Author: kono
Date: 2010-09-16 18:48:41 -0700 (Thu, 16 Sep 2010)
New Revision: 21916
Added:
core3/vizmap-impl/branches/vp-tree/src/integration/
core3/vizmap-impl/branches/vp-tree/src/integration/java/
core3/vizmap-impl/branches/vp-tree/src/integration/java/integration/
core3/vizmap-impl/branches/vp-tree/src/integration/java/integration/ITVzmapImpl.java
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleFactoryImpl.java
core3/vizmap-impl/branches/vp-tree/src/test/java/org/cytoscape/vizmap/VisualStyleTest.java
core3/vizmap-impl/branches/vp-tree/src/test/resources/
core3/vizmap-impl/branches/vp-tree/src/test/resources/log4j.properties
Modified:
core3/vizmap-impl/branches/vp-tree/pom.xml
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
core3/vizmap-impl/branches/vp-tree/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/vizmap-impl/branches/vp-tree/src/main/resources/META-INF/spring/bundle-context.xml
Log:
Refactored version of VP tree. VisualLexicons are moved to presentation layer.
Modified: core3/vizmap-impl/branches/vp-tree/pom.xml
===================================================================
--- core3/vizmap-impl/branches/vp-tree/pom.xml 2010-09-17 01:30:47 UTC (rev
21915)
+++ core3/vizmap-impl/branches/vp-tree/pom.xml 2010-09-17 01:48:41 UTC (rev
21916)
@@ -62,6 +62,50 @@
</instructions>
</configuration>
</plugin>
+
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+
<artifactId>build-helper-maven-plugin</artifactId>
+ <version>1.5</version>
+ <executions>
+ <execution>
+ <id>add-test-source</id>
+
<phase>generate-test-sources</phase>
+ <goals>
+
<goal>add-test-source</goal>
+ </goals>
+ <configuration>
+ <sources>
+
<source>${basedir}/src/integration/java</source>
+ </sources>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-failsafe-plugin</artifactId>
+ <version>2.6</version>
+ <configuration>
+
<testSourceDirectory>${basedir}/src/integration/java</testSourceDirectory>
+
<redirectTestOutputToFile>true</redirectTestOutputToFile>
+ </configuration>
+ <executions>
+ <execution>
+ <id>integration-test</id>
+ <goals>
+
<goal>integration-test</goal>
+ </goals>
+ </execution>
+ <execution>
+ <id>verify</id>
+ <goals>
+ <goal>verify</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
</plugins>
</build>
@@ -107,5 +151,11 @@
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>integration-test-support</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ <scope>test</scope>
+ </dependency>
</dependencies>
</project>
Added:
core3/vizmap-impl/branches/vp-tree/src/integration/java/integration/ITVzmapImpl.java
===================================================================
---
core3/vizmap-impl/branches/vp-tree/src/integration/java/integration/ITVzmapImpl.java
(rev 0)
+++
core3/vizmap-impl/branches/vp-tree/src/integration/java/integration/ITVzmapImpl.java
2010-09-17 01:48:41 UTC (rev 21916)
@@ -0,0 +1,30 @@
+package integration;
+
+import org.cytoscape.integration.AbstractIntegrationTester;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyleFactory;
+
+public class ITVzmapImpl extends AbstractIntegrationTester {
+
+ public ITVzmapImpl() {
+ super("org.cytoscape.view.vizmap-impl",
+
+ new String[] {
+ "org.cytoscape, event-api, 1.0-SNAPSHOT",
+ "org.cytoscape, event-impl, 1.0-SNAPSHOT",
+ "org.cytoscape, model-api, 1.0-SNAPSHOT",
+ "org.cytoscape, integration-test-support,
1.0-SNAPSHOT",
+ "org.cytoscape, service-util, 1.0-SNAPSHOT",
+ "org.cytoscape, viewmodel-api, 1.0-SNAPSHOT",
+ "org.cytoscape, viewmodel-impl, 1.0-SNAPSHOT",
+ "org.cytoscape, vizmap-api, 1.0-SNAPSHOT",
+ "org.cytoscape, vizmap-impl, 1.0-SNAPSHOT",
+ "org.cytoscape, presentation-api, 1.0-SNAPSHOT"
+
+ },
+ new String[] { "visualStyleFactory",
"visualMappingManager" },
+ new Class[] { VisualStyleFactory.class,
VisualMappingManager.class },
+ new String[] { });
+ }
+
+}
Modified:
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
===================================================================
---
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
2010-09-17 01:30:47 UTC (rev 21915)
+++
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
2010-09-17 01:48:41 UTC (rev 21916)
@@ -34,7 +34,6 @@
*/
package org.cytoscape.view.vizmap.internal;
-import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
@@ -42,12 +41,8 @@
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.VisualLexiconManager;
-import org.cytoscape.view.model.VisualProperty;
-import org.cytoscape.view.vizmap.VisualMappingFunction;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyle;
-import org.cytoscape.view.vizmap.events.VisualStyleCreatedEvent;
import org.cytoscape.view.vizmap.events.VisualStyleDestroyedEvent;
@@ -56,30 +51,20 @@
*/
public class VisualMappingManagerImpl implements VisualMappingManager {
- private final Map<CyNetworkView, VisualStyle> vsForNetwork;
+ private final Map<CyNetworkView, VisualStyle> network2VisualStyleMap;
private final Set<VisualStyle> visualStyles;
- private CyEventHelper cyEventHelper;
- private VisualLexiconManager rootLexicon;
+ private final CyEventHelper cyEventHelper;
- /**
- *
- * @param h
- * DOCUMENT ME!
- */
- public VisualMappingManagerImpl(final CyEventHelper eventHelper,
- final VisualLexiconManager rootLexicon)
{
+
+ public VisualMappingManagerImpl(final CyEventHelper eventHelper) {
if (eventHelper == null)
throw new IllegalArgumentException("CyEventHelper
cannot be null");
- if (rootLexicon == null)
- throw new IllegalArgumentException("vpCatalog cannot be
null");
-
this.cyEventHelper = eventHelper;
- this.rootLexicon = rootLexicon;
visualStyles = new HashSet<VisualStyle>();
- vsForNetwork = new HashMap<CyNetworkView, VisualStyle>();
+ network2VisualStyleMap = new HashMap<CyNetworkView,
VisualStyle>();
}
/**
@@ -90,8 +75,8 @@
*
* @return DOCUMENT ME!
*/
- public VisualStyle getVisualStyle(CyNetworkView nv) {
- return vsForNetwork.get(nv);
+ @Override public VisualStyle getVisualStyle(CyNetworkView nv) {
+ return network2VisualStyleMap.get(nv);
}
/**
@@ -102,78 +87,34 @@
* @param nv
* DOCUMENT ME!
*/
- public void setVisualStyle(VisualStyle vs, CyNetworkView nv) {
- vsForNetwork.put(nv, vs);
+ @Override public void setVisualStyle(VisualStyle vs, CyNetworkView nv) {
+ network2VisualStyleMap.put(nv, vs);
}
- /**
- * DOCUMENT ME!
- *
- * @param originalVS DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public VisualStyle copyVisualStyle(VisualStyle originalVS) {
- final VisualStyle copyVS = new VisualStyleImpl(rootLexicon, new
String(originalVS.getTitle()));
- // TODO: copy everything! This is incomplete
- Collection<VisualMappingFunction<?, ?>> allMapping =
originalVS.getAllVisualMappingFunctions();
-
- String attrName;
- VisualProperty<?> vp;
-
- for (VisualMappingFunction<?, ?> mapping : allMapping) {
- attrName = mapping.getMappingAttributeName();
- vp = mapping.getVisualProperty();
- }
-
- visualStyles.add(copyVS);
- cyEventHelper.fireSynchronousEvent(new
VisualStyleCreatedEvent(this,copyVS));
-
- return copyVS;
- }
-
/**
- * DOCUMENT ME!
- *
- * @param title DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public VisualStyle createVisualStyle(String title) {
- final VisualStyle newVS = new VisualStyleImpl(rootLexicon,
title);
- visualStyles.add(newVS);
- cyEventHelper.fireSynchronousEvent(new
VisualStyleCreatedEvent(this,newVS));
-
- return newVS;
- }
-
- /**
* Remove the style from this manager and delete it.
*
* @param vs
* DOCUMENT ME!
*/
- public void removeVisualStyle(VisualStyle vs) {
+ @Override public void removeVisualStyle(VisualStyle vs) {
visualStyles.remove(vs);
cyEventHelper.fireSynchronousEvent(new
VisualStyleDestroyedEvent(this,vs));
vs = null;
}
+
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public Collection<VisualStyle> getAllVisualStyles() {
+ @Override public Set<VisualStyle> getAllVisualStyles() {
return visualStyles;
}
-
- public <K, V> VisualMappingFunction<K, V> createMapping(String
mappingType,
- String attrName, Class<K> attrType, VisualProperty<V>
vp) {
-
-
- return null;
+ @Override public void addVisualStyle(VisualStyle vs) {
+ this.visualStyles.add(vs);
}
}
Added:
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleFactoryImpl.java
===================================================================
---
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleFactoryImpl.java
(rev 0)
+++
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleFactoryImpl.java
2010-09-17 01:48:41 UTC (rev 21916)
@@ -0,0 +1,50 @@
+package org.cytoscape.view.vizmap.internal;
+
+import java.util.Collection;
+
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.view.model.VisualProperty;
+import org.cytoscape.view.presentation.RenderingEngine;
+import org.cytoscape.view.vizmap.VisualMappingFunction;
+import org.cytoscape.view.vizmap.VisualStyle;
+import org.cytoscape.view.vizmap.VisualStyleFactory;
+import org.cytoscape.view.vizmap.events.VisualStyleCreatedEvent;
+
+public class VisualStyleFactoryImpl implements VisualStyleFactory {
+
+ private final CyEventHelper eventHelper;
+
+ public VisualStyleFactoryImpl(final CyEventHelper eventHelper) {
+ this.eventHelper = eventHelper;
+ }
+
+ @Override
+ public VisualStyle createVisualStyle(final VisualStyle original) {
+ final VisualStyle copyVS = new
VisualStyleImpl(original.getTitle(), original.getVisualLexicon());
+
+ // TODO: copy everything! This is incomplete
+ Collection<VisualMappingFunction<?, ?>> allMapping =
original.getAllVisualMappingFunctions();
+
+ String attrName;
+ VisualProperty<?> vp;
+
+ for (VisualMappingFunction<?, ?> mapping : allMapping) {
+ attrName = mapping.getMappingAttributeName();
+ vp = mapping.getVisualProperty();
+ }
+
+ eventHelper.fireSynchronousEvent(new
VisualStyleCreatedEvent(this,copyVS));
+
+ return copyVS;
+ }
+
+
+ @Override
+ public VisualStyle createVisualStyle(String title, RenderingEngine<?>
engine) {
+ final VisualStyle vs = new VisualStyleImpl(title,
engine.getVisualLexicon());
+
+ eventHelper.fireSynchronousEvent(new
VisualStyleCreatedEvent(this,vs));
+ return vs;
+ }
+
+}
Modified:
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
===================================================================
---
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
2010-09-17 01:30:47 UTC (rev 21915)
+++
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
2010-09-17 01:48:41 UTC (rev 21916)
@@ -36,17 +36,14 @@
import java.util.Collection;
import java.util.HashMap;
-import java.util.HashSet;
import java.util.Map;
import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualLexicon;
-import org.cytoscape.view.model.VisualLexiconManager;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.vizmap.VisualMappingFunction;
import org.cytoscape.view.vizmap.VisualStyle;
@@ -64,8 +61,9 @@
private final Map<VisualProperty<?>, VisualMappingFunction<?, ?>>
mappings;
private final Map<VisualProperty<?>, Object> perVSDefaults;
- private final VisualLexiconManager lexiconManager;
+ private final VisualLexicon lexicon;
+
private String title;
/**
@@ -74,8 +72,8 @@
* @param rootLexicon
* DOCUMENT ME!
*/
- public VisualStyleImpl(final VisualLexiconManager lexiconManager) {
- this(lexiconManager, null);
+ public VisualStyleImpl(final VisualLexicon lexicon) {
+ this(null, lexicon);
}
/**
@@ -86,24 +84,22 @@
* @param rootLexicon
* DOCUMENT ME!
*/
- public VisualStyleImpl(final VisualLexiconManager lexiconManager,
- final String title) {
- if (lexiconManager == null)
- throw new NullPointerException("rootLexicon is null");
+ public VisualStyleImpl(final String title, final VisualLexicon lexicon)
{
+ if (lexicon == null)
+ throw new NullPointerException("Lexicon is null");
if (title == null)
this.title = DEFAULT_TITLE;
else
this.title = title;
- this.lexiconManager = lexiconManager;
+ this.lexicon = lexicon;
mappings = new HashMap<VisualProperty<?>,
VisualMappingFunction<?, ?>>();
perVSDefaults = new HashMap<VisualProperty<?>, Object>();
- // Copy immutable defaults from each VP
- final VisualLexicon root = lexiconManager.getLexicon();
+
- for (VisualProperty<?> vp : root.getAllVisualProperties())
+ for (VisualProperty<?> vp : lexicon.getAllVisualProperties())
perVSDefaults.put(vp, vp.getDefault());
logger.info("New Visual Style Created: Style Name = " +
this.title);
@@ -201,7 +197,6 @@
// networkviews.add(networkView);
// Current visual prop tree.
- final VisualLexicon lexicon = lexiconManager.getLexicon();
Collection<View<? extends CyTableEntry>> allViews = networkView
.getAllViews();
applyImpl(allViews, lexicon.getAllVisualProperties());
@@ -321,8 +316,9 @@
}
// TODO Is this the right set of lexicon?
+ @Override
public VisualLexicon getVisualLexicon() {
- return lexiconManager.getLexicon();
+ return lexicon;
}
}
Modified:
core3/vizmap-impl/branches/vp-tree/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/vizmap-impl/branches/vp-tree/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2010-09-17 01:30:47 UTC (rev 21915)
+++
core3/vizmap-impl/branches/vp-tree/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2010-09-17 01:48:41 UTC (rev 21916)
@@ -5,13 +5,18 @@
http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
default-lazy-init="false">
+
+ <!-- Export VMM as an OSGi Service -->
<osgi:service id="visualMappingManagerService"
ref="visualMappingManager"
interface="org.cytoscape.view.vizmap.VisualMappingManager">
</osgi:service>
+
+ <!-- Export Visual Style Factory as an OSGi Service -->
+ <osgi:service id="visualStyleFactoryService" ref="visualStyleFactory"
+ interface="org.cytoscape.view.vizmap.VisualStyleFactory">
+ </osgi:service>
<!-- Import Services -->
<osgi:reference id="cyEventHelperServiceRef"
interface="org.cytoscape.event.CyEventHelper" />
- <osgi:reference id="rootVisualLexiconRef"
- interface="org.cytoscape.view.model.RootVisualLexicon" />
</beans>
Modified:
core3/vizmap-impl/branches/vp-tree/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/vizmap-impl/branches/vp-tree/src/main/resources/META-INF/spring/bundle-context.xml
2010-09-17 01:30:47 UTC (rev 21915)
+++
core3/vizmap-impl/branches/vp-tree/src/main/resources/META-INF/spring/bundle-context.xml
2010-09-17 01:48:41 UTC (rev 21916)
@@ -13,14 +13,19 @@
http://www.springframework.org/schema/lang
http://www.springframework.org/schema/lang/spring-lang-2.5.xsd
http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
default-lazy-init="false">
+
+ <import resource="bundle-context-osgi.xml" />
<context:annotation-config />
<bean id="visualMappingManager"
class="org.cytoscape.view.vizmap.internal.VisualMappingManagerImpl">
<constructor-arg ref="cyEventHelperServiceRef" />
- <constructor-arg ref="rootVisualLexiconRef" />
</bean>
+
+ <bean id="visualStyleFactory"
+
class="org.cytoscape.view.vizmap.internal.VisualStyleFactoryImpl">
+ <constructor-arg ref="cyEventHelperServiceRef" />
+ </bean>
-
</beans>
Added:
core3/vizmap-impl/branches/vp-tree/src/test/java/org/cytoscape/vizmap/VisualStyleTest.java
===================================================================
---
core3/vizmap-impl/branches/vp-tree/src/test/java/org/cytoscape/vizmap/VisualStyleTest.java
(rev 0)
+++
core3/vizmap-impl/branches/vp-tree/src/test/java/org/cytoscape/vizmap/VisualStyleTest.java
2010-09-17 01:48:41 UTC (rev 21916)
@@ -0,0 +1,23 @@
+package org.cytoscape.vizmap;
+
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class VisualStyleTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testVisualStyle() {
+
+ }
+
+}
Added: core3/vizmap-impl/branches/vp-tree/src/test/resources/log4j.properties
===================================================================
--- core3/vizmap-impl/branches/vp-tree/src/test/resources/log4j.properties
(rev 0)
+++ core3/vizmap-impl/branches/vp-tree/src/test/resources/log4j.properties
2010-09-17 01:48:41 UTC (rev 21916)
@@ -0,0 +1,8 @@
+log4j.rootCategory=info, stdout
+log4j.appender.stdout=org.apache.log4j.ConsoleAppender
+log4j.appender.stdout.layout.ConversionPattern=%t %p [%c] - %m%n
+log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
+log4j.appender.stdout.threshold=TRACE
+
+log4j.logger.org.springframework=INFO
+log4j.logger.org.springframework.osgi.test=INFO
Property changes on:
core3/vizmap-impl/branches/vp-tree/src/test/resources/log4j.properties
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