Author: kono
Date: 2011-10-20 17:10:30 -0700 (Thu, 20 Oct 2011)
New Revision: 27258
Modified:
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/CyActivator.java
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderFactory.java
core3/impl/trunk/psi-mi-impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
Log:
Property added to check default layout algorithm.
Modified:
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/CyActivator.java
2011-10-20 23:04:42 UTC (rev 27257)
+++
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/CyActivator.java
2011-10-21 00:10:30 UTC (rev 27258)
@@ -6,6 +6,7 @@
import org.cytoscape.io.util.StreamUtil;
import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.property.CyProperty;
import org.cytoscape.psi_mi.internal.plugin.PsiMiNetworkViewTaskFactory;
import org.cytoscape.psi_mi.internal.plugin.PsiMiTabReaderFactory;
import org.cytoscape.psi_mi.internal.plugin.PsiMiCyFileFilter;
@@ -33,6 +34,8 @@
CyNetworkFactory cyNetworkFactoryServiceRef =
getService(bc,CyNetworkFactory.class);
CyNetworkViewFactory cyNetworkViewFactoryServiceRef =
getService(bc,CyNetworkViewFactory.class);
StreamUtil streamUtilRef = getService(bc,StreamUtil.class);
+ CyProperty cyPropertyServiceRef =
getService(bc,CyProperty.class,"(cyPropertyName=cytoscape3.props)");
+
PsiMiCyFileFilter psiMiFilter = new PsiMiCyFileFilter("PSI-MI
files (*.xml)",streamUtilRef);
PsiMiCyFileFilter psiMi1Filter = new PsiMiCyFileFilter("PSI-MI
Level 1",streamUtilRef);
@@ -41,7 +44,7 @@
PsiMiNetworkViewTaskFactory psiMiNetworkViewTaskFactory = new
PsiMiNetworkViewTaskFactory(psiMiFilter,cyNetworkFactoryServiceRef,cyNetworkViewFactoryServiceRef,cyLayoutsServiceRef);
PsiMiNetworkWriterFactory psiMi1NetworkViewWriterFactory = new
PsiMiNetworkWriterFactory(LEVEL_1,psiMi1Filter);
PsiMiNetworkWriterFactory psiMi25NetworkViewWriterFactory = new
PsiMiNetworkWriterFactory(LEVEL_2_5,psiMi25Filter);
- PsiMiTabReaderFactory psiMiTabReaderFactory = new
PsiMiTabReaderFactory(psiMiTabFilter,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,cyLayoutsServiceRef);
+ PsiMiTabReaderFactory psiMiTabReaderFactory = new
PsiMiTabReaderFactory(psiMiTabFilter,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,cyLayoutsServiceRef,
cyPropertyServiceRef);
Properties psiMiNetworkViewTaskFactoryProps = new Properties();
Modified:
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
2011-10-20 23:04:42 UTC (rev 27257)
+++
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
2011-10-21 00:10:30 UTC (rev 27258)
@@ -2,10 +2,12 @@
import java.io.IOException;
import java.io.InputStream;
+import java.util.Properties;
import org.cytoscape.io.read.CyNetworkReader;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.property.CyProperty;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
@@ -28,15 +30,18 @@
private CyNetwork network;
private TaskMonitor parentTaskMonitor;
+
+ private final CyProperty<Properties> prop;
public PsiMiTabReader(InputStream is,
CyNetworkViewFactory cyNetworkViewFactory,
- CyNetworkFactory cyNetworkFactory, final
CyLayoutAlgorithmManager layouts) {
+ CyNetworkFactory cyNetworkFactory, final
CyLayoutAlgorithmManager layouts, final CyProperty<Properties> prop) {
if (is == null)
throw new NullPointerException("Input stream is null");
this.inputStream = is;
this.cyNetworkViewFactory = cyNetworkViewFactory;
this.layouts = layouts;
+ this.prop = prop;
parser = new PsiMiTabParser(is, cyNetworkFactory);
}
@@ -73,8 +78,12 @@
public CyNetworkView buildCyNetworkView(CyNetwork network) {
final CyNetworkView view =
cyNetworkViewFactory.getNetworkView(network);
+
+ String pref = CyLayoutAlgorithmManager.DEFAULT_LAYOUT_NAME;
+ if(prop != null)
+ pref =
prop.getProperties().getProperty("preferredLayoutAlgorithm", pref);
- final CyLayoutAlgorithm layout = layouts.getDefaultLayout();
+ final CyLayoutAlgorithm layout = layouts.getLayout(pref);
layout.setNetworkView(view);
// Force to run this task here to avoid concurrency problem.
Modified:
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderFactory.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderFactory.java
2011-10-20 23:04:42 UTC (rev 27257)
+++
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderFactory.java
2011-10-21 00:10:30 UTC (rev 27258)
@@ -1,10 +1,12 @@
package org.cytoscape.psi_mi.internal.plugin;
import java.io.InputStream;
+import java.util.Properties;
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.read.InputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.property.CyProperty;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.TaskIterator;
@@ -17,23 +19,26 @@
private final CyNetworkFactory cyNetworkFactory;
private final CyLayoutAlgorithmManager layouts;
+ private final CyProperty<Properties> prop;
+
private InputStream inputStream;
private String inputName;
public PsiMiTabReaderFactory(
CyFileFilter filter,
CyNetworkViewFactory cyNetworkViewFactory,
- CyNetworkFactory cyNetworkFactory,
CyLayoutAlgorithmManager layouts) {
+ CyNetworkFactory cyNetworkFactory,
CyLayoutAlgorithmManager layouts, final CyProperty<Properties> prop) {
this.cyNetworkFactory = cyNetworkFactory;
this.cyNetworkViewFactory = cyNetworkViewFactory;
this.filter = filter;
this.layouts = layouts;
+ this.prop = prop;
}
@Override
public TaskIterator getTaskIterator() {
return new TaskIterator(new PsiMiTabReader(inputStream,
- cyNetworkViewFactory, cyNetworkFactory,
layouts));
+ cyNetworkViewFactory, cyNetworkFactory,
layouts, prop));
}
@Override
Modified:
core3/impl/trunk/psi-mi-impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
2011-10-20 23:04:42 UTC (rev 27257)
+++
core3/impl/trunk/psi-mi-impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
2011-10-21 00:10:30 UTC (rev 27258)
@@ -8,12 +8,14 @@
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
+import java.util.Properties;
import org.cytoscape.ding.NetworkViewTestSupport;
import org.cytoscape.io.read.CyNetworkReader;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.NetworkTestSupport;
+import org.cytoscape.property.CyProperty;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -36,6 +38,9 @@
TaskMonitor taskMonitor;
@Mock
Task task;
+
+ @Mock
+ CyProperty<Properties> props;
private CyNetworkFactory networkFactory;
private CyNetworkViewFactory networkViewFactory;
@@ -79,7 +84,7 @@
private CyNetworkReader createReader(File file) throws IOException {
final InputStream is = new FileInputStream(file);
PsiMiTabReader reader = new PsiMiTabReader(is,
networkViewFactory,
- networkFactory, layouts);
+ networkFactory, layouts, props);
reader.setTaskIterator(new TaskIterator(reader));
return reader;
}
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