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, 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, 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, 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
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):
OWWidget.__init__(self, parent, signalManager, 'ANOVA')
# input / output data: [("name1", [orange.ExampleTable1a,...]), ("name2", [orange.ExampleTable2a,...])]
self.inputs = [("Structured Data", DataFiles, self.onDataInput)]
self.outputs = [("Example Selection", ExampleSelection, Default), ("Selected Structured Data", DataFiles, Default), ("Other Structured Data", DataFiles)]
# data, p-values, selected examples
self.dataStructure = None # input data
self.numExamples = 0
self.numVariables = 0
self.ps = Numeric.ones((3,0), Numeric.Float) # p-values: 2D Numeric.array of shape (3, numExamples)
self.selectorName = "" # for Example Selection output: (self.selectorName, [0,1,0,...])
# Settings
self.anovaType = OWHypTest.StSST
self.popMean = 0 # single sample t-test, value to compare to
self.useFactors = [0,0,0] # [use factor A, use factor B, use interaction]
self._interaction = 0 # to store last setting: 0: no interaction, 1: test for interaction effect (set this value manually !!!)
self.selectorA = True
self.selectorB = False
self.selectorI = False
self.alphaA = "0.05"
self.alphaB = "0.05"
self.alphaI = "0.05"
self.autoUpdateSelName = 1
self.sendNotSelectedData = 1
self.sendProbabilities = 0
self.commitOnChange = 0
self.loadSettings()
# GUI
self.mainArea.setFixedWidth(0)
ca=QFrame(self.controlArea)
gl=QGridLayout(ca,4,1,5)
# info
box = QVGroupBox("Info", ca)
gl.addWidget(box,0,0)
self.infoa = QLabel('No data on input.', box)
self.infob = QLabel('', box)
self.infoc = QLabel('', box)
# ANOVA type
self.boxAnovaType = QVButtonGroup("Statistics", ca)
gl.addWidget(self.boxAnovaType,1,0)
self.boxAnovaType.setDisabled(1)
self.boxAnovaType.setRadioButtonExclusive(1)
self.boxAnovaType.buttons = []
## for i,lbl in enumerate(OWHypTest.StNames):
## w = QRadioButton(lbl, self.boxAnovaType)
## w.setOn(self.anovaType == i)
## self.boxAnovaType.buttons.append(w)
## if i == OWHypTest.StSST:
## self.boxPopMean = QHBox(self.boxAnovaType)
## QLabel(" population mean ", self.boxPopMean)
## OWGUI.lineEdit(self.boxPopMean, self, "popMean", callback=self.onPopMeanChange)
for i,lbl in enumerate(OWHypTest.StNames):
w = QRadioButton(lbl, self.boxAnovaType)
w.setOn(self.anovaType == i)
self.boxAnovaType.buttons.append(w)
if i == OWHypTest.StSST:
self.boxPopMean = QHBox(self.boxAnovaType)
QLabel(" population mean ", self.boxPopMean)
OWGUI.lineEdit(self.boxPopMean, self, "popMean", callback=self.onPopMeanChange)
OWGUI.connectControl(self.boxAnovaType, self, "anovaType", self.onAnovaType, "clicked(int)", OWGUI.CallFront_radioButtons(self.boxAnovaType))
# selection of examples
self.boxSelection = QVGroupBox("Example Selection", ca)
gl.addWidget(self.boxSelection,2,0)
self.lblNumGenes = [] # list of labels
# selector A
self.boxSelectorA = QVBox(self.boxSelection)
self.cbSelectorA = OWGUI.checkBox(self.boxSelectorA, self, "selectorA", "Factor A (variables)", callback=self.onSelectionChange,
tooltip='H0: The mean does not depend on factor A (represented by variables).')
frmA = QFrame(self.boxSelectorA)
glA = QGridLayout(frmA,1,3,5)
leA = OWGUI.lineEdit(frmA, self, "alphaA", orientation="horizontal", controlWidth=None, callback=lambda x=0: self.onAlphaChange(x))
glA.addWidget(leA,0,1) # Qt.AlignRight
glA.addWidget(QLabel(" p <= ", frmA), 0,0)
self.lblNumGenes.append(QLabel('', frmA))
glA.addWidget(self.lblNumGenes[-1],0,2) # Qt.AlignRight | 0x22
# selector B
self.boxSelectorB = QVBox(self.boxSelection)
self.cbSelectorB = OWGUI.checkBox(self.boxSelectorB, self, "selectorB", "Factor B (data sets)", callback=self.onSelectionChange,
tooltip='H0: The mean does not depend on factor B (represented by data sets).')
frmB = QFrame(self.boxSelectorB)
glB = QGridLayout(frmB,1,3,5)
leB = OWGUI.lineEdit(frmB, self, "alphaB", orientation="horizontal", callback=lambda x=1: self.onAlphaChange(x))
glB.addWidget(leB,0,1)
glB.addWidget(QLabel(" p <= ", frmB), 0,0)
self.lblNumGenes.append(QLabel('', frmB))
glB.addWidget(self.lblNumGenes[-1],0,2)
# selector I
self.boxSelectorI = QVBox(self.boxSelection)
self.cbSelectorI = OWGUI.checkBox(self.boxSelectorI, self, "selectorI", "Interaction (variables * data sets)", callback=self.onSelectionChange,
tooltip='H0: There is no interaction between factor A and factor B.')
frmI = QFrame(self.boxSelectorI)
glI = QGridLayout(frmI,1,3,5)
leI = OWGUI.lineEdit(frmI, self, "alphaI", orientation="horizontal", callback=lambda x=2: self.onAlphaChange(x))
## slider could be used to replace lineEdit (but not sensitive enough)
## self.alphaIf = 0.05
## leI = OWGUI.qwtHSlider(self.boxSelectorI, self, "alphaIf", box="", label=" p < ", labelWidth=None, minValue=0.0001, maxValue=1.0, step=0.1, precision=3, callback=lambda x=2: self.onAlphaChange(x), logarithmic=1, ticks=0, maxWidth=None)
glI.addWidget(leI,0,1)
glI.addWidget(QLabel(" p <= ", frmI), 0,0)
self.lblNumGenes.append(QLabel('', frmI))
glI.addWidget(self.lblNumGenes[-1],0,2)
# output
box = QVGroupBox("Output", ca)
gl.addWidget(box,3,0)
self.leSelectorName = OWGUI.lineEdit(box, self, 'selectorName', label='Selector Name: ')
self.leSelectorName.setReadOnly(self.autoUpdateSelName)
OWGUI.checkBox(box, self, 'autoUpdateSelName', 'Automatically update selector name', callback=self.onAutoUpdateSelNameChange)
OWGUI.checkBox(box, self, 'sendNotSelectedData', 'Send not selected data', callback=self.onSendNotSelectedChange)
OWGUI.checkBox(box, self, 'sendProbabilities', 'Show p-values', callback=self.onSendProbabilitiesChange)
OWGUI.checkBox(box, self, 'commitOnChange', 'Commit data on selection change', callback=lambda: self.onCommit(self.commitOnChange))
self.btnCommit = OWGUI.button(box, self, "Commit", callback=self.onCommit)
# enable/disable anova type box, example selection box, commit button, update the number of examples for individual selectors
self.updateAnovaTypeBox()
self.updateSelectorBox()
self.updateSelectorInfos()
self.updateSelectorName()
self.resize(283, self.sizeHint().height())
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,
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()
self.__in_progress_update = False
fbox = gui.widgetBox(self.controlArea, "Filter")
# The completer model token strings
self.completertokens = []
# A 'dynamic' completer item model will be updated with
# 'prefix {token}' where prefix is current 'active' filter list
# (the QCompleter only completes on one item in the model)
self.completermodel = QStringListModel(self)
self.completer = QCompleter(
self.completermodel, 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."
)
gui.rubber(box)
gui.lineEdit(box, self, "accessCode", "Access Code",
orientation="horizontal",
callback=self.RetrieveFilesList)
self.retryButton = gui.button(
box, self, "Retry", callback=self.RetrieveFilesList
)
self.retryButton.hide()
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.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):
OWWidget.__init__(self, parent, signalManager, 'ANOVA')
# input / output data: [("name1", [orange.ExampleTable1a,...]), ("name2", [orange.ExampleTable2a,...])]
self.inputs = [("Structured Data", DataFiles, self.onDataInput)]
self.outputs = [("Example Selection", ExampleSelection, Default), ("Selected Structured Data", DataFiles, Default), ("Other Structured Data", DataFiles)]
# data, p-values, selected examples
self.dataStructure = None # input data
self.numExamples = 0
self.numVariables = 0
self.ps = None # p-values: 2D Numeric.array of shape (3, numExamples)
self.selectorName = "" # for Example Selection output: (self.selectorName, [0,1,0,...])
# Settings
self.anovaType = 0 # 0: single-sample t-test, 1: one-way (A), 2: one-way (B), 3: two-way (A,B), 4: ful factorial (A, B, A*B)
self.compareToValue = 0 # single sample t-test, value to compare to
self._interaction = 0 # 0: no interaction, 1: test for interaction effect (set this value manually !!!)
self.selectorA = True
self.selectorB = False
self.selectorI = False
self.alphaA = "0.05"
self.alphaB = "0.05"
self.alphaI = "0.05"
self.autoUpdateSelName = 1
self.sendNotSelectedData = 1
self.sendProbabilities = 0
self.commitOnChange = 0
self.loadSettings()
# GUI
self.mainArea.setFixedWidth(0)
ca = self.controlArea
# info
box = OWGUI.widgetBox(ca, "Info")
#gl.addWidget(box,0,0)
self.infoa = OWGUI.label(box, self, 'No data on input.')
self.infob = OWGUI.label(box, self, "")
self.infoc = OWGUI.label(box, self, "")
# ANOVA type
# group selection
anovaTypes = ["Single sample t-test",
"Single-factor (A, variables)",
"Single-factor (B, data sets)",
"Two-factor",
"Two-factor with interaction effect"]
self.boxAnovaType = OWGUI.widgetBox(ca, "Anova Type")
self.anovaTypeS = OWGUI.radioButtonsInBox(self.boxAnovaType, self, "anovaType", btnLabels=anovaTypes)
self.boxAnovaType.setDisabled(1)
self.boxCompareTo = OWGUI.widgetBox(self.boxAnovaType)
OWGUI.lineEdit(self.boxCompareTo, self, "compareToValue", callback=self.onCompareToChange, label="compare to")
# selection of examples
self.boxSelection = OWGUI.widgetBox(ca, "Example Selection")
self.lblNumGenes = [] # list of labels
# selector A
self.boxSelectorA = OWGUI.widgetBox(self.boxSelection)
self.cbSelectorA = OWGUI.checkBox(self.boxSelectorA, self, "selectorA", "Factor A (variables)", callback=self.onSelectionChange,
tooltip='H0: The mean does not depend on factor A (represented by variables).')
frmA = OWGUI.widgetBox(self.boxSelectorA)
leA = OWGUI.lineEdit(frmA, self, "alphaA", orientation="horizontal", callback=lambda x=0: self.onAlphaChange(x), label= "p <= ")
self.lblNumGenes.append(OWGUI.label(frmA, self, ""))
# selector B
self.boxSelectorB = OWGUI.widgetBox(self.boxSelection)
self.cbSelectorB = OWGUI.checkBox(self.boxSelectorB, self, "selectorB", "Factor B (data sets)", callback=self.onSelectionChange,
tooltip='H0: The mean does not depend on factor B (represented by data sets).')
frmB = OWGUI.widgetBox(self.boxSelectorB)
leB = OWGUI.lineEdit(frmB, self, "alphaB", orientation="horizontal", callback=lambda x=1: self.onAlphaChange(x), label= "p <= ")
self.lblNumGenes.append(OWGUI.label(frmB, self, ""))
# selector I
self.boxSelectorI = OWGUI.widgetBox(self.boxSelection)
self.cbSelectorI = OWGUI.checkBox(self.boxSelectorI, self, "selectorI", "Interaction (variables * data sets)", callback=self.onSelectionChange,
tooltip='H0: There is no interaction between factor A and factor B.')
frmI = OWGUI.widgetBox(self.boxSelectorI)
leI = OWGUI.lineEdit(frmI, self, "alphaI", orientation="horizontal", callback=lambda x=2: self.onAlphaChange(x), label= "p <= ")
self.lblNumGenes.append(OWGUI.label(frmI, self, ""))
# output
box = OWGUI.widgetBox(ca, "Output")
self.leSelectorName = OWGUI.lineEdit(box, self, 'selectorName', label='Selector Name: ')
self.leSelectorName.setReadOnly(self.autoUpdateSelName)
OWGUI.checkBox(box, self, 'autoUpdateSelName', 'Automatically update selector name', callback=self.onAutoUpdateSelNameChange)
OWGUI.checkBox(box, self, 'sendNotSelectedData', 'Send not selected data', callback=self.onSendNotSelectedChange)
OWGUI.checkBox(box, self, 'sendProbabilities', 'Show p-values', callback=self.onSendProbabilitiesChange)
OWGUI.checkBox(box, self, 'commitOnChange', 'Commit data on selection change', callback=lambda: self.onCommit(self.commitOnChange))
self.btnCommit = OWGUI.button(box, self, "Commit", callback=self.onCommit)
# enable/disable anova type box, example selection box, commit button, update the number of examples for individual selectors
self.updateAnovaTypeBox()
self.updateSelectorBox()
self.updateSelectorInfos()
self.updateSelectorName()
self.resize(283, self.sizeHint().height())
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):
OWWidget.__init__(self, parent, signalManager, "MeshBrowser")
self.inputs = [("Reference data", ExampleTable, self.getReferenceData),
("Cluster data", ExampleTable, self.getClusterData)]
self.outputs = [("Selected examples", ExampleTable)]
# widget variables
self.loadedRef = 0
self.loadedClu = 0
self.maxPValue = 0.05
self.minExamplesInTerm = 5
self.multi = 1
self.reference = None
self.cluster = None
self.loadSettings()
self.mesh = obiMeSH() # main object is created
self.dataLoaded = self.mesh.dataLoaded
# left pane
box = OWGUI.widgetBox(self.controlArea, "Info")
#box = QGroupBox("Info", self.controlArea)
self.infoa = OWGUI.label(box, self, "No reference data.")
self.infob = OWGUI.label(box, self, "No cluster data.")
self.ratio = OWGUI.label(box, self, "")
self.ref_att = OWGUI.label(box, self, "")
self.clu_att = OWGUI.label(box, self, "")
self.resize(960, 600)
OWGUI.separator(self.controlArea)
self.optionsBox = OWGUI.widgetBox(self.controlArea, "Options")
self.maxp = OWGUI.lineEdit(self.optionsBox,
self,
"maxPValue",
label="threshold:",
orientation="horizontal",
labelWidth=120,
valueType=float)
self.minf = OWGUI.lineEdit(self.optionsBox,
self,
"minExamplesInTerm",
label="min. frequency:",
orientation="horizontal",
labelWidth=120,
valueType=int)
#OWGUI.checkBox(self.optionsBox, self, 'multi', 'Multiple selection', callback= self.checkClicked)
OWGUI.button(self.optionsBox, self, "Refresh", callback=self.refresh)
# right pane
self.col_size = [280, 84, 84, 100, 110]
self.sort_col = 0
self.sort_dir = True
self.columns = [
'MeSH term', '# reference', '# cluster', 'p value',
'fold enrichment'
] # both datasets
self.splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(self.splitter)
# list view
self.meshLV = QTreeWidget(self.splitter)
#self.meshLV.setSelectionMode(QAbstractItemView.MultiSelection)
self.meshLV.setAllColumnsShowFocus(1)
self.meshLV.setColumnCount(len(self.columns))
self.meshLV.setHeaderLabels(self.columns)
self.meshLV.header().setClickable(True)
#self.meshLV.header().setSortIndicatorShown(True)
#self.meshLV.setSortingEnabled(True)
self.meshLV.setRootIsDecorated(True)
self.connect(self.meshLV, SIGNAL("itemSelectionChanged()"),
self.viewSelectionChanged)
#self.meshLV.setItemDelegateForColumn(3, EnrichmentColumnItemDelegate(self))
#self.tooltips = ListViewToolTip(self.meshLV,0, self.mesh.toDesc)
# table of significant mesh terms
self.sigTermsTable = QTableWidget(self.splitter)
self.sigTermsTable.setColumnCount(len(self.columns))
self.sigTermsTable.setRowCount(4)
## hide the vertical header
self.sigTermsTable.verticalHeader().hide()
#self.sigTermsTable.setLeftMargin(0)
#self.sigTermsTable.setSelectionMode(QAbstractItemView.MultiSelection)
for i in range(0, len(self.columns)):
self.sigTermsTable.horizontalHeader().resizeSection(
i, self.col_size[i])
self.meshLV.header().resizeSection(i, self.col_size[i])
self.sigTermsTable.setHorizontalHeaderLabels(self.columns)
self.connect(self.sigTermsTable, SIGNAL("itemSelectionChanged()"),
self.tableSelectionChanged)
self.connect(self.sigTermsTable,
SIGNAL("clicked(int,int,int,const QPoint&)"),
self.tableClicked)
self.splitter.show()
self.optionsBox.setDisabled(1)
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 __init__(self, parent=None, signalManager=None):
OWWidget.__init__(self, parent, signalManager, "MeshBrowser")
self.inputs = [("Reference data", ExampleTable, self.getReferenceData), ("Cluster data", ExampleTable, self.getClusterData)]
self.outputs = [("Selected examples", ExampleTable)]
# widget variables
self.loadedRef = 0
self.loadedClu = 0
self.maxPValue = 0.05
self.minExamplesInTerm = 5
self.multi = 1
self.reference = None
self.cluster = None
self.loadSettings()
self.mesh = obiMeSH() # main object is created
self.dataLoaded = self.mesh.dataLoaded
# left pane
box = OWGUI.widgetBox(self.controlArea, "Info")
#box = QGroupBox("Info", self.controlArea)
self.infoa = OWGUI.label(box, self, "No reference data.")
self.infob = OWGUI.label(box, self, "No cluster data.")
self.ratio = OWGUI.label(box, self, "")
self.ref_att = OWGUI.label(box, self, "")
self.clu_att = OWGUI.label(box, self, "")
self.resize(960, 600)
OWGUI.separator(self.controlArea)
self.optionsBox = OWGUI.widgetBox(self.controlArea, "Options")
self.maxp = OWGUI.lineEdit(self.optionsBox, self, "maxPValue", label="threshold:", orientation="horizontal", labelWidth=120, valueType=float)
self.minf = OWGUI.lineEdit(self.optionsBox, self, "minExamplesInTerm", label="min. frequency:", orientation="horizontal", labelWidth=120, valueType=int)
#OWGUI.checkBox(self.optionsBox, self, 'multi', 'Multiple selection', callback= self.checkClicked)
OWGUI.button(self.optionsBox, self, "Refresh", callback=self.refresh)
# right pane
self.col_size = [280, 84, 84, 100, 110]
self.sort_col = 0
self.sort_dir = True
self.columns = ['MeSH term', '# reference', '# cluster', 'p value', 'fold enrichment'] # both datasets
self.splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(self.splitter)
# list view
self.meshLV = QTreeWidget(self.splitter)
#self.meshLV.setSelectionMode(QAbstractItemView.MultiSelection)
self.meshLV.setAllColumnsShowFocus(1)
self.meshLV.setColumnCount(len(self.columns))
self.meshLV.setHeaderLabels(self.columns)
self.meshLV.header().setClickable(True)
#self.meshLV.header().setSortIndicatorShown(True)
#self.meshLV.setSortingEnabled(True)
self.meshLV.setRootIsDecorated(True)
self.connect(self.meshLV, SIGNAL("itemSelectionChanged()"), self.viewSelectionChanged)
#self.meshLV.setItemDelegateForColumn(3, EnrichmentColumnItemDelegate(self))
#self.tooltips = ListViewToolTip(self.meshLV,0, self.mesh.toDesc)
# table of significant mesh terms
self.sigTermsTable = QTableWidget(self.splitter)
self.sigTermsTable.setColumnCount(len(self.columns))
self.sigTermsTable.setRowCount(4)
## hide the vertical header
self.sigTermsTable.verticalHeader().hide()
#self.sigTermsTable.setLeftMargin(0)
#self.sigTermsTable.setSelectionMode(QAbstractItemView.MultiSelection)
for i in range(0, len(self.columns)):
self.sigTermsTable.horizontalHeader().resizeSection(i, self.col_size[i])
self.meshLV.header().resizeSection(i, self.col_size[i])
self.sigTermsTable.setHorizontalHeaderLabels(self.columns)
self.connect(self.sigTermsTable, SIGNAL("itemSelectionChanged()"), self.tableSelectionChanged)
self.connect(self.sigTermsTable, SIGNAL("clicked(int,int,int,const QPoint&)"), self.tableClicked)
self.splitter.show()
self.optionsBox.setDisabled(1)
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()
