/
OptimizerMainWindow.py
504 lines (385 loc) · 21.4 KB
/
OptimizerMainWindow.py
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'''
Created on 14.02.2015
@author: David
'''
from tkinter import Tk, Frame, LabelFrame, Label, Button, Listbox, Scrollbar,\
Toplevel, Entry
from tkinter.scrolledtext import ScrolledText
from tkinter.ttk import Combobox
from tkinter import W, E, N, S
import tkinter.filedialog
from tkinter.messagebox import showinfo
import sequenceIO
import colorsys
from Bio.Restriction.Restriction_Dictionary import rest_dict
import tkinter
from test.test_importlib import source
from SeqUtils import stripCharsNotInList
from fileinput import filename
class SpeciesSearchDialog():
def __init__(self, parent, caller):
# main window
self.parent=parent
# dialog that called this second dialog
self.caller=caller
self.gui = Toplevel(parent.guiRoot)
self.gui.grab_set()
self.gui.focus()
self.gui.columnconfigure(0, weight=1)
self.gui.rowconfigure(1, weight=1)
self.entrySearch = Entry(self.gui)
self.buttonSearch = Button(self.gui, text=" Search ")
self.buttonAdd = Button(self.gui, text=" Add Species ")
self.buttonClose = Button(self.gui, text=" Close Window ")
self.frameResults = Frame(self.gui)
self.frameResults.columnconfigure(0, weight=1)
self.frameResults.rowconfigure(0, weight=1)
self.scrollResults = Scrollbar(self.frameResults, orient="vertical")
self.scrollResults.grid(row=0, column=1, sticky="ns")
self.listResults = Listbox(self.frameResults, width=70, height=20)
self.listResults.grid(row=0, column=0, sticky="nswe")
self.listResults.config(yscrollcommand=self.scrollResults.set)
self.scrollResults.config(command=self.listResults.yview)
self.entrySearch.grid(row=0, column=0, columnspan=2, sticky="we", padx=5, pady=5)
self.frameResults.grid(row=1, column=0, columnspan=3, sticky="nswe", padx=5, pady=5)
self.buttonSearch.grid(row=0, column=2, padx=5, pady=5, sticky="e")
self.buttonAdd.grid(row=2, column=1, padx=5, pady=5, sticky="e")
self.buttonClose.grid(row=2, column=2, padx=5, pady=5, sticky="e")
self.gui.protocol("WM_DELETE_WINDOW", self.actionClose)
self.buttonClose.bind("<ButtonRelease>", self.actionClose)
self.buttonAdd.bind("<ButtonRelease>", self.actionAdd)
self.buttonSearch.bind("<ButtonRelease>", self.actionSearch)
self.entrySearch.bind("<Return>", self.actionSearch)
self.gui.update()
self.gui.minsize(self.gui.winfo_width(), self.gui.winfo_height())
self.gui.mainloop()
def actionAdd(self, event):
try:
selection = self.listResults.selection_get()
selectionSplit = selection.split(":\t", 1)
selectionSplit2 = selectionSplit[1].split("\t")
if not (selectionSplit[0], selectionSplit2[0]) in self.parent.optimizer.speciesList:
self.parent.optimizer.speciesList.append((selectionSplit[0], selectionSplit2[0].strip()))
self.caller.gui.event_generate("<<Update>>")
except tkinter.TclError :
# no selection
pass
def actionSearch(self, event):
query = self.entrySearch.get()
if(query):
self.listResults.delete(0, "end")
results = self.parent.optimizer.SPSUMHandler.search(query)
# sort results by nr of CDS
results = sorted(results.items(), reverse=True, key=lambda x: (int(x[1][1])))
for name, (taxid, ncs) in results:
self.listResults.insert("end", taxid + ":\t " + name + " \t(" + ncs + " CDS)")
def actionClose(self, event=None):
self.caller.gui.event_generate("<<Update>>", when="tail")
self.gui.destroy()
class SpeciesListDialog():
def __init__(self, parent):
self.parent = parent
self.gui = Toplevel(parent.guiRoot)
self.gui.grab_set()
self.gui.focus()
self.gui.columnconfigure(0, weight=1)
self.gui.rowconfigure(1, weight=1)
Label(self.gui, text="Registered Species:").grid(row=0, column=0, pady=5, padx=5, sticky="w")
self.listRegisteredSpecies = Listbox(self.gui, width=70)
self.buttonAdd = Button(self.gui, text=" + ")
self.buttonDel = Button(self.gui, text=" - ")
self.listRegisteredSpecies.grid(row=1, column=0, columnspan=3, sticky="nswe", pady=5, padx=5)
self.buttonAdd.grid(row=2, column=1, pady=5, padx=5)
self.buttonDel.grid(row=2, column=2, pady=5, padx=5)
# Set (minimum + max) Window size
self.gui.update()
self.gui.minsize(self.gui.winfo_width(), self.gui.winfo_height())
# self.gui.maxsize(self.gui.winfo_width(), self.gui.winfo_height())
self.actionUpdate(None)
self.gui.bind("<<Update>>", self.actionUpdate)
self.gui.protocol("WM_DELETE_WINDOW", self.actionClose)
self.buttonDel.bind("<ButtonRelease>", self.actionDel)
self.buttonAdd.bind("<ButtonRelease>", self.actionAdd)
self.gui.mainloop()
def actionClose(self):
self.parent.guiRoot.event_generate("<<Update>>", when="tail")
self.gui.destroy()
def actionUpdate(self, event):
self.listRegisteredSpecies.delete(0, "end")
for (taxid, name) in self.parent.optimizer.speciesList:
self.listRegisteredSpecies.insert("end", taxid + ": " + name)
def actionDel(self, event):
try:
selection = self.listRegisteredSpecies.selection_get()
selectionSplit = selection.split(": ")
self.parent.optimizer.speciesList.remove((selectionSplit[0], selectionSplit[1]))
self.gui.event_generate("<<Update>>")
except tkinter.TclError :
# no selection
pass
def actionAdd(self, Event):
SpeciesSearchDialog(self.parent, self)
class AddRestrictionDialog():
def __init__(self, parent):
self.parent = parent
self.gui = Toplevel(parent.guiRoot)
self.gui.grab_set()
self.gui.focus()
self.gui.columnconfigure(0, weight=1)
self.gui.columnconfigure(1, weight=1)
Label(self.gui, text="Enzyme:").grid(row=0, column=0, sticky="e", padx=5)
self.entryEnzyme = Entry(self.gui)
self.entryEnzyme.grid(row=0, column=1, sticky="w", padx=5, pady=10)
self.frameButtonGroup = Frame(self.gui)
self.frameButtonGroup.grid(row=1, column=0, columnspan=2, pady=10)
self.buttonOK = Button(self.frameButtonGroup, text=" OK ")
self.buttonCancel = Button(self.frameButtonGroup, text=" Cancel ")
self.buttonOK.grid(row=0, column=1, sticky="w", padx=5)
self.buttonCancel.grid(row=0, column=0, sticky="e", padx=5)
# Set (minimum + max) Window size
self.gui.update()
self.gui.minsize(self.gui.winfo_width(), self.gui.winfo_height())
self.gui.maxsize(self.gui.winfo_width(), self.gui.winfo_height())
self.entryEnzyme.focus()
self.buttonOK.bind("<ButtonRelease>", self.actionOK)
self.buttonCancel.bind("<ButtonRelease>", self.actionCancel)
self.entryEnzyme.bind("<Return>", self.actionOK)
self.gui.mainloop()
# self.gui.grab_release()
# self.gui.destroy()
def actionOK(self, event):
enzymeString = self.entryEnzyme.get()
if enzymeString in rest_dict.keys():
if enzymeString in self.parent.optimizer.restrictionEnzymeList:
showinfo("", (enzymeString + " was already added to the list"))
return
self.parent.optimizer.restrictionEnzymeList.append(enzymeString)
self.parent.guiRoot.event_generate("<<Update>>", when="tail")
self.gui.destroy()
else:
showinfo("", (enzymeString + " is not a valid restriction enzyme"))
def actionCancel(self, event):
self.gui.destroy()
class OptimizerMainWindow():
'''
classdocs
'''
#TODO: change that name
def reactToClick(self, event):
a = AddRestrictionDialog(self)
def __init__(self, optimizer):
# always have a reference to model/controller
self.optimizer = optimizer
# setup main GUI and make stretchable
self.guiRoot = Tk()
self.guiRoot.title("OPTIMIZR")
self.guiRoot.columnconfigure(1, weight=1)
self.guiRoot.rowconfigure(0, weight=1)
# left (settings) and right (sequences) part
self.frameLeft = Frame(self.guiRoot)
self.frameLeft.grid(row=0, column=0, sticky=W+E+N+S)
self.frameLeft.columnconfigure(0, weight=1)
self.frameRight = Frame(self.guiRoot)
self.frameRight.grid(row=0, column=1, sticky=W+E+N+S)
self.frameRight.columnconfigure(0, weight=1)
self.frameRight.rowconfigure(0, weight=1)
self.frameRight.rowconfigure(1, weight=1)
self.frameSpeciesControll = LabelFrame(self.frameLeft, text="Species", pady=10, padx=10)
self.frameSpeciesControll.columnconfigure(1, weight=1)
self.frameOptimizationControll = LabelFrame(self.frameLeft, text="Optimization", pady=10, padx=10)
self.frameRestrictionControll = LabelFrame(self.frameLeft, text="Restriction Enzymes", pady=10, padx=10)
self.frameSpeciesControll.grid(row=0, column=0, sticky=W+E, padx=10, pady=10)
self.frameOptimizationControll.grid(row=1, column=0, sticky=W+E, padx=10, pady=10)
self.frameRestrictionControll.grid(row=2, column=0, sticky=W+E, padx=10, pady=10)
# Species Controll
Label(self.frameSpeciesControll, text="Source:").grid(row=0, column=0)
Label(self.frameSpeciesControll, text="Target:").grid(row=1, column=0)
self.comboSourceSpecies = Combobox(self.frameSpeciesControll, state="readonly")
self.comboSourceSpecies.grid(row=0, column=1, pady=5, sticky="ew")
self.comboTargetSpecies = Combobox(self.frameSpeciesControll, state="readonly")
self.comboTargetSpecies.grid(row=1, column=1, pady=5, sticky="we")
self.buttonSpeciesList = Button(self.frameSpeciesControll, text="Edit Species List")
self.buttonSpeciesList.grid(row=2, column=1, pady=5, sticky="e")
self.comboSourceSpecies.bind("<<ComboboxSelected>>", self.actionOptimizerSettingsChanged)
self.comboTargetSpecies.bind("<<ComboboxSelected>>", self.actionOptimizerSettingsChanged)
# Optimization Controll
Label(self.frameOptimizationControll, text="Optimization Strategy:").grid(row=0, column=0)
self.comboOptimizationStrategy = Combobox(self.frameOptimizationControll, state="readonly")
self.comboOptimizationStrategy.grid(row=0, column=1)
self.comboOptimizationStrategy["values"] = self.optimizer.possibleOptimizationStrategies
self.comboOptimizationStrategy.bind("<<ComboboxSelected>>", self.actionOptimizerSettingsChanged)
# Restriction Enzymes
self.listRestriction = Listbox(self.frameRestrictionControll)
self.listRestriction.grid(row=0, column=0, columnspan=3, pady=5, sticky=W+E)
self.frameRestrictionControll.columnconfigure(0, weight=1)
self.buttonRestricionAdd = Button(self.frameRestrictionControll, text=" + ")
self.buttonRestricionDel = Button(self.frameRestrictionControll, text=" - ")
self.buttonRestricionAdd.grid(row=1, column=1, padx=5)
self.buttonRestricionDel.grid(row=1, column=2, padx=5)
# Source Sequence Frame
self.frameSourceSequence = LabelFrame(self.frameRight, text="Source Sequence", padx=10, pady=10)
self.frameResultSequence = LabelFrame(self.frameRight, text="Result Sequence", padx=10, pady=10)
self.frameSourceSequence.grid(row=0, column=0, sticky="wens", padx=10, pady=10)
self.frameResultSequence.grid(row=1, column=0, sticky="wens", padx=10, pady=10)
self.buttonSourceLoad = Button(self.frameSourceSequence, text=" Load ")
self.textSourceSeq = ScrolledText(self.frameSourceSequence, height=10)
self.buttonSourceLoad.grid(row=0, column=1, sticky="e", pady=5)
self.textSourceSeq.grid(row=1, column=0, columnspan=2, sticky="wens")
self.frameSourceSequence.columnconfigure(0, weight=1)
self.frameSourceSequence.rowconfigure(1, weight=1)
self.textSourceSeq.frame.columnconfigure(1, weight=1)
self.textSourceSeq.frame.rowconfigure(0, weight=1)
self.buttonOptimize = Button(self.frameResultSequence, text=" OPTIMIZE! ")
self.buttonOptimize.bind("<ButtonRelease>", self.actionOptimize)
self.buttonRemoveRestriction = Button(self.frameResultSequence, text=" RESTRICTION-B-GONE! ")
self.buttonRemoveRestriction.bind("<ButtonRelease>", self.actionRemoveRestricion)
self.buttonSaveResult = Button(self.frameResultSequence, text=" Save ")
self.textResultSequence = ScrolledText(self.frameResultSequence, height=10)
self.buttonOptimize.grid(column=0, row=0, pady=5, sticky="w")
self.buttonRemoveRestriction.grid(column=1, row=0, pady=5, padx=10, sticky="w")
self.textResultSequence.grid(row=1, column=0, columnspan=4, sticky="wens")
self.buttonSaveResult.grid(row=2, column=3, pady=5, sticky="e")
self.frameResultSequence.columnconfigure(2, weight=1)
self.frameResultSequence.rowconfigure(1, weight=1)
self.textResultSequence.frame.columnconfigure(1, weight=1)
self.textResultSequence.frame.rowconfigure(0, weight=1)
self.textSourceSeq.bind("<<Modified>>", self.actionSequenceModified)
self.textResultSequence.bind("<<Modified>>", self.actionSequenceModified)
#generate color tags for textboxes
for i in range(101):
#green for normal codons
(r,g,b) = colorsys.hsv_to_rgb(210/360, i/100, 1.0)
colorHex = "#%02x%02x%02x" % (int(r*255), int(g*255), int(b*255))
self.textSourceSeq.tag_config("normal"+str(i), background=colorHex)
self.textResultSequence.tag_config("normal"+str(i), background=colorHex)
#red for codons with restriction sites
(r,g,b) = colorsys.hsv_to_rgb(5/360, i/100, 1.0)
colorHex = "#%02x%02x%02x" % (int(r*255), int(g*255), int(b*255))
self.textSourceSeq.tag_config("restrict"+str(i), background=colorHex)
self.textResultSequence.tag_config("restrict"+str(i), background=colorHex)
# Set (minimum + max) Window size
self.guiRoot.update()
self.guiRoot.minsize(self.guiRoot.winfo_width(), self.guiRoot.winfo_height())
self.buttonRestricionAdd.bind("<ButtonRelease>", self.reactToClick)
self.buttonRestricionDel.bind("<ButtonRelease>", self.actionRestrictionEnzymeDelete)
self.buttonSpeciesList.bind("<ButtonRelease>", self.actionEditSpeciesButton)
self.buttonSourceLoad.bind("<ButtonRelease>", self.actionLoadSequence)
self.buttonSaveResult.bind("<ButtonRelease>", self.actionSaveSequence)
# TEST
# self.listRestriction.insert("end", "EcoRI")
# self.listRestriction.insert("end", "BamHI")
#
# dummy event to manually trigger update
self.guiRoot.bind("<<Update>>", self.actionUpdate)
self.actionUpdate(None)
self.guiRoot.mainloop()
def actionRestrictionEnzymeDelete(self, event):
try:
selectedEnzyme = self.listRestriction.selection_get()
self.optimizer.restrictionEnzymeList.remove(selectedEnzyme)
self.guiRoot.event_generate("<<Update>>")
except tkinter.TclError :
# no selection
pass
def actionUpdate(self, event):
# print("update called")
# clear list of restriction enzymes
self.listRestriction.delete(0, "end")
for r in self.optimizer.restrictionEnzymeList:
self.listRestriction.insert("end", r)
self.comboSourceSpecies.delete(0, "end")
self.comboTargetSpecies.delete(0, "end")
speciesValues = list()
for (taxid, name) in self.optimizer.speciesList:
speciesValues.append(taxid + ": " + name)
self.comboSourceSpecies["values"] = speciesValues
self.comboTargetSpecies["values"] = speciesValues
if self.comboSourceSpecies.get() not in speciesValues:
self.comboSourceSpecies.set("")
if self.comboTargetSpecies.get() not in speciesValues:
self.comboTargetSpecies.set("")
self.textSourceSeq.edit_modified(True)
self.textResultSequence.edit_modified(True)
self.optimizer.saveConfig("config.ini")
def actionEditSpeciesButton(self, event):
speciesListDialog = SpeciesListDialog(self)
def actionOptimizerSettingsChanged(self, event=None):
# print("Something happened")
strategy = self.comboOptimizationStrategy.get()
sourceString = self.comboSourceSpecies.get()
targetString = self.comboTargetSpecies.get()
if not (strategy and sourceString and targetString):
return
sourceTaxid = sourceString.split(":")[0]
targetTaxid = targetString.split(":")[0]
self.optimizer.setOptimizer(sourceTaxid, targetTaxid, strategy)
self.textSourceSeq.edit_modified(True)
self.textResultSequence.edit_modified(True)
# self.optimizer.testPrint()
def actionOptimize(self, event=None):
self.optimizer.runOptimization()
self.textSourceSeq.edit_modified(True)
self.textResultSequence.edit_modified(True)
def actionRemoveRestricion(self, event=None):
self.optimizer.runRestricionRemoval()
self.textSourceSeq.edit_modified(True)
self.textResultSequence.edit_modified(True)
def actionSequenceModified(self, event=None):
# necessary if, otherwise -> infinite loop
if self.textSourceSeq.edit_modified():
seq = self.textSourceSeq.get("1.0", "end").strip()
seq = stripCharsNotInList(seq.upper(), ['A', 'C', 'G', 'T'])
self.optimizer.setSourceSeq(seq)
oldInsert = self.textSourceSeq.index("insert")
self.textSourceSeq.delete("1.0", "end")
sourceCodons = self.optimizer.getCodonsForPrint(True)
if not sourceCodons:
self.textSourceSeq.insert("end", self.optimizer.sourceSequence)
else:
for (co, sc, r) in sourceCodons:
if sc:
if not r:
self.textSourceSeq.insert("end", co, "normal"+str(int(sc*100)))
#print("normal"+str(int(sc*100)))
else:
self.textSourceSeq.insert("end", co, "restrict"+str(int(sc*100)))
else:
# remainder without color
self.textSourceSeq.insert("end", co)
self.textSourceSeq.mark_set("insert", oldInsert)
# reset the modified status at the very end
self.textSourceSeq.edit_modified(False)
if self.textResultSequence.edit_modified():
seq = self.textResultSequence.get("1.0", "end").strip()
# self.optimizer.setOptimizedSeq(seq)
oldInsert = self.textResultSequence.index("insert")
self.textResultSequence.delete("1.0", "end")
targetCodons = self.optimizer.getCodonsForPrint(False)
if not targetCodons:
self.textSourceSeq.insert("end", self.optimizer.optimizedSequence)
else:
for (co, sc, r) in targetCodons:
if sc:
if not r:
self.textResultSequence.insert("end", co, "normal"+str(int(sc*100)))
#print("normal"+str(int(sc*100)))
else:
self.textResultSequence.insert("end", co, "restrict"+str(int(sc*100)))
else:
# remainder without color
self.textResultSequence.insert("end", co)
self.textSourceSeq.mark_set("insert", oldInsert)
self.textResultSequence.edit_modified(False)
def actionLoadSequence(self, event=None):
filename = tkinter.filedialog.askopenfilename()
if filename:
seq = sequenceIO.readFile(filename)
self.textSourceSeq.delete("1.0", "end")
self.textSourceSeq.insert("end", seq)
self.textSourceSeq.edit_modified(True)
def actionSaveSequence(self, event=None):
filename = tkinter.filedialog.asksaveasfilename()
if filename:
# print("file is " + filename)
with open(filename, mode='w') as fd:
fd.write(self.optimizer.optimizedSequence)