Author: kono
Date: 2011-05-09 14:15:37 -0700 (Mon, 09 May 2011)
New Revision: 24970
Modified:
core3/sbml-impl/trunk/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewReader.java
core3/sbml-impl/trunk/src/test/java/org/cytoscape/sbml/internal/SBMLNetworkViewReaderTest.java
Log:
Fixed to make it compatible with new network IO API.
Modified:
core3/sbml-impl/trunk/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewReader.java
===================================================================
---
core3/sbml-impl/trunk/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewReader.java
2011-05-09 21:04:03 UTC (rev 24969)
+++
core3/sbml-impl/trunk/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewReader.java
2011-05-09 21:15:37 UTC (rev 24970)
@@ -8,7 +8,7 @@
import java.util.HashMap;
import java.util.Map;
-import org.cytoscape.io.read.CyNetworkViewReader;
+import org.cytoscape.io.read.CyNetworkReader;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
@@ -16,7 +16,6 @@
import org.cytoscape.model.CyRow;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
import org.sbml.jsbml.JSBML;
@@ -29,7 +28,7 @@
import org.sbml.jsbml.Species;
import org.sbml.jsbml.SpeciesReference;
-public class SBMLNetworkViewReader extends AbstractTask implements
CyNetworkViewReader {
+public class SBMLNetworkViewReader extends AbstractTask implements
CyNetworkReader {
private static final int BUFFER_SIZE = 16384;
static final String NODE_NAME_ATTR_LABEL = "name"; //$NON-NLS-1$
@@ -66,7 +65,8 @@
private final CyNetworkFactory networkFactory;
private final CyNetworkViewFactory viewFactory;
- private CyNetworkView view;
+ //private CyNetworkView view;
+ private CyNetwork network;
public SBMLNetworkViewReader(InputStream stream, CyNetworkFactory
networkFactory, CyNetworkViewFactory viewFactory) {
this.stream = stream;
@@ -79,8 +79,8 @@
String xml = readString(stream);
SBMLDocument document = JSBML.readSBMLFromString(xml);
- CyNetwork network = networkFactory.getInstance();
- view = viewFactory.getNetworkView(network);
+ network = networkFactory.getInstance();
+ //view = viewFactory.getNetworkView(network);
Model model = document.getModel();
// Create a node for each Species
@@ -200,11 +200,13 @@
public void cancel() {
}
- public CyNetworkView[] getNetworkViews() {
- return new CyNetworkView[] { view };
+ @Override
+ public CyNetwork[] getCyNetworks() {
+ return new CyNetwork[] { network };
}
- public VisualStyle[] getVisualStyles() {
- return null;
+ @Override
+ public CyNetworkView buildCyNetworkView(CyNetwork network) {
+ return viewFactory.getNetworkView(network);
}
}
Modified:
core3/sbml-impl/trunk/src/test/java/org/cytoscape/sbml/internal/SBMLNetworkViewReaderTest.java
===================================================================
---
core3/sbml-impl/trunk/src/test/java/org/cytoscape/sbml/internal/SBMLNetworkViewReaderTest.java
2011-05-09 21:04:03 UTC (rev 24969)
+++
core3/sbml-impl/trunk/src/test/java/org/cytoscape/sbml/internal/SBMLNetworkViewReaderTest.java
2011-05-09 21:15:37 UTC (rev 24970)
@@ -7,14 +7,13 @@
import java.io.FileInputStream;
import java.io.IOException;
-import org.cytoscape.io.read.CyNetworkViewReader;
+import org.cytoscape.io.read.CyNetworkReader;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
import org.cytoscape.test.support.NetworkTestSupport;
import org.cytoscape.test.support.NetworkViewTestSupport;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TaskMonitor;
@@ -39,7 +38,7 @@
}
- CyNetworkViewReader createReader(File file) throws IOException {
+ CyNetworkReader createReader(File file) throws IOException {
SBMLNetworkViewReader reader = new SBMLNetworkViewReader(new
FileInputStream(file), networkFactory, networkViewFactory);
reader.setTaskIterator(new TaskIterator(reader));
return reader;
@@ -48,17 +47,17 @@
@Test
public void testSBMLLevel2() throws Exception {
File file = new File("src/test/resources/BIOMD0000000003.xml");
- CyNetworkViewReader reader = createReader(file);
+ CyNetworkReader reader = createReader(file);
reader.run(taskMonitor);
- CyNetworkView[] views = reader.getNetworkViews();
+ CyNetwork[] networks = reader.getCyNetworks();
- assertNotNull(views);
- assertEquals(1, views.length);
+ assertNotNull(networks);
+ assertEquals(1, networks.length);
- CyNetworkView view = views[0];
- assertNotNull(view);
+ CyNetwork network = networks[0];
+ assertNotNull(network);
- CyNetwork model = view.getModel();
+ CyNetwork model = network;
assertNotNull(model);
assertEquals(10, model.getNodeCount());
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
