class MSMainWindow(QMainWindow):
"""Gui of the main window"""
# MAX_RECENT_FILES = 10
# start putting links spyder numpy scipy et tutti quanti
links = (
"http://numpy.scipy.org/",
"http://packages.python.org/spyder/",
"http://www.riverbankcomputing.co.uk/software/pyqt/intro",
)
pluginPath = path.normcase("pluginmanager/plugins/")
def __init__(self, availablePlugins):
"""
Constructor with all the models needed setup menus
"""
QMainWindow.__init__(self)
self.setDockOptions(QMainWindow.VerticalTabs | QMainWindow.AnimatedDocks)
self.plugins = availablePlugins
self.pluginsInst = []
settings = QSettings(
"INRA/INSA", "-".join([QApplication.instance().APPLICATION_NAME_STR, QApplication.instance().VERSION_STR])
)
self.recentFiles = list(settings.value("RecentFiles").toStringList())
self.setStyleSheet(stylesheet)
self.pipeline = MSPipelineToolBar("Pipeline toolbar", parent=self)
self.addToolBar(0x1, self.pipeline)
self._setupModels()
self._setupUi()
self._setupMenus()
def _setupModels(self):
"""
Warning:Causes segfault when horizontal labels set to True
on aura peu etre a la fin un model par sampleList c'est ce qui parait
le plus logique
"""
# drag and drop table sample
self.sampleModel = QStandardItemModel(self)
self.sampleModel.setHorizontalHeaderLabels(["Sample", "Class"])
# treeView1
self.spectraModel = QStandardItemModel(self)
# treeview2
self.peakModel = QStandardItemModel(self)
# treeview3
self.clusterModel = QStandardItemModel(self)
def _setupMenus(self):
# file
self.fileMenu = QMenu("&File")
self.fileMenu.setTearOffEnabled(True)
self.op = QMenu("&Open...", self.fileMenu)
self.op.setIcon(QIcon(path.normcase("gui/icons/fileopen.png")))
open_ = QAction("&Open rawfiles", self)
open_.setToolTip("Open an mzXML or netCDF file")
open_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_O))
open_icon = QIcon(path.normcase("gui/icons/fileopen.png"))
open_.setIcon(open_icon)
self.op.addAction(open_)
load_ = QAction("&Open projects...", self)
load_.setToolTip("load binary file containing saved objects")
load_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_S))
load_icon = QIcon(QPixmap(path.normcase("gui/icons/project_open.png")))
load_.setIcon(load_icon)
self.op.addAction(load_)
self.fileMenu.addMenu(self.op)
save_ = QAction("&Save...", self)
save_.setToolTip("save the actual application model")
save_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_S))
save_icon = QIcon(path.normcase("gui/icons/save_all.png"))
save_.setIcon(save_icon)
self.fileMenu.addAction(save_)
pkl = QAction("&load a peaklist", self) # TODO:load peaklist
pkl.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_P))
pkl.setToolTip("load a peaklist and process it")
pkl.setIcon(QIcon(path.normcase("gui/icons/featuredetect.png")))
self.fileMenu.addAction(pkl)
convert_ = QAction("&Convert...", self)
convert_.setEnabled(False)
convert_.setToolTip("Convert a .wiff file if Analyst(c) is installed")
convert_icon = QIcon(path.normcase("gui/icons/goto.png"))
convert_.setIcon(convert_icon)
self.fileMenu.addAction(convert_)
a = self.fileMenu.addAction(QIcon(path.normcase("gui/icons/process.png")), "&Launch a batch")
a.setEnabled(False)
b = self.fileMenu.addAction(QIcon(path.normcase("gui/icons/process.png")), "&Merge")
b.setToolTip("Merge MRM file")
# b.setEnabled(False)
self.fileMenu.addSeparator()
#
# for i in xrange(self.MAX_RECENT_FILES):
# a = QAction('', self)
# a.setVisible(False)
# self.fileMenu.addAction(a)
#
# for i in xrange(min(self.MAX_RECENT_FILES, len(self.recentFiles))):
# self.fileMenu.actions()[5+i].setVisible(True)
# self.fileMenu.actions()[5+i].setText(self.recentFiles[i].split('/')[-1])
exit_action = QAction("&Exit", self)
exit_action.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_Q))
exit_action.setIcon(QIcon(QPixmap(path.normcase("gui/icons/exit.png"))))
self.fileMenu.addAction(exit_action)
self.menuBar().addMenu(self.fileMenu)
self.editMenu = QMenu("&Edit")
self.editMenu.setTearOffEnabled(True)
self.editMenu.addAction(QIcon(path.normcase("gui/icons/edit_undo.png")), "&Undo...")
self.editMenu.addAction(QIcon(path.normcase("gui/icons/edit_redo.png")), "&Redo...")
self.editMenu.actions()[0].setEnabled(False)
self.editMenu.actions()[1].setEnabled(False)
self.editMenu.addSeparator()
self.editMenu.addAction(QIcon(path.normcase("gui/icons/run.png")), "&Preferences")
self.exportMenu = QMenu("&Export...")
self.exportMenu.setIcon(QIcon(path.normcase("gui/icons/file_export.png")))
self.exportMenu.addAction("&Peaklist")
self.exportMenu.addAction("&Clusters intensity matrix")
self.editMenu.addMenu(self.exportMenu)
self.menuBar().addMenu(self.editMenu)
# view
self.viewMenu = QMenu("&View")
self.viewMenu.setTearOffEnabled(True)
self.viewMenu.addAction(
QIcon(path.normcase("gui/icons/window_duplicate")),
"&Cascade View",
self.mdiArea.cascadeSubWindows,
QKeySequence(Qt.CTRL + Qt.Key_K),
)
self.viewMenu.addAction(
QIcon(path.normcase("gui/icons/view_icon")),
"&Title View",
self.mdiArea.tileSubWindows,
QKeySequence(Qt.CTRL + Qt.Key_N),
)
self.viewMenu.addAction(
QIcon(path.normcase("gui/icons/stop_process.png")),
"&Close all subWindows",
self.mdiArea.closeAllSubWindows,
QKeySequence(Qt.CTRL + Qt.Key_W),
)
self.plotting = QMenu("&Plotting...")
self.plotting.setIcon(QIcon(QPixmap(path.normcase("gui/icons/plot.png"))))
self.plotting.addAction("&3D Plot")
# self.plotting.addAction("&Cytoscape web")
self.plotting.addAction("&Spectrogram Plot")
# self.multiplePlot = QAction("&Visualize Raw/Treated Data", self)
# self.multiplePlot.setCheckable(True)
# self.multiplePlot.setEnabled(False)
# self.sub_plot_.addAction(self.multiplePlot)
self.viewMenu.addMenu(self.plotting)
self.viewMenu.addSeparator()
self.show_hide = QMenu("&Show/Hide")
m = self.createPopupMenu()
m.setTitle("&Show/Hide")
self.viewMenu.addMenu(m)
# self.pref = QMenu("&Preferences")
# self.pref.addAction(self.multiplePlot)
# self.viewMenu.addMenu(self.pref)
self.menuBar().addMenu(self.viewMenu)
# algorithm
self.algoMenu = QMenu("&Algorithm")
self.algoMenu.setTearOffEnabled(True)
self.preProcessing = QMenu("&PreProcessing(experimental)")
self.preProcessing.addAction("&Smoothing raw data...")
self.preProcessing.addAction("&Cut off raw data...")
self.preProcessing.addAction("&Calibration (mz dimension)")
self.preProcessing.addAction("&Resize sample...")
self.algoMenu.addMenu(self.preProcessing)
self.peakPickingMenu = QMenu("&Peack Picking & Alignement(XCMS)", self)
self.peakPickingMenu.setIcon(QIcon(path.normcase("gui/icons/pickedpeakicon.png")))
matched = QAction("&MatchedFiltered", self)
matched.setIcon(QIcon(path.normcase("gui/icons/RLogo")))
matched.setToolTip("Peak Detection and Integration using MatchedFiltered algorithm")
self.peakPickingMenu.addAction(matched)
centwave = QAction("&CentWave", self)
centwave.setIcon(QIcon(path.normcase("gui/icons/RLogo")))
centwave.setToolTip("Peak Detection and Integration using CentWave algorithm")
self.peakPickingMenu.addAction(centwave)
# peak_.setShortcut(.QKeySequence(CTRL + Key_P))
# peak_icon=.QIcon(.QPixmap(path.normcase("gui/icons/pickedpeakicon.png")))
# peak_.setIcon(peak_icon)
self.algoMenu.addMenu(self.peakPickingMenu)
self.alignment = QMenu("&Alignment")
self.alignment.setIcon(QIcon(path.normcase("gui/icons/format_indent_more.png")))
self.alignment.addAction("&Polynomial fitting(exp)")
self.alignment.addAction("&DynamicTimeWarping")
self.alignment.addAction("&ObiWarp")
self.alignment.actions()[2].setEnabled(False)
self.algoMenu.addMenu(self.alignment)
self.algoMenu.addAction("Normalization")
clust_ = QAction("&Clustering", self)
clust_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_L))
clust_icon = QIcon(QPixmap(path.normcase("gui/icons/cluster.png")))
clust_.setIcon(clust_icon)
self.algoMenu.addAction(clust_)
id_ = QAction("&Identification", self)
id_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_I))
id_.setToolTip("Try to identify peaks with several methods")
id_.setIcon(QIcon(QPixmap(path.normcase("gui/icons/findcompound.png"))))
self.algoMenu.addAction(id_)
self.menuBar().addMenu(self.algoMenu)
# tools
self.toolsMenu = QMenu("&Tools")
self.toolsMenu.setTearOffEnabled(True)
web = QAction("&Web Browser", self)
web.setIcon(QIcon(QPixmap(path.normcase("gui/icons/applications_internet.png"))))
self.toolsMenu.addAction(web)
# cyto = QAction("&cytoscape", self)
# cyto_icon =QIcon(QPixmap(path.normcase("gui/icons/cytoscape.jpeg")))
# cyto.setIcon(cyto_icon)
# self.toolsMenu.addAction(cyto)
editor = QAction("&Editor", self)
editor.setIcon(QIcon(QPixmap(path.normcase("gui/icons/document_sign.png"))))
self.toolsMenu.addAction(editor)
pet = QAction("&Short Periodic Table", self)
pet.setIcon(QIcon(QPixmap(path.normcase("gui/icons/pet.jpg"))))
self.toolsMenu.addAction(pet)
self.menuBar().addMenu(self.toolsMenu)
# plugins
self.pluginMenu = QMenu("&Plugins")
self.pluginMenu.setTearOffEnabled(True)
instPl = QAction("&Install a plugin", self)
instPl.setIcon(QIcon(path.normcase("gui/icons/pluginInstall.png")))
self.pluginMenu.addAction(instPl)
self.launchingMenu = QMenu("&Launch PLugins", self)
self.launchingMenu.setIcon(QIcon(path.normcase("gui/icons/plugin")))
for plug in self.plugins:
# fullname="".join([self.pluginPath, str(plug)])
mod = imp.load_source(self.__module__, plug)
if mod.autoActivation:
qApp = QApplication.instance()
name = getattr(mod, "className")
cls = getattr(mod, name)
p = cls(qApp.model, self, parent=self)
# p=qApp.pluginManager.loadPlugin(qApp.model, self, plug.split('/')[-1])
self.pluginsInst.append(p)
else:
self.launchingMenu.addAction(plug.split("/")[-1])
self.pluginMenu.addMenu(self.launchingMenu)
self.pluginMenu.addAction(QIcon(path.normcase("gui/icons/process_stop.png")), "&Remove loaded Plugin")
self.menuBar().addMenu(self.pluginMenu)
# about
self.aboutMenu = QMenu("&About")
self.aboutMenu.setTearOffEnabled(True)
metms = QAction(QIcon(path.normcase("gui/icons/deluge.png")), "&about metMS...", self)
self.aboutMenu.addAction(metms)
pyqt = QAction("&about PyQt4...", self)
pyqt_icon = QIcon(QPixmap(path.normcase("gui/icons/logo_QT4.png")))
pyqt.setIcon(pyqt_icon)
self.aboutMenu.addAction(pyqt)
metms = QAction("&metMS Documentation", self)
metms_icon = QIcon(QPixmap(path.normcase("gui/icons/deluge.png")))
metms.setIcon(metms_icon)
self.aboutMenu.addAction(metms)
self.menuBar().addMenu(self.aboutMenu)
def _setupUi(self, background=None):
"""
Make the GUI
"""
# mdi
self.mdiArea = MSMdiArea(self)
self.mdiArea.setBackground(QBrush(QPixmap(path.normcase("gui/icons/blac2.png")))) # QColor(Qt.blue).darker()))
self.setCentralWidget(self.mdiArea)
# sample dock widget
self.sampleDockWidget = QDockWidget("Samples", self)
# sampleWidget = QWidget()
self.sampleTableView = MSDragFromTableView()
self.sampleTableView.setModel(self.sampleModel)
self.sampleTableView.setSelectionBehavior(1)
self.sampleTableView.verticalHeader().hide()
self.sampleTableView.verticalHeader().setDefaultSectionSize(15)
self.sampleTableView.horizontalHeader().setDefaultSectionSize(150)
self.sampleDockWidget.setWidget(self.sampleTableView) # sampleWidget)
self.sampleDockWidget.visible = True
# workflow dock
self.workflowDockWidget = QDockWidget("Visualizer", self)
self.workflowDockWidget.visible = True
a = QWidget(self)
v = QVBoxLayout(a)
q = QToolBar()
# self.workingSample = QLabel("Working Sample:None")
# q.addWidget(self.workingSample)
q.addWidget(QLabel("ppm :"))
self.ppmEditer = QDoubleSpinBox()
self.usePpm = QCheckBox("use ?")
q.addWidget(self.ppmEditer)
q.addWidget(self.usePpm)
q.addSeparator()
self.removeButton = QToolButton(self)
self.removeButton.setIcon(QIcon(path.normcase("gui/icons/delete.png")))
q.addWidget(self.removeButton)
self.markAsGood = QAction(QIcon(path.normcase("gui/icons/button_ok.png")), "mark peak as good", self)
self.markAsBad = QAction(QIcon(path.normcase("gui/icons/stop.png")), "mark peak as bad", self)
self.hideItem = QAction(QIcon(path.normcase("gui/icons/list_remove.png")), "Hide Item", self)
q.addAction(self.markAsGood)
q.addAction(self.markAsBad)
q.addAction(self.hideItem)
v.addWidget(q)
self.tabWidget = QTabWidget()
self.tab = QWidget()
verticalLayout = QVBoxLayout(self.tab)
self.treeView = MSToDropTableView()
self.treeView.verticalHeader().setDefaultSectionSize(20)
self.treeView.setModel(self.spectraModel)
self.spectraLabel = QLabel("Sample: None")
verticalLayout.addWidget(self.treeView)
verticalLayout.addWidget(self.spectraLabel)
self.tabWidget.addTab(self.tab, QIcon(path.normcase("gui/icons/spectrumicon.png")), "Spectra")
self.tab_2 = QWidget()
verticalLayout_4 = QVBoxLayout(self.tab_2)
self.treeView_2 = MSToDropTableView() # MSTreeView(self.tab_2)# QTableView(self)#
self.treeView_2.verticalHeader().setDefaultSectionSize(20)
self.treeView_2.setModel(self.peakModel)
self.peakLabel = QLabel("Sample: None")
verticalLayout_4.addWidget(self.treeView_2)
verticalLayout_4.addWidget(self.peakLabel)
self.tabWidget.addTab(self.tab_2, QIcon(path.normcase("gui/icons/peakicon.png")), "Peaks List")
self.tab_3 = QWidget()
verticalLayout_5 = QVBoxLayout(self.tab_3)
self.treeView_3 = MSToDropTreeView()
self.treeView_3.setAnimated(True)
self.treeView_3.setModel(self.clusterModel)
self.clusterLabel = QLabel("Sample: None")
verticalLayout_5.addWidget(self.treeView_3)
verticalLayout_5.addWidget(self.clusterLabel)
self.tabWidget.addTab(self.tab_3, QIcon(path.normcase("gui/icons/clustering.png")), "Clusters")
self.tabWidget.setCurrentIndex(0)
for l in (self.spectraLabel, self.peakLabel, self.clusterLabel):
l.setAutoFillBackground(True)
v.addWidget(self.tabWidget)
self.workflowDockWidget.setWidget(a)
self.addDockWidget(Qt.DockWidgetArea(0x2), self.workflowDockWidget)
from gui.MetBaseGui import MSIsoCalculator
self.isoCalc = MSIsoCalculator(self)
self.isoCalcDockWidget = QDockWidget("isotopes calculation", self)
self.isoCalcDockWidget.setWidget(self.isoCalc)
self.addDockWidget(Qt.DockWidgetArea(0x2), self.isoCalcDockWidget)
self.isoCalcDockWidget.setVisible(False)
self.isoCalcDockWidget.visible = False
from gui.MetBaseGui import FormulaGenerator
self.generator = FormulaGenerator(self)
self.generatorDockWidget = QDockWidget("formula generator", self)
self.generatorDockWidget.setWidget(self.generator)
self.addDockWidget(Qt.DockWidgetArea(0x2), self.generatorDockWidget)
self.generatorDockWidget.setVisible(False)
self.generatorDockWidget.visible = False
self.compoundTreeView = MSCompoundTreeView(self)
self.compoundDockWidget = QDockWidget("Compounds", self)
self.compoundDockWidget.setWidget(self.compoundTreeView)
self.addDockWidget(Qt.DockWidgetArea(0x2), self.compoundDockWidget)
self.compoundDockWidget.setVisible(False)
self.compoundDockWidget.visible = False
self.comparativeTableView = QTableView(self)
self.comparativeTableView.horizontalHeader().setStretchLastSection(True)
self.comparativeTableView.verticalHeader().setDefaultSectionSize(20)
self.comparativeDock = QDockWidget("Comparative View", self)
self.comparativeDock.setWidget(self.comparativeTableView)
self.addDockWidget(Qt.DockWidgetArea(0x8), self.comparativeDock)
self.comparativeDock.setVisible(False)
self.comparativeDock.visible = False
self.tabifyDockWidget(self.compoundDockWidget, self.isoCalcDockWidget)
self.tabifyDockWidget(self.isoCalcDockWidget, self.workflowDockWidget)
self.tabifyDockWidget(self.workflowDockWidget, self.generatorDockWidget)
# set the end
# WARNING: possible that the internal shell widget cause random segfault
# with the error of QObject::killTimers...? not sure !
self.shell = QWidget() # InternalShell(namespace={'metms': QApplication.instance()},
# parent=self,
# multithreaded=False)
self.shellDock = QDockWidget("Python Shell", self)
self.shellDock.setWindowIcon(QIcon(path.normcase("gui/icons/stop.png")))
self.shellDock.setWidget(self.shell)
self.shellDock.setMinimumWidth(255)
self.shellDock.visible = True
self.addDockWidget(0x2, self.shellDock)
self.addDockWidget(0x2, self.sampleDockWidget)
self.tabifyDockWidget(self.shellDock, self.sampleDockWidget)
self.pb = QProgressBar(self)
self.pb.setMaximumWidth(245)
self.stopProcess = QToolButton(self)
self.stopProcess.setIcon(QIcon(path.normcase("gui/icons/process_stop.png")))
m = QMenu()
# self.connect(m, SIGNAL('triggered(QAction*'), QApplication.instance().taskManager.abortByName)
self.stopProcess.setMenu(m)
self.stopProcess.setPopupMode(1) # Menu Button
# self.connect(self.stopProcess, SIGNAL("clicked()"), self.stopThread)
self.statusBar().addPermanentWidget(self.stopProcess)
self.statusBar().addPermanentWidget(self.pb)
def updateStopProcessMenu(self):
"""
update the menu of the stop process
button, based directly on the processes
stored by the task manager
"""
self.stopProcess.menu().clear()
for c in QApplication.instance().taskManager:
self.stopProcess.menu().addAction(c.title)
# QApplication.instance().taskManager.abort(QApplication.instance().taskManager[-1])
def addMdiSubWindow(self, plot, title="", showMaximized=False):
"""
Allow addition of new window in the mdiarea
"""
win = self.mdiArea.addSubWindow(plot)
# print "widget parent", plot.parent()
win.setAttribute(Qt.WA_DeleteOnClose)
# win.connect(win, SIGNAL('destroyed(QObject *)'), self.testdestroy)
# plot.setParent(win)
win.setWindowTitle(title)
if showMaximized:
win.showMaximized()
else:
win.resize(400, 300)
win.show()
return win
def updateTreeView(self):
"""
Tree View update switch spectre/chromato
"""
if self.treeView.model() == self.spectraModel:
self.treeView.setModel(self.chromaModel)
self.tabWidget.setTabText(0, "Chroma")
else:
self.treeView.setModel(self.spectraModel)
# self.treeView.setSelectionMode(1)
self.tabWidget.setTabText(0, "Spectra")
def addTreeViewModel(self, model1, model2):
"""Add a model """
self.chromaModel.appendRow(model1)
self.spectraModel.appendRow(model2)
def _actionHovered(self, action):
"""emulate tooltip cause they do not work that much"""
tip = action.toolTip()
QToolTip.showText(QCursor.pos(), tip)
def showErrorMessage(self, title, string):
QMessageBox.critical(self, title, string, 0, 0)
def showWarningMessage(self, title, string):
return QMessageBox.warning(self, title, string, QMessageBox.Ok | QMessageBox.Cancel)
def showInformationMessage(self, title, string):
QMessageBox.information(self, title, string, 0)
def updateProgressBar(self, i):
"""update the value of the progress bar for all the treatment"""
self.pb.setValue(min(i, 100))
def to_indetermined_mode(self):
self.pb.setMaximum(0)
def to_determined_mode(self):
self.pb.setMaximum(100)
def showInStatusBar(self, string, time=5000):
self.statusBar().showMessage(string, time)
def addInterpreterDock(self, shell):
self.shellDock = QDockWidget(self)
self.shellDock.setWidget(shell)
self.shellDock.setWindowTitle("shell")
self.addDockWidget(0x2, self.shellDock)
def showMetMSInformation(self):
QMessageBox.about(
self,
self.tr("About %1").arg("metMS"),
self.tr(
"""<b>%1 %2</b>
<br>metabolite Mass Spectrometry
<p>Copyright © 2010 Marco INSA, INRA
<br>Licensed under the terms of the CeciLL License
<p>Developed and maintained by Marco
<br>Bug reports and feature requests:
<a href="http://github.com/jerkos/metms">metMS site</a><br>
Discussions around the project:
<a href="http://groups.google.com/group/spyderlib">Google Group</a>
<p>This project is part of the BRIDGE project
<p>Python %3, Qt %4, PyQt %5"""
)
.arg("metMS")
.arg(__version__)
.arg(platform.python_version())
.arg(QT_VERSION_STR)
.arg(PYQT_VERSION_STR),
)
class MSMainWindow(QMainWindow):
"""Gui of the main window"""
#MAX_RECENT_FILES = 10
#start putting links spyder numpy scipy et tutti quanti
links=('http://numpy.scipy.org/',
'http://packages.python.org/spyder/',
'http://www.riverbankcomputing.co.uk/software/pyqt/intro')
pluginPath=path.normcase('pluginmanager/plugins/')
def __init__(self, availablePlugins):
"""
Constructor with all the models needed setup menus
"""
QMainWindow.__init__(self)
self.setDockOptions(QMainWindow.VerticalTabs | QMainWindow.AnimatedDocks)
self.plugins = availablePlugins
self.pluginsInst=[]
settings=QSettings('INRA/INSA', '-'.join([QApplication.instance().APPLICATION_NAME_STR,
QApplication.instance().VERSION_STR]))
self.recentFiles = list(settings.value("RecentFiles").toStringList())
self.setStyleSheet(stylesheet)
self.pipeline = MSPipelineToolBar("Pipeline toolbar", parent=self)
self.addToolBar(0x1,self.pipeline)
self._setupModels()
self._setupUi()
self._setupMenus()
def _setupModels(self):
"""
Warning:Causes segfault when horizontal labels set to True
on aura peu etre a la fin un model par sampleList c'est ce qui parait
le plus logique
"""
#drag and drop table sample
self.sampleModel = QStandardItemModel(self)
self.sampleModel.setHorizontalHeaderLabels(["Sample", "Class"])
#treeView1
self.spectraModel = QStandardItemModel(self)
#treeview2
self.peakModel = QStandardItemModel(self)
#treeview3
self.clusterModel = QStandardItemModel(self)
def _setupMenus(self):
#file
self.fileMenu = QMenu('&File')
self.fileMenu.setTearOffEnabled(True)
self.op=QMenu("&Open...",self.fileMenu)
self.op.setIcon(QIcon(path.normcase("gui/icons/fileopen.png")))
open_=QAction("&Open rawfiles", self)
open_.setToolTip("Open an mzXML or netCDF file")
open_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_O))
open_icon=QIcon(path.normcase("gui/icons/fileopen.png"))
open_.setIcon(open_icon)
self.op.addAction(open_)
load_=QAction("&Open projects...", self)
load_.setToolTip("load binary file containing saved objects")
load_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_S))
load_icon=QIcon(QPixmap(path.normcase("gui/icons/project_open.png")))
load_.setIcon(load_icon)
self.op.addAction(load_)
self.fileMenu.addMenu(self.op)
save_=QAction("&Save...", self)
save_.setToolTip("save the actual application model")
save_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_S))
save_icon=QIcon(path.normcase("gui/icons/save_all.png"))
save_.setIcon(save_icon)
self.fileMenu.addAction(save_)
pkl = QAction("&load a peaklist", self) #TODO:load peaklist
pkl.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_P))
pkl.setToolTip("load a peaklist and process it")
pkl.setIcon(QIcon(path.normcase("gui/icons/featuredetect.png")))
self.fileMenu.addAction(pkl)
convert_=QAction("&Convert...", self)
convert_.setEnabled(False)
convert_.setToolTip("Convert a .wiff file if Analyst(c) is installed")
convert_icon=QIcon(path.normcase("gui/icons/goto.png"))
convert_.setIcon(convert_icon)
self.fileMenu.addAction(convert_)
a = self.fileMenu.addAction(QIcon(path.normcase("gui/icons/process.png")), "&Launch a batch")
a.setEnabled(False)
b = self.fileMenu.addAction(QIcon(path.normcase("gui/icons/process.png")), "&Merge")
b.setToolTip("Merge MRM file")
#b.setEnabled(False)
self.fileMenu.addSeparator()
#
# for i in xrange(self.MAX_RECENT_FILES):
# a = QAction('', self)
# a.setVisible(False)
# self.fileMenu.addAction(a)
#
# for i in xrange(min(self.MAX_RECENT_FILES, len(self.recentFiles))):
# self.fileMenu.actions()[5+i].setVisible(True)
# self.fileMenu.actions()[5+i].setText(self.recentFiles[i].split('/')[-1])
exit_action =QAction("&Exit", self)
exit_action.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_Q))
exit_action.setIcon(QIcon(QPixmap(path.normcase('gui/icons/exit.png'))))
self.fileMenu.addAction(exit_action)
self.menuBar().addMenu(self.fileMenu)
self.editMenu=QMenu("&Edit")
self.editMenu.setTearOffEnabled(True)
self.editMenu.addAction(QIcon(path.normcase('gui/icons/edit_undo.png')), '&Undo...')
self.editMenu.addAction(QIcon(path.normcase('gui/icons/edit_redo.png')), '&Redo...')
self.editMenu.actions()[0].setEnabled(False)
self.editMenu.actions()[1].setEnabled(False)
self.editMenu.addSeparator()
self.editMenu.addAction(QIcon(path.normcase('gui/icons/run.png')), '&Preferences')
self.exportMenu = QMenu("&Export...")
self.exportMenu.setIcon(QIcon(path.normcase('gui/icons/file_export.png')))
self.exportMenu.addAction("&Peaklist")
self.exportMenu.addAction("&Clusters intensity matrix")
self.editMenu.addMenu(self.exportMenu)
self.menuBar().addMenu(self.editMenu)
#view
self.viewMenu =QMenu("&View")
self.viewMenu.setTearOffEnabled(True)
self.viewMenu.addAction(QIcon(path.normcase('gui/icons/window_duplicate')),
"&Cascade View",
self.mdiArea.cascadeSubWindows,
QKeySequence(Qt.CTRL + Qt.Key_K))
self.viewMenu.addAction(QIcon(path.normcase('gui/icons/view_icon')),
"&Title View",
self.mdiArea.tileSubWindows,
QKeySequence(Qt.CTRL + Qt.Key_N))
self.viewMenu.addAction(QIcon(path.normcase("gui/icons/stop_process.png")),
"&Close all subWindows",
self.mdiArea.closeAllSubWindows,
QKeySequence(Qt.CTRL+Qt.Key_W))
self.plotting =QMenu("&Plotting...")
self.plotting.setIcon(QIcon(QPixmap(path.normcase("gui/icons/plot.png"))))
self.plotting.addAction("&3D Plot")
#self.plotting.addAction("&Cytoscape web")
self.plotting.addAction("&Spectrogram Plot")
#self.multiplePlot = QAction("&Visualize Raw/Treated Data", self)
#self.multiplePlot.setCheckable(True)
#self.multiplePlot.setEnabled(False)
#self.sub_plot_.addAction(self.multiplePlot)
self.viewMenu.addMenu(self.plotting)
self.viewMenu.addSeparator()
self.show_hide=QMenu("&Show/Hide")
m=self.createPopupMenu()
m.setTitle("&Show/Hide")
self.viewMenu.addMenu(m)
#self.pref = QMenu("&Preferences")
#self.pref.addAction(self.multiplePlot)
#self.viewMenu.addMenu(self.pref)
self.menuBar().addMenu(self.viewMenu)
#algorithm
self.algoMenu= QMenu("&Algorithm")
self.algoMenu.setTearOffEnabled(True)
self.preProcessing=QMenu("&PreProcessing(experimental)")
self.preProcessing.addAction("&Smoothing raw data...")
self.preProcessing.addAction("&Cut off raw data...")
self.preProcessing.addAction('&Calibration (mz dimension)')
self.preProcessing.addAction("&Resize sample...")
self.algoMenu.addMenu(self.preProcessing)
self.peakPickingMenu = QMenu("&Peack Picking & Alignement(XCMS)", self)
self.peakPickingMenu.setIcon(QIcon(path.normcase("gui/icons/pickedpeakicon.png")))
matched = QAction("&MatchedFiltered", self)
matched.setIcon(QIcon(path.normcase('gui/icons/RLogo')))
matched.setToolTip("Peak Detection and Integration using MatchedFiltered algorithm")
self.peakPickingMenu.addAction(matched)
centwave=QAction("&CentWave", self)
centwave.setIcon(QIcon(path.normcase('gui/icons/RLogo')))
centwave.setToolTip("Peak Detection and Integration using CentWave algorithm")
self.peakPickingMenu.addAction(centwave)
#peak_.setShortcut(.QKeySequence(CTRL + Key_P))
# peak_icon=.QIcon(.QPixmap(path.normcase("gui/icons/pickedpeakicon.png")))
#peak_.setIcon(peak_icon)
self.algoMenu.addMenu(self.peakPickingMenu)
self.alignment = QMenu("&Alignment")
self.alignment.setIcon(QIcon(path.normcase('gui/icons/format_indent_more.png')))
self.alignment.addAction("&Polynomial fitting(exp)")
self.alignment.addAction("&DynamicTimeWarping")
self.alignment.addAction("&ObiWarp")
self.alignment.actions()[2].setEnabled(False)
self.algoMenu.addMenu(self.alignment)
self.algoMenu.addAction("Normalization")
clust_ = QAction("&Clustering", self)
clust_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_L))
clust_icon=QIcon(QPixmap(path.normcase("gui/icons/cluster.png")))
clust_.setIcon(clust_icon)
self.algoMenu.addAction(clust_)
id_ = QAction("&Identification", self)
id_.setShortcut(QKeySequence(Qt.CTRL + Qt.Key_I))
id_.setToolTip("Try to identify peaks with several methods")
id_.setIcon(QIcon(QPixmap(path.normcase("gui/icons/findcompound.png"))))
self.algoMenu.addAction(id_)
self.menuBar().addMenu(self.algoMenu)
#tools
self.toolsMenu =QMenu("&Tools")
self.toolsMenu.setTearOffEnabled(True)
web = QAction("&Web Browser", self)
web.setIcon(QIcon(QPixmap(path.normcase("gui/icons/applications_internet.png"))))
self.toolsMenu.addAction(web)
#cyto = QAction("&cytoscape", self)
#cyto_icon =QIcon(QPixmap(path.normcase("gui/icons/cytoscape.jpeg")))
#cyto.setIcon(cyto_icon)
#self.toolsMenu.addAction(cyto)
editor = QAction("&Editor", self)
editor.setIcon(QIcon(QPixmap(path.normcase("gui/icons/document_sign.png"))))
self.toolsMenu.addAction(editor)
pet=QAction("&Short Periodic Table", self)
pet.setIcon(QIcon(QPixmap(path.normcase("gui/icons/pet.jpg"))))
self.toolsMenu.addAction(pet)
self.menuBar().addMenu(self.toolsMenu)
#plugins
self.pluginMenu = QMenu('&Plugins')
self.pluginMenu.setTearOffEnabled(True)
instPl= QAction("&Install a plugin", self)
instPl.setIcon(QIcon(path.normcase('gui/icons/pluginInstall.png')))
self.pluginMenu.addAction(instPl)
self.launchingMenu = QMenu("&Launch PLugins", self)
self.launchingMenu.setIcon(QIcon(path.normcase('gui/icons/plugin')))
for plug in self.plugins:
#fullname="".join([self.pluginPath, str(plug)])
mod=imp.load_source(self.__module__, plug)
if mod.autoActivation:
qApp=QApplication.instance()
name=getattr(mod, 'className')
cls=getattr(mod, name)
p=cls(qApp.model, self, parent=self)
#p=qApp.pluginManager.loadPlugin(qApp.model, self, plug.split('/')[-1])
self.pluginsInst.append(p)
else:
self.launchingMenu.addAction(plug.split('/')[-1])
self.pluginMenu.addMenu(self.launchingMenu)
self.pluginMenu.addAction(QIcon(path.normcase("gui/icons/process_stop.png")),
"&Remove loaded Plugin")
self.menuBar().addMenu(self.pluginMenu)
#about
self.aboutMenu= QMenu("&About")
self.aboutMenu.setTearOffEnabled(True)
metms = QAction(QIcon(path.normcase('gui/icons/deluge.png')), "&about metMS...", self)
self.aboutMenu.addAction(metms)
pyqt = QAction("&about PyQt4...", self)
pyqt_icon =QIcon(QPixmap(path.normcase("gui/icons/logo_QT4.png")))
pyqt.setIcon(pyqt_icon)
self.aboutMenu.addAction(pyqt)
metms = QAction("&metMS Documentation", self)
metms_icon =QIcon(QPixmap(path.normcase("gui/icons/deluge.png")))
metms.setIcon(metms_icon)
self.aboutMenu.addAction(metms)
self.menuBar().addMenu(self.aboutMenu)
def _setupUi(self, background=None):
"""
Make the GUI
"""
#mdi
self.mdiArea = MSMdiArea(self)
self.mdiArea.setBackground(QBrush(QPixmap(path.normcase('gui/icons/blac2.png'))))#QColor(Qt.blue).darker()))
self.setCentralWidget(self.mdiArea)
#sample dock widget
self.sampleDockWidget = QDockWidget("Samples", self)
#sampleWidget = QWidget()
self.sampleTableView = MSDragFromTableView()
self.sampleTableView.setModel(self.sampleModel)
self.sampleTableView.setSelectionBehavior(1)
self.sampleTableView.verticalHeader().hide()
self.sampleTableView.verticalHeader().setDefaultSectionSize(15)
self.sampleTableView.horizontalHeader().setDefaultSectionSize(150)
self.sampleDockWidget.setWidget(self.sampleTableView)#sampleWidget)
self.sampleDockWidget.visible=True
#workflow dock
self.workflowDockWidget = QDockWidget("Visualizer", self)
self.workflowDockWidget.visible = True
a=QWidget(self)
v=QVBoxLayout(a)
q=QToolBar()
#self.workingSample = QLabel("Working Sample:None")
#q.addWidget(self.workingSample)
q.addWidget(QLabel("ppm :"))
self.ppmEditer=QDoubleSpinBox()
self.usePpm=QCheckBox("use ?")
q.addWidget(self.ppmEditer)
q.addWidget(self.usePpm)
q.addSeparator()
self.removeButton=QToolButton(self)
self.removeButton.setIcon(QIcon(path.normcase("gui/icons/delete.png")))
q.addWidget(self.removeButton)
self.markAsGood=QAction(QIcon(path.normcase("gui/icons/button_ok.png")),"mark peak as good", self)
self.markAsBad=QAction(QIcon(path.normcase("gui/icons/stop.png")), "mark peak as bad", self)
self.hideItem = QAction(QIcon(path.normcase("gui/icons/list_remove.png")), "Hide Item", self)
q.addAction(self.markAsGood)
q.addAction(self.markAsBad)
q.addAction(self.hideItem)
v.addWidget(q)
self.tabWidget = QTabWidget()
self.tab = QWidget()
verticalLayout = QVBoxLayout(self.tab)
self.treeView = MSToDropTableView()
self.treeView.verticalHeader().setDefaultSectionSize(20)
self.treeView.setModel(self.spectraModel)
self.spectraLabel = QLabel("Sample: None")
verticalLayout.addWidget(self.treeView)
verticalLayout.addWidget(self.spectraLabel)
self.tabWidget.addTab(self.tab, QIcon(path.normcase("gui/icons/spectrumicon.png")),"Spectra")
self.tab_2 = QWidget()
verticalLayout_4 = QVBoxLayout(self.tab_2)
self.treeView_2 = MSToDropTableView()#MSTreeView(self.tab_2)# QTableView(self)#
self.treeView_2.verticalHeader().setDefaultSectionSize(20)
self.treeView_2.setModel(self.peakModel)
self.peakLabel = QLabel("Sample: None")
verticalLayout_4.addWidget(self.treeView_2)
verticalLayout_4.addWidget(self.peakLabel)
self.tabWidget.addTab(self.tab_2,QIcon(path.normcase("gui/icons/peakicon.png")), "Peaks List")
self.tab_3 = QWidget()
verticalLayout_5 = QVBoxLayout(self.tab_3)
self.treeView_3 = MSToDropTreeView()
self.treeView_3.setAnimated(True)
self.treeView_3.setModel(self.clusterModel)
self.clusterLabel = QLabel("Sample: None")
verticalLayout_5.addWidget(self.treeView_3)
verticalLayout_5.addWidget(self.clusterLabel)
self.tabWidget.addTab(self.tab_3, QIcon(path.normcase("gui/icons/clustering.png")), "Clusters")
self.tabWidget.setCurrentIndex(0)
for l in (self.spectraLabel, self.peakLabel, self.clusterLabel):
l.setAutoFillBackground(True)
v.addWidget(self.tabWidget)
self.workflowDockWidget.setWidget(a)
self.addDockWidget(Qt.DockWidgetArea(0x2),self.workflowDockWidget)
from gui.MetBaseGui import MSIsoCalculator
self.isoCalc = MSIsoCalculator(self)
self.isoCalcDockWidget=QDockWidget('isotopes calculation', self)
self.isoCalcDockWidget.setWidget(self.isoCalc)
self.addDockWidget(Qt.DockWidgetArea(0x2), self.isoCalcDockWidget)
self.isoCalcDockWidget.setVisible(False)
self.isoCalcDockWidget.visible=False
from gui.MetBaseGui import FormulaGenerator
self.generator=FormulaGenerator(self)
self.generatorDockWidget=QDockWidget('formula generator', self)
self.generatorDockWidget.setWidget(self.generator)
self.addDockWidget(Qt.DockWidgetArea(0x2), self.generatorDockWidget)
self.generatorDockWidget.setVisible(False)
self.generatorDockWidget.visible=False
self.compoundTreeView = MSCompoundTreeView(self)
self.compoundDockWidget = QDockWidget("Compounds", self)
self.compoundDockWidget.setWidget(self.compoundTreeView)
self.addDockWidget(Qt.DockWidgetArea(0x2),self.compoundDockWidget)
self.compoundDockWidget.setVisible(False)
self.compoundDockWidget.visible=False
self.comparativeTableView = QTableView(self)
self.comparativeTableView.horizontalHeader().setStretchLastSection(True)
self.comparativeTableView.verticalHeader().setDefaultSectionSize(20)
self.comparativeDock = QDockWidget("Comparative View", self)
self.comparativeDock.setWidget(self.comparativeTableView)
self.addDockWidget(Qt.DockWidgetArea(0x8), self.comparativeDock)
self.comparativeDock.setVisible(False)
self.comparativeDock.visible = False
self.tabifyDockWidget(self.compoundDockWidget, self.isoCalcDockWidget)
self.tabifyDockWidget(self.isoCalcDockWidget, self.workflowDockWidget )
self.tabifyDockWidget(self.workflowDockWidget, self.generatorDockWidget)
#set the end
#WARNING: possible that the internal shell widget cause random segfault
#with the error of QObject::killTimers...? not sure !
self.shell = QWidget()#InternalShell(namespace={'metms': QApplication.instance()},
# parent=self,
# multithreaded=False)
self.shellDock = QDockWidget("Python Shell", self)
self.shellDock.setWindowIcon(QIcon(path.normcase('gui/icons/stop.png')))
self.shellDock.setWidget(self.shell)
self.shellDock.setMinimumWidth(255)
self.shellDock.visible=True
self.addDockWidget(0x2, self.shellDock)
self.addDockWidget(0x2, self.sampleDockWidget)
self.tabifyDockWidget(self.shellDock, self.sampleDockWidget)
self.pb = QProgressBar(self)
self.pb.setMaximumWidth(245)
self.stopProcess = QToolButton(self)
self.stopProcess.setIcon(QIcon(path.normcase("gui/icons/process_stop.png")))
m = QMenu()
#self.connect(m, SIGNAL('triggered(QAction*'), QApplication.instance().taskManager.abortByName)
self.stopProcess.setMenu(m)
self.stopProcess.setPopupMode(1) #Menu Button
#self.connect(self.stopProcess, SIGNAL("clicked()"), self.stopThread)
self.statusBar().addPermanentWidget(self.stopProcess)
self.statusBar().addPermanentWidget(self.pb)
def updateStopProcessMenu(self):
"""
update the menu of the stop process
button, based directly on the processes
stored by the task manager
"""
self.stopProcess.menu().clear()
for c in QApplication.instance().taskManager:
self.stopProcess.menu().addAction(c.title)
#QApplication.instance().taskManager.abort(QApplication.instance().taskManager[-1])
def addMdiSubWindow(self, plot, title="", showMaximized=False):
"""
Allow addition of new window in the mdiarea
"""
win=self.mdiArea.addSubWindow(plot)
#print "widget parent", plot.parent()
win.setAttribute(Qt.WA_DeleteOnClose)
#win.connect(win, SIGNAL('destroyed(QObject *)'), self.testdestroy)
#plot.setParent(win)
win.setWindowTitle(title)
if showMaximized:
win.showMaximized()
else:
win.resize(400, 300)
win.show()
return win
def updateTreeView(self):
"""
Tree View update switch spectre/chromato
"""
if self.treeView.model() == self.spectraModel:
self.treeView.setModel(self.chromaModel)
self.tabWidget.setTabText(0, "Chroma")
else:
self.treeView.setModel(self.spectraModel)
#self.treeView.setSelectionMode(1)
self.tabWidget.setTabText(0, "Spectra")
def addTreeViewModel (self,model1, model2):
"""Add a model """
self.chromaModel.appendRow(model1)
self.spectraModel.appendRow(model2)
def _actionHovered(self, action):
"""emulate tooltip cause they do not work that much"""
tip = action.toolTip()
QToolTip.showText(QCursor.pos(), tip)
def showErrorMessage(self, title, string):
QMessageBox.critical(self, title, string, 0, 0)
def showWarningMessage(self, title, string):
return QMessageBox.warning(self, title, string, QMessageBox.Ok|QMessageBox.Cancel)
def showInformationMessage(self, title, string):
QMessageBox.information(self, title, string, 0)
def updateProgressBar(self, i):
"""update the value of the progress bar for all the treatment"""
self.pb.setValue(min(i, 100))
def to_indetermined_mode(self):
self.pb.setMaximum(0)
def to_determined_mode(self):
self.pb.setMaximum(100)
def showInStatusBar(self, string, time=5000):
self.statusBar().showMessage(string, time)
def addInterpreterDock(self, shell):
self.shellDock = QDockWidget(self)
self.shellDock.setWidget(shell)
self.shellDock.setWindowTitle("shell")
self.addDockWidget(0x2, self.shellDock)
def showMetMSInformation(self):
QMessageBox.about(self,
self.tr("About %1").arg("metMS"),
self.tr("""<b>%1 %2</b>
<br>metabolite Mass Spectrometry
<p>Copyright © 2010 Marco INSA, INRA
<br>Licensed under the terms of the CeciLL License
<p>Developed and maintained by Marco
<br>Bug reports and feature requests:
<a href="http://github.com/jerkos/metms">metMS site</a><br>
Discussions around the project:
<a href="http://groups.google.com/group/spyderlib">Google Group</a>
<p>This project is part of the BRIDGE project
<p>Python %3, Qt %4, PyQt %5""") \
.arg("metMS").arg(__version__) \
.arg(platform.python_version()).arg(QT_VERSION_STR) \
.arg(PYQT_VERSION_STR))
def setWindowIcon(self, icon):
QDockWidget.setWindowIcon(self, icon)
self.windowIconChanged.emit(icon)
def setWindowIcon(self, icon):
QDockWidget.setWindowIcon(self, icon)
self.windowIconChanged.emit(icon)