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- GraphNodeAttribute.GraphNodeAttribute
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- PianaGraphNodeAttribute
class PianaGraphNodeAttribute(GraphNodeAttribute.GraphNodeAttribute) |
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Class that implements attributes for Piana Nodes: accessing node values, setting values, ... |
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Methods defined here:
- __deepcopy__(self, memo)
- __getnewargs__(self)
- __getstate__(self)
- __init__(self, proteinPiana_value, piana_access=None, mem_mode='onDemand')
- "proteinPiana_value" is the proteinPiana of this node
"piana_access" is a PianaDBaccess object used to access the database
"mem_mode" can be:
--> onDemand: values are retrieved from DB only when they are needed, and then are stored in memory all remaining time
--> inMemory: values are retrieved from DB at initilisation and stored in memory all time
--> inFlight: values are retrieved from DB when are needed, but never are stored in memory
- __setstate__(self, dict)
- get_associated_node_ids_set(self)
- get_associated_proteinPianas(self)
- Returns the set of associated proteinPianas. The original one too
- get_cell_location(self)
- Returns a dictionary {location:None, location:None, ...} with the cellular locations for this node
- get_descriptions(self)
- returns the list of descriptions for this node
- get_dic_cell_location(self)
- Returns a dictionary {location:None, location:None, ...} with the cellular locations for this node
- get_dic_descriptions(self)
- returns the list of descriptions for this node
- get_dic_functions(self)
- returns the list of functions for this node
- get_dic_keywords_appearing(self, user_keywords=[])
- returns the list of user keywords that appear in the name, description or function of this protein
- get_dic_special_labels(self)
- returns the list of special labels for this node
if no special labels are found, returns empty list
- get_dic_taxonomies(self)
- Returns a dictionary {tax:None, tax:None, ...} with the taxonomies for this node
- get_expression(self)
- returns the expression (over_and_infra_expressed, over_expressed, infra_expressed or None) for this node
- get_functions(self)
- returns the list of functions for this node
- get_isoelectric_point(self)
- Returns the molecular weight of the protein
- get_keywords_appearing(self)
- returns the list of user keywords that appear in the name, description or function of this protein
- get_molecular_weight(self)
- Returns the molecular weight of the protein from the database
- get_node_id(self)
- overwrittes the method in GraphNodeAttribute, identifying this attribute with the proteinPiana
- get_proteinPiana(self)
- get_special_labels(self)
- returns the list of special labels for this node
if no special labels are found, returns empty list
- get_union_neighbours(self)
- returns the set of neighbours for the unified node
(ie. list of neighbours for all nodes that have been 'unified' into this node attribute)
- merge_attribute(self, attribute_object, ignore_ids=0)
- merges existing attribute with atribute_object passed as argument
certain characteristics of the node will only be merged in ignore_ids is 1,
since we are interested in having those characteristics filled
only when we are unifying the nodes (ie. the operation by which PIANA
decides which name will it use for the protein)
Methods inherited from GraphNodeAttribute.GraphNodeAttribute:
- __eq__(self, other)
- When defining new Attribute classes, the equality operator MUST be overridden.
Otherwise, adding further attributes to existing nodes in the graph may cause
duplicated attributes.
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