def test_calctype_not_impemented(qtbot, caplog):
view = MainWindow(controller=None)
qtbot.addWidget(view)
testbutton = QRadioButton()
testbutton.setObjectName('custom')
buttongroup = view._ui.calctype.buttongroup
buttongroup.addButton(testbutton)
assert testbutton in buttongroup.buttons()
testbutton.animateClick(msec=0)
qtbot.wait(100)
assert caplog.records[-1].levelname == 'ERROR'
assert 'button name mismatch' in caplog.text
def configFilterTypeButtons(self,
name=u"default",
checked=False,
xPos=0,
yPos=0,
idButton=0):
button = QRadioButton(self)
button.setObjectName(name)
button.setEnabled(True)
button.setGeometry(QRect(xPos, yPos, 82, 17))
button.setCursor(QCursor(Qt.PointingHandCursor))
button.setChecked(checked)
lam = lambda id=idButton: self.buttonChecked(id)
self.connect(button, SIGNAL("clicked()"), lam)
self.filterTypeButtons.addButton(button, idButton)
class SCOUTS(QMainWindow):
"""Main Window Widget for SCOUTS."""
style = {
'title': 'QLabel {font-size: 18pt; font-weight: 600}',
'header': 'QLabel {font-size: 12pt; font-weight: 520}',
'label': 'QLabel {font-size: 10pt}',
'button': 'QPushButton {font-size: 10pt}',
'md button': 'QPushButton {font-size: 12pt}',
'run button': 'QPushButton {font-size: 18pt; font-weight: 600}',
'line edit': 'QLineEdit {font-size: 10pt}',
'checkbox': 'QCheckBox {font-size: 10pt}',
'radio button': 'QRadioButton {font-size: 10pt}'
}
def __init__(self) -> None:
"""SCOUTS Constructor. Defines all aspects of the GUI."""
# ###
# ### Main Window setup
# ###
# Inherits from QMainWindow
super().__init__()
self.rootdir = get_project_root()
self.threadpool = QThreadPool()
# Sets values for QMainWindow
self.setWindowTitle("SCOUTS")
self.setWindowIcon(
QIcon(
os.path.abspath(os.path.join(self.rootdir, 'src',
'scouts.ico'))))
# Creates StackedWidget as QMainWindow's central widget
self.stacked_pages = QStackedWidget(self)
self.setCentralWidget(self.stacked_pages)
# Creates Widgets for individual "pages" and adds them to the StackedWidget
self.main_page = QWidget()
self.samples_page = QWidget()
self.gating_page = QWidget()
self.pages = (self.main_page, self.samples_page, self.gating_page)
for page in self.pages:
self.stacked_pages.addWidget(page)
# ## Sets widget at program startup
self.stacked_pages.setCurrentWidget(self.main_page)
# ###
# ### MAIN PAGE
# ###
# Main page layout
self.main_layout = QVBoxLayout(self.main_page)
# Title section
# Title
self.title = QLabel(self.main_page)
self.title.setText('SCOUTS - Single Cell Outlier Selector')
self.title.setStyleSheet(self.style['title'])
self.title.adjustSize()
self.main_layout.addWidget(self.title)
# ## Input section
# Input header
self.input_header = QLabel(self.main_page)
self.input_header.setText('Input settings')
self.input_header.setStyleSheet(self.style['header'])
self.main_layout.addChildWidget(self.input_header)
self.input_header.adjustSize()
self.main_layout.addWidget(self.input_header)
# Input frame
self.input_frame = QFrame(self.main_page)
self.input_frame.setFrameShape(QFrame.StyledPanel)
self.input_frame.setLayout(QFormLayout())
self.main_layout.addWidget(self.input_frame)
# Input button
self.input_button = QPushButton(self.main_page)
self.input_button.setStyleSheet(self.style['button'])
self.set_icon(self.input_button, 'x-office-spreadsheet')
self.input_button.setObjectName('input')
self.input_button.setText(' Select input file (.xlsx or .csv)')
self.input_button.clicked.connect(self.get_path)
# Input path box
self.input_path = QLineEdit(self.main_page)
self.input_path.setObjectName('input_path')
self.input_path.setStyleSheet(self.style['line edit'])
# Go to sample naming page
self.samples_button = QPushButton(self.main_page)
self.samples_button.setStyleSheet(self.style['button'])
self.set_icon(self.samples_button, 'preferences-other')
self.samples_button.setText(' Name samples...')
self.samples_button.clicked.connect(self.goto_samples_page)
# Go to gating page
self.gates_button = QPushButton(self.main_page)
self.gates_button.setStyleSheet(self.style['button'])
self.set_icon(self.gates_button, 'preferences-other')
self.gates_button.setText(' Gating && outlier options...')
self.gates_button.clicked.connect(self.goto_gates_page)
# Add widgets above to input frame Layout
self.input_frame.layout().addRow(self.input_button, self.input_path)
self.input_frame.layout().addRow(self.samples_button)
self.input_frame.layout().addRow(self.gates_button)
# ## Analysis section
# Analysis header
self.analysis_header = QLabel(self.main_page)
self.analysis_header.setText('Analysis settings')
self.analysis_header.setStyleSheet(self.style['header'])
self.analysis_header.adjustSize()
self.main_layout.addWidget(self.analysis_header)
# Analysis frame
self.analysis_frame = QFrame(self.main_page)
self.analysis_frame.setFrameShape(QFrame.StyledPanel)
self.analysis_frame.setLayout(QVBoxLayout())
self.main_layout.addWidget(self.analysis_frame)
# Cutoff text
self.cutoff_text = QLabel(self.main_page)
self.cutoff_text.setText('Type of outlier to select:')
self.cutoff_text.setToolTip(
'Choose whether to select outliers using the cutoff value from a reference\n'
'sample (OutR) or by using the cutoff value calculated for each sample\n'
'individually (OutS)')
self.cutoff_text.setStyleSheet(self.style['label'])
# Cutoff button group
self.cutoff_group = QButtonGroup(self)
# Cutoff by sample
self.cutoff_sample = QRadioButton(self.main_page)
self.cutoff_sample.setText('OutS')
self.cutoff_sample.setObjectName('sample')
self.cutoff_sample.setStyleSheet(self.style['radio button'])
self.cutoff_sample.setChecked(True)
self.cutoff_group.addButton(self.cutoff_sample)
# Cutoff by reference
self.cutoff_reference = QRadioButton(self.main_page)
self.cutoff_reference.setText('OutR')
self.cutoff_reference.setObjectName('ref')
self.cutoff_reference.setStyleSheet(self.style['radio button'])
self.cutoff_group.addButton(self.cutoff_reference)
# Both cutoffs
self.cutoff_both = QRadioButton(self.main_page)
self.cutoff_both.setText('both')
self.cutoff_both.setObjectName('sample ref')
self.cutoff_both.setStyleSheet(self.style['radio button'])
self.cutoff_group.addButton(self.cutoff_both)
# Markers text
self.markers_text = QLabel(self.main_page)
self.markers_text.setStyleSheet(self.style['label'])
self.markers_text.setText('Show results for:')
self.markers_text.setToolTip(
'Individual markers: for each marker, select outliers\n'
'Any marker: select cells that are outliers for AT LEAST one marker'
)
# Markers button group
self.markers_group = QButtonGroup(self)
# Single marker
self.single_marker = QRadioButton(self.main_page)
self.single_marker.setText('individual markers')
self.single_marker.setObjectName('single')
self.single_marker.setStyleSheet(self.style['radio button'])
self.single_marker.setChecked(True)
self.markers_group.addButton(self.single_marker)
# Any marker
self.any_marker = QRadioButton(self.main_page)
self.any_marker.setText('any marker')
self.any_marker.setObjectName('any')
self.any_marker.setStyleSheet(self.style['radio button'])
self.markers_group.addButton(self.any_marker)
# Both methods
self.both_methods = QRadioButton(self.main_page)
self.both_methods.setText('both')
self.both_methods.setObjectName('single any')
self.both_methods.setStyleSheet(self.style['radio button'])
self.markers_group.addButton(self.both_methods)
# Tukey text
self.tukey_text = QLabel(self.main_page)
self.tukey_text.setStyleSheet(self.style['label'])
# Tukey button group
self.tukey_text.setText('Tukey factor:')
self.tukey_group = QButtonGroup(self)
# Low Tukey value
self.tukey_low = QRadioButton(self.main_page)
self.tukey_low.setText('1.5')
self.tukey_low.setStyleSheet(self.style['radio button'])
self.tukey_low.setChecked(True)
self.tukey_group.addButton(self.tukey_low)
# High Tukey value
self.tukey_high = QRadioButton(self.main_page)
self.tukey_high.setText('3.0')
self.tukey_high.setStyleSheet(self.style['radio button'])
self.tukey_group.addButton(self.tukey_high)
# Add widgets above to analysis frame layout
self.analysis_frame.layout().addWidget(self.cutoff_text)
self.cutoff_buttons = QHBoxLayout()
for button in self.cutoff_group.buttons():
self.cutoff_buttons.addWidget(button)
self.analysis_frame.layout().addLayout(self.cutoff_buttons)
self.analysis_frame.layout().addWidget(self.markers_text)
self.markers_buttons = QHBoxLayout()
for button in self.markers_group.buttons():
self.markers_buttons.addWidget(button)
self.analysis_frame.layout().addLayout(self.markers_buttons)
self.analysis_frame.layout().addWidget(self.tukey_text)
self.tukey_buttons = QHBoxLayout()
for button in self.tukey_group.buttons():
self.tukey_buttons.addWidget(button)
self.tukey_buttons.addWidget(QLabel()) # aligns row with 2 buttons
self.analysis_frame.layout().addLayout(self.tukey_buttons)
# ## Output section
# Output header
self.output_header = QLabel(self.main_page)
self.output_header.setText('Output settings')
self.output_header.setStyleSheet(self.style['header'])
self.output_header.adjustSize()
self.main_layout.addWidget(self.output_header)
# Output frame
self.output_frame = QFrame(self.main_page)
self.output_frame.setFrameShape(QFrame.StyledPanel)
self.output_frame.setLayout(QFormLayout())
self.main_layout.addWidget(self.output_frame)
# Output button
self.output_button = QPushButton(self.main_page)
self.output_button.setStyleSheet(self.style['button'])
self.set_icon(self.output_button, 'folder')
self.output_button.setObjectName('output')
self.output_button.setText(' Select output folder')
self.output_button.clicked.connect(self.get_path)
# Output path box
self.output_path = QLineEdit(self.main_page)
self.output_path.setStyleSheet(self.style['line edit'])
# Generate CSV checkbox
self.output_csv = QCheckBox(self.main_page)
self.output_csv.setText('Export multiple text files (.csv)')
self.output_csv.setStyleSheet(self.style['checkbox'])
self.output_csv.setChecked(True)
# Generate XLSX checkbox
self.output_excel = QCheckBox(self.main_page)
self.output_excel.setText('Export multiple Excel spreadsheets (.xlsx)')
self.output_excel.setStyleSheet(self.style['checkbox'])
self.output_excel.clicked.connect(self.enable_single_excel)
# Generate single, large XLSX checkbox
self.single_excel = QCheckBox(self.main_page)
self.single_excel.setText(
'Also save one multi-sheet Excel spreadsheet')
self.single_excel.setToolTip(
'After generating all Excel spreadsheets, SCOUTS combines them into '
'a single\nExcel spreadsheet where each sheet corresponds to an output'
'file from SCOUTS')
self.single_excel.setStyleSheet(self.style['checkbox'])
self.single_excel.setEnabled(False)
self.single_excel.clicked.connect(self.memory_warning)
# Add widgets above to output frame layout
self.output_frame.layout().addRow(self.output_button, self.output_path)
self.output_frame.layout().addRow(self.output_csv)
self.output_frame.layout().addRow(self.output_excel)
self.output_frame.layout().addRow(self.single_excel)
# ## Run & help-quit section
# Run button (stand-alone)
self.run_button = QPushButton(self.main_page)
self.set_icon(self.run_button, 'system-run')
self.run_button.setText(' Run!')
self.run_button.setStyleSheet(self.style['run button'])
self.main_layout.addWidget(self.run_button)
self.run_button.clicked.connect(self.run)
# Help-quit frame (invisible)
self.helpquit_frame = QFrame(self.main_page)
self.helpquit_frame.setLayout(QHBoxLayout())
self.helpquit_frame.layout().setMargin(0)
self.main_layout.addWidget(self.helpquit_frame)
# Help button
self.help_button = QPushButton(self.main_page)
self.set_icon(self.help_button, 'help-about')
self.help_button.setText(' Help')
self.help_button.setStyleSheet(self.style['md button'])
self.help_button.clicked.connect(self.get_help)
# Quit button
self.quit_button = QPushButton(self.main_page)
self.set_icon(self.quit_button, 'process-stop')
self.quit_button.setText(' Quit')
self.quit_button.setStyleSheet(self.style['md button'])
self.quit_button.clicked.connect(self.close)
# Add widgets above to help-quit layout
self.helpquit_frame.layout().addWidget(self.help_button)
self.helpquit_frame.layout().addWidget(self.quit_button)
# ###
# ### SAMPLES PAGE
# ###
# Samples page layout
self.samples_layout = QVBoxLayout(self.samples_page)
# ## Title section
# Title
self.samples_title = QLabel(self.samples_page)
self.samples_title.setText('Name your samples')
self.samples_title.setStyleSheet(self.style['title'])
self.samples_title.adjustSize()
self.samples_layout.addWidget(self.samples_title)
# Subtitle
self.samples_subtitle = QLabel(self.samples_page)
string = (
'Please name the samples to be analysed by SCOUTS.\n\nSCOUTS searches the first '
'column of your data\nand locates the exact string as part of the sample name.'
)
self.samples_subtitle.setText(string)
self.samples_subtitle.setStyleSheet(self.style['label'])
self.samples_subtitle.adjustSize()
self.samples_layout.addWidget(self.samples_subtitle)
# ## Sample addition section
# Sample addition frame
self.samples_frame = QFrame(self.samples_page)
self.samples_frame.setFrameShape(QFrame.StyledPanel)
self.samples_frame.setLayout(QGridLayout())
self.samples_layout.addWidget(self.samples_frame)
# Sample name box
self.sample_name = QLineEdit(self.samples_page)
self.sample_name.setStyleSheet(self.style['line edit'])
self.sample_name.setPlaceholderText('Sample name ...')
# Reference check
self.is_reference = QCheckBox(self.samples_page)
self.is_reference.setText('Reference?')
self.is_reference.setStyleSheet(self.style['checkbox'])
# Add sample to table
self.add_sample_button = QPushButton(self.samples_page)
QShortcut(QKeySequence("Return"), self.add_sample_button,
self.write_to_sample_table)
self.set_icon(self.add_sample_button, 'list-add')
self.add_sample_button.setText(' Add sample (Enter)')
self.add_sample_button.setStyleSheet(self.style['button'])
self.add_sample_button.clicked.connect(self.write_to_sample_table)
# Remove sample from table
self.remove_sample_button = QPushButton(self.samples_page)
QShortcut(QKeySequence("Delete"), self.remove_sample_button,
self.remove_from_sample_table)
self.set_icon(self.remove_sample_button, 'list-remove')
self.remove_sample_button.setText(' Remove sample (Del)')
self.remove_sample_button.setStyleSheet(self.style['button'])
self.remove_sample_button.clicked.connect(
self.remove_from_sample_table)
# Add widgets above to sample addition layout
self.samples_frame.layout().addWidget(self.sample_name, 0, 0)
self.samples_frame.layout().addWidget(self.is_reference, 1, 0)
self.samples_frame.layout().addWidget(self.add_sample_button, 0, 1)
self.samples_frame.layout().addWidget(self.remove_sample_button, 1, 1)
# ## Sample table
self.sample_table = QTableWidget(self.samples_page)
self.sample_table.setColumnCount(2)
self.sample_table.setHorizontalHeaderItem(0,
QTableWidgetItem('Sample'))
self.sample_table.setHorizontalHeaderItem(
1, QTableWidgetItem('Reference?'))
self.sample_table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Stretch)
self.sample_table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.ResizeToContents)
self.samples_layout.addWidget(self.sample_table)
# ## Save & clear buttons
# Save & clear frame (invisible)
self.saveclear_frame = QFrame(self.samples_page)
self.saveclear_frame.setLayout(QHBoxLayout())
self.saveclear_frame.layout().setMargin(0)
self.samples_layout.addWidget(self.saveclear_frame)
# Clear samples button
self.clear_samples = QPushButton(self.samples_page)
self.set_icon(self.clear_samples, 'edit-delete')
self.clear_samples.setText(' Clear table')
self.clear_samples.setStyleSheet(self.style['md button'])
self.clear_samples.clicked.connect(self.prompt_clear_data)
# Save samples button
self.save_samples = QPushButton(self.samples_page)
self.set_icon(self.save_samples, 'document-save')
self.save_samples.setText(' Save samples')
self.save_samples.setStyleSheet(self.style['md button'])
self.save_samples.clicked.connect(self.goto_main_page)
# Add widgets above to save & clear layout
self.saveclear_frame.layout().addWidget(self.clear_samples)
self.saveclear_frame.layout().addWidget(self.save_samples)
# ###
# ### GATING PAGE
# ###
# Gating page layout
self.gating_layout = QVBoxLayout(self.gating_page)
# ## Title section
# Title
self.gates_title = QLabel(self.gating_page)
self.gates_title.setText('Gating & outlier options')
self.gates_title.setStyleSheet(self.style['title'])
self.gates_title.adjustSize()
self.gating_layout.addWidget(self.gates_title)
# ## Gating options section
# Gating header
self.gate_header = QLabel(self.gating_page)
self.gate_header.setText('Gating')
self.gate_header.setStyleSheet(self.style['header'])
self.gate_header.adjustSize()
self.gating_layout.addWidget(self.gate_header)
# Gating frame
self.gate_frame = QFrame(self.gating_page)
self.gate_frame.setFrameShape(QFrame.StyledPanel)
self.gate_frame.setLayout(QFormLayout())
self.gating_layout.addWidget(self.gate_frame)
# Gating button group
self.gating_group = QButtonGroup(self)
# Do not gate samples
self.no_gates = QRadioButton(self.gating_page)
self.no_gates.setObjectName('no_gate')
self.no_gates.setText("Don't gate samples")
self.no_gates.setStyleSheet(self.style['radio button'])
self.no_gates.setChecked(True)
self.gating_group.addButton(self.no_gates)
self.no_gates.clicked.connect(self.activate_gate)
# CyToF gating
self.cytof_gates = QRadioButton(self.gating_page)
self.cytof_gates.setObjectName('cytof')
self.cytof_gates.setText('Mass Cytometry gating')
self.cytof_gates.setStyleSheet(self.style['radio button'])
self.cytof_gates.setToolTip(
'Exclude cells for which the average expression of all\n'
'markers is below the selected value')
self.gating_group.addButton(self.cytof_gates)
self.cytof_gates.clicked.connect(self.activate_gate)
# CyToF gating spinbox
self.cytof_gates_value = QDoubleSpinBox(self.gating_page)
self.cytof_gates_value.setMinimum(0)
self.cytof_gates_value.setMaximum(1)
self.cytof_gates_value.setValue(0.1)
self.cytof_gates_value.setSingleStep(0.05)
self.cytof_gates_value.setEnabled(False)
# scRNA-Seq gating
self.rnaseq_gates = QRadioButton(self.gating_page)
self.rnaseq_gates.setText('scRNA-Seq gating')
self.rnaseq_gates.setStyleSheet(self.style['radio button'])
self.rnaseq_gates.setToolTip(
'When calculating cutoff, ignore reads below the selected value')
self.rnaseq_gates.setObjectName('rnaseq')
self.gating_group.addButton(self.rnaseq_gates)
self.rnaseq_gates.clicked.connect(self.activate_gate)
# scRNA-Seq gating spinbox
self.rnaseq_gates_value = QDoubleSpinBox(self.gating_page)
self.rnaseq_gates_value.setMinimum(0)
self.rnaseq_gates_value.setMaximum(10)
self.rnaseq_gates_value.setValue(0)
self.rnaseq_gates_value.setSingleStep(1)
self.rnaseq_gates_value.setEnabled(False)
# export gated population checkbox
self.export_gated = QCheckBox(self.gating_page)
self.export_gated.setText('Export gated cells as an output file')
self.export_gated.setStyleSheet(self.style['checkbox'])
self.export_gated.setEnabled(False)
# Add widgets above to Gate frame layout
self.gate_frame.layout().addRow(self.no_gates, QLabel())
self.gate_frame.layout().addRow(self.cytof_gates,
self.cytof_gates_value)
self.gate_frame.layout().addRow(self.rnaseq_gates,
self.rnaseq_gates_value)
self.gate_frame.layout().addRow(self.export_gated, QLabel())
# ## Outlier options section
# Outlier header
self.outlier_header = QLabel(self.gating_page)
self.outlier_header.setText('Outliers')
self.outlier_header.setStyleSheet(self.style['header'])
self.outlier_header.adjustSize()
self.gating_layout.addWidget(self.outlier_header)
# Outlier frame
self.outlier_frame = QFrame(self.gating_page)
self.outlier_frame.setFrameShape(QFrame.StyledPanel)
self.outlier_frame.setLayout(QVBoxLayout())
self.gating_layout.addWidget(self.outlier_frame)
# Top outliers information
self.top_outliers = QLabel(self.gating_page)
self.top_outliers.setStyleSheet(self.style['label'])
self.top_outliers.setText(
'By default, SCOUTS selects the top outliers from the population')
self.top_outliers.setStyleSheet(self.style['label'])
# Bottom outliers data
self.bottom_outliers = QCheckBox(self.gating_page)
self.bottom_outliers.setText('Include results for low outliers')
self.bottom_outliers.setStyleSheet(self.style['checkbox'])
# Non-outliers data
self.not_outliers = QCheckBox(self.gating_page)
self.not_outliers.setText('Include results for non-outliers')
self.not_outliers.setStyleSheet(self.style['checkbox'])
# Add widgets above to Gate frame layout
self.outlier_frame.layout().addWidget(self.top_outliers)
self.outlier_frame.layout().addWidget(self.bottom_outliers)
self.outlier_frame.layout().addWidget(self.not_outliers)
# ## Save/back button
self.save_gates = QPushButton(self.gating_page)
self.set_icon(self.save_gates, 'go-next')
self.save_gates.setText(' Back to main menu')
self.save_gates.setStyleSheet(self.style['md button'])
self.gating_layout.addWidget(self.save_gates)
self.save_gates.clicked.connect(self.goto_main_page)
# ## Add empty label to take vertical space
self.empty_label = QLabel(self.gating_page)
self.empty_label.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Expanding)
self.gating_layout.addWidget(self.empty_label)
# ###
# ### ICON SETTING
# ###
def set_icon(self, widget: QWidget, icon: str) -> None:
"""Associates an icon to a widget."""
i = QIcon()
i.addPixmap(
QPixmap(
os.path.abspath(
os.path.join(self.rootdir, 'src', 'default_icons',
f'{icon}.svg'))))
widget.setIcon(QIcon.fromTheme(icon, i))
# ###
# ### STACKED WIDGET PAGE SWITCHING
# ###
def goto_main_page(self) -> None:
"""Switches stacked widget pages to the main page."""
self.stacked_pages.setCurrentWidget(self.main_page)
def goto_samples_page(self) -> None:
"""Switches stacked widget pages to the samples table page."""
self.stacked_pages.setCurrentWidget(self.samples_page)
def goto_gates_page(self) -> None:
"""Switches stacked widget pages to the gating & other options page."""
self.stacked_pages.setCurrentWidget(self.gating_page)
# ###
# ### MAIN PAGE GUI LOGIC
# ###
def get_path(self) -> None:
"""Opens a dialog box and sets the chosen file/folder path, depending on the caller widget."""
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
sender_name = self.sender().objectName()
if sender_name == 'input':
query, _ = QFileDialog.getOpenFileName(self,
"Select file",
"",
"All Files (*)",
options=options)
elif sender_name == 'output':
query = QFileDialog.getExistingDirectory(self,
"Select Directory",
options=options)
else:
return
if query:
getattr(self, f'{sender_name}_path').setText(query)
def enable_single_excel(self) -> None:
"""Enables checkbox for generating a single Excel output."""
if self.output_excel.isChecked():
self.single_excel.setEnabled(True)
else:
self.single_excel.setEnabled(False)
self.single_excel.setChecked(False)
# ###
# ### SAMPLE NAME/SAMPLE TABLE GUI LOGIC
# ###
def write_to_sample_table(self) -> None:
"""Writes data to sample table."""
table = self.sample_table
ref = 'no'
sample = self.sample_name.text()
if sample:
for cell in range(table.rowCount()):
item = table.item(cell, 0)
if item.text() == sample:
self.same_sample()
return
if self.is_reference.isChecked():
for cell in range(table.rowCount()):
item = table.item(cell, 1)
if item.text() == 'yes':
self.more_than_one_reference()
return
ref = 'yes'
sample = QTableWidgetItem(sample)
is_reference = QTableWidgetItem(ref)
is_reference.setFlags(Qt.ItemIsEnabled)
row_position = table.rowCount()
table.insertRow(row_position)
table.setItem(row_position, 0, sample)
table.setItem(row_position, 1, is_reference)
self.is_reference.setChecked(False)
self.sample_name.setText('')
def remove_from_sample_table(self) -> None:
"""Removes data from sample table."""
table = self.sample_table
rows = set(index.row() for index in table.selectedIndexes())
for index in sorted(rows, reverse=True):
self.sample_table.removeRow(index)
def prompt_clear_data(self) -> None:
"""Prompts option to clear all data in the sample table."""
if self.confirm_clear_data():
table = self.sample_table
while table.rowCount():
self.sample_table.removeRow(0)
# ###
# ### GATING GUI LOGIC
# ###
def activate_gate(self) -> None:
"""Activates/deactivates buttons related to gating."""
if self.sender().objectName() == 'no_gate':
self.cytof_gates_value.setEnabled(False)
self.rnaseq_gates_value.setEnabled(False)
self.export_gated.setEnabled(False)
self.export_gated.setChecked(False)
elif self.sender().objectName() == 'cytof':
self.cytof_gates_value.setEnabled(True)
self.rnaseq_gates_value.setEnabled(False)
self.export_gated.setEnabled(True)
elif self.sender().objectName() == 'rnaseq':
self.cytof_gates_value.setEnabled(False)
self.rnaseq_gates_value.setEnabled(True)
self.export_gated.setEnabled(True)
# ###
# ### CONNECT SCOUTS TO ANALYTICAL MODULES
# ###
def run(self) -> None:
"""Runs SCOUTS as a Worker, based on user input in the GUI."""
try:
data = self.parse_input()
except Exception as error:
trace = traceback.format_exc()
self.propagate_error((error, trace))
else:
data['widget'] = self
worker = Worker(func=start_scouts, **data)
worker.signals.started.connect(self.analysis_has_started)
worker.signals.finished.connect(self.analysis_has_finished)
worker.signals.success.connect(self.success_message)
worker.signals.error.connect(self.propagate_error)
self.threadpool.start(worker)
def parse_input(self) -> Dict:
"""Returns user input on the GUI as a dictionary."""
# Input and output
input_dict = {
'input_file': str(self.input_path.text()),
'output_folder': str(self.output_path.text())
}
if not input_dict['input_file'] or not input_dict['output_folder']:
raise NoIOPathError
# Set cutoff by reference or by sample rule
input_dict['cutoff_rule'] = self.cutoff_group.checkedButton(
).objectName() # 'sample', 'ref', 'sample ref'
# Outliers for each individual marker or any marker in row
input_dict['marker_rule'] = self.markers_group.checkedButton(
).objectName() # 'single', 'any', 'single any'
# Tukey factor used for calculating cutoff
input_dict['tukey_factor'] = float(
self.tukey_group.checkedButton().text()) # '1.5', '3.0'
# Output settings
input_dict['export_csv'] = True if self.output_csv.isChecked(
) else False
input_dict['export_excel'] = True if self.output_excel.isChecked(
) else False
input_dict['single_excel'] = True if self.single_excel.isChecked(
) else False
# Retrieve samples from sample table
input_dict['sample_list'] = []
for tuples in self.yield_samples_from_table():
input_dict['sample_list'].append(tuples)
if not input_dict['sample_list']:
raise NoSampleError
# Set gate cutoff (if any)
input_dict['gating'] = self.gating_group.checkedButton().objectName(
) # 'no_gate', 'cytof', 'rnaseq'
input_dict['gate_cutoff_value'] = None
if input_dict['gating'] != 'no_gate':
input_dict['gate_cutoff_value'] = getattr(
self, f'{input_dict["gating"]}_gates_value').value()
input_dict['export_gated'] = True if self.export_gated.isChecked(
) else False
# Generate results for non-outliers
input_dict['non_outliers'] = False
if self.not_outliers.isChecked():
input_dict['non_outliers'] = True
# Generate results for bottom outliers
input_dict['bottom_outliers'] = False
if self.bottom_outliers.isChecked():
input_dict['bottom_outliers'] = True
# return dictionary with all gathered inputs
return input_dict
def yield_samples_from_table(
self) -> Generator[Tuple[str, str], None, None]:
"""Yields sample names from the sample table."""
table = self.sample_table
for cell in range(table.rowCount()):
sample_name = table.item(cell, 0).text()
sample_type = table.item(cell, 1).text()
yield sample_name, sample_type
# ###
# ### MESSAGE BOXES
# ###
def analysis_has_started(self) -> None:
"""Disables run button while SCOUTS analysis is underway."""
self.run_button.setText(' Working...')
self.run_button.setEnabled(False)
def analysis_has_finished(self) -> None:
"""Enables run button after SCOUTS analysis has finished."""
self.run_button.setEnabled(True)
self.run_button.setText(' Run!')
def success_message(self) -> None:
"""Info message box used when SCOUTS finished without errors."""
title = "Analysis finished!"
mes = "Your analysis has finished. No errors were reported."
if self.stacked_pages.isEnabled() is True:
QMessageBox.information(self, title, mes)
def memory_warning(self) -> None:
"""Warning message box used when user wants to generate a single excel file."""
if self.sender().isChecked():
title = 'Memory warning!'
mes = (
"Depending on your dataset, this option can consume a LOT of memory and take"
" a long time to process. Please make sure that your computer can handle it!"
)
QMessageBox.information(self, title, mes)
def same_sample(self) -> None:
"""Error message box used when the user tries to input the same sample twice in the sample table."""
title = 'Error: sample name already in table'
mes = (
"Sorry, you can't do this because this sample name is already in the table. "
"Please select a different name.")
QMessageBox.critical(self, title, mes)
def more_than_one_reference(self) -> None:
"""Error message box used when the user tries to input two reference samples in the sample table."""
title = "Error: more than one reference selected"
mes = (
"Sorry, you can't do this because there is already a reference column in the table. "
"Please remove it before adding a reference.")
QMessageBox.critical(self, title, mes)
def confirm_clear_data(self) -> bool:
"""Question message box used to confirm user action of clearing sample table."""
title = 'Confirm Action'
mes = "Table will be cleared. Are you sure?"
reply = QMessageBox.question(self, title, mes,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.No)
if reply == QMessageBox.Yes:
return True
return False
# ###
# ### EXCEPTIONS & ERRORS
# ###
def propagate_error(self, error: Tuple[Exception, str]) -> None:
"""Calls the appropriate error message box based on type of Exception raised."""
if isinstance(error[0], NoIOPathError):
self.no_io_path_error_message()
elif isinstance(error[0], NoReferenceError):
self.no_reference_error_message()
elif isinstance(error[0], NoSampleError):
self.no_sample_error_message()
elif isinstance(error[0], PandasInputError):
self.pandas_input_error_message()
elif isinstance(error[0], SampleNamingError):
self.sample_naming_error_message()
else:
self.generic_error_message(error)
def no_io_path_error_message(self) -> None:
"""Message displayed when the user did not include an input file path, or an output folder path."""
title = 'Error: no file/folder'
message = ("Sorry, no input file and/or output folder was provided. "
"Please add the path to the necessary file/folder.")
QMessageBox.critical(self, title, message)
def no_reference_error_message(self) -> None:
"""Message displayed when the user wants to analyse cutoff based on a reference, but did not specify what
sample corresponds to the reference."""
title = "Error: No reference selected"
message = (
"Sorry, no reference sample was found on the sample list, but analysis was set to "
"reference. Please add a reference sample, or change the rule for cutoff calculation."
)
QMessageBox.critical(self, title, message)
def no_sample_error_message(self) -> None:
"""Message displayed when the user did not add any samples to the sample table."""
title = "Error: No samples selected"
message = (
"Sorry, the analysis cannot be performed because no sample names were input. "
"Please add your sample names.")
QMessageBox.critical(self, title, message)
def pandas_input_error_message(self) -> None:
"""Message displayed when the input file cannot be read (likely because it is not a Excel or csv file)."""
title = 'Error: unexpected input file'
message = (
"Sorry, the input file could not be read. Please make sure that "
"the data is save in a valid format (supported formats are: "
".csv, .xlsx).")
QMessageBox.critical(self, title, message)
def sample_naming_error_message(self) -> None:
"""Message displayed when none of the sample names passed by the user are found in the input DataFrame."""
title = 'Error: sample names not in input file'
message = (
"Sorry, your sample names were not found in the input file. Please "
"make sure that the names were typed correctly (case-sensitive).")
QMessageBox.critical(self, title, message)
def generic_error_message(self, error: Tuple[Exception, str]) -> None:
"""Error message box used to display any error message (including traceback) for any uncaught errors."""
title = 'An error occurred!'
name, trace = error
QMessageBox.critical(self, title,
f"{str(name)}\n\nfull traceback:\n{trace}")
def not_implemented_error_message(self) -> None:
"""Error message box used when the user accesses a functionality that hasn't been implemented yet."""
title = "Not yet implemented"
mes = "Sorry, this functionality has not been implemented yet."
QMessageBox.critical(self, title, mes)
# ###
# ### HELP & QUIT
# ###
@staticmethod
def get_help() -> None:
"""Opens SCOUTS documentation on the browser. Called when the user clicks the "help" button"""
webbrowser.open('https://scouts.readthedocs.io/en/master/')
def closeEvent(self, event: QEvent) -> None:
"""Defines the message box for when the user wants to quit SCOUTS."""
title = 'Quit SCOUTS'
mes = "Are you sure you want to quit?"
reply = QMessageBox.question(self, title, mes,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.No)
if reply == QMessageBox.Yes:
self.stacked_pages.setEnabled(False)
message = self.quit_message()
waiter = Waiter(waiter_func=self.threadpool.activeThreadCount)
waiter.signals.started.connect(message.show)
waiter.signals.finished.connect(message.destroy)
waiter.signals.finished.connect(sys.exit)
self.threadpool.start(waiter)
event.ignore()
def quit_message(self) -> QDialog:
"""Displays a window while SCOUTS is exiting"""
message = QDialog(self)
message.setWindowTitle('Exiting SCOUTS')
message.resize(300, 50)
label = QLabel('SCOUTS is exiting, please wait...', message)
label.setStyleSheet(self.style['label'])
label.adjustSize()
label.setAlignment(Qt.AlignCenter)
label.move(int((message.width() - label.width()) / 2),
int((message.height() - label.height()) / 2))
return message
class Ui_GroupBox(object):
def setupUi(self, GroupBox):
if not GroupBox.objectName():
GroupBox.setObjectName(u"GroupBox")
GroupBox.resize(535, 520)
sizePolicy = QSizePolicy(QSizePolicy.Preferred, QSizePolicy.Minimum)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(GroupBox.sizePolicy().hasHeightForWidth())
GroupBox.setSizePolicy(sizePolicy)
self.verticalLayout_2 = QVBoxLayout(GroupBox)
self.verticalLayout_2.setObjectName(u"verticalLayout_2")
self.groupBox_occupancy_histogram = QGroupBox(GroupBox)
self.groupBox_occupancy_histogram.setObjectName(
u"groupBox_occupancy_histogram")
self.verticalLayout = QVBoxLayout(self.groupBox_occupancy_histogram)
self.verticalLayout.setObjectName(u"verticalLayout")
self.horizontalLayout = QHBoxLayout()
self.horizontalLayout.setObjectName(u"horizontalLayout")
self.label_56 = QLabel(self.groupBox_occupancy_histogram)
self.label_56.setObjectName(u"label_56")
self.label_56.setMaximumSize(QSize(16777215, 16777215))
self.label_56.setAlignment(Qt.AlignRight | Qt.AlignTrailing
| Qt.AlignVCenter)
self.horizontalLayout.addWidget(self.label_56)
self.lineEdit_bins = QLineEdit(self.groupBox_occupancy_histogram)
self.lineEdit_bins.setObjectName(u"lineEdit_bins")
self.lineEdit_bins.setMinimumSize(QSize(50, 0))
self.lineEdit_bins.setMaximumSize(QSize(50, 16777215))
self.horizontalLayout.addWidget(self.lineEdit_bins)
self.horizontalSpacer_3 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout.addItem(self.horizontalSpacer_3)
self.label_55 = QLabel(self.groupBox_occupancy_histogram)
self.label_55.setObjectName(u"label_55")
self.label_55.setMaximumSize(QSize(16777215, 16777215))
self.label_55.setAlignment(Qt.AlignRight | Qt.AlignTrailing
| Qt.AlignVCenter)
self.horizontalLayout.addWidget(self.label_55)
self.lineEdit_minimum = QLineEdit(self.groupBox_occupancy_histogram)
self.lineEdit_minimum.setObjectName(u"lineEdit_minimum")
self.lineEdit_minimum.setMinimumSize(QSize(50, 0))
self.lineEdit_minimum.setMaximumSize(QSize(50, 16777215))
self.horizontalLayout.addWidget(self.lineEdit_minimum)
self.horizontalSpacer_2 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout.addItem(self.horizontalSpacer_2)
self.label_17 = QLabel(self.groupBox_occupancy_histogram)
self.label_17.setObjectName(u"label_17")
self.label_17.setAlignment(Qt.AlignRight | Qt.AlignTrailing
| Qt.AlignVCenter)
self.horizontalLayout.addWidget(self.label_17)
self.lineEdit_maximum = QLineEdit(self.groupBox_occupancy_histogram)
self.lineEdit_maximum.setObjectName(u"lineEdit_maximum")
self.lineEdit_maximum.setMinimumSize(QSize(50, 0))
self.lineEdit_maximum.setMaximumSize(QSize(50, 16777215))
self.horizontalLayout.addWidget(self.lineEdit_maximum)
self.verticalLayout.addLayout(self.horizontalLayout)
self.horizontalLayout_7 = QHBoxLayout()
self.horizontalLayout_7.setObjectName(u"horizontalLayout_7")
self.checkBox_cumulative_histogram = QCheckBox(
self.groupBox_occupancy_histogram)
self.checkBox_cumulative_histogram.setObjectName(
u"checkBox_cumulative_histogram")
self.horizontalLayout_7.addWidget(self.checkBox_cumulative_histogram)
self.horizontalSpacer_12 = QSpacerItem(40, 20, QSizePolicy.Fixed,
QSizePolicy.Minimum)
self.horizontalLayout_7.addItem(self.horizontalSpacer_12)
self.checkBox_stacked_histogram = QCheckBox(
self.groupBox_occupancy_histogram)
self.checkBox_stacked_histogram.setObjectName(
u"checkBox_stacked_histogram")
self.horizontalLayout_7.addWidget(self.checkBox_stacked_histogram)
self.horizontalSpacer_11 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_7.addItem(self.horizontalSpacer_11)
self.verticalLayout.addLayout(self.horizontalLayout_7)
self.horizontalLayout_6 = QHBoxLayout()
self.horizontalLayout_6.setObjectName(u"horizontalLayout_6")
self.checkBox_color_segments_occupancy = QCheckBox(
self.groupBox_occupancy_histogram)
self.checkBox_color_segments_occupancy.setObjectName(
u"checkBox_color_segments_occupancy")
self.checkBox_color_segments_occupancy.setChecked(True)
self.horizontalLayout_6.addWidget(
self.checkBox_color_segments_occupancy)
self.horizontalSpacer_9 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_6.addItem(self.horizontalSpacer_9)
self.verticalLayout.addLayout(self.horizontalLayout_6)
self.horizontalLayout_2 = QHBoxLayout()
self.horizontalLayout_2.setObjectName(u"horizontalLayout_2")
self.horizontalSpacer = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_2.addItem(self.horizontalSpacer)
self.pushButton_save_occupancy = QPushButton(
self.groupBox_occupancy_histogram)
self.pushButton_save_occupancy.setObjectName(
u"pushButton_save_occupancy")
self.horizontalLayout_2.addWidget(self.pushButton_save_occupancy)
self.pushButton_plot_occupancy = QPushButton(
self.groupBox_occupancy_histogram)
self.pushButton_plot_occupancy.setObjectName(
u"pushButton_plot_occupancy")
self.pushButton_plot_occupancy.setAutoDefault(False)
self.horizontalLayout_2.addWidget(self.pushButton_plot_occupancy)
self.verticalLayout.addLayout(self.horizontalLayout_2)
self.verticalLayout_2.addWidget(self.groupBox_occupancy_histogram)
self.verticalSpacer_2 = QSpacerItem(20, 40, QSizePolicy.Minimum,
QSizePolicy.Expanding)
self.verticalLayout_2.addItem(self.verticalSpacer_2)
self.groupBox_nb_connections = QGroupBox(GroupBox)
self.groupBox_nb_connections.setObjectName(u"groupBox_nb_connections")
self.verticalLayout_3 = QVBoxLayout(self.groupBox_nb_connections)
self.verticalLayout_3.setObjectName(u"verticalLayout_3")
self.horizontalLayout_5 = QHBoxLayout()
self.horizontalLayout_5.setObjectName(u"horizontalLayout_5")
self.checkBox_color_segments_timeseries = QCheckBox(
self.groupBox_nb_connections)
self.checkBox_color_segments_timeseries.setObjectName(
u"checkBox_color_segments_timeseries")
self.checkBox_color_segments_timeseries.setChecked(True)
self.horizontalLayout_5.addWidget(
self.checkBox_color_segments_timeseries)
self.horizontalSpacer_7 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_5.addItem(self.horizontalSpacer_7)
self.verticalLayout_3.addLayout(self.horizontalLayout_5)
self.horizontalLayout_4 = QHBoxLayout()
self.horizontalLayout_4.setObjectName(u"horizontalLayout_4")
self.horizontalSpacer_5 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_4.addItem(self.horizontalSpacer_5)
self.pushButton_save_timeseries = QPushButton(
self.groupBox_nb_connections)
self.pushButton_save_timeseries.setObjectName(
u"pushButton_save_timeseries")
self.horizontalLayout_4.addWidget(self.pushButton_save_timeseries)
self.pushButton_plot_timeseries = QPushButton(
self.groupBox_nb_connections)
self.pushButton_plot_timeseries.setObjectName(
u"pushButton_plot_timeseries")
self.pushButton_plot_timeseries.setAutoDefault(False)
self.horizontalLayout_4.addWidget(self.pushButton_plot_timeseries)
self.verticalLayout_3.addLayout(self.horizontalLayout_4)
self.verticalLayout_2.addWidget(self.groupBox_nb_connections)
self.verticalSpacer = QSpacerItem(20, 40, QSizePolicy.Minimum,
QSizePolicy.Expanding)
self.verticalLayout_2.addItem(self.verticalSpacer)
self.groupBox_joint_occupancy = QGroupBox(GroupBox)
self.groupBox_joint_occupancy.setObjectName(
u"groupBox_joint_occupancy")
self.verticalLayout_4 = QVBoxLayout(self.groupBox_joint_occupancy)
self.verticalLayout_4.setObjectName(u"verticalLayout_4")
self.horizontalLayout_10 = QHBoxLayout()
self.horizontalLayout_10.setObjectName(u"horizontalLayout_10")
self.radioButton_scatter = QRadioButton(self.groupBox_joint_occupancy)
self.radioButton_scatter.setObjectName(u"radioButton_scatter")
self.radioButton_scatter.setChecked(True)
self.horizontalLayout_10.addWidget(self.radioButton_scatter)
self.label_3 = QLabel(self.groupBox_joint_occupancy)
self.label_3.setObjectName(u"label_3")
self.horizontalLayout_10.addWidget(self.label_3)
self.lineEdit_scatter_size = QLineEdit(self.groupBox_joint_occupancy)
self.lineEdit_scatter_size.setObjectName(u"lineEdit_scatter_size")
self.lineEdit_scatter_size.setMaximumSize(QSize(50, 16777215))
self.horizontalLayout_10.addWidget(self.lineEdit_scatter_size)
self.horizontalSpacer_10 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_10.addItem(self.horizontalSpacer_10)
self.verticalLayout_4.addLayout(self.horizontalLayout_10)
self.horizontalLayout_3 = QHBoxLayout()
self.horizontalLayout_3.setObjectName(u"horizontalLayout_3")
self.radioButton_heatmap = QRadioButton(self.groupBox_joint_occupancy)
self.radioButton_heatmap.setObjectName(u"radioButton_heatmap")
self.horizontalLayout_3.addWidget(self.radioButton_heatmap)
self.horizontalSpacer_4 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_3.addItem(self.horizontalSpacer_4)
self.pushButton_save_jo = QPushButton(self.groupBox_joint_occupancy)
self.pushButton_save_jo.setObjectName(u"pushButton_save_jo")
self.horizontalLayout_3.addWidget(self.pushButton_save_jo)
self.pushButton_plot_jo = QPushButton(self.groupBox_joint_occupancy)
self.pushButton_plot_jo.setObjectName(u"pushButton_plot_jo")
self.pushButton_plot_jo.setAutoDefault(False)
self.horizontalLayout_3.addWidget(self.pushButton_plot_jo)
self.verticalLayout_4.addLayout(self.horizontalLayout_3)
self.verticalLayout_2.addWidget(self.groupBox_joint_occupancy)
self.retranslateUi(GroupBox)
QMetaObject.connectSlotsByName(GroupBox)
# setupUi
def retranslateUi(self, GroupBox):
GroupBox.setWindowTitle(
QCoreApplication.translate("GroupBox", u"GroupBox", None))
self.groupBox_occupancy_histogram.setTitle(
QCoreApplication.translate("GroupBox", u"Occupancy histogram",
None))
self.label_56.setText(
QCoreApplication.translate("GroupBox", u"# of bins", None))
self.lineEdit_bins.setText(
QCoreApplication.translate("GroupBox", u"10", None))
self.label_55.setText(
QCoreApplication.translate("GroupBox", u"min. occupancy", None))
self.lineEdit_minimum.setText(
QCoreApplication.translate("GroupBox", u"0.0", None))
self.label_17.setText(
QCoreApplication.translate("GroupBox", u"max. occupancy", None))
self.lineEdit_maximum.setText(
QCoreApplication.translate("GroupBox", u"1.0", None))
self.checkBox_cumulative_histogram.setText(
QCoreApplication.translate("GroupBox", u"cumulative", None))
self.checkBox_stacked_histogram.setText(
QCoreApplication.translate("GroupBox", u"stacked", None))
#if QT_CONFIG(tooltip)
self.checkBox_color_segments_occupancy.setToolTip(
QCoreApplication.translate(
"GroupBox",
u"<html><head/><body><p align=\"justify\">Toggle if histogram bars are colored by segment or molecule. With colors turned on, comparing to other analyses is not possible.</p></body></html>",
None))
#endif // QT_CONFIG(tooltip)
self.checkBox_color_segments_occupancy.setText(
QCoreApplication.translate("GroupBox", u"color by segment", None))
self.pushButton_save_occupancy.setText(
QCoreApplication.translate("GroupBox", u"Data", None))
#if QT_CONFIG(tooltip)
self.pushButton_plot_occupancy.setToolTip(
QCoreApplication.translate(
"GroupBox",
u"<html><head/><body><p>Compute histogram of H bond occupancies. Counts the number of H bonds with an occupancy equal or greater than the respective value.</p></body></html>",
None))
#endif // QT_CONFIG(tooltip)
self.pushButton_plot_occupancy.setText(
QCoreApplication.translate("GroupBox", u"Plot", None))
self.groupBox_nb_connections.setTitle(
QCoreApplication.translate("GroupBox",
u"Number of connections time series",
None))
#if QT_CONFIG(tooltip)
self.checkBox_color_segments_timeseries.setToolTip(
QCoreApplication.translate(
"GroupBox",
u"<html><head/><body><p align=\"justify\">Toggle if histogram bars are colored by segment or molecule. With colors turned on, comparing to other analyses is not possible.</p></body></html>",
None))
#endif // QT_CONFIG(tooltip)
self.checkBox_color_segments_timeseries.setText(
QCoreApplication.translate("GroupBox", u"color by segment", None))
self.pushButton_save_timeseries.setText(
QCoreApplication.translate("GroupBox", u"Data", None))
#if QT_CONFIG(tooltip)
self.pushButton_plot_timeseries.setToolTip(
QCoreApplication.translate(
"GroupBox",
u"<html><head/><body><p align=\"justify\">Compute the number of H bonds per frame.</p></body></html>",
None))
#endif // QT_CONFIG(tooltip)
self.pushButton_plot_timeseries.setText(
QCoreApplication.translate("GroupBox", u"Plot", None))
self.groupBox_joint_occupancy.setTitle(
QCoreApplication.translate("GroupBox", u"Joint Occupancy", None))
self.radioButton_scatter.setText(
QCoreApplication.translate("GroupBox", u"scatter plot", None))
self.label_3.setText(
QCoreApplication.translate("GroupBox", u"with dot size", None))
self.lineEdit_scatter_size.setText(
QCoreApplication.translate("GroupBox", u"1", None))
self.lineEdit_scatter_size.setPlaceholderText(
QCoreApplication.translate("GroupBox", u"0 - 100", None))
self.radioButton_heatmap.setText(
QCoreApplication.translate("GroupBox", u"heatmap", None))
self.pushButton_save_jo.setText(
QCoreApplication.translate("GroupBox", u"Data", None))
#if QT_CONFIG(tooltip)
self.pushButton_plot_jo.setToolTip(
QCoreApplication.translate(
"GroupBox",
u"<html><head/><body><p align=\"justify\">Compute the joint occupancy of the H bond network. The joint occupancy is true, if all H bonds of the network are present in a frame and false otherwise.</p></body></html>",
None))
#endif // QT_CONFIG(tooltip)
self.pushButton_plot_jo.setText(
QCoreApplication.translate("GroupBox", u"Plot", None))
class MainWindow(QMainWindow):
def __init__(self, ui_file, devMode, parent=None):
super(MainWindow, self).__init__()
self.uiFileName = ui_file # use this if there are multiple UI files
if devMode == "development": # use ui file directly made by QDesigner
uiFile = QFile(ui_file)
uiFile.open(QFile.ReadOnly) # read in UI for the form
loader = QUiLoader()
self.window = loader.load(uiFile)
uiFile.close()
else: #deployment - use .py version of ui file, with slightly different setup
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.getParts() # identify form objects
self.connectParts() # connect buttons to operations
self.convs = Converters(
) # load converters for main conversion categories
self.yc = YearConverters(
) # load converters for japanese years, zodiac years
self.mess = Mess() # instructions and messages in local language
self.validFloat = QDoubleValidator()
self.validYear = QIntValidator()
self.validYear.setRange(1, 9999) # used for years
self.btnConvert.hide()
self.widgetSetup("start") # initial conditions for form
if devMode == "development": self.window.show()
else: self.show()
def widgetSetup(self, themode): # based on which main button is pressed
self.themode = themode # this is set when a main button is pressed, or on initial load
self.emptyConvLayout(
) # get rid of old radio buttons if they exist, hide input/output, etc.
thetext, thestyle = makeHeader1(
themode, self.uiFileName) # make heading for convType = themode
self.header1.setStyleSheet(
thestyle) # can have different background colors
self.header1.setText(thetext)
self.header1.show()
self.hideBigInstructions()
if themode in self.convs.getValidConvTypes(
): # set up radio buttons for conversions
oneConvTypeInfo = self.convs.convTypeToConvInfo(
themode) # get convCodes, displays for this convType
for ix, (convCode, convDisplay) in enumerate(
oneConvTypeInfo
): # iterate through enumerated list of tuples
self.oneRadio = QRadioButton(
"{}".format(convDisplay)) # text for button
self.oneRadio.setObjectName("object_{}".format(
convCode)) # to be used later by sender()
self.oneRadio.setStyleSheet(
makeStyleSheet("radiobutton", self.uiFileName))
self.layoutConv.addWidget(self.oneRadio)
self.oneRadio.clicked.connect(
self.convSetup
) # convSetup will call sender() to find convCode
if ix == 0:
self.oneRadio.setFocus(
) # set focus on first button in list
if themode == "fromjpyear": # set up radio buttons for modern eras
self.fromjpyearmode = "modern" # start with modern eras only
self.showJpEras()
if themode == "fromjpyearhistoric": # set up radio buttons for all eras
self.fromjpyearmode = "all" # start with modern eras only
self.showJpEras()
if themode == "tojpyear": # no choices, go straight to input box
self.showInstructions(self.mess.getToJpYear(self.yc.getMinYear()),
"")
self.input1.setText(str(
self.yc.getNowYear())) # start with current year
self.setUpValidator()
self.convertUnits()
if themode == "zodiac": # no choices, go straight to input box
self.showInstructions(self.mess.getEnterYearZodiac(), "")
self.input1.setText(str(
self.yc.getNowYear())) # start with current year
self.setUpValidator()
self.convertUnits()
if themode == "start":
self.btnFromMetric.setFocus()
self.showBigInstructions(self.mess.getStartMsg2())
def showBigInstructions(self, themsg):
self.instructions2.setText(themsg)
self.scrollArea.hide()
self.instructions2.show()
def hideBigInstructions(self):
self.scrollArea.show()
self.instructions2.hide()
def showJpEras(self): # display radio buttons for Japanese eras
jpEraList = self.yc.getEraNamesPlusCodes(
self.fromjpyearmode) # modern or all
for ix, (eraText, eraCode) in enumerate(jpEraList):
self.oneRadio = QRadioButton(
"{}".format(eraText)) # text for button
self.oneRadio.setObjectName(
"object_{}".format(eraCode)) # to be used later by sender()
self.oneRadio.setStyleSheet(
makeStyleSheet("radiobutton", self.uiFileName))
self.layoutConv.addWidget(self.oneRadio)
self.oneRadio.clicked.connect(
self.eraSetup) # eraSetup will call sender() to find eraCode
if ix == 0: self.oneRadio.setFocus() # set focus on first button
if self.fromjpyearmode == "modern":
self.oneRadio = QRadioButton(
"{}".format("Show more eras")) # now add option for more eras
self.oneRadio.setObjectName(
"object_{}".format("all")) # to be used later by sender()
else:
self.oneRadio = QRadioButton("{}".format(
"Show fewer eras")) # now add option to return to modern eras
self.oneRadio.setObjectName(
"object_{}".format("modern")) # to be used later by sender()
self.oneRadio.setStyleSheet(
makeStyleSheet("radiobutton", self.uiFileName))
self.layoutConv.addWidget(self.oneRadio)
self.oneRadio.clicked.connect(
self.eraSetup) # eraSetup will call sender() to find eraCode
def eraSetup(self): # this is called when radio button is chosen
theEra = self.getCodeFromSenderName(
) # era or mode is determined by object name of sending radio button
if theEra in ["all", "modern"]: # switch between modern and all
self.fromjpyearmode = theEra # set the mode here
self.emptyConvLayout() # clear former list
if theEra == "all": self.widgetSetup("fromjpyearhistoric")
else: self.widgetSetup("fromjpyear")
else: # theEra will be eraCode for chosen era
self.chosenEra = theEra # set this property
if self.yc.getNowEra() == theEra:
theHint = "(1- )" # no final year if it's the current era
else:
theHint = "(1-{})".format(
self.yc.getNumYears(theEra)) # final year in that era
self.showInstructions(
self.mess.getFromJpYear(self.yc.getENameUnparsed(theEra)),
theHint)
self.output2.hide()
self.setUpValidator()
def setUpValidator(self):
if self.themode in self.convs.getValidConvTypes(): # measures
if self.convs.isTempConv(self.theConvCode):
self.validFloat.setBottom(
-999999) # temperatures can be negative
else:
self.validFloat.setBottom(
0.0) # other measures can't be negative
self.input1.setValidator(self.validFloat)
if self.themode in [
"fromjpyear", "fromjpyearhistoric", "tojpyear", "zodiac"
]:
self.input1.setValidator(
self.validYear) # range already set to 1-9999
def convSetup(self): # set up based on which radio button was set
self.theConvCode = self.getCodeFromSenderName(
) # get the code based on the sending button, and set it
self.showInstructions(self.mess.getEnterAmt())
self.setUpValidator()
self.input1.setText("1") # show units=1 to start
self.convertUnits()
def getCodeFromSenderName(self): # based on objectName of sender button
sending_button = self.sender()
return str(sending_button.objectName()).replace("object_", "")
def convertUnits(self): # main conversion routine
pstart = self.mess.getPstart(
) # get paragraph HTML from Message object
pstopstart = self.mess.getPstopstart()
pstop = self.mess.getPstop()
jcol = self.mess.getJColor() # special color for Japanese text
if len(self.input1.text()) < 1: # test for blank input
self.output2.setText(
self.mess.getBlankConvertMsg()) # show error message
self.output2.show()
return
if self.themode in self.convs.getValidConvTypes(
): # standard conversions: fromjpmeasure, tometric, etc
amt1Text = self.input1.text()
amt1 = strToNum(amt1Text)
if self.convs.isTooCold(self.theConvCode, amt1):
eqString = self.mess.getTooCold(
) #check for temp below abs zero
else:
eqString = self.convs.getEquation(self.theConvCode, amt1,
" =" + pstopstart, jcol)
self.output2.setText(
pstart + eqString +
pstop) # use paragraphs for better control of appearance
elif self.themode == "tojpyear": # int'l year to Japanese year
try:
iYear = int(self.input1.text())
yearDisplay = self.mess.makeJYearDisplay(
self.yc.iYearToJYear(iYear, jcol), iYear)
except ValueError as errorMsg:
yearDisplay = pstart + str(
errorMsg) + pstop # display the error message
self.output2.setText(yearDisplay)
#print (yearDisplay)
elif self.themode in ["fromjpyear", "fromjpyearhistoric"
]: # Japanese year to int'l year
jYear = int(self.input1.text()
) # validator at work, so this should be an integer
try: # raise exception if not in range
iYear = self.yc.jYearToIYear(self.chosenEra, jYear)
yearDisplay = pstart + "{} ({}) {}".format(self.yc.getENameUnparsed(self.chosenEra), \
self.yc.getJName(self.chosenEra, jcol), jYear) + \
pstopstart + self.mess.getIs() + " " + str(iYear) + pstop
except ValueError as errorMsg:
yearDisplay = pstart + str(
errorMsg) + pstop # display the error message
self.output2.setText(yearDisplay)
elif self.themode == "zodiac": # international year to zodiac sign
iYear = int(self.input1.text())
# display is HTML with paragraph, line height, and Japanese characters in color (specified in Mess class)
yearDisplay = pstart + str(iYear) + " " + self.mess.getIs() + ":" + pstopstart + \
self.mess.getYearOfThe().capitalize() + " " + self.yc.getZodEName(iYear) + pstop
self.output2.setText(yearDisplay)
zBig = self.mess.makeZodiacBigDisplay(
self.yc.getZodEName(iYear), self.yc.getZodJName(iYear, jcol),
self.yc.getZodJZName(iYear, jcol))
self.showBigInstructions(zBig)
self.output2.show() # common to all conversion types
def emptyConvLayout(
self): # clear the radio buttons in the converter/jpYear layout
for i in reversed(range(
self.layoutConv.count())): # delete them in reverse order
self.layoutConv.itemAt(i).widget().deleteLater()
self.instructions1.hide()
self.input1.setPlaceholderText("") # clear previous hints
self.input1.hide() # conversion not chosen yet, so hide this
self.btnConvert.hide() # conversion not chosen yet, so hide this
self.output2.hide() # conversion not chosen yet, so hide this
def showInstructions(
self,
instructionsText,
inputHint=""): # position UI elements, set label, show input box
self.instructions1.setText(instructionsText)
self.instructions1.show()
self.input1.setText("")
self.input1.setPlaceholderText(inputHint)
self.input1.show()
self.btnConvert.show()
self.input1.setFocus()
def convertQuickly(self): # testing
if not self.input1.text(): amt = 0
else: amt = float(self.input1.text()) * 2.0
amtString = '{} kilograms'.format(amt)
self.output2.setText(amtString)
def getParts(self): # map form elements to object properties
self.centralw = self.findWidget(QWidget, 'central_widget')
self.input1 = self.findWidget(QLineEdit, 'input1')
self.output2 = self.findWidget(QTextEdit, 'label_output2')
self.header1 = self.findWidget(QLabel, 'label_header1')
self.btnConvert = self.findWidget(QPushButton, 'button_convert')
self.btnExit = self.findWidget(QPushButton, 'button_exit')
self.btnFromMetric = self.findWidget(QPushButton, 'button_from_metric')
self.btnToMetric = self.findWidget(QPushButton, 'button_to_metric')
self.btnFromJpMeasure = self.findWidget(QPushButton,
'button_from_jpmeasure')
self.btnToJpMeasure = self.findWidget(QPushButton,
'button_to_jpmeasure')
self.btnFromJpYear = self.findWidget(QPushButton, 'button_from_jpyear')
self.btnToJpYear = self.findWidget(QPushButton, 'button_to_jpyear')
self.btnZodiac = self.findWidget(QPushButton, 'button_zodiac')
self.scrollArea = self.findWidget(QScrollArea, 'conv_layout')
content_widget = QWidget(
) # now add the QVBoxLayout widget programmatically, for scrolling
self.scrollArea.setWidget(content_widget)
self.scrollArea.setWidgetResizable(True)
self.layoutConv = QVBoxLayout(content_widget)
self.layoutConv.setAlignment(
Qt.AlignTop
) # don't evenly space the radio buttons, but start at the top
self.instructions1 = self.findWidget(QLabel, 'label_instructions1')
self.instructions2 = self.findWidget(QLabel, 'label_instructions2')
self.menuExit = self.findWidget(QAction, 'action_exit')
self.menuFromMetric = self.findWidget(QAction, 'action_from_metric')
self.menuToMetric = self.findWidget(QAction, 'action_to_metric')
self.menuFromJpMeasure = self.findWidget(QAction,
'action_from_jpmeasure')
self.menuToJpMeasure = self.findWidget(QAction, 'action_to_jpmeasure')
self.menuFromJpYear = self.findWidget(QAction, 'action_from_jpyear')
self.menuFromJpYearHistoric = self.findWidget(
QAction, 'action_from_jpyear_historic')
self.menuToJpYear = self.findWidget(QAction, 'action_to_jpyear')
self.menuZodiac = self.findWidget(QAction, 'action_zodiac')
self.menubar = self.findWidget(QMenuBar, 'menubar')
if self.uiFileName == "main3.ui":
self.menubar.setStyleSheet(
getMenuStyle("main3.ui")) # in jpconvhelper.py
def findWidget(self, widgetType, widgetName):
if devMode == "development":
return self.window.findChild(widgetType, widgetName)
else:
return self.findChild(widgetType, widgetName)
def connectParts(self): # connect buttons and menu actions to operations
self.input1.returnPressed.connect(self.convertUnits)
self.btnConvert.clicked.connect(self.convertUnits)
self.btnExit.clicked.connect(self.exitHandler)
self.menuExit.triggered.connect(self.exitHandler)
self.btnFromMetric.clicked.connect(
lambda: self.widgetSetup("frommetric"))
self.menuFromMetric.triggered.connect(
lambda: self.widgetSetup("frommetric"))
self.btnToMetric.clicked.connect(lambda: self.widgetSetup("tometric"))
self.menuToMetric.triggered.connect(
lambda: self.widgetSetup("tometric"))
self.btnFromJpMeasure.clicked.connect(
lambda: self.widgetSetup("fromjpmeasure"))
self.menuFromJpMeasure.triggered.connect(
lambda: self.widgetSetup("fromjpmeasure"))
self.btnToJpMeasure.clicked.connect(
lambda: self.widgetSetup("tojpmeasure"))
self.menuToJpMeasure.triggered.connect(
lambda: self.widgetSetup("tojpmeasure"))
self.btnFromJpYear.clicked.connect(
lambda: self.widgetSetup("fromjpyear"))
self.menuFromJpYear.triggered.connect(
lambda: self.widgetSetup("fromjpyear"))
self.menuFromJpYearHistoric.triggered.connect(
lambda: self.widgetSetup("fromjpyearhistoric"))
self.btnToJpYear.clicked.connect(lambda: self.widgetSetup("tojpyear"))
self.menuToJpYear.triggered.connect(
lambda: self.widgetSetup("tojpyear"))
self.btnZodiac.clicked.connect(lambda: self.widgetSetup("zodiac"))
self.menuZodiac.triggered.connect(lambda: self.widgetSetup("zodiac"))
def exitHandler(self):
app.exit()
class Ui_GroupBox(object):
def setupUi(self, GroupBox):
if not GroupBox.objectName():
GroupBox.setObjectName(u"GroupBox")
GroupBox.resize(528, 576)
sizePolicy = QSizePolicy(QSizePolicy.Preferred, QSizePolicy.Minimum)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(GroupBox.sizePolicy().hasHeightForWidth())
GroupBox.setSizePolicy(sizePolicy)
self.verticalLayout_2 = QVBoxLayout(GroupBox)
self.verticalLayout_2.setObjectName(u"verticalLayout_2")
self.groupBox = QGroupBox(GroupBox)
self.groupBox.setObjectName(u"groupBox")
self.verticalLayout_4 = QVBoxLayout(self.groupBox)
self.verticalLayout_4.setObjectName(u"verticalLayout_4")
self.horizontalLayout_7 = QHBoxLayout()
self.horizontalLayout_7.setObjectName(u"horizontalLayout_7")
self.horizontalSpacer_7 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_7.addItem(self.horizontalSpacer_7)
self.pushButton_degree_save = QPushButton(self.groupBox)
self.pushButton_degree_save.setObjectName(u"pushButton_degree_save")
self.horizontalLayout_7.addWidget(self.pushButton_degree_save)
self.verticalLayout_4.addLayout(self.horizontalLayout_7)
self.verticalLayout_2.addWidget(self.groupBox)
self.verticalSpacer_2 = QSpacerItem(20, 40, QSizePolicy.Minimum,
QSizePolicy.Expanding)
self.verticalLayout_2.addItem(self.verticalSpacer_2)
self.groupBox_degree = QGroupBox(GroupBox)
self.groupBox_degree.setObjectName(u"groupBox_degree")
self.verticalLayout_3 = QVBoxLayout(self.groupBox_degree)
self.verticalLayout_3.setObjectName(u"verticalLayout_3")
self.horizontalLayout_2 = QHBoxLayout()
self.horizontalLayout_2.setObjectName(u"horizontalLayout_2")
self.radioButton_betweenness = QRadioButton(self.groupBox_degree)
self.radioButton_betweenness.setObjectName(u"radioButton_betweenness")
self.horizontalLayout_2.addWidget(self.radioButton_betweenness)
self.radioButton_degree = QRadioButton(self.groupBox_degree)
self.radioButton_degree.setObjectName(u"radioButton_degree")
self.radioButton_degree.setChecked(True)
self.horizontalLayout_2.addWidget(self.radioButton_degree)
self.horizontalSpacer_5 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_2.addItem(self.horizontalSpacer_5)
self.verticalLayout_3.addLayout(self.horizontalLayout_2)
self.checkBox_averaged_frames = QCheckBox(self.groupBox_degree)
self.checkBox_averaged_frames.setObjectName(
u"checkBox_averaged_frames")
self.checkBox_averaged_frames.setChecked(True)
self.verticalLayout_3.addWidget(self.checkBox_averaged_frames)
self.checkBox_normalized = QCheckBox(self.groupBox_degree)
self.checkBox_normalized.setObjectName(u"checkBox_normalized")
self.verticalLayout_3.addWidget(self.checkBox_normalized)
self.groupBox_per_residue = QGroupBox(self.groupBox_degree)
self.groupBox_per_residue.setObjectName(u"groupBox_per_residue")
self.groupBox_per_residue.setCheckable(True)
self.verticalLayout = QVBoxLayout(self.groupBox_per_residue)
self.verticalLayout.setObjectName(u"verticalLayout")
self.horizontalLayout_6 = QHBoxLayout()
self.horizontalLayout_6.setObjectName(u"horizontalLayout_6")
self.label_2 = QLabel(self.groupBox_per_residue)
self.label_2.setObjectName(u"label_2")
self.horizontalLayout_6.addWidget(self.label_2)
self.comboBox = QComboBox(self.groupBox_per_residue)
self.comboBox.setObjectName(u"comboBox")
self.horizontalLayout_6.addWidget(self.comboBox)
self.horizontalSpacer_2 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_6.addItem(self.horizontalSpacer_2)
self.verticalLayout.addLayout(self.horizontalLayout_6)
self.horizontalLayout = QHBoxLayout()
self.horizontalLayout.setObjectName(u"horizontalLayout")
self.label_10 = QLabel(self.groupBox_per_residue)
self.label_10.setObjectName(u"label_10")
self.label_10.setAlignment(Qt.AlignRight | Qt.AlignTrailing
| Qt.AlignVCenter)
self.horizontalLayout.addWidget(self.label_10)
self.lineEdit_degree_residue_ids = QLineEdit(self.groupBox_per_residue)
self.lineEdit_degree_residue_ids.setObjectName(
u"lineEdit_degree_residue_ids")
self.horizontalLayout.addWidget(self.lineEdit_degree_residue_ids)
self.horizontalSpacer_6 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout.addItem(self.horizontalSpacer_6)
self.verticalLayout.addLayout(self.horizontalLayout)
self.verticalLayout_3.addWidget(self.groupBox_per_residue)
self.groupBox_histogram = QGroupBox(self.groupBox_degree)
self.groupBox_histogram.setObjectName(u"groupBox_histogram")
self.groupBox_histogram.setCheckable(True)
self.groupBox_histogram.setChecked(False)
self.verticalLayout_5 = QVBoxLayout(self.groupBox_histogram)
self.verticalLayout_5.setObjectName(u"verticalLayout_5")
self.horizontalLayout_3 = QHBoxLayout()
self.horizontalLayout_3.setObjectName(u"horizontalLayout_3")
self.label_56 = QLabel(self.groupBox_histogram)
self.label_56.setObjectName(u"label_56")
self.label_56.setMaximumSize(QSize(16777215, 16777215))
self.label_56.setAlignment(Qt.AlignRight | Qt.AlignTrailing
| Qt.AlignVCenter)
self.horizontalLayout_3.addWidget(self.label_56)
self.lineEdit_bins = QLineEdit(self.groupBox_histogram)
self.lineEdit_bins.setObjectName(u"lineEdit_bins")
self.lineEdit_bins.setMinimumSize(QSize(50, 0))
self.lineEdit_bins.setMaximumSize(QSize(50, 16777215))
self.horizontalLayout_3.addWidget(self.lineEdit_bins)
self.label_55 = QLabel(self.groupBox_histogram)
self.label_55.setObjectName(u"label_55")
self.label_55.setMaximumSize(QSize(16777215, 16777215))
self.label_55.setAlignment(Qt.AlignRight | Qt.AlignTrailing
| Qt.AlignVCenter)
self.horizontalLayout_3.addWidget(self.label_55)
self.lineEdit_minimum = QLineEdit(self.groupBox_histogram)
self.lineEdit_minimum.setObjectName(u"lineEdit_minimum")
self.lineEdit_minimum.setMinimumSize(QSize(50, 0))
self.lineEdit_minimum.setMaximumSize(QSize(50, 16777215))
self.horizontalLayout_3.addWidget(self.lineEdit_minimum)
self.label_17 = QLabel(self.groupBox_histogram)
self.label_17.setObjectName(u"label_17")
self.label_17.setAlignment(Qt.AlignRight | Qt.AlignTrailing
| Qt.AlignVCenter)
self.horizontalLayout_3.addWidget(self.label_17)
self.lineEdit_maximum = QLineEdit(self.groupBox_histogram)
self.lineEdit_maximum.setObjectName(u"lineEdit_maximum")
self.lineEdit_maximum.setMinimumSize(QSize(50, 0))
self.lineEdit_maximum.setMaximumSize(QSize(50, 16777215))
self.horizontalLayout_3.addWidget(self.lineEdit_maximum)
self.horizontalSpacer_3 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_3.addItem(self.horizontalSpacer_3)
self.verticalLayout_5.addLayout(self.horizontalLayout_3)
self.horizontalLayout_8 = QHBoxLayout()
self.horizontalLayout_8.setObjectName(u"horizontalLayout_8")
self.checkBox_cumulative_histogram = QCheckBox(self.groupBox_histogram)
self.checkBox_cumulative_histogram.setObjectName(
u"checkBox_cumulative_histogram")
self.horizontalLayout_8.addWidget(self.checkBox_cumulative_histogram)
self.horizontalSpacer_12 = QSpacerItem(40, 20, QSizePolicy.Fixed,
QSizePolicy.Minimum)
self.horizontalLayout_8.addItem(self.horizontalSpacer_12)
self.checkBox_stacked_histogram = QCheckBox(self.groupBox_histogram)
self.checkBox_stacked_histogram.setObjectName(
u"checkBox_stacked_histogram")
self.horizontalLayout_8.addWidget(self.checkBox_stacked_histogram)
self.horizontalSpacer_11 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_8.addItem(self.horizontalSpacer_11)
self.verticalLayout_5.addLayout(self.horizontalLayout_8)
self.horizontalLayout_9 = QHBoxLayout()
self.horizontalLayout_9.setObjectName(u"horizontalLayout_9")
self.checkBox_color_segments_occupancy = QCheckBox(
self.groupBox_histogram)
self.checkBox_color_segments_occupancy.setObjectName(
u"checkBox_color_segments_occupancy")
self.checkBox_color_segments_occupancy.setChecked(True)
self.horizontalLayout_9.addWidget(
self.checkBox_color_segments_occupancy)
self.horizontalSpacer_9 = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_9.addItem(self.horizontalSpacer_9)
self.verticalLayout_5.addLayout(self.horizontalLayout_9)
self.verticalLayout_3.addWidget(self.groupBox_histogram)
self.horizontalLayout_5 = QHBoxLayout()
self.horizontalLayout_5.setObjectName(u"horizontalLayout_5")
self.horizontalSpacer = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.horizontalLayout_5.addItem(self.horizontalSpacer)
self.pushButton_degree_plot = QPushButton(self.groupBox_degree)
self.pushButton_degree_plot.setObjectName(u"pushButton_degree_plot")
self.pushButton_degree_plot.setAutoDefault(False)
self.horizontalLayout_5.addWidget(self.pushButton_degree_plot)
self.verticalLayout_3.addLayout(self.horizontalLayout_5)
self.verticalLayout_2.addWidget(self.groupBox_degree)
self.retranslateUi(GroupBox)
QMetaObject.connectSlotsByName(GroupBox)
# setupUi
def retranslateUi(self, GroupBox):
GroupBox.setWindowTitle(
QCoreApplication.translate("GroupBox", u"GroupBox", None))
self.groupBox.setTitle(
QCoreApplication.translate("GroupBox", u"All centrality measures",
None))
self.pushButton_degree_save.setText(
QCoreApplication.translate("GroupBox", u"Data", None))
self.groupBox_degree.setTitle(
QCoreApplication.translate("GroupBox", u"Plots", None))
self.radioButton_betweenness.setText(
QCoreApplication.translate("GroupBox", u"betweenness centrality",
None))
self.radioButton_degree.setText(
QCoreApplication.translate("GroupBox", u"degree centrality", None))
#if QT_CONFIG(tooltip)
self.checkBox_averaged_frames.setToolTip(
QCoreApplication.translate(
"GroupBox",
u"<html><head/><body><p align=\"justify\">Toggle, if absolute number of connections or time averaged number of connections are used.</p></body></html>",
None))
#endif // QT_CONFIG(tooltip)
self.checkBox_averaged_frames.setText(
QCoreApplication.translate("GroupBox", u"average across frames",
None))
self.checkBox_normalized.setText(
QCoreApplication.translate("GroupBox", u"normalized", None))
self.groupBox_per_residue.setTitle(
QCoreApplication.translate("GroupBox", u"Per Residue", None))
self.label_2.setText(
QCoreApplication.translate("GroupBox", u"segment: ", None))
self.label_10.setText(
QCoreApplication.translate("GroupBox", u"residue ids: ", None))
self.lineEdit_degree_residue_ids.setPlaceholderText(
QCoreApplication.translate("GroupBox", u"e.g. 0-12, 20, 70-90",
None))
self.groupBox_histogram.setTitle(
QCoreApplication.translate("GroupBox", u"Histogram", None))
self.label_56.setText(
QCoreApplication.translate("GroupBox", u"# of bins", None))
self.lineEdit_bins.setText(
QCoreApplication.translate("GroupBox", u"10", None))
self.label_55.setText(
QCoreApplication.translate("GroupBox", u"min. value", None))
self.lineEdit_minimum.setText(
QCoreApplication.translate("GroupBox", u"0.0", None))
self.label_17.setText(
QCoreApplication.translate("GroupBox", u"max. value", None))
self.lineEdit_maximum.setText(
QCoreApplication.translate("GroupBox", u"1.0", None))
self.checkBox_cumulative_histogram.setText(
QCoreApplication.translate("GroupBox", u"cumulative", None))
self.checkBox_stacked_histogram.setText(
QCoreApplication.translate("GroupBox", u"stacked", None))
#if QT_CONFIG(tooltip)
self.checkBox_color_segments_occupancy.setToolTip(
QCoreApplication.translate(
"GroupBox",
u"<html><head/><body><p align=\"justify\">Toggle if histogram bars are colored by segment or molecule. With colors turned on, comparing to other analyses is not possible.</p></body></html>",
None))
#endif // QT_CONFIG(tooltip)
self.checkBox_color_segments_occupancy.setText(
QCoreApplication.translate("GroupBox", u"color by segment", None))
#if QT_CONFIG(tooltip)
self.pushButton_degree_plot.setToolTip(
QCoreApplication.translate(
"GroupBox",
u"<html><head/><body><p align=\"justify\">Compute the number of H bonds per residue. Results are colored by segment.</p></body></html>",
None))
#endif // QT_CONFIG(tooltip)
self.pushButton_degree_plot.setText(
QCoreApplication.translate("GroupBox", u"Plot", None))
class Ui_dlg_new_tool(object):
def setupUi(self, dlg_new_tool):
if not dlg_new_tool.objectName():
dlg_new_tool.setObjectName(u"dlg_new_tool")
dlg_new_tool.resize(570, 463)
dlg_new_tool.setModal(True)
self.gridLayout_2 = QGridLayout(dlg_new_tool)
self.gridLayout_2.setObjectName(u"gridLayout_2")
self.gridLayout = QGridLayout()
self.gridLayout.setObjectName(u"gridLayout")
self.te_description = QTextEdit(dlg_new_tool)
self.te_description.setObjectName(u"te_description")
self.gridLayout.addWidget(self.te_description, 3, 0, 1, 6)
self.label = QLabel(dlg_new_tool)
self.label.setObjectName(u"label")
self.gridLayout.addWidget(self.label, 0, 0, 1, 1)
self.lbl_file_exists = QLabel(dlg_new_tool)
self.lbl_file_exists.setObjectName(u"lbl_file_exists")
self.lbl_file_exists.setPixmap(QPixmap(u"../resources/OK.png"))
self.gridLayout.addWidget(self.lbl_file_exists, 0, 5, 1, 1)
self.label_5 = QLabel(dlg_new_tool)
self.label_5.setObjectName(u"label_5")
self.gridLayout.addWidget(self.label_5, 0, 3, 1, 1)
self.chk_mask_required = QCheckBox(dlg_new_tool)
self.chk_mask_required.setObjectName(u"chk_mask_required")
self.gridLayout.addWidget(self.chk_mask_required, 5, 0, 1, 6)
self.label_4 = QLabel(dlg_new_tool)
self.label_4.setObjectName(u"label_4")
self.gridLayout.addWidget(self.label_4, 0, 2, 1, 1)
self.le_tool_name = QLineEdit(dlg_new_tool)
self.le_tool_name.setObjectName(u"le_tool_name")
self.gridLayout.addWidget(self.le_tool_name, 0, 1, 1, 1)
self.label_3 = QLabel(dlg_new_tool)
self.label_3.setObjectName(u"label_3")
self.gridLayout.addWidget(self.label_3, 1, 3, 1, 1)
self.le_file_name = QLineEdit(dlg_new_tool)
self.le_file_name.setObjectName(u"le_file_name")
self.le_file_name.setReadOnly(True)
self.gridLayout.addWidget(self.le_file_name, 0, 4, 1, 1)
self.label_6 = QLabel(dlg_new_tool)
self.label_6.setObjectName(u"label_6")
font = QFont()
font.setPointSize(8)
self.label_6.setFont(font)
self.gridLayout.addWidget(self.label_6, 1, 2, 1, 1)
self.le_class_name = QLineEdit(dlg_new_tool)
self.le_class_name.setObjectName(u"le_class_name")
self.le_class_name.setReadOnly(True)
self.gridLayout.addWidget(self.le_class_name, 1, 4, 1, 1)
self.label_2 = QLabel(dlg_new_tool)
self.label_2.setObjectName(u"label_2")
self.gridLayout.addWidget(self.label_2, 2, 0, 1, 6)
self.label_7 = QLabel(dlg_new_tool)
self.label_7.setObjectName(u"label_7")
self.gridLayout.addWidget(self.label_7, 4, 0, 1, 1)
self.le_package_name = QLineEdit(dlg_new_tool)
self.le_package_name.setObjectName(u"le_package_name")
self.gridLayout.addWidget(self.le_package_name, 4, 1, 1, 5)
self.gridLayout_2.addLayout(self.gridLayout, 0, 0, 1, 2)
self.verticalLayout_4 = QVBoxLayout()
self.verticalLayout_4.setObjectName(u"verticalLayout_4")
self.groupBox = QGroupBox(dlg_new_tool)
self.groupBox.setObjectName(u"groupBox")
self.groupBox.setCheckable(False)
self.verticalLayout = QVBoxLayout(self.groupBox)
self.verticalLayout.setObjectName(u"verticalLayout")
self.rb_output_image = QRadioButton(self.groupBox)
self.rb_output_image.setObjectName(u"rb_output_image")
self.rb_output_image.setChecked(True)
self.verticalLayout.addWidget(self.rb_output_image)
self.rb_output_mask = QRadioButton(self.groupBox)
self.rb_output_mask.setObjectName(u"rb_output_mask")
self.verticalLayout.addWidget(self.rb_output_mask)
self.rb_output_data = QRadioButton(self.groupBox)
self.rb_output_data.setObjectName(u"rb_output_data")
self.verticalLayout.addWidget(self.rb_output_data)
self.rb_output_none = QRadioButton(self.groupBox)
self.rb_output_none.setObjectName(u"rb_output_none")
self.verticalLayout.addWidget(self.rb_output_none)
self.verticalLayout_4.addWidget(self.groupBox)
self.gb_pipeline_tool_groups = QGroupBox(dlg_new_tool)
self.gb_pipeline_tool_groups.setObjectName(u"gb_pipeline_tool_groups")
self.verticalLayout_4.addWidget(self.gb_pipeline_tool_groups)
self.verticalSpacer = QSpacerItem(
20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding
)
self.verticalLayout_4.addItem(self.verticalSpacer)
self.gridLayout_2.addLayout(self.verticalLayout_4, 1, 0, 1, 1)
self.verticalLayout_3 = QVBoxLayout()
self.verticalLayout_3.setObjectName(u"verticalLayout_3")
self.groupBox_2 = QGroupBox(dlg_new_tool)
self.groupBox_2.setObjectName(u"groupBox_2")
self.verticalLayout_2 = QVBoxLayout(self.groupBox_2)
self.verticalLayout_2.setObjectName(u"verticalLayout_2")
self.rb_rt_yes = QRadioButton(self.groupBox_2)
self.rb_rt_yes.setObjectName(u"rb_rt_yes")
self.verticalLayout_2.addWidget(self.rb_rt_yes)
self.rb_rt_no = QRadioButton(self.groupBox_2)
self.rb_rt_no.setObjectName(u"rb_rt_no")
self.rb_rt_no.setChecked(True)
self.verticalLayout_2.addWidget(self.rb_rt_no)
self.rb_rt_widget = QRadioButton(self.groupBox_2)
self.rb_rt_widget.setObjectName(u"rb_rt_widget")
self.verticalLayout_2.addWidget(self.rb_rt_widget)
self.rb_rt_property = QRadioButton(self.groupBox_2)
self.rb_rt_property.setObjectName(u"rb_rt_property")
self.verticalLayout_2.addWidget(self.rb_rt_property)
self.verticalLayout_3.addWidget(self.groupBox_2)
self.gb_no_pipeline_tool_groups = QGroupBox(dlg_new_tool)
self.gb_no_pipeline_tool_groups.setObjectName(u"gb_no_pipeline_tool_groups")
self.verticalLayout_3.addWidget(self.gb_no_pipeline_tool_groups)
self.verticalSpacer_2 = QSpacerItem(
20, 40, QSizePolicy.Minimum, QSizePolicy.Expanding
)
self.verticalLayout_3.addItem(self.verticalSpacer_2)
self.gridLayout_2.addLayout(self.verticalLayout_3, 1, 1, 1, 1)
self.horizontalLayout = QHBoxLayout()
self.horizontalLayout.setObjectName(u"horizontalLayout")
self.horizontalSpacer = QSpacerItem(
40, 20, QSizePolicy.Expanding, QSizePolicy.Minimum
)
self.horizontalLayout.addItem(self.horizontalSpacer)
self.bt_save = QPushButton(dlg_new_tool)
self.bt_save.setObjectName(u"bt_save")
self.horizontalLayout.addWidget(self.bt_save)
self.bt_cancel = QPushButton(dlg_new_tool)
self.bt_cancel.setObjectName(u"bt_cancel")
self.horizontalLayout.addWidget(self.bt_cancel)
self.gridLayout_2.addLayout(self.horizontalLayout, 2, 1, 1, 1)
self.gridLayout_2.setColumnStretch(0, 1)
self.gridLayout_2.setColumnStretch(1, 1)
self.retranslateUi(dlg_new_tool)
QMetaObject.connectSlotsByName(dlg_new_tool)
# setupUi
def retranslateUi(self, dlg_new_tool):
dlg_new_tool.setWindowTitle(
QCoreApplication.translate("dlg_new_tool", u"New tool wizard", None)
)
self.te_description.setPlaceholderText(
QCoreApplication.translate(
"dlg_new_tool",
u"Write your tool's description here.\\nYou can use HTML tags",
None,
)
)
self.label.setText(
QCoreApplication.translate("dlg_new_tool", u"Tool name:", None)
)
self.lbl_file_exists.setText("")
self.label_5.setText(
QCoreApplication.translate("dlg_new_tool", u"File name:", None)
)
self.chk_mask_required.setText(
QCoreApplication.translate("dlg_new_tool", u"Requires mask in input", None)
)
self.label_4.setText(u"\ud83e\udc62")
self.label_6.setText(u"\ud83e\udc62")
self.label_3.setText(
QCoreApplication.translate("dlg_new_tool", u"Class name", None)
)
self.label_2.setText(
QCoreApplication.translate("dlg_new_tool", u"Description:", None)
)
self.label_7.setText(
QCoreApplication.translate("dlg_new_tool", u"Package:", None)
)
self.groupBox.setTitle(
QCoreApplication.translate("dlg_new_tool", u"Output:", None)
)
self.rb_output_image.setText(
QCoreApplication.translate("dlg_new_tool", u"Image", None)
)
self.rb_output_mask.setText(
QCoreApplication.translate("dlg_new_tool", u"Mask", None)
)
self.rb_output_data.setText(
QCoreApplication.translate("dlg_new_tool", u"Data", None)
)
self.rb_output_none.setText(
QCoreApplication.translate("dlg_new_tool", u"None", None)
)
self.gb_pipeline_tool_groups.setTitle(
QCoreApplication.translate(
"dlg_new_tool", u"Groups that can be added to pipelines", None
)
)
self.groupBox_2.setTitle(
QCoreApplication.translate("dlg_new_tool", u"Real time:", None)
)
self.rb_rt_yes.setText(QCoreApplication.translate("dlg_new_tool", u"Yes", None))
self.rb_rt_no.setText(QCoreApplication.translate("dlg_new_tool", u"No", None))
self.rb_rt_widget.setText(
QCoreApplication.translate("dlg_new_tool", u"Widget", None)
)
self.rb_rt_property.setText(
QCoreApplication.translate("dlg_new_tool", u"Property", None)
)
self.gb_no_pipeline_tool_groups.setTitle(
QCoreApplication.translate(
"dlg_new_tool", u"Groups forbiden in pipelines", None
)
)
self.bt_save.setText(QCoreApplication.translate("dlg_new_tool", u"Save", None))
self.bt_cancel.setText(
QCoreApplication.translate("dlg_new_tool", u"Close", None)
)
class AddPlayer(QWidget):
def __init__(self, playerList, parent=None):
super(AddPlayer, self).__init__(parent)
self.playerList = playerList
mainLayout = QHBoxLayout()
mainLayout.setContentsMargins(0, 0, 0, 0)
# self.setMaximumSize(600, 270)
# self.setMinimumSize(600, 100)
# self.resize(600, 270)
self.setLayout(mainLayout)
baseLayout = QGridLayout()
mainLayout.addLayout(baseLayout)
# Labels
lblPlayerName = QLabel("Player name:")
lblPlayerName.setObjectName("addPlayerLabels")
baseLayout.addWidget(lblPlayerName, 0, 0)
lblGender = QLabel("Gender:")
lblGender.setObjectName("addPlayerLabels")
baseLayout.addWidget(lblGender, 1, 0)
lblPlayerGames = QLabel("Games played:")
lblPlayerGames.setObjectName("addPlayerLabels")
baseLayout.addWidget(lblPlayerGames, 2, 0)
lblGamesWon = QLabel("Games won:")
lblGamesWon.setObjectName("addPlayerLabels")
baseLayout.addWidget(lblGamesWon, 3, 0)
lblPlayedRounds = QLabel("Rounds played:")
lblPlayedRounds.setObjectName("addPlayerLabels")
baseLayout.addWidget(lblPlayedRounds, 4, 0)
# Text fields
self.txtPlayerName = QTextEdit()
self.txtPlayerName.setObjectName("addPlayer_txtField")
baseLayout.addWidget(self.txtPlayerName, 0, 1, 1, 2)
self.txtPlayerName.setFixedHeight(35)
self.rbtnMale = QRadioButton("Male")
self.rbtnMale.setObjectName("addPlayerRadioBtn")
baseLayout.addWidget(self.rbtnMale, 1, 1, alignment=Qt.AlignCenter)
self.rbtnMale.setChecked(True)
self.rbtnFemale = QRadioButton("Female")
self.rbtnFemale.setObjectName("addPlayerRadioBtn")
baseLayout.addWidget(self.rbtnFemale, 1, 2)
self.txtPlayerGames = QTextEdit("0")
self.txtPlayerGames.setObjectName("addPlayer_txtField")
baseLayout.addWidget(self.txtPlayerGames, 2, 1, 1, 2)
self.txtPlayerGames.setFixedHeight(35)
self.txtPlayerWins = QTextEdit("0")
self.txtPlayerWins.setObjectName("addPlayer_txtField")
baseLayout.addWidget(self.txtPlayerWins, 3, 1, 1, 2)
self.txtPlayerWins.setFixedHeight(35)
self.txtPlayedRounds = QTextEdit("0")
self.txtPlayedRounds.setObjectName("addPlayer_txtField")
baseLayout.addWidget(self.txtPlayedRounds, 4, 1, 1, 2)
self.txtPlayedRounds.setFixedHeight(35)
self.txtPlayedRounds.setEnabled(False)
# Buttons
btnSavePlayer = QPushButton("Save")
btnSavePlayer.setFixedHeight(50)
baseLayout.addWidget(btnSavePlayer, 5, 0)
btnSavePlayer.clicked.connect(self.savePlayer)
btnCancel = QPushButton("Cancel")
btnCancel.setFixedHeight(50)
baseLayout.addWidget(btnCancel, 5, 1)
btnCancel.clicked.connect(self.cancel)
def clearAll(self):
self.txtPlayerName.clear()
self.txtPlayerWins.clear()
self.txtPlayerGames.clear()
def cancel(self):
self.hide()
self.playerList.btnAddPlayer.show()
self.playerList.btnEditPlayer.show()
self.playerList.browser.show()
self.playerList.btnRemovePlayer.show()
self.playerList.mainWindow.btnBack.show()
self.playerList.mainWindow.btnStartGame.show()
self.playerList.setMaximumSize(600, 800)
self.playerList.browser.refreshView()
def savePlayer(self):
name = self.txtPlayerName.toPlainText()
# check name
if name:
if len(name) < 1:
raise TypeError
else:
msg1 = QMessageBox()
msg1.setText("Player name is not given.")
msg1.exec_()
return
# Check radiobuttons value
if self.rbtnMale.isChecked():
gender = "male"
elif self.rbtnFemale.isChecked():
gender = "female"
else:
msg1 = QMessageBox()
msg1.setText("Select gender.")
msg1.exec_()
gamesPlayed = self.txtPlayerGames.toPlainText()
# Check games played
if gamesPlayed:
try:
gamesPlayed = int(gamesPlayed)
if gamesPlayed < 0:
raise TypeError
else:
gamesPlayed = str(gamesPlayed)
except:
msg2 = QMessageBox()
msg2.setText(
"Invalid number in Games played.\n\nValid: 0-9999")
msg2.exec_()
return
else:
msg2 = QMessageBox()
msg2.setText("Number of played games is not given.")
msg2.exec_()
return
wins = self.txtPlayerWins.toPlainText()
# Check number of wins
if wins:
try:
wins = int(wins)
if wins < 0:
raise TypeError
else:
wins = str(wins)
except:
msg3 = QMessageBox()
msg3.setText("Invalid number in Wins field.\n\nValid: 0-9999")
msg3.exec_()
return
else:
msg3 = QMessageBox()
msg3.setText("Number of won games is not given.")
msg3.exec_()
return
dbu.Database().addPlayer(name, gender, gamesPlayed, wins, 0)
self.hide()
self.playerList.btnAddPlayer.show()
self.playerList.btnEditPlayer.show()
self.playerList.browser.show()
self.playerList.btnRemovePlayer.show()
self.playerList.mainWindow.btnBack.show()
self.playerList.mainWindow.btnStartGame.show()
self.playerList.setMaximumSize(600, 850)
self.playerList.browser.refreshView()
