netconv.network.Network

Package netconv :: Module network :: Class Network

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Class Network

Stores information of network

Methods for importing/exporting network are provided

Method Summary
	`__init__(self, nnodes, nedges)`
	`attributes2Cluster(self, attr)` Converts attributes to cluster
	`cluster2Attributes(self, attr, s)` Converts cluster info to attributes
	`findId(self, id)` Finds node by Id
	`findNode(self, node)` Finds node by name
	`fromList(self, list, nodesList)` reads the network from a list of interactions.
	`getAllNodes(self)` Returns a list with all nodes names.
	`getAttribute(self, attr, attribs)` Return generic attribute for the network
	`pajek2pos(self, mult)` Converts pajek node positions (range from 0 to 1) to graph position
	`pos2pajek(self)` Converts node positions to pajek format (range from 0 to 1)
	`reset(self)` Cleans the network
	`setAttribute(self, attr, value, attribs)` Defines generic attribute for the network
	`toList(self)` Converts the network to a list of interactions.

Instance Variable Summary
`str`	`coordsModel`: set the model used to store network coords

Method Details

init(self, nnodes=0, nedges=0)
(Constructor)

Parameters:: nnodes - number of nodes; nedges - number of edges

attributes2Cluster(self, attr=('cluster', 'cluster'))

Converts attributes to cluster

Parameters:: attr - attribute to convert from (defaults to 'Cluster')

cluster2Attributes(self, attr=('cluster', 'cluster'), s='')

Converts cluster info to attributes

Parameters:: attr - attribute that will receive the information (defaults to 'Cluster'); s - string to add at the begining of the value of attribute to avoids problems with "numerical" nodes with the VisualMapper from Cytoscape

findId(self, id)

Finds node by Id

Parameters:: id - Id of node

Returns:: index in the network

findNode(self, node)

Finds node by name

Parameters:: node - name (canonical) of node

Returns:: index in the network

fromList(self, list, nodesList=None)

reads the network from a list of interactions.

Parameters:: list - list of interactions

getAllNodes(self)

Returns a list with all nodes names.

getAttribute(self, attr, attribs=None)

Parameters:: attr - attribute to be read; attribs - dict of attributes

Returns:: generic attribute for the network

pajek2pos(self, mult)

Converts pajek node positions (range from 0 to 1) to graph position

Parameters:: mult - valut to multiply the pajek value

pos2pajek(self)

Converts node positions to pajek format (range from 0 to 1)

reset(self)

Cleans the network

setAttribute(self, attr, value, attribs=None)

Defines generic attribute for the network

Parameters:: attr - attribute to be set (can be a tuple); value - value of attribute; attribs - dict of attributes

toList(self)

Converts the network to a list of interactions.

Returns:: list of interactions

Instance Variable Details

coordsModel

set the model used to store network coords

pajek: coords range from 0 to 1
pos: coords are the position in graph

Type:: str
Value:: 'pos'

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