Author: jm
Date: 2011-05-04 06:58:51 -0700 (Wed, 04 May 2011)
New Revision: 24915
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader.java
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
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/xgmml/XGMMLNetworkViewReaderTest.java
Log:
Fixed unit tests in io-impl
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader.java
2011-05-04 13:57:31 UTC (rev 24914)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader.java
2011-05-04 13:58:51 UTC (rev 24915)
@@ -154,7 +154,9 @@
private void createView(CyNetwork network) {
view = cyNetworkViewFactory.getNetworkView(network);
- layout();
+ if (!view.isEmptyView()) {
+ layout();
+ }
this.cyNetworkViews = new CyNetworkView[]{view};
}
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
2011-05-04 13:57:31 UTC (rev 24914)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
2011-05-04 13:58:51 UTC (rev 24915)
@@ -7,6 +7,7 @@
import static org.mockito.Mockito.when;
import java.util.List;
+import java.util.Properties;
import org.cytoscape.io.internal.util.ReadUtils;
import org.cytoscape.io.internal.util.StreamUtilImpl;
@@ -14,6 +15,9 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNode;
+import org.cytoscape.property.BasicCyProperty;
+import org.cytoscape.property.CyProperty;
+import org.cytoscape.property.CyProperty.SavePolicy;
import org.cytoscape.test.support.NetworkTestSupport;
import org.cytoscape.test.support.NetworkViewTestSupport;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
@@ -39,7 +43,7 @@
protected ReadUtils readUtil;
protected CyLayoutAlgorithmManager layouts;
- protected int viewThreshold = DEF_THRESHOLD;
+ private Properties properties;
@Before
public void setUp() throws Exception {
@@ -54,12 +58,20 @@
NetworkTestSupport nts = new NetworkTestSupport();
netFactory = nts.getNetworkFactory();
- NetworkViewTestSupport nvts = new NetworkViewTestSupport();
+ 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());
}
+ protected void setViewThreshold(int threshold) {
+ properties.setProperty("viewThreshold", String.valueOf(threshold));
+ }
+
/**
* Will fail if it doesn't find the specified interaction.
*/
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 13:57:31 UTC (rev 24914)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
2011-05-04 13:58:51 UTC (rev 24915)
@@ -30,11 +30,10 @@
findInteraction(net, "YNL312W", "YPL111W", "pd", 1);
// Test low threshold
- this.viewThreshold = 5;
+ setViewThreshold(5);
CyNetworkView[] nullViews = getViews("sample.sif");
assertNotNull(nullViews);
assertTrue(nullViews[0].isEmptyView());
- this.viewThreshold = this.DEF_THRESHOLD;
}
/**
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderTest.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderTest.java
2011-05-04 13:57:31 UTC (rev 24914)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderTest.java
2011-05-04 13:58:51 UTC (rev 24915)
@@ -66,12 +66,11 @@
findInteraction(net, "YGR136W", "YGR058W", "pp", 1);
// Test low threshold
- this.viewThreshold = 5;
+ setViewThreshold(5);
CyNetworkView[] nullViews = getViews("galFiltered.xgmml");
assertNotNull(nullViews);
assertEquals(1, nullViews.length);
assertTrue(nullViews[0].isEmptyView());
- this.viewThreshold = this.DEF_THRESHOLD;
}
private CyNetworkView[] getViews(String file) throws Exception {
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