Examples with GraphMLReader org.cytoscape.io.internal.read.graphml.GraphMLReader used on opensource projects

Example 1 with GraphMLReader

use of org.cytoscape.io.internal.read.graphml.GraphMLReader in project cytoscape-impl by cytoscape.

the class GraphMLReaderTest method testReadAttedOutput.

@Test
public void testReadAttedOutput() throws Exception {
    File file = new File("src/test/resources/atted.graphml");
    InputStream stream = file.toURI().toURL().openStream();
    GraphMLReader reader = new GraphMLReader(stream, layouts, appManager, netFactory, networkManager, rootFactory);
    assertNotNull(reader);
    reader.run(tm);
    final CyNetwork[] networks = reader.getNetworks();
    assertNotNull(networks);
    assertEquals(1, networks.length);
    final CyNetwork network = networks[0];
// nodes = network.getno
// 
// assertEquals("AtbZIP52", nodeAttr.getAttribute("At1g06850", "symbol"));
// assertEquals("bZIP", nodeAttr.getAttribute("At1g06850", "TF_family"));
// 
// assertEquals("correlation", edgeAttr.getAttribute("At5g48880 (pp) At1g65060", "label"));
// assertEquals(5.20, edgeAttr.getAttribute("At5g48880 (pp) At1g65060", "mr_all"));
}

Example 2 with GraphMLReader

use of org.cytoscape.io.internal.read.graphml.GraphMLReader in project cytoscape-impl by cytoscape.

the class GraphMLReaderTest method testReadSimpleGraph.

@Test
public void testReadSimpleGraph() throws Exception {
    File file = new File("src/test/resources/testGraph1.xml");
    InputStream stream = file.toURI().toURL().openStream();
    GraphMLReader reader = new GraphMLReader(stream, layouts, appManager, netFactory, networkManager, rootFactory);
    assertNotNull(reader);
    reader.run(tm);
    final CyNetwork[] networks = reader.getNetworks();
    assertNotNull(networks);
    assertEquals(1, networks.length);
    final CyNetwork network = networks[0];
    assertEquals(11, network.getNodeCount());
    assertEquals(12, network.getEdgeCount());
}

Example 3 with GraphMLReader

use of org.cytoscape.io.internal.read.graphml.GraphMLReader in project cytoscape-impl by cytoscape.

the class GraphMLReaderTest method testReadAttrGraph.

@Test
public void testReadAttrGraph() throws Exception {
    File file = new File("src/test/resources/simpleWithAttributes.xml");
    InputStream stream = file.toURI().toURL().openStream();
    GraphMLReader reader = new GraphMLReader(stream, layouts, appManager, netFactory, networkManager, rootFactory);
    assertNotNull(reader);
    reader.run(tm);
    final CyNetwork[] networks = reader.getNetworks();
    assertNotNull(networks);
    assertEquals(1, networks.length);
    final CyNetwork net = networks[0];
    assertEquals(6, net.getNodeCount());
    assertEquals(7, net.getEdgeCount());
    // Check Network Attributes
    final String networkName = net.getDefaultNetworkTable().getRow(net.getSUID()).get(NAME, String.class);
    final Number networkNumber = net.getDefaultNetworkTable().getRow(net.getSUID()).get("number_test", Double.class);
    assertEquals("Small GraphML Network", networkName);
    assertEquals(100.123, networkNumber);
    final CyNode n1 = getNodeByName(net, "n0");
    assertNotNull(n1);
    final CyEdge e1 = getEdgeByName(net, "n0 (-) n1");
    assertNotNull(e1);
    final CyColumn colorCol = net.getDefaultNodeTable().getColumn("color");
    final CyColumn rankCol = net.getDefaultNodeTable().getColumn("rank");
    final CyColumn degreeCol = net.getDefaultNodeTable().getColumn("degree");
    final CyColumn scoreCol = net.getDefaultNodeTable().getColumn("score");
    final CyColumn taggedCol = net.getDefaultNodeTable().getColumn("tagged");
    final CyColumn weightCol = net.getDefaultEdgeTable().getColumn("weight");
    assertNotNull(colorCol);
    assertNotNull(rankCol);
    assertNotNull(degreeCol);
    assertNotNull(scoreCol);
    assertNotNull(taggedCol);
    assertNotNull(weightCol);
    assertEquals(String.class, colorCol.getType());
    assertEquals(Integer.class, rankCol.getType());
    assertEquals(Long.class, degreeCol.getType());
    // GraphML "float" is converted to Double by Cytoscape
    assertEquals(Double.class, scoreCol.getType());
    assertEquals(Boolean.class, taggedCol.getType());
    assertEquals(Double.class, weightCol.getType());
    assertEquals("green", net.getRow(n1).get("color", String.class));
    assertEquals(Integer.valueOf(3), net.getRow(n1).get("rank", Integer.class));
    assertEquals(Long.valueOf(2), net.getRow(n1).get("degree", Long.class));
    assertEquals(Double.valueOf(0.95d), net.getRow(n1).get("score", Double.class));
    assertEquals(Boolean.TRUE, net.getRow(n1).get("tagged", Boolean.class));
    assertEquals(Double.valueOf(1.0d), net.getRow(e1).get("weight", Double.class));
}

Example 4 with GraphMLReader

use of org.cytoscape.io.internal.read.graphml.GraphMLReader in project cytoscape-impl by cytoscape.

the class GraphMLReaderTest method testReadNestedSubgraphs.

@Test
public void testReadNestedSubgraphs() throws Exception {
    File file = new File("src/test/resources/nested.xml");
    InputStream stream = file.toURI().toURL().openStream();
    GraphMLReader reader = new GraphMLReader(stream, layouts, appManager, netFactory, networkManager, rootFactory);
    assertNotNull(reader);
    reader.run(tm);
    final CyNetwork[] networks = reader.getNetworks();
    assertNotNull(networks);
    assertEquals(4, networks.length);
    final CyNetwork rootNetwork = networks[0];
    for (CyNode node : rootNetwork.getNodeList()) System.out.println("In root network: " + rootNetwork.getRow(node).get(CyNetwork.NAME, String.class));
    assertEquals(11, rootNetwork.getNodeCount());
    assertEquals(12, rootNetwork.getEdgeCount());
    final CyNetwork child1 = networks[1];
    assertEquals(3, child1.getNodeCount());
    assertEquals(2, child1.getEdgeCount());
    final CyNetwork child2 = networks[2];
    assertEquals(3, child2.getNodeCount());
    assertEquals(2, child2.getEdgeCount());
    final CyNetwork child3 = networks[3];
    assertEquals(1, child3.getNodeCount());
    assertEquals(0, child3.getEdgeCount());
}

Example 5 with GraphMLReader

use of org.cytoscape.io.internal.read.graphml.GraphMLReader in project cytoscape-impl by cytoscape.

the class GraphMLReaderTest method testReadNestedSubgraphs2.

@Test
public void testReadNestedSubgraphs2() throws Exception {
    File file = new File("src/test/resources/nested2.xml");
    InputStream stream = file.toURI().toURL().openStream();
    GraphMLReader reader = new GraphMLReader(stream, layouts, appManager, netFactory, networkManager, rootFactory);
    assertNotNull(reader);
    reader.run(tm);
    final CyNetwork[] networks = reader.getNetworks();
    assertNotNull(networks);
    assertEquals(4, networks.length);
    final CyNetwork rootNetwork = networks[0];
    for (CyNode node : rootNetwork.getNodeList()) System.out.println("In root network: " + rootNetwork.getRow(node).get(CyNetwork.NAME, String.class));
    assertEquals(8, rootNetwork.getNodeCount());
    assertEquals(10, rootNetwork.getEdgeCount());
    final CyNetwork child1 = networks[1];
    assertEquals(6, child1.getNodeCount());
    assertEquals(7, child1.getEdgeCount());
    final CyNetwork child2 = networks[2];
    assertEquals(3, child2.getNodeCount());
    assertEquals(3, child2.getEdgeCount());
    final CyNetwork child3 = networks[3];
    assertEquals(2, child3.getNodeCount());
    assertEquals(1, child3.getEdgeCount());
}