Author: jm
Date: 2011-01-25 08:53:35 -0800 (Tue, 25 Jan 2011)
New Revision: 23600
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/GMLNetworkViewReaderFactory.java
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
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
Log:
Updated GMLNetworkViewReader to use default VisualLexicon instead of that of
current RenderingEngine
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
2011-01-25 16:05:48 UTC (rev 23599)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReader.java
2011-01-25 16:53:35 UTC (rev 23600)
@@ -31,7 +31,6 @@
import java.awt.Color;
-import java.awt.Paint;
import java.io.InputStream;
import java.io.StringWriter;
import java.util.ArrayList;
@@ -59,6 +58,7 @@
import org.cytoscape.view.model.VisualLexicon;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.presentation.RenderingEngine;
+import org.cytoscape.view.presentation.RenderingEngineManager;
import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.AbstractTask;
@@ -187,7 +187,7 @@
private final InputStream inputStream;
private final CyNetworkFactory networkFactory;
private final CyNetworkViewFactory viewFactory;
- private final CyApplicationManager applicationManager;
+ private final RenderingEngineManager renderingEngineManager;
private CyNetwork network;
private CyNetworkView view;
@@ -202,12 +202,12 @@
*
*/
public GMLNetworkViewReader(InputStream inputStream, CyNetworkFactory
networkFactory,
- CyNetworkViewFactory
viewFactory, CyApplicationManager applicationManager)
+ CyNetworkViewFactory
viewFactory, RenderingEngineManager renderingEngineManager)
{
this.inputStream = inputStream;
this.networkFactory = networkFactory;
this.viewFactory = viewFactory;
- this.applicationManager = applicationManager;
+ this.renderingEngineManager = renderingEngineManager;
// Set new style name
edge_names = new Vector<CyEdge>();
@@ -698,70 +698,52 @@
* matches to the "graphics" key word
*/
private void layoutNodeGraphics(CyNetworkView myView, List<KeyValue>
list, View<CyNode> nodeView) {
- RenderingEngine<CyNetwork> engine =
applicationManager.getCurrentRenderingEngine();
- if (engine == null) {
- // TODO: Remove this once CyNetworkManager can provide
an engine
- // instance with zero networks loaded.
- return;
- }
- VisualLexicon lexicon = engine.getVisualLexicon();
-
+ VisualLexicon lexicon =
renderingEngineManager.getDefaultVisualLexicon();
Collection<VisualProperty<?>> properties =
lexicon.getAllDescendants(TwoDVisualLexicon.NODE);
for (VisualProperty<?> property : properties) {
String id = property.getIdString();
for (KeyValue keyVal : list) {
if (keyVal.key.equals(X) &&
id.equals("NODE_X_LOCATION")) {
- nodeView.setVisualProperty(property,
(Object) asDouble(keyVal.value));
+ nodeView.setVisualProperty(property,
(Object) property.parseSerializableString(keyVal.value.toString()));
} else if (keyVal.key.equals(Y) &&
id.equals("NODE_Y_LOCATION")) {
- nodeView.setVisualProperty(property,
(Object) asDouble(keyVal.value));
+ nodeView.setVisualProperty(property,
(Object) property.parseSerializableString(keyVal.value.toString()));
} else if (keyVal.key.equals(W) &&
id.equals("NODE_X_SIZE")) {
- nodeView.setVisualProperty(property,
(Object) asDouble(keyVal.value));
+ nodeView.setVisualProperty(property,
(Object) property.parseSerializableString(keyVal.value.toString()));
} else if (keyVal.key.equals(H) &&
id.equals("NODE_Y_SIZE")) {
- nodeView.setVisualProperty(property,
(Object) asDouble(keyVal.value));
+ nodeView.setVisualProperty(property,
(Object) property.parseSerializableString(keyVal.value.toString()));
} else if (keyVal.key.equals(FILL) &&
id.equals("NODE_COLOR")) {
- nodeView.setVisualProperty(property,
(Object) asPaint(keyVal.value));
+ nodeView.setVisualProperty(property,
(Object) property.parseSerializableString(keyVal.value.toString()));
} else if (keyVal.key.equals(OUTLINE) &&
id.equals("NODE_BORDER_PAINT")) {
- nodeView.setVisualProperty(property,
(Object) asPaint(keyVal.value));
+ nodeView.setVisualProperty(property,
(Object) property.parseSerializableString(keyVal.value.toString()));
} else if (keyVal.key.equals(OUTLINE_WIDTH) &&
id.equals("NODE_BORDER_WIDTH")) {
- nodeView.setVisualProperty(property,
(Object) asDouble(keyVal.value));
+ nodeView.setVisualProperty(property,
(Object) property.parseSerializableString(keyVal.value.toString()));
+ } else if (keyVal.key.equals(TYPE) &&
id.equals("NODE_SHAPE")) {
+ String type = (String) keyVal.value;
+ String value = null;
+ if (type.equals(ELLIPSE)) {
+ value = "ELLIPSE";
+ } else if (type.equals(RECTANGLE)) {
+ value = "RECT";
+ } else if (type.equals(DIAMOND)) {
+ value = "DIAMOND";
+ } else if (type.equals(HEXAGON)) {
+ value = "HEXAGON";
+ } else if (type.equals(OCTAGON)) {
+ value = "OCTAGON";
+ } else if (type.equals(PARALELLOGRAM)) {
+ value = "PARALLELOGRAM";
+ } else if (type.equals(TRIANGLE)) {
+ value = "TRIANGLE";
+ }
+ if (value != null) {
+
nodeView.setVisualProperty(property, (Object)
property.parseSerializableString(value));
+ }
}
}
}
-// } else if (keyVal.key.equals(TYPE)) {
-// String type = (String) keyVal.value;
-//
-// if (type.equals(ELLIPSE)) {
-// nodeView.setShape(NodeView.ELLIPSE);
-// } else if (type.equals(RECTANGLE)) {
-// nodeView.setShape(NodeView.RECTANGLE);
-// } else if (type.equals(DIAMOND)) {
-// nodeView.setShape(NodeView.DIAMOND);
-// } else if (type.equals(HEXAGON)) {
-// nodeView.setShape(NodeView.HEXAGON);
-// } else if (type.equals(OCTAGON)) {
-// nodeView.setShape(NodeView.OCTAGON);
-// } else if (type.equals(PARALELLOGRAM)) {
-//
nodeView.setShape(NodeView.PARALELLOGRAM);
-// } else if (type.equals(TRIANGLE)) {
-// nodeView.setShape(NodeView.TRIANGLE);
-// }
}
- private Paint asPaint(Object object) {
- if (object instanceof String) {
- return getColor((String) object);
- }
- return null;
- }
-
- private Double asDouble(Object object) {
- if (object instanceof Number) {
- return ((Number) object).doubleValue();
- }
- return null;
- }
-
//
// Extract node attributes from GML file
private void extractNodeAttributes(List<KeyValue> list, CyNode node) {
@@ -913,13 +895,7 @@
//
@SuppressWarnings("unchecked")
private void layoutEdgeGraphics(CyNetworkView myView, List<KeyValue>
list, View<CyEdge> edgeView) {
- RenderingEngine<CyNetwork> engine =
applicationManager.getCurrentRenderingEngine();
- if (engine == null) {
- // TODO: Remove this once CyNetworkManager can provide
an engine
- // instance with zero networks loaded.
- return;
- }
- VisualLexicon lexicon = engine.getVisualLexicon();
+ VisualLexicon lexicon =
renderingEngineManager.getDefaultVisualLexicon();
Collection<VisualProperty<?>> properties =
lexicon.getAllDescendants(TwoDVisualLexicon.NODE);
for (VisualProperty<?> property : properties) {
String id = property.getIdString();
@@ -930,9 +906,23 @@
if (keyVal.key.equals(LINE)) {
layoutEdgeGraphicsLine(myView,
(List<KeyValue>) keyVal.value, edgeView);
} else if (keyVal.key.equals(WIDTH) &&
id.equals("EDGE_WIDTH")) {
- edgeView.setVisualProperty(property,
(Object) asDouble(keyVal.value));
+ edgeView.setVisualProperty(property,
(Object) property.parseSerializableString(keyVal.value.toString()));
} else if (keyVal.key.equals(FILL) &&
id.equals("EDGE_COLOR")) {
- edgeView.setVisualProperty(property,
(Object) asPaint(keyVal.value));
+ edgeView.setVisualProperty(property,
(Object) property.parseSerializableString(keyVal.value.toString()));
+ } else if (keyVal.key.equals(ARROW) &&
id.equals("EDGE_SOURCE_ARROW_SHAPE")) {
+ String value = (String) keyVal.value;
+ if (value.equals(ARROW_BOTH) ||
value.equals(ARROW_FIRST)) {
+
edgeView.setVisualProperty(property, (Object)
property.parseSerializableString("ARROW"));
+ }
+ } else if (keyVal.key.equals(ARROW) &&
id.equals("EDGE_TARGET_ARROW_SHAPE")) {
+ String value = (String) keyVal.value;
+ if (value.equals(ARROW_BOTH) ||
value.equals(ARROW_LAST)) {
+
edgeView.setVisualProperty(property, (Object)
property.parseSerializableString("ARROW"));
+ }
+ } else if (keyVal.key.equals(SOURCE_ARROW) &&
id.equals("EDGE_SOURCE_ARROW_SHAPE")) {
+ edgeView.setVisualProperty(property,
(Object) property.parseSerializableString("ARROW"));
+ } else if (keyVal.key.equals(TARGET_ARROW) &&
id.equals("EDGE_TARGET_ARROW_SHAPE")) {
+ edgeView.setVisualProperty(property,
(Object) property.parseSerializableString("ARROW"));
}
}
}
@@ -945,24 +935,6 @@
// } else if (value.equals(CURVED_LINES)) {
//
edgeView.setLineType(EdgeView.CURVED_LINES);
// }
-// } else if (keyVal.key.equals(ARROW)) {
-// // The position of the arrow.
-// // There are 4 states: no arrows, both ends
have arrows, source,
-// // or target.
-// //
-// // The arrow type below is hard-coded since GML
does not
-// // support shape of the arrow.
-// if (keyVal.value.equals(ARROW_FIRST)) {
-// edgeView.setSourceEdgeEnd(2);
-// } else if (keyVal.value.equals(ARROW_LAST)) {
-// edgeView.setTargetEdgeEnd(2);
-// } else if (keyVal.value.equals(ARROW_BOTH)) {
-// edgeView.setSourceEdgeEnd(2);
-// edgeView.setTargetEdgeEnd(2);
-// } else if (keyVal.value.equals(ARROW_NONE)) {
-// // Do nothing. No arrows.
-// }
-//
// if (keyVal.key.equals(SOURCE_ARROW)) {
// edgeView.setSourceEdgeEnd(((Number)
keyVal.value).intValue());
// } else if (keyVal.value.equals(TARGET_ARROW)) {
@@ -1002,11 +974,4 @@
}
*/
}
-
- /**
- * Create a color object from the string like it is stored in a gml file
- */
- private Color getColor(String colorString) {
- return new Color(Integer.parseInt(colorString.substring(1),
16));
- }
}
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
2011-01-25 16:05:48 UTC (rev 23599)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReaderFactory.java
2011-01-25 16:53:35 UTC (rev 23600)
@@ -4,25 +4,25 @@
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.internal.read.AbstractNetworkViewReaderFactory;
import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.session.CyApplicationManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.presentation.RenderingEngineManager;
import org.cytoscape.work.TaskIterator;
public class GMLNetworkViewReaderFactory extends
AbstractNetworkViewReaderFactory {
- private final CyApplicationManager applicationManager;
+ private final RenderingEngineManager renderingEngineManager;
public GMLNetworkViewReaderFactory(CyFileFilter filter,
CyNetworkViewFactory networkViewFactory,
CyNetworkFactory networkFactory,
- CyApplicationManager applicationManager) {
+ RenderingEngineManager renderingEngineManager) {
super(filter, networkViewFactory, networkFactory);
- this.applicationManager = applicationManager;
+ this.renderingEngineManager = renderingEngineManager;
}
@Override
public TaskIterator getTaskIterator() {
- return new TaskIterator(new GMLNetworkViewReader(inputStream,
cyNetworkFactory, cyNetworkViewFactory, applicationManager));
+ return new TaskIterator(new GMLNetworkViewReader(inputStream,
cyNetworkFactory, cyNetworkViewFactory, renderingEngineManager));
}
}
Modified:
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-01-25 16:05:48 UTC (rev 23599)
+++
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-01-25 16:53:35 UTC (rev 23600)
@@ -39,6 +39,9 @@
interface="org.cytoscape.view.vizmap.VisualMappingFunctionFactory"
filter="(mapping.type=discrete)" />
+ <osgi:reference id="renderingEngineManagerServiceRef"
+
interface="org.cytoscape.view.presentation.RenderingEngineManager" />
+
<!-- Export services -->
<osgi:service id="cyNetworkViewReaderManagerService"
ref="cyNetworkViewReaderManager"
interface="org.cytoscape.io.read.CyNetworkViewReaderManager">
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
2011-01-25 16:05:48 UTC (rev 23599)
+++ core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-01-25 16:53:35 UTC (rev 23600)
@@ -266,7 +266,7 @@
<constructor-arg ref="gmlFilter" />
<constructor-arg ref="cyNetworkViewFactoryServiceRef" />
<constructor-arg ref="cyNetworkFactoryServiceRef" />
- <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="renderingEngineManagerServiceRef" />
</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
2011-01-25 16:05:48 UTC (rev 23599)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/gml/GMLNetworkViewReaderTest.java
2011-01-25 16:53:35 UTC (rev 23600)
@@ -2,28 +2,23 @@
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.util.LinkedList;
import org.cytoscape.io.internal.read.AbstractNetworkViewReaderTester;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.session.CyApplicationManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.VisualLexicon;
-import org.cytoscape.view.model.VisualProperty;
-import org.cytoscape.view.presentation.RenderingEngine;
+import org.cytoscape.view.presentation.RenderingEngineManager;
import org.junit.Before;
import org.junit.Test;
import org.mockito.Mock;
import org.mockito.MockitoAnnotations;
public class GMLNetworkViewReaderTest extends AbstractNetworkViewReaderTester {
- @Mock private CyApplicationManager applicationManager;
- @Mock private RenderingEngine<CyNetwork> engine;
+ @Mock private RenderingEngineManager renderingEngineManager;
@Mock private VisualLexicon lexicon;
@Before
@@ -32,8 +27,7 @@
MockitoAnnotations.initMocks(this);
-
when(applicationManager.getCurrentRenderingEngine()).thenReturn(engine);
- when(engine.getVisualLexicon()).thenReturn(lexicon);
+
when(renderingEngineManager.getDefaultVisualLexicon()).thenReturn(lexicon);
// FIXME
//when(lexicon.getVisualProperties(any(String.class))).thenReturn(new
LinkedList<VisualProperty<?>>());
@@ -43,7 +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, applicationManager);
+ new GMLNetworkViewReader(new FileInputStream(file),
netFactory, viewFactory, renderingEngineManager);
reader.run(taskMonitor);
CyNetworkView[] networkViews = reader.getNetworkViews();
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