I find the answer to my question. Methods to do this is part of the
RootGraph class. See it at the page:
http://chianti.ucsd.edu/Cyto-2_6_1/javadoc/index.html?cytoscape/package-summary.html
and use functions like:
int[] getAdjacentEdgeIndicesArray(int node_index, boolean
undirected_edges, boolean incoming_directed_edges, boolean
outgoing_directed_edges)
Returns indices of all edges adjacent to the node at
specified index.
int[] getChildlessMetaDescendants(int node_index)
Nodes and Edges comprise an additional directed graph
through the contains-a relationship, in which a MetaParent Node
contains each of its MetaChild Nodes and Edges.
int[] getConnectingEdgeIndicesArray(int[] node_indices)
This will return an array of edge indices that are the edges
between nodes.
cheers
Franktwis