Author: kono
Date: 2011-05-02 17:47:13 -0700 (Mon, 02 May 2011)
New Revision: 24895
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyNetworkViewReader.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReader.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderFactory.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReader.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReaderFactory.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderFactory.java
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/XGMMLNetworkViewReaderFactory.java
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReaderTest.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
core3/viewmodel-impl/trunk/pom.xml
Log:
NullCyNetworkView is hidden in implementation bundle. To test null object or
not, use isNullView() method instead.
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewTask.java
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewTask.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -53,7 +53,8 @@
taskMonitor.setProgress(-1.0);
try {
- final CyNetworkView view = viewFactory.getNetworkView(network);
+ // By calling this task, actual view will be created even if it's a
large network.
+ final CyNetworkView view = viewFactory.getNetworkView(network,
false);
networkViewManager.addNetworkView(view);
} catch (Exception e) {
throw new Exception("Could not create network view for network: "
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -43,7 +43,6 @@
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewManager;
-import org.cytoscape.view.model.NullCyNetworkView;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
@@ -121,7 +120,7 @@
networkManager.addNetwork(cyNetwork);
// Do the following only for non-null views.
- if (view instanceof NullCyNetworkView == false) {
+ if (view.isNullView() == false) {
networkViewManager.addNetworkView(view);
view.fitContent();
} else {
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyNetworkViewReader.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyNetworkViewReader.java
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyNetworkViewReader.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -15,11 +15,6 @@
* {@link org.cytoscape.io.CyFileFilter}.
*/
public interface CyNetworkViewReader extends Task {
-
- /**
- * By default, this value will be used as the View Threshold.
- */
- static final int DEF_VIEW_THRESHOLD = 3000;
/**
* Return an array of {@link org.cytoscape.view.model.CyNetworkView}
objects
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReader.java
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReader.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -3,18 +3,14 @@
import java.io.InputStream;
import org.cytoscape.io.read.CyNetworkViewReader;
-import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.view.model.NullCyNetworkView;
import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.AbstractTask;
public abstract class AbstractNetworkViewReader extends AbstractTask
implements CyNetworkViewReader {
- protected CyNetwork[] networks;
-
protected CyNetworkView[] cyNetworkViews;
protected VisualStyle[] visualstyles;
@@ -23,33 +19,23 @@
protected final CyNetworkViewFactory cyNetworkViewFactory;
protected final CyNetworkFactory cyNetworkFactory;
- // If number of graph objects is above this value, NullCyNetworkView will
be
- // created instead of actual view.
- protected final int viewThreshold;
public AbstractNetworkViewReader(InputStream inputStream, final
CyNetworkViewFactory cyNetworkViewFactory,
- final CyNetworkFactory cyNetworkFactory, final Integer
viewThreshold) {
+ final CyNetworkFactory cyNetworkFactory) {
if (inputStream == null)
throw new NullPointerException("Input stream is null");
if (cyNetworkViewFactory == null)
throw new NullPointerException("CyNetworkViewFactory is null");
if (cyNetworkFactory == null)
throw new NullPointerException("CyNetworkFactory is null");
+
this.inputStream = inputStream;
this.cyNetworkViewFactory = cyNetworkViewFactory;
this.cyNetworkFactory = cyNetworkFactory;
-
- if (viewThreshold != null)
- this.viewThreshold = viewThreshold;
- else
- this.viewThreshold = DEF_VIEW_THRESHOLD;
}
@Override
public CyNetworkView[] getNetworkViews() {
- if(cyNetworkViews == null)
- this.createViews();
-
return cyNetworkViews;
}
@@ -57,21 +43,4 @@
public VisualStyle[] getVisualStyles() {
return visualstyles;
}
-
- protected void createViews() {
- if (networks == null || networks.length == 0)
- throw new IllegalStateException("No network model is available.");
- this.cyNetworkViews = new CyNetworkView[networks.length];
-
- for (int i = 0; i < networks.length; i++) {
- final CyNetwork network = networks[i];
- final int objectCount = network.getEdgeCount() +
network.getNodeCount();
- if (this.viewThreshold < objectCount)
- cyNetworkViews[i] = new NullCyNetworkView(network);
- else
- cyNetworkViews[i] = createView(network);
- }
- }
-
- abstract protected CyNetworkView createView(final CyNetwork network);
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderFactory.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderFactory.java
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderFactory.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -28,13 +28,10 @@
package org.cytoscape.io.internal.read;
import java.io.InputStream;
-import java.util.Properties;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.CyNetworkViewReader;
import org.cytoscape.io.read.InputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.property.CyProperty;
import org.cytoscape.view.model.CyNetworkViewFactory;
public abstract class AbstractNetworkViewReaderFactory implements
InputStreamTaskFactory {
@@ -47,20 +44,12 @@
protected InputStream inputStream;
protected String inputName;
- private final Properties props;
-
- //TODO: is this the right place to save this constant?
- private final String VIEW_THRESHOLD = "viewThreshold";
-
- protected int threshold;
public AbstractNetworkViewReaderFactory(CyFileFilter filter,
CyNetworkViewFactory cyNetworkViewFactory,
- CyNetworkFactory cyNetworkFactory, final CyProperty<Properties>
prop) {
+ CyNetworkFactory cyNetworkFactory) {
this.filter = filter;
this.cyNetworkViewFactory = cyNetworkViewFactory;
this.cyNetworkFactory = cyNetworkFactory;
-
- this.props = prop.getProperties();
}
public void setInputStream(InputStream is, String in) {
@@ -68,21 +57,7 @@
throw new NullPointerException("Input stream is null");
inputStream = is;
inputName = in;
-
- this.threshold = getViewThreshold();
}
-
- private int getViewThreshold() {
- final String vts = props.getProperty(VIEW_THRESHOLD);
- int threshold;
- try {
- threshold = Integer.parseInt(vts);
- } catch (Exception e) {
- threshold = CyNetworkViewReader.DEF_VIEW_THRESHOLD;
- }
-
- return threshold;
- }
public CyFileFilter getCyFileFilter() {
return filter;
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReader.java
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReader.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -49,7 +49,6 @@
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.view.model.NullCyNetworkView;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualLexicon;
import org.cytoscape.view.model.VisualProperty;
@@ -179,6 +178,7 @@
private final RenderingEngineManager renderingEngineManager;
private CyNetworkView view;
+ private CyNetwork network;
/**
* Constructor.<br>
@@ -192,8 +192,8 @@
public GMLNetworkViewReader(InputStream inputStream,
CyNetworkFactory networkFactory,
CyNetworkViewFactory viewFactory,
- RenderingEngineManager renderingEngineManager,
final int viewThreshold) {
- super(inputStream, viewFactory, networkFactory, viewThreshold);
+ RenderingEngineManager renderingEngineManager)
{
+ super(inputStream, viewFactory, networkFactory);
this.renderingEngineManager = renderingEngineManager;
// Set new style name
@@ -214,14 +214,15 @@
readGML(keyVals, taskMonitor); // read the GML file
- this.networks = new CyNetwork[1];
- this.networks[0] = cyNetworkFactory.getInstance();
- createGraph(taskMonitor); // create the graph AND new visual style
+ network = cyNetworkFactory.getInstance();
+ createGraph(taskMonitor);
+ createView();
}
- @Override
- protected CyNetworkView createView(CyNetwork network) {
+ private void createView() {
view = cyNetworkViewFactory.getNetworkView(network);
+ if(view.isNullView())
+ return;
// New features are called here:
@@ -233,10 +234,9 @@
extract();
releaseStructures();
-
layout(view);
- return view;
+ this.cyNetworkViews = new CyNetworkView[]{view};
}
@Override
@@ -296,7 +296,7 @@
String label = node_labels.get(idx);
if (nodeNameSet.add(label)) {
- CyNode node = networks[0].addNode();
+ CyNode node = network.addNode();
//FIXME this fires too many events!!
node.getCyRow().set(CyTableEntry.NAME, label);
@@ -337,7 +337,7 @@
CyNode node_1 = nodeIDMap.get(sourceName);
CyNode node_2 = nodeIDMap.get(targetName);
- CyEdge edge = networks[0].addEdge(node_1, node_2,
isDirected.booleanValue());
+ CyEdge edge = network.addEdge(node_1, node_2,
isDirected.booleanValue());
edge.getCyRow().set(CyTableEntry.NAME, edgeName);
edge.getCyRow().set("interaction", label);
edge_names.add(idx, edge);
@@ -506,7 +506,7 @@
*/
@SuppressWarnings("unchecked")
public void layout(CyNetworkView view) {
- if ((view == null) || (networks[0].getNodeCount() == 0)) {
+ if ((view == null) || (network.getNodeCount() == 0)) {
return;
}
@@ -667,7 +667,7 @@
// System.out.print( "In layout, Root index is: " + root_index );
// System.out.print( " Checking label: " + label );
- View<CyNode> view =
myView.getNodeView(networks[0].getNode(root_index.intValue()));
+ View<CyNode> view =
myView.getNodeView(network.getNode(root_index.intValue()));
// TODO update for new view
// if (label != null) {
@@ -825,7 +825,7 @@
return;
}
- edgeView = myView.getEdgeView(networks[0].getEdge(((Integer)
keyVal.value).intValue()));
+ edgeView = myView.getEdgeView(network.getEdge(((Integer)
keyVal.value).intValue()));
} else if (keyVal.key.equals(GRAPHICS)) {
graphics_list = (List<KeyValue>) keyVal.value;
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReaderFactory.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReaderFactory.java
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReaderFactory.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -1,11 +1,8 @@
package org.cytoscape.io.internal.read.gml;
-import java.util.Properties;
-
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.internal.read.AbstractNetworkViewReaderFactory;
import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.property.CyProperty;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.presentation.RenderingEngineManager;
import org.cytoscape.work.TaskIterator;
@@ -14,15 +11,15 @@
private final RenderingEngineManager renderingEngineManager;
public GMLNetworkViewReaderFactory(CyFileFilter filter,
CyNetworkViewFactory networkViewFactory,
- CyNetworkFactory networkFactory, RenderingEngineManager
renderingEngineManager, CyProperty<Properties> props) {
- super(filter, networkViewFactory, networkFactory, props);
+ CyNetworkFactory networkFactory, RenderingEngineManager
renderingEngineManager) {
+ super(filter, networkViewFactory, networkFactory);
this.renderingEngineManager = renderingEngineManager;
}
@Override
public TaskIterator getTaskIterator() {
return new TaskIterator(new GMLNetworkViewReader(inputStream,
cyNetworkFactory, cyNetworkViewFactory,
- renderingEngineManager, threshold));
+ renderingEngineManager));
}
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -69,8 +69,8 @@
public SIFNetworkViewReader(InputStream is, CyLayoutAlgorithmManager
layouts,
CyNetworkViewFactory cyNetworkViewFactory, CyNetworkFactory
cyNetworkFactory,
- final CyEventHelper eventHelper, final int viewThreshold) {
- super(is, cyNetworkViewFactory, cyNetworkFactory, viewThreshold);
+ final CyEventHelper eventHelper) {
+ super(is, cyNetworkViewFactory, cyNetworkFactory);
this.layouts = layouts;
this.eventHelper = eventHelper;
}
@@ -139,8 +139,7 @@
nMap.clear();
nMap = null;
- this.networks = new CyNetwork[]{network};
- createViews();
+ createView(network);
tm.setProgress(1.0);
}
@@ -166,10 +165,14 @@
}
}
- @Override
- protected CyNetworkView createView(final CyNetwork network) {
+ private CyNetworkView createView(final CyNetwork network) {
final CyNetworkView view = cyNetworkViewFactory.getNetworkView(network);
+ this.cyNetworkViews = new CyNetworkView[]{view};
+
+ if(view.isNullView())
+ return view;
+
final CyLayoutAlgorithm layout = layouts.getDefaultLayout();
layout.setNetworkView(view);
insertTasksAfterCurrentTask(layout.getTaskIterator());
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderFactory.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderFactory.java
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderFactory.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -27,13 +27,10 @@
*/
package org.cytoscape.io.internal.read.sif;
-import java.util.Properties;
-
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.internal.read.AbstractNetworkViewReaderFactory;
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;
@@ -45,14 +42,14 @@
public SIFNetworkViewReaderFactory(CyFileFilter filter,
CyLayoutAlgorithmManager layouts,
CyNetworkViewFactory cyNetworkViewFactory, CyNetworkFactory
cyNetworkFactory,
- final CyEventHelper eventHelper, CyProperty<Properties> prop) {
- super(filter, cyNetworkViewFactory, cyNetworkFactory, prop);
+ final CyEventHelper eventHelper) {
+ super(filter, cyNetworkViewFactory, cyNetworkFactory);
this.layouts = layouts;
this.eventHelper = eventHelper;
}
public TaskIterator getTaskIterator() {
return new TaskIterator(new SIFNetworkViewReader(inputStream, layouts,
cyNetworkViewFactory,
- cyNetworkFactory, eventHelper, threshold));
+ cyNetworkFactory, eventHelper));
}
}
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
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -116,8 +116,8 @@
final CyNetworkViewFactory cyNetworkViewFactory, final
CyNetworkFactory cyNetworkFactory,
final ReadDataManager readDataManager, final AttributeValueUtil
attributeValueUtil,
final VisualStyleFactory styleFactory, final VisualMappingManager
visMappingManager,
- final XGMMLParser parser, final CyProperty<Properties> properties,
final int viewThreshold) {
- super(inputStream, cyNetworkViewFactory, cyNetworkFactory,
viewThreshold);
+ final XGMMLParser parser, final CyProperty<Properties> properties) {
+ super(inputStream, cyNetworkViewFactory, cyNetworkFactory);
this.readDataManager = readDataManager;
this.attributeValueUtil = attributeValueUtil;
@@ -139,7 +139,8 @@
try {
readXGMML();
- networks = new CyNetwork[]{readDataManager.getNetwork()};
+ final CyNetwork network = readDataManager.getNetwork();
+ createView(network);
} catch (SAXException e) {
throw new IOException("Could not parse XGMML file: ");
}
@@ -151,14 +152,10 @@
public void cancel() {
}
- @Override
- protected CyNetworkView createView(CyNetwork network) {
-
+ private void createView(CyNetwork network) {
view = cyNetworkViewFactory.getNetworkView(network);
layout();
-
- return view;
-
+ this.cyNetworkViews = new CyNetworkView[]{view};
}
/**
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderFactory.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderFactory.java
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderFactory.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -59,7 +59,7 @@
private XGMMLParser parser;
private ReadDataManager readDataManager;
private AttributeValueUtil attributeValueUtil;
- private CyProperty<Properties> properties;
+ private final CyProperty<Properties> properties;
public XGMMLNetworkViewReaderFactory(CyFileFilter filter,
RenderingEngineManager
renderingEngineManager,
@@ -70,21 +70,21 @@
VisualStyleFactory styleFactory,
VisualMappingManager
visMappingManager,
VisualMappingFunctionFactory
discreteMappingFactory,
- XGMMLParser parser,
- CyProperty<Properties> properties) {
- super(filter, cyNetworkViewFactory, cyNetworkFactory, properties);
+ XGMMLParser parser, final
CyProperty<Properties> properties) {
+ super(filter, cyNetworkViewFactory, cyNetworkFactory);
this.renderingEngineManager = renderingEngineManager;
this.readDataManager = readDataManager;
this.attributeValueUtil = attributeValueUtil;
this.styleFactory = styleFactory;
this.visMappingManager = visMappingManager;
this.parser = parser;
+
this.properties = properties;
}
public TaskIterator getTaskIterator() {
return new TaskIterator(new XGMMLNetworkViewReader(inputStream,
renderingEngineManager, cyNetworkViewFactory,
cyNetworkFactory,
readDataManager, attributeValueUtil,
- styleFactory,
visMappingManager, parser, properties, threshold));
+ styleFactory,
visMappingManager, parser, properties));
}
}
Modified:
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
--- core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-05-03 00:46:04 UTC (rev 24894)
+++ core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-05-03 00:47:13 UTC (rev 24895)
@@ -254,7 +254,6 @@
<constructor-arg ref="cyNetworkViewFactoryServiceRef" />
<constructor-arg ref="cyNetworkFactoryServiceRef" />
<constructor-arg ref="cyEventHelperRef" />
- <constructor-arg ref="cyPropertyServiceRef" />
</bean>
<bean id="gmlNetworkViewReaderFactory"
class="org.cytoscape.io.internal.read.gml.GMLNetworkViewReaderFactory">
@@ -262,7 +261,6 @@
<constructor-arg ref="cyNetworkViewFactoryServiceRef" />
<constructor-arg ref="cyNetworkFactoryServiceRef" />
<constructor-arg ref="renderingEngineManagerServiceRef" />
- <constructor-arg ref="cyPropertyServiceRef" />
</bean>
<!-- Writer Factories -->
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReaderTest.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReaderTest.java
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReaderTest.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -37,7 +37,7 @@
public void testLoadGml() throws Exception {
File file = new
File("src/test/resources/testData/gml/example1.gml");
GMLNetworkViewReader reader =
- new GMLNetworkViewReader(new FileInputStream(file),
netFactory, viewFactory, renderingEngineManager, viewThreshold);
+ new GMLNetworkViewReader(new FileInputStream(file),
netFactory, viewFactory, renderingEngineManager);
reader.run(taskMonitor);
CyNetworkView[] networkViews = reader.getNetworkViews();
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
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -1,6 +1,6 @@
package org.cytoscape.io.internal.read.sif;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.mockito.Mockito.mock;
@@ -12,7 +12,6 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.NullCyNetworkView;
import org.cytoscape.work.TaskIterator;
import org.junit.Test;
@@ -34,7 +33,7 @@
this.viewThreshold = 5;
CyNetworkView[] nullViews = getViews("sample.sif");
assertNotNull(nullViews);
- assertTrue(nullViews[0] instanceof NullCyNetworkView);
+ assertTrue(nullViews[0].isNullView());
this.viewThreshold = this.DEF_THRESHOLD;
}
@@ -83,7 +82,7 @@
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, viewThreshold);
+ netFactory, eventHelper);
new TaskIterator(snvp);
snvp.run(taskMonitor);
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
2011-05-03 00:46:04 UTC (rev 24894)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderTest.java
2011-05-03 00:47:13 UTC (rev 24895)
@@ -1,6 +1,6 @@
package org.cytoscape.io.internal.read.xgmml;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.mockito.Mockito.mock;
@@ -16,7 +16,6 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.property.CyProperty;
import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.NullCyNetworkView;
import org.cytoscape.view.presentation.RenderingEngineManager;
import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
import org.cytoscape.view.presentation.property.NullVisualProperty;
@@ -24,7 +23,6 @@
import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.view.vizmap.VisualStyleFactory;
import org.cytoscape.view.vizmap.mappings.DiscreteMappingFactory;
-import org.cytoscape.work.TaskMonitor;
import org.junit.Before;
import org.junit.Test;
@@ -72,7 +70,7 @@
CyNetworkView[] nullViews = getViews("galFiltered.xgmml");
assertNotNull(nullViews);
assertEquals(1, nullViews.length);
- assertTrue(nullViews[0] instanceof NullCyNetworkView);
+ assertTrue(nullViews[0].isNullView());
this.viewThreshold = this.DEF_THRESHOLD;
}
@@ -80,7 +78,7 @@
File f = new File("./src/test/resources/testData/xgmml/" + file);
XGMMLNetworkViewReader snvp = new XGMMLNetworkViewReader(new
FileInputStream(f), renderingEngineManager,
viewFactory, netFactory, readDataManager, attributeValueUtil,
styleFactory, visMappingManager, parser,
- properties, viewThreshold);
+ properties);
snvp.run(taskMonitor);
return snvp.getNetworkViews();
Modified: core3/viewmodel-impl/trunk/pom.xml
===================================================================
--- core3/viewmodel-impl/trunk/pom.xml 2011-05-03 00:46:04 UTC (rev 24894)
+++ core3/viewmodel-impl/trunk/pom.xml 2011-05-03 00:47:13 UTC (rev 24895)
@@ -1,4 +1,5 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd";>
+<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd";>
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.cytoscape</groupId>
@@ -24,7 +25,7 @@
</scm>
<build>
- <plugins>
+ <plugins>
<plugin>
<inherited>false</inherited>
<groupId>org.apache.maven.plugins</groupId>
@@ -67,11 +68,9 @@
</repository>
</repositories>
- <!--
- Dependencies included here should *ONLY* be for the impl bundle.
- All additional dependencies necessary for the integration tests (it)
- should be kept in the it/pom.xml
- -->
+ <!-- Dependencies included here should *ONLY* be for the impl bundle.
All
+ additional dependencies necessary for the integration tests
(it) should be
+ kept in the it/pom.xml -->
<dependencies>
<dependency>
<groupId>org.cytoscape</groupId>
@@ -98,6 +97,12 @@
<scope>provided</scope>
</dependency>
<dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>property-api</artifactId>
+ <version>3.0.0-alpha4-SNAPSHOT</version>
+ </dependency>
+
+ <dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
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