def generar_menu_dist(*args):
"""
Subprograma que genera los campos correspondientes al tipo de distribución seleccionada por el distribucion_seleccionada.
"""
try:
dic = distribuciones[distribucion_seleccionada.get()].dict_params
except KeyError:
distribucion_seleccionada.set("Binomial")
dic = distribuciones["Binomial"].dict_params
# busca los widgets que no se ocupan y los destruye
flush_widgets(app)
# genera los widgets necesarios de la distribucion
for campo in dic.keys():
if modo_seleccionado.get() == "Acumulada" and campo == "x":
label = Label(app, text="Inicio", font=("sans", "12", "bold"))
# agregar un form
txtfld = Entry(app, text="Inicio")
txtfld.tag = "inicio"
tooltip = CreateToolTip(txtfld, text="x inicial")
# vincularlos a la app
label.pack()
txtfld.pack()
label = Label(app, text="Fin", font=("sans", "12", "bold"))
# agregar un form
txtfld = Entry(app, text="Fin")
txtfld.tag = "fin"
tooltip = CreateToolTip(txtfld, text="x final")
# vincularlos a la app
label.pack()
txtfld.pack()
continue
label = Label(app, text=campo, font=("sans", "12", "bold"))
# agregar un form
txtfld = Entry(app, text=campo)
txtfld.tag = campo
tooltip = CreateToolTip(txtfld, text=dic[campo])
# vincularlos a la app
label.pack()
txtfld.pack()
button = Button(
app,
text="Calcular!",
command=(lambda e=app.winfo_children(): calcular_distribucion(e)))
button.pack()
# texto por defecto para flushear bonito
txt = '''
Probabilidad: -
Esperanza: -
Varianza: -
'''
label = Label(app, text=txt, font=("sans", "12", "bold"))
label.pack()
def openAnnotFile(self, var=None):
var.set(askopenfilename())
row = 2
master = self.master
try:
with open(var.get(), 'r') as ANNOT:
keyList = ANNOT.readline().strip().split("\t")[1:]
#print(keyList)
keyList.sort()
keyString = ",".join(keyList)
except FileNotFoundError:
return
self.optionLabel = Label(master, text="Annotation keys")
self.optionLabel.grid(row=row, column=0, sticky=W, padx=3)
self.k = StringVar()
self.k.set(keyString)
self.optionEntry = Entry(master, width=WIDTH, textvariable=self.k)
self.optionEntry.grid(row=row, column=1, padx=3)
self.optionLabel2 = Label(master, text="comma-separated")
self.optionLabel2.grid(row=row, column=3, sticky=W, padx=3)
ann = os.path.basename(self.a.get())
CreateToolTip(
self.optionEntry,
"""List of available attributes in file %s.\nIf you wish to remove some, click on line and edit."""
% ann)
self.master.update_idletasks()
RHeight = self.master.winfo_reqheight()
RWidth = self.master.winfo_reqwidth()
self.master.geometry(("%dx%d+300+300") % (RWidth, RHeight))
center(self.master)
def __init__(self, master, title=None, args=None):
self.master = master
self.args = args
self.name = title
master.title("Startup interface for %s" % title)
self.arguments = dict()
style = Style()
style.configure(".", background="lightgrey")
labelStyle = Style()
labelStyle.configure("TLabel", background="lightgrey")
buttonStyle = Style()
buttonStyle.configure("TButton", background="lightgrey")
chkbuttonStyle = Style()
chkbuttonStyle.configure("TCheckbutton", background="lightgrey")
rbuttonStyle = Style()
rbuttonStyle.configure("TRadiobutton", background="lightgrey")
row = 0
column = 0
# Input edge file
self.inEdgeLabel = Label(master, text="Input edge file")
self.inEdgeLabel.grid(row=row, column=column, sticky=W, padx=3)
self.inEdgeFile = StringVar()
if self.args.i:
self.inEdgeFile.set(self.args.i)
self.inEdgeEntry = Entry(master,
width=WIDTH,
textvariable=self.inEdgeFile)
column += 1
self.inEdgeEntry.grid(row=row, column=column, padx=3)
self.inEdgeSelect = Button(master, text = "Select",\
command = lambda: self.setOutputFiles2(IN=self.inEdgeFile,OUT=[(self.configFile,"config"),(self.outFile,"desc"),(self.outFile2,"xml_desc")]))
column += 1
self.inEdgeSelect.grid(row=row, column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text="required")
column += 1
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText1 = "Edge file for input graph (two columns, tab-delimited)."
self.inEdgeTip = CreateToolTip(self.inEdgeEntry, helpText1)
##
row += 1
column = 0
self.annotLabel = Label(master, text="Annotation file")
self.annotLabel.grid(row=row, column=column, sticky=W, padx=3)
self.a = StringVar()
if self.args.a:
self.a.set(os.path.abspath(os.path.normpath(self.args.a)))
self.annotEntry = Entry(master, width=WIDTH, textvariable=self.a)
column += 1
self.annotEntry.grid(row=row, column=column, padx=3)
self.annotSelect = Button(
master,
text="Select",
command=lambda: self.openAnnotFile(var=self.a))
column += 1
self.annotSelect.grid(row=row, column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text="required")
column += 1
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
CreateToolTip(
self.annotEntry,
"Common annotation file for genomes and genes.\nTab-delimited, compulsory header with attribute names.\nSpecify empty annotations with '-'."
)
row += 1
column = 0
self.k = StringVar()
if self.a.get():
with open(self.a.get(), 'r') as ANNOT:
keyList = ANNOT.readline().strip().split("\t")[1:]
#print(keyList)
keyList.sort()
keyString = ",".join(keyList)
self.optionLabel = Label(master, text="Annotation keys")
self.optionLabel.grid(row=row, column=0, sticky=W, padx=3)
self.k = StringVar()
self.k.set(keyString)
self.optionEntry = Entry(master, width=WIDTH, textvariable=self.k)
self.optionEntry.grid(row=row, column=1, padx=3)
self.optionLabel2 = Label(master, text="comma-separated")
self.optionLabel2.grid(row=row, column=3, sticky=W, padx=3)
CreateToolTip(
self.optionEntry,
"List of available attributes in file %s.\nIf you wish to remove some, click on line and edit."
% self.args.a)
row += 1
self.configLabel = Label(master, text="Configuration file")
self.configLabel.grid(row=row, column=column, sticky=W, padx=3)
self.configFile = StringVar()
self.generateConfig = BooleanVar()
self.generateConfig.set(bool(self.args.X))
self.useConfig = BooleanVar()
self.useConfig.set(bool(self.args.x))
if self.args.x or self.args.X:
if self.args.x and self.args.X:
if self.args.x == self.args.X:
cFile = self.args.x
self.configFile.set(cFile)
else:
sys.exit(
"Conflicting fields -x and -X. Check and run again.")
elif self.args.x:
cFile = self.args.x
else:
cFile = self.args.X
self.configFile.set(cFile)
else:
self.configFile.set('')
self.configEntry = Entry(master,
width=WIDTH,
textvariable=self.configFile)
column += 1
self.configEntry.grid(row=row, column=column, padx=3)
self.configSelect = Button(
master,
text="Select",
command=lambda: self.setFile(var1=self.configFile,
var2=self.outTrailFile))
column += 1
self.configSelect.grid(row=row, column=column, sticky=W, padx=3)
"""self.optionLabel2 = Label(master, text = "optional")
column += 1
self.optionLabel2.grid(row=row,column=column,sticky=W, padx=3)
"""
# tip
helpText3 = "XML file specifying component, trails and annotations for all node types."
self.configTip = CreateToolTip(self.configEntry, helpText3)
#
column += 1
#row += 1
#column = 0
cbFrame = Frame(master)
chk1 = Checkbutton(cbFrame, text="Generate", var=self.generateConfig)
chk1.pack(side="left", fill=None, expand=False, padx=3)
CreateToolTip(chk1,
"Generate configuration file %s" % self.configFile.get())
chk2 = Checkbutton(cbFrame, text="Use", var=self.useConfig)
chk2.pack(side="left", fill=None, expand=False, padx=3)
CreateToolTip(chk2,
"Use configuration file %s" % self.configFile.get())
cbFrame.grid(row=row, column=column, sticky=W)
row += 1
column = 0
self.TrailLabel = Label(master, text="Use trail file")
self.TrailLabel.grid(row=row, column=column, sticky=W, padx=3)
self.inTrailFile = StringVar()
self.T = StringVar()
if self.args.t:
self.T.set("1")
self.inTrailFile.set(self.args.t)
elif self.args.H:
self.T.set("2")
self.inTrailFile.set(self.args.H)
else:
self.T.set("0")
MODES = [
("No", "0"),
("Unique level", "1"),
("Follow history", "2"),
]
trailVal = {
"0": "Toto",
"1": self.inTrailFile.get(),
"2": self.inTrailFile.get()
}
helpVal = {
"0":
"Do not use trail file.\nCheck that annotations refer to IDs of current graph.",
"1": "Use only level described by trail file.",
"2": "Use all levels found in the trail history."
}
rbFrame = Frame(master) # create subframe for radiobuttons
i = 0
MODE = MODES[0]
b = Radiobutton(rbFrame,
text=MODE[0],
variable=self.T,
value=MODE[1],
command=lambda: self.inTrailFile.set(''))
# tip
CreateToolTip(b, helpVal[str(i)])
##
b.pack(side="left", fill=None, expand=False, padx=3)
for text, mode in MODES[1:]:
b = Radiobutton(
rbFrame,
text=text,
variable=self.T,
value=mode,
command=lambda: self.openFileCheck(var=self.inTrailFile))
# tip
CreateToolTip(b, helpVal[mode])
##
b.pack(side="left", fill=None, expand=False, padx=3)
rbFrame.grid(row=row, column=1)
row += 1
column = 0
self.inTrailLabel = Label(master, text="Trail file")
self.inTrailLabel.grid(row=row, column=column, sticky=W, padx=18)
#self.inTrailEntry = Entry(master, width = WIDTH, textvariable = self.inTrailFile)
self.inTrailEntry = Entry(master,
width=WIDTH,
textvariable=self.inTrailFile,
validate='focusin',
validatecommand=lambda: self.T.set("2"))
CreateToolTip(
self.inTrailEntry,
"""Select node type file for multipartite graphs.\nThis will reset the partiteness to "Multipartite"."""
)
column += 1
self.inTrailEntry.grid(row=row, column=column, padx=3)
self.inTrailSelect = Button(
master,
text="Select",
command=lambda: self.openFile2(
var=self.inTrailFile, var2=self.T, value="2"))
column += 1
self.inTrailSelect.grid(row=row, column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text="if option set")
column += 1
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText3 = "Links IDs of current graph to IDs of ROOT graph (two columns, tab-delimited).\nIf skipped, current graph is considered ROOT."
self.inTrailTip = CreateToolTip(self.inTrailEntry, helpText3)
#
"""
cbFrame = Frame(master)
self.uniqueTrail = BooleanVar()
chk1 = Checkbutton(cbFrame, text="Unique trail file", var = self.uniqueTrail)
chk1.pack(side="left", fill=None, expand=False, padx=3)
CreateToolTip(chk1, "Consider only level given by %s" % self.inTrailFile.get())
self.history = BooleanVar()
chk2 = Checkbutton(cbFrame, text="Use trail history", var = self.history)
chk2.pack(side="left", fill=None, expand=False, padx=3)
CreateToolTip(chk2, "Follow trail history of trail file %s" % self.inTrailFile.get())
cbFrame.grid(row=row,column=1)
"""
row += 1
column = 0
# Component file
self.CompLabel = Label(master, text="Component file ")
self.CompLabel.grid(row=row, column=column, sticky=W, padx=3)
self.CompFile = StringVar()
if self.args.c:
self.CompFile.set(self.args.c)
self.CompEntry = Entry(master, width=WIDTH, textvariable=self.CompFile)
column += 1
self.CompEntry.grid(row=row, column=column, padx=3)
self.CompSelect = Button(
master,
text="Select",
command=lambda: self.openFile(var=self.CompFile))
column += 1
self.CompSelect.grid(row=row, column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text="optional")
column += 1
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText3 = "Links a nodeID and its neighbours to the twin class ID.\nThis is usually an overlapping clustering.\nIf left empty, consider nodes of current graph as components."
self.CompTip = CreateToolTip(self.CompEntry, helpText3)
##
row += 1
column = 0
# Partiteness options
self.inNodeLabel = Label(master, text="Partiteness")
self.inNodeLabel.grid(row=row, column=column, sticky=W, padx=3)
column += 1
MODES = [
("Unipartite", "1"),
("Bipartite", "2"),
]
self.inNodeType = StringVar()
self.v = StringVar()
if str(self.args.N) == '1' or str(self.args.N) == '2':
self.v.set(self.args.N) # initialize at value
elif self.args.N:
self.v.set("m")
self.inNodeType.set(self.args.N)
else:
self.v.set("2")
rbFrame = Frame(master) # create subframe for radiobuttons
for text, mode in MODES:
b = Radiobutton(rbFrame,
text=text,
variable=self.v,
value=mode,
command=lambda: self.inNodeType.set(''))
# tip
CreateToolTip(b, "Select if graph is %s" % text.lower())
##
b.pack(side="left", fill=None, expand=False, padx=3)
b = Radiobutton(rbFrame,
text="Multipartite",
variable=self.v,
value="m",
command=lambda: self.openFile(var=self.inNodeType))
CreateToolTip(
b,
"Select if graph is multipartite.\nThis will open a select box for the node type file."
)
b.pack(side="left", fill=None, expand=False, padx=3)
rbFrame.grid(row=row, column=column, padx=3)
row += 1
column = 0
self.Label = Label(master, text="Node type file")
self.Label.grid(row=row, column=column, sticky=W, padx=18)
self.inNodeEntry = Entry(master,
width=WIDTH,
textvariable=self.inNodeType,
validate='focusin',
validatecommand=lambda: self.v.set("m"))
CreateToolTip(
self.inNodeEntry,
"""Select node type file for multipartite graphs.\nThis will reset the partiteness to "Multipartite"."""
)
column += 1
self.inNodeEntry.grid(row=row, column=column, padx=3)
self.inNodeSelect = Button(
master,
text="Select",
command=lambda: self.openFile2(
var=self.inNodeType, var2=self.v, value="m")
) # reset value to "multipartite" when type file is chosen.
column += 1
self.inNodeSelect.grid(row=row, column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text="for multipartite only")
column += 1
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
CreateToolTip(
self.inNodeSelect,
"""Select node type file for multipartite graphs.\nThis will reset the partiteness to "Multipartite"."""
)
row += 1
column = 0
# Output file
self.outLabel = Label(master, text="Output plain file")
self.outLabel.grid(row=row, column=column, sticky=W, padx=3)
self.outFile = StringVar()
if self.args.o:
self.outFile.set(self.args.o)
self.outEntry = Entry(master, width=WIDTH, textvariable=self.outFile)
column += 1
self.outEntry.grid(row=row, column=column, padx=3)
self.outSelect = Button(
master,
text="Select",
command=lambda: self.openFile(var=self.outFile))
column += 1
self.outSelect.grid(row=row, column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text="required")
column += 1
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText2 = "Set name of the plain text description file"
self.outTip = CreateToolTip(self.outEntry, helpText2)
##
row += 1
column = 0
# Output file
self.outLabel2 = Label(master, text="Output XML file")
self.outLabel2.grid(row=row, column=column, sticky=W, padx=3)
self.outFile2 = StringVar()
if self.args.O:
self.outFile.set(self.args.O)
self.outEntry2 = Entry(master, width=WIDTH, textvariable=self.outFile2)
column += 1
self.outEntry2.grid(row=row, column=column, padx=3)
self.outSelect2 = Button(
master,
text="Select",
command=lambda: self.openFile(var=self.outFile2))
column += 1
self.outSelect2.grid(row=row, column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text="optional")
column += 1
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText2 = "Set name of the XML description file"
self.outTip = CreateToolTip(self.outEntry2, helpText2)
##
row += 1
column = 0
self.optionLabel = Label(master, text="Unique node identifier")
self.optionLabel.grid(row=row, column=0, sticky=W, padx=3)
self.I = StringVar()
if self.args.I:
self.I.set(self.args.I)
self.optionEntry = Entry(master, width=WIDTH, textvariable=self.I)
self.optionEntry.grid(row=row, column=1, padx=3)
CreateToolTip(
self.optionEntry,
"""Name of first column in annotation %s file.\nCheck that the items in this column match the node IDs in the ROOT graph."""
% os.path.basename(self.a.get()))
row += 1
column = 0
self.trackLabel = Label(master, text="Missing annotation label")
self.trackLabel.grid(row=row, column=column, sticky=W, padx=3)
self.trackName = StringVar()
if self.args.T:
self.trackName.set(self.args.T)
self.trackEntry = Entry(master,
width=WIDTH,
textvariable=self.trackName)
column += 1
self.trackEntry.grid(row=row, column=column, padx=3)
# tip
helpText3 = "Name replacing missing annotations"
self.trackTip = CreateToolTip(self.trackEntry, helpText3)
#
column += 2
self.Track = BooleanVar()
chk1 = Checkbutton(master, text="Skip", var=self.Track)
CreateToolTip(chk1, "Skip missing annotations")
chk1.grid(row=row, column=column, sticky=W, padx=9)
row += 1
column = 0
self.optionLabel = Label(master,
text="Graphic interface for %s" %
self.configFile.get())
self.optionLabel.grid(row=row, column=0, sticky=W, padx=3)
self.K = BooleanVar()
self.K.set(self.args.K)
self.chk = Checkbutton(master, text="Display?", var=self.K)
self.chk.grid(row=row, column=1, padx=3, sticky=W)
CreateToolTip(
self.chk,
"Displays graphic customization interface for the last description.py step.\nIf not selected, displays all attributes for all key types and all trail levels."
)
row += 1
column = 0
# Log
self.optionLabel = Label(master, text="Log file")
self.optionLabel.grid(row=row, column=0, sticky=W, padx=3)
self.l = StringVar()
try:
log = self.args.l.name.strip("(<,>")
except:
log = log
self.l.set(log)
self.optionEntry = Entry(master, width=WIDTH, textvariable=self.l)
self.optionEntry.grid(row=row, column=1, padx=3)
row += 2
# Populate outFiles if edge file given
if self.args.i:
self.setOutputFiles2(IN=self.inEdgeFile,
OUT=[(self.configFile, "config"),
(self.outFile, "desc"),
(self.outFile2, "xml_desc")],
OPEN=False)
cbFrame = Frame(master) # create subframe for command buttons
self.run_button = Button(cbFrame, text="Run", command=self.run)
self.run_button.grid(row=row, column=0, padx=12)
self.close_button = Button(cbFrame, text="Close", command=self.Quit)
self.close_button.grid(row=row, column=1, padx=12)
cbFrame.grid(row=row, column=1, columnspan=2, sticky=E + W)
helpText = description.processArgs().format_help()
self.helpbutton = Button(
master,
text="Help",
command=lambda: HelpWindow(text=helpText, name=self.name))
self.helpbutton.grid(row=row, column=2, sticky=W, padx=3)
def widget(self):
Info(
self,
text="Updates to settings require the script to be restarted.",
center=True,
)._pack(pady=5)
settings_frame = tk.Frame(self)
settings_frame.grid_columnconfigure(1, weight=1)
inputs = [] # may be better known as entries
def on_change(_):
if list(self.settings.values()) == [
_entry.sv.get() for _entry in inputs
]:
save["state"] = "disabled"
else:
save["state"] = "normal"
## CREATE INPUT WIDGETS
for i, (name, setting) in enumerate(self.settings.items()):
### CREATE LABEL WIDGET
label = tk.Label(settings_frame, text=name)
label.grid(row=i, column=0, padx=10)
CreateToolTip(label, self.tooltips[name])
### CREATE ENTRY WIDGET
if (name == "Pause When Locked" or name == "Push To Back"
or name == "Create Shortcut"):
entry = Dropdown(
settings_frame,
name,
self.yes_no_options,
self.yes_no_options.index(setting),
)
elif name == "Spotify Path":
entry = FileSelector(settings_frame,
name,
setting,
on_change=on_change)
else:
entry = Input(settings_frame, name=name, value=setting)
CreateToolTip(entry, self.tooltips[name])
entry.grid(
row=i,
column=1,
padx=15,
sticky=tk.W + tk.E,
pady=2 if name == "Spotify Path" else 0,
)
inputs.append(entry)
entry.on_change = on_change
### CREATE SAVE BUTTON WIDGET
def on_click():
settings = {}
for input in inputs:
value = input.sv.get()
if value:
settings[input.name] = value
else:
settings[input.name] = self.settings[input.name]
self.settings = settings
save_settings(settings)
save["state"] = "disabled"
self.master.focus()
save = tk.Button(
settings_frame,
text="Save Settings",
command=on_click,
state="disabled",
)
save.grid(row=i + 1,
column=0,
columnspan=2,
pady=10,
padx=40,
sticky=tk.W + tk.E)
settings_frame.pack(fill="x")
def __init__(self, master,title=None,args=None):
self.master = master
self.args = args
self.name = title
master.title("Startup interface for %s" % title)
self.arguments = dict()
style = Style()
style.configure(".",background="lightgrey")
labelStyle = Style()
labelStyle.configure("TLabel", background="lightgrey")
buttonStyle = Style()
buttonStyle.configure("TButton", background = "lightgrey")
chkbuttonStyle = Style()
chkbuttonStyle.configure("TCheckbutton", background = "lightgrey")
rbuttonStyle = Style()
rbuttonStyle.configure("TRadiobutton", background = "lightgrey")
row = 0
column = 0
# Input edge file
self.inEdgeLabel = Label(master, text = "Input edge file")
self.inEdgeLabel.grid(row=row,column=column, sticky=W, padx=3)
self.inEdgeFile = StringVar()
if self.args.input_edge_file:
self.inEdgeFile.set(self.args.input_edge_file)
self.inEdgeEntry = Entry(master, width = WIDTH, textvariable = self.inEdgeFile)
column += 1
self.inEdgeEntry.grid(row=row,column=column, padx=3)
self.inEdgeSelect = Button(master, text = "Select", command = lambda: self.setOutputFiles(IN=self.inEdgeFile,TWIN=self.outTwinFile,TWINCOMP=self.twinCompFile))
column += 1
self.inEdgeSelect.grid(row=row,column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text = "required")
column += 1
self.optionLabel2.grid(row=row,column=column,sticky=W, padx=3)
# tip
helpText1 = "Edge file for input graph (two columns, tab-delimited)."
self.inEdgeTip = CreateToolTip(self.inEdgeEntry, helpText1)
##
row += 1
column = 0
# Output twin file
self.outTwinLabel = Label(master, text = "Output twin file")
self.outTwinLabel.grid(row=row,column=column, sticky=W, padx=3)
self.outTwinFile = StringVar()
if self.args.o:
self.outTwinFile.set(self.args.o)
self.outTwinEntry = Entry(master, width = WIDTH, textvariable = self.outTwinFile)
column += 1
self.outTwinEntry.grid(row=row,column=column, padx=3)
self.outTwinSelect = Button(master, text = "Select", command = lambda: self.openFile(var=self.outTwinFile))
column += 1
self.outTwinSelect.grid(row=row,column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text = "required")
column += 1
self.optionLabel2.grid(row=row,column=column,sticky=W, padx=3)
# tip
helpText2 = "Links a nodeID to its twin class ID (two columns, tab-delimited)."
self.outTwinTip = CreateToolTip(self.outTwinEntry, helpText2)
##
row += 1
column = 0
# Twin component file
self.twinCompLabel = Label(master, text = "Twin component file ")
self.twinCompLabel.grid(row=row,column=column, sticky=W, padx=3)
self.twinCompFile = StringVar()
if self.args.c:
self.twinCompFile.set(self.args.c)
self.twinCompEntry = Entry(master, width = WIDTH, textvariable = self.twinCompFile)
column += 1
self.twinCompEntry.grid(row=row,column=column, padx=3)
self.twinCompSelect = Button(master, text = "Select", command = lambda: self.openFile(var=self.twinCompFile))
column += 1
self.twinCompSelect.grid(row=row,column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text = "optional")
column += 1
self.optionLabel2.grid(row=row,column=column,sticky=W, padx=3)
# tip
helpText3 = "Links a nodeID and its neighbours to the twin class ID.\nThis is usually an overlapping clustering."
self.twinCompTip = CreateToolTip(self.twinCompEntry, helpText3)
##
row += 1
column = 0
# Populate outFiles if edge file given
if self.args.input_edge_file:
inFile = os.path.split(self.args.input_edge_file)[1]
inRad = inFile.split(".")[0]
twin = inRad+".twins"
twinComp = inRad+".twin_comp"
self.outTwinFile.set(twin)
self.twinCompFile.set(twinComp)
# Partiteness options
self.inNodeLabel = Label(master, text = "Partitneness")
self.inNodeLabel.grid(row=row,column=column, sticky=W, padx=3)
column += 1
MODES = [("Unipartite", "1"),("Bipartite", "2"),]
self.inNodeType = StringVar()
self.v = StringVar()
if str(self.args.n) == '1' or str(self.args.n) == '2':
self.v.set(self.args.n) # initialize at bipartite
elif self.args.n:
self.v.set("m")
self.inNodeType.set(self.args.n)
rbFrame = Frame(master) # create subframe for radiobuttons
for text,mode in MODES:
b = Radiobutton(rbFrame, text=text, variable=self.v, value=mode, command = lambda: self.inNodeType.set(''))
# tip
CreateToolTip(b,"Select if graph is %s" % text.lower())
##
b.pack(side="left", fill=None, expand=False, padx=3)
b = Radiobutton(rbFrame, text="Multipartite", variable=self.v, value="m", command = lambda: self.openFile(var=self.inNodeType))
CreateToolTip(b,"Select if graph is multipartite.\nThis will open a select box for the node type file.")
b.pack(side="left", fill=None, expand=False, padx=3)
rbFrame.grid(row=row,column=column, padx=3)
row += 1
column = 0
self.inNodeEntry = Entry(master, width = WIDTH, textvariable = self.inNodeType, validate='focusin',validatecommand = lambda: self.v.set("m"))
CreateToolTip(self.inNodeEntry,"""Select node type file for multipartite graphs.\nThis will reset the partiteness to "Multipartite".""")
column += 1
self.inNodeEntry.grid(row=row,column=column, padx=3)
self.inNodeSelect = Button(master, text = "Select", command = lambda: self.openFile2(var=self.inNodeType,var2=self.v,value="m")) # reset value to "multipartite" when type file is chosen.
column += 1
self.inNodeSelect.grid(row=row,column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text = "for multipartite")
column += 1
self.optionLabel2.grid(row=row,column=column,sticky=W, padx=3)
CreateToolTip(self.inNodeSelect,"""Select node type file for multipartite graphs.\nThis will reset the partiteness to "Multipartite".""")
row += 1
column = 0
# unilat
self.twinSelectLabel = Label(master, text = "Restrict to node types")
self.twinSelectLabel.grid(row=row,column=column, sticky=W, padx=3)
column += 1
self.unilat = StringVar()
if self.args.u:
self.unilat.set(self.args.u)
self.twinSelectEntry = Entry(master, width = WIDTH, textvariable = self.unilat)
self.twinSelectEntry.grid(row=row,column=column, padx=3)
column += 2
self.optionLabel2 = Label(master, text = "optional (comma-separated)")
self.optionLabel2.grid(row=row,column=column, padx=3)
CreateToolTip(self.twinSelectEntry,"Computes twins for nodes of specified types only.")
row += 1
column = 0
# Min support
self.minsuppLabel = Label(master, text = "Minimum support")
self.minsuppLabel.grid(row=row,column=column, sticky=W, padx=3)
column += 1
self.minsupp = StringVar()
if self.args.thr:
self.minsupp.set(self.args.thr)
self.minsuppEntry = Entry(master, width = WIDTH, textvariable = self.minsupp)
self.minsuppEntry.grid(row=row,column=column, padx=3)
column += 2
self.optionLabel2 = Label(master, text = "optional")
self.optionLabel2.grid(row=row,column=column, padx=3,sticky=W)
CreateToolTip(self.minsuppEntry,"Returns twins only if their neighbourhood has at least this number of elements.")
row += 1
column = 0
# min size
self.minsizeLabel = Label(master, text = "Minimum twin size")
self.minsizeLabel.grid(row=row,column=column, sticky=W, padx=3)
column += 1
self.minsize = StringVar()
if self.args.M:
self.minsize.set(self.args.M)
self.minsizeEntry = Entry(master, width = WIDTH, textvariable = self.minsize)
self.minsizeEntry.grid(row=row,column=column, padx=3)
column += 2
self.optionLabel2 = Label(master, text = "optional")
self.optionLabel2.grid(row=row,column=column, padx=3,sticky=W)
CreateToolTip(self.minsizeEntry,"Returns twins only if they have at least this number of elements.")
row += 1
column = 0
# Log
self.optionLabel = Label(master, text = "Log file")
self.optionLabel.grid(row=row,column=0, sticky=W, padx=3)
self.l = StringVar()
try:
log = self.args.l.name.strip("(<,>")
except:
log = log
self.l.set(log)
self.optionEntry = Entry(master, width = WIDTH, textvariable = self.l)
self.optionEntry.grid(row=row,column=1, padx=3)
row += 2
cbFrame = Frame(master) # create subframe for command buttons
self.run_button = Button(cbFrame, text="Run", command=self.run)
self.run_button.grid(row=row,column=0,padx=12)
self.close_button = Button(cbFrame, text="Close", command=self.Quit)
self.close_button.grid(row=row,column=1,padx=12)
cbFrame.grid(row=row,column=1,columnspan=2,sticky=E+W)
helpText = detect_twins.processArgs().format_help()
self.helpbutton = Button(master, text="Help", command = lambda: HelpWindow(text=helpText,name=self.name))
self.helpbutton.grid(row=row,column=2,sticky=W,padx=3)
def __init__(self, master,title=None,args=None):
self.master = master
self.args = args
self.name = title
master.title("Startup interface for %s" % title)
self.arguments = dict()
style = Style()
style.configure(".",background="lightgrey")
labelStyle = Style()
labelStyle.configure("TLabel", background="lightgrey")
buttonStyle = Style()
buttonStyle.configure("TButton", background = "lightgrey")
chkbuttonStyle = Style()
chkbuttonStyle.configure("TCheckbutton", background = "lightgrey")
rbuttonStyle = Style()
rbuttonStyle.configure("TRadiobutton", background = "lightgrey")
row = 0
self.blastLabel = Label(master, text = "Blast/Diamond output file")
self.blastLabel.grid(row=row,column=0, sticky=W, padx=3)
self.blastFile = StringVar()
if self.args.b:
self.blastFile.set(self.args.b)
self.blastEntry = Entry(master, width = WIDTH, textvariable = self.blastFile)
self.blastEntry.grid(row=row,column=1, padx=3)
self.blastSelect = Button(master, text = "Select", command = lambda: self.openFile(var=self.blastFile))
self.blastSelect.grid(row=row,column=2, sticky=W, padx=3)
self.optionLabel2 = Label(master, text = "required")
self.optionLabel2.grid(row=row,column=3,sticky=W, padx=3)
CreateToolTip(self.blastEntry,"Sequence similarity file produced by BLAST or DIAMOND.\nUses specific format (see README).")
row += 1
self.networkLabel = Label(master, text = "Genome to gene file")
self.networkLabel.grid(row=row,column=0, sticky=W, padx=3)
self.networkFile = StringVar()
if self.args.g:
self.networkFile.set(self.args.g)
self.networkEntry = Entry(master, width = WIDTH, textvariable = self.networkFile)
self.networkEntry.grid(row=row,column=1, padx=3)
self.networkSelect = Button(master, text = "Select", command = lambda: self.openFile(var=self.networkFile))
self.networkSelect.grid(row=row,column=2, sticky=W, padx=3)
self.optionLabel2 = Label(master, text = "required")
self.optionLabel2.grid(row=row,column=3,sticky=W, padx=3)
CreateToolTip(self.networkEntry,"Input bipartite graph edge file (Tab-separated).\nCheck for the ordering of the items on each line:\nGenome first, then sequence ID.")
row += 1
self.annotLabel = Label(master, text = "Annotation file")
self.annotLabel.grid(row=row,column=0, sticky=W, padx=3)
self.a = StringVar()
if self.args.a:
self.a.set(self.args.a)
self.annotEntry = Entry(master, width = WIDTH, textvariable = self.a)
self.annotEntry.grid(row=row,column=1, padx=3)
self.annotSelect = Button(master, text = "Select", command = lambda: self.openAnnotFile(var=self.a))
self.annotSelect.grid(row=row,column=2, sticky=W, padx=3)
self.optionLabel2 = Label(master, text = "recommended")
self.optionLabel2.grid(row=row,column=3,sticky=W, padx=3)
CreateToolTip(self.annotEntry,"Common annotation file for genomes and genes.\nTab-delimited, compulsory header with attribute names.\nSpecify empty annotations with '-'.")
row += 1
self.k = StringVar()
if self.a.get():
with open(self.a.get(),'r') as ANNOT:
keyList = ANNOT.readline().strip().split("\t")[1:]
#print(keyList)
keyList.sort()
keyString = ",".join(keyList)
self.optionLabel = Label(master, text = "Annotation keys")
self.optionLabel.grid(row=row,column=0, sticky=W, padx=3)
self.k = StringVar()
self.k.set(keyString)
self.optionEntry = Entry(master, width = WIDTH, textvariable = self.k)
self.optionEntry.grid(row=row,column=1, padx=3)
self.optionLabel2 = Label(master, text = "comma-separated")
self.optionLabel2.grid(row=row,column=3,sticky=W, padx=3)
CreateToolTip(self.optionEntry,"List of available attributes in file %s.\nIf you wish to remove some, click on line and edit." % self.args.a)
row += 1
self.optionLabel = Label(master, text = "Identity threshold(s)")
self.optionLabel.grid(row=row,column=0, sticky=W, padx=3)
self.n = StringVar()
if self.args.n:
self.n.set(self.args.n)
self.optionEntry = Entry(master, width = WIDTH, textvariable = self.n)
self.optionEntry.grid(row=row,column=1, padx=3)
self.optionLabel2 = Label(master, text = "comma-separated")
self.optionLabel2.grid(row=row,column=3,sticky=W, padx=3)
CreateToolTip(self.optionEntry,"List of thresholds considered.\nOne subdirectory will be created for each value.")
row += 1
self.optionLabel = Label(master, text = "Mutual cover")
self.optionLabel.grid(row=row,column=0, sticky=W, padx=3)
self.c = StringVar()
if self.args.c:
self.c.set(self.args.c)
self.optionEntry = Entry(master, width = WIDTH, textvariable = self.c)
self.optionEntry.grid(row=row,column=1, sticky=W, padx=3)
CreateToolTip(self.optionEntry,"Set new value for minimum mutual cover for sequence similarity.")
row += 1
self.optionLabel = Label(master, text = "Clustering method")
self.optionLabel.grid(row=row,column=0, sticky=W, padx=3)
option_list = ["cc","families"]
self.C = StringVar()
self.C.set(option_list[0])
self.optionEntry = Combobox(master, width = 10, textvariable = self.C)
self.optionEntry['values'] = option_list
self.optionEntry.grid(row=row,column=1,sticky=W, padx=3)
CreateToolTip(self.optionEntry,"""Select method for the definition of gene families.\ncc = connected components of sequence similarity network.\nfamilies = communities produced by the "Louvain" multilevel algorithm.""")
row += 1
self.optionLabel = Label(master, text = "Input network")
self.optionLabel.grid(row=row,column=0, sticky=W, padx=3)
self.I = StringVar()
if self.args.I:
self.I.set(self.args.I)
self.optionEntry = Entry(master, width = WIDTH, textvariable = self.I)
self.optionEntry.grid(row=row,column=1, padx=3)
self.optionSelect = Button(master, text = "Select", command = lambda: self.openFile(var=self.I))
self.optionSelect.grid(row=row,column=2, sticky=W, padx=3)
self.optionLabel2 = Label(master, text = "optional")
self.optionLabel2.grid(row=row,column=3,sticky=W, padx=3)
CreateToolTip(self.optionEntry,"Supply directly sequence similarity network.\nSkips use of cleanblast on the blast file output.")
row += 1
self.optionLabel = Label(master, text = "Fasta file")
self.optionLabel.grid(row=row,column=0, sticky=W, padx=3)
self.f = StringVar()
if self.args.f:
self.f.set(self.args.f)
self.optionEntry = Entry(master, width = WIDTH, textvariable = self.f)
self.optionEntry.grid(row=row,column=1, padx=3)
self.optionSelect = Button(master, text = "Select", command = lambda: self.openFile(var=self.f))
self.optionSelect.grid(row=row,column=2, sticky=W, padx=3)
self.optionLabel2 = Label(master, text = "optional")
self.optionLabel2.grid(row=row,column=3,sticky=W, padx=3)
CreateToolTip(self.optionEntry,"Supply fasta file for the protein sequences.\nAdds sequence similarity detection step.\nWARNING: this could take a long time.")
row += 1
self.optionLabel = Label(master, text = "Similarity search software")
self.optionLabel.grid(row=row,column=0, sticky=W, padx=3)
option_list = ["Blast","Diamond"]
self.A = StringVar()
self.A.set(option_list[0])
self.optionEntry = Combobox(master, width =10, textvariable = self.A)
self.optionEntry['values'] = option_list
self.optionEntry.grid(row=row,column=1,sticky=W, padx=3)
self.optionLabel2 = Label(master, text = "optional (requires fasta file)")
self.optionLabel2.grid(row=row,column=3,sticky=W, padx=3)
CreateToolTip(self.optionEntry,"Selects sequence similarity detection software.\nSilently ignored if no fasta file is given.")
row += 1
self.optionLabel = Label(master, text = "Unique node identifier")
self.optionLabel.grid(row=row,column=0, sticky=W, padx=3)
self.i = StringVar()
if self.args.i:
self.i.set(self.args.i)
self.optionEntry = Entry(master, width = WIDTH, textvariable = self.i)
self.optionEntry.grid(row=row,column=1, padx=3)
CreateToolTip(self.optionEntry,"""Name of first column in %s file.\nCheck that the items in this column match the node IDs in the ROOT graph.""" % self.args.a)
row += 1
self.optionLabel = Label(master, text = "Graphic interface for Description")
self.optionLabel.grid(row=row,column=0, sticky=W, padx=3)
self.K = BooleanVar()
self.K.set(self.args.K)
self.chk = Checkbutton(master, text="Display?", var = self.K)
self.chk.grid (row=row,column=1,padx=3,sticky=W)
CreateToolTip(self.chk,"Displays graphic customization interface for the last description.py step.\nIf not selected, displays all attributes for all key types and all trail levels.")
row += 1
column = 0
self.outDirLabel = Label(master, text = "Output directory")
self.outDirLabel.grid(row=row,column=column, sticky=W, padx=3)
self.outDir = StringVar()
if self.args.D:
self.outDir.set(self.args.D)
else:
self.outDir.set('')
self.outDirEntry = Entry(master, width = WIDTH, textvariable = self.outDir)
column += 1
self.outDirEntry.grid(row=row,column=column, padx=3)
self.optionLabel2 = Label(master, text = "optional")
column += 2
self.optionLabel2.grid(row=row,column=column,sticky=W, padx=3)
# tip
helpText8 = "Storage directory for output files."
self.outDirTip = CreateToolTip(self.outDirEntry, helpText8)
#
row += 1
self.optionLabel = Label(master, text = "Log file")
self.optionLabel.grid(row=row,column=0, sticky=W, padx=3)
self.l = StringVar()
try:
log = self.args.l.name.strip("(<,>")
except:
log = log
self.l.set(log)
self.optionEntry = Entry(master, width = WIDTH, textvariable = self.l)
self.optionEntry.grid(row=row,column=1, padx=3)
row += 2
cbFrame = Frame(master) # create subframe for command buttons
self.run_button = Button(cbFrame, text="Run", command=self.run)
self.run_button.grid(row=row,column=0,padx=12)
self.close_button = Button(cbFrame, text="Close", command=self.Quit)
self.close_button.grid(row=row,column=1,padx=12)
cbFrame.grid(row=row,column=1,columnspan=2,sticky=E+W)
helpText = bitwin.processArgs().format_help()
self.helpbutton = Button(master, text="Help", command = lambda: HelpWindow(text=helpText,name=self.name))
self.helpbutton.grid(row=row,column=2,sticky=W,padx=3)
def initUI(self):
# set frame title
self.parent.title("Configuration settings for %s" % self.XML)
# pack frame
self.pack(fill=BOTH, expand=1)
# configure grid columns
#NCols = max(3,self.K+1)
NCols = 3
for i in range(NCols):
self.columnconfigure(i, pad=3)
# configure grid rows
NRows = self.M + self.T + self.A
for i in range(NRows):
self.rowconfigure(i, pad=3)
row = 0
label = Label(self, text="ROOT directory: %s" % self.RootDir)
label.grid(row=row, columnspan=WIDTH, sticky=W, padx=3)
row += 1
# Module selection
# File
self.compLabel = Label(self, text="Component file")
self.compLabel.grid(row=row, column=0, sticky=W, padx=3)
self.compEntry = Entry(self,
width=WIDTH,
textvariable=self.mod.ModFile)
self.compEntry.grid(row=row, column=1, padx=3)
self.compSelect = Button(self,
text="Select",
command=self.selectModFile)
self.compSelect.grid(row=row, column=2, sticky=W, padx=3)
helpText1 = "Terminal clustering file whose component's contents one wishes to analyze.\nIf left empty, each node of the graph is a component."
self.compTip = CreateToolTip(self.compEntry, helpText1)
row += 1
# Name
self.lab1 = StringVar()
#self.lab1.set("Name of components")
modfile = os.path.split(self.mod.ModFile.get())[1]
#comp_name = os.path.relpath(self.mod.ModFile.get(), start=self.RootDir)
self.lab1.set("Name of components in file %s" % modfile)
label1 = Label(self, textvariable=self.lab1)
label1.grid(row=row, column=0, sticky=W, padx=3)
entry1 = Entry(self, width=WIDTH, textvariable=self.mod.ModName)
entry1.grid(row=row, column=1)
CreateToolTip(entry1, "Name that will identify each component")
row += 1
# Module keys
"""
if self.mod.Keys:
for nT in self.nodeTypes:
label = Label (self,text = "Name of type %d nodes" % nT)
label.grid (row=row,column=0,sticky=W,padx=3)
entry = Entry (self,width=WIDTH,textvariable = self.mod.Keys[nT].name)
entry.grid (row=row,column=1)
chk = Checkbutton(self, text="Display?", var = self.mod.Keys[nT].display)
chk.grid (row=row,column=2)
row +=1
"""
# Trails selection
for trail_index in self.trails:
trail = self.trails[trail_index]
fname = os.path.relpath(trail.filename, start=self.RootDir)
label = Label(self,
text="Trail file ROOT/%s of rank %d" %
(fname, trail_index))
#label = Label (self,text = "Trail file %s of rank %d" % (trail.filename,trail_index))
label.grid(row=row, columnspan=WIDTH, sticky=W, padx=3)
row += 1
# Trail keys
for nT in self.nodeTypes:
label = Label(self, text="Name of type %d nodes" % nT)
label.grid(row=row, column=0, sticky=W, padx=3)
entry = Entry(self,
width=WIDTH,
textvariable=trail.Keys[nT].name)
entry.grid(row=row, column=1)
CreateToolTip(
entry,
"Name for node of type %d in trail file of rank %d" %
(nT, trail_index))
chk = Checkbutton(self,
text="Display?",
var=trail.Keys[nT].display)
chk.grid(row=row, column=2, sticky=W)
CreateToolTip(
chk,
"Select if node of type %d should appear in description" %
nT)
row += 1
Separator(self, orient=HORIZONTAL).grid(row=row,
column=0,
columnspan=WIDTH,
sticky=E + W)
row += 1
label = Label(self, text="List of attributes")
label.grid(row=row, column=0, sticky=W, padx=3)
label = Label(self, text="Display attribute for key type?")
label.grid(row=row, column=1)
row += 1
Separator(self, orient=HORIZONTAL).grid(row=row,
column=0,
columnspan=WIDTH,
sticky=E + W)
row += 1
# Attributes selection
for attr_index in self.attrs:
attr = self.attrs[attr_index]
label = Label(self, text=attr.name)
label.grid(row=row, column=0, sticky=W, padx=3)
# Attr Keys
column = 0
cbFrame = Frame(self)
for nT in self.nodeTypes:
chk = Checkbutton(cbFrame,
text="Key " + str(nT),
var=attr.Keys[nT].display)
chk.pack(side="left", fill=None, expand=False, padx=3)
CreateToolTip(
chk,
"Select if attribute %s is relevant for node of type %d" %
(attr.name, nT))
cbFrame.grid(row=row, column=1)
row += 1
# create OK button
button1 = Button(self, text="OK", command=self.onOK)
button1.grid(row=row, column=0, sticky=E)
self.parent.bind("<Return>", self.onOK)
# create Cancel button
button2 = Button(self, text="Cancel", command=self.onCancel)
button2.grid(row=row, column=2, sticky=W)
self.parent.bind("<Escape>", self.onCancel)
def __init__(self, master, title=None, args=None):
self.master = master
self.args = args
self.name = title
master.title("Startup interface for %s" % title)
self.arguments = dict()
style = Style()
style.configure(".", background="lightgrey")
labelStyle = Style()
labelStyle.configure("TLabel", background="lightgrey")
buttonStyle = Style()
buttonStyle.configure("TButton", background="lightgrey")
chkbuttonStyle = Style()
chkbuttonStyle.configure("TCheckbutton", background="lightgrey")
rbuttonStyle = Style()
rbuttonStyle.configure("TRadiobutton", background="lightgrey")
row = 0
column = 0
self.inEdgeLabel = Label(master, text="Input edge file")
self.inEdgeLabel.grid(row=row, column=column, sticky=W, padx=3)
self.inEdgeFile = StringVar()
if self.args.input_edge_file:
self.inEdgeFile.set(self.args.input_edge_file)
self.inEdgeEntry = Entry(master,
width=WIDTH,
textvariable=self.inEdgeFile)
column += 1
self.inEdgeEntry.grid(row=row, column=column, padx=3)
self.inEdgeSelect = Button(
master,
text="Select",
command=lambda: self.setRequiredFiles(IN=self.inEdgeFile,
OUT=self.outEdgeFile,
TRAIL=self.outTrailFile))
column += 1
self.inEdgeSelect.grid(row=row, column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text="required")
column += 1
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText1 = "Edge file for input graph (two columns, tab-delimited)."
self.inEdgeTip = CreateToolTip(self.inEdgeEntry, helpText1)
##
column += 2
self.outEdgeLabel = Label(master, text="Output edge file")
self.outEdgeLabel.grid(row=row, column=column, sticky=W, padx=3)
self.outEdgeFile = StringVar()
if self.args.output_edge_file:
self.outEdgeFile.set(self.args.output_edge_file)
self.outEdgeEntry = Entry(master,
width=WIDTH,
textvariable=self.outEdgeFile)
column += 1
self.outEdgeEntry.grid(row=row, column=column, padx=3)
self.outEdgeSelect = Button(
master,
text="Select",
command=lambda: self.openFile(var=self.outEdgeFile))
column += 1
self.outEdgeSelect.grid(row=row, column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text="required")
column += 1
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText2 = "Edge file for output graph"
self.outEdgeTip = CreateToolTip(self.outEdgeEntry, helpText2)
#
row += 1
column = 0
self.inTrailLabel = Label(master, text="Input trail file")
self.inTrailLabel.grid(row=row, column=column, sticky=W, padx=3)
self.inTrailFile = StringVar()
if self.args.t:
self.inTrailFile.set(self.args.t)
self.inTrailEntry = Entry(master,
width=WIDTH,
textvariable=self.inTrailFile)
column += 1
self.inTrailEntry.grid(row=row, column=column, padx=3)
self.inTrailSelect = Button(
master,
text="Select",
command=lambda: self.setFile(var1=self.inTrailFile,
var2=self.outTrailFile))
column += 1
self.inTrailSelect.grid(row=row, column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text="optional")
column += 1
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText3 = "Links IDs of current graph to IDs of ROOT graph (two columns, tab-delimited).\nIf skipped, current graph is considered ROOT."
self.inTrailTip = CreateToolTip(self.inTrailEntry, helpText3)
#
column += 2
self.outTrailLabel = Label(master, text="Output trail file")
self.outTrailLabel.grid(row=row, column=column, sticky=W, padx=3)
self.outTrailFile = StringVar()
if self.args.output_trail_file:
self.outTrailFile.set(self.args.output_trail_file)
column += 1
self.outTrailEntry = Entry(master,
width=WIDTH,
textvariable=self.outTrailFile)
self.outTrailEntry.grid(row=row, column=column, padx=3)
column += 1
self.outTrailSelect = Button(
master,
text="Select",
command=lambda: self.openFile(var=self.outTrailFile))
self.outTrailSelect.grid(row=row, column=column, sticky=W, padx=3)
column += 1
self.optionLabel2 = Label(master, text="required")
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText4 = "Links new IDs to ROOT graph"
self.outTrailTip = CreateToolTip(self.outTrailEntry, helpText4)
#
row += 1
column = 0
self.inNodeLabel = Label(master, text="Input node type file")
self.inNodeLabel.grid(row=row, column=column, sticky=W, padx=3)
self.inNodeType = StringVar()
if self.args.n:
self.inNodeType.set(self.args.n)
self.inNodeEntry = Entry(master,
width=WIDTH,
textvariable=self.inNodeType)
column += 1
self.inNodeEntry.grid(row=row, column=column, padx=3)
self.inNodeSelect = Button(
master,
text="Select",
command=lambda: self.setFile(var1=self.inNodeType,
var2=self.outNodeType))
column += 1
self.inNodeSelect.grid(row=row, column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text="for k-partite")
column += 1
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText5 = "Stores node types (two columns, tab-delimited).\nRequired for multipartite (more than bipartite)."
self.inNodeTip = CreateToolTip(self.inNodeEntry, helpText5)
#
column += 2
self.outNodeLabel = Label(master, text="Output node type file")
self.outNodeLabel.grid(row=row, column=column, sticky=W, padx=3)
self.outNodeType = StringVar()
if self.args.N:
self.outNodeType.set(self.args.N)
self.outNodeEntry = Entry(master,
width=WIDTH,
textvariable=self.outNodeType)
column += 1
self.outNodeEntry.grid(row=row, column=column, padx=3)
self.outNodeSelect = Button(
master,
text="Select",
command=lambda: self.openFile(var=self.outNodeType))
column += 1
self.outNodeSelect.grid(row=row, column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text="for k-partite")
column += 1
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText6 = "Updates node types with new nodeIDs.\nRequired when input node type file is given."
self.outNodeTip = CreateToolTip(self.outNodeEntry, helpText6)
#
row += 1
column = 0
self.componentLabel = Label(master, text="Community file")
self.componentLabel.grid(row=row, column=column, sticky=W, padx=3)
self.componentFile = StringVar()
if self.args.c:
self.componentFile.set(self.args.c)
self.componentEntry = Entry(master,
width=WIDTH,
textvariable=self.componentFile)
column += 1
self.componentEntry.grid(row=row, column=column, padx=3)
self.componentSelect = Button(
master,
text="Select",
command=lambda: self.openFile(var=self.componentFile))
column += 1
self.componentSelect.grid(row=row, column=column, sticky=W, padx=3)
self.optionLabel2 = Label(master, text="optional")
column += 1
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText7 = "Specifies grouping of nodes into communities or super-nodes.\nIf not given, input graph is simply renumbered."
self.componentTip = CreateToolTip(self.componentEntry, helpText7)
#
column += 2
self.outDirLabel = Label(master, text="Output directory")
self.outDirLabel.grid(row=row, column=column, sticky=W, padx=3)
self.outDir = StringVar()
if self.args.d:
self.outDir.set(self.args.d)
else:
self.outDir.set("OutputDir")
self.outDirEntry = Entry(master, width=WIDTH, textvariable=self.outDir)
column += 1
self.outDirEntry.grid(row=row, column=column, padx=3)
self.optionLabel2 = Label(master, text="optional")
column += 2
self.optionLabel2.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText8 = "Storage directory for output files.\nIf suppressed, check that in- and output filenames do not collide."
self.outDirTip = CreateToolTip(self.outDirEntry, helpText8)
#
row += 1
column = 0
self.optionLabel = Label(master, text="Clustering file format")
self.optionLabel.grid(row=row, column=column, sticky=W, padx=3)
option_list = ["Component", "Fasta"]
self.C = StringVar()
self.C.set(option_list[0])
if self.args.f:
self.C.set(option_list[1])
self.optionEntry = Combobox(master, width=10, textvariable=self.C)
self.optionEntry['values'] = option_list
column += 1
self.optionEntry.grid(row=row, column=column, sticky=W, padx=3)
# tip
helpText9 = """Specifies format of community file \nComponent=two columns, tab-delimited\nFasta=one line per node, ">" for community ID"""
self.optionTip = CreateToolTip(self.optionEntry, helpText9)
#
column += 2
self.w = BooleanVar()
self.w.set(self.args.w)
self.chk = Checkbutton(master, text="Use weights", var=self.w)
self.chk.grid(row=row, column=column, padx=3, sticky=W)
# tip
helpText10 = "Weighs super-nodes with log(size_of_community)"
self.chkTip = CreateToolTip(self.chk, helpText10)
#
column += 2
self.optionLabel = Label(master, text="Keep community IDs")
self.optionLabel.grid(row=row, column=column, sticky=W, padx=3)
self.K = BooleanVar()
self.K.set(self.args.C)
self.chk = Checkbutton(master, text="", var=self.K)
column += 1
self.chk.grid(row=row, column=column, padx=3, sticky=W)
# tip
helpText11 = "Gives to super-nodes the same ID as in the community file"
self.keepTip = CreateToolTip(self.optionLabel, helpText11)
#
row += 1
column = 1
self.optionLabel = Label(master, text="Log file")
self.optionLabel.grid(row=row, column=0, sticky=W, padx=3)
self.l = StringVar()
try:
log = self.args.l.name.strip("(<,>")
except:
log = log
self.l.set(log)
self.optionEntry = Entry(master, width=WIDTH, textvariable=self.l)
self.optionEntry.grid(row=row, column=1, padx=3)
row += 2
self.run_button = Button(master, text="Run", command=self.run)
self.run_button.grid(row=row, column=2)
self.close_button = Button(master, text="Close", command=self.Quit)
self.close_button.grid(row=row, column=4)
helpText = factorgraph.processArgs().format_help()
self.helpbutton = Button(
master,
text="Help",
command=lambda: HelpWindow(text=helpText, name=self.name))
self.helpbutton.grid(row=row, column=6, sticky=W, padx=3)