def make_gdna_frame(self, parent):
gdna_f = Frame(parent, borderwidth=1, relief="sunken")
self.gdna = IntVar(gdna_f, value=1)
cb = Checkbutton(gdna_f, variable=self.gdna, text="get gDNA sequence")
cb.bind("<Button-1>", self.check_box_callback)
cb.grid(row=1, column=1, sticky="W", columnspan=2)
self.flank = IntVar(gdna_f, value=0)
Entry(gdna_f, width=6, text=self.flank,
justify="right").grid(row=2, column=1, sticky="W")
Label(gdna_f, text="bp flanking gene").grid(row=2,
column=2,
sticky="W")
self.check_box_callback(cb)
return gdna_f
def __init__(self, parent, funnel, index, command_stack):
tk.Frame.__init__(self, parent, borderwidth=4, relief="raised")
Subscriber.__init__(self, funnel)
Observable.__init__(self)
self._funnel = funnel
self._command_stack = command_stack
self._active_var = tk.IntVar()
self._active_var.trace_add("write", self._switch_active)
self._y_var = tk.StringVar()
self._y_var.set(0)
self._y_var.trace_add("write", self._set_position)
self._x_var = tk.StringVar()
self._x_var.set(0)
self._x_var.trace_add("write", self._set_position)
self._oval_var = tk.IntVar()
self._oval_var.trace_add("write", self._switch_oval)
self._update()
self.bind("<Button-1>", self._on_click)
is_active = Checkbutton(
self, text=f"Funnel n°{index}: ", variable=self._active_var)
is_active.grid(columnspan=3)
is_active.bind("<FocusIn>", self._on_get_focus)
is_active.bind("<FocusOut>", self._on_lost_focus)
x_label = Label(self, text="\u21d5", anchor=tk.CENTER)
x_label.grid(sticky=tk.E + tk.W)
x_label.bind("<Button-1>", self._on_click)
self.x_entry = Entry(self, textvariable=self._x_var, width=6)
self.x_entry.grid(row=2, column=0, sticky=tk.W + tk.E)
self.x_entry.bind("<FocusIn>", self._on_get_focus)
self.x_entry.bind("<FocusOut>", self._on_lost_focus)
y_label = Label(self, text="\u21d4", anchor=tk.CENTER)
y_label.grid(row=1, column=1, sticky=tk.E+tk.W)
y_label.bind("<Button-1>", self._on_click)
self.y_entry = Entry(self, textvariable=self._y_var, width=6)
self.y_entry.grid(row=2, column=1, sticky=tk.W + tk.E)
self.y_entry.bind("<FocusIn>", self._on_get_focus)
self.y_entry.bind("<FocusOut>", self._on_lost_focus)
is_oval = Checkbutton(self, text="Is Oval", variable=self._oval_var)
is_oval.grid(row=1, column=2)
is_oval.bind("<FocusIn>", self._on_get_focus)
is_oval.bind("<FocusOut>", self._on_lost_focus)
force_centerline = Button(
self, text="force on centerline", command=self._force_centerline)
force_centerline.grid(row=2, column=2)
self.columnconfigure(0, weight=1)
self.columnconfigure(1, weight=1)
self.columnconfigure(2, weight=1)
def make_cdna_frame(self, parent):
cdna_f = Frame(parent, borderwidth=1, relief="sunken")
self.cdna = IntVar(cdna_f, value=1)
cb = Checkbutton(cdna_f, variable=self.cdna, text="get cDNA sequence")
cb.bind("<Button-1>", self.check_box_callback)
cb.grid(row=1, column=1, sticky="W")
self.splice = StringVar(cdna_f)
[Radiobutton(cdna_f,text=label[1],variable=self.splice,value=label[0])\
.grid(column=1,row=num+2,sticky="W") for num,label in \
enumerate(self.splice_values)]
self.splice.set("cds")
self.check_box_callback(cb)
return cdna_f
def make_feature_frame(self, parent):
primer_f = Frame(parent, borderwidth=1, relief="sunken")
self.get_primers = IntVar(primer_f, 0)
cb = Checkbutton(primer_f,
text="Import primers from file",
variable=self.get_primers)
cb.bind("<Button-1>", self.check_box_callback)
cb.grid(row=1, column=1, sticky="SNW", columnspan=3)
if self.default_primer_path and self.default_primer_path.exists():
self.primer_path = self.default_primer_path
else:
self.primer_path = plp().home().resolve()
primer_path_view = StringVar(primer_f, "")
self.text_view_limit(self.primer_path,
primer_path_view,
width=self.width)
Label(primer_f, text="Select primer file:",
justify="left").grid(row=2,
column=1,
sticky="SNEW",
columnspan=2)
kw = {
"method": tfd.askopenfilename,
"path_var": "primer_path",
"width": self.width,
"title": "Select primer file",
"str_var": primer_path_view
}
Button(primer_f,
textvariable=primer_path_view,
command=self.path_callback(**kw),
width=35,
style="B.TButton").grid(row=2,
column=3,
sticky="SNEW",
columnspan=3)
Label(primer_f, text="Allow up to", justify="left").grid(row=3,
column=1,
sticky="NWS")
self.mismatch = IntVar(primer_f, "0")
Entry(primer_f, textvariable=self.mismatch, justify="center",
width=3).grid(row=3, column=2, sticky="NWS")
Label(primer_f, text="mismatches in primers",
justify="left").grid(row=3, column=3, sticky="NWS")
self.check_box_callback(cb)
return primer_f
def make_auto_open(self, parent):
auto_f = Frame(parent)
self.do_open = IntVar(auto_f, value=1)
cb = Checkbutton(
auto_f,
variable=self.do_open,
text="Automatically open files after annotation complete")
cb.bind("<Button-1>", self.check_box_callback)
cb.grid(row=1, column=1, sticky="NW", columnspan=3)
if self.default_program_path and self.default_program_path.exists():
self.program_path = self.default_program_path
else:
self.program_path = plp.home()
for i in self.program_locations:
if i.exists():
self.program_path = i
program_path_view = StringVar(auto_f, "")
self.text_view_limit(self.program_path,
program_path_view,
width=self.width)
Label(auto_f, text="Select ApE program:",
justify="left").grid(row=2, column=1, sticky="SNW", columnspan=2)
kw = {
"method": tfd.askopenfilename,
"path_var": "program_path",
"title": "Select ApE program",
"str_var": program_path_view,
"width": self.width
}
Button(auto_f,
textvariable=program_path_view,
command=self.path_callback(**kw),
width=35,
style="B.TButton").grid(row=2,
column=3,
sticky="NSW",
columnspan=3)
self.check_box_callback(cb)
return auto_f
def __init__(self, parent, funnel, index, command_stack):
tk.Frame.__init__(self, parent, borderwidth=4, relief="raised")
Subscriber.__init__(self, funnel)
Observable.__init__(self)
self._funnel = funnel
self._command_stack = command_stack
self._active_var = tk.IntVar()
self._active_var.trace_add("write", self._switch_active)
self._position_var = tk.StringVar()
self._position_var.trace_add("write", self._set_position)
self._oval_var = tk.IntVar()
self._oval_var.trace_add("write", self._switch_oval)
self._update()
self.bind("<Button-1>", self._on_click)
is_active = Checkbutton(self,
text=f"Funnel n°{index}: ",
variable=self._active_var)
is_active.grid(columnspan=3)
is_active.bind("<FocusIn>", self._on_get_focus)
is_active.bind("<FocusOut>", self._on_lost_focus)
pos_label = Label(self, text=" Position: ")
pos_label.grid(sticky=tk.E)
pos_label.bind("<Button-1>", self._on_click)
self._pos_entry = Entry(self, textvariable=self._position_var, width=6)
self._pos_entry.grid(row=1, column=1, sticky=tk.W)
self._pos_entry.bind("<FocusIn>", self._on_get_focus)
self._pos_entry.bind("<FocusOut>", self._on_lost_focus)
is_oval = Checkbutton(self, text="Is Oval", variable=self._oval_var)
is_oval.grid(row=1, column=2)
is_oval.bind("<FocusIn>", self._on_get_focus)
is_oval.bind("<FocusOut>", self._on_lost_focus)
self.columnconfigure(0, weight=1)
self.columnconfigure(1, weight=1)
self.columnconfigure(2, weight=1)
class ManagerItem(Frame):
def __init__(self, master, note_data, toggle_visibility_cmd):
Frame.__init__(self,
master,
class_='ManagerItem',
style='manager.TFrame')
self.columnconfigure(0, weight=0, minsize=18)
self.columnconfigure(1, weight=1, minsize=198)
self.columnconfigure(2, weight=1, minsize=198)
self.columnconfigure(3, weight=0, minsize=85)
self.columnconfigure(4, weight=0, minsize=22)
self.toggle_visibility_cmd = toggle_visibility_cmd
title = note_data['title']
if title:
title = title[:17] + (len(title) > 17) * '...'
title = title.replace('\t', ' ')
date = note_data.get('date', '??')
txt = note_data['txt'].splitlines()
if txt:
txt = txt[0][:17] + (len(txt[0]) > 17 or len(txt) > 1) * '...'
else:
txt = ''
txt = txt.replace('\t', ' ')
self._data = {'title': title, 'text': txt, 'date': date}
self.title = Label(self,
text=title,
anchor='w',
style='manager.TLabel')
self.text = Label(self, text=txt, anchor='w', style='manager.TLabel')
self.date = Label(self,
text=date,
anchor='center',
style='manager.TLabel')
self.checkbutton = Checkbutton(self, style='manager.TCheckbutton')
self.visibility = BooleanVar(self, note_data['visible'])
self.toggle_visibility = Checkbutton(self,
style='manager.Toggle',
variable=self.visibility,
command=self.toggle_visibility)
self.checkbutton.grid(row=0,
column=0,
padx=(2, 0),
pady=4,
sticky='nsew')
self.title.grid(row=0, column=1, padx=4, pady=4, sticky='ew')
self.text.grid(row=0, column=2, padx=4, pady=4, sticky='ew')
self.date.grid(row=0, column=3, padx=4, pady=4, sticky='ew')
self.toggle_visibility.grid(row=0,
column=4,
padx=(0, 2),
pady=4,
sticky='wens')
self.bind('<Enter>', self._on_enter)
self.bind('<Leave>', self._on_leave)
self.checkbutton.bind('<Enter>',
self._on_enter) # override class binding
self.checkbutton.bind('<Leave>',
self._on_leave) # override class binding
self.toggle_visibility.bind('<Enter>',
self._on_enter) # override class binding
self.toggle_visibility.bind('<Leave>',
self._on_leave) # override class binding
self.bind('<ButtonRelease-1>', self._on_click)
self.text.bind('<ButtonRelease-1>', self._on_click)
self.title.bind('<ButtonRelease-1>', self._on_click)
self.date.bind('<ButtonRelease-1>', self._on_click)
def state(self, statespec=None):
return self.checkbutton.state(statespec)
def toggle_visibility(self):
self.toggle_visibility_cmd(self.visibility.get())
def get(self, key):
if key == 'visibility':
return self.visibility.get()
else:
return self._data[key]
def get_values(self):
return (self._data['title'], self._data['text'], self._data['date'],
self.visibility.get())
def _on_enter(self, event):
self.title.state(('active', ))
self.text.state(('active', ))
self.date.state(('active', ))
self.checkbutton.state(('active', ))
self.toggle_visibility.state(('active', ))
Frame.state(self, ('active', ))
return "break"
def _on_leave(self, event):
self.title.state(('!active', ))
self.text.state(('!active', ))
self.date.state(('!active', ))
self.checkbutton.state(('!active', ))
self.toggle_visibility.state(('!active', ))
Frame.state(self, ('!active', ))
return "break"
def _on_click(self, event):
self.checkbutton.invoke()
return "break"
def makegridsquare(self, parent, imageobj, setguidata):
frame = tk.Frame(parent,
width=self.thumbnailsize + 14,
height=self.thumbnailsize + 24)
frame.obj = imageobj
try:
if setguidata:
if not os.path.exists(imageobj.thumbnail):
self.fileManager.makethumb(imageobj)
try:
buffer = pyvips.Image.new_from_file(imageobj.thumbnail)
img = ImageTk.PhotoImage(
Image.frombuffer("RGB", [buffer.width, buffer.height],
buffer.write_to_memory()))
except: # Pillow fallback
img = ImageTk.PhotoImage(Image.open(imageobj.thumbnail))
else:
img = imageobj.guidata['img']
canvas = tk.Canvas(frame,
width=self.thumbnailsize,
height=self.thumbnailsize)
tooltiptext = tk.StringVar(frame, self.tooltiptext(imageobj))
ToolTip(canvas, msg=tooltiptext.get, delay=1)
canvas.create_image(self.thumbnailsize / 2,
self.thumbnailsize / 2,
anchor="center",
image=img)
check = Checkbutton(frame,
textvariable=imageobj.name,
variable=imageobj.checked,
onvalue=True,
offvalue=False)
canvas.grid(column=0, row=0, sticky="NSEW")
check.grid(column=0, row=1, sticky="N")
frame.rowconfigure(0, weight=4)
frame.rowconfigure(1, weight=1)
frame.config(height=self.thumbnailsize + 12)
if (
setguidata
): # save the data to the image obj to both store a reference and for later manipulation
imageobj.setguidata({
"img": img,
"frame": frame,
"canvas": canvas,
"check": check,
"show": True,
"tooltip": tooltiptext
})
# anything other than rightclicking toggles the checkbox, as we want.
canvas.bind("<Button-1>", partial(bindhandler, check, "invoke"))
canvas.bind("<Button-3>", partial(self.displayimage, imageobj))
check.bind("<Button-3>", partial(self.displayimage, imageobj))
canvas.bind("<MouseWheel>", partial(bindhandler, parent, "scroll"))
frame.bind("<MouseWheel>",
partial(bindhandler, self.imagegrid, "scroll"))
check.bind("<MouseWheel>",
partial(bindhandler, self.imagegrid, "scroll"))
if imageobj.moved:
frame.configure(highlightbackground="green",
highlightthickness=2)
if os.path.dirname(
imageobj.path) in self.fileManager.destinationsraw:
color = self.fileManager.destinations[indexOf(
self.fileManager.destinationsraw,
os.path.dirname(imageobj.path))]['color']
frame['background'] = color
canvas['background'] = color
frame.configure(height=self.thumbnailsize + 10)
if imageobj.dupename:
frame.configure(highlightbackground="yellow",
highlightthickness=2)
except Exception as e:
logging.error(e)
return frame
