def __init__(self, master, model, height=300, width=800):
FramePlot.FramePlot.__init__(self,
master,
model,
xTitle="Glyco Score",
yTitle="Counts")
glyxtoolms.lib.Histogram.__init__(self, 0.2)
self.canvas.config(height=height)
self.canvas.config(width=width)
self.master = master
self.logScore = 0.0
self.NrXScales = 5.0
self.coord = Tkinter.StringVar()
l = ttk.Label(self, textvariable=self.coord)
l.grid(row=4, column=0, sticky="NS")
self.keepZoom = Tkinter.IntVar()
c = Appearance.Checkbutton(self,
text="keep zoom fixed",
variable=self.keepZoom)
c.grid(row=5, column=0, sticky="NS")
self.grid_rowconfigure(0, weight=1)
self.grid_columnconfigure(0, weight=1)
def addFont(self, frame, optionname, text):
label = Appearance.Label(frame, text=text)
label.grid(row=frame.row, column=0, sticky="NW")
var = Tkinter.IntVar()
var.set(self.master.options[optionname]["font"].config()["size"])
entry = Tkinter.Entry(frame, textvariable=var)
entry.grid(row=frame.row, column=1, sticky="NW")
entry.config(bg="white")
var.trace("w",
lambda a, b, c, d=optionname: self.setFontSize(a, b, c, d))
self.addVariable(optionname, "font", var)
var.entry = entry
frame.row += 1
def addPlotMargins(self):
frame = self.addLabelFrame(text="margins")
for name in ["left", "right", "bottom", "top"]:
label = Appearance.Label(frame, text=name + " Margin: ")
label.grid(row=frame.row, column=0, sticky="NW")
var = Tkinter.IntVar()
var.set(self.master.options["margins"][name])
var.trace("w", lambda a, b, c, d=name: self.setMargin(a, b, c, d))
entry = Tkinter.Entry(frame, textvariable=var)
entry.grid(row=frame.row, column=1, sticky="NW")
entry.config(bg="white")
self.addVariable("margins", name, var)
var.entry = entry
frame.row += 1
def addFragmentHighlight(showName=None, text=None, colorName=None):
if showName != None and text != None:
var = Tkinter.BooleanVar()
var.set(self.options["annotations"][showName])
optionsFrame.addVariable("annotations", showName, var)
c = Appearance.Checkbutton(frame, text=text, variable=var)
c.grid(row=frame.row, column=0, columnspan=2, sticky="NWS")
var.trace("w", lambda a,b,c,d=showName,e=var: toggleVisbility(a,b,c,d,e))
if colorName != None:
botton = Tkinter.Button(frame, text="Set Color")
botton.grid(row=frame.row, column=2, sticky="NW")
botton.config(fg=self.options["annotations"][colorName])
botton.config(activeforeground=self.options["annotations"][colorName])
botton.config(command=lambda a=colorName, b=botton: self.setColor(a,b))
frame.row += 1
def createOptions(self, optionsFrame):
def togglePictogram(a, b, c, var):
self.options["axislabel"]["showpicto"] = var.get()
self._paintCanvas(False)
super(OxoniumIonPlot, self).createOptions(optionsFrame)
frameAxis = optionsFrame.getLabelFrame("Axis")
pictogramVar = Tkinter.BooleanVar()
pictogramVar.set(self.options["axislabel"]["showpicto"])
optionsFrame.addVariable("axislabel", "showPicto", pictogramVar)
c = Appearance.Checkbutton(frameAxis,
text="Use Glycan Pictograms",
variable=pictogramVar)
c.grid(row=frameAxis.row, column=0, columnspan=2, sticky="NWS")
frameAxis.row += 1
pictogramVar.trace(
"w", lambda a, b, c, d=pictogramVar: togglePictogram(a, b, c, d))
def __init__(self, master, model):
AnnotatedPlot.AnnotatedPlot.__init__(self,
master,
model,
xTitle="m/z",
yTitle="Intensity [counts]")
self.master = master
self.consensus = None
self.feature = None
self.hit = None
self.selectedFragments = []
self.NrXScales = 5.0
self.referenceMass = 0
self.annotationItems = {}
self.annotations = {}
self.currentAnnotation = None
self.peaksByItem = {}
self.coord = Tkinter.StringVar()
l = ttk.Label(self, textvariable=self.coord)
l.grid(row=4, column=0, sticky="NS")
self.keepZoom = Tkinter.IntVar()
c = Appearance.Checkbutton(self,
text="keep zoom fixed",
variable=self.keepZoom)
c.grid(row=5, column=0, sticky="NS")
self.grid_rowconfigure(0, weight=0)
self.grid_rowconfigure(1, weight=1)
self.grid_columnconfigure(0, weight=1)
# register additional button bindings
self.canvas.bind("<Button-2>", self.button2, "+")
self.canvas.bind("<Button-3>", self.button3, "+")
def __init__(self, master, model):
Tkinter.Toplevel.__init__(self, master=master)
#self.minsize(600, 300)
self.master = master
self.title("Configure glyXtoolMS, and TOPPAS scripts")
self.model = model
self.columnconfigure(0, weight=1)
self.rowconfigure(0, weight=0)
self.rowconfigure(1, weight=0)
self.rowconfigure(2, weight=0)
self.rowconfigure(3, weight=0)
self.rowconfigure(4, weight=1)
self.columnconfigure(0, weight=1)
frameOpenMS = ttk.Labelframe(self, text="OpenMS/TOPPAS Installation")
frameOpenMS.grid(row=0, column=0, sticky="NWES")
frameOpenMS.columnconfigure(0, weight=0)
frameOpenMS.columnconfigure(3, weight=1)
buttonOpenMS = Tkinter.Button(frameOpenMS,
text="Set OpenMS Path",
command=self.setOpenMSPath)
buttonOpenMS.grid(row=0, column=0, sticky="NWES")
self.openMSPathVar = Tkinter.StringVar()
self.openMSPathVar.set(self.model.openMSDir)
self.openMSPathEntry = Tkinter.Entry(frameOpenMS,
textvariable=self.openMSPathVar,
width=60)
self.openMSPathEntry.grid(row=0, column=1, columnspan=3, sticky="NWES")
self.openMSPathEntry.config(bg="white")
self.openMSPathVar.trace("w", self.setTOPPASButtonState)
self.buttonScripts = Tkinter.Button(frameOpenMS,
text="Copy SCRIPTS into OpenMS",
command=self.copyTOPPASFiles)
self.buttonScripts.grid(row=1, column=1)
self.buttonWorkflows = Tkinter.Button(
frameOpenMS,
text="Edit Scriptspath in TOPPAS Workflows",
command=self.editWorkflows)
self.buttonWorkflows.grid(row=1, column=2)
#frameOutput = ttk.Labelframe(self, text="Set TOPPAS output folder")
#frameOutput.grid(row=1, column=0, sticky="NWES")
#frameOutput.columnconfigure(0, weight=0)
#frameOutput.columnconfigure(1, weight=1)
#buttonOutput = Tkinter.Button(frameOutput, text="Set TOPPAS output folder", command=self.setTOPPASOutput)
#self.outputVar = Tkinter.StringVar()
#self.outputVar.set(self.model.toppasOutputDir)
#entryOutput = Tkinter.Entry(frameOutput, textvariable=self.outputVar, width=60)
#entryOutput.config(bg="white")
#
#buttonOutput.grid(row=0, column=0, sticky="NWES")
#entryOutput.grid(row=0, column=1, sticky="NWES")
frameWorkspace = ttk.Labelframe(self, text="Set Workspace")
frameWorkspace.grid(row=2, column=0, sticky="NWES")
frameWorkspace.columnconfigure(0, weight=0)
frameWorkspace.columnconfigure(1, weight=1)
buttonWorkspace = Tkinter.Button(frameWorkspace,
text="Set workspace",
command=self.setWorkspace)
self.workspaceVar = Tkinter.StringVar()
self.workspaceVar.set(self.model.workingdir)
entryWorkspace = Tkinter.Entry(frameWorkspace,
textvariable=self.workspaceVar,
width=60)
entryWorkspace.config(bg="white")
buttonWorkspace.grid(row=0, column=0, sticky="NWES")
entryWorkspace.grid(row=0, column=1, sticky="NWES")
frameTimeAxis = ttk.Labelframe(self, text="Timeaxis")
frameTimeAxis.grid(row=3, column=0, sticky="NWES")
self.timeAxisVar = Tkinter.StringVar()
self.timeAxisVar.set(self.model.timescale)
timeAxisChoice1 = Appearance.Radiobutton(frameTimeAxis,
text="In seconds",
variable=self.timeAxisVar,
value="seconds")
timeAxisChoice2 = Appearance.Radiobutton(frameTimeAxis,
text="In minutes",
variable=self.timeAxisVar,
value="minutes")
timeAxisChoice1.grid(row=0, column=0, sticky="NWS")
timeAxisChoice2.grid(row=0, column=1, sticky="NWS")
frameError = ttk.Labelframe(self, text="Mass Error")
frameError.grid(row=4, column=0, sticky="NWES")
self.errorVar = Tkinter.StringVar()
self.errorVar.set(self.model.errorType)
errorChoice1 = Appearance.Radiobutton(frameError,
text="In Dalton",
variable=self.errorVar,
value="Da")
errorChoice2 = Appearance.Radiobutton(frameError,
text="In ppm",
variable=self.errorVar,
value="ppm")
errorChoice1.grid(row=0, column=0, sticky="NWS")
errorChoice2.grid(row=0, column=1, sticky="NWS")
frameClipboard = ttk.Labelframe(self, text="Clipboard")
frameClipboard.grid(row=5, column=0, sticky="NWES")
self.clipVar = Tkinter.StringVar()
self.clipVar.set(self.model.clipboard)
boards = ('osx', 'qt', 'xclip', 'xsel', 'klipper', 'windows')
# test which boards are available here
avlBoards = []
for board in boards:
try:
pyperclip.set_clipboard(board)
avlBoards.append(board)
except:
pass
avlBoards = ['Tkinter'] + avlBoards
for i, board in enumerate(avlBoards):
clipboardChoice = Appearance.Radiobutton(frameClipboard,
text=board,
variable=self.clipVar,
value=board)
clipboardChoice.grid(row=5 + i / 3, column=1 + i % 3, sticky="NWS")
frameDifferences = ttk.Labelframe(self, text="Massdifferences")
frameDifferences.grid(row=6, column=0, sticky="NWES")
scrollbar = Tkinter.Scrollbar(frameDifferences)
self.tree = ttk.Treeview(frameDifferences,
yscrollcommand=scrollbar.set,
selectmode='browse')
self.columns = ("Mass", "Charge", "Type")
self.tree["columns"] = self.columns
self.tree.grid(row=0, column=0, sticky="NWES")
self.tree["columns"] = self.columns
self.tree.heading("#0",
text="Name",
command=lambda col="#0": self.sortColumn(col))
for col in self.columns:
self.tree.heading(col,
text=col,
command=lambda col=col: self.sortColumn(col))
scrollbar.grid(row=0, column=1, sticky="NWES")
scrollbar.config(command=self.tree.yview)
self.tree.bind("<<TreeviewSelect>>", self.clickedTree)
frameEntry = ttk.Labelframe(frameDifferences, text="Entry")
frameEntry.grid(row=0, column=2, sticky="NWE")
l1 = ttk.Label(frameEntry, text="Name:")
l2 = ttk.Label(frameEntry, text="Mass:")
l3 = ttk.Label(frameEntry, text="Charge:")
l4 = ttk.Label(frameEntry, text="Type:")
l1.grid(row=0, column=0, sticky="NW")
l2.grid(row=1, column=0, sticky="NW")
l3.grid(row=2, column=0, sticky="NW")
l4.grid(row=3, column=0, sticky="NW")
self.v1 = Tkinter.StringVar()
self.v2 = Tkinter.StringVar()
self.v3 = Tkinter.StringVar()
self.v4 = Tkinter.StringVar()
self.v1.trace("w", lambda a, b, c: self.valueChanged("v1"))
self.v2.trace("w", lambda a, b, c: self.valueChanged("v2"))
self.v3.trace("w", lambda a, b, c: self.valueChanged("v3"))
self.v4.trace("w", lambda a, b, c: self.valueChanged("v4"))
self.e1 = Tkinter.Entry(frameEntry, textvariable=self.v1)
self.e2 = Tkinter.Entry(frameEntry, textvariable=self.v2)
self.e3 = Tkinter.Entry(frameEntry, textvariable=self.v3)
self.e4 = Tkinter.Entry(frameEntry, textvariable=self.v4)
self.e1.grid(row=0, column=1, sticky="NW")
self.e2.grid(row=1, column=1, sticky="NW")
self.e3.grid(row=2, column=1, sticky="NW")
self.e4.grid(row=3, column=1, sticky="NW")
self.e1.config(bg="white")
self.e2.config(bg="white")
self.e3.config(bg="white")
self.e4.config(bg="white")
frameEntry2 = ttk.Frame(frameEntry)
frameEntry2.grid(row=4, column=0, columnspan=2, sticky="NWES")
self.b1 = Tkinter.Button(frameEntry2,
text="Delete Entry",
command=self.deleteEntry)
self.b2 = Tkinter.Button(frameEntry2,
text="New Entry",
command=self.newEntry)
self.b1.grid(row=0, column=0, sticky="SW")
self.b2.grid(row=0, column=1, sticky="SE")
# add data
for mass, name, charge, typ in self.model.massdifferences:
self.tree.insert("",
"end",
text=name,
values=(str(round(mass, 4)), str(charge), typ))
self.sorting = ("#0", False)
frameButtons = ttk.Frame(self)
frameButtons.grid(row=7, column=0, sticky="NWES")
cancelButton = Tkinter.Button(frameButtons,
text="Cancel",
command=self.cancel)
self.saveButton = Tkinter.Button(frameButtons,
text="Save options",
command=self.save)
cancelButton.grid(row=0, column=0, sticky="NWES")
self.saveButton.grid(row=0, column=1, sticky="NWES")
# run OpenMS Check
self.setTOPPASButtonState()
self.model.centerWidget(self.master, self)