__main__.py 14.6 KB
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#!/usr/bin/env python3

from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
from matplotlib.widgets import SpanSelector
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from matplotlib.gridspec import GridSpec
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from PyQt5 import QtCore
from PyQt5 import QtWidgets
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from PyQt5 import QtGui
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from PyQt5 import QtPrintSupport
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from rawprasslib import load_raw
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from rawprasslib import rawprasslib
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from prasopes.predictmz import predict as getmzpattern
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from io import BytesIO
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import numpy as np
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import prasopes.graphtools as gt
import prasopes.filetools as ft
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import prasopes.zcetools as zce
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import prasopes.drltools as drl
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import prasopes.config as cf
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import prasopes.tangoicons
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import sys
import matplotlib
import logging
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import os.path
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matplotlib.use("Qt5Agg")


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class update_signal(QtCore.QObject):
    signal = QtCore.pyqtSignal()


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def load_file(parent, chrom_plot, spc, d_set, ms_s, fn, chrom_s,
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              update, settings, filename=None):
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    """populates dataset and plots it"""
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    directory=settings.value("open_folder")
    if fn[0] is not None:
        directory=fn[0]
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    if filename == None:
        filename = QtWidgets.QFileDialog.getOpenFileName(
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            caption="Open spectrum",
            directory=directory,
            filter="Finnigan RAW files (*.raw, *.RAW)")[0]
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    if filename is not '' and os.path.isfile(filename):
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        try:
            d_set['chrom_dat'], d_set['masses'], d_set['matrix'] \
                = load_raw(filename, settings.value("tmp_location"))
        except rawprasslib.ParsingException as pex:
            QtWidgets.QMessageBox.critical(
                parent, "Opening of the file has failed!",
                "File is incompatible with the rawprasslib, "
                "canceling request!\n\n"
                "Error message:\n{}".format(pex.args[0]))
            return

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        gt.populate(chrom_plot, spc, d_set, ms_s, chrom_s)
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        fn[0] = filename
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        parent.setWindowTitle("Prasopes - {}".format(
            os.path.basename(filename)))
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        update.signal.emit()
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def print_graph(data_set, mass_spec, chrom_spec, spect, fn):
    def printimage(printdevice, img):
        painter = QtGui.QPainter(printdevice)
        painter.drawImage(QtCore.QPoint(0,0), img)
        painter.end()
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    printfig = Figure(figsize=(10, 4), dpi=300)
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    canvas = FigureCanvas(printfig)
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    printplot = printfig.add_subplot(111)
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    printplot.set_xlim(spect.get_xlim())
    printplot.set_ylim(spect.get_ylim())
    ydata = [line.get_data()[1] for line in spect.lines]
    for yline in ydata:
        spect = mass_spec.copy()
        spect['y'] = yline
        gt.pop_plot(printplot,spect)
    cache_file = BytesIO()
    printfig.savefig(cache_file)
    cache_file.seek(0)
    image = QtGui.QImage.fromData(cache_file.read())
    #TODO: substitute the QPrintPreviewDialog with QPrintPreviewWidget
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    printPreview = QtPrintSupport.QPrintPreviewDialog()
    printer = printPreview.printer()
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    printer.setResolution(600)
    printer.setPageSize(printer.A5)
    printer.setDuplex(printer.DuplexNone)
    printPreview.paintRequested.connect(lambda:
            printimage(printer, image))
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    printPreview.exec()


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def update_spectrum(condition, chromatogram, spect, ds,
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                    ms, fn, chrom, config):
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    if fn[0] is not None and condition:
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        slims = [spect.get_xlim(), spect.get_ylim()]
        ds['chrom_dat'], ds['masses'], ds['matrix'] \
            = load_raw(fn[0], config.value("tmp_location"))
        gt.populate(chromatogram, spect, ds, ms, chrom)
        spect.set_xlim(slims[0])
        spect.set_ylim(slims[1])
        spect.get_figure().canvas.draw()


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def dropped(event, parent, chromatogram, spectrum, ds, ms, filename,
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            chrom, update, config):
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    dropurl = event.mimeData().urls()[0].toLocalFile()
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    load_file(parent, chromatogram, spectrum, ds, ms, filename,
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              chrom, update, config, filename=dropurl)
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def drag_entered(event):
    if event.mimeData().hasUrls() and event.mimeData().urls()[0]\
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        .toLocalFile().lower().endswith('.raw'):
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        event.accept()


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def predictmz(form, chromatogram, spect, ds, ms, chrom):
    text = form.text()
    if text == "":
        ms["predict"] = None
        return
    slims = [spect.get_xlim(), spect.get_ylim()]
    ms["predict"] = getmzpattern(text)
    gt.populate(chromatogram, spect, ds, ms, chrom)
    spect.set_xlim(slims[0])
    spect.set_ylim(slims[1])
    spect.get_figure().canvas.draw()


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def about(parent):
    """constructs window with "about" info"""
    QtWidgets.QMessageBox.information(
            parent, "About Prasopes",
            "Prasopes Finnigan raw file viewer\n\n"
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            "Version: 0.0.10 (alpha)")
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def main():
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    # ds for data_set, ms for mass_spec_dataset, chrom for chrom_dataset
    ds = dict(chrom_dat=None, masses=None, matrix=None)
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    ms = dict(x=[0], y=[0], annotation=[],
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              name="Spectrum", xlabel="m/z", ylabel="ion count",
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              xtics=20, predict=None)
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    chrom = dict(x=[0], y=[0], t_start=None, t_end=None,
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                 name="Chromatogram", xlabel="time(min)",
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                 ylabel="total ion count", timesarg=None)
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    filename = [None]
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    drlcache = [None, None]
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    update = update_signal()
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    config = cf.settings()

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    p_logger = logging.getLogger('parseLogger')
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    drl_logger = logging.getLogger('drlLogger')
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    zce_logger = logging.getLogger('zceLogger')
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    logging.basicConfig()
    p_logger.setLevel("WARN")
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    #drl_logger.setLevel("INFO")
    drl_logger.setLevel("DEBUG")
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    zce_logger.setLevel("DEBUG")
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    graph = Figure(figsize=(5, 4), dpi=100, facecolor="None")
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    grid = graph.add_gridspec(2, 1)
    chromatogram = graph.add_subplot(grid[0,0], facecolor=(1, 1, 1, 0.8))
    spectrum = graph.add_subplot(grid[1,0], facecolor=(1, 1, 1, 0.8))
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    graph.tight_layout()
    mpl_canvas = FigureCanvas(graph)
    mpl_canvas.setStyleSheet("background-color:transparent;")
    mpl_canvas.setAutoFillBackground(False)
    mpl_canvas.setFocusPolicy(QtCore.Qt.ClickFocus)
    
    gt.pan_factory(chromatogram)
    gt.zoom_factory(chromatogram, 1.15)
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    gt.arrow_factory(spectrum, chromatogram, ds, ms, chrom)
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    gt.pan_factory(spectrum, ms)
    gt.zoom_factory(spectrum, 1.15, ms)
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    mass_selector = SpanSelector(
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        spectrum, lambda x_min, x_max: gt.pick_masses(
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            x_min, x_max, spectrum, ms), 'horizontal', minspan=0.01,
        useblit=True, rectprops=dict(alpha=0.15, facecolor='purple'),
        button=3)
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    time_selector = SpanSelector(
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         chromatogram, lambda x_min, x_max: gt.pick_times(
             x_min, x_max, spectrum, ds, chromatogram, ms, chrom), 
         'horizontal', useblit=True, rectprops=dict(
             alpha=0.15, facecolor='purple'), button=3)

    app = QtWidgets.QApplication(sys.argv)
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    main_window = QtWidgets.QMainWindow(windowTitle="Prasopes")
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    if QtGui.QIcon.themeName() is "":
        QtGui.QIcon.setThemeName("TangoMFK")

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    openact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
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        "document-open"), "&Open...", None)
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    openact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_O)
    openact.triggered.connect(lambda: load_file(
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        main_window, chromatogram, spectrum, ds, ms, filename, chrom,
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        update, config))
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    exportact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
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        "document-save-as"), "&Export...", None)
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    exportact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_E)
    exportact.triggered.connect(lambda: ft.export_dial(
        ms, chrom, filename, main_window))
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    printact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "document-print"), "&Print", None)
    printact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_P)
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    printact.triggered.connect(lambda: print_graph(
        ds, ms, chrom, spectrum, filename))
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    settingsact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
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        "preferences-system"), "&Settings...", None)
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    settingsact.triggered.connect(lambda: cf.dial(main_window))
    quitact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
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        "application-exit"), "&Quit", None)
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    quitact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_Q)
    quitact.triggered.connect(main_window.close)
    zceact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
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        "applications-utilities"), "&TSQ zce...", None)
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    zceact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_T)
    zceact.triggered.connect(lambda: zce.dialog(
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        main_window, ds, filename, update))
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    drlact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
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        "applications-utilities"), "&DRL...", None)
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    drlact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_D)
    drlact.triggered.connect(lambda: drl.main_window(
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        main_window, ds, filename, drlcache, update))
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    aboutact = QtWidgets.QAction("&About Prasopes", None)
    aboutact.triggered.connect(lambda: about(main_window))
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    autozoomy = QtWidgets.QAction(QtGui.QIcon.fromTheme(
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        "zoom-original"), "Auto Zoom Y", None, checkable=True,
        checked=config.value("view/autozoomy", type=bool))
    autozoomy.triggered.connect(lambda: config.setValue(
                                "view/autozoomy", autozoomy.isChecked()))
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    autozoomy.triggered.connect(lambda: gt.autozoomy(spectrum))
    intensitiesact = QtWidgets.QAction("&Show intensities", None,
            checkable=True, checked=config.value("view/intensities",
                type=bool))
    intensitiesact.triggered.connect(lambda: config.setValue(
        "view/intensities", intensitiesact.isChecked()))
    intensitiesact.triggered.connect(lambda: gt.ann_spec(spectrum, ms))
    intensitiesact.triggered.connect(lambda: spectrum.figure.canvas.draw())
    oddevenact = QtWidgets.QAction("&Odd / even", None, checkable=True,
            checked=config.value("view/oddeven", type=bool))
    oddevenact.triggered.connect(lambda: config.setValue(
        "view/oddeven", oddevenact.isChecked()))
    oddevenact.triggered.connect(lambda:
        update_spectrum(True, chromatogram, spectrum, ds, ms,
                        filename, chrom, config))
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    filebrowseract = QtWidgets.QAction(
            "&File browser", None, checkable=True,
            checked=config.value("view/filebrowservisible", type=bool))
    filebrowseract.triggered.connect(lambda: config.setValue(
        "view/filebrowservisible", filebrowseract.isChecked()))
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    filebrowseract.triggered.connect(
        lambda: treedock.show() if filebrowseract.isChecked() == True
                else treedock.hide())
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    predictform = QtWidgets.QLineEdit(maximumWidth=150)
    predictform.editingFinished.connect(lambda: predictmz(
        predictform, chromatogram, spectrum, ds, ms, chrom))

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    file_menu = QtWidgets.QMenu('&File', main_window)
    main_window.menuBar().addMenu(file_menu)
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    file_menu.addAction(openact)
    file_menu.addAction(exportact)
    file_menu.addSeparator()
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    file_menu.addAction(printact)
    file_menu.addSeparator()
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    file_menu.addAction(settingsact)
    file_menu.addSeparator()
    file_menu.addAction(quitact)
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    tools_menu = QtWidgets.QMenu('&Tools', main_window)
    main_window.menuBar().addMenu(tools_menu)
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    tools_menu.addAction(zceact)
    tools_menu.addAction(drlact)
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    tools_menu.addSeparator()
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    view_menu = QtWidgets.QMenu('&View', main_window)
    view_menu.addAction(filebrowseract)
    view_menu.addAction(autozoomy)
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    view_menu.addAction(intensitiesact)
    view_menu.addSeparator()
    view_menu.addAction(oddevenact)
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    main_window.menuBar().addMenu(view_menu)
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    help_menu = QtWidgets.QMenu('&Help', main_window)
    main_window.menuBar().addMenu(help_menu)
    help_menu.addAction(aboutact)
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    main_widget = QtWidgets.QWidget(main_window)
    main_window.setCentralWidget(main_widget)

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    toolBar = QtWidgets.QToolBar(main_window)
    toolBar.setAllowedAreas(QtCore.Qt.TopToolBarArea)
    toolBar.setFloatable(False)
    toolBar.setMovable(False)
    toolBar.setToolButtonStyle(QtCore.Qt.ToolButtonTextBesideIcon)
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    toolBar.addAction(openact)
    toolBar.addAction(exportact)
    toolBar.addSeparator()
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    toolBar.addWidget(QtWidgets.QLabel("Predict Formula:"))
    toolBar.addWidget(predictform)
    toolBar.addSeparator()
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    toolBar.addAction(zceact)
    toolBar.addAction(drlact)
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    toolBar.addSeparator()
    toolBar.addAction(autozoomy)
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    fileModel = QtWidgets.QFileSystemModel()
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    fileModel.setRootPath('')
    activeDir = fileModel.index(config.value("open_folder"))
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    treeview = QtWidgets.QTreeView()
    treeview.setModel(fileModel)
    treeview.setCurrentIndex(activeDir)
    treeview.expand(activeDir)
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    dirview = QtWidgets.QListView()
    dirview.setModel(fileModel)
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    treedock = QtWidgets.QDockWidget()
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    if not config.value("view/filebrowservisible",type=bool):
        treedock.hide()
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    treedock.setWidget(QtWidgets.QWidget())
    treedock_layout = QtWidgets.QVBoxLayout(treedock.widget())
    treedock_layout.addWidget(treeview)
    treedock_layout.addWidget(dirview)
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    update.signal.connect(
        lambda: treeview.setCurrentIndex(fileModel.index(filename[0])))
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    update.signal.connect(
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        lambda: dirview.setRootIndex(fileModel.index(
            os.path.dirname(os.path.realpath(filename[0])))))
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    treeview.doubleClicked.connect(lambda index: load_file(
        main_window, chromatogram, spectrum, ds, ms, filename, chrom,
        update, config, filename=fileModel.filePath(index)))
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    dirview.doubleClicked.connect(lambda index: load_file(
        main_window, chromatogram, spectrum, ds, ms, filename, chrom,
        update, config, filename=fileModel.filePath(index)))
    dirview.clicked.connect(lambda index: load_file(
        main_window, chromatogram, spectrum, ds, ms, filename, chrom,
        update, config, filename=fileModel.filePath(index)))
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    def closeOverride(event, dock, action):
        action.setChecked(False)
        dock.hide()
        event.ignore()
    treedock.closeEvent = lambda event: closeOverride(
            event, treedock, filebrowseract)
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    main_window.addDockWidget(QtCore.Qt.LeftDockWidgetArea, treedock)

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    layout = QtWidgets.QVBoxLayout(main_widget)
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    layout.addWidget(toolBar)
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    layout.addWidget(mpl_canvas)
    mpl_canvas.setFocus()

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    mpl_canvas.mpl_connect('key_press_event', lambda event:
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        update_spectrum(event.key == "f5", chromatogram, spectrum, ds, ms,
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                        filename, chrom, config))
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    main_window.dragEnterEvent = lambda event: drag_entered(event)
    main_window.dropEvent = lambda event: dropped(
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        event, main_window, chromatogram, spectrum, ds, ms, filename,
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        chrom, update, config)
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    main_window.setAcceptDrops(True)
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    if len(sys.argv) == 2:
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        load_file(main_window, chromatogram, spectrum, ds, ms,
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                  filename, chrom, update, config, filename=sys.argv[1])
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    else:
        gt.pop_plot(spectrum, ms)
        gt.pop_plot(chromatogram, chrom)

    main_window.show()
    sys.exit(app.exec_())
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if __name__ == "__main__":
    main()