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

Example 96 with CyEdge

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

the class SourceID method evaluateFunction.

@Override
public Object evaluateFunction(final Object[] args) {
    final Long edgeID = FunctionUtil.getArgAsLong(args[0]);
    final CyNetwork currentNetwork = serviceRegistrar.getService(CyApplicationManager.class).getCurrentNetwork();
    if (currentNetwork == null)
        return (Long) (-1L);
    final CyEdge edge = currentNetwork.getEdge(edgeID);
    if (edge == null)
        throw new IllegalArgumentException("\"" + edgeID + "\" is not a valid edge identifier.");
    return edge.getSource().getSUID();
}

Example 97 with CyEdge

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

the class DegreeTest method init.

@Before
public void init() {
    final CyNode node = mock(CyNode.class);
    when(node.getSUID()).thenReturn(101L);
    final List<CyEdge> edgeList = mock(List.class);
    when(edgeList.size()).thenReturn(3);
    final CyNetwork network = mock(CyNetwork.class);
    when(network.getAdjacentEdgeList(node, CyEdge.Type.ANY)).thenReturn(edgeList);
    when(network.getNode(101L)).thenReturn(node);
    Collection<CyNode> nodes = new ArrayList<>(1);
    nodes.add(node);
    applicationManager = mock(CyApplicationManager.class);
    when(applicationManager.getCurrentNetwork()).thenReturn(network);
    eventHelper = new DummyCyEventHelper();
    serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyApplicationManager.class)).thenReturn(applicationManager);
    when(serviceRegistrar.getService(CyEventHelper.class)).thenReturn(eventHelper);
}

Example 98 with CyEdge

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

the class TargetIDTest method init.

@Before
public void init() {
    final CyNode node = mock(CyNode.class);
    when(node.getSUID()).thenReturn(101L);
    final List<CyEdge> edgeList = mock(List.class);
    when(edgeList.size()).thenReturn(3);
    final CyNetwork network = mock(CyNetwork.class);
    final CyEdge edge = mock(CyEdge.class);
    when(edge.getSUID()).thenReturn(11L);
    when(edge.getTarget()).thenReturn(node);
    Collection<CyEdge> edges = new ArrayList<CyEdge>(1);
    edges.add(edge);
    when(network.getEdge(11L)).thenReturn(edge);
    applicationManager = mock(CyApplicationManager.class);
    when(applicationManager.getCurrentNetwork()).thenReturn(network);
    eventHelper = new DummyCyEventHelper();
    serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyApplicationManager.class)).thenReturn(applicationManager);
    when(serviceRegistrar.getService(CyEventHelper.class)).thenReturn(eventHelper);
}

Example 99 with CyEdge

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

the class GMLNetworkReaderTest method testReadYEdArrows.

@Test
public void testReadYEdArrows() throws Exception {
    final GMLNetworkReader reader = readGML("src/test/resources/testData/gml/yed_arrows.gml");
    final CyNetwork[] networks = reader.getNetworks();
    assertEquals(1, networks.length);
    final CyNetwork net = networks[0];
    final CyNetworkView view = reader.buildCyNetworkView(net);
    final CyEdge e1 = getEdgeByName(net, "n1 () n2");
    final CyEdge e2 = getEdgeByName(net, "n2 () n3");
    final CyEdge e3 = getEdgeByName(net, "n3 () n1");
    final CyEdge e4 = getEdgeByName(net, "n3 () n4");
    // Test arrows as specified here: http://docs.yworks.com/yfiles/doc/developers-guide/gml.html
    final View<CyEdge> ev1 = view.getEdgeView(e1);
    assertEquals(ArrowShapeVisualProperty.NONE, ev1.getVisualProperty(EDGE_SOURCE_ARROW_SHAPE));
    assertEquals(ArrowShapeVisualProperty.ARROW, ev1.getVisualProperty(EDGE_TARGET_ARROW_SHAPE));
    final View<CyEdge> ev2 = view.getEdgeView(e2);
    assertEquals(ArrowShapeVisualProperty.DELTA, ev2.getVisualProperty(EDGE_SOURCE_ARROW_SHAPE));
    assertEquals(ArrowShapeVisualProperty.NONE, ev2.getVisualProperty(EDGE_TARGET_ARROW_SHAPE));
    final View<CyEdge> ev3 = view.getEdgeView(e3);
    assertEquals(ArrowShapeVisualProperty.DIAMOND, ev3.getVisualProperty(EDGE_SOURCE_ARROW_SHAPE));
    assertEquals(ArrowShapeVisualProperty.CIRCLE, ev3.getVisualProperty(EDGE_TARGET_ARROW_SHAPE));
    final View<CyEdge> ev4 = view.getEdgeView(e4);
    assertEquals(ArrowShapeVisualProperty.NONE, ev4.getVisualProperty(EDGE_SOURCE_ARROW_SHAPE));
    assertEquals(ArrowShapeVisualProperty.NONE, ev4.getVisualProperty(EDGE_TARGET_ARROW_SHAPE));
}

Example 100 with CyEdge

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

the class GMLNetworkReaderTest method testReadOldGalFilteredArrows.

@Test
public void testReadOldGalFilteredArrows() throws Exception {
    // This file is distributed in the sampleData folder of previous Cy2 versions
    // and uses only the attribute key "arrow" (not "sourceArrow" or "source_Arrow", as yEd and Cy3)
    final GMLNetworkReader reader = readGML("src/test/resources/testData/gml/galFiltered_old.gml");
    final CyNetwork[] networks = reader.getNetworks();
    assertEquals(1, networks.length);
    final CyNetwork net = networks[0];
    final CyNetworkView view = reader.buildCyNetworkView(net);
    final CyEdge e1 = getEdgeByName(net, "YPR124W (pd) YMR021C");
    final CyEdge e2 = getEdgeByName(net, "YGR074W (pp) YBR043C");
    final View<CyEdge> ev1 = view.getEdgeView(e1);
    assertEquals(ArrowShapeVisualProperty.NONE, ev1.getVisualProperty(EDGE_SOURCE_ARROW_SHAPE));
    assertEquals(ArrowShapeVisualProperty.ARROW, ev1.getVisualProperty(EDGE_TARGET_ARROW_SHAPE));
    final View<CyEdge> ev2 = view.getEdgeView(e2);
    assertEquals(ArrowShapeVisualProperty.NONE, ev2.getVisualProperty(EDGE_SOURCE_ARROW_SHAPE));
    assertEquals(ArrowShapeVisualProperty.NONE, ev2.getVisualProperty(EDGE_TARGET_ARROW_SHAPE));
}