Esempio n. 1
0
    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)
Esempio n. 2
0
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 &copy; 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))
Esempio n. 3
0
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 &copy; 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),
        )
Esempio n. 4
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    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)