def populate(self):
"""Fill combobox with samples from databases
"""
self.mother_combo.clear()
self.father_combo.clear()
self.child_combo.clear()
samples = [i["name"] for i in sql.get_samples(self.conn)]
for sample in samples:
self.mother_combo.addItem(FIcon(0xF1077), sample)
self.father_combo.addItem(FIcon(0xF0643), sample)
self.child_combo.addItem(FIcon(0xF0E7D), sample)
def __init__(self):
super().__init__()
self.setWindowTitle(self.tr("Network"))
self.setWindowIcon(FIcon(0xF0484))
self.combo_box = QComboBox()
self.host_edit = QLineEdit()
self.port_edit = QSpinBox()
self.user_edit = QLineEdit()
self.pass_edit = QLineEdit()
# Load proxy type
for key in network.PROXY_TYPES:
self.combo_box.addItem(key, network.PROXY_TYPES[key])
# edit restriction
self.pass_edit.setEchoMode(QLineEdit.PasswordEchoOnEdit)
f_layout = QFormLayout()
f_layout.addRow(self.tr("Type"), self.combo_box)
f_layout.addRow(self.tr("Proxy host"), self.host_edit)
f_layout.addRow(self.tr("Proxy Port"), self.port_edit)
f_layout.addRow(self.tr("Username"), self.user_edit)
f_layout.addRow(self.tr("Password"), self.pass_edit)
self.combo_box.currentIndexChanged.connect(self.on_combo_changed)
self.setLayout(f_layout)
def load_plugins(self):
""" Add plugins settings """
from cutevariant.gui import plugin
for extension in plugin.find_plugins():
if "setting" in extension:
settings_widget_class = extension["setting"]
if not settings_widget_class.ENABLE:
# Skip disabled plugins
continue
widget = settings_widget_class()
# Create rprefix settings ! For instance [VariantView]
# widget.prefix_settings = widget.__class__.__name__.replace(
# "SettingsWidget", ""
# )
if not widget.windowTitle():
widget.setWindowTitle(extension["name"])
if not widget.windowIcon():
widget.setWindowIcon(FIcon(0xF0431))
self.add_section(widget)
def __init__(self):
super().__init__()
self.setWindowTitle(self.tr("Translation"))
self.setWindowIcon(FIcon(0xF05CA))
self.locales_combobox = QComboBox()
mainLayout = QFormLayout()
mainLayout.addRow(self.tr("&Choose a locale:"), self.locales_combobox)
self.setLayout(mainLayout)
def __init__(self):
super().__init__()
self.setWindowTitle(self.tr("Path"))
self.setWindowIcon(FIcon(0xF1080))
self.edit = widgets.FileEdit()
self.edit.set_path_type("dir")
main_layout = QFormLayout()
main_layout.addRow("path", self.edit)
self.setLayout(main_layout)
def populate(self):
"""Actualize the list of word sets"""
self.view.clear()
self.set_names = list()
for data in get_wordsets(self.conn):
set_name = data["name"]
item = QListWidgetItem()
item.setText(set_name)
item.setIcon(FIcon(0xF0A38))
self.view.addItem(item)
self.set_names.append(set_name)
def __init__(self):
super().__init__()
self.setWindowTitle(self.tr("Plugins"))
self.setWindowIcon(FIcon(0xF0431))
self.view = QTreeWidget()
self.view.setColumnCount(3)
self.view.setHeaderLabels(["Name", "Description", "Version"])
self.view.header().setSectionResizeMode(QHeaderView.ResizeToContents)
main_layout = QVBoxLayout()
main_layout.addWidget(self.view)
self.setLayout(main_layout)
def setup_toolbar(self):
"""Top tool bar setup: items and actions
.. note:: Require selection_widget and some actions of Menubar
"""
# Tool bar
self.toolbar.setToolButtonStyle(Qt.ToolButtonTextUnderIcon)
self.toolbar.addAction(self.new_project_action)
self.toolbar.addAction(self.open_project_action)
self.toolbar.addAction(FIcon(0xF02D7), self.tr("Help"),
QWhatsThis.enterWhatsThisMode)
self.toolbar.addSeparator()
def __init__(self, parent=None):
super().__init__(parent)
self.setWindowTitle(self.tr("About Cutevariant"))
self.setWindowIcon(QIcon(cm.DIR_ICONS + "app.png"))
self.tab_widget = QTabWidget()
self.header_lbl = QLabel()
self.button_box = QDialogButtonBox()
github_button = self.button_box.addButton("GitHub", QDialogButtonBox.HelpRole)
twitter_button = self.button_box.addButton("Twitter", QDialogButtonBox.HelpRole)
self.button_box.addButton(QDialogButtonBox.Ok)
github_button.setIcon(FIcon(0xF02A4))
twitter_button.setIcon(FIcon(0xF0544))
vLayout = QVBoxLayout()
vLayout.addWidget(self.header_lbl)
vLayout.addWidget(self.tab_widget)
vLayout.addWidget(self.button_box)
self.setLayout(vLayout)
self.addTab("LICENSE")
# self.addTab("AUTHORS")
# self.addTab("CREDITS")
# self.addTab("CHANGELOG")
self.drawHeader()
# Connexions
self.button_box.button(QDialogButtonBox.Ok).clicked.connect(self.close)
github_button.clicked.connect(self.open_github_page)
twitter_button.clicked.connect(self.open_twitter_page)
self.resize(600, 400)
def __init__(self, parent=None):
super().__init__(parent)
self.conn = None
self.set_names = list()
self.setWindowTitle(self.tr("Word Sets"))
self.toolbar = QToolBar()
self.view = QListWidget()
self.view.setIconSize(QSize(20, 20))
self.view.itemDoubleClicked.connect(self.open_wordset)
self.view.setSelectionMode(QAbstractItemView.ExtendedSelection)
# setup tool bar
self.toolbar.setIconSize(QSize(16, 16))
self.toolbar.addAction(FIcon(0xF0415), self.tr("Add Word set"),
self.add_wordset)
self.edit_action = self.toolbar.addAction(FIcon(0xF0DC9),
self.tr("Edit Word set"),
self.open_wordset)
self.remove_action = self.toolbar.addAction(FIcon(0xF0A7A),
self.tr("Remove Word set"),
self.remove_wordset)
self.edit_action.setEnabled(False)
self.remove_action.setEnabled(False)
v_layout = QVBoxLayout()
v_layout.setContentsMargins(0, 0, 0, 0)
v_layout.setSpacing(0)
v_layout.addWidget(self.view)
v_layout.addWidget(self.toolbar)
self.setLayout(v_layout)
# Item selected in view
self.view.selectionModel().selectionChanged.connect(
self.on_item_selected)
def __init__(self):
"""Init StyleSettingsWidget
Args:
mainwindow (QMainWindow): Current main ui of cutevariant;
Used to refresh the plugins
"""
super().__init__()
self.setWindowTitle(self.tr("Styles"))
self.setWindowIcon(FIcon(0xF03D8))
self.styles_combobox = QComboBox()
mainLayout = QFormLayout()
mainLayout.addRow(self.tr("&Choose a style:"), self.styles_combobox)
self.setLayout(mainLayout)
def load_plugins(self):
""" Add plugins settings """
from cutevariant.gui import plugin
for extension in plugin.find_plugins():
if "setting" in extension:
settings_widget_class = extension["setting"]
if not settings_widget_class.ENABLE:
# Skip disabled plugins
continue
widget = settings_widget_class()
if not widget.windowTitle():
widget.setWindowTitle(extension["name"])
if not widget.windowIcon():
widget.setWindowIcon(FIcon(0xF0431))
self.addPanel(widget)
def __init__(self):
super().__init__()
self.group_parent = None
self.settings = QSettings()
self.setWindowTitle("base")
self.setWindowIcon(FIcon(0xF5CA))
def __init__(self):
super().__init__()
self.setWindowTitle("base")
self.setWindowIcon(FIcon(0xF5CA))
self.section_widget = None
def __init__(self, parent=None):
super().__init__(parent)
self.setWindowTitle(self.tr("Cutevariant - Settings"))
self.setWindowIcon(QIcon(cm.DIR_ICONS + "app.png"))
self.widgets = []
self.list_widget = QListWidget()
self.stack_widget = QStackedWidget()
self.button_box = QDialogButtonBox(
QDialogButtonBox.SaveAll | QDialogButtonBox.Cancel | QDialogButtonBox.Reset
)
self.list_widget.setFixedWidth(200)
self.list_widget.setIconSize(QSize(32, 32))
h_layout = QHBoxLayout()
h_layout.addWidget(self.list_widget)
h_layout.addWidget(self.stack_widget)
v_layout = QVBoxLayout()
v_layout.addLayout(h_layout)
v_layout.addWidget(self.button_box)
self.setLayout(v_layout)
# Instantiate subwidgets on panels
# Similar widgets for general configuration
general_settings = SectionWidget() # Not a title !
general_settings.setWindowTitle(self.tr("General"))
general_settings.setWindowIcon(FIcon(0xF0614))
general_settings.add_page(PathSettingsWidget())
# Cutevariant is not yet translated ..
# general_settings.add_page(TranslationSettingsWidget())
general_settings.add_page(ProxySettingsWidget())
general_settings.add_page(StyleSettingsWidget())
# Activation status of plugins
plugin_settings = PluginsSettingsWidget()
# BOF...
if parent:
plugin_settings.registerPlugin.connect(parent.register_plugin)
plugin_settings.deregisterPlugin.connect(parent.deregister_plugin)
# Specialized widgets on panels
self.add_section(general_settings)
# self.add_section(plugin_settings)
self.load_plugins()
self.resize(800, 400)
self.button_box.button(QDialogButtonBox.SaveAll).clicked.connect(self.save_all)
self.button_box.button(QDialogButtonBox.Reset).clicked.connect(self.load_all)
self.button_box.button(QDialogButtonBox.Cancel).clicked.connect(self.close)
# Connection events
self.list_widget.currentRowChanged.connect(self.stack_widget.setCurrentIndex)
# Load settings
self.load_all()
self.accepted.connect(self.close)
def __init__(self, parent=None, default_text=""):
"""Init Markdown editor
:param default_text: Populate source edit with current comment in db.
:type default_text: <str>
"""
super().__init__(parent)
self.setWindowTitle("Cutevariant - " + self.tr("Comment editor"))
self.setWindowIcon(QIcon(cm.DIR_ICONS + "app.png"))
main_vlayout = QVBoxLayout()
# main_vlayout.setContentsMargins(0, 0, 0, 0)
self.setLayout(main_vlayout)
# Setup edit view
self.rich_edit = QTextEdit() # Rich text result
self.source_edit = QPlainTextEdit() # Markdown content
self.source_edit.setPlainText(default_text)
vlayout = QVBoxLayout()
vlayout.setSpacing(1)
vlayout.setContentsMargins(0, 0, 0, 0)
main_vlayout.addLayout(vlayout)
self.splitter = QSplitter(Qt.Horizontal)
self.splitter.addWidget(self.source_edit)
if parse_version(pyside_version) >= parse_version("5.14"):
# RichText in Markdown is supported starting PySide 5.14
self.splitter.addWidget(self.rich_edit)
# self.rich_edit.setStyleSheet(
# "QWidget {background-color:'lightgray'}")
self.rich_edit.setAcceptRichText(True)
self.rich_edit.setAutoFormatting(QTextEdit.AutoAll)
self.rich_edit.setReadOnly(True)
# Update preview with Markdown content
self.source_edit.textChanged.connect(self.update_rich_text)
# Auto refresh rich text content now
self.update_rich_text()
# Setup toolbar
self.toolbar = QToolBar()
self.act_undo = self.toolbar.addAction(self.tr("undo"), self.source_edit.undo)
self.act_undo.setIcon(FIcon(0xF054C))
self.act_undo.setShortcut(QKeySequence.Undo)
self.act_redo = self.toolbar.addAction(self.tr("redo"), self.source_edit.redo)
self.act_redo.setIcon(FIcon(0xF044E))
self.act_redo.setShortcut(QKeySequence.Redo)
self.act_bold = self.toolbar.addAction(
self.tr("bold"), lambda: self.infix("**")
)
self.act_bold.setIcon(FIcon(0xF0264))
self.act_bold.setShortcut(QKeySequence("CTRL+B"))
self.act_italic = self.toolbar.addAction(
self.tr("italic"), lambda: self.infix("*")
)
self.act_italic.setIcon(FIcon(0xF0277))
self.act_italic.setShortcut(QKeySequence("CTRL+I"))
self.act_heading = self.toolbar.addAction(
self.tr("insert title"), lambda: self.heading()
)
self.act_heading.setShortcut(QKeySequence("CTRL+H"))
self.act_heading.setIcon(FIcon(0xF0274))
self.act_unorder_list = self.toolbar.addAction(
self.tr("insert list item"), self.unorder_list
)
self.act_unorder_list.setIcon(FIcon(0xF0279))
self.act_quote = self.toolbar.addAction(self.tr("quote"), self.quote)
self.act_quote.setIcon(FIcon(0xF027E))
self.act_link = self.toolbar.addAction(self.tr("insert link"), self.link)
self.act_link.setIcon(FIcon(0xF0339))
vlayout.addWidget(self.toolbar)
vlayout.addWidget(self.splitter)
# Add buttons
buttons = QDialogButtonBox(QDialogButtonBox.Save | QDialogButtonBox.Cancel)
buttons.accepted.connect(self.accept)
buttons.rejected.connect(self.reject)
main_vlayout.addWidget(buttons)
def __init__(self, parent=None):
super().__init__(parent)
self.setWindowTitle(self.tr("Info variants"))
# Current variant => set by on_refresh and on_open_project
self.current_variant = None
self.view = QTabWidget()
self.toolbar = QToolBar()
self.toolbar.setIconSize(QSize(16, 16))
# Build variant tab
self.variant_view = QTreeWidget()
self.variant_view.setColumnCount(2)
self.variant_view.setAlternatingRowColors(True)
# self.variant_view.setHeaderLabels(["Field", "Value"])
self.variant_view.header().setVisible(False)
self.view.addTab(self.variant_view, self.tr("Variant"))
# Build transcript tab
self.transcript_combo = QComboBox()
self.transcript_view = QTreeWidget()
self.transcript_view.setColumnCount(2)
self.transcript_view.setAlternatingRowColors(True)
# self.transcript_view.setHeaderLabels(["Field", "Value"])
self.transcript_view.header().setVisible(False)
tx_layout = QVBoxLayout()
tx_layout.addWidget(self.transcript_combo)
tx_layout.addWidget(self.transcript_view)
tx_widget = QWidget()
tx_widget.setLayout(tx_layout)
self.view.addTab(tx_widget, self.tr("Transcripts"))
self.transcript_combo.currentIndexChanged.connect(
self.on_transcript_changed)
# Build Samples tab
self.sample_combo = QComboBox()
self.sample_view = QTreeWidget()
self.sample_view.setAlternatingRowColors(True)
self.sample_view.setColumnCount(2)
# self.sample_view.setHeaderLabels(["Field", "Value"])
self.sample_view.header().setVisible(False)
tx_layout = QVBoxLayout()
tx_layout.addWidget(self.sample_combo)
tx_layout.addWidget(self.sample_view)
tx_widget = QWidget()
tx_widget.setLayout(tx_layout)
self.view.addTab(tx_widget, self.tr("Samples"))
self.sample_combo.currentIndexChanged.connect(self.on_sample_changed)
# Build genotype tab
self.genotype_view = QListWidget()
self.genotype_view.setIconSize(QSize(20, 20))
self.view.addTab(self.genotype_view, self.tr("Genotypes"))
# Build comments tab
# Build Editor
# TODO: edit comment on variant is disabled
self.comment_input = QTextBrowser()
self.comment_input.setAlignment(Qt.AlignTop | Qt.AlignLeft)
self.comment_input.setOpenExternalLinks(True)
self.editor = QWidget()
self.editor_layout = QVBoxLayout()
# Save comment functionality
# sub_edit_layout = QFormLayout()
# editor_layout.setRowWrapPolicy(QFormLayout.WrapAllRows)
# sub_edit_layout.addWidget(self.comment_input)
# sub_edit_layout.addWidget(self.save_button)
# self.save_button.clicked.connect(self.on_save_clicked)
self.editor_layout.addWidget(self.comment_input)
self.editor.setLayout(self.editor_layout)
self.view.addTab(self.editor, self.tr("Comments"))
v_layout = QVBoxLayout()
v_layout.setContentsMargins(0, 0, 0, 0)
v_layout.addWidget(self.view)
self.setLayout(v_layout)
# # Create menu
# TODO: restore this
# self.context_menu = VariantPopupMenu()
# # Ability to trigger the menu
# self.view.setContextMenuPolicy(Qt.CustomContextMenu)
# self.view.customContextMenuRequested.connect(self.show_menu)
# self.add_tab("variants")
# Cache all database fields and their descriptions for tooltips
# Field names as keys, descriptions as values
self.fields_descriptions = None
# Cache genotype icons
# Values in gt field as keys (str), FIcon as values
self.genotype_icons = {
key: FIcon(val)
for key, val in cm.GENOTYPE_ICONS.items()
}
def setup_menubar(self):
"""Menu bar setup: items and actions
.. note:: Setup tools menu that could be dynamically augmented by plugins.
"""
## File Menu
self.file_menu = self.menuBar().addMenu(self.tr("&File"))
self.new_project_action = self.file_menu.addAction(
FIcon(0xF01BA), self.tr("&New project"), self.new_project,
QKeySequence.New)
self.open_project_action = self.file_menu.addAction(
FIcon(0xF095D),
self.tr("&Open project..."),
self.open_project,
QKeySequence.Open,
)
### Recent projects
self.recent_files_menu = self.file_menu.addMenu(self.tr("Open recent"))
self.setup_recent_menu()
### Export projects as
self.export_csv_action = self.file_menu.addAction(
self.tr("Export as csv"), self.export_as_csv)
self.export_ped_action = self.file_menu.addAction(
self.tr("Export pedigree PED/PLINK"), self.export_ped)
self.file_menu.addSeparator()
### Misc
self.file_menu.addAction(FIcon(0xF0493), self.tr("Settings..."),
self.show_settings)
self.file_menu.addSeparator()
self.file_menu.addAction(self.tr("&Quit"), self.close,
QKeySequence.Quit)
## Edit
# TODO: if variant_view plugin is not loaded, disable this menu entries...
self.edit_menu = self.menuBar().addMenu(self.tr("&Edit"))
self.edit_menu.addAction(
FIcon(0xF018F),
self.tr("&Copy selected variants"),
self.copy_variants_to_clipboard,
"ctrl+shift+c",
)
self.edit_menu.addSeparator()
self.edit_menu.addAction(
FIcon(0xF0486),
self.tr("&Select all variants"),
self.select_all_variants,
QKeySequence.SelectAll,
)
## View
self.view_menu = self.menuBar().addMenu(self.tr("&View"))
self.view_menu.addAction(self.tr("Reset widgets positions"),
self.reset_ui)
# Set toggle footer visibility action
show_action = self.view_menu.addAction(FIcon(0xF018D),
self.tr("Show bottom toolbar"))
show_action.setCheckable(True)
show_action.setChecked(True)
show_action.toggled.connect(self.toggle_footer_visibility)
self.view_menu.addSeparator()
## Tools
self.tool_menu = self.menuBar().addMenu(self.tr("&Tools"))
## Help
self.help_menu = self.menuBar().addMenu(self.tr("Help"))
self.help_menu.addAction(
FIcon(0xF02D6),
self.tr("What's this"),
QWhatsThis.enterWhatsThisMode,
QKeySequence.WhatsThis,
)
self.help_menu.addAction(
FIcon(0xF059F),
self.tr("Documentation..."),
partial(QDesktopServices.openUrl,
QUrl(cm.WIKI_URL, QUrl.TolerantMode)),
)
self.help_menu.addAction(
FIcon(0xF0A30),
self.tr("Report a bug..."),
partial(QDesktopServices.openUrl,
QUrl(cm.REPORT_BUG_URL, QUrl.TolerantMode)),
)
self.help_menu.addSeparator()
self.help_menu.addAction(self.tr("About Qt..."),
QApplication.instance().aboutQt)
self.help_menu.addAction(
QIcon(DIR_ICONS + "app.png"),
self.tr("About Cutevariant..."),
self.about_cutevariant,
)
