def __init__(self, parent=None, **kwargs):
# type: (Optional[QWidget], Any) -> None
super().__init__(parent, **kwargs)
self.setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Expanding)
self.__model = QStandardItemModel() # type: QAbstractItemModel
self.__flattened = False
self.__actionRole = Qt.UserRole
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
view = QTreeView(objectName="tool-tree-view")
view.setUniformRowHeights(True)
view.setFrameStyle(QTreeView.NoFrame)
view.setModel(self.__model)
view.setRootIsDecorated(False)
view.setHeaderHidden(True)
view.setItemsExpandable(True)
view.setEditTriggers(QTreeView.NoEditTriggers)
view.activated.connect(self.__onActivated)
view.clicked.connect(self.__onActivated)
view.entered.connect(self.__onEntered)
view.installEventFilter(self)
self.__view = view # type: QTreeView
layout.addWidget(view)
self.setLayout(layout)
def __init__(self):
super().__init__()
self.source = None
self.group_index = -1
self.filter_text = ""
self.group_cb = gui.comboBox(self.controlArea, self, "group_index")
self.group_cb.activated[int].connect(self.set_group_index)
# TODO: to avoid this, marker genes table should have 'tax_id' column
self.map_group_to_taxid = {'Human': '9606', 'Mouse': '10090'}
filter = gui.lineEdit(self.controlArea, self,
"filter_text") # type: QLineEdit
filter.setPlaceholderText("Filter...")
filter.textEdited.connect(self.set_filter_str)
self.view = view = QTreeView(
rootIsDecorated=False,
uniformRowHeights=True,
selectionMode=QTreeView.ExtendedSelection,
sortingEnabled=True,
)
self.proxy_model = FilterProxyModel(
self,
filterCaseSensitivity=Qt.CaseInsensitive,
)
view.setModel(self.proxy_model)
view.selectionModel().selectionChanged.connect(
self._on_selection_changed)
view.viewport().setMouseTracking(True)
self.controlArea.layout().addWidget(view)
self.read_data()
if self.header_state:
view.header().restoreState(self.header_state)
def __setupUi(self):
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
view = QTreeView(objectName="tool-tree-view")
view.setUniformRowHeights(True)
view.setFrameStyle(QTreeView.NoFrame)
view.setModel(self.__model)
view.setRootIsDecorated(False)
view.setHeaderHidden(True)
view.setItemsExpandable(True)
view.setEditTriggers(QTreeView.NoEditTriggers)
view.setItemDelegate(ToolTreeItemDelegate(self))
view.activated.connect(self.__onActivated)
view.clicked.connect(self.__onActivated)
view.entered.connect(self.__onEntered)
view.installEventFilter(self)
self.__view = view
layout.addWidget(view)
self.setLayout(layout)
def main(argv):
app = QApplication(argv)
mw = QMainWindow()
dock = CollapsibleDockWidget()
w1 = QTreeView()
w1.header().hide()
w2 = QToolButton()
w2.setFixedSize(38, 200)
dock.setExpandedWidget(w1)
dock.setCollapsedWidget(w2)
mw.addDockWidget(Qt.LeftDockWidgetArea, dock)
mw.setCentralWidget(QTextEdit())
mw.show()
a = QAction("Expand",
mw,
checkable=True,
shortcut=QKeySequence(Qt.ControlModifier | Qt.Key_D))
a.triggered[bool].connect(dock.setExpanded)
mw.addAction(a)
return app.exec()
def test_settings_model(self):
store = QSettings(
QSettings.IniFormat,
QSettings.UserScope,
"biolab.si",
"Orange Canvas UnitTests",
)
defaults = [
config_slot("S1", bool, True, "Something"),
config_slot("S2", str, "I an not a String",
"Disregard the string."),
]
settings = Settings(defaults=defaults, store=store)
model = UserSettingsModel(settings=settings)
self.assertEqual(model.rowCount(), len(settings))
view = QTreeView()
view.setHeaderHidden(False)
view.setModel(model)
view.show()
self.app.exec_()
def _setup_gui_labels(self):
vlayout = QVBoxLayout()
vlayout.setContentsMargins(0, 0, 0, 0)
vlayout.setSpacing(1)
self.labels_edit = QTreeView()
self.labels_edit.setEditTriggers(QTreeView.CurrentChanged)
self.labels_edit.setRootIsDecorated(False)
self.labels_model = DictItemsModel()
self.labels_edit.setModel(self.labels_model)
self.labels_edit.selectionModel().selectionChanged.connect(
self.on_label_selection_changed)
# Necessary signals to know when the labels change
self.labels_model.dataChanged.connect(self.on_labels_changed)
self.labels_model.rowsInserted.connect(self.on_labels_changed)
self.labels_model.rowsRemoved.connect(self.on_labels_changed)
vlayout.addWidget(self.labels_edit)
hlayout = QHBoxLayout()
hlayout.setContentsMargins(0, 0, 0, 0)
hlayout.setSpacing(1)
self.add_label_action = QAction(
"+",
self,
toolTip="Add a new label.",
triggered=self.on_add_label,
enabled=False,
shortcut=QKeySequence(QKeySequence.New),
)
self.remove_label_action = QAction(
unicodedata.lookup("MINUS SIGN"),
self,
toolTip="Remove selected label.",
triggered=self.on_remove_label,
enabled=False,
shortcut=QKeySequence(QKeySequence.Delete),
)
button_size = gui.toolButtonSizeHint()
button_size = QSize(button_size, button_size)
button = QToolButton(self)
button.setFixedSize(button_size)
button.setDefaultAction(self.add_label_action)
hlayout.addWidget(button)
button = QToolButton(self)
button.setFixedSize(button_size)
button.setDefaultAction(self.remove_label_action)
hlayout.addWidget(button)
hlayout.addStretch(10)
vlayout.addLayout(hlayout)
self.main_form.addRow("Labels:", vlayout)
def __init__(self, parent=None, **kwargs):
super(AddonManagerWidget, self).__init__(parent, **kwargs)
#: list of Available | Installed
self.__items = []
self.setLayout(QVBoxLayout())
self.__header = QLabel(
wordWrap=True,
textFormat=Qt.RichText
)
self.__search = QLineEdit(
placeholderText=self.tr("Filter")
)
self.layout().addWidget(self.__search)
self.__view = view = QTreeView(
rootIsDecorated=False,
editTriggers=QTreeView.NoEditTriggers,
selectionMode=QTreeView.SingleSelection,
alternatingRowColors=True
)
self.__view.setItemDelegateForColumn(0, TristateCheckItemDelegate())
self.layout().addWidget(view)
self.__model = model = QStandardItemModel()
model.setHorizontalHeaderLabels(["", "Name", "Version", "Action"])
model.dataChanged.connect(self.__data_changed)
proxy = QSortFilterProxyModel(
filterKeyColumn=1,
filterCaseSensitivity=Qt.CaseInsensitive
)
proxy.setSourceModel(model)
self.__search.textChanged.connect(proxy.setFilterFixedString)
view.setModel(proxy)
view.selectionModel().selectionChanged.connect(
self.__update_details
)
header = self.__view.header()
header.setSectionResizeMode(0, QHeaderView.Fixed)
header.setSectionResizeMode(2, QHeaderView.ResizeToContents)
self.__details = QTextBrowser(
frameShape=QTextBrowser.NoFrame,
readOnly=True,
lineWrapMode=QTextBrowser.WidgetWidth,
openExternalLinks=True,
)
self.__details.setWordWrapMode(QTextOption.WordWrap)
palette = QPalette(self.palette())
palette.setColor(QPalette.Base, Qt.transparent)
self.__details.setPalette(palette)
self.layout().addWidget(self.__details)
def __init__(self):
super().__init__()
self._data = None
self._available_db_sources = None
self.output = None
self._timer = QTimer()
self._timer.timeout.connect(self._filter_table)
self._timer.setSingleShot(True)
self.info.set_input_summary("0")
self.info.set_output_summary("0")
box = gui.widgetBox(self.controlArea, 'Database', margin=0)
self.db_source_index = -1
self.db_source_cb = gui.comboBox(box, self, 'db_source_index')
self.db_source_cb.activated[int].connect(self.handle_source_changed)
box = gui.widgetBox(self.controlArea, 'Organism', margin=0)
self.group_index = -1
self.group_cb = gui.comboBox(box, self, 'group_index')
self.group_cb.activated[int].connect(self.set_group_index)
gui.rubber(self.controlArea)
gui.auto_commit(self.controlArea, self, "auto_commit", "Commit",
"Commit Automatically")
# TODO: to avoid this, marker genes table should have 'tax_id' column
self.map_group_to_taxid = {'Human': '9606', 'Mouse': '10090'}
filter_line_edit = gui.lineEdit(self.mainArea, self,
"filter_text") # type: QLineEdit
filter_line_edit.setPlaceholderText("Filter...")
filter_line_edit.textEdited.connect(self.call_filter_timer)
self.view = view = QTreeView(
rootIsDecorated=False,
uniformRowHeights=True,
selectionMode=QTreeView.ExtendedSelection,
sortingEnabled=True,
)
view.viewport().setMouseTracking(True)
self.mainArea.layout().addWidget(view)
self._load_data()
if self.header_state:
view.header().restoreState(self.header_state)
def setup_gui(self):
# control area
info_box = vBox(self.controlArea, 'Input info')
self.input_info = widgetLabel(info_box)
hierarchy_box = widgetBox(self.controlArea, "Entity Sets")
self.hierarchy_widget = QTreeWidget(self)
self.hierarchy_widget.setEditTriggers(QTreeView.NoEditTriggers)
self.hierarchy_widget.setHeaderLabels(HIERARCHY_HEADER_LABELS)
self.hierarchy_widget.itemClicked.connect(self.display_gene_sets)
hierarchy_box.layout().addWidget(self.hierarchy_widget)
self.commit_button = auto_commit(self.controlArea,
self,
"auto_commit",
"&Commit",
box=False)
# rubber(self.controlArea)
# main area
self.filter_proxy_model = QSortFilterProxyModel(self.data_view)
self.filter_proxy_model.setFilterKeyColumn(3)
self.data_view = QTreeView()
self.data_view.setModel(self.filter_proxy_model)
self.data_view.setAlternatingRowColors(True)
self.data_view.sortByColumn(2, Qt.DescendingOrder)
self.data_view.setSortingEnabled(True)
self.data_view.setSelectionMode(QTreeView.ExtendedSelection)
self.data_view.setEditTriggers(QTreeView.NoEditTriggers)
self.data_view.viewport().setMouseTracking(True)
self.data_view.setItemDelegateForColumn(
TERM, LinkStyledItemDelegate(self.data_view))
self.data_view.selectionModel().selectionChanged.connect(self.commit)
self.lineEdit_filter = lineEdit(self.mainArea, self, 'search_pattern',
'Filter gene sets:')
self.lineEdit_filter.setPlaceholderText('search pattern ...')
self.lineEdit_filter.textChanged.connect(
self.filter_proxy_model.setFilterRegExp)
self.mainArea.layout().addWidget(self.data_view)
def make_continent_view(self, type, callback, append_to):
cc = ContinentCountries()
if (type == 'rep'):
data = cc.rep_continents
elif (type == 'par'):
data = cc.par_continents
list = QTreeView()
model = QStandardItemModel(0, 1)
for key, values in sorted(data.items()):
continent = QStandardItem(key)
continent.setCheckable(True)
for country in values:
country = QStandardItem(country)
country.setCheckable(True)
continent.setChild(continent.rowCount(), country)
model.setItem(model.rowCount(), continent)
if (type == 'rep'):
self.rep_top_item = model.index(0, 0)
elif (type == 'par'):
self.par_top_item = model.index(0, 0)
model.itemChanged.connect(callback)
list.setModel(model)
list.setEditTriggers(QAbstractItemView.NoEditTriggers)
list.setHeaderHidden(True)
list.expandAll()
proxy_model = FindFilterProxyModel()
proxy_model.setSourceModel(model)
proxy_model.setFilterKeyColumn(-1)
list.setModel(proxy_model)
list.expandAll()
append_to.layout().addWidget(list)
return [list, proxy_model, model]
def setup_gui(self):
# control area
self.setup_control_area()
# main area
self.data_view = QTreeView()
self.setup_filter_model()
self.setup_filter_area()
self.data_view.setAlternatingRowColors(True)
self.data_view.sortByColumn(self.COUNT, Qt.DescendingOrder)
self.data_view.setSortingEnabled(True)
self.data_view.setSelectionMode(QTreeView.ExtendedSelection)
self.data_view.setEditTriggers(QTreeView.NoEditTriggers)
self.data_view.viewport().setMouseTracking(False)
self.data_view.setItemDelegateForColumn(self.TERM, LinkStyledItemDelegate(self.data_view))
self.mainArea.layout().addWidget(self.data_view)
self.data_view.header().setSectionResizeMode(QHeaderView.ResizeToContents)
self.assign_delegates()
def __init__(self, parent=None):
super().__init__(parent)
self.data = None
# Info
infobox = gui.widgetBox(self.controlArea, "Info")
self.info_label = gui.widgetLabel(infobox, "No data on input.")
# Link method
method_box = gui.widgetBox(self.controlArea, "Method")
gui.comboBox(method_box,
self,
"link_method",
items=LinkMethod.items(),
callback=self.__link_method_changed)
gui.separator(method_box)
self.skip_zeros_check = gui.checkBox(
method_box,
self,
"skip_zeros",
"Skip zero expressions",
enabled=self.link_method != LinkMethod.LOG_LINK,
callback=lambda: self.commit())
# Batch Variable Selection
header_shema = (("selected", ""), ("variable", "Variable"),
("count", "#"), ("score", "Score"))
header_labels = labels = [label for _, label in header_shema]
header = namedtuple("header", [tag for tag, _ in header_shema])
self.Header = header(*[index for index, _ in enumerate(labels)])
batch_box = gui.widgetBox(self.controlArea, "Batch Variable Selection")
self.view = QTreeView()
self.model = QStandardItemModel()
self.model.itemChanged.connect(self.__selected_batch_vars_changed)
self.model.setHorizontalHeaderLabels(header_labels)
batch_box.layout().addWidget(self.view)
self._setup_view()
gui.auto_commit(self.controlArea, self, "auto_commit", "Apply",
"Apply Automatically")
def __init__(self, data_objects, descriptor_schema, *args, **kwargs):
super().__init__(*args, **kwargs)
self.ow = kwargs.get('parent', None)
self._data_objects = data_objects
self.descriptor_schema = descriptor_schema
self.header_schema = None
self.header = None
# set layout
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(layout)
self.view = QTreeView()
self.view.setSortingEnabled(False)
self.view.setAlternatingRowColors(True)
self.view.setEditTriggers(QTreeView.NoEditTriggers)
self.view.setSelectionMode(QTreeView.SingleSelection)
self.model = QStandardItemModel()
self.display_data_objects()
self.layout().addWidget(self.view)
def __init__(self, parent=None):
super().__init__(parent)
self.geneMatcherSettings = [False, False, True, False]
self.data = None
self.referenceData = None
self.taxid_list = []
self.__genematcher = (None, fulfill(gene.matcher([])))
self.__invalidated = False
self.currentAnnotatedCategories = []
self.state = None
self.__state = OWSetEnrichment.Initializing
box = gui.widgetBox(self.controlArea, "Info")
self.infoBox = gui.widgetLabel(box, "Info")
self.infoBox.setText("No data on input.\n")
self.speciesComboBox = gui.comboBox(
self.controlArea,
self,
"speciesIndex",
"Species",
callback=self.__on_speciesIndexChanged)
box = gui.widgetBox(self.controlArea, "Entity names")
self.geneAttrComboBox = gui.comboBox(box,
self,
"geneattr",
"Entity feature",
sendSelectedValue=0,
callback=self.updateAnnotations)
cb = gui.checkBox(box,
self,
"genesinrows",
"Use feature names",
callback=self.updateAnnotations,
disables=[(-1, self.geneAttrComboBox)])
cb.makeConsistent()
# gui.button(box, self, "Gene matcher settings",
# callback=self.updateGeneMatcherSettings,
# tooltip="Open gene matching settings dialog")
self.referenceRadioBox = gui.radioButtonsInBox(
self.controlArea,
self,
"useReferenceData", ["All entities", "Reference set (input)"],
tooltips=[
"Use entire genome (for gene set enrichment) or all " +
"available entities for reference",
"Use entities from Reference Examples input signal " +
"as reference"
],
box="Reference",
callback=self.updateAnnotations)
box = gui.widgetBox(self.controlArea, "Entity Sets")
self.groupsWidget = QTreeWidget(self)
self.groupsWidget.setHeaderLabels(["Category"])
box.layout().addWidget(self.groupsWidget)
hLayout = QHBoxLayout()
hLayout.setSpacing(10)
hWidget = gui.widgetBox(self.mainArea, orientation=hLayout)
gui.spin(hWidget,
self,
"minClusterCount",
0,
100,
label="Entities",
tooltip="Minimum entity count",
callback=self.filterAnnotationsChartView,
callbackOnReturn=True,
checked="useMinCountFilter",
checkCallback=self.filterAnnotationsChartView)
pvalfilterbox = gui.widgetBox(hWidget, orientation="horizontal")
cb = gui.checkBox(pvalfilterbox,
self,
"useMaxPValFilter",
"p-value",
callback=self.filterAnnotationsChartView)
sp = gui.doubleSpin(
pvalfilterbox,
self,
"maxPValue",
0.0,
1.0,
0.0001,
tooltip="Maximum p-value",
callback=self.filterAnnotationsChartView,
callbackOnReturn=True,
)
sp.setEnabled(self.useMaxFDRFilter)
cb.toggled[bool].connect(sp.setEnabled)
pvalfilterbox.layout().setAlignment(cb, Qt.AlignRight)
pvalfilterbox.layout().setAlignment(sp, Qt.AlignLeft)
fdrfilterbox = gui.widgetBox(hWidget, orientation="horizontal")
cb = gui.checkBox(fdrfilterbox,
self,
"useMaxFDRFilter",
"FDR",
callback=self.filterAnnotationsChartView)
sp = gui.doubleSpin(
fdrfilterbox,
self,
"maxFDR",
0.0,
1.0,
0.0001,
tooltip="Maximum False discovery rate",
callback=self.filterAnnotationsChartView,
callbackOnReturn=True,
)
sp.setEnabled(self.useMaxFDRFilter)
cb.toggled[bool].connect(sp.setEnabled)
fdrfilterbox.layout().setAlignment(cb, Qt.AlignRight)
fdrfilterbox.layout().setAlignment(sp, Qt.AlignLeft)
self.filterLineEdit = QLineEdit(self, placeholderText="Filter ...")
self.filterCompleter = QCompleter(self.filterLineEdit)
self.filterCompleter.setCaseSensitivity(Qt.CaseInsensitive)
self.filterLineEdit.setCompleter(self.filterCompleter)
hLayout.addWidget(self.filterLineEdit)
self.mainArea.layout().addWidget(hWidget)
self.filterLineEdit.textChanged.connect(
self.filterAnnotationsChartView)
self.annotationsChartView = QTreeView(
alternatingRowColors=True,
sortingEnabled=True,
selectionMode=QTreeView.ExtendedSelection,
rootIsDecorated=False,
editTriggers=QTreeView.NoEditTriggers,
)
self.annotationsChartView.viewport().setMouseTracking(True)
self.mainArea.layout().addWidget(self.annotationsChartView)
contextEventFilter = gui.VisibleHeaderSectionContextEventFilter(
self.annotationsChartView)
self.annotationsChartView.header().installEventFilter(
contextEventFilter)
self.groupsWidget.itemClicked.connect(self.subsetSelectionChanged)
gui.auto_commit(self.controlArea, self, "autocommit", "Commit")
self.setBlocking(True)
task = EnsureDownloaded([(taxonomy.Taxonomy.DOMAIN,
taxonomy.Taxonomy.FILENAME),
(geneset.sfdomain, "index.pck")])
task.finished.connect(self.__initialize_finish)
self.setStatusMessage("Initializing")
self._executor = ThreadExecutor(parent=self,
threadPool=QThreadPool(self))
self._executor.submit(task)
def __init__(self):
super().__init__()
self.local_cache_path = os.path.join(data_dir(), self.DATASET_DIR)
self.__awaiting_state = None # type: Optional[_FetchState]
box = gui.widgetBox(self.controlArea, "Info")
self.infolabel = QLabel(text="Initializing...\n\n")
box.layout().addWidget(self.infolabel)
gui.widgetLabel(self.mainArea, "Filter")
self.filterLineEdit = QLineEdit(
textChanged=self.filter
)
self.mainArea.layout().addWidget(self.filterLineEdit)
self.splitter = QSplitter(orientation=Qt.Vertical)
self.view = QTreeView(
sortingEnabled=True,
selectionMode=QTreeView.SingleSelection,
alternatingRowColors=True,
rootIsDecorated=False,
editTriggers=QTreeView.NoEditTriggers,
)
box = gui.widgetBox(self.splitter, "Description", addToLayout=False)
self.descriptionlabel = QLabel(
wordWrap=True,
textFormat=Qt.RichText,
)
self.descriptionlabel = QTextBrowser(
openExternalLinks=True,
textInteractionFlags=(Qt.TextSelectableByMouse |
Qt.LinksAccessibleByMouse)
)
self.descriptionlabel.setFrameStyle(QTextBrowser.NoFrame)
# no (white) text background
self.descriptionlabel.viewport().setAutoFillBackground(False)
box.layout().addWidget(self.descriptionlabel)
self.splitter.addWidget(self.view)
self.splitter.addWidget(box)
self.splitter.setSizes([300, 200])
self.splitter.splitterMoved.connect(
lambda:
setattr(self, "splitter_state", bytes(self.splitter.saveState()))
)
self.mainArea.layout().addWidget(self.splitter)
self.controlArea.layout().addStretch(10)
gui.auto_commit(self.controlArea, self, "auto_commit", "Send Data")
model = QStandardItemModel(self)
model.setHorizontalHeaderLabels(HEADER)
proxy = QSortFilterProxyModel()
proxy.setSourceModel(model)
proxy.setFilterKeyColumn(-1)
proxy.setFilterCaseSensitivity(False)
self.view.setModel(proxy)
if self.splitter_state:
self.splitter.restoreState(self.splitter_state)
self.view.setItemDelegateForColumn(
Header.Size, SizeDelegate(self))
self.view.setItemDelegateForColumn(
Header.Local, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.view.setItemDelegateForColumn(
Header.Instances, NumericalDelegate(self))
self.view.setItemDelegateForColumn(
Header.Variables, NumericalDelegate(self))
self.view.resizeColumnToContents(Header.Local)
if self.header_state:
self.view.header().restoreState(self.header_state)
self.setBlocking(True)
self.setStatusMessage("Initializing")
self._executor = ThreadPoolExecutor(max_workers=1)
f = self._executor.submit(self.list_remote)
w = FutureWatcher(f, parent=self)
w.done.connect(self.__set_index)
def init_form(self):
self._form = QTreeView()
super(ControlFilesTree, self).init_form()
def __init__(self, parent=None, **kwargs):
super().__init__(parent, **kwargs)
self.var = None # type: Optional[Variable]
layout = QVBoxLayout()
self.setLayout(layout)
self.form = form = QFormLayout(
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow,
objectName="editor-form-layout")
layout.addLayout(self.form)
self.name_edit = QLineEdit(objectName="name-editor")
self.name_edit.editingFinished.connect(
lambda: self.name_edit.isModified() and self.on_name_changed())
form.addRow("Name:", self.name_edit)
vlayout = QVBoxLayout(margin=0, spacing=1)
self.labels_edit = view = QTreeView(
objectName="annotation-pairs-edit",
rootIsDecorated=False,
editTriggers=QTreeView.DoubleClicked | QTreeView.EditKeyPressed,
)
self.labels_model = model = DictItemsModel()
view.setModel(model)
view.selectionModel().selectionChanged.connect(
self.on_label_selection_changed)
agrp = QActionGroup(view, objectName="annotate-action-group")
action_add = QAction("+",
self,
objectName="action-add-label",
toolTip="Add a new label.",
shortcut=QKeySequence(QKeySequence.New),
shortcutContext=Qt.WidgetShortcut)
action_delete = QAction("\N{MINUS SIGN}",
self,
objectName="action-delete-label",
toolTip="Remove selected label.",
shortcut=QKeySequence(QKeySequence.Delete),
shortcutContext=Qt.WidgetShortcut)
agrp.addAction(action_add)
agrp.addAction(action_delete)
view.addActions([action_add, action_delete])
def add_label():
row = [QStandardItem(), QStandardItem()]
model.appendRow(row)
idx = model.index(model.rowCount() - 1, 0)
view.setCurrentIndex(idx)
view.edit(idx)
def remove_label():
rows = view.selectionModel().selectedRows(0)
if rows:
assert len(rows) == 1
idx = rows[0].row()
model.removeRow(idx)
action_add.triggered.connect(add_label)
action_delete.triggered.connect(remove_label)
agrp.setEnabled(False)
self.add_label_action = action_add
self.remove_label_action = action_delete
# Necessary signals to know when the labels change
model.dataChanged.connect(self.on_labels_changed)
model.rowsInserted.connect(self.on_labels_changed)
model.rowsRemoved.connect(self.on_labels_changed)
vlayout.addWidget(self.labels_edit)
hlayout = QHBoxLayout()
hlayout.setContentsMargins(0, 0, 0, 0)
button = FixedSizeButton(
self,
defaultAction=self.add_label_action,
accessibleName="Add",
)
hlayout.addWidget(button)
button = FixedSizeButton(
self,
defaultAction=self.remove_label_action,
accessibleName="Remove",
)
hlayout.addWidget(button)
hlayout.addStretch(10)
vlayout.addLayout(hlayout)
form.addRow("Labels:", vlayout)
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_form(self):
self._form = QTreeView()
def __init__(
self,
parent=None,
):
super().__init__(self, parent)
self.selectionChangedFlag = False
self.__initialized = False
self.initfuture = None
self.itemsfuture = None
self.infoLabel = gui.widgetLabel(
gui.widgetBox(self.controlArea, "Info", addSpace=True),
"Initializing\n")
self.organisms = None
self.organismBox = gui.widgetBox(self.controlArea,
"Organism",
addSpace=True)
self.organismComboBox = gui.comboBox(
self.organismBox,
self,
"organism_index",
callback=self._onSelectedOrganismChanged)
# For now only support one alt source, with a checkbox
# In the future this can be extended to multiple selections
self.altSourceCheck = gui.checkBox(self.organismBox,
self,
"useAltSource",
"Show information from dictyBase",
callback=self.onAltSourceChange)
self.altSourceCheck.hide()
box = gui.widgetBox(self.controlArea, "Gene names", addSpace=True)
self.geneAttrComboBox = gui.comboBox(box,
self,
"gene_attr",
"Gene attribute",
callback=self.updateInfoItems)
self.geneAttrComboBox.setEnabled(not self.useAttr)
cb = gui.checkBox(box,
self,
"useAttr",
"Use attribute names",
callback=self.updateInfoItems)
cb.toggled[bool].connect(self.geneAttrComboBox.setDisabled)
gui.auto_commit(self.controlArea, self, "auto_commit", "Commit")
# A label for dictyExpress link (Why oh god why???)
self.dictyExpressBox = gui.widgetBox(self.controlArea, "Dicty Express")
self.linkLabel = gui.widgetLabel(self.dictyExpressBox, "")
self.linkLabel.setOpenExternalLinks(False)
self.linkLabel.linkActivated.connect(self.onDictyExpressLink)
self.dictyExpressBox.hide()
gui.rubber(self.controlArea)
gui.lineEdit(self.mainArea,
self,
"search_string",
"Filter",
callbackOnType=True,
callback=self.searchUpdate)
self.treeWidget = QTreeView(self.mainArea,
selectionMode=QTreeView.ExtendedSelection,
rootIsDecorated=False,
uniformRowHeights=True,
sortingEnabled=True)
self.treeWidget.setItemDelegate(
gui.LinkStyledItemDelegate(self.treeWidget))
self.treeWidget.viewport().setMouseTracking(True)
self.mainArea.layout().addWidget(self.treeWidget)
box = gui.widgetBox(self.mainArea, "", orientation="horizontal")
gui.button(box, self, "Select Filtered", callback=self.selectFiltered)
gui.button(box,
self,
"Clear Selection",
callback=self.treeWidget.clearSelection)
self.geneinfo = []
self.cells = []
self.row2geneinfo = {}
self.data = None
# : (# input genes, # matches genes)
self.matchedInfo = 0, 0
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):
super().__init__()
# OWWidget.__init__(self)
ConcurrentWidgetMixin.__init__(self)
# Control area
box = vBox(self.controlArea, True, margin=0)
self.gs_selection_component: GeneSetSelection = GeneSetSelection(self, box)
self.gs_selection_component.selection_changed.connect(self._on_selection_changed)
self.reference_radio_box = radioButtonsInBox(
self.controlArea,
self,
'use_reference_data',
['Entire genome', 'Reference gene set (input)'],
tooltips=['Use entire genome (for gene set enrichment)', 'Use reference set of genes'],
box='Reference',
callback=self._on_selection_changed,
)
self.reference_radio_box.setEnabled(False)
self.reference_genes: Optional[List[str]] = None
# Main area
self.filter_proxy_model = FilterProxyModel()
self.filter_proxy_model.setFilterKeyColumn(Header.term)
self.tree_view = QTreeView()
self.tree_view.setAlternatingRowColors(True)
self.tree_view.setSortingEnabled(True)
self.tree_view.sortByColumn(Header.count, Qt.DescendingOrder)
self.tree_view.setSelectionMode(QTreeView.ExtendedSelection)
self.tree_view.setEditTriggers(QTreeView.NoEditTriggers)
self.tree_view.viewport().setMouseTracking(True)
self.tree_view.setItemDelegateForColumn(Header.term, LinkStyledItemDelegate(self.tree_view))
self.tree_view.setItemDelegateForColumn(Header.genes, NumericalColumnDelegate(self))
self.tree_view.setItemDelegateForColumn(Header.count, NumericalColumnDelegate(self))
self.tree_view.setItemDelegateForColumn(Header.p_val, NumericalColumnDelegate(self, precision=2, notation='e'))
self.tree_view.setItemDelegateForColumn(Header.fdr, NumericalColumnDelegate(self, precision=2, notation='e'))
self.tree_view.setItemDelegateForColumn(Header.enrichment, NumericalColumnDelegate(self, precision=1))
self.tree_view.setItemDelegateForColumn(Header.reference, NumericalColumnDelegate(self))
self.tree_view.setModel(self.filter_proxy_model)
h_layout = QHBoxLayout()
h_layout.setSpacing(100)
h_widget = widgetBox(self.mainArea, orientation=h_layout)
spin(
h_widget,
self,
'min_count',
0,
1000,
label='Count',
tooltip='Minimum genes count',
checked='use_min_count',
callback=self.filter_view,
callbackOnReturn=True,
checkCallback=self.filter_view,
)
doubleSpin(
h_widget,
self,
'max_p_value',
0.0,
1.0,
0.0001,
label='p-value',
tooltip='Maximum p-value of the enrichment score',
checked='use_p_value',
callback=self.filter_view,
callbackOnReturn=True,
checkCallback=self.filter_view,
)
doubleSpin(
h_widget,
self,
'max_fdr',
0.0,
1.0,
0.0001,
label='FDR',
tooltip='Maximum false discovery rate',
checked='use_max_fdr',
callback=self.filter_view,
callbackOnReturn=True,
checkCallback=self.filter_view,
)
self.line_edit_filter = lineEdit(h_widget, self, 'search_pattern')
self.line_edit_filter.setPlaceholderText('Filter gene sets ...')
self.line_edit_filter.textChanged.connect(self.filter_view)
self.mainArea.layout().addWidget(self.tree_view)
self.tree_view.header().setSectionResizeMode(QHeaderView.ResizeToContents)
self.commit_button = auto_commit(self.controlArea, self, 'auto_commit', '&Commit', box=False)
self.input_data: Optional[Table] = None
self.num_of_selected_genes: int = 0
self.gene_info: Optional[GeneInfo] = None
def __init__(
self,
parent=None,
):
super().__init__(self, parent)
self.selectionChangedFlag = False
self.__initialized = False
self.initfuture = None
self.itemsfuture = None
self.map_input_to_ensembl = None
self.infoLabel = gui.widgetLabel(
gui.widgetBox(self.controlArea, "Info", addSpace=True),
"Initializing\n")
self.organisms = None
self.organismBox = gui.widgetBox(self.controlArea,
"Organism",
addSpace=True)
self.organismComboBox = gui.comboBox(
self.organismBox,
self,
"organism_index",
callback=self._onSelectedOrganismChanged)
box = gui.widgetBox(self.controlArea, "Gene names", addSpace=True)
self.geneAttrComboBox = gui.comboBox(box,
self,
"gene_attr",
"Gene attribute",
callback=self.updateInfoItems)
self.geneAttrComboBox.setEnabled(not self.useAttr)
self.geneAttrCheckbox = gui.checkBox(box,
self,
"useAttr",
"Use column names",
callback=self.updateInfoItems)
self.geneAttrCheckbox.toggled[bool].connect(
self.geneAttrComboBox.setDisabled)
gui.auto_commit(self.controlArea, self, "auto_commit", "Commit")
gui.rubber(self.controlArea)
gui.lineEdit(self.mainArea,
self,
"search_string",
"Filter",
callbackOnType=True,
callback=self.searchUpdate)
self.treeWidget = QTreeView(self.mainArea)
self.treeWidget.setAlternatingRowColors(True)
self.treeWidget.setSortingEnabled(True)
self.treeWidget.setSelectionMode(QTreeView.ExtendedSelection)
self.treeWidget.setUniformRowHeights(True)
self.treeWidget.setRootIsDecorated(False)
self.treeWidget.setItemDelegateForColumn(
HEADER_SCHEMA['NCBI ID'],
gui.LinkStyledItemDelegate(self.treeWidget))
self.treeWidget.setItemDelegateForColumn(
HEADER_SCHEMA['Ensembl ID'],
gui.LinkStyledItemDelegate(self.treeWidget))
self.treeWidget.viewport().setMouseTracking(True)
self.mainArea.layout().addWidget(self.treeWidget)
box = gui.widgetBox(self.mainArea, "", orientation="horizontal")
gui.button(box, self, "Select Filtered", callback=self.selectFiltered)
gui.button(box,
self,
"Clear Selection",
callback=self.treeWidget.clearSelection)
self.geneinfo = []
self.cells = []
self.row2geneinfo = {}
self.data = None
# : (# input genes, # matches genes)
self.matchedInfo = 0, 0
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):
super().__init__()
self.local_cache_path = os.path.join(data_dir(), self.DATASET_DIR)
self._header_labels = [header['label'] for _, header in self.HEADER_SCHEMA]
self._header_index = namedtuple('_header_index', [info_tag for info_tag, _ in self.HEADER_SCHEMA])
self.Header = self._header_index(*[index for index, _ in enumerate(self._header_labels)])
self.__awaiting_state = None # type: Optional[_FetchState]
box = gui.widgetBox(self.controlArea, "Info")
self.infolabel = QLabel(text="Initializing...\n\n")
box.layout().addWidget(self.infolabel)
gui.widgetLabel(self.mainArea, "Filter")
self.filterLineEdit = QLineEdit(
textChanged=self.filter
)
self.mainArea.layout().addWidget(self.filterLineEdit)
self.splitter = QSplitter(orientation=Qt.Vertical)
self.view = QTreeView(
sortingEnabled=True,
selectionMode=QTreeView.SingleSelection,
alternatingRowColors=True,
rootIsDecorated=False,
editTriggers=QTreeView.NoEditTriggers,
uniformRowHeights=True,
)
box = gui.widgetBox(self.splitter, "Description", addToLayout=False)
self.descriptionlabel = QLabel(
wordWrap=True,
textFormat=Qt.RichText,
)
self.descriptionlabel = QTextBrowser(
openExternalLinks=True,
textInteractionFlags=(Qt.TextSelectableByMouse |
Qt.LinksAccessibleByMouse)
)
self.descriptionlabel.setFrameStyle(QTextBrowser.NoFrame)
# no (white) text background
self.descriptionlabel.viewport().setAutoFillBackground(False)
box.layout().addWidget(self.descriptionlabel)
self.splitter.addWidget(self.view)
self.splitter.addWidget(box)
self.splitter.setSizes([300, 200])
self.splitter.splitterMoved.connect(
lambda:
setattr(self, "splitter_state", bytes(self.splitter.saveState()))
)
self.mainArea.layout().addWidget(self.splitter)
self.controlArea.layout().addStretch(10)
gui.auto_commit(self.controlArea, self, "auto_commit", "Send Data")
proxy = QSortFilterProxyModel()
proxy.setFilterKeyColumn(-1)
proxy.setFilterCaseSensitivity(False)
self.view.setModel(proxy)
if self.splitter_state:
self.splitter.restoreState(self.splitter_state)
self.assign_delegates()
self.setBlocking(True)
self.setStatusMessage("Initializing")
self._executor = ThreadPoolExecutor(max_workers=1)
f = self._executor.submit(self.list_remote)
w = FutureWatcher(f, parent=self)
w.done.connect(self.__set_index)
def __init__(self):
super().__init__()
# OWWidget.__init__(self)
ConcurrentWidgetMixin.__init__(self)
# Control area
box = vBox(self.controlArea, True, margin=0)
self.gs_selection_component: GeneSetSelection = GeneSetSelection(
self, box)
self.gs_selection_component.selection_changed.connect(
self._on_selection_changed)
# Main area
self.filter_proxy_model = FilterProxyModel()
self.filter_proxy_model.setFilterKeyColumn(Header.term)
self.tree_view = QTreeView()
self.tree_view.setAlternatingRowColors(True)
self.tree_view.setSortingEnabled(True)
self.tree_view.sortByColumn(Header.count, Qt.DescendingOrder)
self.tree_view.setSelectionMode(QTreeView.ExtendedSelection)
self.tree_view.setEditTriggers(QTreeView.NoEditTriggers)
self.tree_view.viewport().setMouseTracking(True)
self.tree_view.setItemDelegateForColumn(
Header.term, LinkStyledItemDelegate(self.tree_view))
self.tree_view.setItemDelegateForColumn(Header.genes,
NumericalColumnDelegate(self))
self.tree_view.setItemDelegateForColumn(Header.count,
NumericalColumnDelegate(self))
self.tree_view.setModel(self.filter_proxy_model)
h_layout = QHBoxLayout()
h_layout.setSpacing(100)
h_widget = widgetBox(self.mainArea, orientation=h_layout)
spin(
h_widget,
self,
'min_count',
0,
1000,
label='Count',
tooltip='Minimum genes count',
checked='use_min_count',
callback=self.filter_view,
callbackOnReturn=True,
checkCallback=self.filter_view,
)
self.line_edit_filter = lineEdit(h_widget, self, 'search_pattern')
self.line_edit_filter.setPlaceholderText('Filter gene sets ...')
self.line_edit_filter.textChanged.connect(self.filter_view)
self.mainArea.layout().addWidget(self.tree_view)
self.tree_view.header().setSectionResizeMode(
QHeaderView.ResizeToContents)
self.commit_button = auto_commit(self.controlArea,
self,
'auto_commit',
'&Commit',
box=False)
self.input_data: Optional[Table] = None
self.num_of_selected_genes: int = 0
