def __init__(self, **kwargs):
super(PathwayMiningApp, self).__init__(**kwargs)
# Define automatic mapping (settings will determine the route; allow manual tweaks later)
self.addDataToolBar()
#self.addExperimentToolBar()
self.config.set_defaults({
'/Data/MiningActive': False,
'/Data/MiningDepth': 5,
'/Data/MiningType': 'c',
'/Data/MiningRelative': False,
'/Data/MiningShared': True,
})
#t = self.getCreatedToolbar('Pathway mining', 'pathway_mining')
#miningSetup = QAction( QIcon( os.path.join( self.plugin.path, 'icon-16.png' ) ), 'Set up pathway mining \u2026', self.m)
#miningSetup.setStatusTip('Set parameters for pathway mining')
#miningSetup.triggered.connect(self.onMiningSettings)
#t.addAction(miningSetup)
self.data.add_input('input_1') # Add input slot
self.data.add_input('input_2') # Add input slot
self.data.add_input('input_3') # Add input slot
self.data.add_input('input_4') # Add input slot
self.data.add_output('output')
self.table = TableView()
self.table.setModel(self.data.o['output'].as_table)
self.views.addView(self.table, 'Table', unfocus_on_refresh=True)
# Setup data consumer options
self.data.consumer_defs.extend([
DataDefinition('input_1', {
'entities_t': (None, ['Compound', 'Gene', 'Protein']),
},
title='Source compound, gene or protein data'),
DataDefinition('input_2', {
'entities_t': (None, ['Compound', 'Gene', 'Protein']),
},
title='Source compound, gene or protein data'),
DataDefinition('input_3', {
'entities_t': (None, ['Compound', 'Gene', 'Protein']),
},
title='Source compound, gene or protein data'),
DataDefinition('input_4', {
'entities_t': (None, ['Compound', 'Gene', 'Protein']),
},
title='Source compound, gene or protein data'),
])
self.addConfigPanel(PathwayMiningConfigPanel, 'Pathway Mining')
self.finalise()
def __init__(self, **kwargs):
super(MapEntityApp, self).__init__(**kwargs)
# Define automatic mapping (settings will determine the route; allow manual tweaks later)
self.addDataToolBar()
self.addFigureToolBar()
self.data.add_input('input') # Add input slot
self.data.add_output('output')
self.table = TableView()
self.table.setItemDelegate(EntityItemDelegate())
self.data.o['output'].register_interface('as_entity_table',
EntityTableInterface)
self.views.addView(self.table, 'Table', unfocus_on_refresh=True)
self.table.setModel(self.data.o['output'].as_entity_table)
# Deprecate as too slow for large mappings
#self.views.addTab(WheezyView(self), 'Entities')
t = self.getCreatedToolbar('Entity mapping', 'external-data')
import_dataAction = QAction(
QIcon(os.path.join(utils.scriptdir, 'icons', 'disk--arrow.png')),
'Load annotations from file\\u2026', self.m)
import_dataAction.setStatusTip('Load annotations from .csv. file')
import_dataAction.triggered.connect(self.onImportEntities)
t.addAction(import_dataAction)
self.addExternalDataToolbar() # Add standard source data options
self.config.set_defaults({
'map_object_type': MAP_ENTITY_ALL,
})
self._entity_mapping_table = {}
# Setup data consumer options
self.data.consumer_defs.append(
DataDefinition('input', {
'labels_n': (None, '>0'),
'entities_t': (None, None),
}))
self.addConfigPanel(MapEntityConfigPanel, 'Mapping')
self.finalise()
