Python OWGUI.widgetLabel方法代码示例

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager = None, loaddata=1):
        OWWidget.__init__(self, parent, signalManager, 'Data Files', wantMainArea = 0, resizingEnabled = 1)

        self.callbackDeposit = []

        self.inputs = []
        self.outputs = [("Examples", ExampleTable), ("Structured Data", DataFiles)]

        self.dataStructure = []
        self.datasets = None
        self.lastSentIds = []

        # Settings
        self.recentDirs=[]  
        self.selectedDirName = "None"
        self.applyOnChange = 0
        self.loadSettings()

        # CONTROLS
        box = OWGUI.widgetBox(self.controlArea, "Directory", addSpace = True, orientation=0)
        self.dircombo=QComboBox(box)
        box.layout().addWidget(self.dircombo)
        button = OWGUI.button(box, self, '...', callback = self.browseDirectory, disabled=0)
        button.setMaximumWidth(25)
        # connecting GUI to code
        self.connect(self.dircombo,SIGNAL('activated(int)'),self.selectDir)

        # info
        box = OWGUI.widgetBox(self.controlArea, "Info", addSpace = True)
        self.infoa = OWGUI.widgetLabel(box, 'No data loaded.')
        self.infob = OWGUI.widgetLabel(box, '')
        self.infoc = OWGUI.widgetLabel(box, '')
            
        # LIST VIEW
        frmListView = OWGUI.widgetBox(self.controlArea, None, addSpace = True)
        self.tree = QTreeWidget(frmListView)
        self.tree.setSelectionMode(QAbstractItemView.MultiSelection)
        self.tree.setHeaderLabel("Directory/Data File")
        frmListView.layout().addWidget(self.tree)
        self.connect(self.tree,SIGNAL('itemSelectionChanged()'),self.selectionChanged)

        # Output
        box = OWGUI.widgetBox(self.controlArea, "Output", addSpace = True)
        OWGUI.checkBox(box, self, 'applyOnChange', 'Commit data on selection change')
        self.commitBtn = OWGUI.button(box, self, "Commit", callback=self.sendData, disabled=1)
        self.resize(300,600)

        # initial settings            
        self.recentDirs=filter(os.path.exists,self.recentDirs)
        self.setDirlist()
        self.dircombo.setCurrentIndex(0)
        if self.recentDirs!=[] and loaddata:
            self.loadData(self.recentDirs[0])

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager=None, title="Databases Pack"):

        super(OWDatabasesPack, self).__init__(parent, signalManager, title, wantMainArea=False)

        self.fileslist = [("Taxonomy", "ncbi_taxonomy.tar.gz")]
        self.downloadurl = "https://dl.dropboxusercontent.com/u/100248799/sf_pack.tar.gz"
        self.downloadmessage = (
            "Downloading a subset of available databases for a smoother " + "ride through the workshop"
        )
        self.loadSettings()
        self._tmpfile = None
        self.reply = None

        # Locks held on server files
        self.locks = []
        self.net_manager = QNetworkAccessManager()
        # Lock all files in files list so any other (in process) atempt to
        # download the files waits)
        box = OWGUI.widgetBox(self.controlArea, "Info")
        self.info = OWGUI.widgetLabel(box, self.downloadmessage)
        self.info.setWordWrap(True)

        box = OWGUI.widgetBox(self.controlArea, "Status")
        self.statusinfo = OWGUI.widgetLabel(box, "Please wait")
        self.statusinfo.setWordWrap(True)
        self.progressbar = QProgressBar()
        box.layout().addWidget(self.progressbar)

        self.setMinimumWidth(250)

        already_available = [
            (domain, filename) for domain in serverfiles.listdomains() for filename in serverfiles.listfiles(domain)
        ]

        if set(self.fileslist) <= set(already_available):
            # All files are already downloaded
            self.statusinfo.setText("All files already available")
            self.setStatusMessage("Done")
        else:
            for domain, filename in self.fileslist + [("_tmp_cache_", "pack")]:
                manager = serverfiles._lock_file(domain, filename)
                try:
                    manager.__enter__()
                except Exception:
                    warnings.warn("Could not acquire lock for {0} {0}".format(domain, filename))
                    self.warning(0, "...")
                else:
                    self.locks.append(manager)

            QTimer.singleShot(0, self.show)
            QTimer.singleShot(0, self.run)

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager = None):
        OWWidget.__init__(self, parent, signalManager, "Save Data Files", wantMainArea = 0, resizingEnabled = 1)

        self.inputs = [("Structured Data", DataFiles, self.structuredData, Default)]
        self.outputs = []
        self.dataStructure = None

        # Settings
        self.recentDirs=[]
        self.selectedDirName = "(none)"
        self.loadSettings()

        # GUI
        rfbox = OWGUI.widgetBox(self.controlArea, "Directory", orientation="horizontal", addSpace = True)
        self.dircombo = QComboBox(rfbox)
        rfbox.layout().addWidget(self.dircombo)
        browse = OWGUI.button(rfbox, self, '&...', callback = self.browseDirectory, disabled=0)
        browse.setMaximumWidth(25)
        # info
        box = OWGUI.widgetBox(self.controlArea, "Info", addSpace = True)
        self.infoa = OWGUI.widgetLabel(box, 'No data on input.')
        # Output
        box = OWGUI.widgetBox(self.controlArea, "Output", addSpace = True)
        self.save = OWGUI.button(box, self, '&Save', callback = self.saveData, disabled=1)
        self.adjustSize()
           
        # initial settings            
        self.recentDirs=filter(os.path.exists, self.recentDirs)
        self.setDirlist()
        self.dircombo.setCurrentIndex(0)
        self.resize(300,self.height())

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager = None):
        OWWidget.__init__(self, parent, signalManager, 'Data Files Selector', wantMainArea = 0, resizingEnabled = 1)

        self.callbackDeposit = []

        self.inputs = [("Structured Data", DataFiles, self.onDataInput)]
        self.outputs = [("Examples", ExampleTable), ("Structured Data", DataFiles)]

        self.dataStructure = None
        self.datasets = None
        self.lastSentIds = []

        # Settings
        self.applyOnChange = 0
        self.loadSettings()

        # GUI
        # info
        box = OWGUI.widgetBox(self.controlArea, "Info", addSpace = True)
        self.infoa = OWGUI.widgetLabel(box, 'No data loaded.')
        self.infob = OWGUI.widgetLabel(box, '')
        self.infoc = OWGUI.widgetLabel(box, '')
            
        # LIST VIEW
        frmListView = OWGUI.widgetBox(self.controlArea, None, addSpace = True)
        self.tree = QTreeWidget(frmListView)
        self.tree.setSelectionMode(QAbstractItemView.MultiSelection)
        self.tree.setHeaderLabel("Directory/Data File")
        frmListView.layout().addWidget(self.tree)
        self.connect(self.tree,SIGNAL('itemSelectionChanged()'),self.selectionChanged)

        # Output
        box = OWGUI.widgetBox(self.controlArea, "Output", addSpace = True)
        OWGUI.checkBox(box, self, 'applyOnChange', 'Commit data on selection change')
        self.commitBtn = OWGUI.button(box, self, "Commit", callback=self.sendData, disabled=1)
        self.resize(300,600)

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"):
        OWWidget.__init__(self, parent, signalManager, name)

        self.selectionChanged = False
        self.filterString = ""
        self.datasetName = ""

        ## GUI
        box = gui.widgetBox(self.controlArea, "Info", addSpace=True)
        self.infoBox = gui.widgetLabel(box, "Initializing\n\n")

        box = gui.widgetBox(self.controlArea, "Output", addSpace=True)
        gui.radioButtonsInBox(box, self, "outputRows",
                              ["Genes in rows", "Samples in rows"], "Rows",
                              callback=self.commitIf)

        gui.checkBox(box, self, "mergeSpots", "Merge spots of same gene",
                     callback=self.commitIf)

        gui.separator(box)
        self.nameEdit = gui.lineEdit(
            box, self, "datasetName", "Data set name",
            tooltip="Override the default output data set name",
            callback=self.onNameEdited
        )
        self.nameEdit.setPlaceholderText("")

        if sys.version_info < (3, ):
            box = gui.widgetBox(self.controlArea, "Commit", addSpace=True)
            self.commitButton = gui.button(
                box, self, "Commit", callback=self.commit)
            cb = gui.checkBox(box, self, "autoCommit", "Commit on any change")
            gui.setStopper(self, self.commitButton, cb, "selectionChanged",
                           self.commit)
        else:
            gui.auto_commit(self.controlArea, self, "autoCommit", "Commit",
                            box="Commit")
            self.commitIf = self.commit

        gui.rubber(self.controlArea)

        gui.widgetLabel(self.mainArea, "Filter")
        self.filterLineEdit = QLineEdit(
            textChanged=self.filter
        )
        self.completer = TokenListCompleter(
            self, caseSensitivity=Qt.CaseInsensitive
        )
        self.filterLineEdit.setCompleter(self.completer)

        self.mainArea.layout().addWidget(self.filterLineEdit)

        splitter = QSplitter(Qt.Vertical, self.mainArea)
        self.mainArea.layout().addWidget(splitter)
        self.treeWidget = QTreeView(splitter)

        self.treeWidget.setSelectionMode(QTreeView.SingleSelection)
        self.treeWidget.setRootIsDecorated(False)
        self.treeWidget.setSortingEnabled(True)
        self.treeWidget.setAlternatingRowColors(True)
        self.treeWidget.setUniformRowHeights(True)
        self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers)

        linkdelegate = LinkStyledItemDelegate(self.treeWidget)
        self.treeWidget.setItemDelegateForColumn(1, linkdelegate)
        self.treeWidget.setItemDelegateForColumn(8, linkdelegate)
        self.treeWidget.setItemDelegateForColumn(
            0, gui.IndicatorItemDelegate(self.treeWidget,
                                         role=Qt.DisplayRole))

        proxyModel = MySortFilterProxyModel(self.treeWidget)
        self.treeWidget.setModel(proxyModel)
        self.treeWidget.selectionModel().selectionChanged.connect(
            self.updateSelection
        )
        self.treeWidget.viewport().setMouseTracking(True)

        splitterH = QSplitter(Qt.Horizontal, splitter)

        box = gui.widgetBox(splitterH, "Description")
        self.infoGDS = gui.widgetLabel(box, "")
        self.infoGDS.setWordWrap(True)
        gui.rubber(box)

        box = gui.widgetBox(splitterH, "Sample Annotations")
        self.annotationsTree = QTreeWidget(box)
        self.annotationsTree.setHeaderLabels(
            ["Type (Sample annotations)", "Sample count"]
        )
        self.annotationsTree.setRootIsDecorated(True)
        box.layout().addWidget(self.annotationsTree)
        self.annotationsTree.itemChanged.connect(
            self.annotationSelectionChanged
        )
        self._annotationsUpdating = False
        self.splitters = splitter, splitterH

        for sp, setting in zip(self.splitters, self.splitterSettings):
            sp.splitterMoved.connect(self.splitterMoved)
            sp.restoreState(setting)
#.........这里部分代码省略.........

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager=None, title="Expression Profile Distances"):
        OWWidget.__init__(self, parent, signalManager, title)

        self.inputs = [("Example Table", ExampleTable, self.set_data)]
        self.outputs = [("Distances", Orange.core.SymMatrix), ("Sorted Example Table", ExampleTable)]

        self.distance_measure = 0
        self.auto_commit = False
        self.changed_flag = False

        self.loadSettings()

        ########
        # GUI
        ########

        self.info_box = OWGUI.widgetLabel(
            OWGUI.widgetBox(self.controlArea, "Input", addSpace=True), "No data on input\n"
        )

        box = OWGUI.widgetBox(self.controlArea, "Separate By", addSpace=True)
        self.separate_view = QListView()
        self.separate_view.setSelectionMode(QListView.MultiSelection)
        box.layout().addWidget(self.separate_view)

        box = OWGUI.widgetBox(self.controlArea, "Sort By", addSpace=True)
        self.relevant_view = QListView()
        self.relevant_view.setSelectionMode(QListView.MultiSelection)
        box.layout().addWidget(self.relevant_view)

        self.distance_view = OWGUI.comboBox(
            self.controlArea,
            self,
            "distance_measure",
            box="Distance Measure",
            items=[d[0] for d in self.DISTANCE_FUNCTIONS],
        )

        OWGUI.rubber(self.controlArea)

        box = OWGUI.widgetBox(self.controlArea, "Commit")
        cb = OWGUI.checkBox(
            box,
            self,
            "auto_commit",
            "Commit on any change",
            tooltip="Compute and send the distances on any change.",
            callback=self.commit_if,
        )

        b = OWGUI.button(
            box,
            self,
            "Commit",
            tooltip="Compute the distances and send the output signals.",
            callback=self.commit,
            default=True,
        )

        OWGUI.setStopper(self, b, cb, "changed_flag", callback=self.commit)

        self.groups_box = OWGUI.widgetBox(self.mainArea, "Groups")
        self.groups_scroll_area = QScrollArea()
        self.groups_box.layout().addWidget(self.groups_scroll_area)

        self.data = None
        self.partitions = []
        self.matrix = None
        self.split_groups = []
        self._disable_updates = False

        self.resize(800, 600)

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager=None, title="Gene Network"):
        super(OWGeneNetwork, self).__init__(
            parent, signalManager, title, wantMainArea=False,
            resizingEnabled=False
        )

        self.taxid = "9606"
        self.gene_var_index = -1
        self.use_attr_names = False
        self.network_source = 1
        self.include_neighborhood = True
        self.autocommit = False
        self.min_score = 0.9
        self.loadSettings()

        self.taxids = taxonomy.common_taxids()
        self.current_taxid_index = self.taxids.index(self.taxid)

        self.data = None
        self.geneinfo = None
        self.nettask = None
        self._invalidated = False

        box = OWGUI.widgetBox(self.controlArea, "Info")
        self.info = OWGUI.widgetLabel(box, "No data on input\n")

        box = OWGUI.widgetBox(self.controlArea, "Organism")
        self.organism_cb = OWGUI.comboBox(
            box, self, "current_taxid_index",
            items=map(taxonomy.name, self.taxids),
            callback=self._update_organism
        )
        box = OWGUI.widgetBox(self.controlArea, "Genes")
        self.genes_cb = OWGUI.comboBox(
            box, self, "gene_var_index", callback=self._update_query_genes
        )
        self.varmodel = OWItemModels.VariableListModel()
        self.genes_cb.setModel(self.varmodel)

        OWGUI.checkBox(
            box, self, "use_attr_names",
            "Use attribute names",
            callback=self._update_query_genes
        )

        box = OWGUI.widgetBox(self.controlArea, "Network")
        OWGUI.comboBox(
            box, self, "network_source",
            items=[s.name for s in SOURCES],
            callback=self._on_source_db_changed
        )
        OWGUI.checkBox(
            box, self, "include_neighborhood",
            "Include immediate gene neighbors",
            callback=self.invalidate
        )
        self.score_spin = OWGUI.doubleSpin(
            box, self, "min_score", 0.0, 1.0, step=0.001,
            label="Minimal edge score",
            callback=self.invalidate
        )
        self.score_spin.setEnabled(SOURCES[self.network_source].score_filter)

        box = OWGUI.widgetBox(self.controlArea, "Commit")
        OWGUI.button(box, self, "Commit", callback=self.commit, default=True)

        self.executor = ThreadExecutor()

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager=None, title="Gene Atlas Tissue Expression"):
        OWWidget.__init__(self, parent, signalManager, title)
        
        self.inputs = [("Example Table", Orange.data.Table, self.set_data)]
        self.outputs = [("Selected Genes", Orange.data.Table)]
        
        self.selected_organism = "Homo sapiens"
        self.selected_gene_attr = 0
        self.genes_in_columns = False
        self.selected_ef = 0
        self.selected_ef_value = 0
        
        self.loadSettings()
        
        #####
        # GUI
        #####
        box = OWGUI.widgetBox(self.controlArea, "Info", addSpace=True)
        self.info_label = OWGUI.widgetLabel(box, "No data on input.\n")
        
        box = OWGUI.widgetBox(self.controlArea, "Organism", addSpace=True)
        cb = OWGUI.comboBox(box, self, "selected_organism",
                            items=self.ORGANISMS,
                            tooltip="Organism name",
                            callback=self.on_organism_change,
                            sendSelectedValue=True,
                            valueType=str
                            )
        cb.setMaximumWidth(250)
        
        box = OWGUI.widgetBox(self.controlArea, "Gene Attribute", addSpace=True)
        self.gene_attr_cb = OWGUI.comboBox(box, self, "selected_gene_attr",
                              tooltip="Attribute (column) containing the gene names.",
                              callback=self.on_gene_attr_change,
                              )
        self.gene_attr_cb.setMaximumWidth(250)
        
        cb = OWGUI.checkBox(box, self, "genes_in_columns", "Use attribute names",
                       tooltip="Gene names in columns.",
                       callback=self.on_genes_change,)
        cb.disables.append((-1, self.gene_attr_cb))
        cb.makeConsistent()
        
        box = OWGUI.widgetBox(self.controlArea, "Tissues", addSpace=True)
        self.categories_cb = OWGUI.comboBox(box, self, "selected_ef",
                                box="Categories", 
                                items=self.FACTORS,
                                tooltip="Experimental factor.",
                                callback=self.on_ef_change,
                                )
        self.categories_cb.box.setFlat(True)
        
        self.values_cb = OWGUI.comboBox(box, self, "selected_ef_value",
                                box="Values",
                                tooltip="Experimental factor value.",
                                callback=self.on_ef_value_change
                                )
        self.values_cb.setMaximumWidth(250)
        self.values_cb.box.setFlat(True)
        
        box = OWGUI.widgetBox(self.controlArea, "Cache", addSpace=True)
        OWGUI.button(box, self, "Clear cache",
                     callback=self.on_cache_clear,
                     tooltip="Clear Gene Atlas cache.")
        
        OWGUI.rubber(self.controlArea)
        
        OWGUI.button(self.controlArea, self, label="Commit",
                     callback=self.commit,
                     tooltip="Send selected genes")
        
        self.report_view = QTreeView(self.mainArea)
        self.report_view.setSelectionMode(QTreeView.ExtendedSelection)
        self.report_view.setSortingEnabled(True)
        self.report_view.setRootIsDecorated(False)
        self.report_view.setAlternatingRowColors(True)
        self.report_view.setEditTriggers(QTreeView.NoEditTriggers)
        self.mainArea.layout().addWidget(self.report_view)
        self.report_header = ["Gene symbol", "Up", "Down"]
        
        model = QStandardItemModel()
        model.setHorizontalHeaderLabels(self.report_header)
        self.report_view.setModel(model)
        
        self.data = None
        self.candidate_vars = []
        self.candidate_var_names = []
        self.results = {}, {}, {}
        
        self.ensembl_info = None
        self.gene_matcher = obiGene.GMDirect()
        self.loaded_matcher_taxid = None
        self.unknown_genes = []
        self.query_genes = []
        
#        self.set_organism(self.selected_organism, update_results=False)
        
        self.get_atlas_summary = obiGeneAtlas.get_atlas_summary
        
        #Cached construct_matcher
#.........这里部分代码省略.........

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"):
        OWWidget.__init__(self, parent, signalManager, name)

        self.outputs = [("Expression Data", ExampleTable)]

        ## Settings
        self.selectedAnnotation = 0
        self.includeIf = False
        self.minSamples = 3
        self.autoCommit = False
        self.outputRows = 0
        self.mergeSpots = True
        self.filterString = ""
        self.currentGds = None
        self.selectionChanged = False
        self.autoCommit = False
        self.gdsSelectionStates = {}
        self.splitterSettings = [
            '\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xea\x00\x00\x00\xd7\x01\x00\x00\x00\x07\x01\x00\x00\x00\x02',
            '\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xb5\x00\x00\x02\x10\x01\x00\x00\x00\x07\x01\x00\x00\x00\x01'
        ]
        self.datasetNames = {}
        self.loadSettings()

        self.datasetName = ""

        ## GUI
        self.infoBox = OWGUI.widgetLabel(
            OWGUI.widgetBox(self.controlArea, "Info", addSpace=True),
            "Initializing\n\n"
        )

        box = OWGUI.widgetBox(self.controlArea, "Output", addSpace=True)
        OWGUI.radioButtonsInBox(box, self, "outputRows",
                                ["Genes or spots", "Samples"], "Rows",
                                callback=self.commitIf)
        OWGUI.checkBox(box, self, "mergeSpots", "Merge spots of same gene",
                       callback=self.commitIf)

        OWGUI.separator(box)
        self.nameEdit = OWGUI.lineEdit(
            box, self, "datasetName", "Data set name",
            tooltip="Override the default output data set name",
            callback=self.onNameEdited
        )
        self.nameEdit.setPlaceholderText("")

        box = OWGUI.widgetBox(self.controlArea, "Commit", addSpace=True)
        self.commitButton = OWGUI.button(box, self, "Commit",
                                         callback=self.commit)
        cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on any change")
        OWGUI.setStopper(self, self.commitButton, cb, "selectionChanged",
                         self.commit)
        OWGUI.rubber(self.controlArea)

        self.filterLineEdit = OWGUIEx.lineEditHint(
            self.mainArea, self, "filterString", "Filter",
            caseSensitive=False, matchAnywhere=True,
            callback=self.filter,  delimiters=" ")

        splitter = QSplitter(Qt.Vertical, self.mainArea)
        self.mainArea.layout().addWidget(splitter)
        self.treeWidget = QTreeView(splitter)

        self.treeWidget.setSelectionMode(QAbstractItemView.SingleSelection)
        self.treeWidget.setRootIsDecorated(False)
        self.treeWidget.setSortingEnabled(True)
        self.treeWidget.setAlternatingRowColors(True)
        self.treeWidget.setUniformRowHeights(True)
        self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers)

        linkdelegate = LinkStyledItemDelegate(self.treeWidget)
        self.treeWidget.setItemDelegateForColumn(1, linkdelegate)
        self.treeWidget.setItemDelegateForColumn(8, linkdelegate)
        self.treeWidget.setItemDelegateForColumn(
            0, OWGUI.IndicatorItemDelegate(self.treeWidget,
                                           role=Qt.DisplayRole))

        proxyModel = MySortFilterProxyModel(self.treeWidget)
        self.treeWidget.setModel(proxyModel)
        self.treeWidget.selectionModel().selectionChanged.connect(
            self.updateSelection
        )
        self.treeWidget.viewport().setMouseTracking(True)

        splitterH = QSplitter(Qt.Horizontal, splitter)

        box = OWGUI.widgetBox(splitterH, "Description")
        self.infoGDS = OWGUI.widgetLabel(box, "")
        self.infoGDS.setWordWrap(True)
        OWGUI.rubber(box)

        box = OWGUI.widgetBox(splitterH, "Sample Annotations")
        self.annotationsTree = QTreeWidget(box)
        self.annotationsTree.setHeaderLabels(
            ["Type (Sample annotations)", "Sample count"]
        )
        self.annotationsTree.setRootIsDecorated(True)
        box.layout().addWidget(self.annotationsTree)
        self.annotationsTree.itemChanged.connect(
#.........这里部分代码省略.........

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager=None, name="Gene Info"):
        OWWidget.__init__(self, parent, signalManager, name)

        self.inputs = [("Examples", Orange.data.Table, self.setData)]
        self.outputs = [("Selected Examples", Orange.data.Table)]

        self.organismIndex = 0
        self.taxid = None
        self.geneAttr = 0
        self.useAttr = False
        self.autoCommit = False
        self.searchString = ""
        self.selectionChangedFlag = False
        self.useAltSource = 0
        self.loadSettings()

        self.__initialized = False
        self.initfuture = None
        self.itemsfuture = None

        self.infoLabel = OWGUI.widgetLabel(
            OWGUI.widgetBox(self.controlArea, "Info", addSpace=True),
            "Initializing\n"
        )

        self.organisms = None
        self.organismBox = OWGUI.widgetBox(
            self.controlArea, "Organism", addSpace=True)

        self.organismComboBox = OWGUI.comboBox(
            self.organismBox, self, "organismIndex",
            callback=self._onSelectedOrganismChanged,
            debuggingEnabled=0)

        # For now only support one alt source, with a checkbox
        # In the future this can be extended to multiple selections
        self.altSourceCheck = OWGUI.checkBox(self.organismBox, self,
                            "useAltSource", "Show information from dictyBase",
                            callback=self.onAltSourceChange,
#                            debuggingEnabled=0,
                            )
        self.altSourceCheck.hide()

        box = OWGUI.widgetBox(self.controlArea, "Gene names", addSpace=True)
        self.geneAttrComboBox = OWGUI.comboBox(
            box, self, "geneAttr",
            "Gene atttibute", callback=self.updateInfoItems
        )
        OWGUI.checkBox(box, self, "useAttr", "Use attribute names",
                       callback=self.updateInfoItems,
                       disables=[(-1, self.geneAttrComboBox)])

        self.geneAttrComboBox.setDisabled(bool(self.useAttr))

        box = OWGUI.widgetBox(self.controlArea, "Commit", addSpace=True)
        b = OWGUI.button(box, self, "Commit", callback=self.commit)
        c = OWGUI.checkBox(box, self, "autoCommit", "Commit on change")
        OWGUI.setStopper(self, b, c, "selectionChangedFlag",
                         callback=self.commit)

        # A label for dictyExpress link
        self.dictyExpressBox = OWGUI.widgetBox(
            self.controlArea, "Dicty Express")
        self.linkLabel = OWGUI.widgetLabel(self.dictyExpressBox, "")
        self.linkLabel.setOpenExternalLinks(False)
        self.connect(self.linkLabel, SIGNAL("linkActivated(QString)"),
                     self.onDictyExpressLink)
        self.dictyExpressBox.hide()

        OWGUI.rubber(self.controlArea)

        OWGUI.lineEdit(self.mainArea, self, "searchString", "Filter",
                       callbackOnType=True, callback=self.searchUpdate)

        self.treeWidget = QTreeView(self.mainArea)
        self.treeWidget.setRootIsDecorated(False)
        self.treeWidget.setSelectionMode(
            QAbstractItemView.ExtendedSelection)
        self.treeWidget.setItemDelegate(
            LinkStyledItemDelegate(self.treeWidget))
        self.treeWidget.setUniformRowHeights(True)
        self.treeWidget.viewport().setMouseTracking(True)
        self.treeWidget.setSortingEnabled(True)
        self.mainArea.layout().addWidget(self.treeWidget)

        box = OWGUI.widgetBox(self.mainArea, "",
                              orientation="horizontal")
        OWGUI.button(box, self, "Select Filtered",
                     callback=self.selectFiltered)
        OWGUI.button(box, self, "Clear Selection",
                     callback=self.treeWidget.clearSelection)

        self.resize(1000, 700)

        self.geneinfo = []
        self.cells = []
        self.row2geneinfo = {}
        self.data = None

        # : (# input genes, # matches genes)
#.........这里部分代码省略.........

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager=None, name="KEGG Pathways"):
        OWWidget.__init__(self, parent, signalManager, name, wantGraph=True)
        self.inputs = [("Examples", Orange.data.Table, self.SetData),
                       ("Reference", Orange.data.Table, self.SetRefData)]
        self.outputs = [("Selected Examples", Orange.data.Table),
                        ("Unselected Examples", Orange.data.Table)]
        self.organismIndex = 0
        self.geneAttrIndex = 0
        self.autoCommit = False
        self.autoResize = True
        self.useReference = False
        self.useAttrNames = 0
        self.showOrthology = True

        self.loadSettings()

        self.organismCodes = []
        self._changedFlag = False

        self.controlArea.setMaximumWidth(250)
        box = OWGUI.widgetBox(self.controlArea, "Info")
        self.infoLabel = OWGUI.widgetLabel(box, "No data on input\n")

        # Organism selection.
        box = OWGUI.widgetBox(self.controlArea, "Organism")
        self.organismComboBox = OWGUI.comboBox(
            box, self, "organismIndex",
            items=[],
            callback=self.Update,
            addSpace=True,
            debuggingEnabled=0,
            tooltip="Select the organism of the input genes")

        # Selection of genes attribute
        box = OWGUI.widgetBox(self.controlArea, "Gene attribute")
        self.geneAttrCandidates = VariableListModel(parent=self)
        self.geneAttrCombo = OWGUI.comboBox(
            box, self, "geneAttrIndex", callback=self.Update)
        self.geneAttrCombo.setModel(self.geneAttrCandidates)

        OWGUI.checkBox(box, self, "useAttrNames",
                       "Use variable names",
                       disables=[(-1, self.geneAttrCombo)],
                       callback=self.Update)

        self.geneAttrCombo.setDisabled(bool(self.useAttrNames))

        OWGUI.separator(self.controlArea)

        OWGUI.checkBox(self.controlArea, self, "useReference",
                       "From signal",
                       box="Reference",
                       callback=self.Update)

        OWGUI.separator(self.controlArea)

        OWGUI.checkBox(self.controlArea, self, "showOrthology",
                       "Show pathways in full orthology",
                       box="Orthology",
                       callback=self.UpdateListView)

        OWGUI.checkBox(self.controlArea, self, "autoResize",
                       "Resize to fit",
                       box="Image",
                       callback=self.UpdatePathwayViewTransform)

        box = OWGUI.widgetBox(self.controlArea, "Cache Control")

        OWGUI.button(box, self, "Clear cache",
                     callback=self.ClearCache,
                     tooltip="Clear all locally cached KEGG data.")

        OWGUI.separator(self.controlArea)

        box = OWGUI.widgetBox(self.controlArea, "Selection")
        cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on update")
        button = OWGUI.button(box, self, "Commit", callback=self.Commit,
                              default=True)
        OWGUI.setStopper(self, button, cb, "_changedFlag", self.Commit)

        OWGUI.rubber(self.controlArea)

        spliter = QSplitter(Qt.Vertical, self.mainArea)
        self.pathwayView = PathwayView(self, spliter)
        self.pathwayView.scene().selectionChanged.connect(
            self._onSelectionChanged
        )
        self.mainArea.layout().addWidget(spliter)

        self.listView = QTreeWidget(spliter)
        spliter.addWidget(self.listView)

        self.listView.setAllColumnsShowFocus(1)
        self.listView.setColumnCount(4)
        self.listView.setHeaderLabels(["Pathway", "P value",
                                       "Genes", "Reference"])

        self.listView.setSelectionMode(QTreeWidget.SingleSelection)

        self.listView.setSortingEnabled(True)
#.........这里部分代码省略.........

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager=None,
                 title="Venn Diagram"):
        super(OWVennDiagram, self).__init__(parent, signalManager, title,
                                            wantGraph=True)

        self.autocommit = False
        # Selected disjoint subset indices
        self.selection = []

        # Stored input set hints
        # {(index, inputname, attributes): (selectedattrname, itemsettitle)}
        # The 'selectedattrname' can be None
        self.inputhints = {}

        # Use identifier columns for instance matching
        self.useidentifiers = 1

        self.loadSettings()

        # Output changed flag
        self._changed = False
        # Diagram update is in progress
        self._updating = False
        # Input update is in progress
        self._inputUpdate = False
        # All input tables have the same domain.
        self.samedomain = True
        # Input datasets in the order they were 'connected'.
        self.data = OrderedDict()
        # Extracted input item sets in the order they were 'connected'
        self.itemsets = OrderedDict()

        # GUI
        box = OWGUI.widgetBox(self.controlArea, "Info")
        self.info = OWGUI.widgetLabel(box, "No data on input\n")

        self.identifiersBox = OWGUI.radioButtonsInBox(
            self.controlArea, self, "useidentifiers", [],
            box="Data Instance Identifiers",
            callback=self._on_useidentifiersChanged
        )
        self.useequalityButton = OWGUI.appendRadioButton(
            self.identifiersBox, self, "useidentifiers",
            "Use instance equality"
        )
        rb = OWGUI.appendRadioButton(
            self.identifiersBox, self, "useidentifiers",
            "Use identifiers"
        )
        self.inputsBox = OWGUI.indentedBox(
            self.identifiersBox, sep=OWGUI.checkButtonOffsetHint(rb)
        )
        self.inputsBox.setEnabled(self.useidentifiers == 1)

        for i in range(5):
            box = OWGUI.widgetBox(self.inputsBox, "Data set #%i" % (i + 1),
                                  flat=True)
            model = OWItemModels.VariableListModel(parent=self)
            cb = QComboBox()
            cb.setModel(model)
            cb.activated[int].connect(self._on_inputAttrActivated)
            box.setEnabled(False)
            # Store the combo in the box for later use.
            box.combo_box = cb
            box.layout().addWidget(cb)

        OWGUI.rubber(self.controlArea)

        box = OWGUI.widgetBox(self.controlArea, "Output")
        cb = OWGUI.checkBox(box, self, "autocommit", "Commit on any change")
        b = OWGUI.button(box, self, "Commit", callback=self.commit,
                         default=True)
        OWGUI.setStopper(self, b, cb, "_changed", callback=self.commit)

        # Main area view
        self.scene = QGraphicsScene()
        self.view = QGraphicsView(self.scene)
        self.view.setRenderHint(QPainter.Antialiasing)
        self.view.setBackgroundRole(QPalette.Window)
        self.view.setFrameStyle(QGraphicsView.StyledPanel)

        self.mainArea.layout().addWidget(self.view)
        self.vennwidget = VennDiagram()
        self.vennwidget.resize(400, 400)
        self.vennwidget.itemTextEdited.connect(self._on_itemTextEdited)
        self.scene.selectionChanged.connect(self._on_selectionChanged)

        self.scene.addItem(self.vennwidget)

        self.resize(self.controlArea.sizeHint().width() + 550,
                    max(self.controlArea.sizeHint().height(), 550))

        self._queue = []
        self.graphButton.clicked.connect(self.saveImage)

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
 def __init__(self, parent=None, signalManager=None, name="Normalize Expression Array"):
     OWWidget.__init__(self, parent, signalManager, name, wantGraph=True)
     
     self.inputs = [("Expression array", ExampleTable, self.setData)]
     self.outputs = [("Normalized expression array", ExampleTable, Default), ("Filtered expression array", ExampleTable)]
     
     self.selectedGroup = 0
     self.selectedCenterMethod = 0
     self.selectedMergeMethod = 0
     self.zCutoff = 1.96
     self.appendZScore = False
     self.appendRIValues = False
     self.autoCommit = False
     
     self.loadSettings()
     ## GUI
     self.infoBox = OWGUI.widgetLabel(OWGUI.widgetBox(self.controlArea, "Info", addSpace=True),
                                      "No data on input.")
     
     box = OWGUI.widgetBox(self.controlArea, "Split by", addSpace=True)
     self.groupCombo = OWGUI.comboBox(box, self, "selectedGroup", 
                                      callback=self.onGroupSelection
                                      )
     
     self.centerCombo = OWGUI.comboBox(self.controlArea, self, "selectedCenterMethod",
                                       box="Center Fold-change Using",
                                       items=[name for name, _ in self.CENTER_METHODS],
                                       callback=self.onCenterMethodChange,
                                       addSpace=True
                                       )
     
     self.mergeCombo = OWGUI.comboBox(self.controlArea, self, "selectedMergeMethod",
                                      box="Merge Replicates",
                                      items=[name for name, _ in self.MERGE_METHODS],
                                      tooltip="Select the method for replicate merging",
                                      callback=self.onMergeMethodChange,
                                      addSpace=True
                                      )
     
     box = OWGUI.doubleSpin(self.controlArea, self, "zCutoff", 0.0, 3.0, 0.01,
                            box="Z-Score Cutoff",
                            callback=[self.replotMA, self.commitIf])
     
     OWGUI.separator(self.controlArea)
     
     box = OWGUI.widgetBox(self.controlArea, "Ouput")
     OWGUI.checkBox(box, self, "appendZScore", "Append Z-Scores",
                    tooltip="Append calculated Z-Scores to output",
                    callback=self.commitIf
                    )
     
     OWGUI.checkBox(box, self, "appendRIValues", "Append Log Ratio and Intensity values",
                    tooltip="Append calculated Log Ratio and Intensity values to output data",
                    callback=self.commitIf
                    )
     
     cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on change",
                    tooltip="Commit data on any change",
                    callback=self.commitIf
                    )
     
     b = OWGUI.button(box, self, "Commit", callback=self.commit)
     OWGUI.setStopper(self, b, cb, "changedFlag", callback=self.commit)
     
     self.connect(self.graphButton, SIGNAL("clicked()"), self.saveGraph)
     
     OWGUI.rubber(self.controlArea)
     self.graph = OWGraph(self.mainArea)
     self.graph.setAxisTitle(QwtPlot.xBottom, "Intensity: log<sub>10</sub>(R*G)")
     self.graph.setAxisTitle(QwtPlot.yLeft, "Log ratio: log<sub>2</sub>(R/G)")
     self.graph.showFilledSymbols = True
     self.mainArea.layout().addWidget(self.graph)
     self.groups = []
     self.split_data = None, None
     self.merged_splits = None, None
     self.centered = None, None
     self.changedFlag = False
     self.data = None
     
     self.resize(800, 600)

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager=None,
                 title="Quality Control"):
        OWWidget.__init__(self, parent, signalManager, title,
                          wantGraph=True)

        self.inputs = [("Experiment Data", Orange.data.Table, self.set_data)]

        ## Settings
        self.selected_distance_index = 0

        ## Attributes
        self.data = None
        self.distances = None
        self.groups = None
        self.unique_pos = None
        self.base_group_index = 0

        ## GUI
        box = OWGUI.widgetBox(self.controlArea, "Info")
        self.info_box = OWGUI.widgetLabel(box, "\n")

        ## Separate By box
        box = OWGUI.widgetBox(self.controlArea, "Separate By")
        self.split_by_model = PyListModel()
        self.split_by_view = QListView()
        self.split_by_view.setSelectionMode(QListView.ExtendedSelection)
        self.split_by_view.setModel(self.split_by_model)
        box.layout().addWidget(self.split_by_view)

        self.connect(self.split_by_view.selectionModel(),
                     SIGNAL("selectionChanged(QItemSelection, QItemSelection)"),
                     self.on_split_key_changed)

        ## Sort By box
        box = OWGUI.widgetBox(self.controlArea, "Sort By")
        self.sort_by_model = PyListModel()
        self.sort_by_view = QListView()
        self.sort_by_view.setSelectionMode(QListView.ExtendedSelection)
        self.sort_by_view.setModel(self.sort_by_model)
        box.layout().addWidget(self.sort_by_view)
        
        self.connect(self.sort_by_view.selectionModel(),
                     SIGNAL("selectionChanged(QItemSelection, QItemSelection)"),
                     self.on_sort_key_changed)

        ## Distance box
        box = OWGUI.widgetBox(self.controlArea, "Distance Measure")
        OWGUI.comboBox(box, self, "selected_distance_index",
                       items=[t[0] for t in self.DISTANCE_FUNCTIONS],
                       callback=self.on_distance_measure_changed)

        self.connect(self.graphButton,
                     SIGNAL("clicked()"),
                     self.save_graph)
        
        self.scene = QGraphicsScene()
        self.scene_view = QualityGraphicsView(self.scene)
        self.scene_view.setRenderHints(QPainter.Antialiasing)
        self.scene_view.setAlignment(Qt.AlignLeft | Qt.AlignVCenter)
        self.mainArea.layout().addWidget(self.scene_view)
        
        self.connect(self.scene_view,
                     SIGNAL("view_size_changed(QSize)"),
                     self.on_view_resize)

        self._disable_updates = False
        self._cached_distances = {}
        self._base_index_hints = {}
        self.main_widget = None
        
        self.resize(800, 600)

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import widgetLabel [as 别名]
    def __init__(self, parent=None, signalManager=None, name="Gene selection"):
        OWWidget.__init__(self, parent, signalManager, name, wantGraph=True, showSaveGraph=True)
        self.inputs = [("Examples", ExampleTable, self.set_data)]
        self.outputs = [("Example table with selected genes", ExampleTable), ("Example table with remaining genes", ExampleTable), ("Selected genes", ExampleTable)]

        self.method_index = 0
        self.genes_in_columns = False
        self.compute_null = False
        self.permutations_count = 10
        self.auto_commit = False
        self.selectNBest = 20
        self.selectPValue = 0.01
        self.data_changed_flag = False
        self.add_scores_to_output = True
        self.thresholds = {
            "fold change": (0.5, 2.),
            "log2 fold change": (-1, 1),
            "t-test": (-2, 2),
            "t-test p-value": (0.01, 0.01),
        }

        self.oneTailTestHi = oneTailTestHi = lambda array, low, hi: array >= hi
        self.oneTailTestLow = oneTailTestLow = lambda array, low, hi: array <= low
        self.twoTailTest = twoTailTest = lambda array, low, hi: (array >= hi) | (array <= low)
        self.middleTest = middleTest = lambda array, low, hi: (array <= hi) | (array >= low)
        
        self.histType = {oneTailTestHi:"hiTail", oneTailTestLow:"lowTail", twoTailTest:"twoTail", middleTest:"middle"}

        # [(name, func, tail test, two sample test), ...]
        self.score_methods = [("fold change", ExpressionSignificance_FoldChange, twoTailTest, True),
                             ("log2 fold change", ExpressionSignificance_Log2FoldChange, twoTailTest, True),
                             ("t-test", ExpressionSignificance_TTest_T, twoTailTest, True),
                             ("t-test p-value", ExpressionSignificance_TTest_PValue, oneTailTestLow, True),
                             ("anova", ExpressionSignificance_ANOVA_F, oneTailTestHi, False),
                             ("anova p-value", ExpressionSignificance_ANOVA_PValue, oneTailTestLow, False),
                             ("signal to noise ratio", ExpressionSignificance_SignalToNoise, twoTailTest, True),
                             ("info gain", ExpressionSignificance_Info, oneTailTestHi, True),
                             ("chi-square", ExpressionSignificance_ChiSquare, oneTailTestHi, True),
                             ("mann-whitney", ExpressionSignigicance_MannWhitneyu_U, oneTailTestLow, True)]

        boxHistogram = OWGUI.widgetBox(self.mainArea)
        self.histogram = ScoreHist(self, boxHistogram)
        boxHistogram.layout().addWidget(self.histogram)
        self.histogram.show()
        
        box = OWGUI.widgetBox(self.controlArea, "Info")
        self.dataInfoLabel = OWGUI.widgetLabel(box, "\n\n")
        self.dataInfoLabel.setWordWrap(True)
        self.selectedInfoLabel = OWGUI.widgetLabel(box, "")

        box1 = OWGUI.widgetBox(self.controlArea, "Scoring Method")
        self.testRadioBox = OWGUI.comboBox(box1, self, "method_index",
                                    items=[sm[0] for sm in self.score_methods],
                                    callback=[self.on_scoring_method_changed, self.update_scores])
        
        box = OWGUI.widgetBox(self.controlArea, "Target Labels")
        self.label_selection_widget = LabelSelectionWidget(self)
        self.label_selection_widget.setMaximumHeight(150)
        box.layout().addWidget(self.label_selection_widget)
        self.connect(self.label_selection_widget,
                     SIGNAL("selection_changed()"),
                     self.on_target_changed)
        
        self.connect(self.label_selection_widget,
                     SIGNAL("label_activated(int)"),
                     self.on_label_activated)
        
        self.genes_in_columns_check = OWGUI.checkBox(box, self, "genes_in_columns",
                                                  "Genes in columns",
                                                  callback=self.on_genes_in_columns_change)

        box = OWGUI.widgetBox(self.controlArea, "Selection")
        box.layout().setSpacing(0)

        self.upperBoundarySpin = OWGUI.doubleSpin(box, self, "histogram.upperBoundary",
                                                  min=-1e6, max=1e6, step= 1e-6,
                                                  label="Upper threshold:", 
                                                  callback=self.update_boundary, 
                                                  callbackOnReturn=True)
        
        self.lowerBoundarySpin = OWGUI.doubleSpin(box, self, "histogram.lowerBoundary", 
                                                  min=-1e6, max=1e6, step= 1e-6, 
                                                  label="Lower threshold:", 
                                                  callback=self.update_boundary, 
                                                  callbackOnReturn=True)
        
        check = OWGUI.checkBox(box, self, "compute_null", "Compute null distribution",
                               callback=self.update_scores)

        check.disables.append(OWGUI.spin(box, self, "permutations_count", min=1, max=10, 
                                         label="Permutations:", callback=self.update_scores, 
                                         callbackOnReturn=True))

        box1 = OWGUI.widgetBox(box, orientation='horizontal')
        check.disables.append(OWGUI.doubleSpin(box1, self, "selectPValue", 
                                               min=2e-7, max=1.0, step=1e-7, 
                                               label="P-value:"))
        check.disables.append(OWGUI.button(box1, self, "Select", callback=self.select_p_best))
        check.makeConsistent()

#.........这里部分代码省略.........