Author: kono
Date: 2011-05-09 14:32:27 -0700 (Mon, 09 May 2011)
New Revision: 24975
Modified:
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
Log:
Fixed to make this bundle compatible with new network IO API.
Modified:
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
===================================================================
---
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
2011-05-09 21:21:50 UTC (rev 24974)
+++
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
2011-05-09 21:32:27 UTC (rev 24975)
@@ -7,7 +7,7 @@
import java.io.StringWriter;
import java.util.ArrayList;
-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.psi_mi.internal.cyto_mapper.MapToCytoscape;
@@ -21,11 +21,11 @@
import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.Task;
-import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TaskMonitor;
-public class PsiMiNetworkViewReader extends AbstractTask implements
CyNetworkViewReader {
+public class PsiMiNetworkViewReader extends AbstractTask implements
CyNetworkReader {
+
private static final int BUFFER_SIZE = 16384;
private final CyNetworkViewFactory networkViewFactory;
@@ -33,7 +33,7 @@
private InputStream inputStream;
- private CyNetworkView networkView;
+ private CyNetwork network;
private CyLayoutAlgorithmManager layouts;
@@ -64,32 +64,14 @@
taskMonitor.setProgress(0.25);
// Now map to Cytoscape network objects.
- CyNetwork network = networkFactory.getInstance();
+ network = networkFactory.getInstance();
MapToCytoscape mapper2 = new MapToCytoscape(network,
interactions, MapToCytoscape.SPOKE_VIEW);
mapper2.doMapping();
-
- taskMonitor.setProgress(0.5);
-
- networkView = networkViewFactory.getNetworkView(network);
-
- CyLayoutAlgorithm taskFactory = layouts.getDefaultLayout();
- taskFactory.setNetworkView(networkView);
- TaskIterator taskIterator = taskFactory.getTaskIterator();
- Task task = taskIterator.next();
- insertTasksAfterCurrentTask(task);
taskMonitor.setProgress(1.0);
}
- @Override
- public CyNetworkView[] getNetworkViews() {
- return new CyNetworkView[] { networkView };
- }
- @Override
- public VisualStyle[] getVisualStyles() {
- return null;
- }
private static String readString(InputStream source) throws IOException
{
StringWriter writer = new StringWriter();
@@ -106,4 +88,23 @@
}
return writer.toString();
}
+
+ @Override
+ public CyNetwork[] getCyNetworks() {
+ return new CyNetwork[] { network };
+ }
+
+ @Override
+ public CyNetworkView buildCyNetworkView(CyNetwork network) {
+
+ final CyNetworkView networkView =
networkViewFactory.getNetworkView(network);
+
+ CyLayoutAlgorithm taskFactory = layouts.getDefaultLayout();
+ taskFactory.setNetworkView(networkView);
+ TaskIterator taskIterator = taskFactory.getTaskIterator();
+ Task task = taskIterator.next();
+ insertTasksAfterCurrentTask(task);
+
+ return networkView;
+ }
}
Modified:
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
===================================================================
---
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
2011-05-09 21:21:50 UTC (rev 24974)
+++
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
2011-05-09 21:32:27 UTC (rev 24975)
@@ -3,32 +3,29 @@
import java.io.IOException;
import java.io.InputStream;
-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.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
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.Task;
-import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TaskMonitor;
-public class PsiMiTabReader extends AbstractTask implements
CyNetworkViewReader {
+public class PsiMiTabReader extends AbstractTask implements CyNetworkReader {
private InputStream inputStream;
private final CyNetworkViewFactory cyNetworkViewFactory;
-
- private CyNetworkView[] cyNetworkViews;
- private VisualStyle[] visualstyles;
private final CyLayoutAlgorithmManager layouts;
private final PsiMiTabParser parser;
+
+ private CyNetwork network;
public PsiMiTabReader(InputStream is,
CyNetworkViewFactory cyNetworkViewFactory,
@@ -43,16 +40,6 @@
}
@Override
- public CyNetworkView[] getNetworkViews() {
- return cyNetworkViews;
- }
-
- @Override
- public VisualStyle[] getVisualStyles() {
- return visualstyles;
- }
-
- @Override
public void run(TaskMonitor taskMonitor) throws Exception {
try {
createNetwork(taskMonitor);
@@ -68,8 +55,19 @@
taskMonitor.setProgress(0.0);
- final CyNetwork network = parser.parse();
+ network = parser.parse();
+ taskMonitor.setProgress(1.0);
+
+ }
+
+ @Override
+ public CyNetwork[] getCyNetworks() {
+ return new CyNetwork[] {network};
+ }
+
+ @Override
+ public CyNetworkView buildCyNetworkView(CyNetwork network) {
final CyNetworkView view =
cyNetworkViewFactory.getNetworkView(network);
CyLayoutAlgorithm tf = layouts.getDefaultLayout();
@@ -78,10 +76,6 @@
Task task = ti.next();
insertTasksAfterCurrentTask(task);
- // SIF always creates only one network.
- this.cyNetworkViews = new CyNetworkView[] { view };
-
- taskMonitor.setProgress(1.0);
-
+ return view;
}
}
Modified:
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
===================================================================
---
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
2011-05-09 21:21:50 UTC (rev 24974)
+++
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
2011-05-09 21:32:27 UTC (rev 24975)
@@ -2,21 +2,19 @@
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
-import static org.mockito.Matchers.any;
import static org.mockito.Mockito.when;
import java.io.File;
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.test.support.NetworkTestSupport;
import org.cytoscape.test.support.NetworkViewTestSupport;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskIterator;
@@ -46,7 +44,7 @@
networkViewFactory = new
NetworkViewTestSupport().getNetworkViewFactory();
}
- CyNetworkViewReader createReader(File file) throws IOException {
+ CyNetworkReader createReader(File file) throws IOException {
PsiMiNetworkViewReader reader = new PsiMiNetworkViewReader(new
FileInputStream(file), networkFactory, networkViewFactory, layouts);
reader.setTaskIterator(new TaskIterator(reader));
return reader;
@@ -55,17 +53,14 @@
@Test
public void testReadPsiMi1() throws Exception {
File file = new
File("src/test/resources/testData/dip_sample.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 = view.getModel();
+ CyNetwork network = networks[0];
assertNotNull(network);
// 2 interactors, 4 distinct bits of evidence supporting
@@ -76,17 +71,14 @@
@Test
public void testReadPsiMi25() throws Exception {
File file = new
File("src/test/resources/testData/psi_sample_2_5_1.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 = view.getModel();
+ CyNetwork network = networks[0];
assertNotNull(network);
// Spoke model: 40 interactors, 1 bait = 39 interactions
Modified:
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
===================================================================
---
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
2011-05-09 21:21:50 UTC (rev 24974)
+++
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
2011-05-09 21:32:27 UTC (rev 24975)
@@ -1,7 +1,7 @@
package org.cytoscape.psi_mi.internal.plugin;
-import static org.junit.Assert.*;
-import static org.mockito.Matchers.any;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
import static org.mockito.Mockito.when;
import java.io.File;
@@ -9,14 +9,13 @@
import java.io.IOException;
import java.io.InputStream;
-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.test.support.NetworkTestSupport;
import org.cytoscape.test.support.NetworkViewTestSupport;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskIterator;
@@ -61,18 +60,15 @@
public void testPsiMiTabReader() throws Exception {
final File file = new File(
"src/test/resources/testData/BIOGRID-ORGANISM-Bos_taurus-3.1.74.mitab");
- final CyNetworkViewReader reader = createReader(file);
+ final 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);
-
- final CyNetwork network = view.getModel();
+ final CyNetwork network = networks[0];
assertNotNull(network);
assertEquals(109, network.getNodeCount());
@@ -80,7 +76,7 @@
}
- private CyNetworkViewReader createReader(File file) throws IOException {
+ private CyNetworkReader createReader(File file) throws IOException {
final InputStream is = new FileInputStream(file);
PsiMiTabReader reader = new PsiMiTabReader(is,
networkViewFactory,
networkFactory, layouts);
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