Examples with CyNetworkReader org.cytoscape.io.read.CyNetworkReader used on opensource projects

Example 6 with CyNetworkReader

use of org.cytoscape.io.read.CyNetworkReader in project cytoscape-impl by cytoscape.

the class LoadNetworkURLTaskFactoryImpl method loadCyNetworks.

@Override
public TaskIterator loadCyNetworks(final URL url) {
    // Code adapted from LoadNetworkURLTask
    // TODO: Refactor to avoid duplication of code
    final String urlString = url.getFile();
    final String[] parts = urlString.split("/");
    final String name = parts[parts.length - 1];
    CyNetworkReader reader = null;
    try {
        reader = serviceRegistrar.getService(CyNetworkReaderManager.class).getReader(url.toURI(), url.toURI().toString());
    } catch (URISyntaxException e) {
        e.printStackTrace();
    }
    return new TaskIterator(2, new LoadNetworkTask(reader, name, serviceRegistrar));
}

Example 7 with CyNetworkReader

use of org.cytoscape.io.read.CyNetworkReader in project cytoscape-impl by cytoscape.

the class Cy3SessionReaderImpl method extractNetworks.

private void extractNetworks(InputStream is, String entryName) throws Exception {
    CyNetworkReader reader = networkReaderMgr.getReader(is, entryName);
    reader.run(taskMonitor);
    final CyRootNetworkManager rootNetworkManager = serviceRegistrar.getService(CyRootNetworkManager.class);
    final CyNetwork[] netArray = reader.getNetworks();
    for (final CyNetwork net : netArray) {
        // Add its root-network to the lookup map first
        final CyRootNetwork rootNet = rootNetworkManager.getRootNetwork(net);
        if (!networkLookup.containsKey(rootNet.getSUID()))
            ;
        networkLookup.put(rootNet.getSUID(), rootNet);
        networkLookup.put(net.getSUID(), net);
        // Note: do NOT add the root-network to this set!
        networks.add(net);
    }
}