Example #1
0
    def __init__(self, parent=None, signalManager=None, name="dictyExpress"):
        OWWidget.__init__(self, parent, signalManager, name)
        self.outputs = [("Example table", ExampleTable)]
        self.serverToken = ""
        self.server = obiDicty.defaddress

        self.platform = None

        self.selectedExperiments = []
        self.buffer = obiDicty.CacheSQLite(bufferfile)

        self.searchString = ""
        self.excludeconstant = False

        box = OWGUI.widgetBox(self.controlArea, "Cache")
        OWGUI.button(box, self, "Clear cache", callback=self.clear_buffer)

        OWGUI.checkBox(self.controlArea, self, "excludeconstant",
                       "Exclude labels with constant values")

        OWGUI.button(self.controlArea, self, "&Commit", callback=self.Commit)
        box = OWGUI.widgetBox(self.controlArea, "Server")
        OWGUI.lineEdit(box,
                       self,
                       "serverToken",
                       "Token",
                       callback=self.Connect)
        OWGUI.rubber(self.controlArea)

        OWGUI.lineEdit(self.mainArea,
                       self,
                       "searchString",
                       "Search",
                       callbackOnType=True,
                       callback=self.SearchUpdate)
        self.experimentsWidget = QTreeWidget()
        self.experimentsWidget.setHeaderLabels([
            "Strain", "Treatment", "Growth condition", "Platform", "N", "Chips"
        ])
        self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection)
        self.experimentsWidget.setRootIsDecorated(False)
        self.experimentsWidget.setSortingEnabled(True)
        ##        self.experimentsWidget.setAlternatingRowColors(True)

        self.mainArea.layout().addWidget(self.experimentsWidget)

        self.loadSettings()
        self.dbc = None

        QTimer.singleShot(0, self.UpdateExperiments)

        self.resize(800, 600)
Example #2
0
    def __init__(self, parent=None, signalManager=None, name="dictyExpress"):
        OWWidget.__init__(self, parent, signalManager, name)
        self.outputs = [("Example table", ExampleTable)]
        self.serverToken = ""
        self.server = obiDicty.defaddress

        self.platform = None

        self.selectedExperiments = []
        self.buffer = obiDicty.CacheSQLite(bufferfile)

        self.searchString = ""
        self.excludeconstant = False
        
        box = OWGUI.widgetBox(self.controlArea, "Cache")
        OWGUI.button(box, self, "Clear cache", callback=self.clear_buffer)

        OWGUI.checkBox(self.controlArea, self, "excludeconstant", "Exclude labels with constant values" )

        OWGUI.button(self.controlArea, self, "&Commit", callback=self.Commit)
        box  = OWGUI.widgetBox(self.controlArea, "Server")
        OWGUI.lineEdit(box, self, "serverToken","Token", callback=self.Connect)
        OWGUI.rubber(self.controlArea)

        OWGUI.lineEdit(self.mainArea, self, "searchString", "Search", callbackOnType=True, callback=self.SearchUpdate)
        self.experimentsWidget = QTreeWidget()
        self.experimentsWidget.setHeaderLabels(["Strain", "Treatment", "Growth condition", "Platform", "N", "Chips"]) 
        self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection)
        self.experimentsWidget.setRootIsDecorated(False)
        self.experimentsWidget.setSortingEnabled(True)
##        self.experimentsWidget.setAlternatingRowColors(True)

        self.mainArea.layout().addWidget(self.experimentsWidget)

        self.loadSettings()
        self.dbc = None        

        QTimer.singleShot(0, self.UpdateExperiments)        

        self.resize(800, 600)
    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 = "H**o 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
        @lru_cache(maxsize=3)
        def my_cached_matcher(org):
            return obiGeneAtlas.default_gene_matcher(org)
        self.construct_matcher = my_cached_matcher
    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()

        box1 = OWGUI.widgetBox(box, orientation='horizontal')
        OWGUI.spin(box1, self, "selectNBest", 0, 10000, step=1, label="Best Ranked:")
        OWGUI.button(box1, self, "Select", callback=self.select_n_best)

        box = OWGUI.widgetBox(self.controlArea, "Output")
        b = OWGUI.button(box, self, "&Commit", callback=self.commit)
        cb = OWGUI.checkBox(box, self, "auto_commit", "Commit on change")
        OWGUI.setStopper(self, b, cb, "data_changed_flag", self.commit)
        OWGUI.checkBox(box, self, "add_scores_to_output", "Add gene scores to output",
                       callback=self.commit_if) 
        
        OWGUI.rubber(self.controlArea)

        self.connect(self.graphButton, SIGNAL("clicked()"), self.histogram.saveToFile)
        
        self.loadSettings()

        self.data = None
        self.discData = None
        self.scoreCache = {}
        self.nullDistCache = {}
        self.cuts = {}
        self.null_dist = []
        self.targets = []
        self.scores = {}
        self.genes_in_columns = True
        self.target_selections = None
        
        self.on_scoring_method_changed()
        
        self.resize(800, 600)
    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)
    def __init__(self, parent=None, signalManager=None,
                 name="Databases update"):
        OWWidget.__init__(self, parent, signalManager, name,
                          wantMainArea=False)

        self.searchString = ""

        fbox = gui.widgetBox(self.controlArea, "Filter")
        self.completer = TokenListCompleter(
            self, caseSensitivity=Qt.CaseInsensitive)
        self.lineEditFilter = QLineEdit(textChanged=self.SearchUpdate)
        self.lineEditFilter.setCompleter(self.completer)

        fbox.layout().addWidget(self.lineEditFilter)

        box = gui.widgetBox(self.controlArea, "Files")

        self.filesView = QTreeWidget(self)
        self.filesView.setHeaderLabels(
            ["", "Data Source", "Update", "Last Updated", "Size"])

        self.filesView.setRootIsDecorated(False)
        self.filesView.setUniformRowHeights(True)
        self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
        self.filesView.setSortingEnabled(True)
        self.filesView.sortItems(1, Qt.AscendingOrder)
        self.filesView.setItemDelegateForColumn(
            0, UpdateOptionsItemDelegate(self.filesView))

        self.filesView.model().layoutChanged.connect(self.SearchUpdate)

        box.layout().addWidget(self.filesView)

        box = gui.widgetBox(self.controlArea, orientation="horizontal")
        self.updateButton = gui.button(
            box, self, "Update all",
            callback=self.UpdateAll,
            tooltip="Update all updatable files",
         )

        self.downloadButton = gui.button(
            box, self, "Download all",
            callback=self.DownloadFiltered,
            tooltip="Download all filtered files shown"
        )

        self.cancelButton = gui.button(
            box, self, "Cancel", callback=self.Cancel,
            tooltip="Cancel scheduled downloads/updates."
        )

        self.retryButton = gui.button(
            box, self, "Reconnect", callback=self.RetrieveFilesList
        )
        self.retryButton.hide()

        gui.rubber(box)
        self.warning(0)

        box = gui.widgetBox(self.controlArea, orientation="horizontal")
        gui.rubber(box)

        self.infoLabel = QLabel()
        self.infoLabel.setAlignment(Qt.AlignCenter)

        self.controlArea.layout().addWidget(self.infoLabel)
        self.infoLabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)

        self.updateItems = []

        self.resize(800, 600)

        self.progress = ProgressState(self, maximum=3)
        self.progress.valueChanged.connect(self._updateProgress)
        self.progress.rangeChanged.connect(self._updateProgress)
        self.executor = ThreadExecutor(
            threadPool=QThreadPool(maxThreadCount=2)
        )

        task = Task(self, function=self.RetrieveFilesList)
        task.exceptionReady.connect(self.HandleError)
        task.start()

        self._tasks = []
        self._haveProgress = False
Example #7
0
    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(
            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)

        self.searchKeys = ["dataset_id", "title", "platform_organism",
                           "description"]

        self.gds = []
        self.gds_info = None

        self.resize(1000, 600)

        self.setBlocking(True)
        self.setEnabled(False)
        self.progressBarInit()

        self._executor = ThreadExecutor()

        func = partial(get_gds_model,
                       methodinvoke(self, "_setProgress", (float,)))
        self._inittask = Task(function=func)
        self._inittask.finished.connect(self._initializemodel)
        self._executor.submit(self._inittask)

        self._datatask = None
Example #8
0
    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)

        self.searchKeys = ["dataset_id", "title", "platform_organism",
                           "description"]

        self.gds = []
        self.gds_info = None

        self.resize(1000, 600)

        self.setBlocking(True)
        self.setEnabled(False)
        self.progressBarInit()

        self._executor = ThreadExecutor()

        func = partial(get_gds_model,
                       methodinvoke(self, "_setProgress", (float,)))
        self._inittask = Task(function=func)
        self._inittask.finished.connect(self._initializemodel)
        self._executor.submit(self._inittask)

        self._datatask = None
Example #9
0
    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 = 1
        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 in rows", "Samples in rows"], "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(
            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)

        self.searchKeys = ["dataset_id", "title", "platform_organism",
                           "description"]

        self.gds = []
        self.gds_info = None

        self.resize(1000, 600)

        self.setBlocking(True)
        self.setEnabled(False)
        self.progressBarInit()

        self._executor = ThreadExecutor()

        func = partial(get_gds_model,
                       methodinvoke(self, "_setProgress", (float,)))
        self._inittask = Task(function=func)
        self._inittask.finished.connect(self._initializemodel)
        self._executor.submit(self._inittask)

        self._datatask = None
    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)

        self.listView.setMaximumHeight(200)

        self.connect(self.listView,
                     SIGNAL("itemSelectionChanged()"),
                     self.UpdatePathwayView)

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

        select = QAction(
            "Select All", self,
            shortcut=QKeySequence.SelectAll
        )
        select.triggered.connect(self.selectAll)
        self.addAction(select)

        self.data = None
        self.refData = None

        self.resize(800, 600)

        self.connect(self,
                     SIGNAL("widgetStateChanged(QString, int, QString)"),
                     self.onStateChange)

        self.has_new_data = False
        self.has_new_reference_set = False

        self._executor = ThreadExecutor()
        self.setEnabled(False)
        self.setBlocking(True)
        QTimer.singleShot(0, self._initialize)
        self.infoLabel.setText("Fetching organism definitions\n")
Example #11
0
    def __init__(self, parent=None, signalManager=None,
                 title="Venn Diagram"):
        super(OWVennDiagram, self).__init__(parent, signalManager, title,
                                            wantGraph=True)

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

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

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

        self.loadSettings()

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

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

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

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

        OWGUI.rubber(self.controlArea)

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

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

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

        self.scene.addItem(self.vennwidget)

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

        self._queue = []
        self.graphButton.clicked.connect(self.saveImage)
Example #12
0
    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,
            tooltip=
            "Show bars with distribution of class values (only for discrete attributes)"
        )

        box = OWGUI.widgetBox(self.SettingsTab,
                              "Colors",
                              orientation="horizontal")
        OWGUI.button(
            box,
            self,
            "Set colors",
            self.setColors,
            tooltip=
            "Set the canvas background color and color palette for coloring continuous variables",
            debuggingEnabled=0)

        box = OWGUI.widgetBox(self.SettingsTab,
                              "Auto Send Selected Data When...")
        OWGUI.checkBox(
            box,
            self,
            'autoSendSelection',
            'Adding/Removing selection areas',
            callback=self.selectionChanged,
            tooltip=
            "Send selected data whenever a selection area is added or removed")
        OWGUI.checkBox(
            box,
            self,
            'graph.sendSelectionOnUpdate',
            'Moving/Resizing selection areas',
            tooltip=
            "Send selected data when a user moves or resizes an existing selection area"
        )
        self.graph.autoSendSelectionCallback = self.selectionChanged

        self.SettingsTab.layout().addStretch(100)
        self.icons = self.createAttributeIconDict()

        dlg = self.createColorDialog()
        self.graph.contPalette = dlg.getContinuousPalette("contPalette")
        self.graph.discPalette = dlg.getDiscretePalette("discPalette")
        self.graph.setCanvasBackground(dlg.getColor("Canvas"))
        apply([
            self.zoomSelectToolbar.actionZooming,
            self.zoomSelectToolbar.actionRectangleSelection,
            self.zoomSelectToolbar.actionPolygonSelection
        ][self.toolbarSelection], [])
        self.cbShowAllAttributes()

        self.resize(900, 700)
Example #13
0
 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)
    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)

        if pybel:
            self.listBox = QListWidget(spliter)
        else:
            self.listBox = QListWidget(None)
            self.listBox.setHidden(True)

        self.listBox.itemClicked.connect(self.fragmentSelection)

        self.fragmentSmilesCombo.box.setDisabled(not pybel)

        self.data = None
        self.data_subset = []
        self.fragment_data = None
        self.resize(800, 600)
        self.listBox.setMaximumHeight(150)
        self.fragmentSmilesCombo.setDisabled(True)
        self.selectMarkedMoleculesButton.setDisabled(True)
        self.markFragmentsCheckBox.setDisabled(True)
        self.showFragmentsRadioButton.setDisabled(True)

        self.loadSettings()

        if not pybel:
            self.showFragments = 0
            self.warning(10,
                         "Pybel module not installed. To view molecule fragments\n"
                         "please install openbabel python extension.")

        self.__loop = None
Example #15
0
    def __init__(self, parent=None, signalManager=None, name="Vulcano Plot"):
        OWWidget.__init__(self, parent, signalManager, name, wantGraph=True)

        self.inputs = [("Examples", ExampleTable, self.setData)]
        self.outputs = [("Examples with selected attributes", ExampleTable)]

        self.genes_in_columns = False

        self.showXTitle = True
        self.showYTitle = True

        self.auto_commit = False
        self.selection_changed_flag = False
        self.target_group = None, []
        self.label_selections = []

        self.graph = VulcanoGraph(self)
        self.connect(self.graph, SIGNAL("selectionChanged()"),
                     self.on_selection_changed)
        self.mainArea.layout().addWidget(self.graph)

        self.loadSettings()

        ## GUI
        box = OWGUI.widgetBox(self.controlArea, "Info")
        self.infoLabel = OWGUI.label(box, self, "")
        self.infoLabel.setText("No data on input")
        self.infoLabel2 = OWGUI.label(box, self, "")
        self.infoLabel2.setText("0 selected genes")
        
        box = OWGUI.widgetBox(self.controlArea, "Target Labels")
        
        self.target_widget = LabelSelectionWidget(self)
        self.connect(self.target_widget,
                     SIGNAL("selection_changed(PyQt_PyObject, PyQt_PyObject)"),
                     self.on_target_changed)
        self.connect(self.target_widget,
                     SIGNAL("label_activated(int)"),
                     self.on_label_activated)
        
        box.layout().addWidget(self.target_widget)
        
        self.genesInColumnsCheck = OWGUI.checkBox(box, self, "genes_in_columns",
                                    "Genes in columns", 
                                    callback=[self.init_from_data, self.plot])

        box = OWGUI.widgetBox(self.controlArea, "Settings")
        OWGUI.hSlider(box, self, "graph.symbolSize", label="Symbol size:   ", minValue=2, maxValue=20, step=1, callback = self.graph.updateSymbolSize)
        OWGUI.checkBox(box, self, "showXTitle", "X axis title", callback=self.setAxesTitles)
        OWGUI.checkBox(box, self, "showYTitle", "Y axis title", callback=self.setAxesTitles)
        
        toolbar = ZoomSelectToolbar(self, self.controlArea, self.graph, buttons=[ZoomSelectToolbar.IconSelect, ZoomSelectToolbar.IconZoom, ZoomSelectToolbar.IconPan])
        
        top_layout = toolbar.layout()
        top_layout.setDirection(QBoxLayout.TopToBottom)
        button_layotu = QHBoxLayout()
        top_layout.insertLayout(0, button_layotu)
        
        for i in range(1, top_layout.count()):
            item = top_layout.itemAt(1)
            top_layout.removeItem(item)
            button_layotu.addItem(item)
        
        OWGUI.checkBox(toolbar, self, "graph.symetricSelections", "Symetric selection", callback=self.graph.reselect)

        box = OWGUI.widgetBox(self.controlArea, "Commit")
        b = OWGUI.button(box, self, "Commit", callback=self.commit, default=True)
        cb = OWGUI.checkBox(box, self, "auto_commit", "Commit automatically")
        OWGUI.setStopper(self, b, cb, "selection_changed_flag", self.commit_if)

        self.connect(self.graphButton, SIGNAL("clicked()"), self.graph.saveToFile)
        
        OWGUI.rubber(self.controlArea)

        self.data = None
        self.target_group = None, []
        self.current_selection = []

        self.graph.reselect(True)
        self.resize(800, 600)
    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)
Example #17
0
    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)
Example #18
0
    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 = "H**o 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
        @lru_cache(maxsize=3)
        def my_cached_matcher(org):
            return obiGeneAtlas.default_gene_matcher(org)

        self.construct_matcher = my_cached_matcher
    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
Example #20
0
    def __init__(self, parent=None, signalManager=None,
                 name="Databases update", domains=None):
        OWWidget.__init__(self, parent, signalManager, name,
                          wantMainArea=False)

        self.searchString = ""
        self.accessCode = ""
        self.domains = domains or DOMAINS
        self.serverFiles = serverfiles.ServerFiles()

        fbox = gui.widgetBox(self.controlArea, "Filter")
        self.completer = TokenListCompleter(
            self, caseSensitivity=Qt.CaseInsensitive)
        self.lineEditFilter = QLineEdit(textChanged=self.SearchUpdate)
        self.lineEditFilter.setCompleter(self.completer)

        fbox.layout().addWidget(self.lineEditFilter)

        box = gui.widgetBox(self.controlArea, "Files")

        self.filesView = QTreeWidget(self)
        self.filesView.setHeaderLabels(
            ["", "Data Source", "Update", "Last Updated", "Size"])

        self.filesView.setRootIsDecorated(False)
        self.filesView.setUniformRowHeights(True)
        self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
        self.filesView.setSortingEnabled(True)
        self.filesView.sortItems(1, Qt.AscendingOrder)
        self.filesView.setItemDelegateForColumn(
            0, UpdateOptionsItemDelegate(self.filesView))

        self.filesView.model().layoutChanged.connect(self.SearchUpdate)

        box.layout().addWidget(self.filesView)

        box = gui.widgetBox(self.controlArea, orientation="horizontal")
        self.updateButton = gui.button(
            box, self, "Update all",
            callback=self.UpdateAll,
            tooltip="Update all updatable files",
         )

        self.downloadButton = gui.button(
            box, self, "Download all",
            callback=self.DownloadFiltered,
            tooltip="Download all filtered files shown"
        )

        self.cancelButton = gui.button(
            box, self, "Cancel", callback=self.Cancel,
            tooltip="Cancel scheduled downloads/updates."
        )

        self.retryButton = gui.button(
            box, self, "Reconnect", callback=self.RetrieveFilesList
        )
        self.retryButton.hide()

        gui.rubber(box)

        gui.lineEdit(box, self, "accessCode", "Access Code",
                     orientation="horizontal",
                     callback=self.RetrieveFilesList)

        self.warning(0)

        box = gui.widgetBox(self.controlArea, orientation="horizontal")
        gui.rubber(box)

        self.infoLabel = QLabel()
        self.infoLabel.setAlignment(Qt.AlignCenter)

        self.controlArea.layout().addWidget(self.infoLabel)
        self.infoLabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)

        self.updateItems = []

        self.resize(800, 600)

        self.progress = ProgressState(self, maximum=3)
        self.progress.valueChanged.connect(self._updateProgress)
        self.progress.rangeChanged.connect(self._updateProgress)
        self.executor = ThreadExecutor(
            threadPool=QThreadPool(maxThreadCount=2)
        )

        task = Task(self, function=self.RetrieveFilesList)
        task.exceptionReady.connect(self.HandleError)
        task.start()

        self._tasks = []
        self._haveProgress = False
Example #21
0
    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)
        self.matchedInfo = 0, 0
        self.selectionUpdateInProgress = False

        self.setBlocking(True)
        self.executor = ThreadExecutor(self)

        self.progressBarInit()

        task = Task(
            function=partial(
                taxonomy.ensure_downloaded,
                callback=methodinvoke(self, "advance", ())
            )
        )

        task.resultReady.connect(self.initialize)
        task.exceptionReady.connect(self._onInitializeError)

        self.initfuture = self.executor.submit(task)
    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)

        if pybel:
            self.listBox = QListWidget(spliter)
        else:
            self.listBox = QListWidget(None)
            self.listBox.setHidden(True)

        self.listBox.itemClicked.connect(self.fragmentSelection)

        self.fragmentSmilesCombo.box.setDisabled(not pybel)

        self.data = None
        self.data_subset = []
        self.fragment_data = None
        self.resize(800, 600)
        self.listBox.setMaximumHeight(150)
        self.fragmentSmilesCombo.setDisabled(True)
        self.selectMarkedMoleculesButton.setDisabled(True)
        self.markFragmentsCheckBox.setDisabled(True)
        self.showFragmentsRadioButton.setDisabled(True)

        self.loadSettings()

        if not pybel:
            self.showFragments = 0
            self.warning(
                10, "Pybel module not installed. To view molecule fragments\n"
                "please install openbabel python extension.")

        self.__loop = None
Example #23
0
    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()

        box1 = OWGUI.widgetBox(box, orientation='horizontal')
        OWGUI.spin(box1,
                   self,
                   "selectNBest",
                   0,
                   10000,
                   step=1,
                   label="Best Ranked:")
        OWGUI.button(box1, self, "Select", callback=self.select_n_best)

        box = OWGUI.widgetBox(self.controlArea, "Output")
        b = OWGUI.button(box, self, "&Commit", callback=self.commit)
        cb = OWGUI.checkBox(box, self, "auto_commit", "Commit on change")
        OWGUI.setStopper(self, b, cb, "data_changed_flag", self.commit)
        OWGUI.checkBox(box,
                       self,
                       "add_scores_to_output",
                       "Add gene scores to output",
                       callback=self.commit_if)

        OWGUI.rubber(self.controlArea)

        self.connect(self.graphButton, SIGNAL("clicked()"),
                     self.histogram.saveToFile)

        self.loadSettings()

        self.data = None
        self.discData = None
        self.scoreCache = {}
        self.nullDistCache = {}
        self.cuts = {}
        self.null_dist = []
        self.targets = []
        self.scores = {}
        self.genes_in_columns = True
        self.target_selections = None

        self.on_scoring_method_changed()

        self.resize(800, 600)
Example #24
0
    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)

        self.searchKeys = [
            "dataset_id", "title", "platform_organism", "description"
        ]

        self.gds = []
        self.gds_info = None

        self.resize(1000, 600)

        self.setBlocking(True)
        self.setEnabled(False)
        self.progressBarInit()

        self._executor = ThreadExecutor()

        func = partial(get_gds_model,
                       methodinvoke(self, "_setProgress", (float, )))
        self._inittask = Task(function=func)
        self._inittask.finished.connect(self._initializemodel)
        self._executor.submit(self._inittask)

        self._datatask = None
    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,
                       tooltip="Show bars with distribution of class values (only for discrete attributes)")

        box = OWGUI.widgetBox(self.SettingsTab, "Colors", orientation="horizontal")
        OWGUI.button(box, self, "Set colors", self.setColors,
                     tooltip="Set the canvas background color and color palette for coloring continuous variables",
                     debuggingEnabled=0)

        box = OWGUI.widgetBox(self.SettingsTab, "Auto Send Selected Data When...")
        OWGUI.checkBox(box, self, 'autoSendSelection', 'Adding/Removing selection areas',
                       callback=self.selectionChanged,
                       tooltip="Send selected data whenever a selection area is added or removed")
        OWGUI.checkBox(box, self, 'graph.sendSelectionOnUpdate', 'Moving/Resizing selection areas',
                       tooltip="Send selected data when a user moves or resizes an existing selection area")
        self.graph.autoSendSelectionCallback = self.selectionChanged

        self.SettingsTab.layout().addStretch(100)
        self.icons = self.createAttributeIconDict()

        dlg = self.createColorDialog()
        self.graph.contPalette = dlg.getContinuousPalette("contPalette")
        self.graph.discPalette = dlg.getDiscretePalette("discPalette")
        self.graph.setCanvasBackground(dlg.getColor("Canvas"))
        apply([self.zoomSelectToolbar.actionZooming, self.zoomSelectToolbar.actionRectangleSelection,
               self.zoomSelectToolbar.actionPolygonSelection][self.toolbarSelection], [])
        self.cbShowAllAttributes()

        self.resize(900, 700)