def create_UI(self):
self.grid_rowconfigure(0, weight = 1)
self.grid_columnconfigure(0, weight = 1)
central_panel = tkinter.PanedWindow(self, orient = tkinter.HORIZONTAL, sashwidth = self.p * 2, sashrelief = tkinter.RIDGE, background = self.host.back)
central_panel.grid(row = 0, column = 0, sticky = "NSEW")
self.fixed = Aln_basic.TextFrameWithLabelAndButton(central_panel, self.p, None, None,
"'Fixed' alignment:", "Save to file")
self.fixed.button.configure(command = self.save_fixed)
sort_by_tree = tkinter.Button(self.fixed.panel, background = self.host.header, foreground = "#FFFFFF", text = "Sort by tree", command = self.sort_by_tree)
sort_by_tree.grid(row = 0, column = 2, sticky = "NSW", padx = self.p, pady = self.p)
central_panel.add(self.fixed)
self.pure = Aln_basic.TextFrameWithLabelAndButton(central_panel, self.p, None, None,
"'Pure names':", "Save to file")
self.pure.button.configure(command = self.save_pure)
self.run_hmmsearch_Pfam = tkinter.Button(self.pure.panel, state = tkinter.DISABLED, text = "HMM search (Pfam)", command = self.hmmsearch_Pfam)
self.run_hmmsearch_Pfam.grid(row = 0, column = 2, sticky = "NSW", padx = self.p, pady = self.p)
self.run_hmmsearch_COG = tkinter.Button(self.pure.panel, state = tkinter.DISABLED, text = "HMM search (COG)", command = self.hmmsearch_COG)
self.run_hmmsearch_COG.grid(row = 0, column = 3, sticky = "NSW", padx = self.p, pady = self.p)
self.run_TMHMM = tkinter.Button(self.pure.panel, state = tkinter.DISABLED, text = "TMHMM", command = self.TMHMM)
self.run_TMHMM.grid(row = 0, column = 4, sticky = "NSW", padx = self.p, pady = self.p)
tkinter.Label(self.pure.panel, text = "Enter begin, step and nsteps:").grid(row = 1, column = 0, sticky = "NSW")
self.begin_entry = tkinter.Entry(self.pure.panel, width = 8)
self.begin_entry.grid(row = 1, column = 1, sticky = "NSW", padx = self.p, pady = self.p)
self.begin_entry.insert(tkinter.END, 200)
self.step_entry = tkinter.Entry(self.pure.panel, width = 8)
self.step_entry.grid(row = 1, column = 2, sticky = "NSW", padx = self.p, pady = self.p)
self.step_entry.insert(tkinter.END, 50)
self.nsteps_entry = tkinter.Entry(self.pure.panel, width = 8)
self.nsteps_entry.grid(row = 1, column = 3, sticky = "NSW", padx = self.p, pady = self.p)
self.nsteps_entry.insert(tkinter.END, 10)
self.length_histo = tkinter.Button(self.pure.panel, text = "To log", state = tkinter.DISABLED, command = self.histo_to_log)
self.length_histo.grid(row = 1, column = 4, sticky = "NSW", padx = self.p, pady = self.p)
central_panel.add(self.pure)
self.blocks = Aln_basic.TextFrameWithLabelAndButton(central_panel, self.p, None, None,
"Blocks regions:", "Save to file")
self.blocks.button.configure(command = self.save_blocks)
central_panel.add(self.blocks)
self.IDs = Aln_basic.TextFrameWithLabelAndButton(central_panel, self.p, None, None,
"List of IDs:", "Save to file")
self.IDs.button.configure(command = self.save_IDs)
self.ID_save_mode = tkinter.StringVar()
self.ID_save_mode.set("No change")
ID_save_mode = tkinter.OptionMenu(self.IDs.panel, self.ID_save_mode, "No change", " -> gi ", "fix gi-gi", "fix & ->")
ID_save_mode.grid(row = 0, column = 2, sticky = "NW", padx = self.p, pady = self.p)
try: #FIX: version 1.0.0 (if no assignment between gi and id/locus was given, conversion options are disabled)
curr_table = self.host.settings.table_filename
except AttributeError:
ID_save_mode.configure(state = tkinter.DISABLED)
central_panel.add(self.IDs)
self.update_idletasks()
central_panel.sash_place(0, 300, 1)
central_panel.sash_place(1, 1100, 1)
central_panel.sash_place(2, 1500, 1)
def create_UI(self):
self.grid_rowconfigure(0, weight = 1)
self.grid_columnconfigure(0, weight = 1)
central_panel = tkinter.PanedWindow(self, orient = tkinter.HORIZONTAL, sashwidth = self.p * 2, sashrelief = tkinter.RIDGE, background = self.host.back)
central_panel.grid(row = 0, column = 0, sticky = "NSEW")
self.auto_log = Aln_basic.TextFrameWithLabelAndButton(central_panel, self.p, None, None,
"Automatically generated log:", "")
self.auto_log.button.grid_forget()
self.auto_log.text_widget.tag_configure("important", background = "#FFFF00")
self.wrap_auto = tkinter.BooleanVar()
c = tkinter.Checkbutton(self.auto_log.panel, text = "Wrap text", variable = self.wrap_auto, command = self.wrap_configure)
c.grid(row = 0, column = 1, sticky ="NSE", padx = self.p, pady = self.p)
central_panel.add(self.auto_log)
self.manual_log = Aln_basic.TextFrameWithLabelAndButton(central_panel, self.p, None, None,
"Manually generated log:", "")
self.manual_log.button.grid_forget()
self.wrap_manual = tkinter.BooleanVar()
c = tkinter.Checkbutton(self.manual_log.panel, text = "Wrap text", variable = self.wrap_manual, command = self.wrap_configure)
c.grid(row = 0, column = 1, sticky ="NSE", padx = self.p, pady = self.p)
central_panel.add(self.manual_log)
def create_UI(self):
self.grid_rowconfigure(0, weight = 1)
self.grid_columnconfigure(0, weight = 1)
central_panel = tkinter.PanedWindow(self, orient = tkinter.HORIZONTAL, sashwidth = self.p * 2, sashrelief = tkinter.RIDGE, background = self.host.back)
central_panel.grid(row = 0, column = 0, sticky = "NSEW")
self.aln_input_frame = Aln_basic.TextFrameWithLabelAndButton(central_panel, self.p, self.host.header, "#FFFFFF",
"Insert multiple alignment or generate it from the left panel:", "Check input")
self.aln_input_frame.button.configure(command = self.check_input)
central_panel.add(self.aln_input_frame)
self.seq_input_frame = Aln_basic.TextFrameWithLabelAndButton(central_panel, self.p, self.host.header, "#FFFFFF",
"Insert unaligned sequences:", "Align now!")
self.seq_input_frame.button.configure(command = self.align)
central_panel.add(self.seq_input_frame)
self.insert_blocks = tkinter.BooleanVar()
self.insert_blocks.set(False)
c = tkinter.Checkbutton(self.seq_input_frame.panel, text = "Insert BLOCKS & SITE", variable = self.insert_blocks)
c.grid(row = 0, column = 2, sticky ="NSW", padx = self.p, pady = self.p)
tkinter.Label(self.seq_input_frame.panel, text = "maxiters").grid(row = 0, column = 3, sticky = "NSW")
self.maxiters = tkinter.Entry(self.seq_input_frame.panel, width = 2)
self.maxiters.insert(tkinter.END, "2")
self.maxiters.grid(row = 0, column = 4, sticky = "NSW", padx = self.p, pady = self.p)
tkinter.Label(self.seq_input_frame.panel, text = "gapopen").grid(row = 0, column = 5, sticky = "NSW")
self.gapopen = tkinter.Entry(self.seq_input_frame.panel, width = 3)
self.gapopen.insert(tkinter.END, "")
self.gapopen.grid(row = 0, column = 6, sticky = "NSW", padx = self.p, pady = self.p)
tkinter.Label(self.seq_input_frame.panel, text = "gapextend").grid(row = 0, column = 7, sticky = "NSW")
self.gapextend = tkinter.Entry(self.seq_input_frame.panel, width = 3)
self.gapextend.insert(tkinter.END, "")
self.gapextend.grid(row = 0, column = 8, sticky = "NSW", padx = self.p, pady = self.p)
filter_identical = tkinter.Button(self.seq_input_frame.panel, text = "Filter identical", command = self.filter_seq)
filter_identical.grid(row = 0, column = 9, sticky = "NSW", padx = self.p, pady = self.p)
def create_UI(self):
self.grid_rowconfigure(0, weight = 1)
self.grid_columnconfigure(0, weight = 1)
self.input_frame = Aln_basic.TextFrameWithLabelAndButton(self, self.p, self.host.header, "#FFFFFF",
"Insert sequences in FASTA format:", "Obtain taxonomy units")
self.input_frame.grid(row = 0, column = 0, sticky = "NSEW", padx = self.p, pady = self.p)
self.input_frame.button.configure(command = self.filter)
tkinter.Label(self.input_frame.panel, text = "Input format:").grid(row = 0, column = 2, sticky = "NSW")
self.input_format = tkinter.StringVar()
self.input_format.set("My")
input_format = tkinter.OptionMenu(self.input_frame.panel, self.input_format, "URef", "NCBI", "Uniprot", "PDB", "COGalyser", "Basic", "COG", "OldRef", "My_Ref", "My", "Olesya", "German")
input_format.grid(row = 0, column = 3, sticky = "NSW", padx = self.p, pady = self.p)
help_button = tkinter.Button(self.input_frame.panel, state = tkinter.DISABLED, text = "Format help", command = self.show_help)
help_button.grid(row = 0, column = 4, sticky = "NSW", padx = self.p, pady = self.p)
self.configure_frame =
def create_UI(self):
self.grid_rowconfigure(0, weight=1)
self.grid_columnconfigure(0, weight=1)
central_panel = tkinter.PanedWindow(self,
orient=tkinter.HORIZONTAL,
sashwidth=self.p * 2,
sashrelief=tkinter.RIDGE,
background=self.host.back)
central_panel.grid(row=0, column=0, sticky="NSEW")
base_frame = tkinter.Frame(central_panel)
base_frame.columnconfigure(0, weight=1)
base_frame.rowconfigure(1, weight=1)
top_frame = tkinter.Frame(base_frame)
tkinter.Label(top_frame, text="Max e-value:").grid(row=0,
column=0,
sticky="NSW")
self.evalue_threshold = tkinter.Entry(top_frame,
state=tkinter.DISABLED,
width=8)
self.evalue_threshold.grid(row=0,
column=1,
sticky="NSW",
padx=self.p,
pady=self.p)
tkinter.Label(top_frame, text="# of σ (hit):").grid(row=0,
column=2,
sticky="NSW")
self.sigma_num_self = tkinter.Entry(top_frame,
state=tkinter.DISABLED,
width=4)
self.sigma_num_self.grid(row=0,
column=3,
sticky="NSW",
padx=self.p,
pady=self.p)
self.self_hits_button = tkinter.Button(top_frame,
state=tkinter.DISABLED,
text="Find self-hits",
command=self.find_self_hits)
self.self_hits_button.grid(row=0,
column=4,
sticky="NSW",
padx=self.p,
pady=self.p)
self.white_crow_button = tkinter.Button(
top_frame,
state=tkinter.DISABLED,
text="Apply options",
command=self.apply_purification_options)
self.white_crow_button.grid(row=1,
column=4,
sticky="NSW",
padx=self.p,
pady=self.p)
tkinter.Label(top_frame, text="Min length:").grid(row=1,
column=0,
sticky="NSW")
self.min_length = tkinter.Entry(top_frame, width=6)
self.min_length.insert(tkinter.END, "0")
self.min_length.grid(row=1,
column=1,
sticky="NSW",
padx=self.p,
pady=self.p)
tkinter.Label(top_frame, text="Max length:").grid(row=1,
column=2,
sticky="NSW")
self.max_length = tkinter.Entry(top_frame, width=6)
self.max_length.insert(tkinter.END, "10000")
self.max_length.grid(row=1,
column=3,
sticky="NSW",
padx=self.p,
pady=self.p)
top_frame.grid(row=0, column=0, columnspan=2, sticky="NSEW")
y_scrollbar = tkinter.Scrollbar(base_frame)
y_scrollbar.grid(row=1, column=1, sticky="NS")
actions = ttk.Treeview(base_frame,
columns=("action", "organism"),
selectmode="extended",
yscrollcommand=y_scrollbar.set)
y_scrollbar.config(command=actions.yview)
actions.grid(row=1, column=0, sticky="NSEW")
actions.column("action", width=50, anchor="w")
actions.heading("action", text="Action")
actions.column("organism", width=50, anchor="w")
actions.heading("organism", text="Organism")
actions.bind("<Double-Button-1>", self.get_click)
self.actions = actions
self.actions.menu_available = True # To show <ActionMenu> only at this widget
central_panel.add(base_frame)
self.alignment = Aln_basic.TextFrameWithLabelAndButton(
central_panel, self.p, self.host.header, "#FFFFFF",
"Suggested changes in alignment:", "Load domains")
self.alignment.button.configure(state=tkinter.DISABLED,
command=self.create_domain_tags)
self.alignment.text_widget.purify_text_widget = True # To show <TextMenu> only at this widget
self.show_features = tkinter.Button(self.alignment.panel,
state=tkinter.DISABLED,
text="Show domains",
command=self.show_domains)
self.show_features.grid(row=0,
column=2,
sticky="NSW",
padx=self.p,
pady=self.p)
self.hide_features = tkinter.Button(self.alignment.panel,
state=tkinter.DISABLED,
text="Hide domains",
command=self.hide_domains)
self.hide_features.grid(row=0,
column=3,
sticky="NSW",
padx=self.p,
pady=self.p)
self.load_taxonomy = tkinter.Button(self.alignment.panel,
state=tkinter.DISABLED,
text="Color taxonomy",
command=self.color_taxonomy)
self.load_taxonomy.grid(row=0,
column=4,
sticky="NSW",
padx=self.p,
pady=self.p)
self.act = tkinter.Button(self.alignment.panel,
state=tkinter.DISABLED,
text="Apply actions",
background=self.host.header,
foreground="#FFFFFF",
command=self.apply_actions)
self.act.grid(row=0,
column=5,
sticky="NSW",
padx=self.p * 3,
pady=self.p)
tkinter.Label(self.alignment.panel,
text="Presence required (%):").grid(row=0, column=6)
self.presence_entry = tkinter.Entry(self.alignment.panel, width=3)
self.presence_entry.insert(tkinter.END, "0")
self.presence_entry.grid(row=0, column=7, padx=self.p, pady=self.p)
central_panel.add(self.alignment)
self.update_idletasks()
central_panel.sash_place(0, base_frame.winfo_reqwidth(), 1)
def create_UI(self):
self.grid_rowconfigure(0, weight=1)
self.grid_columnconfigure(0, weight=1)
central_panel = tkinter.PanedWindow(self,
orient=tkinter.HORIZONTAL,
sashwidth=self.p * 2,
sashrelief=tkinter.RIDGE,
background=self.host.back)
central_panel.grid(row=0, column=0, sticky="NSEW")
self.input_frame = Aln_basic.TextFrameWithLabelAndButton(
central_panel, self.p, self.host.header, "#FFFFFF",
"Insert FASTA-format sequences:", "=> Convert =>")
self.input_frame.button.configure(command=self.convert)
tkinter.Label(self.input_frame.panel,
text="Input format:").grid(row=0, column=2, sticky="NSW")
self.input_format = tkinter.StringVar()
self.input_format.set("Basic")
#input_format = tkinter.OptionMenu(self.input_frame.panel, self.input_format, "URef", "NCBI", "NCBI_2016", "Uniprot", "PDB", "COGcollator", "Basic", "COG", "OldRef", "My_Ref", "My", "Olesya", "German")
input_format = tkinter.OptionMenu(self.input_frame.panel,
self.input_format, "Basic", "NCBI",
"NCBI_2016-", "Uniprot", "PDB",
"COGcollator", "URef", "My")
input_format.grid(row=0,
column=3,
sticky="NSW",
padx=self.p,
pady=self.p)
help_button = tkinter.Button(self.input_frame.panel,
state=tkinter.DISABLED,
text="Format help",
command=self.show_help)
help_button.grid(row=0,
column=4,
sticky="NSW",
padx=self.p,
pady=self.p)
central_panel.add(self.input_frame)
self.output_frame = Aln_basic.TextFrameWithLabelAndButton(
central_panel, self.p, self.host.header, "#FFFFFF",
"Your result will be shown here:", "")
self.output_frame.button.grid_forget()
tkinter.Label(self.output_frame.panel,
text="Output format:").grid(row=0,
column=1,
sticky="NSW")
self.output_format = tkinter.StringVar()
self.output_format.set("My")
output_format = tkinter.OptionMenu(self.output_frame.panel,
self.output_format, "My", "Basic",
"NCBI", "ID", "Table",
"Same but fixed")
output_format.grid(row=0,
column=2,
sticky="NSW",
padx=self.p,
pady=self.p)
tkinter.Label(self.output_frame.panel,
text="Group label (optional):").grid(row=0,
column=3,
sticky="NSW")
self.output_class = tkinter.Entry(self.output_frame.panel, width=15)
self.output_class.grid(row=0,
column=4,
sticky="NSW",
padx=self.p,
pady=self.p)
self.replace_spaces = tkinter.BooleanVar()
self.replace_spaces.set(True)
c = tkinter.Checkbutton(self.output_frame.panel,
text="Replace spaces",
variable=self.replace_spaces)
c.grid(row=0, column=5, sticky="NSW", padx=self.p, pady=self.p)
self.id_mode = tkinter.StringVar()
self.id_mode.set("GI")
radio = tkinter.Radiobutton(self.output_frame.panel,
text="GI",
variable=self.id_mode,
value="GI")
radio.grid(row=0, column=6, sticky="NSW", padx=self.p, pady=self.p)
radio = tkinter.Radiobutton(self.output_frame.panel,
text="protein_id",
variable=self.id_mode,
value="ID")
radio.grid(row=0, column=7, sticky="NSW", padx=self.p, pady=self.p)
radio = tkinter.Radiobutton(self.output_frame.panel,
text="locus",
variable=self.id_mode,
value="locus")
radio.grid(row=0, column=8, sticky="NSW", padx=self.p, pady=self.p)
self.unalign = tkinter.BooleanVar()
self.unalign.set(False)
c = tkinter.Checkbutton(self.output_frame.panel,
text="Unalign",
variable=self.unalign)
c.grid(row=0, column=9, sticky="NSW", padx=self.p, pady=self.p)
central_panel.add(self.output_frame)
def create_UI(self):
self.grid_rowconfigure(0, weight=1)
self.grid_columnconfigure(0, weight=1)
central_panel = tkinter.PanedWindow(self,
orient=tkinter.HORIZONTAL,
sashwidth=self.p * 2,
sashrelief=tkinter.RIDGE,
background=self.host.back)
central_panel.grid(row=0, column=0, sticky="NSEW")
self.hmmresults_COG = Aln_basic.TextFrameWithLabelAndButton(
central_panel, self.p, None, None, "HMMer (COG):", "")
self.hmmresults_COG.button.grid_forget()
central_panel.add(self.hmmresults_COG)
self.hmmresults_Pfam = Aln_basic.TextFrameWithLabelAndButton(
central_panel, self.p, None, None, "HMMer (Pfam):", "")
self.hmmresults_Pfam.button.grid_forget()
central_panel.add(self.hmmresults_Pfam)
self.TMHMM_results = Aln_basic.TextFrameWithLabelAndButton(
central_panel, self.p, None, None, "TMHMM results:", "Save")
self.TMHMM_results.button.configure(command=self.save_TMHMM)
central_panel.add(self.TMHMM_results)
self.features = Aln_basic.TextFrameWithLabelAndButton(
central_panel, self.p, None, None, "Resulting features:",
"Save to file")
self.features.button.configure(command=self.save_features)
tkinter.Label(self.features.panel,
text="Max e-value:").grid(row=0, column=2, sticky="NSW")
self.evalue_threshold = tkinter.Entry(self.features.panel, width=8)
self.evalue_threshold.insert(tkinter.END, "1e-5")
self.evalue_threshold.grid(row=0,
column=3,
sticky="NSW",
padx=self.p,
pady=self.p)
tkinter.Label(self.features.panel,
text="Min overlap/max_domain_length (%):").grid(
row=0, column=4, sticky="NSW")
self.overlap_threshold = tkinter.Entry(self.features.panel, width=3)
self.overlap_threshold.insert(tkinter.END, "20")
self.overlap_threshold.grid(row=0,
column=5,
sticky="NSW",
padx=self.p,
pady=self.p)
self.feature_mode = tkinter.StringVar()
self.feature_mode.set("COG")
radio = tkinter.Radiobutton(self.features.panel,
text="COG",
variable=self.feature_mode,
value="COG")
radio.grid(row=0, column=6, sticky="NSW", padx=self.p, pady=self.p)
radio = tkinter.Radiobutton(self.features.panel,
text="Pfam",
variable=self.feature_mode,
value="Pfam")
radio.grid(row=0, column=7, sticky="NSW", padx=self.p, pady=self.p)
obtain = tkinter.Button(self.features.panel,
text="Obtain",
background=self.host.header,
foreground="#FFFFFF",
command=self.obtain_features)
obtain.grid(row=0, column=8, sticky="NSW", padx=self.p, pady=self.p)
central_panel.add(self.features)
self.update_idletasks()
central_panel.sash_place(0, 200, 1)
central_panel.sash_place(1, 400, 1)
central_panel.sash_place(2, 600, 1)