def progressBarSet(self, value):
if not self.__in_progress_update:
self.__in_progress_update = True
try:
OWWidget.progressBarSet(self, value)
finally:
self.__in_progress_update = False
def handleNewSignals(self):
self._inputUpdate = False
# Check if all inputs are from the same domain.
domains = [input.table.domain for input in self.data.values()]
# samedomain = all(d1 == d2 for d1, d2 in pairwise(domains))
samedomain = all(domain_eq(d1, d2) for d1, d2 in pairwise(domains))
self.useequalityButton.setEnabled(samedomain)
self.samedomain = samedomain
has_identifiers = all(source_attributes(input.table.domain)
for input in self.data.values())
if not samedomain and not self.useidentifiers:
self.useidentifiers = 1
elif samedomain and not has_identifiers:
self.useidentifiers = 0
incremental = all(inc for _, inc in self._queue)
if incremental:
# Only received updated data on existing link.
self._updateItemsets()
else:
# Links were removed and/or added.
self._createItemsets()
self._restoreHints()
self._updateItemsets()
del self._queue[:]
self._createDiagram()
if self.data:
self.info.setText(
"{} data sets on input.\n".format(len(self.data)))
else:
self.info.setText("No data on input\n")
self._updateInfo()
OWWidget.handleNewSignals(self)
def handleNewSignals(self):
self._inputUpdate = False
incremental = all(inc for _, inc in self._queue)
if incremental:
self._updateItemsets()
else:
self._createItemsets()
self._restoreHints()
self._updateItemsets()
del self._queue[:]
self._createDiagram()
if self.data:
self.info.setText(
"{} data sets on input.\n".format(len(self.data)))
else:
self.info.setText("No data on input\n")
OWWidget.handleNewSignals(self)
def onDeleteWidget(self):
self.Cancel()
self.executor.shutdown(wait=False)
OWWidget.onDeleteWidget(self)
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
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 or spots", "Samples"], "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")
gui.rubber(self.controlArea)
# self.filterLineEdit = OWGUIEx.lineEditHint(
# self.mainArea, self, "filterString", "Filter",
# caseSensitive=False, matchAnywhere=True,
# callback=self.filter, delimiters=" ")
gui.widgetLabel(self.mainArea, "Filter")
self.filterLineEdit = QLineEdit(
textChanged=self.filter
)
self.completer = QCompleter(
caseSensitivity=Qt.CaseInsensitive
)
self.completer.setModel(QStringListModel(self))
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 getSettings(self, *args, **kwargs):
self._storeHints()
return OWWidget.getSettings(self, *args, **kwargs)
def closeEvent(self, ce):
self.optimizationDlg.hide()
OWWidget.closeEvent(self, ce)
def onDeleteWidget(self):
self.Cancel()
self.executor.shutdown(wait=False)
OWWidget.onDeleteWidget(self)
def __init__(self, parallelWidget, parent=None, signalManager=None):
OWWidget.__init__(self, parent, signalManager,
"Parallel Optimization Dialog", False)
self.setCaption("Parallel Optimization Dialog")
self.parallelWidget = parallelWidget
self.optimizationMeasure = 0
self.attributeCount = 5
self.numberOfAttributes = 6
self.fileName = ""
self.lastSaveDirName = os.getcwd() + "/"
self.fileBuffer = []
self.projections = []
self.allResults = []
self.canOptimize = 0
self.orderAllAttributes = 1 # do we wish to order all attributes or find just an interesting subset
self.worstVal = -1 # used in heuristics to stop the search in uninteresting parts of the graph
self.loadSettings()
self.measureBox = OWGUI.radioButtonsInBox(
self.controlArea,
self,
"optimizationMeasure", ["Correlation", "VizRank"],
box="Select optimization measure",
callback=self.updateGUI)
self.vizrankSettingsBox = OWGUI.widgetBox(self.controlArea,
"VizRank settings")
self.optimizeBox = OWGUI.widgetBox(self.controlArea, "Optimize")
self.manageBox = OWGUI.widgetBox(self.controlArea, "Manage results")
self.resultsBox = OWGUI.widgetBox(self.mainArea, "Results")
self.resultList = OWGUI.listBox(self.resultsBox, self)
self.resultList.setMinimumSize(200, 200)
self.connect(self.resultList, SIGNAL("itemSelectionChanged()"),
self.showSelectedAttributes)
# remove non-existing files
names = []
for i in range(len(self.fileBuffer) - 1, -1, -1):
(short, longName) = self.fileBuffer[i]
if not os.path.exists(longName):
self.fileBuffer.remove((short, longName))
else:
names.append(short)
names.append("(None)")
self.fileName = "(None)"
self.hbox1 = OWGUI.widgetBox(self.vizrankSettingsBox,
"VizRank projections file",
orientation="horizontal")
self.vizrankFileCombo = OWGUI.comboBox(
self.hbox1,
self,
"fileName",
items=names,
tooltip=
"File that contains information about interestingness of scatterplots\n"
"generated by VizRank method in scatterplot widget",
callback=self.changeProjectionFile,
sendSelectedValue=1,
valueType=str)
self.browseButton = OWGUI.button(self.hbox1,
self,
"...",
callback=self.loadProjections)
self.browseButton.setMaximumWidth(20)
self.resultsInfoBox = OWGUI.widgetBox(self.vizrankSettingsBox,
"VizRank parameters")
self.kNeighborsLabel = OWGUI.widgetLabel(self.resultsInfoBox,
"Number of neighbors (k):")
self.percentDataUsedLabel = OWGUI.widgetLabel(self.resultsInfoBox,
"Percent of data used:")
self.testingMethodLabel = OWGUI.widgetLabel(self.resultsInfoBox,
"Testing method used:")
self.qualityMeasureLabel = OWGUI.widgetLabel(self.resultsInfoBox,
"Quality measure used:")
self.allAttributesRadio = QRadioButton("Order all attributes",
self.optimizeBox)
self.optimizeBox.layout().addWidget(self.allAttributesRadio)
self.connect(self.allAttributesRadio, SIGNAL("clicked()"),
self.setAllAttributeRadio)
box = OWGUI.widgetBox(self.optimizeBox, orientation="horizontal")
self.subsetAttributeRadio = QRadioButton("Find subsets of", box)
box.layout().addWidget(self.subsetAttributeRadio)
self.connect(self.subsetAttributeRadio, SIGNAL("clicked()"),
self.setSubsetAttributeRadio)
self.subsetAttributeEdit = OWGUI.lineEdit(box,
self,
"numberOfAttributes",
valueType=int)
self.subsetAttributeEdit.setMaximumWidth(30)
OWGUI.widgetLabel(box, "attributes")
self.startOptimizationButton = OWGUI.button(
self.optimizeBox,
self,
"Start Optimization",
callback=self.startOptimization)
f = self.startOptimizationButton.font()
f.setBold(1)
self.startOptimizationButton.setFont(f)
self.stopOptimizationButton = OWGUI.button(
self.optimizeBox,
self,
"Stop Evaluation",
callback=self.stopOptimizationClick)
self.stopOptimizationButton.setFont(f)
self.stopOptimizationButton.hide()
self.connect(self.stopOptimizationButton, SIGNAL("clicked()"),
self.stopOptimizationClick)
self.clearButton = OWGUI.button(self.manageBox, self, "Clear Results",
self.clearResults)
self.loadButton = OWGUI.button(self.manageBox, self, "Load",
self.loadResults)
self.saveButton = OWGUI.button(self.manageBox, self, "Save",
self.saveResults)
self.closeButton = OWGUI.button(self.manageBox, self, "Close Dialog",
self.hide)
self.changeProjectionFile()
self.updateGUI()
if self.orderAllAttributes:
self.setAllAttributeRadio()
else:
self.setSubsetAttributeRadio()
def closeEvent(self, ce):
self.optimizationDlg.hide()
OWWidget.closeEvent(self, ce)
def saveSettings(self):
OWWidget.saveSettings(self)
self.optimizationDlg.saveSettings()
def onDeleteWidget(self):
OWWidget.onDeleteWidget(self)
if self.__loop is not None:
self.__loop.close()
self.__loop = 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)
def __init__(self, parallelWidget, parent=None, signalManager=None):
OWWidget.__init__(self, parent, signalManager, "Parallel Optimization Dialog", False)
self.setCaption("Parallel Optimization Dialog")
self.parallelWidget = parallelWidget
self.optimizationMeasure = 0
self.attributeCount = 5
self.numberOfAttributes = 6
self.fileName = ""
self.lastSaveDirName = os.getcwd() + "/"
self.fileBuffer = []
self.projections = []
self.allResults = []
self.canOptimize = 0
self.orderAllAttributes = 1 # do we wish to order all attributes or find just an interesting subset
self.worstVal = -1 # used in heuristics to stop the search in uninteresting parts of the graph
self.loadSettings()
self.measureBox = OWGUI.radioButtonsInBox(self.controlArea, self, "optimizationMeasure",
["Correlation", "VizRank"], box="Select optimization measure",
callback=self.updateGUI)
self.vizrankSettingsBox = OWGUI.widgetBox(self.controlArea, "VizRank settings")
self.optimizeBox = OWGUI.widgetBox(self.controlArea, "Optimize")
self.manageBox = OWGUI.widgetBox(self.controlArea, "Manage results")
self.resultsBox = OWGUI.widgetBox(self.mainArea, "Results")
self.resultList = OWGUI.listBox(self.resultsBox, self)
self.resultList.setMinimumSize(200, 200)
self.connect(self.resultList, SIGNAL("itemSelectionChanged()"), self.showSelectedAttributes)
# remove non-existing files
names = []
for i in range(len(self.fileBuffer) - 1, -1, -1):
(short, longName) = self.fileBuffer[i]
if not os.path.exists(longName):
self.fileBuffer.remove((short, longName))
else:
names.append(short)
names.append("(None)")
self.fileName = "(None)"
self.hbox1 = OWGUI.widgetBox(self.vizrankSettingsBox, "VizRank projections file", orientation="horizontal")
self.vizrankFileCombo = OWGUI.comboBox(self.hbox1, self, "fileName", items=names,
tooltip="File that contains information about interestingness of scatterplots\n"
"generated by VizRank method in scatterplot widget",
callback=self.changeProjectionFile, sendSelectedValue=1, valueType=str)
self.browseButton = OWGUI.button(self.hbox1, self, "...", callback=self.loadProjections)
self.browseButton.setMaximumWidth(20)
self.resultsInfoBox = OWGUI.widgetBox(self.vizrankSettingsBox, "VizRank parameters")
self.kNeighborsLabel = OWGUI.widgetLabel(self.resultsInfoBox, "Number of neighbors (k):")
self.percentDataUsedLabel = OWGUI.widgetLabel(self.resultsInfoBox, "Percent of data used:")
self.testingMethodLabel = OWGUI.widgetLabel(self.resultsInfoBox, "Testing method used:")
self.qualityMeasureLabel = OWGUI.widgetLabel(self.resultsInfoBox, "Quality measure used:")
self.allAttributesRadio = QRadioButton("Order all attributes", self.optimizeBox)
self.optimizeBox.layout().addWidget(self.allAttributesRadio)
self.connect(self.allAttributesRadio, SIGNAL("clicked()"), self.setAllAttributeRadio)
box = OWGUI.widgetBox(self.optimizeBox, orientation="horizontal")
self.subsetAttributeRadio = QRadioButton("Find subsets of", box)
box.layout().addWidget(self.subsetAttributeRadio)
self.connect(self.subsetAttributeRadio, SIGNAL("clicked()"), self.setSubsetAttributeRadio)
self.subsetAttributeEdit = OWGUI.lineEdit(box, self, "numberOfAttributes", valueType=int)
self.subsetAttributeEdit.setMaximumWidth(30)
OWGUI.widgetLabel(box, "attributes")
self.startOptimizationButton = OWGUI.button(self.optimizeBox, self, "Start Optimization",
callback=self.startOptimization)
f = self.startOptimizationButton.font()
f.setBold(1)
self.startOptimizationButton.setFont(f)
self.stopOptimizationButton = OWGUI.button(self.optimizeBox, self, "Stop Evaluation",
callback=self.stopOptimizationClick)
self.stopOptimizationButton.setFont(f)
self.stopOptimizationButton.hide()
self.connect(self.stopOptimizationButton, SIGNAL("clicked()"), self.stopOptimizationClick)
self.clearButton = OWGUI.button(self.manageBox, self, "Clear Results", self.clearResults)
self.loadButton = OWGUI.button(self.manageBox, self, "Load", self.loadResults)
self.saveButton = OWGUI.button(self.manageBox, self, "Save", self.saveResults)
self.closeButton = OWGUI.button(self.manageBox, self, "Close Dialog", self.hide)
self.changeProjectionFile()
self.updateGUI()
if self.orderAllAttributes:
self.setAllAttributeRadio()
else:
self.setSubsetAttributeRadio()
def onDeleteWidget(self):
OWWidget.onDeleteWidget(self)
if self.__loop is not None:
self.__loop.close()
self.__loop = None
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
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)
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 saveSettings(self):
OWWidget.saveSettings(self)
self.optimizationDlg.saveSettings()
