(self)
self.modelGraphFrame = GraphFrame(self.graphNotebook, dim=2)
self.modelGraphFrame.axes.set_ylabel(r'$thickness(m)$')
self.regressionGraphFrame = GraphFrame(self.graphNotebook, dim=2)
self.regressionGraphFrame.axes.set_ylabel(r'$\log{(thickness(m))}$')
self.errorSurfaceGraphFrame = GraphFrame(self.graphNotebook, dim=3)
self.errorSurfaceGraphFrame.axes.set_zlabel(r'$error$')
self.graphNotebook.addFrame(self.modelGraphFrame, text="Model")
def statistics(df, dictionaries):
""" фомрмирование статистик """
global stat
report = Toplevel()
qty = StringVar(report)
headers = [item for item in df if item not in ['Цена', 'Билет', 'Время']]
q1 = LabelFrame(report, text='Качественные')
q2 = LabelFrame(report, text='Количественные')
choice = Combobox(q1, values=headers, textvariable=qty)
qty.trace('w', lambda name, index, mode, sv=qty: updateBoxes(sv))
qty.set(headers[0])
choice.current(0)
choice.pack(side=LEFT, padx=5, pady=5)
q1.pack(side=TOP, padx=10, pady=10)
choice2 = Combobox(q2, values=['Цена'])
choice2.pack(side=LEFT, padx=5, pady=5)
choice2.current(0)
choice2.config(state=DISABLED)
q2.pack(side=TOP, padx=10, pady=10)
bframe = Frame(report)
Button(bframe, text='Сформировать', command=lambda frame=df: text_report_old(frame))\
.pack(side=LEFT, padx=10, pady=10)
Button(bframe, text='Закрыть', command=lambda: report.destroy())\
.pack(side=LEFT, padx=10, pady=10)
bframe.pack(side=TOP)
def build_widgets(self):
"Build the various widgets that will be used in the program."
# Create processing frame widgets.
self.processing_frame = LabelFrame(self, text='Processing Mode:')
self.mode_var = StringVar(self, 'encode')
self.decode_button = Radiobutton(self.processing_frame,
text='Decode Cipher-Text',
command=self.handle_radiobuttons,
value='decode',
variable=self.mode_var)
self.encode_button = Radiobutton(self.processing_frame,
text='Encode Plain-Text',
command=self.handle_radiobuttons,
value='encode',
variable=self.mode_var)
self.freeze_var = BooleanVar(self, False)
self.freeze_button = Checkbutton(self.processing_frame,
text='Freeze Key & Primer',
command=self.handle_checkbutton,
offvalue=False,
onvalue=True,
variable=self.freeze_var)
# Create encoding frame widgets.
self.encoding_frame = LabelFrame(self, text='Encoding Options:')
self.chain_size_label = Label(self.encoding_frame, text='Chain Size:')
self.chain_size_entry = Entry(self.encoding_frame)
self.plain_text_label = Label(self.encoding_frame, text='Plain-Text:')
self.plain_text_entry = Entry(self.encoding_frame)
# Create input frame widgets.
self.input_frame = LabelFrame(self, text='Input Area:')
self.input_text = ScrolledText(self.input_frame, **self.TEXT)
# Create output frame widgets.
self.output_frame = LabelFrame(self, text='Output Area:')
self.output_text = ScrolledText(self.output_frame, **self.TEXT)
def __init__(self, parent):
LabelFrame.__init__(self, parent, text="Calculate", borderwidth=5)
self.startCalculationB = Button(self,
text="Start calculation",
width=20)
self.startCalculationB.grid(row=0, column=0, padx=10, pady=5)
self.endCalculationB = Button(self,
text="Cancel calculation",
width=20)
self.endCalculationB.grid(row=1, column=0, padx=10, pady=5)
self.calculationPB = Progressbar(self,
mode="indeterminate",
length=128)
self.calculationPB.grid(row=2, column=0, padx=10, pady=5)
def create_widgets(self):
''' creates GUI for app '''
# expand widget to fill the grid
# self.columnconfigure(1, weight=1, pad=100)
# self.rowconfigure(1, weight=1, pad=20)
lframe = LabelFrame(self, text="Combobox", width=100, height=100)
lframe.grid(row=1, column=1, sticky=N + S + E + W)
self.cbov = StringVar()
cbox = Combobox(lframe, textvariable=self.cbov)
cbox['values'] = ('value1', 'value2', 'value3')
# COMBO.bind('<<ComboboxSelected>>', self.ONCOMBOSELECT)
cbox.current(0)
cbox.grid(row=1, column=1, sticky=E + W, padx=10, pady=20)
def reset_content(self):
self._heading.destroy()
self._heading = Frame(self)
self._inventory_display.destroy()
self._inventory_display = Frame(self)
self._die_field.destroy()
self._die_field = Frame(self)
self._score_field.destroy()
self._score_field = LabelFrame(self)
self._turn_order.destroy()
self._turn_order = Frame(self)
if self.die:
self.die.destroy()
self.die = None
self._load_content()
def get_info(self):
x, y = (self.size[0]/2, self.size[1]/2)
for i in self.info:
label_frame= LabelFrame(self, text="name")
label_frame.pack(fill="y")
for entry in self.info[i]["Entry"]:
frame = Frame(label_frame)
frame.pack(fill="x")
label = Label(label_frame, text=self.info[i]["Entry"][entry], width=6)
label.pack(side="left", anchor="n", padx=5, pady=5)
for text in self.info[i]["Text"]:
frame = Frame(label_frame)
frame.pack(fill="x")
label = Label(label_frame, text=self.info[i]["Text"][text], width=6)
label.pack(side="left", anchor="n", padx=5, pady=5)
window = self.canvas.create_window(x, y, window=label_frame, tag="test")
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
Pipelines = ["CAPmirseq-plus"]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe,
Pipeline,
*Pipelines,
command=self.option_controller)
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
self.add_info(eframe)
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline:")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
Pipelines=["InitialChIPseqQC", "ChIPseq" ]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
om.config()#bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=20,pady=5)
#readtypes = ['Single', 'Paired']
#self.readtype = readtype = StringVar()
#readtype.set(readtypes[0])
#readtype_menu = OptionMenu(eframe, readtype, *readtypes)
#readtype_menu.grid(row=3, column=3, sticky=E, pady=5)
#readtype_label = Label(eframe, text="-end ")
#readtype_label.grid( row=3, column=4, stick=W, pady=5)
self.add_info(eframe)
self.option_controller()
self.peakinfo_fn = 'peakcall.tab'
self.contrast_fn = 'contrast.tab'
def add_pairs( self, parent ) :
if not self.pairs :
self.pairs = LabelFrame(parent, text='Pairs')
self.pairs_text = Text( self.pairs,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold","11")
)
self.pairs_save_button = Button(self.pairs,
text="Save",
command = self.writepair )
self.pairs_load_button = Button(self.pairs,
text="Load",
command = self.readpair )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.pairs_load_button.grid( row=5, column=5, padx=10, pady=5 )
self.pairs_save_button.grid( row=5, column=6, padx=10, pady=5 )
self.pairs_text.grid( row=1, rowspan=3,
column=1, columnspan=7,
padx=5, pady=5 )
self.pairs.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
def _create_label_frame(self):
''' Creates label frame.
'''
self.panel = panel = LabelFrame(self, text=TEXT_FOR_PANEL)
panel.columnconfigure(0, weight=1)
panel.rowconfigure(0, weight=1)
panel.grid(row=1, column=0, padx=5, pady=5, sticky=E + W + S + N)
def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.pairs = None
eframe = self.eframe = LabelFrame(self, text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)
label = Label(eframe,
text="Pipeline") #,fg=textLightColor,bg=baseColor)
label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
PipelineLabels = [
'Initial QC', 'Germline', 'Somatic Tumor-Normal',
'Somatic Tumor-Only'
]
Pipelines = [
"initialqcgenomeseq", "wgslow", 'wgs-somatic',
'wgs-somatic-tumoronly'
]
self.label2pipeline = {k: v for k, v in zip(PipelineLabels, Pipelines)}
PipelineLabel = self.PipelineLabel = StringVar()
Pipeline = self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
#om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
om = OptionMenu(eframe,
PipelineLabel,
*PipelineLabels,
command=self.option_controller)
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3, column=1, sticky=W, padx=10, pady=5)
def on_create_labelframe(self,
frame_name,
col,
row,
colpad,
rowpad,
pos,
pic=None):
if pic is None:
self.panel_control_lf = LabelFrame(master=self.dev_control_panel,
text=frame_name)
self.panel_control_lf.grid(column=col,
row=row,
padx=colpad,
pady=rowpad,
sticky=pos)
else:
self.house_plan_lf = LabelFrame(master=self.dev_control_panel,
text=frame_name)
self.house_plan_lf.grid(column=col,
row=row,
padx=colpad,
pady=rowpad,
sticky=pos)
img = None
try:
img = Image.open(
os.path.join(self.imgpath, str(self.plan[pic])))
print(str(self.plan[pic]))
except IOError:
pass
print(img.mode, '- - - - ', img.size)
img.rotate(90) # Bild Umdrehen
img.thumbnail((self.pic_width, self.pic_height),
Image.ANTIALIAS) # groesse des Bild anpassen
img_lbl = ImageTk.PhotoImage(
image=img
) # ohne dass --> UnboundLocalError: local variable 'img'
# referenced before assignment img_lbl musst als label image zugewiesen werden
# ohne dass - - > _tkinter.TclError: image specification must contain an odd number of elements
self.house_lbl = Label(self.house_plan_lf, image=img_lbl)
self.house_lbl.grid(column=0, row=0, padx=8, pady=5)
self.house_lbl = img_lbl # und diese Zuweisung am Ende
def __init__(self, parent, calculationTimeEstimationFunction):
LabelFrame.__init__(self, parent, text="Isopachs", borderwidth=5)
self.numberOfIsopachs = DEFAULT_NUMBER_OF_ISOPACHS
self.calculationTimeEstimationFunction = calculationTimeEstimationFunction
openButtonImage = tkinter.PhotoImage(file=IMAGE_DIR +
"open_file-icon.gif")
self.tickImage = tkinter.PhotoImage(file=IMAGE_DIR + "tick.gif")
self.loadFromFileButton = Button(self, image=openButtonImage)
self.loadFromFileButton.grid(row=0,
column=0,
padx=self.buttonPadding,
pady=10)
self.loadFromFileButton.bind("<Button-1>", self.loadFromFile)
self.loadFromFileButton.image = openButtonImage
self.addButton = Button(self,
text="Add isopach",
width=self.buttonWidth)
self.addButton.grid(row=0, column=1, padx=self.buttonPadding, pady=10)
self.addButton.bind("<Button-1>", self.addIsopach)
self.removeButton = Button(self,
text="Remove isopach",
width=self.buttonWidth)
self.removeButton.grid(row=0,
column=2,
padx=self.buttonPadding,
pady=10)
self.removeButton.bind("<Button-1>", self.removeIsopach)
self.scrollFrame = ScrollFrame(self)
self.scrollFrame.grid(row=1, column=0, columnspan=3, sticky="NS")
self.innerFrame = self.scrollFrame.innerFrame
self.grid_rowconfigure(1, weight=1)
self.rows = [self.createRow(i) for i in range(self.numberOfIsopachs)]
thicknessM_L = Label(self.innerFrame, text="Thickness (m)")
thicknessM_L.grid(column=1, row=1, padx=5, pady=5)
sqrtAreaKM_L = Label(self.innerFrame, text="\u221AArea (km)")
sqrtAreaKM_L.grid(column=2, row=1, padx=5, pady=5)
include_L = Label(self.innerFrame, text="Use?")
include_L.grid(column=3, row=1, padx=5, pady=5)
def init_ui(self):
self.master.title("Speech Demo")
self.pack(fill=BOTH, expand=True)
label_frame = LabelFrame(self, text="System words")
label_frame.pack(fill=X, padx=40, pady=20)
self.labels = []
rows = 8
cols = 2
for j in range(rows):
for i in range(cols):
k = i + j * cols
label = Label(label_frame, text=labels[k])
label.config(font=("Cambria Math", 20))
label.grid(row=j, column=i, padx=20, pady=10)
self.labels += [label]
self.selected = None
self.after(100, self.ontick)
def __init__(self,parent):
LabelFrame.__init__(self, parent,text="Results", width=825, height=485)
# Terrible kludgy hack to force the app to stay the right size
# Need to work out how to remove
self.grid_propagate(False)
self.resultsDict = None
self.modelType = None
self.currentSegment = 0
# Stats frame
self.statsFrame = StatsFrame(self, self.padX, self.padY)
self.statsFrame.calculate_B.bind("<Button-1>", self._parametersChanged)
self.statsFrame.reset_B.bind("<Button-1>", self._parametersReset)
def onComboBoxSelect(e):
self.currentSegment = e.widget.current()
self._updateDisplay(True)
self.statsFrame.expSeg_CB.bind("<<ComboboxSelected>>", onComboBoxSelect)
# Error frame
self.errorSurfaceFrame = ErrorSurfaceFrame(self)
self.errorSurfaceFrame.errorSurfaceB.bind("<Button-1>", self._displayErrorSurface)
# Graph notebook
self.errorSurfaceSeperator = Separator(self,orient=tkinter.HORIZONTAL)
self.graphNotebook = ImprovedNotebook(self)
self.modelGraphFrame = GraphFrame(self.graphNotebook, dim=2)
self.modelGraphFrame.axes.set_ylabel(r'$thickness(m)$')
self.regressionGraphFrame = GraphFrame(self.graphNotebook, dim=2)
self.regressionGraphFrame.axes.set_ylabel(r'$\ln{(thickness(m))}$')
self.errorSurfaceGraphFrame = GraphFrame(self.graphNotebook, dim=3)
self.errorSurfaceGraphFrame.axes.set_zlabel(r'$error$')
self.graphNotebook.addFrame(self.modelGraphFrame, text="Model")
def __init__(self):
self.BTL = [110, 300, 600, 1200, 2400, 4800, 9600, 14400, 19200, 38400, 56000, 57600, 115200, 128000, 256000] # 波特率下拉列表框内容
self.JYW = ['NONE', 'ODD', 'EVEN', 'MARK', 'SPACE'] # 校验位下拉列表框内容
self.SJW = [5, 6, 7, 8] # 数据位下拉列表内容
self.TZW = [1, 1.5, 2] # 停止位下拉列表内容
self.CKXX = self.read_serial_info()
self.PZMC = ['串口号','波特率','校验位','数据位','停止位']
self.serial_res_hex_bzw = False # 接收数据框内容显示hex标志位
self.serial_sen_hex_bzw = False # 发送数据框内容显示hex标志位
self.radiobutton_sen_ascii_click_count = 1 # 设置发送ASCII单选框点击次数为0
self.radiobutton_sen_hex_click_count = 0 # 设置发送HEX单选框点击次数为0
self.root = Tk(className='串口调试助手') # 创建一个主窗体，并命名为‘串口调试助手’
self.root.protocol('WM_DELETE_WINDOW',self.close_window) # 实现点击窗口关闭按钮，调用self.close_window方法，关闭已经打开的串口，销毁窗口
self.root.geometry('630x580') # 设置窗体大小
self.root.minsize(width=630, height=435) # 这两句语言限制窗口不能随意变化
self.root.maxsize(width=630, height=435)
self.lf = LabelFrame(self.root, text='串口设置') # 创建标签容器，并且命名为‘串口设置’
self.lf.grid(padx=8, pady=10,ipadx=3, ipady=5,row=1,column=1,sticky='n') # 设置标签容器在窗口中的位置
self.text_res_con = LabelFrame(master=self.root,text='接收设置') # 创建标签容器，并命名为接收设置
self.text_res_con.grid(row=1,column=1,sticky='s') # 设置标签容器在窗口中的位置
self.text_sen_con = LabelFrame(master=self.root,text='发送设置') # 创建标签容器，并命名为接收设置
self.text_sen_con.grid(padx=8, pady=10,row=2,column=1,sticky='nesw') # 设置标签容器在窗口中的位置
self.data_rec = LabelFrame(self.root, text='数据日志') # 创建标签容器，并且命名为‘数据日志’
self.data_rec.grid(ipadx=3, ipady=5,row=1, column=2, sticky='e') # 设置标签容器在窗口中的位置
self.y_scroll = Scrollbar(self.data_rec) # 创建接收文本框的Y轴下拉框
self.y_scroll.pack(side=RIGHT,fill=Y) # 确定位置
self.result_text = Text(master=self.data_rec,height=22,width=66,yscrollcommand=self.y_scroll.set) # 创建一个多文本组件，用来显示接收的串口信息，并且配置关联滚轴
self.result_text.pack(side=RIGHT,fill=Y) # 设置多文本组件在窗口中的位置
self.y_scroll.config(command=self.result_text.yview) # 让文本框和滚轴关联起来
self.data_sen = LabelFrame(self.root, text='数据发送') # 创建标签容器，并且命名为‘数据日志’
self.data_sen.grid(ipadx=3, ipady=5,row=2, column=2, sticky='w') # 设置标签容器在窗口中的位置
self.send_text = Text(master=self.data_sen,height=6,width=60) # 创建一个发送文本框
self.send_text.grid(row=1,column=1,sticky='n') # 设置标签容器在窗口中的位置
self.button_send = Button(self.data_sen,text='发送消息',command=self.button_send_serial_click,width=7) # 创建一个发送文本框
self.button_send.grid(row=1,column=2,sticky='NSEW') # 设置串口打开按钮的位置
def servicepanel(server):
''' Draws the panel with the service information '''
global servv, spanel
servicepanel = LabelFrame(win, text = "Service Details")
servicepanel.grid(column = 0, row = 1, padx = 5, pady = 5, sticky = W+E)
services = server.getservices()
scount = 0
for service in services:
servv[service] = StringVar()
Label(servicepanel, text = service + ": ").grid(column = 0, row = scount, sticky = W)
Label(servicepanel, textvariable = servv[service]).grid(column = 1, row = scount, sticky = W)
servicestatus(server, service)
scount += 1
spanel = Label(servicepanel, textvariable = status).grid(column = 0, row = scount + 1, columnspan = 2, sticky = W)
status.set("")
def popup_window( self, text, filename ) :
top = Toplevel()
info = LabelFrame(top, text=text )#"Group Information")
info_text = Text(info,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold","11")
)
def savefunc() :
self.writepaste( filename, info_text )
def loadfunc() :
self.readpaste( filename, info_text )
info_save_button = Button(info,
text="Save",
command = savefunc )
info_load_button = Button(info,
text="Load",
command = loadfunc )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
info_load_button.grid( row=5, column=5, padx=10, pady=5 )
info_save_button.grid( row=5, column=6, padx=10, pady=5 )
info_text.grid(row=1, rowspan=3,
column=1, columnspan=7,
padx=5, pady=5 )
info.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
top.focus_force()
def __init__(self,parent,calculationTimeEstimationFunction):
LabelFrame.__init__(self,parent,text="Isopachs",borderwidth=5)
self.numberOfIsopachs = DEFAULT_NUMBER_OF_ISOPACHS
self.calculationTimeEstimationFunction = calculationTimeEstimationFunction
openButtonImage = tkinter.PhotoImage(file=IMAGE_DIR + "open_file-icon.gif")
self.tickImage = tkinter.PhotoImage(file=IMAGE_DIR + "tick.gif")
self.loadFromFileButton = Button(self,image=openButtonImage)
self.loadFromFileButton.grid(row=0,column=0,padx=self.buttonPadding,pady=10)
self.loadFromFileButton.bind("<Button-1>",self.loadFromFile)
self.loadFromFileButton.image = openButtonImage
self.addButton = Button(self,text="Add isopach",width=self.buttonWidth)
self.addButton.grid(row=0,column=1,padx=self.buttonPadding,pady=10)
self.addButton.bind("<Button-1>",self.addIsopach)
self.removeButton = Button(self,text="Remove isopach",width=self.buttonWidth)
self.removeButton.grid(row=0,column=2,padx=self.buttonPadding,pady=10)
self.removeButton.bind("<Button-1>",self.removeIsopach)
self.scrollFrame = ScrollFrame(self)
self.scrollFrame.grid(row=1,column=0,columnspan=3, sticky="NS")
self.innerFrame = self.scrollFrame.innerFrame
self.grid_rowconfigure(1,weight=1)
self.rows = [self.createRow(i) for i in range(self.numberOfIsopachs)]
thicknessM_L = Label(self.innerFrame, text="Thickness (m)")
thicknessM_L.grid(column=1, row=1, padx=5, pady=5)
sqrtAreaKM_L = Label(self.innerFrame, text="\u221AArea (km)")
sqrtAreaKM_L.grid(column=2, row=1, padx=5, pady=5)
include_L = Label(self.innerFrame, text="Use?")
include_L.grid(column=3, row=1, padx=5, pady=5)
def __init__(self,parent): LabelFrame.__init__(self, parent, borderwidth=0) entryWidth = 7 xPad1 = 30 xPad2 = 5 self.errorXLowerLimitL = Label(self) self.errorXLowerLimitE = CustomEntry(self,width=entryWidth,justify="right") self.errorXLowerLimitL.grid(row=0,column=0,padx=(10,xPad2),pady=5,sticky="W") self.errorXLowerLimitE.grid(row=0,column=1,padx=(xPad2,xPad1),pady=5) self.errorXUpperLimitL = Label(self) self.errorXUpperLimitE = CustomEntry(self,width=entryWidth,justify="right") self.errorXUpperLimitL.grid(row=1,column=0,padx=(10,xPad2),pady=5,sticky="W") self.errorXUpperLimitE.grid(row=1,column=1,padx=(xPad2,xPad1),pady=5) self.errorYLowerLimitL = Label(self) self.errorYLowerLimitE = CustomEntry(self,width=entryWidth,justify="right") self.errorYLowerLimitL.grid(row=0,column=2,padx=(xPad1,xPad2),pady=5,sticky="W") self.errorYLowerLimitE.grid(row=0,column=3,padx=(xPad2,xPad1),pady=5) self.errorYUpperLimitL = Label(self) self.errorYUpperLimitE = CustomEntry(self,width=entryWidth,justify="right") self.errorYUpperLimitL.grid(row=1,column=2,padx=(xPad1,xPad2),pady=5,sticky="W") self.errorYUpperLimitE.grid(row=1,column=3,padx=(xPad2,xPad1),pady=5) self.errorResolutionL = Label(self,text="Resolution: ") self.errorResolutionE = CustomEntry(self,width=entryWidth,justify="right") self.errorResolutionE.insert(0,ERROR_SURFACE_DEFAULT_RESOLUTION) self.errorResolutionL.grid(row=0,column=4,padx=(xPad1,xPad2),pady=5,sticky="W") self.errorResolutionE.grid(row=0,column=5,padx=(xPad2,xPad1),pady=5,sticky="E") self.errorSurfaceB = Button(self,text=" Calculate error surface ") self.errorSurfaceB.grid(row=1,column=4,columnspan=2,padx=(xPad1,xPad1),sticky="EW") self.errorSurfaceB.configure(state=tkinter.ACTIVE)
def add_info( self, parent ) :
if not self.info :
self.info = LabelFrame(parent, text="Sample Information")
self.groups_button = Button(self.info,
text="Set Groups",
command = self.popup_groups )
self.contrasts_button = Button(self.info,
text="Set Contrasts",
command = self.popup_contrasts )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.groups_button.grid( row=5, column=5, padx=10, pady=5 )
self.contrasts_button.grid( row=5, column=6, padx=10, pady=5 )
self.info.grid(row=10,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
def create_widgets(self):
''' Creates all widgets.
'''
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
validate_btn = Button(self, text='Validate weight restrictions',
command=self.on_validate_weights)
validate_btn.grid(row=0, column=0, padx=10, pady=5, sticky=N+W)
panel = LabelFrame(self, text='Weight restrictions')
panel.columnconfigure(0, weight=1)
panel.rowconfigure(0, weight=1)
panel.grid(row=1, column=0,
padx=5, pady=5, sticky=E+W+S+N)
weight_tab_main = VerticalScrolledFrame(panel)
weight_tab_main.grid(row=0, column=0, sticky=E+W+S+N)
weights_tab = weight_tab_main.interior
self.abs_weights = TextForWeights(weights_tab, 'absolute',
'Input1 <= 0.02',
self.current_categories, self.params,
'ABS_WEIGHT_RESTRICTIONS')
self.abs_weights.grid(row=0, column=0, padx=10, pady=5, sticky=N+W)
self.virtual_weights = TextForWeights(weights_tab, 'virtual',
'Input1 >= 0.34',
self.current_categories,
self.params,
'VIRTUAL_WEIGHT_RESTRICTIONS')
self.virtual_weights.grid(row=1, column=0, padx=10, pady=5, sticky=N+W)
self.price_ratio_weights = TextForWeights(weights_tab, 'price ratio',
'Input1/Input2 <= 5',
self.current_categories,
self.params,
'PRICE_RATIO_RESTRICTIONS',
True)
self.price_ratio_weights.grid(row=2, column=0, padx=10, pady=5,
sticky=N+W)
class GenomeSeqFrame( PipelineFrame ) :
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.pairs = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
PipelineLabels = ['Initial QC',
'Germline',
'Somatic Tumor-Normal',
'Somatic Tumor-Only']
Pipelines=["initialqcgenomeseq",
"wgslow",
'wgs-somatic',
'wgs-somatic-tumoronly']
self.label2pipeline = { k:v for k,v in zip(PipelineLabels, Pipelines)}
PipelineLabel = self.PipelineLabel = StringVar()
Pipeline = self.Pipeline = StringVar()
PipelineLabel.set(PipelineLabels[0])
#om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
om = OptionMenu(eframe, PipelineLabel, *PipelineLabels, command=self.option_controller)
om.config()#bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
def option_controller( self, *args, **kwargs ) :
PipelineFrame.option_controller( self )
self.Pipeline.set( self.label2pipeline[self.PipelineLabel.get()] )
print( self.Pipeline.get() )
if self.Pipeline.get() == 'wgs-somatic' :
self.add_pairs( self.eframe )
#self.dry_button.config( state="disabled" )
elif self.Pipeline.get() != 'wgs-somatic' :
self.del_pairs( self.eframe )
#if self.workpath.get() :
# self.dry_button.config( state='active' )
def add_pairs( self, parent ) :
if not self.pairs :
self.pairs = LabelFrame(parent, text='Pairs')
self.pairs_text = Text( self.pairs,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold","11")
)
self.pairs_save_button = Button(self.pairs,
text="Save",
command = self.writepair )
self.pairs_load_button = Button(self.pairs,
text="Load",
command = self.readpair )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.pairs_load_button.grid( row=5, column=5, padx=10, pady=5 )
self.pairs_save_button.grid( row=5, column=6, padx=10, pady=5 )
self.pairs_text.grid( row=1, rowspan=3,
column=1, columnspan=7,
padx=5, pady=5 )
self.pairs.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
def del_pairs( self, parent ) :
if self.pairs :
self.pairs.grid_forget()
def writepair( self ) :
self.writepaste( 'pairs', self.pairs_text )
#self.dry_button.config( state='active' )
def readpair( self ) :
self.readpaste( 'pairs', self.pairs_text )
def make_widgets(frame: ttk.LabelFrame, pane: SubPane) -> SelectorWin:
"""Generate the UI components, and return the base window."""
def for_channel(channel: MusicChannel) -> List[SelItem]:
"""Get the items needed for a specific channel."""
music_list = []
for music in Music.all():
if music.provides_channel(channel):
selitem = SEL_ITEMS[music.id].copy()
selitem.snd_sample = music.get_sample(channel)
music_list.append(selitem)
return music_list
# This gets overwritten when making windows.
last_selected = {
channel: GEN_OPTS.get_val(
'Last_Selected',
'music_' + channel.name.casefold(),
'<NONE>',
) for channel in MusicChannel
}
base_win = WINDOWS[MusicChannel.BASE] = SelectorWin(
TK_ROOT,
for_channel(MusicChannel.BASE),
title=_('Select Background Music - Base'),
desc=_('This controls the background music used for a map. Expand '
'the dropdown to set tracks for specific test elements.'),
has_none=True,
sound_sys=filesystem,
none_desc=_('Add no music to the map at all. Testing Element-specific '
'music may still be added.'),
callback=selwin_callback,
callback_params=[MusicChannel.BASE],
attributes=[
SelAttr.bool('SPEED', _('Propulsion Gel SFX')),
SelAttr.bool('BOUNCE', _('Repulsion Gel SFX')),
SelAttr.bool('TBEAM', _('Excursion Funnel Music')),
SelAttr.bool('TBEAM_SYNC', _('Synced Funnel Music')),
],
)
WINDOWS[MusicChannel.TBEAM] = SelectorWin(
TK_ROOT,
for_channel(MusicChannel.TBEAM),
title=_('Select Excursion Funnel Music'),
desc=_('Set the music used while inside Excursion Funnels.'),
has_none=True,
sound_sys=filesystem,
none_desc=_('Have no music playing when inside funnels.'),
callback=selwin_callback,
callback_params=[MusicChannel.TBEAM],
attributes=[
SelAttr.bool('TBEAM_SYNC', _('Synced Funnel Music')),
],
)
WINDOWS[MusicChannel.BOUNCE] = SelectorWin(
TK_ROOT,
for_channel(MusicChannel.BOUNCE),
title=_('Select Repulsion Gel Music'),
desc=_('Select the music played when players jump on Repulsion Gel.'),
has_none=True,
sound_sys=filesystem,
none_desc=_('Add no music when jumping on Repulsion Gel.'),
callback=selwin_callback,
callback_params=[MusicChannel.BOUNCE],
)
WINDOWS[MusicChannel.SPEED] = SelectorWin(
TK_ROOT,
for_channel(MusicChannel.SPEED),
title=_('Select Propulsion Gel Music'),
desc=_('Select music played when players have large amounts of horizontal velocity.'),
has_none=True,
sound_sys=filesystem,
none_desc=_('Add no music while running fast.'),
callback=selwin_callback,
callback_params=[MusicChannel.SPEED],
)
assert set(WINDOWS.keys()) == set(MusicChannel), "Extra channels?"
# Widgets we want to remove when collapsing.
exp_widgets = [] # type: List[tkinter.Widget]
def toggle_btn_enter(event=None):
toggle_btn['text'] = BTN_EXPAND_HOVER if is_collapsed else BTN_CONTRACT_HOVER
def toggle_btn_exit(event=None):
toggle_btn['text'] = BTN_EXPAND if is_collapsed else BTN_CONTRACT
def set_collapsed():
"""Configure for the collapsed state."""
global is_collapsed
is_collapsed = True
GEN_OPTS['Last_Selected']['music_collapsed'] = '1'
base_lbl['text'] = _('Music: ')
toggle_btn_exit()
# Set all music to the children - so those are used.
set_suggested(WINDOWS[MusicChannel.BASE].chosen_id, sel_item=True)
for wid in exp_widgets:
wid.grid_remove()
def set_expanded():
"""Configure for the expanded state."""
global is_collapsed
is_collapsed = False
GEN_OPTS['Last_Selected']['music_collapsed'] = '0'
base_lbl['text'] = _('Base: ')
toggle_btn_exit()
for wid in exp_widgets:
wid.grid()
pane.update_idletasks()
pane.move()
def toggle(event=None):
if is_collapsed:
set_expanded()
else:
set_collapsed()
pane.update_idletasks()
pane.move()
frame.columnconfigure(2, weight=1)
base_lbl = ttk.Label(frame)
base_lbl.grid(row=0, column=1)
toggle_btn = ttk.Label(frame, text=' ')
toggle_btn.bind('<Enter>', toggle_btn_enter)
toggle_btn.bind('<Leave>', toggle_btn_exit)
toggle_btn.bind('<ButtonPress-1>', toggle)
toggle_btn.grid(row=0, column=0)
for row, channel in enumerate(MusicChannel):
btn = WINDOWS[channel].widget(frame)
if row:
exp_widgets.append(btn)
btn.grid(row=row, column=2, sticky='EW')
for row, text in enumerate([
_('Funnel:'),
_('Bounce:'),
_('Speed:'),
], start=1):
label = ttk.Label(frame, text=text)
exp_widgets.append(label)
label.grid(row=row, column=1, sticky='EW')
if GEN_OPTS.get_bool('Last_Selected', 'music_collapsed', True):
set_collapsed()
else:
set_expanded()
for channel, win in WINDOWS.items():
win.sel_item_id(last_selected[channel])
return base_win
def init_project_frame( self ) :
projframe = Frame(self)
######################
#The Project Entry Form
#
#Current design inherited from others
#is very bad. It should have been made as
#json or dictionary as is in this point
#then the subsequent coding will be much
#eaiser.
#BK
######################
BS=StringVar()
self.eprojectid = eprojectid= StringVar()
self.eorganism = eorganism=StringVar()
self.eanalyst = eanalyst=StringVar()
self.epoc = epoc=StringVar()
self.epi = epi=StringVar()
self.euser = euser=StringVar()
self.eflowcell = eflowcell=StringVar()
self.eplatform = eplatform=StringVar()
eplatform.set("Illumina")
self.technique = technique=StringVar()
self.pipehome = pipehome=StringVar()
pipehome.set(PIPELINER_HOME)
editframe = Frame( self )
editframe.grid( column=0, row=3, columnspan=3 )
projpanel1 = LabelFrame(editframe,text="Project Information")
#,fg=textLightColor,bg=baseColor)
projpanel1.pack( side = TOP, fill=X, padx=10, pady=5, expand=YES )
pipeline_panel = LabelFrame(editframe, text="Global Settings")
pipeline_panel.pack( side=TOP, fill=X, padx=10, pady=5, expand=YES )
l=Label( pipeline_panel, text="Genome:" )
l.grid(row=1,column=3,sticky=W,padx=0,pady=5)
l = Label( pipeline_panel, text="Pipeline Family:" )
l.grid(row=1,column=1,sticky=W,padx=0,pady=5)
annotations=['hg19','mm10','mm9','hg38','GRCh38']
self.annotation = annotation = StringVar()
annotation.set(annotations[0])
#annotation.trace('w', lambda *_ :settargets(annotation) )
om = OptionMenu(pipeline_panel, annotation, *annotations, command=self.set_pipeline)
#, command=lambda _:makejson("refsets"))
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
om.grid(row=1,column=4,sticky=W,padx=10,pady=10)
pfamilys = ['exomeseq', 'rnaseq', 'genomeseq', 'mirseq', 'ChIPseq', 'scrnaseq']
self.pfamily = pfamily = StringVar()
pfamily.set('Select a pipeline')
om = OptionMenu(pipeline_panel, pfamily, *pfamilys, command=self.set_pipeline)
#, command=lambda _:makejson(pfamily.get()))
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
om.grid(row=1,column=2,sticky=W,padx=10,pady=5)
#add_button = Button( pipeline_panel,
# text="Set a pipeline",
# command=self.add_pipeline
# )
#add_button.grid(row=1, column=5, sticky=W, padx=10, pady=5)
self.notebook = notebook = Notebook( editframe )
self.pipelineframe = None #the pipeline frame in the notebook frame!
projpanel2 = Frame(notebook) #,fg=textLightColor,bg=baseColor)
projpanel2.pack( side = LEFT, fill=BOTH, padx=10, pady=5, expand=YES )
notebook.add( projpanel2, text="Project Description" )
notebook.pack( side=LEFT, fill=BOTH, padx=10, pady=5, expand=YES )
Dscrollbar = Scrollbar(projpanel2)
Dscrollbar.grid(row=2,column=4,rowspan=40)
self.description =description= Text(projpanel2,
width=75,
height=28,
#bg=commentBgColor,
#fg=commentFgColor,
font=("nimbus mono bold","10"),
yscrollcommand = Dscrollbar.set)
description.delete("1.0", END)
description.insert(INSERT, "Enter CCBR Project Description and Notes here.")
#description.bind('<FocusOut>',lambda _:makejson("none"))
description.grid(row=2,column=3,sticky="e",padx=10,pady=5)
Dscrollbar['command']=description.yview
L=Label(projpanel1, text="Project Id", anchor="ne" )
#,bg=baseColor,fg=textLightColor)
E = Entry(projpanel1,
bd =2,
width=20,
#bg=entryBgColor,
#fg=entryFgColor,
textvariable=eprojectid
)
#L.pack(pady=5,padx=5)
#E.pack(pady=1,padx=5)
L.grid(row=0, column=0, sticky=W, padx=10, pady=5)
E.grid(row=0, column=2, sticky=W, padx=10, pady=5)
eprojectid.set("project")
#eprojectid.trace('w', makejson)
L2=Label(projpanel1,
text = "(Examples: CCBR-nnn,Labname or short project name)",
anchor="ne"
)#,bg="firebrick",fg="white")
L2.grid(row=0, column=3, padx=10, pady=5, sticky="w")
L=Label( projpanel1,
text="Email address",
anchor="ne")#,bg=baseColor,fg=textLightColor)
E = Entry( projpanel1,
bd =2,
width=20,
#bg=entryBgColor,
#fg=entryFgColor,
textvariable=euser)
L3 = Label(projpanel1,
text ="(Mandatory field: must use @nih.gov email address)",
anchor="ne")
L3.grid(row=1,column=3,padx=10,pady=5,sticky="w")
L.grid(row=1,column=0,sticky=W,padx=10,pady=5)
E.grid(row=1,column=2,sticky=W,padx=10,pady=5)
#euser.trace('w', makejson)
L=Label(projpanel1,text="Flow Cell ID",anchor="ne")
E = Entry(projpanel1, bd =2, width=20, textvariable=eflowcell )#, bg=entryBgColor)
L4=Label( projpanel1,
text="(Examples: FlowCellID, Labname, date or short project name)",
anchor="ne"
)#,bg="firebrick",fg="white")
L4.grid(row=2,column=3,padx=10,pady=5,sticky="w")
L.grid(row=2,column=0,sticky=W,padx=10,pady=5)
E.grid(row=2,column=2,sticky=W,padx=10,pady=5)
eflowcell.set("stats")
#eflowcell.trace('w', makejson)
Projscrollbar = Scrollbar(projframe)
Projscrollbar.grid(row=2,column=4,rowspan=30 )
self.jsonconf = jsonconf = Text( projframe,
width=80,
height=30,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold","11"),
yscrollcommand = Projscrollbar.set)
Projscrollbar['command']=jsonconf.yview
jsonconf.grid(row=3,column=0,sticky="e",padx=10,pady=5)
def _gui():
try:
from tkinter import Tk, ttk, filedialog, messagebox, StringVar, IntVar
from tkinter.ttk import Button, Entry, Frame, Label, LabelFrame, Notebook, Radiobutton, Style
except:
sys.exit("Unable to load tkinter. Aborting.")
def _check_single(): #check the input and accordingly give the output... for the f_single tab
if txt_f_single_entry.get()=="":
lbl_f_single_result.config(text="", style="TLabel")
elif check_afm(txt_f_single_entry.get()):
lbl_f_single_result.config(text="Έγκυρο ΑΦΜ.", style="valid.TLabel")
else:
lbl_f_single_result.config(text="Άκυρο ΑΦΜ.", style="invalid.TLabel")
def _select_input_file():
strv_f_file_input.set(filedialog.askopenfilename(title="Άνοιγμα αρχείου"))
if strv_f_file_input.get() != "" and strv_f_file_output.get() != "":
btn_f_file_submit.config(state="normal")
else: btn_f_file_submit.config(state="disabled")
#TODO a much better mechanism to enable / disable btn_f_file_submit is needed.
def _select_output_file():
strv_f_file_output.set(filedialog.asksaveasfilename(title="Αποθήκευση ως..."))
if strv_f_file_input.get() != "" and strv_f_file_output.get() != "":
btn_f_file_submit.config(state="normal")
else: btn_f_file_submit.config(state="disabled")
def _check_file():#TODO this could / should be merged with the TUI version...
input_filepath = strv_f_file_input.get()
output_filepath = strv_f_file_output.get()
filter_output = intvar_filter_sel.get()
try:
input_file = open(input_filepath, "r")
output_file = open(output_filepath, "w")
except:
messagebox.showerror(title="Σφάλμα", message="Αδυναμία διαχείρησης των αρχείων που ορίσατε.\n\nΠαρακαλώ επιβεβαιώστε πως το αρχείο με τα δεδομένα υπάρχει, πως έχετε δικαιώματα ανάγνωσης, και πως έχετε δικαιώματα εγγραφής στον κατάλογο εξαγωγής των αποτελεσμάτων.")
return
counter = {True:0, False:0}
for entry in input_file:
validation = check_afm(entry.strip())
counter[validation]+=1
if filter_output == 3 and validation == False:
output_file.write(entry)
elif filter_output == 2 and validation == True:
output_file.write(entry)
elif filter_output == 1:
output_file.write(entry.strip() + "\t" + str(validation) + "\n\r")
lbl_f_file_result.config(text="Σύνολο: "+str(counter[True]+counter[False])+"\nΈγκυρα: "+str(counter[True])+"\nΆκυρα: "+str(counter[False]))
#create the window
main_window = Tk()
main_window.title("Έλεγχος εγκυρότητας Α.Φ.Μ. (v 2.0)")
main_window.geometry("600x180")
main_window.minsize(600,180)
#fool arround with styling
style = ttk.Style()
style.configure("valid.TLabel", background="green")
style.configure("empty.TLabel", background="white")
style.configure("invalid.TLabel", background="red")
style.configure("TNotebook", padding = 10)
#create the Notebook
tabs = Notebook(main_window)
f_single = Frame(tabs)
f_file = Frame(tabs)
tabs.add(f_single, text="Μεμονομένα Α.Φ.Μ.")
tabs.add(f_file, text="Λίστα από αρχείο")#add state="disabled" prior to git push until ready
tabs.pack(anchor="nw")
#add some widgets in f_single tab
lbl_f_single_instructions = Label(f_single, text="Εισάγετε έναν ΑΦΜ για έλεγχο")
lbl_f_single_instructions.grid(column=0, row=0)
lbl_f_single_result = Label(f_single, text="", width=10, justify="center")
lbl_f_single_result.grid(column=1, row=0, rowspan=2, sticky="ewns")
txt_f_single_entry = Entry(f_single, width=11)
txt_f_single_entry.focus()
txt_f_single_entry.bind("<KeyRelease>", lambda e: _check_single() )
txt_f_single_entry.grid(column=0,row=1)
#btn_f_single_submit = Button(f_single, text="Έλεγχος", command=_check_single)
#btn_f_single_submit.grid(column=0,row=2)
#add some widgets in f_file tab
lbl_f_file_finput = Label(f_file, text="Άνοιγμα...")
lbl_f_file_finput.grid(column=0, row=0)
strv_f_file_input = StringVar()
txt_f_file_finput = Entry(f_file, textvariable = strv_f_file_input)
txt_f_file_finput.grid(column=1, row=0)
btn_f_file_finput = Button(f_file, text="...", width=3, command=_select_input_file)
btn_f_file_finput.grid(column=2, row=0, sticky="W")
lbl_f_file_foutput = Label(f_file, text="Αποθήκευση ως...")
lbl_f_file_foutput.grid(column=0, row=1)
strv_f_file_output = StringVar()
txt_f_file_foutput = Entry(f_file, textvariable = strv_f_file_output)
txt_f_file_foutput.grid(column=1, row=1)
btn_f_file_foutput = Button(f_file, text="...", width=3, command=_select_output_file)
btn_f_file_foutput.grid(column=2, row=1, sticky="W")
lf_filter = LabelFrame(f_file, text="Επιστροφή")
lf_filter.grid(column=3, row=0, rowspan=2, sticky="ewns")
intvar_filter_sel = IntVar()
rb_filter_all = Radiobutton(lf_filter, text="Όλων", variable=intvar_filter_sel, value=1) #TODO maybe add command
rb_filter_all.pack(anchor="w")
rb_filter_all.invoke()
rb_filter_true = Radiobutton(lf_filter, text="Έγκυρων", variable=intvar_filter_sel, value=2)
rb_filter_true.pack(anchor="w")
rb_filter_false = Radiobutton(lf_filter, text="Άκυρων", variable=intvar_filter_sel, value=3)
rb_filter_false.pack(anchor="w")
lf_result = LabelFrame(f_file, text="Σύνοψη")
lf_result.grid(column=4, row=0, rowspan=2, sticky="ewns")
lbl_f_file_result = Label(lf_result, text="", width=12)#TODO bring results
lbl_f_file_result.pack()
btn_f_file_submit = Button(f_file, text="Επεξεργασία", state="disabled", command=_check_file)
btn_f_file_submit.grid(column=0, row=2, columnspan=3)
btn_main_exit = Button(main_window, text="Έξοδος", command=sys.exit)
btn_main_exit.pack(anchor="se")
main_window.mainloop()
def __init__(self,parent): LabelFrame.__init__(self,parent,text="Model",borderwidth=5) self.selection = tkinter.IntVar() self.exponential = Radiobutton(self,text="Exponential model",variable=self.selection,value=Model.EXP.value,command=self.changeSelection) self.powerlaw = Radiobutton(self,text="Power law model",variable=self.selection,value=Model.POW.value,command=self.changeSelection) self.weibull = Radiobutton(self,text="Weibull model",variable=self.selection,value=Model.WEI.value,command=self.changeSelection) self.exponential.grid(row=0,column=0,sticky="W",padx=10,pady=(self.topPadding,5)) self.powerlaw.grid(row=1,column=0,sticky="W",padx=10,pady=5) self.weibull.grid(row=2,column=0,sticky="W",padx=10,pady=(5,0)) seperator = Separator(self, orient=tkinter.VERTICAL) seperator.grid(row=0, column=1, rowspan=3, sticky="NS", padx=(20,10), pady=(self.topPadding,0)) ## Exponential setup self.expNumberOfSegments_L = Label(self,text="Number of segments: ") self.expNumberOfSegments_E = Entry(self,width=5, justify="right") self.expNumberOfSegments_E.insert(0, settings.EXP_DEFAULT_NUMBER_OF_SEGMENTS) self.expWidgets = [self.expNumberOfSegments_L,self.expNumberOfSegments_E] ## Power law setup self.powProximalLimit_L = Label(self,text="Proximal limit of integration: ") self.powProximalLimit_E = Entry(self,width=5, justify="right") self.powDistalLimit_L = Label(self,text="Distal limit of integration: ") self.powDistalLimit_E = Entry(self,width=5, justify="right") self.powProximalLimit_E.insert(0, settings.POW_DEFAULT_PROXIMAL_LIMIT) self.powDistalLimit_E.insert(0, settings.POW_DEFAULT_DISTAL_LIMIT) self.powWidgets = [self.powProximalLimit_L,self.powProximalLimit_E, self.powDistalLimit_L,self.powDistalLimit_E] ## Weibull setup self.weiNumberOfRuns_L = Label(self,text="Number of runs: ") self.weiNumberOfRuns_E = Entry(self,width=5, justify="right") self.weiIterationsPerRun_L = Label(self,text="Iterations per run: ") self.weiIterationsPerRun_E = Entry(self,width=5, justify="right") self.weiEstimatedTime_L = Label(self,text="Estimated time (s): ") self.weiEstimatedTime_E = CustomEntry(self,width=5, justify="right") self.weiEstimatedTime_E.setUserEditable(False) self.weiLambdaLowerBoundL = Label(self,text="\u03BB lower bound:") self.weiLambdaUpperBoundL = Label(self,text="\u03BB upper bound:") self.weiLambdaLowerBoundE = Entry(self,width=5, justify="right") self.weiLambdaUpperBoundE = Entry(self,width=5, justify="right") self.weiKLowerBoundL = Label(self,text="k lower bound:") self.weiKUpperBoundL = Label(self,text="k upper bound:") self.weiKLowerBoundE = Entry(self,width=5, justify="right") self.weiKUpperBoundE = Entry(self,width=5, justify="right") self.weiNumberOfRuns_E.insert(0, settings.WEI_DEFAULT_NUMBER_OF_RUNS) self.weiIterationsPerRun_E.insert(0, settings.WEI_DEFAULT_ITERATIONS_PER_RUN) self.weiLambdaLowerBoundE.insert(0, settings.WEI_DEFAULT_LAMBDA_LOWER_BOUND) self.weiLambdaUpperBoundE.insert(0, settings.WEI_DEFAULT_LAMBDA_UPPER_BOUND) self.weiKLowerBoundE.insert(0, settings.WEI_DEFAULT_K_LOWER_BOUND) self.weiKUpperBoundE.insert(0, settings.WEI_DEFAULT_K_UPPER_BOUND) self.weiWidgets = [self.weiNumberOfRuns_L,self.weiNumberOfRuns_E, self.weiIterationsPerRun_L,self.weiIterationsPerRun_E, self.weiEstimatedTime_L,self.weiEstimatedTime_E, self.weiLambdaLowerBoundL,self.weiLambdaUpperBoundL,self.weiLambdaLowerBoundE,self.weiLambdaUpperBoundE, self.weiKLowerBoundL,self.weiKUpperBoundL,self.weiKLowerBoundE,self.weiKUpperBoundE] ## General self.currentWidgets = [] self.selection.set(Model.EXP.value) self.changeSelection()
class ExomeSeqFrame( PipelineFrame ) :
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.pairs = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
Pipelines=["initialqc","exomeseq-somatic","exomeseq-germline"]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
#om.config()#bg = widgetBgColor,fg=widgetFgColor)
#om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
targetsL=Label(eframe,
text="Target Capture Kit")
#,fg=textLightColor,bg=baseColor)
targetsL.grid(row=5,column=0,sticky=W,padx=10,pady=5)
targetsE = Entry(eframe,textvariable=self.targetspath, width=50)
if self.genome=="hg19":
self.targetspath.set(
"/data/CCBR_Pipeliner/db/PipeDB/lib/SS_v5_UTRs_hg19.bed" )
else:
self.targetspath.set(
"/data/CCBR_Pipeliner/db/PipeDB/lib/SureSelect_mm10.bed")
targetsE.grid(row=5,column=1,columnspan=6,sticky=W,padx=10,pady=5)
self.targetspath.trace('w', lambda a,b,c,x="targetspath":self.makejson(x))
label = Label (eframe,
text =
"By default, the path to the Agilent V5+UTR targets file is filled in here" )
label.grid(row=6, column=0, columnspan=5, sticky=W, padx=10, pady=5)
def option_controller( self, *args, **kwargs ) :
PipelineFrame.option_controller( self )
if self.Pipeline.get() == 'exomeseq-somatic' :
self.add_pairs( self.eframe )
#self.dry_button.config( state="disabled" )
elif self.Pipeline.get() != 'exomeseq-somatic' :
self.del_pairs( self.eframe )
#if self.workpath.get() :
# self.dry_button.config( state='active' )
def add_pairs( self, parent ) :
if not self.pairs :
self.pairs = LabelFrame(parent, text='Pairs')
self.pairs_text = Text( self.pairs,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold","11")
)
self.pairs_save_button = Button(self.pairs,
text="Save",
command = self.writepair )
self.pairs_load_button = Button(self.pairs,
text="Load",
command = self.readpair )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.pairs_load_button.grid( row=5, column=5, padx=10, pady=5 )
self.pairs_save_button.grid( row=5, column=6, padx=10, pady=5 )
self.pairs_text.grid( row=1, rowspan=3,
column=1, columnspan=7,
padx=5, pady=5 )
self.pairs.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
def del_pairs( self, parent ) :
if self.pairs :
self.pairs.grid_forget()
def writepair( self ) :
self.writepaste( 'pairs', self.pairs_text )
#self.dry_button.config( state='active' )
def readpair( self ) :
self.readpaste( 'pairs', self.pairs_text )
class MiRSeqFrame( PipelineFrame ) :
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
Pipelines=["CAPmirseq-plus"]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
om.config()#bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
self.add_info( eframe )
def add_info( self, parent ) :
if not self.info :
self.info = LabelFrame(parent, text="Sample Information")
self.groups_button = Button(self.info,
text="Set Groups",
command = self.popup_groups )
self.contrasts_button = Button(self.info,
text="Set Contrasts",
command = self.popup_contrasts )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.groups_button.grid( row=5, column=5, padx=10, pady=5 )
self.contrasts_button.grid( row=5, column=6, padx=10, pady=5 )
self.info.grid(row=10,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
def popup_groups( self ) :
self.popup_window( "Groups Information", "groups.tab" )
def popup_contrasts( self ) :
self.popup_window( "Contrasts Information", "contrasts.tab" )
def popup_window( self, text, filename ) :
top = Toplevel()
info = LabelFrame(top, text=text )#"Group Information")
info_text = Text(info,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold","11")
)
def savefunc() :
self.writepaste( filename, info_text )
def loadfunc() :
self.readpaste( filename, info_text )
info_save_button = Button(info,
text="Save",
command = savefunc )
info_load_button = Button(info,
text="Load",
command = loadfunc )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
info_load_button.grid( row=5, column=5, padx=10, pady=5 )
info_save_button.grid( row=5, column=6, padx=10, pady=5 )
info_text.grid(row=1, rowspan=3,
column=1, columnspan=7,
padx=5, pady=5 )
info.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
top.focus_force()
def makejson(self, *args):
#print(args[0])
caller=args[0]
#global PD
#global UnitsBak
#global RGbak
D=dict()
try:
F=open(self.workpath.get()+"/samples","r")
f=F.read().split("\n")
F.close()
for line in f:
L=line.split()
a=L.pop(0)
D[a]=L
samples=D
except:
samples={"na":"na"}
D=dict()
try:
F=open(self.workpath.get()+"/pairs","r")
f=F.read().split()
F.close()
for i in range(0,len(f),2):
# a=f[i].split(".")[0]
# b=f[i+1].split(".")[0]
a=f[i]
b=f[i+1]
D[a+"+"+b]=[a,b]
pairs=D
except:
pairs={"na":"na"}
D=dict()
try:
F=open(self.workpath.get()+"/contrasts.tab","r")
# f=F.read().split('\n')
# F.close()
# D["rsamps"]=f[0].split()
# D["rgroups"]=f[1].split()
# D["rcontrasts"]=f[2].split()
# D["rlabels"]=f[3].split()
f=F.readlines()
F.close()
## sampl=[]
## grp=[]
cont=[]
## lbl=[]
for x in f:
if len(x.split()) == 2:
cont.append(x.split()[0])
cont.append(x.split()[1])
D["rcontrasts"]=cont
# contrasts["rcontrasts"]=cont
contrasts=D
except:
contrasts={"rcontrasts":"na"}
## contrasts={"rsamps":"na","rgroups":"na","rcontrasts":"na","rlabels":"na"}
##------
D=dict()
try:
F=open(self.workpath.get()+"/groups.tab","r")
f=F.readlines()
F.close()
sampl=[]
grp=[]
# cont=[]
lbl=[]
for x in f:
# if len(x.split()) == 4 or len(x.split()) == 3:
if len(x.split()) == 3:
sampl.append(x.split()[0])
grp.append(x.split()[1])
lbl.append(x.split()[2])
D["rsamps"]=sampl
D["rgroups"]=grp
D["rlabels"]=lbl
# D["rcontrasts"]="na"
# contrasts=D
groups=D
except:
# contrasts={"rsamps":"na","rgroups":"na","rcontrasts":"na","rlabels":"na"}
groups={"rsamps":"na","rgroups":"na","rlabels":"na"}
##------
D=dict()
FT = filetype#.get()
# p = Popen("ls "+workpath.get()+"/*."+FT, shell=True, stdin=PIPE, stdout=PIPE, stderr=DEVNULL, close_fds=True)
p = Popen("find "+self.workpath.get()+" -maxdepth 1 -type l -printf '%f\n' ", shell=True, stdin=PIPE, stdout=PIPE, stderr=DEVNULL, close_fds=True)
a = p.stdout.read().decode(encoding='UTF-8').split("\n")
RG=dict()
b=a.pop()
# tkinter.messagebox.showerror("",a)
# if freezeunits.get()=="no":
for i in a:
key=re.sub(".realign","",i.split("/")[-1])
key=re.sub(".bai","",key)
key=re.sub(".bam","",key)
key=re.sub(".sam","",key)
key=re.sub(".recal","",key)
key=re.sub(".dedup","",key)
key=re.sub(".sorted","",key)
key=re.sub(".fin","",key)
key=re.sub(".R[12]","",key)
key=re.sub("_R[12]","",key)
key=re.sub(".fastq","",key)
key=re.sub(".gz","",key)
# key=re.sub("[\._](R[12]\.)*"+FT+"$","",i.split("/")[-1])
# key=re.sub(".R[12]."+FT+"$","",i.split("/")[-1])
# key=re.sub("([._]R[12][._])*([fin|sorted|dedup|recal|realign])*\.{0}$".format(FT),"",i.split("/")[-1])
D[key]=key
RG[key]={'rgsm':key,'rglb':'na','rgpu':'na','rgpl':'ILLUMINA','rgcn':'na'}
units=D
UnitsBak=D
try:
F=open(self.workpath.get()+"/rg.tab","r")
f=F.read().splitlines()
F.close()
for theLine in f:
if not re.match("^ID",theLine):
(rgid,rgsm,rglb,rgpl,rgpu,rgcn)=theLine.split("\t")
RG[rgid]={'rgsm':rgsm,'rglb':rglb,'rgpu':rgpu,'rgpl':rgpl,'rgcn':rgcn}
except:
pass
RGbak=RG
# else:
# units=UnitsBak
# RG=RGbak
#
PD=dict()
smparams=[]
for i in range(len(self.parameters)):
if cp[i].var.get()=="1":
smparams.append(parameters[i])
AD=eval( open( join(PIPELINER_HOME,
self.annotation.get()+".json"
), "r"
).read()
)
SD=AD['references']['rnaseq']['STARDIR']
# tkinter.messagebox.showinfo("initLock","SD={0}".format(SD))
gi = self.global_info
PD={
'project': {
'pfamily': gi.pfamily.get(),
'units': units,
'samples': samples,
'pairs': pairs,
'id': gi.eprojectid.get(),
'pi': gi.epi.get(),
'organism': gi.eorganism.get(),
'analyst': gi.eanalyst.get(),
'poc': gi.epoc.get(),
'pipeline': self.Pipeline.get(),
'version':"1.0",
'annotation': gi.annotation.get(),
'datapath': self.datapath.get(),
'targetspath': self.targetspath.get(),
'filetype': filetype ,
'binset': "standard-bin",
'username': gi.euser.get(),
'flowcellid': gi.eflowcell.get(),
'platform': gi.eplatform.get(),
'custom': customRules,
'efiletype': efiletype,
'workpath': self.workpath.get(),
'batchsize': batchsize,
"smparams": smparams,
"rgid": RG,
"cluster": "cluster_medium.json",
"description": gi.description.get('1.0',END),
"technique" : gi.technique.get(),
"TRIM": "yes",
"groups": groups,
"contrasts": contrasts,
}
}
J=json.dumps(PD, sort_keys = True, indent = 4, ensure_ascii=True)
gi.jsonconf.delete("1.0", END)
gi.jsonconf.insert(INSERT, J)
self.saveproject(gi.jsonconf.get("1.0",END))
def popup_window_contrast(self) :
text = "Comparing ChIP-seq Peaks"
contrast_fn = join(self.workpath.get(),self.contrast_fn)
peakinfo_fn = join(self.workpath.get(),self.peakinfo_fn)
NA='N/A'
try :
groups = list(set([l.split('\t')[-1].strip() for l in open(peakinfo_fn) if l.split('\t')[-1].strip()]))
if len(groups) < 2 :
showwarning( 'WARNING!', "More than one groups need to be fefined in Peak Information File!" )
print( 'groups:', groups )
return
except IOError :
showerror( 'Error', "Did you set peak information?" )
print('Error:', 'Cannot process peakcall.tab file:')
return
top = Toplevel()
info = LabelFrame(top, text=text )#"Group Information")
print( groups )
contrast_vars = []
contrast_menus = []
n = 0
groups.insert(0, NA)
for i in range( int((len(groups)-1)*(len(groups)-2)/2) ):
n = n + 1
v1, v2 = StringVar(), StringVar()
contrast_vars.append( [v1, v2] )
o1, o2 = OptionMenu(info, v1, *groups), OptionMenu(info, v2, *groups)
contrast_menus.append( [o1, o2] )
v1.set(NA)
v2.set(NA)
vslabel = Label(info, text=" VS ")
o1.grid( row=n, column=0, padx=4, pady=1 )
o2.grid( row=n, column=2, padx=4, pady=1 )
vslabel.grid( row=n, column=1, padx=4, pady=1 )
def savefunc() :
info_text = StringIO()
for v1, v2 in contrast_vars :
v1 = v1.get() if v1.get() != NA else ""
v2 = v2.get() if v2.get() != NA else ""
if v1 and v2 :
pass
elif v1 or v2 :
showerror( 'Error', "None or Both columns should be selected!" )
return
else:
continue
print( v1, v2, file=info_text, sep="\t" )
fp = open( contrast_fn, 'w' )
fp.write( info_text.getvalue() )
fp.close()
def loadfunc() :
#self.readpaste( filename, info_text )
for i, l in enumerate(open( contrast_fn )) :
v1, v2 = l.split('\t')
v1 = v1.strip()
v2 = v2.strip()
if v1 :
try : assert v1 in groups
except :
showwarning('WARNING', 'Group name is not in the selection list!' )
print( 'v1:',v1 )
print( 'group:', groups )
continue
if v2 :
try: assert v2 in groups
except :
showwarning('WARNING', 'Group name is not in the selection list!' )
print( 'v2:',v2 )
print( 'group:', groups )
continue
contrast_vars[i][0].set(v1)
contrast_vars[i][1].set(v2)
def clearfunc() :
for v1, v2 in contrast_vars :
v1.set(NA)
v2.set(NA)
info_clear_button = Button(top,
text="Clear",
command = clearfunc )
info_save_button = Button(top,
text="Save",
command = savefunc )
info_load_button = Button(top,
text="Load",
command = loadfunc )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
info_clear_button.grid( row=5, column=3, padx=10, pady=5 )
info_load_button.grid( row=5, column=4, padx=10, pady=5 )
info_save_button.grid( row=5, column=5, padx=10, pady=5 )
info.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
top.focus_force()
def popup_window_peakinfo( self, text, filename ) :
NA = 'N/A'
selections = [fn.split('.R1.fastq.gz')[0]
for fn in self.datafiles if fn.endswith( ".R1.fastq.gz" )]
################################
#check availablity of the files before moving on!
if not selections :
showerror( "No FASTQ files available matching the pattern *.R1.fastq.gz" )
return
################################
selections.insert(0, NA) #Adding N/A for the groups where no input is available
groups = ['Grp%d'%i for i in range(1, len(selections)+1)]
##checking for debugging purpose
print( selections )
assert len(selections) == len(set(selections))
##
top = Toplevel()
info = LabelFrame(top, text=text )#"Group Information")
chip_vars = [ StringVar() for s in selections[1:] ]
input_vars = [ StringVar() for s in selections[1:] ]
group_vars = [ StringVar() for s in selections[1:] ]
chip_menus = [OptionMenu(info,var,*selections) for var in chip_vars]
input_menus = [OptionMenu(info,var,*selections) for var in input_vars]
group_menus = [OptionMenu(info,var,*groups) for var in group_vars]
group_entries = [Entry(info, bd=2, width=8, textvariable=var) for var in group_vars]
chiplabel = Label(info, text= "ChIP Names")
inputlabel = Label(info, text="Input Names")
grouplabel = Label(info, text="Group Names")
chiplabel.grid( row = 0, column = 1, padx=4, pady=1)
inputlabel.grid( row = 0, column = 2, padx=4, pady=1)
grouplabel.grid( row = 0, column = 3, padx=4, pady=1 )
for i, (chvar, invar) in enumerate(zip(chip_vars, input_vars)) :
chvar.set(selections[0])
invar.set(selections[0])
chip_menus[i].grid( row = i+1, column = 1, padx=4, pady=1 )
input_menus[i].grid( row = i+1, column = 2, padx=4, pady=1 )
group_entries[i].grid( row = i+1, column = 3, padx=4, pady=1 )
group_menus[i].grid( row = i+1, column = 4, padx=4, pady=1 )
def savefunc() :
info_text = StringIO()
for v1, v2, v3 in zip( chip_vars, input_vars, group_vars ) :
v1 = v1.get().strip() if v1.get().strip() != NA else ""
if not v1 :
continue
v2 = v2.get().strip() if v2.get().strip() != NA else ""
v3 = v3.get().strip() if v3.get().strip() != NA else ""
if not v3 :
showerror( "Error", "Missing Replicate group name detected.\nReplicate group names should be given!" )
print( "Error", "Missing Replicate group name detected.\nReplicate group names should be given!" )
return
print( v1, v2, v3, file=info_text, sep="\t" )
fp = open( filename, 'w' )
fp.write( info_text.getvalue() )
fp.close()
def loadfunc() :
if not exists(filename) :
print( filename, 'does not exists!' )
return
for i, l in enumerate(open( filename )) :
v1, v2, v3 = l.split('\t')
if v1 :
try : assert v1 in selections
except :
showwarning('WARNING', 'ChIP name is not in the selection list!' )
print( 'v1:',v1 )
print( 'selection:', selection )
continue
if v2 :
try: assert v2 in selections
except :
showwarning('WARNING', 'Input name is not in the selection list!' )
print( 'v2:',v2 )
print( 'selection:', selection )
return
chip_vars[i].set(v1.strip())
input_vars[i].set(v2.strip())
group_vars[i].set(v3.strip())
def clearfunc() :
for i, (chvar, invar, grvar) in enumerate(zip(chip_vars, input_vars, group_vars)) :
chvar.set(selections[0])
invar.set(selections[0])
grvar.set('')
info_clear_button = Button(top,
text="Clear",
command = clearfunc )
info_save_button = Button(top,
text="Save",
command = savefunc )
info_load_button = Button(top,
text="Load",
command = loadfunc )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
info_clear_button.grid( row=5, column=3, padx=10, pady=5 )
info_load_button.grid( row=5, column=4, padx=10, pady=5 )
info_save_button.grid( row=5, column=5, padx=10, pady=5 )
info.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
top.focus_force()
class MarkovDemo(Frame):
"MarkovDemo(master=None, **kw) -> MarkovDemo instance"
TEXT = dict(height=2, width=46, wrap=WORD) # Text Options
GRID = dict(padx=5, pady=5) # Grid Options
# Initialize a MarkovDemo instance with a GUI for interaction.
def __init__(self, master=None, **kw):
"Initialize the MarkovDemo instance's widgets and settings."
super().__init__(master, **kw)
self.build_widgets()
self.place_widgets()
self.setup_widgets()
self.grid_rowconfigure(2, weight=1)
self.grid_rowconfigure(3, weight=1)
self.grid_columnconfigure(0, weight=1)
self.key = self.primer = None
def build_widgets(self):
"Build the various widgets that will be used in the program."
# Create processing frame widgets.
self.processing_frame = LabelFrame(self, text='Processing Mode:')
self.mode_var = StringVar(self, 'encode')
self.decode_button = Radiobutton(self.processing_frame,
text='Decode Cipher-Text',
command=self.handle_radiobuttons,
value='decode',
variable=self.mode_var)
self.encode_button = Radiobutton(self.processing_frame,
text='Encode Plain-Text',
command=self.handle_radiobuttons,
value='encode',
variable=self.mode_var)
self.freeze_var = BooleanVar(self, False)
self.freeze_button = Checkbutton(self.processing_frame,
text='Freeze Key & Primer',
command=self.handle_checkbutton,
offvalue=False,
onvalue=True,
variable=self.freeze_var)
# Create encoding frame widgets.
self.encoding_frame = LabelFrame(self, text='Encoding Options:')
self.chain_size_label = Label(self.encoding_frame, text='Chain Size:')
self.chain_size_entry = Entry(self.encoding_frame)
self.plain_text_label = Label(self.encoding_frame, text='Plain-Text:')
self.plain_text_entry = Entry(self.encoding_frame)
# Create input frame widgets.
self.input_frame = LabelFrame(self, text='Input Area:')
self.input_text = ScrolledText(self.input_frame, **self.TEXT)
# Create output frame widgets.
self.output_frame = LabelFrame(self, text='Output Area:')
self.output_text = ScrolledText(self.output_frame, **self.TEXT)
def place_widgets(self):
"Place the widgets where they belong in the MarkovDemo frame."
# Locate processing frame widgets.
self.processing_frame.grid(sticky=EW, **self.GRID)
self.decode_button.grid(row=0, column=0, **self.GRID)
self.encode_button.grid(row=0, column=1, **self.GRID)
self.freeze_button.grid(row=0, column=2, **self.GRID)
# Locate encoding frame widgets.
self.encoding_frame.grid(sticky=EW, **self.GRID)
self.chain_size_label.grid(row=0, column=0, sticky=W, **self.GRID)
self.chain_size_entry.grid(row=0, column=1, sticky=EW, **self.GRID)
self.plain_text_label.grid(row=1, column=0, sticky=W, **self.GRID)
self.plain_text_entry.grid(row=1, column=1, sticky=EW, **self.GRID)
self.encoding_frame.grid_columnconfigure(1, weight=1)
# Locate input frame widgets.
self.input_frame.grid(sticky=NSEW, **self.GRID)
self.input_text.grid(sticky=NSEW, **self.GRID)
self.input_frame.grid_rowconfigure(0, weight=1)
self.input_frame.grid_columnconfigure(0, weight=1)
# Locate output frame widgets.
self.output_frame.grid(sticky=NSEW, **self.GRID)
self.output_text.grid(sticky=NSEW, **self.GRID)
self.output_frame.grid_rowconfigure(0, weight=1)
self.output_frame.grid_columnconfigure(0, weight=1)
def setup_widgets(self):
"Setup each widget's configuration for the events they handle."
self.input_text.bind('<Key>', self.handle_key_events)
self.input_text.bind('<Control-Key-a>', self.handle_control_a)
self.input_text.bind('<Control-Key-/>', lambda event: 'break')
self.output_text['state'] = DISABLED
self.output_text.bind('<Control-Key-a>', self.handle_control_a)
self.output_text.bind('<Control-Key-/>', lambda event: 'break')
########################################################################
# Take care of any special event needing dedicated processing.
def handle_radiobuttons(self):
"Change the interface based on the encoding / decoding setting."
if self.encrypting:
self.freeze_button.grid()
if not self.freeze_var.get():
self.encoding_frame.grid()
else:
self.freeze_button.grid_remove()
if not self.freeze_var.get():
self.encoding_frame.grid_remove()
self.handle_key_events(None)
def handle_checkbutton(self):
"Change the interface based on the key / primer freeze setting."
if self.freeze_var.get():
self.encoding_frame.grid_remove()
else:
self.encoding_frame.grid()
def handle_key_events(self, event):
"Schedule refreshing the output area after an input area event."
if event is None or event.char and event.state | 0o11 == 0o11:
self.after_idle(self.refresh)
@staticmethod
def handle_control_a(event):
"Select all text in the widget associated with the given event."
event.widget.tag_add(SEL, 1.0, END + '-1c')
return 'break'
########################################################################
# Handle interface's updates when either encoding or decoding.
def refresh(self):
"Refresh the output based on the value of the input."
text = self.input_text.get(1.0, END + '-1c')
if not text:
self.output = text
elif self.encrypting:
self.encode(text)
else:
self.decode(text)
def output(self, value):
"Set the text in the output area to the string value."
self.output_text['state'] = NORMAL
self.output_text.delete(1.0, END)
self.output_text.insert(END, value)
if self.encrypting and self.freeze_var.get():
self.output_text.see(END)
self.output_text['state'] = DISABLED
output = property(fset=output, doc='Output area property.')
@property
def chain_size(self):
"Chain size for the Markov chains used when encrypting."
try:
value = ast.literal_eval(self.chain_size_entry.get())
assert isinstance(value, int) and 2 <= value <= 256
return value
except:
self.chain_size_entry.delete(0, END)
self.chain_size_entry.insert(0, '2')
return 2
@property
def plain_text(self):
"Plain text or ignored characters in encryption process."
try:
value = self.repr_to_obj(self.plain_text_entry.get(), '')
assert isinstance(value, str)
return value
except:
self.plain_text_entry.delete(0, END)
return ''
########################################################################
# Encrypt a string for display in the interface's output area.
def encode(self, string):
"Encode the string and show the cipher-text in the output."
try:
cipher = self.build_cipher(string)
except ValueError:
self.output = ''
except:
self.output = traceback.format_exc()
else:
self.output = self.build_header() + '\n\n' + cipher
def build_cipher(self, string):
"Build cipher-text based on plain-text and return answer."
if self.key and self.freeze_var.get():
cipher, primer = me.encrypt_str(string, self.key, self.primer)
else:
args = string, self.chain_size, self.plain_text
cipher, self.key, self.primer = me.auto_encrypt_str(*args)
return cipher
def build_header(self):
"Build header from key and primer values in current use."
header = '\n'.join(map(self.bytes_to_repr, self.key.data))
header += '\n' + self.bytes_to_repr(self.primer.data)
return header
########################################################################
# Decrypt a string for display in the interface's output area.
def decode(self, string):
"Decode encrypted message and display plain-text in output."
try:
cipher = self.extract_keys(string)
text = self.extract_text(cipher)
except ValueError:
self.output = ''
except:
self.output = traceback.format_exc()
else:
self.output = text
def extract_keys(self, string):
"Extract keys to decryption and return the cipher-text area."
header, cipher = string.split('\n\n', 1)
*key, primer = map(self.repr_to_obj, header.split('\n'))
self.key, self.primer = me.Key(tuple(key)), me.Primer(primer)
return cipher
def extract_text(self, string):
"Extract text message from string using built key and primer."
text, primer = me.decrypt_str(string, self.key, self.primer)
return text
########################################################################
# Provide some special methods to simplify the program's code.
@property
def encrypting(self):
"Encrypting boolean stating current operations mode."
return {'encode': True, 'decode': False}[self.mode_var.get()]
@staticmethod
def bytes_to_repr(obj):
"Convert bytes object into suitable representation."
if not isinstance(obj, bytes):
raise TypeError('Object must be a bytes instance!')
return repr(obj)[2:-1]
@staticmethod
def repr_to_obj(string, prefix='b'):
"Convert representation into an equivalent object."
for template in '{}"{}"', "{}'{}'":
try:
return ast.literal_eval(template.format(prefix, string))
except:
pass
raise ValueError('Cannot convert {!r} to object!'.format(string))
@classmethod
def main(cls):
"Create context for demo and run a test instance."
NoDefaultRoot()
root = Tk()
root.minsize(420, 330)
root.title('Markov Demo 2')
test = cls(root)
test.grid(sticky=NSEW)
root.grid_rowconfigure(0, weight=1)
root.grid_columnconfigure(0, weight=1)
root.mainloop()
def __init__(self,parent, padX, padY):
LabelFrame.__init__(self,parent,borderwidth=0)
# Total volume
self.totalEstimatedVolume_L = Label(self,text="Estimated total volume (km\u00B3): ")
self.totalEstimatedVolume_E = CustomEntry(self,width=10,justify="right")
self.totalEstimatedVolume_E.setUserEditable(False)
self.totalEstimatedVolume_E.grid(row=0,column=1,padx=10,pady=padY,sticky="E")
self.totalEstimatedVolume_L.grid(row=0,column=0,sticky="W",padx=10)
# Relative squared error
self.relativeSquaredError_L = Label(self,text="Mean relative squared error: ")
self.relativeSquaredError_L.grid(row=1,column=0,sticky="W",padx=10,pady=padY)
self.relativeSquaredError_E = CustomEntry(self,width=10,justify="right")
self.relativeSquaredError_E.grid(row=1,column=1,padx=10,sticky="E")
self.relativeSquaredError_E.setUserEditable(False)
# Equation
self.equation_L = Label(self,text="Equation: ")
self.equation_E = CustomEntry(self,width=10,justify="right")
self.equation_E.setUserEditable(False)
# General
self.parameters_L = Label(self,text="Parameters:")
self.calculate_B = Button(self,text="Recalculate",width=12)
self.reset_B = Button(self,text="Reset",width=8)
#########
## Exp ##
#########
# Segment combobox
self.expSeg_CB = Combobox(self,state="readonly",width=10)
# Segment volume
self.expSegVolume_L = Label(self,text="Segment volume (km\u00B3): ")
self.expSegVolume_E = CustomEntry(self, width=10, justify="right")
self.expSegVolume_E.setUserEditable(False)
# Segment start
self.expSegStartLimit_L = Label(self,text="Start of segment: ")
self.expSegStartLimit_E = NumericEntry(self, width=10, justify="right")
self.expSegStartLimit_E.setSF(NUMBER_OF_SF)
# Segment end
self.expSegEndLimit_L = Label(self,text="End of segment: ")
self.expSegEndLimit_E = NumericEntry(self, width=10, justify="right")
self.expSegEndLimit_E.setSF(NUMBER_OF_SF)
# Segment coefficient
self.expSegCoefficent_L = Label(self,text="Segment coefficient, c: ")
self.expSegCoefficent_E = NumericEntry(self, width=10, justify="right")
self.expSegCoefficent_E.setSF(NUMBER_OF_SF)
# Segment exponent
self.expSegExponent_L = Label(self,text="Segment exponent, m: ")
self.expSegExponent_E = NumericEntry(self, width=10, justify="right")
self.expSegExponent_E.setSF(NUMBER_OF_SF)
#########
## Pow ##
#########
# Coefficient
self.powCoefficient_L = Label(self,text="Coefficient, c: ")
self.powCoefficient_E = NumericEntry(self,width=10, justify="right")
self.powCoefficient_E.setSF(NUMBER_OF_SF)
# Exponent
self.powExponent_L = Label(self,text="Exponent, m: ")
self.powExponent_E = NumericEntry(self,width=10, justify="right")
self.powExponent_E.setSF(NUMBER_OF_SF)
# Proximal limit
self.powProximalLimit_L = Label(self,text="Proximal limit: ")
self.powProximalLimit_E = NumericEntry(self,width=10, justify="right")
self.powProximalLimit_E.setSF(NUMBER_OF_SF)
# Distal limit
self.powDistalLimit_L = Label(self,text="Distal limit: ")
self.powDistalLimit_E = NumericEntry(self,width=10, justify="right")
self.powDistalLimit_E.setSF(NUMBER_OF_SF)
# Suggested proximal limit
self.powSuggestedProximalLimit_L = Label(self,text="Suggested proximal limit: ")
self.powSuggestedProximalLimit_E = CustomEntry(self,width=10, justify="right")
self.powSuggestedProximalLimit_E.setUserEditable(False)
#########
## Wei ##
#########
# lambda
self.weiLambdaL = Label(self,text="Estimated \u03BB: ")
self.weiLambdaE = NumericEntry(self,width=10, justify="right")
self.weiLambdaE.setSF(NUMBER_OF_SF)
# k
self.weiKL = Label(self,text="Estimated k: ")
self.weiKE = NumericEntry(self,width=10, justify="right")
self.weiKE.setSF(NUMBER_OF_SF)
# theta
self.weiThetaL = Label(self,text="Estimated \u03B8: ")
self.weiThetaE = NumericEntry(self,width=10, justify="right")
self.weiThetaE.setSF(NUMBER_OF_SF)
self.components = {
Model.EXP : [
self.expSeg_CB,
self.expSegVolume_L, self.expSegVolume_E,
self.expSegStartLimit_L, self.expSegStartLimit_E,
self.expSegEndLimit_L, self.expSegEndLimit_E,
self.expSegCoefficent_L, self.expSegCoefficent_E,
self.expSegExponent_L, self.expSegExponent_E
],
Model.POW : [
self.powCoefficient_L, self.powCoefficient_E,
self.powExponent_L, self.powExponent_E,
self.powProximalLimit_L, self.powProximalLimit_E,
self.powDistalLimit_L, self.powDistalLimit_E,
self.powSuggestedProximalLimit_L, self.powSuggestedProximalLimit_E
],
Model.WEI : [
self.weiLambdaL, self.weiLambdaE,
self.weiKL, self.weiKE,
self.weiThetaL, self.weiThetaE,
],
}
class ChIPSeqFrame( PipelineFrame ) :
def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
self.info = None
eframe = self.eframe = LabelFrame(self,text="Options")
#,fg=textLightColor,bg=baseColor)
eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
Pipelines=["ChIPSeq"]
Pipeline = self.Pipeline = StringVar()
Pipeline.set(Pipelines[0])
om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
om.config()#bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
#om.pack(side=LEFT,padx=20,pady=5)
om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
label.grid(row=6, column=0, columnspan=5, sticky=W, padx=10, pady=5)
self.add_info(eframe)
'''
def set_data_directory( self ):
fname = askdirectory( initialdir = USER_HOME,
title="Select Data Directory")
self.datapath.set(fname)
#count number
self.data_count['text'] = str(
len([fn for fn in listdir(fname) if fn.endswith(filetype) or fn.endswith('.fastq')] )
)
print( "Found", self.data_count['text'], filetype, "files!" )
'''
def add_info( self, parent ) :
if not self.info :
self.info = LabelFrame(parent, text='Peak Call Info')
self.info_text = Text( self.info,
width=50,
height=8,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold","11")
)
self.info_save_button = Button(self.info,
text="Save",
command = self.writeinfo )
self.info_load_button = Button(self.info,
text="Load",
command = self.readinfo )
#self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
#self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )
self.info_load_button.grid( row=5, column=5, padx=10, pady=5 )
self.info_save_button.grid( row=5, column=6, padx=10, pady=5 )
self.info_text.grid( row=1, rowspan=3,
column=1, columnspan=7,
padx=5, pady=5 )
self.info.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
def writeinfo( self ) :
self.writepaste( 'peakcallinfo.csv', self.info_text )
def readinfo( self ) :
self.readpaste( 'peakcallinfo.csv', self.info_text )
