$LastChangedRevision: 688 $
my $hInteractions = $oTransport->query('interactorA'); my $hInteractions = $oTransport->query('interactorA', 'interactorB');
A data transport exposing interactions stored in a SIF file, along with attributes stored in Cytoscape attribute files. Access is via the 'query' method.
Each line of a Simple Interaction Format (SIF) file describes one or more binary interactions, and takes the form: nodeA lineType nodeB [nodeC ...]
This example describes a protein-protein interaction between interactorA and interactorB: interactorA pp interactorB
This example describes three separate interactions, each involving interactorA: interactorA pp interactorB interactorC interactor D
Node attribute files may be used to add DAS 'detail' elements to interactors: description interactorA = An example interactor interactorB = Another example of an interactor ...
Edge attribute files may be used to add DAS 'detail' elements to interactions: score interactorA pp interactorB = 2.43 interactorX pp interactorY = 5.1 ...
Configured as part of each source's ProServer 2 INI file:
[mysif] ... source configuration ... transport = sif filename = /data/interactions.sif attributes = /data/node-attribute.noa ; /data/edge-attributes.eda
Retrieves interactions involving interactorA: $hInteractions = $oTransport->query('interactorA'); Retrieves an interaction involving both interactorA and interactorB: $hInteractions = $oTransport->query('interactorA', 'interactorB'); The returned hash is of the structure expected by ProServer.
Generally not directly invoked, but if you really want to: $transport->DESTROY();
Run ProServer with the -debug flag.
The Simple Interaction Format is very simple, and therefore only supports a limited range of DAS annotation details. It also only handles binary interactions (i.e. those with exactly two interactors).
Andy Jenkinson <firstname.lastname@example.org>
Copyright (c) 2008 EMBL-EBI