__main__.py 17.7 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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try:
    from rawautoparams import load_params
    autoparams = True
except:
    autoparams = False
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import numpy as np
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import prasopes.config as cf
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import prasopes.datatools as dt
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import prasopes.drltools as drl
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import prasopes.filetools as ft
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import prasopes.graphtools as gt
import prasopes.imagetools as imgt
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import prasopes.zcetools as zce
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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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class QStatusBarLogger(logging.Handler):
    def __init__(self, parent=None):
        super().__init__()
        self.statusBar = QtWidgets.QStatusBar(parent)
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        self.trigger = update_signal()
        self.msg = str("")
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    def emit(self, record):
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        self.msg = self.format(record)
        self.trigger.signal.emit()
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def load_file(parent, chrom_plot, spc, d_set, ms_s, fn, chrom_s,
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              update, settings, loadthread, 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)\
                          and not os.path.isdir(filename):
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        error = update_signal()
        errormsg = []
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        def runfnc():
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            try:
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                [i.clear() for i in (
                    d_set, chrom_s['timesarg'], ms_s['params'],ms_s['headers'])]
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                [d_set.append(dict(chrom_dat=i[0], masses=i[1], matrix=i[2]))
                    for i in load_raw(filename, settings.value("tmp_location"))]
            except rawprasslib.ParsingException as pex:
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                errormsg.append("Opening of the file has failed!")
                errormsg.append(
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                    "File is incompatible with the rawprasslib, "
                    "canceling request!\n\n"
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                    "Error message:\n{}".format(pex.args[0]))
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                error.signal.emit()
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                return
            if autoparams == True:
                try:
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                    ms_s['params'], rawheaders, chrom_s['machtype'] = load_params(filename)
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                    segments = [len(subset['chrom_dat'][0]) for subset in d_set]
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                    indicies = [sum(segments[:i+1]) for i in range(len(segments))]
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                    ms_s['headers'] = np.split(rawheaders, indicies)[:-1]
                except Exception as pex:
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                    errormsg.append("File is incompatible with the rawautoparams,")
                    errormsg.append(
                            "no parameters loaded!\n\n"
                            "Error message:\n{}".format(pex.args[0]))
                    error.signal.emit()
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            gt.populate(chrom_plot, spc, d_set, ms_s, chrom_s)
            fn[0] = filename
            parent.setWindowTitle("Prasopes - {}".format(
                os.path.basename(filename)))
            update.signal.emit()
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        error.signal.connect(lambda:
            QtWidgets.QMessageBox.critical(parent, errormsg[0], errormsg[1]))
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        loadthread.run = runfnc
        loadthread.start()
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def print_graph(data_set, mass_spec, chrom_spec, spect, fn, table):
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    def printimage(printdevice, img):
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        printer.setResolution(600)
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        painter = QtGui.QPainter(printdevice)
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        font = painter.font()
        linesize = printer.resolution()/15
        font.setPixelSize(linesize)
        painter.setFont(font)
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        painter.drawImage(0,0,img)
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        offset = img.size().height()
        line = 1
        spacing = 1.5
        for row in range(table.rowCount()):
            if table.cellWidget(row,0).checkState() == 2:
                text = table.item(row,1).text() + table.item(row,2).text()
                painter.drawText(300,int(offset+line*linesize*spacing), text)
                line += 1
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        painter.end()
    #TODO: substitute the QPrintPreviewDialog with QPrintPreviewWidget
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    printPreview = QtPrintSupport.QPrintPreviewDialog()
    printer = printPreview.printer()
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    printer.setPageSize(printer.A5)
    printer.setDuplex(printer.DuplexNone)
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    image = imgt.paint_image(mass_spec, spect, printer)
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    printPreview.paintRequested.connect(lambda:
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                                        printimage(printer, image))
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    printPreview.exec()


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def update_spectrum(chromatogram, spect, ds, ms, fn, chrom, config):
    if fn[0] is not None:
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        slims = [spect.get_xlim(), spect.get_ylim()]
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        ds.clear()
        [ds.append(dict(chrom_dat=i[0], masses=i[1], matrix=i[2])) for i
                in load_raw(fn[0], config.value("tmp_location"))]
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        gt.populate(chromatogram, spect, ds, ms, chrom)
        spect.set_xlim(slims[0])
        spect.set_ylim(slims[1])
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        gt.ann_spec(spect, ms)
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        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, loadthread):
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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, loadthread, 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 oddeven_changed(chromatogram, spectrum, ds, ms, filename, chrom, config,
        oddevenact):
    config.setValue("view/oddeven", oddevenact.isChecked())
    update_spectrum(chromatogram, spectrum, ds, ms, filename, chrom, config)


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def key_pressed(event, chrom, spect, ds, ms_ds, fn, chrom_ds, config):
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    if event.key() == QtCore.Qt.Key_F5:
        update_spectrum(chrom, spect, ds, ms_ds, fn, chrom_ds, config)
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    if event.key() == QtCore.Qt.Key_C:
        if event.modifiers().__int__() == QtCore.Qt.ControlModifier:
            imgt.clip_spect_img(ms_ds, spect)
        if event.modifiers().__int__() == QtCore.Qt.ControlModifier+\
                                          QtCore.Qt.ShiftModifier:
            dt.clip_spectstr(spect, chrom_ds, fn)
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    if event.key() in (QtCore.Qt.Key_Left, QtCore.Qt.Key_Right):
        gt.shift_times(event, spect, chrom, ds, ms_ds, chrom_ds)
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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: 0.0.12 (alpha)")
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def main():
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    app = QtWidgets.QApplication(sys.argv)
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    loadthread = QtCore.QThread()
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    ds = []
    ms = dict(annotation=[], name="Spectrum", xlabel="m/z",
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              ylabel="ion count", xtics=20, predict=None,
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              params=[], headers=[], texts=[])
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    chrom = dict(x=[0], y=[0], t_start=None, t_end=None, machtype=None,
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                 name="Chromatogram", xlabel="time(min)",
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                 ylabel="total ion count", timesarg=[])
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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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    barHandler = QStatusBarLogger()
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    barHandler.trigger.signal.connect(lambda:
            barHandler.statusBar.showMessage(barHandler.msg))
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    p_logger = logging.getLogger('parseLogger')
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    params_logger = logging.getLogger('acqLogLogger')
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    drl_logger = logging.getLogger('drlLogger')
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    zce_logger = logging.getLogger('zceLogger')
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    #mpl_logger = logging.getLogger('matplotlib')
    #mpl_logger.setLevel("DEBUG")
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    logging.basicConfig()
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    #p_logger.setLevel("WARN")
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    #p_logger.setLevel("DEBUG")
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    #drl_logger.setLevel("INFO")
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    drl_logger.setLevel("DEBUG")
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    zce_logger.setLevel("DEBUG")
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    params_logger.setLevel("DEBUG")
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    p_logger.addHandler(barHandler)
    zce_logger.addHandler(barHandler)
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    params_logger.addHandler(barHandler)
    barHandler.setLevel("DEBUG")
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    paramstable = dt.table(["","name","value"], 100)
    paramstable.horizontalHeader().setSectionResizeMode(
            0, QtWidgets.QHeaderView.ResizeToContents)
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    graph = Figure(figsize=(5, 4), dpi=100, facecolor="None", constrained_layout=True)
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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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    mpl_canvas = FigureCanvas(graph)
    mpl_canvas.setStyleSheet("background-color:transparent;")
    mpl_canvas.setAutoFillBackground(False)
    
    gt.pan_factory(chromatogram)
    gt.zoom_factory(chromatogram, 1.15)
    gt.pan_factory(spectrum, ms)
    gt.zoom_factory(spectrum, 1.15, ms)
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    gt.textedit_factory(spectrum, ms)
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    mass_selector = gt.AugSpanSelector(spectrum, ms)
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    time_selector = SpanSelector(chromatogram, lambda x_min, x_max:
            gt.pick_times( x_min, x_max, spectrum, ds, chromatogram, ms, chrom,
                paramstable), 'horizontal', useblit=True, rectprops=dict(
                    alpha=0.15, facecolor='purple'), button=3)
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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, loadthread))
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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(
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        spectrum, 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(
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        ds, ms, chrom, spectrum, filename, paramstable))
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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:
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        oddeven_changed(chromatogram, spectrum, ds, ms, filename, chrom,
            config, oddevenact))
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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_window.setCentralWidget(mpl_canvas)
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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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    paramsdock = QtWidgets.QDockWidget()
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    update.signal.connect(lambda: gt.update_paramstable(paramstable, ms, chrom))
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    paramsdock.setWidget(paramstable)

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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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    def scrolltoonce():
        fileModel.directoryLoaded.disconnect(scrolltoonce)
        treeview.scrollTo(fileModel.index(config.value("open_folder")), 1)
    fileModel.directoryLoaded.connect(scrolltoonce)
    fileModel.directoryLoaded.connect(
            lambda: treeview.resizeColumnToContents(0))
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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])))
    update.signal.connect(lambda: dirview.setRootIndex(fileModel.index(
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            os.path.dirname(os.path.realpath(filename[0])))))
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    clickload = lambda index: load_file(
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        main_window, chromatogram, spectrum, ds, ms, filename, chrom,
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        update, config, loadthread, filename=fileModel.filePath(index))
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    for i in [treeview.doubleClicked, dirview.doubleClicked, dirview.clicked]:
        i.connect(clickload)
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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.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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    main_window.keyPressEvent = lambda event: key_pressed(event, chromatogram,
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            spectrum, ds, ms, filename, chrom, config)
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    main_window.addToolBar(QtCore.Qt.TopToolBarArea, toolBar)
    main_window.addDockWidget(QtCore.Qt.LeftDockWidgetArea, treedock)
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    main_window.addDockWidget(QtCore.Qt.RightDockWidgetArea, paramsdock)
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    main_window.setStatusBar(barHandler.statusBar)
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    main_window.setFocus()

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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, loadthread,
                  filename=sys.argv[1])
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    else:
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        gt.pop_plot(0, 0, spectrum, ms)
        gt.pop_plot(0, 0, chromatogram, chrom)
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    main_window.show()
    sys.exit(app.exec_())
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if __name__ == "__main__":
    main()