Author: kono
Date: 2011-05-04 12:35:31 -0700 (Wed, 04 May 2011)
New Revision: 24920
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
Log:
Broken formats are fixed.
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
2011-05-04 19:33:22 UTC (rev 24919)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
2011-05-04 19:35:31 UTC (rev 24920)
@@ -17,74 +17,74 @@
public class SIFNetworkViewReaderTest extends AbstractNetworkViewReaderTester {
- /**
- * 'typical' means that all lines have the form "node1 pd node2 [node3
node4
- * ...]
- */
- @Test
- public void testReadFromTypicalFile() throws Exception {
+ /**
+ * 'typical' means that all lines have the form "node1 pd node2 [node3
node4
+ * ...]
+ */
+ @Test
+ public void testReadFromTypicalFile() throws Exception {
- CyNetworkView[] views = getViews("sample.sif");
- CyNetwork net = checkSingleNetwork(views, 31, 27);
+ CyNetworkView[] views = getViews("sample.sif");
+ CyNetwork net = checkSingleNetwork(views, 31, 27);
- findInteraction(net, "YNL312W", "YPL111W", "pd", 1);
+ findInteraction(net, "YNL312W", "YPL111W", "pd", 1);
- // Test low threshold
- setViewThreshold(5);
- CyNetworkView[] nullViews = getViews("sample.sif");
- assertNotNull(nullViews);
- assertTrue(nullViews[0].isEmptyView());
- }
+ // Test low threshold
+ setViewThreshold(5);
+ CyNetworkView[] nullViews = getViews("sample.sif");
+ assertNotNull(nullViews);
+ assertTrue(nullViews[0].isEmptyView());
+ }
- /**
- * all lines have the degenerate form "node1" that is, with no interaction
- * type and no target
- */
- @Test
- public void testReadFileWithNoInteractions() throws Exception {
- CyNetworkView[] views = getViews("degenerate.sif");
+ /**
+ * all lines have the degenerate form "node1" that is, with no
interaction
+ * type and no target
+ */
+ @Test
+ public void testReadFileWithNoInteractions() throws Exception {
+ CyNetworkView[] views = getViews("degenerate.sif");
- CyNetwork net = checkSingleNetwork(views, 9, 0);
+ CyNetwork net = checkSingleNetwork(views, 9, 0);
- for (CyNode n : net.getNodeList())
- assertTrue(n.getCyRow().get("name", String.class).startsWith("Y"));
- }
+ for (CyNode n : net.getNodeList())
+ assertTrue(n.getCyRow().get("name",
String.class).startsWith("Y"));
+ }
- @Test
- public void testReadMultiWordProteinsFile() throws Exception {
+ @Test
+ public void testReadMultiWordProteinsFile() throws Exception {
- CyNetworkView[] views = getViews("multiWordProteins.sif");
+ CyNetworkView[] views = getViews("multiWordProteins.sif");
- CyNetwork net = checkSingleNetwork(views, 28, 31);
+ CyNetwork net = checkSingleNetwork(views, 28, 31);
- findInteraction(net, "26S ubiquitin dependent proteasome",
"I-kappa-B-alpha", "interactsWith", 1);
- findInteraction(net, "TRAF6", "RIP2", "interactsWith", 13);
- findInteraction(net, "TRAF6", "ABCDE oopah", "interactsWith", 13);
- findInteraction(net, "TRAF6", "HJKOL coltrane", "interactsWith", 13);
+ findInteraction(net, "26S ubiquitin dependent proteasome",
"I-kappa-B-alpha", "interactsWith", 1);
+ findInteraction(net, "TRAF6", "RIP2", "interactsWith", 13);
+ findInteraction(net, "TRAF6", "ABCDE oopah", "interactsWith",
13);
+ findInteraction(net, "TRAF6", "HJKOL coltrane",
"interactsWith", 13);
- }
+ }
- @Test
- public void testReadMultiWordProteinsFileWithErrantSpaces() throws
Exception {
+ @Test
+ public void testReadMultiWordProteinsFileWithErrantSpaces() throws
Exception {
- CyNetworkView[] views =
getViews("multiWordProteinsFileTrailingSpaces.sif");
+ CyNetworkView[] views =
getViews("multiWordProteinsFileTrailingSpaces.sif");
- CyNetwork net = checkSingleNetwork(views, 28, 31);
+ CyNetwork net = checkSingleNetwork(views, 28, 31);
- findInteraction(net, "26S ubiquitin dependent proteasome",
"I-kappa-B-alpha", "interactsWith", 1);
- findInteraction(net, "TRAF6", "RIP2", "interactsWith", 13);
- findInteraction(net, "TRAF6", "ABCDE oopah", "interactsWith", 13);
- findInteraction(net, "TRAF6", "HJKOL coltrane", "interactsWith", 13);
- }
+ findInteraction(net, "26S ubiquitin dependent proteasome",
"I-kappa-B-alpha", "interactsWith", 1);
+ findInteraction(net, "TRAF6", "RIP2", "interactsWith", 13);
+ findInteraction(net, "TRAF6", "ABCDE oopah", "interactsWith",
13);
+ findInteraction(net, "TRAF6", "HJKOL coltrane",
"interactsWith", 13);
+ }
- private CyNetworkView[] getViews(String file) throws Exception {
- File f = new File("./src/test/resources/testData/sif/" + file);
- final CyEventHelper eventHelper = mock(CyEventHelper.class);
- SIFNetworkViewReader snvp = new SIFNetworkViewReader(new
FileInputStream(f), layouts, viewFactory,
- netFactory, eventHelper);
- new TaskIterator(snvp);
- snvp.run(taskMonitor);
+ private CyNetworkView[] getViews(String file) throws Exception {
+ File f = new File("./src/test/resources/testData/sif/" + file);
+ final CyEventHelper eventHelper = mock(CyEventHelper.class);
+ SIFNetworkViewReader snvp = new SIFNetworkViewReader(new
FileInputStream(f), layouts, viewFactory, netFactory,
+ eventHelper);
+ new TaskIterator(snvp);
+ snvp.run(taskMonitor);
- return snvp.getNetworkViews();
- }
+ return snvp.getNetworkViews();
+ }
}
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