def createNetworkView(self, parent=None):
"""
Creates the internal NetworkView. Returns the network view.
@return: The internal NetworkView.
@param parent: QWidget parent that is passed to the NetworkView
@type parent: QWidget
"""
self.networkView = NetworkView(parent, controller=self)
#self.networkView.setViewport(QGLWidget) # would improve performance
#for debugging:
#self.networkView.setWindowTitle("Test") # works
# self._connectViews()
if self.graph is not None:
self.networkView.draw_graph(self.graph)
self.networkView.species = self.modelController.sbmlModel.SbmlSpecies
self.networkView.reactions = self.modelController.sbmlModel.SbmlReactions
self.updateUI()
return self.networkView
def createNetworkView(self, parent=None):
"""
Creates the internal NetworkView. Returns the network view.
@return: The internal NetworkView.
@param parent: QWidget parent that is passed to the NetworkView
@type parent: QWidget
"""
self.networkView = NetworkView(parent, controller=self)
# self.networkView.setViewport(QGLWidget) # would improve performance
# for debugging:
# self.networkView.setWindowTitle("Test") # works
# self._connectViews()
if self.graph is not None:
self.networkView.draw_graph(self.graph)
self.networkView.species = self.modelController.sbmlModel.SbmlSpecies
self.networkView.reactions = self.modelController.sbmlModel.SbmlReactions
self.updateUI()
return self.networkView
class NetworkViewController(QObject):
"""
This controller works as an adapter between main program logic (like
in ModelController) and the NetworkView.
The code in this class could have been included in NetworkView but
was kept separate for historical and housekeeping reasons.
@since: 2011-05-13
"""
__author__ = "Moritz Wade"
__contact__ = "*****@*****.**"
__copyright__ = "Zuse Institute Berlin 2011"
def __init__(self, modelController):
super(NetworkViewController, self).__init__()
if not modelController:
logging.error(
"NetworkViewController: Can't initialize without reference to ModelController."
)
return
self.modelController = modelController
self.modelController.dirtyChanged.connect(self.updateUI)
self.networkView = None
self.reactionsToHyperNodes = None
self.subWindow = None # a place to hold the QSubWindow where self.networkView ic placed
self.graph = None
self.modelController.on_structuralChange.connect(self._updateGraph)
def createNetworkView(self, parent=None):
"""
Creates the internal NetworkView. Returns the network view.
@return: The internal NetworkView.
@param parent: QWidget parent that is passed to the NetworkView
@type parent: QWidget
"""
self.networkView = NetworkView(parent, controller=self)
#self.networkView.setViewport(QGLWidget) # would improve performance
#for debugging:
#self.networkView.setWindowTitle("Test") # works
# self._connectViews()
if self.graph is not None:
self.networkView.draw_graph(self.graph)
self.networkView.species = self.modelController.sbmlModel.SbmlSpecies
self.networkView.reactions = self.modelController.sbmlModel.SbmlReactions
self.updateUI()
return self.networkView
def addReactionToGraph(self,
products,
reactants,
wrappedReaction,
networkView=None):
reaction = wrappedReaction.Item
if len(reactants) == 1 and len(
products) == 1: # normal case for non-hyperedge
self.graph.add_edge(reactants[0],
products[0],
reaction=wrappedReaction)
else: # build an hyperedge
if reaction.getName() == None or reaction.getName() == "":
node = HyperEdgeNode(reaction=reaction)
else:
node = HyperEdgeNode(reaction=reaction,
label=reaction.getName())
# for hyperedge management
if wrappedReaction not in self.reactionsToHyperNodes:
self.reactionsToHyperNodes[wrappedReaction] = set([node])
else:
self.reactionsToHyperNodes[wrappedReaction].add(node)
self.graph.add_node(node)
for reactant in reactants:
self.graph.add_edge(reactant, node, reaction=wrappedReaction)
for product in products:
self.graph.add_edge(node, product, reaction=wrappedReaction)
def _createGraph(self):
"""
Basically builds a networkx graph out
of the SBML model which is ready to be painted.
Hyperedges (edges connecting more than one node)
are built using dummy nodes of type HyperEdgeNode.
"""
self.graph = networkx.DiGraph()
reactions = self.modelController.sbmlModel.SbmlReactions
self.SpeciesRowIndexToSpeciesMapper = {
} # important for syncing index-based table views to network view
if self.modelController.sbmlModel.SbmlSpecies is not None:
for (i, species) in enumerate(
self.modelController.sbmlModel.SbmlSpecies):
self.SpeciesRowIndexToSpeciesMapper[i] = species
self.SpeciesRowIndexToSpeciesMapper[species] = i
if reactions is None:
logging.info("Empty model.")
return
# building the graph from the reactions
self.reactionsToHyperNodes = {}
if reactions is not None and len(reactions) > 1:
for (wrappedReaction, reactants, products) in reactions:
self.addReactionToGraph(products, reactants, wrappedReaction)
else:
for species in self.modelController.sbmlModel.SbmlSpecies:
self.graph.add_node(species)
#self.register_model_signals(self.sbmlModel)
if self.networkView is not None:
self.networkView.draw_graph(self.graph)
#@Slot("structuralChange(SBMLEntity)")
def _updateGraph(self, sbmlEntity, changeType):
"""
Updates the graph, when the MainModel signals a structural change,
e.g. a Species has been added/removed, ...
"""
#print sbmlEntity
if changeType == sbml_mainmodel.CHANGETYPE.ADD:
#print "add"
if sbmlEntity.Type == sbml_entities.TYPE.SPECIES:
i = len(self.SpeciesRowIndexToSpeciesMapper)
self.SpeciesRowIndexToSpeciesMapper[i] = sbmlEntity
self.SpeciesRowIndexToSpeciesMapper[sbmlEntity] = i
self.graph.add_node(
sbmlEntity) # for Node that is not in a Reaction
self.networkView.addNode(sbmlEntity)
elif changeType == sbml_mainmodel.CHANGETYPE.REMOVE:
# TODO: Add support for this type of change
logging.error(
"NetworkViewController: Removing a network entity is not yet supported."
)
elif changeType == sbml_mainmodel.CHANGETYPE.CHANGE_REACTANTS:
self.updateReaction(sbmlEntity)
elif changeType == sbml_mainmodel.CHANGETYPE.CHANGE_PRODUCTS:
self.updateReaction(sbmlEntity)
else:
logging.error(
"NetworkViewController: Unsupported type of change in the main model."
)
self.networkView.redraw()
def updateReaction(self, reactionWrapper):
"""
Searches the graph for the given Reaction, removes all Edges and then creates
new edges in and out of this Reaction node.
"""
# remove hyper node that represents the reaction (if there is one)
if reactionWrapper in self.reactionsToHyperNodes:
nodeSet = self.reactionsToHyperNodes[reactionWrapper]
for hyperEdgeNode in nodeSet:
edges = self.graph.edges([hyperEdgeNode], data=True)
self.graph.remove_edges_from(
edges) #remove structural (!) edges
self.graph.remove_nodes_from([hyperEdgeNode
]) # remove structural (!) node(s)
if self.networkView:
self.networkView.removeSpeciesNode(
hyperEdgeNode) # remove graphical(!) node(s)
#for (u,v,edata['reaction']) in [for u,v,edata in self.graph.edges(data=True) if 'reaction' in edata]:
for (sourceSpecies, targetSpecies,
edata) in self.graph.edges(data=True):
if "reaction" not in edata:
logging.debug(
"Encountered a graph edge without associated Reaction.")
continue
currentReaction = edata["reaction"]
if reactionWrapper == currentReaction:
self.graph.remove_edge(sourceSpecies, targetSpecies)
break
# remove graphical (!) edges (1 or more)
if self.networkView:
self.networkView.removeReaction(reactionWrapper)
# create Reaction in graph
if not self.modelController.sbmlModel:
return
reactionTuples = self.modelController.sbmlModel.SbmlReactions
for (wrappedReaction, newReactants, newProducts) in reactionTuples:
if wrappedReaction == reactionWrapper:
self.addReactionToGraph(newProducts,
newReactants,
wrappedReaction,
networkView=self.networkView)
#debugging
logging.debug("Adding Reaction between...")
for reactant in newReactants:
logging.debug("Reactant: %s" % reactant.getId())
for product in newProducts:
logging.debug("Product: %s" % product.getId())
self.networkView.updateNodesAndEdges()
self.networkView.redraw()
def updateUI(self):
"""
Updates dynamic aspects of the UI, e.g. depending
on whether the current model needs saving, etc.
"""
if self.modelController.Dirty:
windowTitle = self.modelController.filename + " (*)"
else:
windowTitle = self.modelController.filename
if self.networkView is not None:
self.networkView.setWindowTitle(windowTitle)
def setModel(self, model):
self.networkView.setModel(model)
def setSelectionModel(self, selectionModel):
self.networkView.setSelectionModel(selectionModel)
def getGlobalSelectionModel(self):
return self.modelController.selectionModel
class NetworkViewController(QObject):
"""
This controller works as an adapter between main program logic (like
in ModelController) and the NetworkView.
The code in this class could have been included in NetworkView but
was kept separate for historical and housekeeping reasons.
@since: 2011-05-13
"""
__author__ = "Moritz Wade"
__contact__ = "*****@*****.**"
__copyright__ = "Zuse Institute Berlin 2011"
def __init__(self, modelController):
super(NetworkViewController, self).__init__()
if not modelController:
logging.error("NetworkViewController: Can't initialize without reference to ModelController.")
return
self.modelController = modelController
self.modelController.dirtyChanged.connect(self.updateUI)
self.networkView = None
self.reactionsToHyperNodes = None
self.subWindow = None # a place to hold the QSubWindow where self.networkView ic placed
self.graph = None
self.modelController.on_structuralChange.connect(self._updateGraph)
def createNetworkView(self, parent=None):
"""
Creates the internal NetworkView. Returns the network view.
@return: The internal NetworkView.
@param parent: QWidget parent that is passed to the NetworkView
@type parent: QWidget
"""
self.networkView = NetworkView(parent, controller=self)
# self.networkView.setViewport(QGLWidget) # would improve performance
# for debugging:
# self.networkView.setWindowTitle("Test") # works
# self._connectViews()
if self.graph is not None:
self.networkView.draw_graph(self.graph)
self.networkView.species = self.modelController.sbmlModel.SbmlSpecies
self.networkView.reactions = self.modelController.sbmlModel.SbmlReactions
self.updateUI()
return self.networkView
def addReactionToGraph(self, products, reactants, wrappedReaction, networkView=None):
reaction = wrappedReaction.Item
if len(reactants) == 1 and len(products) == 1: # normal case for non-hyperedge
self.graph.add_edge(reactants[0], products[0], reaction=wrappedReaction)
else: # build an hyperedge
if reaction.getName() == None or reaction.getName() == "":
node = HyperEdgeNode(reaction=reaction)
else:
node = HyperEdgeNode(reaction=reaction, label=reaction.getName())
# for hyperedge management
if wrappedReaction not in self.reactionsToHyperNodes:
self.reactionsToHyperNodes[wrappedReaction] = set([node])
else:
self.reactionsToHyperNodes[wrappedReaction].add(node)
self.graph.add_node(node)
for reactant in reactants:
self.graph.add_edge(reactant, node, reaction=wrappedReaction)
for product in products:
self.graph.add_edge(node, product, reaction=wrappedReaction)
def _createGraph(self):
"""
Basically builds a networkx graph out
of the SBML model which is ready to be painted.
Hyperedges (edges connecting more than one node)
are built using dummy nodes of type HyperEdgeNode.
"""
self.graph = networkx.DiGraph()
reactions = self.modelController.sbmlModel.SbmlReactions
self.SpeciesRowIndexToSpeciesMapper = {} # important for syncing index-based table views to network view
if self.modelController.sbmlModel.SbmlSpecies is not None:
for (i, species) in enumerate(self.modelController.sbmlModel.SbmlSpecies):
self.SpeciesRowIndexToSpeciesMapper[i] = species
self.SpeciesRowIndexToSpeciesMapper[species] = i
if reactions is None:
logging.info("Empty model.")
return
# building the graph from the reactions
self.reactionsToHyperNodes = {}
if reactions is not None and len(reactions) > 1:
for (wrappedReaction, reactants, products) in reactions:
self.addReactionToGraph(products, reactants, wrappedReaction)
else:
for species in self.modelController.sbmlModel.SbmlSpecies:
self.graph.add_node(species)
# self.register_model_signals(self.sbmlModel)
if self.networkView is not None:
self.networkView.draw_graph(self.graph)
# @Slot("structuralChange(SBMLEntity)")
def _updateGraph(self, sbmlEntity, changeType):
"""
Updates the graph, when the MainModel signals a structural change,
e.g. a Species has been added/removed, ...
"""
# print sbmlEntity
if changeType == sbml_mainmodel.CHANGETYPE.ADD:
# print "add"
if sbmlEntity.Type == sbml_entities.TYPE.SPECIES:
i = len(self.SpeciesRowIndexToSpeciesMapper)
self.SpeciesRowIndexToSpeciesMapper[i] = sbmlEntity
self.SpeciesRowIndexToSpeciesMapper[sbmlEntity] = i
self.graph.add_node(sbmlEntity) # for Node that is not in a Reaction
self.networkView.addNode(sbmlEntity)
elif changeType == sbml_mainmodel.CHANGETYPE.REMOVE:
# TODO: Add support for this type of change
logging.error("NetworkViewController: Removing a network entity is not yet supported.")
elif changeType == sbml_mainmodel.CHANGETYPE.CHANGE_REACTANTS:
self.updateReaction(sbmlEntity)
elif changeType == sbml_mainmodel.CHANGETYPE.CHANGE_PRODUCTS:
self.updateReaction(sbmlEntity)
else:
logging.error("NetworkViewController: Unsupported type of change in the main model.")
self.networkView.redraw()
def updateReaction(self, reactionWrapper):
"""
Searches the graph for the given Reaction, removes all Edges and then creates
new edges in and out of this Reaction node.
"""
# remove hyper node that represents the reaction (if there is one)
if reactionWrapper in self.reactionsToHyperNodes:
nodeSet = self.reactionsToHyperNodes[reactionWrapper]
for hyperEdgeNode in nodeSet:
edges = self.graph.edges([hyperEdgeNode], data=True)
self.graph.remove_edges_from(edges) # remove structural (!) edges
self.graph.remove_nodes_from([hyperEdgeNode]) # remove structural (!) node(s)
if self.networkView:
self.networkView.removeSpeciesNode(hyperEdgeNode) # remove graphical(!) node(s)
# for (u,v,edata['reaction']) in [for u,v,edata in self.graph.edges(data=True) if 'reaction' in edata]:
for (sourceSpecies, targetSpecies, edata) in self.graph.edges(data=True):
if "reaction" not in edata:
logging.debug("Encountered a graph edge without associated Reaction.")
continue
currentReaction = edata["reaction"]
if reactionWrapper == currentReaction:
self.graph.remove_edge(sourceSpecies, targetSpecies)
break
# remove graphical (!) edges (1 or more)
if self.networkView:
self.networkView.removeReaction(reactionWrapper)
# create Reaction in graph
if not self.modelController.sbmlModel:
return
reactionTuples = self.modelController.sbmlModel.SbmlReactions
for (wrappedReaction, newReactants, newProducts) in reactionTuples:
if wrappedReaction == reactionWrapper:
self.addReactionToGraph(newProducts, newReactants, wrappedReaction, networkView=self.networkView)
# debugging
logging.debug("Adding Reaction between...")
for reactant in newReactants:
logging.debug("Reactant: %s" % reactant.getId())
for product in newProducts:
logging.debug("Product: %s" % product.getId())
self.networkView.updateNodesAndEdges()
self.networkView.redraw()
def updateUI(self):
"""
Updates dynamic aspects of the UI, e.g. depending
on whether the current model needs saving, etc.
"""
if self.modelController.Dirty:
windowTitle = self.modelController.filename + " (*)"
else:
windowTitle = self.modelController.filename
if self.networkView is not None:
self.networkView.setWindowTitle(windowTitle)
def setModel(self, model):
self.networkView.setModel(model)
def setSelectionModel(self, selectionModel):
self.networkView.setSelectionModel(selectionModel)
def getGlobalSelectionModel(self):
return self.modelController.selectionModel
