def __init__(self, label_text="Input", buttons=[]):
PyMod_form_item.__init__(self)
# Label.
self.label = QtWidgets.QLabel(label_text)
# Buttons.
self.input = QtWidgets.QVBoxLayout()
if not buttons:
raise ValueError("Please provide a list of button names")
if len(buttons) != len(set(buttons)):
raise ValueError("Please provide a non redundant list of buttons")
self.button_group = QtWidgets.QButtonGroup()
self.buttons_names = []
self.buttons_dict = {}
for button_name in buttons:
button = QtWidgets.QPushButton(button_name)
button.setCheckable(True)
self.input.addWidget(button)
self.buttons_names.append(button_name)
self.buttons_dict[button_name] = button
self.button_group.addButton(button)
def build_alignment_mode_frame(self):
"""
Builds a frame with some options to choose the alignment mode.
"""
# Vbox which will store all the widgets for the alignment mode options.
self.alignment_mode_vbox = QtWidgets.QVBoxLayout()
self.alignment_mode_label = QtWidgets.QLabel("Alignment Mode")
self.alignment_mode_vbox.addWidget(self.alignment_mode_label)
self.alignment_mode_button_group = QtWidgets.QButtonGroup()
self.build_strategy_specific_modes_frames() # Defined in child classes.
self.middle_formlayout.addRow(self.alignment_mode_vbox)
def __init__(self, *args, **kwargs):
super(PyMod_plot_window_qt, self).__init__(*args, **kwargs)
# Central widget.
self.central_widget = QtWidgets.QWidget()
self.setCentralWidget(self.central_widget)
self.central_widget_layout = QtWidgets.QGridLayout()
self.central_widget.setLayout(self.central_widget_layout)
#------------------------------------------------
# Upper frame (contains the plot and controls). -
#------------------------------------------------
expanding_size_policy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
preferred_size_policy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred,
QtWidgets.QSizePolicy.Preferred)
# The upper frame contains three frames: info, plot and controls frames.
# The infor and controls frames will be displayed only if the 'use_controls'
# argument is set to 'True' when calling the 'build_plotting_area' method.
self.upper_frame = QtWidgets.QFrame()
self.upper_frame.setStyleSheet("background-color: #646464")
self.upper_frame_layout = QtWidgets.QGridLayout()
self.upper_frame.setLayout(self.upper_frame_layout)
self.upper_frame.setSizePolicy(expanding_size_policy)
self.central_widget_layout.addWidget(self.upper_frame, 0, 0)
# Info frame, it contains the messagebar of the plot.
self.info_frame = QtWidgets.QFrame()
self.info_frame_layout = QtWidgets.QHBoxLayout()
self.info_frame.setLayout(self.info_frame_layout)
self.info_frame.setSizePolicy(preferred_size_policy)
self.info_label = QtWidgets.QLabel("")
self.info_frame_layout.addWidget(self.info_label)
# Plot frame.
self.plot_frame = QtWidgets.QFrame()
# self.plot_frame.setStyleSheet("background-color: red")
self.plot_frame_layout = QtWidgets.QGridLayout()
self.plot_frame.setLayout(self.plot_frame_layout)
self.plot_frame.setSizePolicy(expanding_size_policy)
self.build_plot_widget()
# Controls frame.
self.controls_frame = QtWidgets.QWidget()
self.controls_frame.setStyleSheet("background-color: #747474")
self.controls_frame_layout = QtWidgets.QGridLayout()
self.controls_frame.setLayout(self.controls_frame_layout)
self.controls_frame_layout.setAlignment(QtCore.Qt.AlignLeft | QtCore.Qt.AlignTop)
self.controls_scrollarea = QtWidgets.QScrollArea()
self.controls_scrollarea.setWidgetResizable(True)
self.controls_scrollarea.setWidget(self.controls_frame)
self.labels_title = QtWidgets.QLabel("Plots list")
# Middle splitter.
self.middle_splitter = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
self.middle_splitter.setSizePolicy(expanding_size_policy)
#---------------------------------------
# Lower frame (contains some options). -
#---------------------------------------
self.lower_frame = QtWidgets.QFrame()
self.lower_frame_layout = QtWidgets.QGridLayout()
self.lower_frame.setLayout(self.lower_frame_layout)
self.central_widget_layout.addWidget(self.lower_frame, 1, 0)
# View buttons.
self.view_label = QtWidgets.QLabel("View:")
self.lower_frame_layout.addWidget(self.view_label, 0, 0)
self.home_view_button = QtWidgets.QPushButton("Fit to data")
self.home_view_button.clicked.connect(self.on_home_button_click)
self.lower_frame_layout.addWidget(self.home_view_button, 0, 1)
# On click behaviour. The buttons will be shown later, in the
# 'build_plotting_area' metohd.
self.interact_buttons_group = QtWidgets.QButtonGroup()
self.on_click_label = QtWidgets.QLabel("Interact on click:")
self.interact_button = QtWidgets.QPushButton("Yes")
self.interact_button.setCheckable(True)
self.interact_buttons_group.addButton(self.interact_button)
self.interact_button.clicked.connect(self.on_interact_button_click)
self.no_interaction_button = QtWidgets.QPushButton("No")
self.no_interaction_button.setCheckable(True)
self.no_interaction_button.setChecked(True)
self.interact_buttons_group.addButton(self.no_interaction_button)
self.no_interaction_button.clicked.connect(self.on_no_interaction_button_click)
# Show/hide all buttons. They will be shown later, in the 'build_plotting_area'
# method.
self.show_label = QtWidgets.QLabel("Show:")
self.show_all_button = QtWidgets.QPushButton("All")
self.show_all_button.clicked.connect(self.show_all_command)
self.hide_all_button = QtWidgets.QPushButton("None")
self.hide_all_button.clicked.connect(self.hide_all_command)
self.lower_frame_layout.setAlignment(QtCore.Qt.AlignLeft)
#---------------------
# Build a main menu. -
#---------------------
self.save_to_csv_action = QtWidgets.QAction('Save to CSV', self)
self.save_to_csv_action.triggered.connect(lambda a=None: self.save_to_csv_event())
self.save_to_png_action = QtWidgets.QAction('Save to PNG', self)
self.save_to_png_action.triggered.connect(lambda a=None: self.save_to_png_event())
self.main_menubar = self.menuBar()
self.file_menu = self.main_menubar.addMenu('File')
def build_protocol_middle_frame(self):
#------------------
# Simple options. -
#------------------
# Let users decide how to import new sequences when the query is a child element (that
# is, it is already present in a cluster).
if self.protocol.blast_query_element.is_child():
self.import_mode_vbox = QtWidgets.QVBoxLayout()
self.import_mode_label = QtWidgets.QLabel("Hit Import Mode")
self.import_mode_vbox.addWidget(self.import_mode_label)
self.import_mode_button_group = QtWidgets.QButtonGroup()
self.middle_formlayout.addRow(self.import_mode_vbox)
# Build new alignment.
new_alignment_radiobutton = QtWidgets.QRadioButton("Build a new alignment with the query and the new hit sequences")
new_alignment_radiobutton._value = "build-new"
new_alignment_radiobutton.setChecked(True)
self.import_mode_vbox.addWidget(new_alignment_radiobutton)
self.import_mode_button_group.addButton(new_alignment_radiobutton)
# Expand alignment.
expand_alignment_radiobutton = QtWidgets.QRadioButton("Expand the existing alignment by appending the new hit sequences")
# "Expand the already existing cluster by appending to it the new hit sequences"
expand_alignment_radiobutton._value = "expand"
self.import_mode_vbox.addWidget(expand_alignment_radiobutton)
self.import_mode_button_group.addButton(expand_alignment_radiobutton)
# Each algorithm will have its own standard widgets.
self.build_algorithm_standard_options_widgets()
# E-value selection.
if self.protocol.protocol_name in hmmer_protocols_names:
e_value_threshold_enf_text = "c-Evalue Threshold"
else:
e_value_threshold_enf_text = "E-value Threshold"
self.e_value_threshold_enf = PyMod_entryfield_qt(label_text=e_value_threshold_enf_text,
value=str(self.protocol.e_value_threshold_default),
validate={'validator': 'real',
'min': 0.0, 'max': 1000.0})
self.middle_formlayout.add_widget_to_align(self.e_value_threshold_enf, validate=True)
# Max hit number selection.
self.max_hits_enf = PyMod_entryfield_qt(label_text="Max Number of Hits",
value=str(self.protocol.default_max_number_of_hits),
validate={'validator': 'integer',
'min': 1, 'max': 5000})
self.middle_formlayout.add_widget_to_align(self.max_hits_enf, validate=True)
# -------------------
# Advanced options. -
# -------------------
self.show_advanced_button()
# Minimum id% on with query.
self.min_id_enf = PyMod_entryfield_qt(label_text="Min Id% Threshold",
value="0",
validate={'validator': 'integer',
'min': 0, 'max': 100})
self.middle_formlayout.add_widget_to_align(self.min_id_enf, advanced_option=True, validate=True)
# Maximum id% on with query.
self.max_id_enf = PyMod_entryfield_qt(label_text="Max Id% Threshold",
value="100",
validate={'validator': 'integer',
'min': 0, 'max': 100})
self.middle_formlayout.add_widget_to_align(self.max_id_enf, advanced_option=True, validate=True)
# Minimum coverage on the query.
self.min_coverage_enf = PyMod_entryfield_qt(label_text="Min Coverage% Threshold",
value="0",
validate={'validator': 'integer',
'min': 0, 'max': 100})
self.middle_formlayout.add_widget_to_align(self.min_coverage_enf, advanced_option=True, validate=True)
# Advanced options for a specific algorithm.
self.build_algorithm_advanced_options_widgets()
self.middle_formlayout.set_input_widgets_width("auto")
def __init__(self):
QtWidgets.QWidget.__init__(self, parent, Qt.Window)
self.setMinimumSize(400, 500)
self.setWindowTitle('Register File Extensions')
self.model = QtGui.QStandardItemModel(self)
layout = QtWidgets.QVBoxLayout(self)
self.setLayout(layout)
label = QtWidgets.QLabel(
"Select file types to register them with PyMOL", self)
layout.addWidget(label)
alluserslayout = QtWidgets.QHBoxLayout()
alluserslayout.setObjectName("alluserslayout")
layout.addLayout(alluserslayout)
buttonlayout = QtWidgets.QHBoxLayout()
buttonlayout.setObjectName("buttonlayout")
layout.addLayout(buttonlayout)
self.table = QtWidgets.QTableView(self)
self.table.setModel(self.model)
layout.addWidget(self.table)
button = QtWidgets.QPushButton("Register Recommended (*)", self)
buttonlayout.addWidget(button)
button.pressed.connect(self.setRecommended)
button = QtWidgets.QPushButton("Register All", self)
buttonlayout.addWidget(button)
button.pressed.connect(self.setAll)
button = QtWidgets.QPushButton("Clear", self)
button.setToolTip("Clean up Registry")
buttonlayout.addWidget(button)
button.pressed.connect(self.clear)
if isAdmin():
r0 = QtWidgets.QRadioButton("Only for me")
r0.setToolTip("HKEY_CURRENT_USER registry branch")
r0.setChecked(True)
r1 = QtWidgets.QRadioButton("For all users")
r1.setToolTip("HKEY_LOCAL_MACHINE registry branch")
allusersgroup = QtWidgets.QButtonGroup(self)
allusersgroup.addButton(r0)
allusersgroup.addButton(r1)
allusersgroup.buttonClicked.connect(self.populateData)
alluserslayout.addWidget(r0)
alluserslayout.addWidget(r1)
alluserslayout.addStretch()
self.allusersbutton = r1
else:
self.allusersbutton = None
self.finalize_timer = QtCore.QTimer()
self.finalize_timer.setSingleShot(True)
self.finalize_timer.setInterval(500)
self.finalize_timer.timeout.connect(finalize)
self.populateData()
# keep reference to window, otherwise Qt will auto-close it
self._self_ref = self