Author: mes
Date: 2011-09-23 10:29:19 -0700 (Fri, 23 Sep 2011)
New Revision: 26950
Modified:
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
Log:
reformatted
Modified:
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
2011-09-23 17:27:56 UTC (rev 26949)
+++
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
2011-09-23 17:29:19 UTC (rev 26950)
@@ -30,85 +30,85 @@
import org.junit.Before;
public class AbstractNetworkViewReaderTester {
- static class SimpleTask extends AbstractTask {
- public void run(final TaskMonitor tm) {
+ static class SimpleTask extends AbstractTask {
+ public void run(final TaskMonitor tm) {
+ }
}
- }
- protected static final int DEF_THRESHOLD = 10000;
-
- protected TaskMonitor taskMonitor;
- protected CyNetworkFactory netFactory;
- protected CyNetworkViewFactory viewFactory;
- protected ReadUtils readUtil;
- protected CyLayoutAlgorithmManager layouts;
+ protected static final int DEF_THRESHOLD = 10000;
+
+ protected TaskMonitor taskMonitor;
+ protected CyNetworkFactory netFactory;
+ protected CyNetworkViewFactory viewFactory;
+ protected ReadUtils readUtil;
+ protected CyLayoutAlgorithmManager layouts;
private Properties properties;
- @Before
- public void setUp() throws Exception {
- taskMonitor = mock(TaskMonitor.class);
+ @Before
+ public void setUp() throws Exception {
+ taskMonitor = mock(TaskMonitor.class);
- CyLayoutAlgorithm def = mock(CyLayoutAlgorithm.class);
- when(def.getTaskIterator()).thenReturn(new TaskIterator(new
SimpleTask()));
+ CyLayoutAlgorithm def = mock(CyLayoutAlgorithm.class);
+ when(def.getTaskIterator()).thenReturn(new TaskIterator(new
SimpleTask()));
- layouts = mock(CyLayoutAlgorithmManager.class);
- when(layouts.getDefaultLayout()).thenReturn(def);
+ layouts = mock(CyLayoutAlgorithmManager.class);
+ when(layouts.getDefaultLayout()).thenReturn(def);
- NetworkTestSupport nts = new NetworkTestSupport();
- netFactory = nts.getNetworkFactory();
+ NetworkTestSupport nts = new NetworkTestSupport();
+ netFactory = nts.getNetworkFactory();
- properties = new Properties();
- CyProperty<Properties> cyProperties = new BasicCyProperty(properties,
SavePolicy.DO_NOT_SAVE);
- NetworkViewTestSupport nvts = new NetworkViewTestSupport(cyProperties);
- setViewThreshold(DEF_THRESHOLD);
-
- viewFactory = nvts.getNetworkViewFactory();
+ properties = new Properties();
+ CyProperty<Properties> cyProperties = new
BasicCyProperty(properties, SavePolicy.DO_NOT_SAVE);
+ NetworkViewTestSupport nvts = new
NetworkViewTestSupport(cyProperties);
+ setViewThreshold(DEF_THRESHOLD);
+
+ viewFactory = nvts.getNetworkViewFactory();
- readUtil = new ReadUtils(new StreamUtilImpl());
- }
+ readUtil = new ReadUtils(new StreamUtilImpl());
+ }
- protected void setViewThreshold(int threshold) {
- properties.setProperty("viewThreshold", String.valueOf(threshold));
- }
-
- /**
- * Will fail if it doesn't find the specified interaction.
- */
- protected void findInteraction(CyNetwork net, String source, String
target, String interaction, int count) {
- for (CyNode n : net.getNodeList()) {
- if (n.getCyRow().get("name", String.class).equals(source)) {
- List<CyNode> neigh = net.getNeighborList(n, CyEdge.Type.ANY);
- assertEquals(count, neigh.size());
- for (CyNode nn : neigh) {
- if (nn.getCyRow().get("name", String.class).equals(target))
{
- List<CyEdge> con = net.getConnectingEdgeList(n, nn,
CyEdge.Type.ANY);
- for (CyEdge e : con) {
- if (e.getCyRow().get("interaction",
String.class).equals(interaction)) {
- return;
- }
+ protected void setViewThreshold(int threshold) {
+ properties.setProperty("viewThreshold",
String.valueOf(threshold));
+ }
+
+ /**
+ * Will fail if it doesn't find the specified interaction.
+ */
+ protected void findInteraction(CyNetwork net, String source, String
target, String interaction, int count) {
+ for (CyNode n : net.getNodeList()) {
+ if (n.getCyRow().get("name",
String.class).equals(source)) {
+ List<CyNode> neigh = net.getNeighborList(n,
CyEdge.Type.ANY);
+ assertEquals("wrong number of neighbors",
count, neigh.size());
+ for (CyNode nn : neigh) {
+ if (nn.getCyRow().get("name",
String.class).equals(target)) {
+ List<CyEdge> con =
net.getConnectingEdgeList(n, nn, CyEdge.Type.ANY);
+ for (CyEdge e : con) {
+ if
(e.getCyRow().get("interaction", String.class).equals(interaction)) {
+ return;
+ }
+ }
+ }
+ }
}
- }
}
- }
+ fail("couldn't find interaction: " + source + " " + interaction
+ " " + target);
}
- fail("couldn't find interaction: " + source + " " + interaction + " " +
target);
- }
- /**
- * Assuming we only create one network.
- */
- protected CyNetwork checkSingleNetwork(CyNetworkView[] views, int
numNodes, int numEdges) {
- assertNotNull(views);
- assertEquals(1, views.length);
+ /**
+ * Assuming we only create one network.
+ */
+ protected CyNetwork checkSingleNetwork(CyNetworkView[] views, int
numNodes, int numEdges) {
+ assertNotNull(views);
+ assertEquals(1, views.length);
- CyNetwork net = views[0].getModel();
+ CyNetwork net = views[0].getModel();
- assertNotNull(net);
+ assertNotNull(net);
- assertEquals(numNodes, net.getNodeCount());
- assertEquals(numEdges, net.getEdgeCount());
+ assertEquals(numNodes, net.getNodeCount());
+ assertEquals(numEdges, net.getEdgeCount());
- return net;
- }
+ return net;
+ }
}
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