__main__.py 17.3 KB
Newer Older
Yan's avatar
Yan committed
1
2
3
4
5
#!/usr/bin/env python3

from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
from matplotlib.widgets import SpanSelector
Yan's avatar
Yan committed
6
from matplotlib.gridspec import GridSpec
Yan's avatar
Yan committed
7
8
from PyQt5 import QtCore
from PyQt5 import QtWidgets
Yan's avatar
Yan committed
9
from PyQt5 import QtGui
10
from PyQt5 import QtPrintSupport
Yan's avatar
Yan committed
11
from rawprasslib import load_raw
Yan's avatar
Yan committed
12
from rawprasslib import rawprasslib
Yan's avatar
Yan committed
13
from prasopes.predictmz import predict as getmzpattern
Yan's avatar
Yan committed
14
15
16
17
18
try:
    from rawautoparams import load_params
    autoparams = True
except:
    autoparams = False
Yan's avatar
Yan committed
19
import numpy as np
Yan's avatar
Yan committed
20
import prasopes.config as cf
21
import prasopes.datatools as dt
Yan's avatar
Yan committed
22
import prasopes.drltools as drl
Yan's avatar
Yan committed
23
import prasopes.filetools as ft
Yan's avatar
Yan committed
24
25
import prasopes.graphtools as gt
import prasopes.imagetools as imgt
Yan's avatar
Yan committed
26
import prasopes.zcetools as zce
Yan's avatar
Yan committed
27
import prasopes.tangoicons
Yan's avatar
Yan committed
28
29
30
import sys
import matplotlib
import logging
3Yan's avatar
3Yan committed
31
import os.path
Yan's avatar
Yan committed
32
33
34
matplotlib.use("Qt5Agg")


35
36
37
38
class update_signal(QtCore.QObject):
    signal = QtCore.pyqtSignal()


39
40
41
42
43
44
45
46
47
48
class QStatusBarLogger(logging.Handler):
    def __init__(self, parent=None):
        super().__init__()
        self.statusBar = QtWidgets.QStatusBar(parent)

    def emit(self, record):
        msg = self.format(record)
        self.statusBar.showMessage(msg)


49
def load_file(parent, chrom_plot, spc, d_set, ms_s, fn, chrom_s,
50
              update, settings, loadthread, filename=None):
Yan's avatar
Yan committed
51
    """populates dataset and plots it"""
3Yan's avatar
3Yan committed
52
53
54
    directory=settings.value("open_folder")
    if fn[0] is not None:
        directory=fn[0]
Yan's avatar
Yan committed
55
56
    if filename == None:
        filename = QtWidgets.QFileDialog.getOpenFileName(
3Yan's avatar
3Yan committed
57
58
59
            caption="Open spectrum",
            directory=directory,
            filter="Finnigan RAW files (*.raw, *.RAW)")[0]
60
61
    if filename is not '' and os.path.isfile(filename)\
                          and not os.path.isdir(filename):
Yan's avatar
Yan committed
62
63
        error = update_signal()
        errormsg = []
64
        def runfnc():
Yan's avatar
Yan committed
65
            try:
Yan's avatar
Yan committed
66
67
                [i.clear() for i in (
                    d_set, chrom_s['timesarg'], ms_s['params'],ms_s['headers'])]
68
69
70
                [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:
Yan's avatar
Yan committed
71
72
                errormsg.append("Opening of the file has failed!")
                errormsg.append(
73
74
                    "File is incompatible with the rawprasslib, "
                    "canceling request!\n\n"
Yan's avatar
Yan committed
75
                    "Error message:\n{}".format(pex.args[0]))
Yan's avatar
Yan committed
76
                error.signal.emit()
77
78
79
80
81
                return
            if autoparams == True:
                try:
                    ms_s['params'], rawheaders = load_params(filename)
                    segments = [len(subset['chrom_dat'][0]) for subset in d_set]
Yan's avatar
Yan committed
82
                    indicies = [sum(segments[:i+1]) for i in range(len(segments))]
83
84
                    ms_s['headers'] = np.split(rawheaders, indicies)[:-1]
                except Exception as pex:
Yan's avatar
Yan committed
85
86
87
88
89
90
                    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()
                    print("panoc baby")
91
92
93
94
95
            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()
Yan's avatar
Yan committed
96
97
        error.signal.connect(lambda:
            QtWidgets.QMessageBox.critical(parent, errormsg[0], errormsg[1]))
98
99
        loadthread.run = runfnc
        loadthread.start()
3Yan's avatar
3Yan committed
100

Yan's avatar
Yan committed
101

Yan's avatar
Yan committed
102
103
def print_graph(data_set, mass_spec, chrom_spec, spect, fn):
    def printimage(printdevice, img):
Yan's avatar
Yan committed
104
        printer.setResolution(600)
Yan's avatar
Yan committed
105
        painter = QtGui.QPainter(printdevice)
Yan's avatar
Yan committed
106
        painter.drawImage(0,0,img)
Yan's avatar
Yan committed
107
108
        painter.end()
    #TODO: substitute the QPrintPreviewDialog with QPrintPreviewWidget
109
110
    printPreview = QtPrintSupport.QPrintPreviewDialog()
    printer = printPreview.printer()
Yan's avatar
Yan committed
111
112
    printer.setPageSize(printer.A5)
    printer.setDuplex(printer.DuplexNone)
Yan's avatar
Yan committed
113
    image = imgt.paint_image(mass_spec, spect, printer)
Yan's avatar
Yan committed
114
    printPreview.paintRequested.connect(lambda:
Yan's avatar
Yan committed
115
                                        printimage(printer, image))
116
117
118
    printPreview.exec()


Yan's avatar
Yan committed
119
120
def update_spectrum(chromatogram, spect, ds, ms, fn, chrom, config):
    if fn[0] is not None:
Yan's avatar
Yan committed
121
        slims = [spect.get_xlim(), spect.get_ylim()]
3Yan's avatar
3Yan committed
122
123
124
        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"))]
Yan's avatar
Yan committed
125
126
127
        gt.populate(chromatogram, spect, ds, ms, chrom)
        spect.set_xlim(slims[0])
        spect.set_ylim(slims[1])
Yan's avatar
Yan committed
128
        gt.ann_spec(spect, ms)
Yan's avatar
Yan committed
129
130
131
        spect.get_figure().canvas.draw()


132
def dropped(event, parent, chromatogram, spectrum, ds, ms, filename,
133
            chrom, update, config, loadthread):
134
    dropurl = event.mimeData().urls()[0].toLocalFile()
135
    load_file(parent, chromatogram, spectrum, ds, ms, filename,
136
              chrom, update, config, loadthread, filename=dropurl)
Yan's avatar
Yan committed
137
138
139
140


def drag_entered(event):
    if event.mimeData().hasUrls() and event.mimeData().urls()[0]\
141
        .toLocalFile().lower().endswith('.raw'):
Yan's avatar
Yan committed
142
143
144
        event.accept()


Yan's avatar
Yan committed
145
146
147
148
149
150
151
152
153
154
155
156
157
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()


3Yan's avatar
3Yan committed
158
159
160
161
162
163
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)


Yan's avatar
Yan committed
164
165
166
def key_pressed(event, chrom, spect, ds, ms_ds, fn, chrom_ds, config):
    if event.key() == QtCore.Qt.Key_F5:
        update_spectrum(chrom, spect, ds, ms_ds, fn, chrom_ds, config)
167
168
169
170
171
172
    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)
Yan's avatar
Yan committed
173
174
    if event.key() in (QtCore.Qt.Key_Left, QtCore.Qt.Key_Right):
        gt.shift_times(event, spect, chrom, ds, ms_ds, chrom_ds)
Yan's avatar
Yan committed
175
176


Yan's avatar
Yan committed
177
178
179
180
181
def about(parent):
    """constructs window with "about" info"""
    QtWidgets.QMessageBox.information(
            parent, "About Prasopes",
            "Prasopes Finnigan raw file viewer\n\n"
182
            "Version: 0.0.12 (alpha)")
Yan's avatar
Yan committed
183
184


Yan's avatar
Yan committed
185
def main():
186
    app = QtWidgets.QApplication(sys.argv)
187
    loadthread = QtCore.QThread()
188

3Yan's avatar
3Yan committed
189
190
    ds = []
    ms = dict(annotation=[], name="Spectrum", xlabel="m/z",
Yan's avatar
Yan committed
191
192
              ylabel="ion count", xtics=20, predict=None,
              params=[], headers=[])
193
    chrom = dict(x=[0], y=[0], t_start=None, t_end=None,
Yan's avatar
Yan committed
194
                 name="Chromatogram", xlabel="time(min)",
3Yan's avatar
3Yan committed
195
                 ylabel="total ion count", timesarg=[])
Yan's avatar
Yan committed
196
    filename = [None]
3Yan's avatar
3Yan committed
197
    drlcache = [None, None]
198
    update = update_signal()
Yan's avatar
Yan committed
199

Yan's avatar
Yan committed
200
201
    config = cf.settings()

202
203
    barHandler = QStatusBarLogger()

Yan's avatar
Yan committed
204
    p_logger = logging.getLogger('parseLogger')
205
    params_logger = logging.getLogger('acqLogLogger')
Yan's avatar
Yan committed
206
    drl_logger = logging.getLogger('drlLogger')
207
    zce_logger = logging.getLogger('zceLogger')
Yan's avatar
Yan committed
208
    logging.basicConfig()
209
210
    p_logger.setLevel("WARN")
    #p_logger.setLevel("DEBUG")
Yan's avatar
Yan committed
211
    #drl_logger.setLevel("INFO")
212
    #drl_logger.setLevel("DEBUG")
213
    zce_logger.setLevel("DEBUG")
214
    params_logger.setLevel("DEBUG")
215
216
    p_logger.addHandler(barHandler)
    zce_logger.addHandler(barHandler)
217
218
    params_logger.addHandler(barHandler)
    barHandler.setLevel("DEBUG")
Yan's avatar
Yan committed
219

Yan's avatar
Yan committed
220
    paramstable = dt.table(["name","value"], 100)
Yan's avatar
Yan committed
221
    graph = Figure(figsize=(5, 4), dpi=100, facecolor="None")
Yan's avatar
Yan committed
222
223
224
    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))
Yan's avatar
Yan committed
225
226
227
228
229
230
231
232
233
    graph.tight_layout()
    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)
234
    mass_selector = SpanSelector(
Yan's avatar
Yan committed
235
        spectrum, lambda x_min, x_max: gt.pick_masses(
236
237
238
            x_min, x_max, spectrum, ms), 'horizontal', minspan=0.01,
        useblit=True, rectprops=dict(alpha=0.15, facecolor='purple'),
        button=3)
239
    time_selector = SpanSelector(
Yan's avatar
Yan committed
240
         chromatogram, lambda x_min, x_max: gt.pick_times(
Yan's avatar
Yan committed
241
             x_min, x_max, spectrum, ds, chromatogram, ms, chrom, paramstable),
Yan's avatar
Yan committed
242
243
244
         'horizontal', useblit=True, rectprops=dict(
             alpha=0.15, facecolor='purple'), button=3)

Yan's avatar
Yan committed
245
    main_window = QtWidgets.QMainWindow(windowTitle="Prasopes")
Yan's avatar
Yan committed
246

Yan's avatar
Yan committed
247
248
249
    if QtGui.QIcon.themeName() is "":
        QtGui.QIcon.setThemeName("TangoMFK")

Yan's avatar
Yan committed
250
    openact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
Yan's avatar
Yan committed
251
        "document-open"), "&Open...", None)
Yan's avatar
Yan committed
252
253
    openact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_O)
    openact.triggered.connect(lambda: load_file(
254
        main_window, chromatogram, spectrum, ds, ms, filename, chrom,
255
        update, config, loadthread))
Yan's avatar
Yan committed
256
    exportact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
Yan's avatar
Yan committed
257
        "document-save-as"), "&Export...", None)
Yan's avatar
Yan committed
258
259
    exportact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_E)
    exportact.triggered.connect(lambda: ft.export_dial(
260
        spectrum, chrom, filename, main_window))
261
262
263
    printact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
        "document-print"), "&Print", None)
    printact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_P)
Yan's avatar
Yan committed
264
265
    printact.triggered.connect(lambda: print_graph(
        ds, ms, chrom, spectrum, filename))
Yan's avatar
Yan committed
266
    settingsact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
Yan's avatar
Yan committed
267
        "preferences-system"), "&Settings...", None)
Yan's avatar
Yan committed
268
269
    settingsact.triggered.connect(lambda: cf.dial(main_window))
    quitact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
Yan's avatar
Yan committed
270
        "application-exit"), "&Quit", None)
Yan's avatar
Yan committed
271
272
273
    quitact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_Q)
    quitact.triggered.connect(main_window.close)
    zceact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
Yan's avatar
Yan committed
274
        "applications-utilities"), "&TSQ zce...", None)
Yan's avatar
Yan committed
275
276
    zceact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_T)
    zceact.triggered.connect(lambda: zce.dialog(
277
        main_window, ds, filename, update))
Yan's avatar
Yan committed
278
    drlact = QtWidgets.QAction(QtGui.QIcon.fromTheme(
Yan's avatar
Yan committed
279
        "applications-utilities"), "&DRL...", None)
Yan's avatar
Yan committed
280
281
    drlact.setShortcut(QtCore.Qt.CTRL + QtCore.Qt.Key_D)
    drlact.triggered.connect(lambda: drl.main_window(
282
        main_window, ds, filename, drlcache, update))
Yan's avatar
Yan committed
283
284
    aboutact = QtWidgets.QAction("&About Prasopes", None)
    aboutact.triggered.connect(lambda: about(main_window))
Yan's avatar
Yan committed
285
    autozoomy = QtWidgets.QAction(QtGui.QIcon.fromTheme(
Yan's avatar
Yan committed
286
287
288
289
        "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()))
290
291
292
293
294
295
296
297
298
299
300
    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:
3Yan's avatar
3Yan committed
301
302
        oddeven_changed(chromatogram, spectrum, ds, ms, filename, chrom,
            config, oddevenact))
Yan's avatar
Yan committed
303
304
305
306
307
    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()))
308
309
310
    filebrowseract.triggered.connect(
        lambda: treedock.show() if filebrowseract.isChecked() == True
                else treedock.hide())
Yan's avatar
Yan committed
311

Yan's avatar
Yan committed
312
313
314
315
    predictform = QtWidgets.QLineEdit(maximumWidth=150)
    predictform.editingFinished.connect(lambda: predictmz(
        predictform, chromatogram, spectrum, ds, ms, chrom))

Yan's avatar
Yan committed
316
317
    file_menu = QtWidgets.QMenu('&File', main_window)
    main_window.menuBar().addMenu(file_menu)
Yan's avatar
Yan committed
318
319
320
    file_menu.addAction(openact)
    file_menu.addAction(exportact)
    file_menu.addSeparator()
321
322
    file_menu.addAction(printact)
    file_menu.addSeparator()
Yan's avatar
Yan committed
323
324
325
    file_menu.addAction(settingsact)
    file_menu.addSeparator()
    file_menu.addAction(quitact)
Yan's avatar
Yan committed
326
327
    tools_menu = QtWidgets.QMenu('&Tools', main_window)
    main_window.menuBar().addMenu(tools_menu)
Yan's avatar
Yan committed
328
329
    tools_menu.addAction(zceact)
    tools_menu.addAction(drlact)
330
    tools_menu.addSeparator()
Yan's avatar
Yan committed
331
332
333
    view_menu = QtWidgets.QMenu('&View', main_window)
    view_menu.addAction(filebrowseract)
    view_menu.addAction(autozoomy)
334
335
336
    view_menu.addAction(intensitiesact)
    view_menu.addSeparator()
    view_menu.addAction(oddevenact)
Yan's avatar
Yan committed
337
    main_window.menuBar().addMenu(view_menu)
Yan's avatar
Yan committed
338
339
340
    help_menu = QtWidgets.QMenu('&Help', main_window)
    main_window.menuBar().addMenu(help_menu)
    help_menu.addAction(aboutact)
Yan's avatar
Yan committed
341

342
    main_window.setCentralWidget(mpl_canvas)
Yan's avatar
Yan committed
343

Yan's avatar
Yan committed
344
345
346
347
348
    toolBar = QtWidgets.QToolBar(main_window)
    toolBar.setAllowedAreas(QtCore.Qt.TopToolBarArea)
    toolBar.setFloatable(False)
    toolBar.setMovable(False)
    toolBar.setToolButtonStyle(QtCore.Qt.ToolButtonTextBesideIcon)
Yan's avatar
Yan committed
349

Yan's avatar
Yan committed
350
351
352
    toolBar.addAction(openact)
    toolBar.addAction(exportact)
    toolBar.addSeparator()
Yan's avatar
Yan committed
353
354
355
    toolBar.addWidget(QtWidgets.QLabel("Predict Formula:"))
    toolBar.addWidget(predictform)
    toolBar.addSeparator()
Yan's avatar
Yan committed
356
357
    toolBar.addAction(zceact)
    toolBar.addAction(drlact)
Yan's avatar
Yan committed
358
359
    toolBar.addSeparator()
    toolBar.addAction(autozoomy)
Yan's avatar
Yan committed
360

Yan's avatar
Yan committed
361
    paramsdock = QtWidgets.QDockWidget()
Yan's avatar
Yan committed
362
    update.signal.connect(lambda: gt.update_paramstable(paramstable, ms, chrom))
Yan's avatar
Yan committed
363
364
    paramsdock.setWidget(paramstable)

3Yan's avatar
3Yan committed
365
    fileModel = QtWidgets.QFileSystemModel()
366
367
    fileModel.setRootPath('')
    activeDir = fileModel.index(config.value("open_folder"))
3Yan's avatar
3Yan committed
368
369
370
371
    treeview = QtWidgets.QTreeView()
    treeview.setModel(fileModel)
    treeview.setCurrentIndex(activeDir)
    treeview.expand(activeDir)
372
373
    dirview = QtWidgets.QListView()
    dirview.setModel(fileModel)
3Yan's avatar
3Yan committed
374
    treedock = QtWidgets.QDockWidget()
375
376
377
378
379
380
    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))
Yan's avatar
Yan committed
381
382
    if not config.value("view/filebrowservisible",type=bool):
        treedock.hide()
383
384
385
386
    treedock.setWidget(QtWidgets.QWidget())
    treedock_layout = QtWidgets.QVBoxLayout(treedock.widget())
    treedock_layout.addWidget(treeview)
    treedock_layout.addWidget(dirview)
387
388
389
    update.signal.connect(lambda: treeview.setCurrentIndex(fileModel.index(
                                  filename[0])))
    update.signal.connect(lambda: dirview.setRootIndex(fileModel.index(
3Yan's avatar
3Yan committed
390
            os.path.dirname(os.path.realpath(filename[0])))))
391
    clickload = lambda index: load_file(
3Yan's avatar
3Yan committed
392
        main_window, chromatogram, spectrum, ds, ms, filename, chrom,
393
        update, config, loadthread, filename=fileModel.filePath(index))
394
395
    for i in [treeview.doubleClicked, dirview.doubleClicked, dirview.clicked]:
        i.connect(clickload)
396
397
398
399
400
401
    #fileModel gots stuck sometimes, better give it a separate thread
    #it complains at the start, but still works later 
    #and I did not found better solution
    treedockThread = QtCore.QThread()
    treedockThread.start()
    fileModel.moveToThread(treedockThread)
402
403
404
405
406
407
    def closeOverride(event, dock, action):
        action.setChecked(False)
        dock.hide()
        event.ignore()
    treedock.closeEvent = lambda event: closeOverride(
            event, treedock, filebrowseract)
Yan's avatar
Yan committed
408

Yan's avatar
Yan committed
409
    main_window.closeEvent = lambda event: treedockThread.quit()
Yan's avatar
Yan committed
410
411
    main_window.dragEnterEvent = lambda event: drag_entered(event)
    main_window.dropEvent = lambda event: dropped(
412
        event, main_window, chromatogram, spectrum, ds, ms, filename,
3Yan's avatar
3Yan committed
413
        chrom, update, config)
Yan's avatar
Yan committed
414
    main_window.setAcceptDrops(True)
Yan's avatar
Yan committed
415
416
    main_window.keyPressEvent = lambda event: key_pressed(event, chromatogram,
            spectrum, ds, ms, filename, chrom, config)
Yan's avatar
Yan committed
417

418
419
    main_window.addToolBar(QtCore.Qt.TopToolBarArea, toolBar)
    main_window.addDockWidget(QtCore.Qt.LeftDockWidgetArea, treedock)
Yan's avatar
Yan committed
420
    main_window.addDockWidget(QtCore.Qt.RightDockWidgetArea, paramsdock)
421
    main_window.setStatusBar(barHandler.statusBar)
422
423
424

    main_window.setFocus()

Yan's avatar
Yan committed
425
    if len(sys.argv) == 2:
426
        load_file(main_window, chromatogram, spectrum, ds, ms,
427
428
                  filename, chrom, update, config, loadthread,
                  filename=sys.argv[1])
Yan's avatar
Yan committed
429
    else:
3Yan's avatar
3Yan committed
430
431
        gt.pop_plot(0, 0, spectrum, ms)
        gt.pop_plot(0, 0, chromatogram, chrom)
Yan's avatar
Yan committed
432
433
434

    main_window.show()
    sys.exit(app.exec_())
Yan's avatar
Yan committed
435

436

Yan's avatar
Yan committed
437
438
if __name__ == "__main__":
    main()