Python OWGUI.comboBox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 comboBox [as 别名]
    def __init__(self, parent=None, signalManager = None):
        OWWidget.__init__(self, parent, signalManager, 'Process Chip Data')
        self.callbackDeposit = []

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

        self.chipdata = None; self.datasets = None
        self.std = [("No preprocessing", None),
                    ("Array-based standardization", chipstat.standardize_arrays),
                    ("Gene-based standardization", chipstat.standardize_genes),
                    ("First array-, then gene-based standardization", lambda e,r: chipstat.standardize_genes(chipstat.standardize_arrays(e,r),r)),
                    ("First gene-, then array-based standardization", lambda e,r: chipstat.standardize_arrays(chipstat.standardize_genes(e,r),r))]
        # Settings
        self.data = None
        self.preStdMethod = 0; self.preStdRob = 1
        self.postStdMethod = 0; self.postStdRob = 1
        
        self.mergeType = 0
        self.commitOnChange = 0
        self.loadSettings()

        # GUI
        # info
        box = QVGroupBox("Info", self.controlArea)
        self.infoa = QLabel('No data on input.', box)
        self.infob = QLabel('', box)
        
        # preprocessing
        OWGUI.separator(self.controlArea)
        box = QVGroupBox("Preprocessing", self.controlArea)
        labels = [x[0] for x in self.std]
        OWGUI.comboBox(box, self, 'preStdMethod', label=None, labelWidth=None, orientation='vertical', items=labels, callback=self.selectionChange)
        self.preRobBtn = OWGUI.checkBox(box, self, "preStdRob", "Robust standardization", callback=self.selectionChange)
        
        # merge
        OWGUI.separator(self.controlArea)
        self.mergeTypes = [(0, "No merging"), ('mean', 'Mean'), ('median', 'Median'), ('min', 'Minimum expression'), ('max', 'Maximum expression')]
        labels = [x[1] for x in self.mergeTypes]
        OWGUI.radioButtonsInBox(self.controlArea, self, 'mergeType', labels, box='Merge Replicas', tooltips=None, callback=self.selectionChange)

        # postprocessing
        OWGUI.separator(self.controlArea)
        self.boxPostproc = QVGroupBox("Postprocessing", self.controlArea)
        labels = [x[0] for x in self.std]
        OWGUI.comboBox(self.boxPostproc, self, 'postStdMethod', label=None, labelWidth=None, orientation='vertical', items=labels, callback=self.selectionChange)
        self.postRobBtn = OWGUI.checkBox(self.boxPostproc, self, "postStdRob", "Robust standardization", callback=self.selectionChange)

        # output
        OWGUI.separator(self.controlArea)
        box = QVGroupBox("Output", self.controlArea)
        OWGUI.checkBox(box, self, 'commitOnChange', 'Commit data on selection change')
        self.commitBtn = OWGUI.button(box, self, "Commit", callback=self.selectionChange, disabled=1)

        self.setBtnsState()
        self.resize(100,100)

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import comboBox [as 别名]
    def __init__(self,parent=None, signalManager = None):
        OWWidget.__init__(self, parent, signalManager, "&Display Motifs", 0)

        # set default settings
        self.colorBy = None
        self.pvalThresholdIndex = None
        self.pvalThreshold = None

        #load settings
        self.loadSettings()

        # GUI
        self.graph = OWGraph(self.mainArea)
        self.graph.setYRlabels(None)
        self.graph.enableGridXB(0)
        self.graph.enableGridYL(1)
        self.graph.setAxisMaxMinor(QwtPlot.xBottom, 10)
        self.graph.setAxisMaxMajor(QwtPlot.xBottom, 10)
        self.graph.setAxisAutoScale(QwtPlot.xBottom)
        self.graph.setAxisScale(QwtPlot.xBottom, -1020, 0, 0)
        self.mainArea.layout().addWidget(self.graph)
        
        # inputs
        # data and graph temp variables
        self.inputs = [("Examples", ExampleTable, self.cdata, Default), ("Genes", list, self.newGeneList, Default), ("Motifs", list, self.newMotifList, Default)]

        self.data = None
        self.motifLines = []
        self.visibleValues = []
        self.valueToCurve = {}
        self.allGenes = [] ## genes displayed always in same order
        self.geneList = [] ## selected genes
        self.motifList = [] ## selected motifs
        self.valuesPresentInData = []

        self.clusterPostProbThreshold = 0

        # GUI
        self.selValues = OWGUI.widgetBox(self.controlArea, "Values")
        self.selcolorBy = OWGUI.widgetBox(self.controlArea, "Color By")

        self.colorByCombo = OWGUI.comboBox(self.selcolorBy, self, "colorBy",
                                           items=[],
                                           callback=self.colorByChanged)
        
        self.pvalThresholdCombo = OWGUI.comboBox(self.selValues, self, "pvalThresholdIndex",
                                                 items=[],
                                                 callback=self.pvalThresholdChanged)
        
        self.valuesQLB = QListWidget(self.selValues)
        self.valuesQLB.setSelectionMode(QListWidget.MultiSelection)
        self.connect(self.valuesQLB, SIGNAL("itemSelectionChanged()"), self.valuesSelectionChange)
        self.selValues.layout().addWidget(self.valuesQLB)
        
        self.unselectAllQLB = OWGUI.button(self.selValues, self, "Unselect all",
                                           callback = self.unselAll)

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import comboBox [as 别名]
    def __init__(self, parent=None, signalManager = None, name='Approximate Profiles'):
        self.callbackDeposit = [] # deposit for OWGUI callback functions
        OWWidget.__init__(self, parent, signalManager, name)

        self._data = None       # exampleTable
        self._dataN = None      # 2d numeric array
        self._chipdata = None       # [(dirname0, [et0, et1, ...]), ...]
        self._chipdataN = None      # 3d numeric array
        self.kernel = 0
        self.kernels = ["Orthogonal polynomials", "Trigonometric functions"]
        self.kernelSize = None
        self.kernelSizes = [    ["Const"] + map(lambda x: "degree <= %i"%x, range(1,99)),
                                ["Const", "cos x", "sin x"] + reduce(lambda x,y: x+[y[0],y[1]], map(lambda i: ("cos %ix"%i, "sin %ix"%i), range(2,99)), [])
                            ]
        self.useSignificance = 0
        self.alpha = 3
        self.alphas = [0.0001, 0.001, 0.01, 0.05, 0.1, 0.2, 0.5]
        self.commitOnChange = 1
               
        # Settings
        self.loadSettings()

        # GUI: info, comboKernelSize, cbUseSignificance, vboxSignificance, commitBtn
        # info
        box = QVGroupBox("Info", self.controlArea)
        self.infoa = QLabel("No examples on input", box)
        OWGUI.separator(box,250)
        self.infob = QLabel("No structured data on input", box)
        OWGUI.separator(self.controlArea)

        # kernel selection
        box = QVGroupBox("Kernel functions", self.controlArea)
        OWGUI.comboBox(box, self, "kernel", items=self.kernels, callback=self.kernelChange)
        OWGUI.separator(self.controlArea)

        # kernel settings
        box = QVGroupBox("Kernel settings", self.controlArea)
        self.comboKernelSize = OWGUI.comboBox(box, self, "kernelSize", callback=self.kernelSizeChange, label="Number of kernel functions", labelWidth=135, orientation="horizontal", valueType=int)
        self.comboKernelSize.setDisabled(1)
        self.cbUseSignificance = OWGUI.checkBox(box, self, "useSignificance", "Significance of coefficients (F-statistics)", callback=self.useSignificanceChange, tooltip="Use kernels with coefficients significantly different from 0.")
        self.vboxSignificance = QVBox(box)
        OWGUI.comboBox(self.vboxSignificance, self, "alpha", items = self.alphas, callback=self.alphaChange, label="p <", labelWidth=20, orientation="horizontal")
        OWGUI.separator(self.controlArea)

        # output
        box = QVGroupBox("Output", self.controlArea)
        OWGUI.checkBox(box, self, 'commitOnChange', 'Commit data on selection change')
        self.commitBtn = OWGUI.button(box, self, "Commit", callback=self.senddata, disabled=1)

        self.inputs = [("Examples", ExampleTable, self.data), ("Structured Data", DataFiles, self.chipdata)]
        self.outputs = [("Approximated Examples", ExampleTable, Default), ("Approximation Coefficients", ExampleTable), ("Approximated Structured Data", DataFiles, Default), ("Structured Approximation Coefficients", DataFiles)]
        self.resize(200,100)

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import comboBox [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 comboBox [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 comboBox [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 comboBox [as 别名]
    def __init__(self, parent=None, signalManager = None):
#        self.callbackDeposit = [] # deposit for OWGUI callback functions
        OWWidget.__init__(self, parent, signalManager, 'Expression Profiles', 1)

        #set default settings
        self.ShowAverageProfile = 1
        self.ShowSingleProfiles = 0
        self.PointWidth = 2
        self.CurveWidth = 1
        self.AverageCurveWidth = 4
        self.BoxPlotWidth = 2
        self.SelectedClasses = []
        self.Classes = []
        self.autoSendSelected = 0
        self.selectionChangedFlag = False

        self.CutLow = 0; self.CutHigh = 0; self.CutEnabled = 0
        
        self.profileLabel = None

        #load settings
        self.loadSettings()

        # GUI
        self.graph = profilesGraph(self, self.mainArea, "")
        self.mainArea.layout().addWidget(self.graph)
        self.graph.hide()
        self.connect(self.graphButton, SIGNAL("clicked()"), self.graph.saveToFile)

        # GUI definition
        self.tabs = OWGUI.tabWidget(self.space)

        # GRAPH TAB
        GraphTab = OWGUI.createTabPage(self.tabs, "Graph")

        ## display options
        self.infoLabel = OWGUI.widgetLabel(OWGUI.widgetBox(GraphTab, "Info"), "No data on input.")
        displayOptBox = OWGUI.widgetBox(GraphTab, "Display") #QVButtonGroup("Display", GraphTab)
        displayOptButtons = ['Majority Class', 'Majority Class Probability', 'Target Class Probability', 'Number of Instances']
        OWGUI.checkBox(displayOptBox, self, 'ShowSingleProfiles', 'Expression Profiles', tooltip='', callback=self.updateShowSingleProfiles)
        OWGUI.checkBox(displayOptBox, self, 'ShowAverageProfile', 'Box Plot', tooltip='', callback=self.updateShowAverageProfile)

        ## class selection (classQLB)
        self.classQVGB = OWGUI.widgetBox(GraphTab, "Classes") #QVGroupBox(GraphTab)
##        self.classQVGB.setTitle("Classes")
        self.classQLB = OWGUI.listBox(self.classQVGB, self, "SelectedClasses", "Classes", selectionMode=QListWidget.MultiSelection, callback=self.classSelectionChange) #QListBox(self.classQVGB)
##        self.classQLB.setSelectionMode(QListBox.Multi)
        self.unselectAllClassedQLB = OWGUI.button(self.classQVGB, self, "Unselect all", callback=self.SUAclassQLB) #QPushButton("(Un)Select All", self.classQVGB)
##        self.connect(self.unselectAllClassedQLB, SIGNAL("clicked()"), self.SUAclassQLB)
##        self.connect(self.classQLB, SIGNAL("selectionChanged()"), self.classSelectionChange)

        ## show single/average profile
##        self.showAverageQLB = QPushButton("Box Plot", self.classQVGB)
##        self.showAverageQLB.setToggleButton(1)
##        self.showAverageQLB.setOn(self.ShowAverageProfile)
##        self.showSingleQLB = QPushButton("Single Profiles", self.classQVGB)
##        self.showSingleQLB.setToggleButton(1)
##        self.showSingleQLB.setOn(self.ShowSingleProfiles)
##        self.connect(self.showAverageQLB, SIGNAL("toggled(bool)"), self.updateShowAverageProfile)
##        self.connect(self.showSingleQLB, SIGNAL("toggled(bool)"), self.updateShowSingleProfiles)

##        self.tabs.insertTab(GraphTab, "Graph")

        # SETTINGS TAB
        SettingsTab = OWGUI.createTabPage(self.tabs, "Settings") #QVGroupBox(self)

        self.profileLabelComboBox = OWGUI.comboBox(SettingsTab, self, 'profileLabel', 'Profile Labels', sendSelectedValue=True, valueType=str)
        OWGUI.hSlider(SettingsTab, self, 'PointWidth', box='Point Width', minValue=0, maxValue=9, step=1, callback=self.updatePointWidth, ticks=1)
        OWGUI.hSlider(SettingsTab, self, 'CurveWidth', box='Profile Width', minValue=1, maxValue=9, step=1, callback=self.updateCurveWidth, ticks=1)
        OWGUI.hSlider(SettingsTab, self, 'AverageCurveWidth', box='Average Profile Width', minValue=1, maxValue=9, step=1, callback=self.updateAverageCurveWidth, ticks=1)
        OWGUI.hSlider(SettingsTab, self, 'BoxPlotWidth', box='Box Plot Width', minValue=0, maxValue=9, step=1, callback=self.updateBoxPlotWidth, ticks=1)
        OWGUI.checkBox(SettingsTab, self, 'graph.renderAntialiased', "Render antialiased", callback=self.graph.setCurveRenderHints)


    ## graph y scale
        box = OWGUI.widgetBox(SettingsTab, "Threshold/ Values") #QVButtonGroup("Threshol/ Values", SettingsTab)
        OWGUI.checkBox(box, self, 'CutEnabled', "Enabled", callback=self.setCutEnabled)
        self.sliderCutLow = OWGUI.qwtHSlider(box, self, 'CutLow', label='Low:', labelWidth=33, minValue=-20, maxValue=0, step=0.1, precision=1, ticks=0, maxWidth=80, callback=self.updateYaxis)
        self.sliderCutHigh = OWGUI.qwtHSlider(box, self, 'CutHigh', label='High:', labelWidth=33, minValue=0, maxValue=20, step=0.1, precision=1, ticks=0, maxWidth=80, callback=self.updateYaxis)
        if not self.CutEnabled:
            self.sliderCutLow.box.setDisabled(1)
            self.sliderCutHigh.box.setDisabled(1)

##        self.tabs.insertTab(SettingsTab, "Settings")

        self.toolbarSelection = ZoomSelectToolbar(self, self.controlArea, self.graph, self.autoSendSelected, buttons=(ZoomSelectToolbar.IconZoom, ZoomSelectToolbar.IconPan, ZoomSelectToolbar.IconSelect, ZoomSelectToolbar.IconSpace,
                                                                       ZoomSelectToolbar.IconRemoveLast, ZoomSelectToolbar.IconRemoveAll, ZoomSelectToolbar.IconSendSelection))
        cb = OWGUI.checkBox(self.controlArea, self, "autoSendSelected", "Auto send on selection change")
        OWGUI.setStopper(self, self.toolbarSelection.buttonSendSelections, cb, "selectionChangedFlag", self.commit)
        
        # inputs
        # data and graph temp variables
        
        self.inputs = [("Examples", ExampleTable, self.data, Default + Multiple)]
        self.outputs = [("Examples", ExampleTable, Default)]

        # temp variables
        self.MAdata = []
        self.classColor = None
        self.classBrighterColor = None
#.........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 comboBox [as 别名]
    def __init__(self, parent=None, signalManager=None):
        OWWidget.__init__(self, parent, signalManager, "Parallel Coordinates", True)

        #add a graph widget
        self.graph = OWParallelGraph(self, self.mainArea)
        self.mainArea.layout().addWidget(self.graph)

        self.showAllAttributes = 0

        self.inputs = [("Data", ExampleTable, self.setData, Default),
                       ("Data Subset", ExampleTable, self.setSubsetData),
                       ("Features", AttributeList, self.setShownAttributes)]
        self.outputs = [("Selected Data", ExampleTable),
                        ("Other Data", ExampleTable),
                        ("Features", AttributeList)]

        #set default settings
        self.data = None
        self.subsetData = None
        self.autoSendSelection = 1
        self.attrDiscOrder = "Unordered"
        self.attrContOrder = "Unordered"
        self.projections = None
        self.correlationDict = {}
        self.middleLabels = "Correlations"
        self.attributeSelectionList = None
        self.toolbarSelection = 0
        self.colorSettings = None
        self.selectedSchemaIndex = 0

        self.graph.jitterSize = 10
        self.graph.showDistributions = 1
        self.graph.showStatistics = 0
        self.graph.showAttrValues = 1
        self.graph.useSplines = 0
        self.graph.enabledLegend = 1

        #load settings
        self.loadSettings()

        #GUI
        self.tabs = OWGUI.tabWidget(self.controlArea)
        self.GeneralTab = OWGUI.createTabPage(self.tabs, "Main")
        self.SettingsTab = OWGUI.createTabPage(self.tabs, "Settings")

        self.createShowHiddenLists(self.GeneralTab, callback=self.updateGraph)
        self.connect(self.shownAttribsLB, SIGNAL('itemDoubleClicked(QListWidgetItem*)'), self.flipAttribute)

        self.optimizationDlg = ParallelOptimization(self, signalManager=self.signalManager)
        self.optimizationDlgButton = OWGUI.button(self.GeneralTab, self, "Optimization Dialog",
                                                  callback=self.optimizationDlg.reshow, debuggingEnabled=0)

        self.zoomSelectToolbar = OWToolbars.ZoomSelectToolbar(self, self.GeneralTab, self.graph, self.autoSendSelection,
                                                              buttons=(1, 2, 0, 7, 8))
        self.connect(self.zoomSelectToolbar.buttonSendSelections, SIGNAL("clicked()"), self.sendSelections)

        #connect controls to appropriate functions
        self.connect(self.graphButton, SIGNAL("clicked()"), self.graph.saveToFile)

        # ####################################
        # SETTINGS functionality
        box = OWGUI.widgetBox(self.SettingsTab, "Transparency")
        OWGUI.hSlider(box, self, 'graph.alphaValue', label="Examples: ", minValue=0, maxValue=255, step=10,
                      callback=self.updateGraph, tooltip="Alpha value used for drawing example lines")
        OWGUI.hSlider(box, self, 'graph.alphaValue2', label="Rest:     ", minValue=0, maxValue=255, step=10,
                      callback=self.updateGraph, tooltip="Alpha value used to draw statistics, example subsets, ...")

        box = OWGUI.widgetBox(self.SettingsTab, "Jittering Options")
        OWGUI.comboBox(box, self, "graph.jitterSize", label='Jittering size (% of size):  ', orientation='horizontal',
                       callback=self.setJitteringSize, items=self.jitterSizeNums, sendSelectedValue=1, valueType=float)

        # visual settings
        box = OWGUI.widgetBox(self.SettingsTab, "Visual Settings")

        OWGUI.checkBox(box, self, 'graph.showAttrValues', 'Show attribute values', callback=self.updateGraph)
        OWGUI.checkBox(box, self, 'graph.useAntialiasing', 'Use antialiasing', callback=self.updateGraph)
        OWGUI.checkBox(box, self, 'graph.useSplines', 'Show splines', callback=self.updateGraph,
                       tooltip="Show lines using splines")
        OWGUI.checkBox(box, self, 'graph.enabledLegend', 'Show legend', callback=self.updateGraph)

        box = OWGUI.widgetBox(self.SettingsTab, "Axis Distance")
        resizeColsBox = OWGUI.widgetBox(box, 0, "horizontal", 0)
        OWGUI.label(resizeColsBox, self, "Increase/decrease distance: ")
        OWGUI.toolButton(resizeColsBox, self, "+", callback=self.increaseAxesDistance,
                         tooltip="Increase the distance between the axes", width=30, height=20)
        OWGUI.toolButton(resizeColsBox, self, "-", callback=self.decreaseAxesDistance,
                         tooltip="Decrease the distance between the axes", width=30, height=20)
        OWGUI.rubber(resizeColsBox)
        OWGUI.checkBox(box, self, "graph.autoUpdateAxes", "Auto scale X axis",
                       tooltip="Auto scale X axis to show all visualized attributes", callback=self.updateGraph)

        box = OWGUI.widgetBox(self.SettingsTab, "Statistical Information")
        OWGUI.comboBox(box, self, "graph.showStatistics", label="Statistics: ", orientation="horizontal", labelWidth=90,
                       items=["No statistics", "Means, deviations", "Median, quartiles"], callback=self.updateGraph,
                       sendSelectedValue=0, valueType=int)
        OWGUI.comboBox(box, self, "middleLabels", label="Middle labels: ", orientation="horizontal", labelWidth=90,
                       items=["No labels", "Correlations", "VizRank"], callback=self.updateGraph,
                       tooltip="The information do you wish to view on top in the middle of coordinate axes",
                       sendSelectedValue=1, valueType=str)
        OWGUI.checkBox(box, self, 'graph.showDistributions', 'Show distributions', callback=self.updateGraph,
#.........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 comboBox [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 comboBox [as 别名]
    def __init__(self,parent=None, signalManager = None):
        OWWidget.__init__(self, parent, signalManager, "Nomogram", 1)

        #self.setWFlags(Qt.WResizeNoErase | Qt.WRepaintNoErase) #this works like magic.. no flicker during repaint!
        self.parent = parent
#        self.setWFlags(self.getWFlags()+Qt.WStyle_Maximize)

        self.callbackDeposit = [] # deposit for OWGUI callback functions
        self.alignType = 0
        self.contType = 0
        self.yAxis = 0
        self.probability = 0
        self.verticalSpacing = 60
        self.verticalSpacingContinuous = 100
        self.diff_between_ordinal = 30
        self.fontSize = 9
        self.lineWidth = 1
        self.histogram = 0
        self.histogram_size = 10
        self.data = None
        self.cl = None
        self.confidence_check = 0
        self.confidence_percent = 95
        self.sort_type = 0

        self.loadSettings()

        self.pointsName = ["Total", "Total"]
        self.totalPointsName = ["Probability", "Probability"]
        self.bnomogram = None


        self.inputs=[("Classifier", orange.Classifier, self.classifier), ("Data", Orange.data.Table, self.data)]


        self.TargetClassIndex = 0
        self.targetCombo = OWGUI.comboBox(self.controlArea, self, "TargetClassIndex", " Target Class ", addSpace=True, tooltip='Select target (prediction) class in the model.', callback = self.setTarget)

        self.alignRadio = OWGUI.radioButtonsInBox(self.controlArea, self,  'alignType', ['Align left', 'Align by zero influence'], box='Attribute placement',
                                                  tooltips=['Attributes in nomogram are left aligned', 'Attributes are not aligned, top scale represents true (normalized) regression coefficient value'],
                                                  addSpace=True,
                                                  callback=self.showNomogram)
        self.verticalSpacingLabel = OWGUI.spin(self.alignRadio, self, 'verticalSpacing', 15, 200, label = 'Vertical spacing:',  orientation = 0, tooltip='Define space (pixels) between adjacent attributes.', callback = self.showNomogram)

        self.ContRadio = OWGUI.radioButtonsInBox(self.controlArea, self, 'contType',   ['1D projection', '2D curve'], 'Continuous attributes',
                                tooltips=['Continuous attribute are presented on a single scale', 'Two dimensional space is used to present continuous attributes in nomogram.'],
                                addSpace=True,
                                callback=[lambda:self.verticalSpacingContLabel.setDisabled(not self.contType), self.showNomogram])

        self.verticalSpacingContLabel = OWGUI.spin(OWGUI.indentedBox(self.ContRadio, sep=OWGUI.checkButtonOffsetHint(self.ContRadio.buttons[-1])), self, 'verticalSpacingContinuous', 15, 200, label = "Height", orientation=0, tooltip='Define space (pixels) between adjacent 2d presentation of attributes.', callback = self.showNomogram)
        self.verticalSpacingContLabel.setDisabled(not self.contType)

        self.yAxisRadio = OWGUI.radioButtonsInBox(self.controlArea, self, 'yAxis', ['Point scale', 'Log odds ratios'], 'Scale',
                                tooltips=['values are normalized on a 0-100 point scale','values on top axis show log-linear contribution of attribute to full model'],
                                addSpace=True,
                                callback=self.showNomogram)

        layoutBox = OWGUI.widgetBox(self.controlArea, "Display", orientation=1, addSpace=True)

        self.probabilityCheck = OWGUI.checkBox(layoutBox, self, 'probability', 'Show prediction',  tooltip='', callback = self.setProbability)

        self.CICheck, self.CILabel = OWGUI.checkWithSpin(layoutBox, self, 'Confidence intervals (%):', min=1, max=99, step = 1, checked='confidence_check', value='confidence_percent', checkCallback=self.showNomogram, spinCallback = self.showNomogram)

        self.histogramCheck, self.histogramLabel = OWGUI.checkWithSpin(layoutBox, self, 'Show histogram, size', min=1, max=30, checked='histogram', value='histogram_size', step = 1, tooltip='-(TODO)-', checkCallback=self.showNomogram, spinCallback = self.showNomogram)

        OWGUI.separator(layoutBox)
        self.sortOptions = ["No sorting", "Absolute importance", "Positive influence", "Negative influence"]
        self.sortBox = OWGUI.comboBox(layoutBox, self, "sort_type", label="Sort by ", items=self.sortOptions, callback = self.sortNomogram, orientation="horizontal")


        OWGUI.rubber(self.controlArea)

        self.connect(self.graphButton, SIGNAL("clicked()"), self.menuItemPrinter)



        #add a graph widget
        self.header = OWNomogramHeader(None, self.mainArea)
        self.header.setFixedHeight(60)
        self.header.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
        self.header.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
        self.graph = OWNomogramGraph(self.bnomogram, self.mainArea)
        self.graph.setMinimumWidth(200)
        self.graph.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
        self.footer = OWNomogramHeader(None, self.mainArea)
        self.footer.setFixedHeight(60*2+10)
        self.footer.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
        self.footer.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)

        self.mainArea.layout().addWidget(self.header)
        self.mainArea.layout().addWidget(self.graph)
        self.mainArea.layout().addWidget(self.footer)
        self.resize(700,500)
        #self.repaint()
        #self.update()

        # mouse pressed flag
        self.mousepr = False

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import comboBox [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 comboBox [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 comboBox [as 别名]
    def __init__(self, parent=None, signalManager=None,
                 title="Molecule visualizer"):
        super(OWMoleculeVisualizer, self).__init__(parent, signalManager, title)

        self.colorFragments = 1
        self.showFragments = 0
        self.selectedFragment = ""
        self.moleculeSmiles = []
        self.fragmentSmiles = []
        self.defFragmentSmiles = []
        self.smiles_var = 0
        self.moleculeTitleAttr = 0
        self.moleculeTitleAttributeList = []
        self.selectedMoleculeTitleAttrs = []
        self.fragmentSmilesAttr = 0
        self.imageSize = 200
        self.numColumns = 4
        self.commitOnChange = 0

        ## GUI
        box = OWGUI.widgetBox(self.controlArea, "Info", addSpace=True)
        self.infoLabel = OWGUI.label(box, self, "Chemicals:")
        box = OWGUI.radioButtonsInBox(
            self.controlArea, self, "showFragments",
            ["Show molecules", "Show fragments"], "Show",
            callback=self.updateitems
        )

        self.showFragmentsRadioButton = box.buttons[-1]
        self.markFragmentsCheckBox = OWGUI.checkBox(
            box, self, "colorFragments", "Mark fragments",
            callback=self._update
        )
        box.setSizePolicy(
            QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Maximum))
        OWGUI.separator(self.controlArea)

        self.moleculeSmilesCombo = OWGUI.comboBox(
            self.controlArea, self, "smiles_var",
            "Molecule SMILES Attribute",
            callback=self.updateitems
        )
        self.moleculeSmilesCombo.box.setSizePolicy(
            QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Maximum)
        )
        self.smiles_var_model = VariableListModel(parent=self)
        self.moleculeSmilesCombo.setModel(self.smiles_var_model)

        OWGUI.separator(self.controlArea)
        box = OWGUI.widgetBox(self.controlArea, "Molecule Title Attributes",
                              addSpace=True)

        self.title_var_view = QListView(
            selectionMode=QListView.ExtendedSelection
        )
        self.title_var_model = VariableListModel(parent=self)
        self.title_var_view.setModel(self.title_var_model)
        self.title_var_view.selectionModel().selectionChanged.connect(
            self._title_selection_changed
        )
        box.layout().addWidget(self.title_var_view)

        OWGUI.separator(self.controlArea)
        self.fragmentSmilesCombo = OWGUI.comboBox(
            self.controlArea, self, "fragmentSmilesAttr",
            "Fragment SMILES Attribute",
            callback=self.updateFragmentsListBox
        )

        self.fragmentSmilesCombo.setModel(VariableListModel(parent=self))
        self.fragmentSmilesCombo.box.setSizePolicy(
            QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Maximum)
        )
        OWGUI.separator(self.controlArea)
        box = OWGUI.spin(self.controlArea, self, "imageSize", 50, 500, 10,
                         box="Image Size", callback=self._image_size_changed)

        box.setSizePolicy(
            QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Maximum))

        OWGUI.separator(self.controlArea)
        box = OWGUI.widgetBox(self.controlArea, "Selection", addSpace=True)
        OWGUI.checkBox(box, self, "commitOnChange", "Commit on change")

        self.selectMarkedMoleculesButton = OWGUI.button(
            box, self, "Select &matched molecules", self.select_marked
        )
        OWGUI.button(box, self, "&Commit", callback=self.commit, default=True)
        OWGUI.separator(self.controlArea)
        OWGUI.rubber(self.controlArea)

        spliter = QSplitter(Qt.Vertical)
        self.scrollArea = ScrollArea(spliter)

        self.grid = GridWidget()
        self.grid.selectionChanged.connect(self._on_selection_changed)

        self.scrollArea.setWidget(self.grid)
        self.scrollArea.setWidgetResizable(True)
        self.mainArea.layout().addWidget(spliter)
#.........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 comboBox [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 comboBox [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.........