def parse_configuration(self, config_file=None):
#parse configuration
if config_file:
DegenPrimerConfig.parse_configuration(self, unicode(config_file))
else: DegenPrimerConfig.parse_configuration(self)
#update form fields
self._update_fields()
self._fields_empty = False
def parse_configuration(self, config_file=None):
#parse configuration
if config_file:
DegenPrimerConfig.parse_configuration(self, unicode(config_file))
else:
DegenPrimerConfig.parse_configuration(self)
#update form fields
self._update_fields()
self._fields_empty = False
def __init__(self):
#parent's constructors
DegenPrimerConfig.__init__(self)
QMainWindow.__init__(self)
#working directory
self._cwdir = os.getcwd()
#session independent configuration
self._settings = QSettings()
#try to load UI
self.load_ui(self._ui_file, self)
#fields
Field.customize_field = self._customize_field
self._fields = dict()
#config and cwdir path choosers
self._build_group_gui(self._config_group)
#job-id label
self._job_id_label = QLabel(self)
self.configForm.addWidget(self._job_id_label)
#sequence db view
self._loaded_files = []
self._seq_db_widget = None
self._seq_db_box = None
self._seq_db_button = None
for group in self._option_groups: self._build_group_gui(group)
#setup default values
self._reset_fields()
#setup buttons
self._run_widgets = (self.abortButton,
self.elapsedTimeLineEdit,
self.elapsedTimeLabel,)
self._idle_widgets = (self.saveButton,
self.runButton,
self.resetButton,
self.reloadButton,)
self.reloadButton.clicked.connect(self.reload_config)
self.resetButton.clicked.connect(self._reset_fields)
self.saveButton.clicked.connect(self._save_config)
self.runButton.clicked.connect(self._analyse)
self.abortButton.clicked.connect(self._abort_analysis)
self._show_run_specific_widgets(False)
#setup terminal output
self._append_terminal_output.connect(self.terminalOutput.insertPlainText)
self.terminalOutput.textChanged.connect(self.terminalOutput.ensureCursorVisible)
#pipeline thread
self._pipeline_thread = SubprocessThread(degen_primer_pipeline)
self._pipeline_thread.started.connect(self.lock_buttons)
self._pipeline_thread.results_received.connect(self.register_reports)
self._pipeline_thread.finished.connect(self.show_results)
self._pipeline_thread.finished.connect(self.unlock_buttons)
self._pipeline_thread.update_timer.connect(self.update_timer)
self._pipeline_thread.message_received.connect(self.show_message)
self._pipeline_thread_stop.connect(self._pipeline_thread.stop)
#restore GUI state
self._restore_mainwindow_state()
def _do_work(self, options):
#read in configuration
config = DegenPrimerConfig.from_options(options)
#else, run the pipeline
if self._pipeline.run(config) == 0: #pass back collected reports
self._con.send(config.reports)
return 0
def __init__(self):
#parent's constructors
DegenPrimerConfig.__init__(self)
QMainWindow.__init__(self)
#working directory
self._cwdir = os.getcwd()
#session independent configuration
self._settings = QSettings()
#try to load UI
self.load_ui(self._ui_file, self)
#fields
Field.customize_field = self._customize_field
self._fields = dict()
#config and cwdir path choosers
self._build_group_gui(self._config_group)
#job-id label
self._job_id_label = QLabel(self)
self.configForm.addWidget(self._job_id_label)
#sequence db view
self._loaded_files = []
self._seq_db_widget = None
self._seq_db_box = None
self._seq_db_button = None
for group in self._option_groups:
self._build_group_gui(group)
#setup default values
self._reset_fields()
#setup buttons
self._run_widgets = (
self.abortButton,
self.elapsedTimeLineEdit,
self.elapsedTimeLabel,
)
self._idle_widgets = (
self.saveButton,
self.runButton,
self.resetButton,
self.reloadButton,
)
self.reloadButton.clicked.connect(self.reload_config)
self.resetButton.clicked.connect(self._reset_fields)
self.saveButton.clicked.connect(self._save_config)
self.runButton.clicked.connect(self._analyse)
self.abortButton.clicked.connect(self._abort_analysis)
self._show_run_specific_widgets(False)
#setup terminal output
self._append_terminal_output.connect(
self.terminalOutput.insertPlainText)
self.terminalOutput.textChanged.connect(
self.terminalOutput.ensureCursorVisible)
#pipeline thread
self._pipeline_thread = SubprocessThread(degen_primer_pipeline)
self._pipeline_thread.started.connect(self.lock_buttons)
self._pipeline_thread.results_received.connect(self.register_reports)
self._pipeline_thread.finished.connect(self.show_results)
self._pipeline_thread.finished.connect(self.unlock_buttons)
self._pipeline_thread.update_timer.connect(self.update_timer)
self._pipeline_thread.message_received.connect(self.show_message)
self._pipeline_thread_stop.connect(self._pipeline_thread.stop)
#restore GUI state
self._restore_mainwindow_state()
def _override_option(self, option):
return DegenPrimerConfig._override_option(self, option)
