Examples with CySubNetwork org.cytoscape.model.subnetwork.CySubNetwork used on opensource projects

Example 26 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class GenericXGMMLWriterTest method testSecondNetworkPointerRefenceSavedAsXLink.

@Test
public void testSecondNetworkPointerRefenceSavedAsXLink() throws UnsupportedEncodingException {
    // Same root!
    CySubNetwork sn = rootNet.addSubNetwork();
    setRegistered(sn, true);
    CyNode n1 = net.getNodeList().get(0);
    CyNode n2 = net.getNodeList().get(1);
    n1.setNetworkPointer(sn);
    n2.setNetworkPointer(sn);
    write(net);
    // Only one of the nested graphs is an XLink!
    assertEquals(1, evalNumber("count(//x:node/x:att/x:graph[@id=" + sn.getSUID() + "])"));
    // The other one must be an XLINK
    assertEquals(1, evalNumber("count(//x:node/x:att/x:graph[@xlink:href=\"#" + sn.getSUID() + "\"])"));
    // it should have no children, because it's an XLink
    assertEquals(0, evalNumber("count(//x:node/x:att/x:graph[@xlink:href]/*)"));
}

Example 27 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class GenericXGMMLWriterTest method testNetworkPointerSavedIfSameRootNetwork.

@Test
public void testNetworkPointerSavedIfSameRootNetwork() throws UnsupportedEncodingException {
    // Create a subnetwork from the same root
    // Of course the save policy cannot be DO_NOT_SAVE!
    CySubNetwork sn1 = rootNet.addSubNetwork();
    CySubNetwork sn2 = rootNet.addSubNetwork();
    setRegistered(sn1, true);
    setRegistered(sn2, false);
    // Set it as network pointer
    CyNode n1 = net.getNodeList().get(0);
    CyNode n2 = net.getNodeList().get(1);
    n1.setNetworkPointer(sn1);
    n2.setNetworkPointer(sn2);
    write(net);
    // Test:
    // It is saved as a full nested node graph, not an XLink
    assertEquals("" + sn1.getSUID(), evalString("//x:node[@id=" + n1.getSUID() + "]/x:att/x:graph/@id"));
    assertEquals("1", evalString("//x:graph[@id=" + sn1.getSUID() + "]/@cy:registered"));
    // Unregistered net pointer is also saved:
    assertEquals("" + sn2.getSUID(), evalString("//x:node[@id=" + n2.getSUID() + "]/x:att/x:graph/@id"));
    // But it must NOT be registered!
    assertEquals("0", evalString("//x:graph[@id=" + sn2.getSUID() + "]/@cy:registered"));
}

Example 28 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class SessionXGMMLNetworkWriterTest method testUnregisteredNetworkPointerSavedIfSessionSavePolicy.

@Test
public void testUnregisteredNetworkPointerSavedIfSessionSavePolicy() throws UnsupportedEncodingException {
    // Create a subnetwork from the same root
    CySubNetwork sn = rootNet.addSubNetwork();
    // It doesn't matter
    setRegistered(sn, false);
    // Set it as network pointer
    CyNode n = net.getNodeList().get(0);
    n.setNetworkPointer(sn);
    write(rootNet);
    // Test
    // It is saved as a nested node graph
    assertEquals("" + sn.getSUID(), evalString("//x:node[@id=" + n.getSUID() + "]/x:att/x:graph/@id"));
    // But it must NOT be registered!
    assertEquals("0", evalString("/x:graph//x:att/x:graph[@id=" + sn.getSUID() + "]/@cy:registered"));
}

Example 29 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class SessionXGMMLNetworkWriterTest method testRootNetworkOnlySavedIfSessionSavePolicy.

@Test(expected = IllegalArgumentException.class)
public void testRootNetworkOnlySavedIfSessionSavePolicy() throws UnsupportedEncodingException {
    CyRootNetwork newRoot = ((CySubNetwork) netFactory.createNetwork(SavePolicy.DO_NOT_SAVE)).getRootNetwork();
    // Registering it doesn't make any difference
    setRegistered(newRoot, true);
    write(newRoot);
}

Example 30 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class ReadCache method deleteUnresolvedNodes.

public void deleteUnresolvedNodes() {
    // Delete unresolved nodes from
    for (Map.Entry<CySubNetwork, Set<CyNode>> entry : unresolvedNodeMap.entrySet()) {
        final CySubNetwork net = entry.getKey();
        final Set<CyNode> nodes = entry.getValue();
        if (net != null && nodes != null && !nodes.isEmpty()) {
            logger.error("The following nodes can't be resolved and will be deleted from network \"" + net + "\": " + nodes);
            net.removeNodes(nodes);
        }
    }
}