Python OWGUI.separator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 separator [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 separator [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 separator [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 separator [as 别名]
    def __init__(self, parent=None, signalManager = None, name='GSEA'):
        OWWidget.__init__(self, parent, signalManager, name)

        self.inputs = [("Examples", ExampleTable, self.setData)]
        self.outputs = [("Examples with selected genes only", ExampleTable), ("Results", ExampleTable), ("Distance Matrix", orange.SymMatrix) ]

        self.res = None
        self.dm = None
        
        self.name = 'GSEA'
        self.minSubsetSize = 3
        self.minSubsetSizeC = True
        self.maxSubsetSize = 1000
        self.maxSubsetSizeC = True
        self.minSubsetPart = 10
        self.minSubsetPartC = True
        self.perms = 100
        self.csgm = False
        self.gsgo = False
        self.gskegg = False
        self.buildDistances = False
        self.selectedPhenVar = 0
        self.organismIndex = 0
        self.atLeast = 3

        self.permutationTypes =  [("Phenotype", "p"),("Gene", "g") ]
        self.ptype = 0

        self.correlationTypes = [ ("Signal2Noise", "s2n") ]
        self.ctype = 0
        
        self.data = None
        self.geneSets = {}

        self.tabs = OWGUI.tabWidget(self.controlArea)

        ca = OWGUI.createTabPage(self.tabs, "Basic")

        box = OWGUI.widgetBox(ca, 'Organism')
        #FROM KEGG WIDGET - organism selection
        self.organismTaxids = []
        self.organismComboBox = cb = OWGUI.comboBox(box, self, "organismIndex", items=[], debuggingEnabled=0) #changed
        cb.setMaximumWidth(200)

        #OWGUI.checkBox(box, self, "csgm", "Case sensitive gene matching")

        box2 = OWGUI.widgetBox(ca, "Descriptors")
        self.phenCombo = OWGUI.comboBox(box2, self, "selectedPhenVar", items=[], callback=self.phenComboChange, label="Phenotype:")
        self.geneCombo = OWGUI.comboBox(box2, self, "selectedGeneVar", items=[], label = "Gene:")

        self.allowComboChangeCallback = False

        ma = self.mainArea

        self.listView = QTreeWidget(ma)
        ma.layout().addWidget(self.listView)
        self.listView.setAllColumnsShowFocus(1)
        self.listView.setColumnCount(9)
        self.listView.setHeaderLabels(["Collection", "Geneset", "NES", "ES", "P-value", "FDR", "Size", "Matched Size", "Genes"])
        
        self.listView.header().setStretchLastSection(True)
        self.listView.header().setClickable(True)
        self.listView.header().setSortIndicatorShown(True)
        self.listView.setSortingEnabled(True)
        #self.listView.header().setResizeMode(0, QHeaderView.Stretch)
        
        self.listView.setSelectionMode(QAbstractItemView.NoSelection)
        self.connect(self.listView, SIGNAL("itemSelectionChanged()"), self.newPathwaySelected)

        OWGUI.separator(ca)

        OWGUI.widgetLabel(ca, "Phenotype selection:")
        self.psel = PhenotypesSelection(ca)
        
        self.resize(600,50)
 
        OWGUI.separator(ca)

        OWGUI.checkBox(ca, self, "buildDistances", "Compute geneset distances")

        self.btnApply = OWGUI.button(ca, self, "&Compute", callback = self.compute, disabled=0)
        
        fileBox = OWGUI.widgetBox(ca, orientation='horizontal')
        OWGUI.button(fileBox, self, "Load", callback = self.loadData, disabled=0, debuggingEnabled=0)
        OWGUI.button(fileBox, self, "Save", callback = self.saveData, disabled=0, debuggingEnabled=0)
 
        #ca.layout().addStretch(1)

        ca = OWGUI.createTabPage(self.tabs, "Gene sets")
        
        box = OWGUI.widgetBox(ca)

        self.gridSel = []
        self.geneSel = []  #FIXME temporary disabled - use the same as in new "David" widget
        self.lbgs = OWGUI.listBox(box, self, "gridSel", "geneSel", selectionMode = QListWidget.MultiSelection)
        OWGUI.button(box, self, "From &File", callback = self.addCollection, disabled=0, debuggingEnabled=0)

        box = OWGUI.widgetBox(box, "Additional sources:")
        OWGUI.checkBox(box, self, "gskegg", "KEGG pathways")
        OWGUI.checkBox(box, self, "gsgo", "GO terms")
#.........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 separator [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 separator [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 separator [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 separator [as 别名]
    def __init__(self, parent=None, signalManager=None):
        OWWidget.__init__(self, parent, signalManager, "MeshBrowser")
        self.inputs = [("Reference data", ExampleTable, self.getReferenceData), ("Cluster data", ExampleTable, self.getClusterData)]
        self.outputs = [("Selected examples", ExampleTable)]

        # widget variables
        self.loadedRef = 0
        self.loadedClu = 0
        self.maxPValue = 0.05
        self.minExamplesInTerm = 5
        self.multi = 1
        self.reference = None
        self.cluster = None
        self.loadSettings()
        self.mesh = obiMeSH() # main object is created
        self.dataLoaded = self.mesh.dataLoaded

        # left pane
        box = OWGUI.widgetBox(self.controlArea, "Info")
        #box = QGroupBox("Info", self.controlArea)
        self.infoa = OWGUI.label(box, self, "No reference data.")
        self.infob = OWGUI.label(box, self, "No cluster data.")
        self.ratio = OWGUI.label(box, self, "")
        self.ref_att = OWGUI.label(box, self, "")
        self.clu_att = OWGUI.label(box, self, "")
        self.resize(960, 600)
        OWGUI.separator(self.controlArea)

        self.optionsBox = OWGUI.widgetBox(self.controlArea, "Options")
        self.maxp = OWGUI.lineEdit(self.optionsBox, self, "maxPValue", label="threshold:", orientation="horizontal", labelWidth=120, valueType=float)
        self.minf = OWGUI.lineEdit(self.optionsBox, self, "minExamplesInTerm", label="min. frequency:", orientation="horizontal", labelWidth=120, valueType=int)
        #OWGUI.checkBox(self.optionsBox, self, 'multi', 'Multiple selection', callback= self.checkClicked)
        OWGUI.button(self.optionsBox, self, "Refresh", callback=self.refresh)

        # right pane
        self.col_size = [280, 84, 84, 100, 110]
        self.sort_col = 0
        self.sort_dir = True
        self.columns = ['MeSH term', '# reference', '# cluster', 'p value', 'fold enrichment'] # both datasets

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

        # list view
        self.meshLV = QTreeWidget(self.splitter)
        #self.meshLV.setSelectionMode(QAbstractItemView.MultiSelection)
        self.meshLV.setAllColumnsShowFocus(1)
        self.meshLV.setColumnCount(len(self.columns))
        self.meshLV.setHeaderLabels(self.columns)

        self.meshLV.header().setClickable(True)
        #self.meshLV.header().setSortIndicatorShown(True)
        #self.meshLV.setSortingEnabled(True)
        self.meshLV.setRootIsDecorated(True)
        self.connect(self.meshLV, SIGNAL("itemSelectionChanged()"), self.viewSelectionChanged)
        #self.meshLV.setItemDelegateForColumn(3, EnrichmentColumnItemDelegate(self))
        #self.tooltips = ListViewToolTip(self.meshLV,0, self.mesh.toDesc)

        # table of significant mesh terms
        self.sigTermsTable = QTableWidget(self.splitter)
        self.sigTermsTable.setColumnCount(len(self.columns))
        self.sigTermsTable.setRowCount(4)
        ## hide the vertical header
        self.sigTermsTable.verticalHeader().hide()
        #self.sigTermsTable.setLeftMargin(0)
        #self.sigTermsTable.setSelectionMode(QAbstractItemView.MultiSelection)

        for i in range(0, len(self.columns)):
            self.sigTermsTable.horizontalHeader().resizeSection(i, self.col_size[i])
            self.meshLV.header().resizeSection(i, self.col_size[i])

        self.sigTermsTable.setHorizontalHeaderLabels(self.columns)

        self.connect(self.sigTermsTable, SIGNAL("itemSelectionChanged()"), self.tableSelectionChanged)
        self.connect(self.sigTermsTable, SIGNAL("clicked(int,int,int,const QPoint&)"), self.tableClicked)
        self.splitter.show()
        self.optionsBox.setDisabled(1)

# 需要导入模块: from Orange.OrangeWidgets import OWGUI [as 别名]
# 或者: from Orange.OrangeWidgets.OWGUI import separator [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 separator [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.........