Examples with CyEdge org.cytoscape.model.CyEdge used on opensource projects

Example 46 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-api by cytoscape.

the class AbstractCyIdentifiableTest method testGetSUID.

@Test
public void testGetSUID() {
    CyNode n1 = net.addNode();
    assertTrue("suid >= 0", n1.getSUID() >= 0);
    CyNode n2 = net.addNode();
    assertTrue("suid >= 0", n2.getSUID() >= 0);
    CyEdge e1 = net.addEdge(n1, n2, true);
    assertTrue("suid >= 0", e1.getSUID() >= 0);
    CyEdge e2 = net.addEdge(n1, n2, false);
    assertTrue("suid >= 0", e2.getSUID() >= 0);
    assertTrue("suid >= 0", net.getSUID() >= 0);
}

Example 47 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-api by cytoscape.

the class AbstractCyRootNetworkTest method testAddSubNetworkWithGoodNodesAndInvalidEdges.

@Test(expected = IllegalArgumentException.class)
public void testAddSubNetworkWithGoodNodesAndInvalidEdges() {
    CyNode n1 = root.addNode();
    CyNode n2 = root.addNode();
    CyNode n3 = root.addNode();
    CyEdge ex = new DummyCyEdge(null, null, false, 50);
    List<CyNode> nodes = Arrays.asList(n1, n2, n3);
    List<CyEdge> edges = Arrays.asList(ex);
    CySubNetwork n = root.addSubNetwork(nodes, edges);
}

Example 48 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-api by cytoscape.

the class AbstractCyRootNetworkTest method testAddNode.

@Test
public void testAddNode() {
    System.out.println("---> testAddNode");
    CyNode n1 = root.getBaseNetwork().addNode();
    CyNode n2 = root.getBaseNetwork().addNode();
    CyNode n3 = root.getBaseNetwork().addNode();
    CyNode n4 = root.getBaseNetwork().addNode();
    CyEdge e1 = root.getBaseNetwork().addEdge(n1, n2, true);
    CyEdge e2 = root.getBaseNetwork().addEdge(n2, n3, false);
    CyEdge e3 = root.getBaseNetwork().addEdge(n2, n4, false);
    assertEquals("node list size", 4, root.getNodeList().size());
    CySubNetwork s1 = root.addSubNetwork();
    s1.addNode(n1);
    s1.addNode(n2);
    s1.addEdge(e1);
    assertEquals("base node list size", 4, root.getBaseNetwork().getNodeList().size());
    assertEquals("node list size", 4, root.getNodeList().size());
    CyNode n5 = root.getBaseNetwork().addNode();
    assertEquals("node list size", 5, root.getNodeList().size());
    assertEquals("base node list size", 5, root.getBaseNetwork().getNodeList().size());
    CyNode n6 = root.getBaseNetwork().addNode();
    assertEquals("node list size", 6, root.getNodeList().size());
    assertEquals("base node list size", 6, root.getBaseNetwork().getNodeList().size());
    assertTrue("root does contain node5", root.containsNode(n5));
    boolean ret = root.removeNodes(Collections.singletonList(n5));
    assertTrue("removed node5", ret);
    assertFalse("root doesn't contain node5", root.containsNode(n5));
    assertEquals("node list size", 5, root.getNodeList().size());
    assertEquals("base node list size", 5, root.getBaseNetwork().getNodeList().size());
    ret = root.removeNodes(Collections.singletonList(n6));
    assertTrue("removed node6", ret);
    assertEquals("node list size", 4, root.getNodeList().size());
    assertEquals("base node list size", 4, root.getBaseNetwork().getNodeList().size());
}

Example 49 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-api by cytoscape.

the class AbstractCySubNetworkTest method testAddEdgeNotYetAddedTarget.

@Test
public void testAddEdgeNotYetAddedTarget() {
    defaultSetup();
    CyEdge e4 = root.addEdge(n4, n1, true);
    assertTrue(sub.addEdge(e4));
}

Example 50 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-api by cytoscape.

the class CySessionTest method testSetObjectMap.

@Test
public void testSetObjectMap() {
    Map<Object, CyNetwork> netMap = new HashMap<Object, CyNetwork>();
    CyNetwork net1 = mock(CyNetwork.class);
    netMap.put("A", net1);
    CyNetwork net2 = mock(CyNetwork.class);
    netMap.put("B", net2);
    Map<Object, CyNetworkView> viewMap = new HashMap<Object, CyNetworkView>();
    CyNetworkView view1 = mock(CyNetworkView.class);
    viewMap.put("A", view1);
    Map<Object, CyNode> nodeMap = new HashMap<Object, CyNode>();
    CyNode n1 = mock(CyNode.class);
    nodeMap.put(new Long(1), n1);
    CyNode n2 = mock(CyNode.class);
    nodeMap.put(new Long(2), n2);
    Map<Object, CyEdge> edgeMap = new HashMap<Object, CyEdge>();
    CyEdge e1 = mock(CyEdge.class);
    edgeMap.put(new Long(3), e1);
    Map<Class<? extends CyIdentifiable>, Map<Object, ? extends CyIdentifiable>> objMap = new HashMap<Class<? extends CyIdentifiable>, Map<Object, ? extends CyIdentifiable>>();
    objMap.put(CyNetwork.class, netMap);
    objMap.put(CyNetworkView.class, viewMap);
    objMap.put(CyNode.class, nodeMap);
    objMap.put(CyEdge.class, edgeMap);
    session = new CySession.Builder().objectMap(objMap).build();
    assertNotNull(session);
    assertSame(net1, session.getObject("A", CyNetwork.class));
    assertSame(net2, session.getObject("B", CyNetwork.class));
    assertSame(view1, session.getObject("A", CyNetworkView.class));
    assertSame(n1, session.getObject(new Long(1), CyNode.class));
    assertSame(n2, session.getObject(new Long(2), CyNode.class));
    assertSame(e1, session.getObject(new Long(3), CyEdge.class));
    assertNull(session.getObject("A", View.class));
    assertNull(session.getObject("B", CyNetworkView.class));
}