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- Expansion
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- EdgeExpansion
- NodeExpansion
class EdgeExpansion(Expansion) |
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The base class for expansion of nodes. All node expansions must be subclasses of this class.
TO CHECK!!! Does it make sense to expand an edge? What characteristics might share two edges that expands one to the other (interchange the nodes
that they join...) |
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Methods defined here:
- get_expanded_edges(self, edge)
- This should be overridden with a method that returns a list of edges that pass the expansion test
In its current form this will return 1 if argument "edge" is a GraphNode object or 0 otherwise.
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class NodeExpansion(Expansion) |
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The base class for expansion of nodes. All node expansions must be subclasses of this class.
A node will borrow interactions from other nodes (even if they do not appear in the graph) if condition X is shared between the source node
and the other nodes existing in the database. |
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Methods defined here:
- __init__(self)
- class_test(self, node_id=None, class_name=None)
- This must be overridden with a method that tests whether the node_id belongs to class_name or not
returns 1 if class test is passed, 0 otherwise
- create_new_edge_attribute(self, edge_db_id=None, expansion_type=None, propagated_from_node=None, propagated_from_edge_id=None, propagated_from_db_edge_id=None, extended_from_node=None)
- This must be overridden with a method that creates and attribute of type PianaGraphEdgeAttribute with given characteristics
- create_new_node_attribute(self, node_id=None)
- This must be overridden with a method that creates an node attribute
- get_db_edge_ids_from_node(self, node_id)
- This must be overridden with a method that returns a list of database ids for node_id
- get_edges_attributes_from_node(self, node_id)
- This must be overridden with a method that returns from a database edges attributes of edges where "node_id" appears
- get_expansion_name(self)
- This must be overridden with a method that returns the name of the expansion
- get_external_code(self, node_id, id_type=None, alternative_id_types=None)
- This must be overridden with a method that returns the external database code for node_id
- get_partner_ids(self, node_id)
- This must be overridden with a method that returns a list of partner_ids of node_id
- get_partner_node_id(self, edge_id, node_id)
- This must be overridden with a method that returns from a database the partner node of "node_id" in edge "edge_id"
- get_partners_of_nodes_sharing_characteristic(self, node_id)
- Returns a list of partner proteins of proteins that share cog with proteinPiana node_id
returns empty list if nothing found
ATTENTION: currently not being used!!!
- get_sharing_nodes(self, node_id)
- This must be overridden with a method that returns a list of nodes that share a characteristic with node_id
This characteristic will determine the expansion: edges will be propagated between nodes that share that characteristic.
This method is the only one that is specific to this characteristic: all the other methods that have to be overridden
are specific to the external database, but not to the characteristic
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