Author: kono
Date: 2011-04-01 09:29:46 -0700 (Fri, 01 Apr 2011)
New Revision: 24641
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java
core3/layout-jgraph-impl/trunk/pom.xml
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapperTask.java
core3/presentation-api/trunk/src/main/java/org/cytoscape/view/presentation/property/MinimalVisualLexicon.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/select/SelectRegisterListener.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderFactory.java
core3/webservice-biomart-client-impl/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportTableTask.java
core3/webservice-biomart-client-impl/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
core3/webservice-biomart-client-impl/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
Log:
Bugs related to 2D->minimal lexicon are fixed.
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java
2011-04-01 00:00:53 UTC (rev 24640)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java
2011-04-01 16:29:46 UTC (rev 24641)
@@ -17,9 +17,12 @@
import org.slf4j.Logger;
public class GenericReaderManager<T extends InputStreamTaskFactory, R extends
Task> {
+
+ private static final Logger logger = LoggerFactory.getLogger(
GenericReaderManager.class );
+
protected final DataCategory category;
protected final Set<T> factories;
- private static final Logger logger = LoggerFactory.getLogger(
GenericReaderManager.class );
+
public GenericReaderManager(DataCategory category) {
this.category = category;
@@ -32,8 +35,7 @@
* @param factory
* @param props
*/
- @SuppressWarnings("unchecked")
- public void addInputStreamTaskFactory(T factory, Map props) {
+ public void addInputStreamTaskFactory(T factory,
@SuppressWarnings("rawtypes") Map props) {
if (factory == null)
logger.warn("Specified factory is null!");
else if (factory.getCyFileFilter().getDataCategory() ==
category) {
@@ -49,8 +51,7 @@
* @param factory
* @param props
*/
- @SuppressWarnings("unchecked")
- public void removeInputStreamTaskFactory(T factory, Map props) {
+ public void removeInputStreamTaskFactory(T factory,
@SuppressWarnings("rawtypes") Map props) {
factories.remove(factory);
}
@@ -62,26 +63,28 @@
* @return GraphReader capable of reading the specified file.
*/
public R getReader(URI uri, String inputName) {
+
+ logger.debug("Number of factories: " + factories.size());
for (T factory : factories) {
- CyFileFilter cff = factory.getCyFileFilter();
- logger.debug("trying factory: " + factory + " with
filter: " + cff);
+ final CyFileFilter cff = factory.getCyFileFilter();
+ logger.debug("Trying factory: " + factory + " with
filter: " + cff);
if (cff.accepts(uri, category) && uri != null ) {
try {
- logger.debug("successfully matched
factory " + factory);
+ logger.debug("Successfully found
matched factory " + factory);
InputStream stream =
uri.toURL().openStream();
if ( !stream.markSupported() )
stream = new MarkSupportedInputStream(stream);
factory.setInputStream( stream,
inputName );
- return
(R)factory.getTaskIterator().next();
+ return (R)
factory.getTaskIterator().next();
} catch (IOException e) {
logger.warn("Error opening stream to
URI: " + uri.toString(), e);
}
}
}
- logger.info("No reader found for uri: " + uri.toString());
+ logger.warn("No reader found for uri: " + uri.toString());
return null;
}
@@ -108,7 +111,7 @@
logger.warn("Error setting input stream", ioe);
}
- logger.info("No reader found for input stream");
+ logger.warn("No reader found for input stream");
return null;
}
}
Modified: core3/layout-jgraph-impl/trunk/pom.xml
===================================================================
--- core3/layout-jgraph-impl/trunk/pom.xml 2011-04-01 00:00:53 UTC (rev
24640)
+++ core3/layout-jgraph-impl/trunk/pom.xml 2011-04-01 16:29:46 UTC (rev
24641)
@@ -1,25 +1,27 @@
<?xml version="1.0" encoding="UTF-8"?>
-<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd";
xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";>
+<project
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd";
+ xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";>
- <parent>
- <groupId>org.cytoscape</groupId>
- <artifactId>parent</artifactId>
- <version>3.0.0-alpha6-SNAPSHOT</version>
- </parent>
+ <parent>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>3.0.0-alpha6-SNAPSHOT</version>
+ </parent>
- <properties>
- <bundle.symbolicName>org.cytoscape.layout-jgraph-impl</bundle.symbolicName>
- <bundle.namespace>csplugins.layout</bundle.namespace>
- </properties>
+ <properties>
+
<bundle.symbolicName>org.cytoscape.layout-jgraph-impl</bundle.symbolicName>
+ <bundle.namespace>csplugins.layout</bundle.namespace>
+ </properties>
- <modelVersion>4.0.0</modelVersion>
- <groupId>org.cytoscape</groupId>
- <artifactId>layout-jgraph-impl</artifactId>
- <version>1.0-SNAPSHOT</version>
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>layout-jgraph-impl</artifactId>
+ <version>1.0-SNAPSHOT</version>
- <name>${bundle.symbolicName} [${bundle.namespace}]</name>
+ <name>${bundle.symbolicName} [${bundle.namespace}]</name>
- <packaging>bundle</packaging>
+ <packaging>bundle</packaging>
<build>
@@ -28,21 +30,17 @@
<groupId>org.ops4j</groupId>
<artifactId>maven-pax-plugin</artifactId>
<version>${maven-pax-plugin.version}</version>
- <!--
- | enable improved OSGi compilation
support for the bundle
- life-cycle. | to switch back to the
standard bundle life-cycle,
- move this setting | down to the
maven-bundle-plugin section
- -->
+ <!-- | enable improved OSGi compilation support
for the bundle life-cycle.
+ | to switch back to the standard bundle
life-cycle, move this setting | down
+ to the maven-bundle-plugin section -->
<extensions>true</extensions>
</plugin>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>${maven-bundle-plugin.version}</version>
- <!--
- | the following instructions build a
simple set of public/private
- classes into an OSGi bundle
- -->
+ <!-- | the following instructions build a
simple set of public/private
+ classes into an OSGi bundle -->
<configuration>
<instructions>
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
@@ -55,47 +53,27 @@
</plugins>
</build>
- <dependencies>
- <dependency>
- <groupId>org.cytoscape</groupId>
- <artifactId>model-api</artifactId>
- <version>3.0.0-alpha3-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>org.cytoscape</groupId>
- <artifactId>viewmodel-api</artifactId>
- <version>1.0-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>org.cytoscape</groupId>
- <artifactId>layout-api</artifactId>
- <version>1.0-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>org.cytoscape</groupId>
- <artifactId>presentation-api</artifactId>
- <version>1.0-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>org.cytoscape</groupId>
- <artifactId>work-api</artifactId>
- <version>1.0-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>cytoscape-temp</groupId>
- <artifactId>org.jgraph.jgraph</artifactId>
- <version>5.10.0.2</version>
- </dependency>
- <dependency>
- <groupId>cytoscape-temp</groupId>
- <artifactId>org.jgraph.layouts</artifactId>
- <version>5.10.0.2</version>
- </dependency>
- <dependency>
- <groupId>cytoscape-temp</groupId>
- <artifactId>org.jgraph.jgraphpad</artifactId>
- <version>5.10.0.2</version>
- </dependency>
- </dependencies>
+ <dependencies>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>layout-api</artifactId>
+ <version>3.0.0-alpha2-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>org.jgraph.jgraph</artifactId>
+ <version>5.10.0.2</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>org.jgraph.layouts</artifactId>
+ <version>5.10.0.2</version>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>org.jgraph.jgraphpad</artifactId>
+ <version>5.10.0.2</version>
+ </dependency>
+ </dependencies>
</project>
Modified:
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
===================================================================
---
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
2011-04-01 00:00:53 UTC (rev 24640)
+++
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
2011-04-01 16:29:46 UTC (rev 24641)
@@ -2,7 +2,6 @@
import org.cytoscape.view.layout.AbstractLayout;
import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
import org.cytoscape.work.undo.UndoSupport;
import org.jgraph.plugins.layouts.AnnealingLayoutAlgorithm;
Modified:
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapperTask.java
===================================================================
---
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapperTask.java
2011-04-01 00:00:53 UTC (rev 24640)
+++
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapperTask.java
2011-04-01 16:29:46 UTC (rev 24641)
@@ -15,7 +15,7 @@
import org.cytoscape.view.layout.LayoutTask;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
-import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
+import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
import org.cytoscape.work.TaskMonitor;
import org.jgraph.JGraph;
import org.jgraph.graph.CellView;
@@ -139,10 +139,10 @@
// Set bounds
Rectangle2D bounds = new Rectangle2D.Double(
-
node_view.getVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION),
-
node_view.getVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION),
-
node_view.getVisualProperty(TwoDVisualLexicon.NODE_X_SIZE),
-
node_view.getVisualProperty(TwoDVisualLexicon.NODE_Y_SIZE)
+
node_view.getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION),
+
node_view.getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION),
+
node_view.getVisualProperty(MinimalVisualLexicon.NODE_WIDTH),
+
node_view.getVisualProperty(MinimalVisualLexicon.NODE_HEIGHT)
);
GraphConstants.setBounds(jcell.getAttributes(), bounds);
@@ -216,8 +216,8 @@
Rectangle2D rect =
graph.getCellBounds(cell_view.getCell());
CyNode giny = (CyNode)
j_giny_node_map.get(cell_view.getCell());
View<CyNode> node_view =
networkView.getNodeView(giny);
-
node_view.setVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION, rect.getX());
-
node_view.setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION, rect.getY());
+
node_view.setVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION, rect.getX());
+
node_view.setVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION, rect.getY());
// update progress bar
currentProgress += percentProgressPerIter;
Modified:
core3/presentation-api/trunk/src/main/java/org/cytoscape/view/presentation/property/MinimalVisualLexicon.java
===================================================================
---
core3/presentation-api/trunk/src/main/java/org/cytoscape/view/presentation/property/MinimalVisualLexicon.java
2011-04-01 00:00:53 UTC (rev 24640)
+++
core3/presentation-api/trunk/src/main/java/org/cytoscape/view/presentation/property/MinimalVisualLexicon.java
2011-04-01 16:29:46 UTC (rev 24641)
@@ -157,13 +157,13 @@
"Network Center Y Location", true, CyNetwork.class);
public static final VisualProperty<Double> NETWORK_SIZE = new
DoubleVisualProperty(
- 100.0, NONE_ZERO_POSITIVE_DOUBLE_RANGE, "NETWORK_SIZE",
+ 550.0, NONE_ZERO_POSITIVE_DOUBLE_RANGE, "NETWORK_SIZE",
"Network Size", true, CyNetwork.class);
public static final VisualProperty<Double> NETWORK_WIDTH = new
DoubleVisualProperty(
- 100.0, NONE_ZERO_POSITIVE_DOUBLE_RANGE, "NETWORK_WIDTH",
+ 550.0, NONE_ZERO_POSITIVE_DOUBLE_RANGE, "NETWORK_WIDTH",
"Network Width", true, CyNetwork.class);
public static final VisualProperty<Double> NETWORK_HEIGHT = new
DoubleVisualProperty(
- 100.0, NONE_ZERO_POSITIVE_DOUBLE_RANGE,
"NETWORK_HEIGHT",
+ 400.0, NONE_ZERO_POSITIVE_DOUBLE_RANGE,
"NETWORK_HEIGHT",
"Network Height", true, CyNetwork.class);
public static final VisualProperty<String> NETWORK_TITLE = new
StringVisualProperty(
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/select/SelectRegisterListener.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/select/SelectRegisterListener.java
2011-04-01 00:00:53 UTC (rev 24640)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/select/SelectRegisterListener.java
2011-04-01 16:29:46 UTC (rev 24641)
@@ -2,20 +2,14 @@
package org.cytoscape.internal.select;
-import java.util.Properties;
-
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableManager;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyTable;
import org.cytoscape.model.events.RowSetMicroListener;
-import org.cytoscape.service.util.CyServiceRegistrar;
-import org.cytoscape.view.model.events.NetworkViewAddedEvent;
-import org.cytoscape.view.model.events.NetworkViewAddedListener;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
+import org.cytoscape.view.model.events.NetworkViewAddedEvent;
+import org.cytoscape.view.model.events.NetworkViewAddedListener;
public class SelectRegisterListener implements NetworkViewAddedListener {
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
2011-04-01 00:00:53 UTC (rev 24640)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
2011-04-01 16:29:46 UTC (rev 24641)
@@ -47,11 +47,11 @@
import javax.swing.JInternalFrame;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
-import javax.swing.event.InternalFrameListener;
import org.cytoscape.application.swing.CyHelpBroker;
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.events.RowSetMicroListener;
import org.cytoscape.property.CyProperty;
import org.cytoscape.property.session.Cysession;
@@ -81,28 +81,28 @@
/**
- * Actually, this is a presentation manager.
+ * Managing views (presentations) in current session.
+ *
*/
-public class NetworkViewManager implements InternalFrameListener,
+public class NetworkViewManager extends InternalFrameAdapter implements
NetworkViewAddedListener, NetworkViewAboutToBeDestroyedListener,
SetCurrentNetworkViewListener, SetCurrentNetworkListener,
SessionLoadedListener {
private static final Logger logger =
LoggerFactory.getLogger(NetworkViewManager.class);
+ private static final int MINIMUM_WIN_WIDTH = 200;
+ private static final int MINIMUM_WIN_HEIGHT = 200;
+
private final JDesktopPane desktopPane;
// Key is MODEL ID
private final Map<Long, JInternalFrame> presentationContainerMap;
private final Map<Long, RenderingEngine<CyNetwork>> presentationMap;
- private final Map<JInternalFrame, Long> componentMap;
-
- protected final int MINIMUM_WIN_WIDTH = 200;
- protected final int MINIMUM_WIN_HEIGHT = 200;
-
+ private final Map<JInternalFrame, Long> iFrameMap;
+ private final Properties props;
+
private Long currentPresentationContainerID;
-
- private Properties props;
// Supports multiple presentations
private final Map<String, RenderingEngineFactory<CyNetwork>> factories;
@@ -130,21 +130,29 @@
*/
public NetworkViewManager(CyApplicationManager appMgr,
CyNetworkViewManager netViewMgr, CyProperty<Properties> cyProps,
CyHelpBroker help, CyEventHelper eventHelper) {
+
+ if(appMgr == null)
+ throw new NullPointerException("CyApplicationManager is
null.");
+ if(eventHelper == null)
+ throw new NullPointerException("CyEventHelper is
null.");
+ if(netViewMgr == null)
+ throw new NullPointerException("CyNetworkViewManager is
null.");
+
this.factories = new HashMap<String,
RenderingEngineFactory<CyNetwork>>();
this.networkViewManager = netViewMgr;
this.applicationManager = appMgr;
this.props = cyProps.getProperties();
this.eventHelper = eventHelper;
- desktopPane = new JDesktopPane();
+
+ this.desktopPane = new JDesktopPane();
// add Help hooks
- help.getHelpBroker().enableHelp(desktopPane,
"network-view-manager",
- null);
+ help.getHelpBroker().enableHelp(desktopPane,
"network-view-manager", null);
presentationContainerMap = new HashMap<Long, JInternalFrame>();
presentationMap = new HashMap<Long,
RenderingEngine<CyNetwork>>();
- componentMap = new HashMap<JInternalFrame, Long>();
+ iFrameMap = new HashMap<JInternalFrame, Long>();
currentPresentationContainerID = null;
netViewChangeListeners = new HashMap<CyNetworkView,
NetworkViewChangeMicroListener>();
@@ -152,12 +160,12 @@
}
/**
- * Dynamically add rendering engine factories.
+ * Dynamically add rendering engine factories. Will be used by Spring
DM.
*
* @param factory
* @param props
*/
- public void addPresentationFactory(RenderingEngineFactory<CyNetwork>
factory, Map props) {
+ public void addPresentationFactory(RenderingEngineFactory<CyNetwork>
factory, @SuppressWarnings("rawtypes") Map props) {
logger.info("Adding New Rendering Engine Factory...");
Object rendererID = props.get(ID);
@@ -173,7 +181,7 @@
logger.info("New Rendering Engine is Available: " + rendererID);
}
- public void removePresentationFactory(RenderingEngineFactory<CyNetwork>
factory, Map props) {
+ public void removePresentationFactory(RenderingEngineFactory<CyNetwork>
factory, @SuppressWarnings("rawtypes") Map props) {
factories.remove(props.get(ID));
}
@@ -210,7 +218,7 @@
* View switched
*/
public void internalFrameActivated(InternalFrameEvent e) {
- final Long networkId = componentMap.get(e.getInternalFrame());
+ final Long networkId = iFrameMap.get(e.getInternalFrame());
if (networkId == null) return;
final RenderingEngine<CyNetwork> currentEngine =
applicationManager.getCurrentRenderingEngine();
@@ -223,59 +231,12 @@
/**
* Fire Events when a Managed Network View gets the Focus.
*/
- public void internalFrameOpened(InternalFrameEvent e) {
+ @Override public void internalFrameOpened(InternalFrameEvent e) {
internalFrameActivated(e);
}
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void internalFrameClosed(InternalFrameEvent e) {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void internalFrameClosing(InternalFrameEvent e) {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void internalFrameDeactivated(InternalFrameEvent e) {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void internalFrameDeiconified(InternalFrameEvent e) {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void internalFrameIconified(InternalFrameEvent e) {
- }
-
//// Event Handlers ////
-
public void handleEvent(SetCurrentNetworkViewEvent e) {
if ( e.getNetworkView() == null ) {
logger.info("Attempting to set current network view
model: null view " );
@@ -304,11 +265,12 @@
/**
* Adding new network view model to this manager.
- * Then, create default presentation.
+ * Then, render presentation.
*/
public void handleEvent(final NetworkViewAddedEvent nvae) {
- logger.info("Adding view to manager: NetworkViewManager: View
ID = "
- + nvae.getNetworkView().getSUID());
+ logger.info("\n\n\n **** View got Network view added event.
Adding view to manager: NetworkViewManager: View ID = "
+ + nvae.getNetworkView().getSUID() + "\n\n\n");
+
render(nvae.getNetworkView());
}
@@ -334,15 +296,15 @@
* Create a visualization container and add presentation to it.
*
*/
- protected void render(final CyNetworkView view) {
- final Long netModelId = view.getModel().getSUID();
+ private void render(final CyNetworkView view) {
+ final Long modelID = view.getModel().getSUID();
// If already registered in this manager, do not render.
- if (presentationContainerMap.containsKey(netModelId))
+ if (presentationContainerMap.containsKey(modelID))
return;
// Create a new InternalFrame and put the CyNetworkView
Component into it
- final String title = view.getModel().getCyRow().get("name",
String.class);
+ final String title =
view.getModel().getCyRow().get(CyTableEntry.NAME, String.class);
final JInternalFrame iframe = new JInternalFrame(title, true,
true, true, true);
iframe.addInternalFrameListener(new InternalFrameAdapter() {
@@ -352,14 +314,14 @@
});
desktopPane.add(iframe);
- presentationContainerMap.put(netModelId, iframe);
- componentMap.put(iframe, netModelId);
+ presentationContainerMap.put(modelID, iframe);
+ iFrameMap.put(iframe, modelID);
- long start = System.currentTimeMillis();
- logger.debug("Rendering view model: " + view.getSUID());
+ final long start = System.currentTimeMillis();
+ logger.debug("Rendering start: view model = " + view.getSUID());
final RenderingEngine<CyNetwork> renderingEngine =
currentRenderingEngineFactory.getInstance(iframe, view);
logger.debug("Rendering finished in " +
(System.currentTimeMillis() - start) + " m sec.");
- presentationMap.put(netModelId, renderingEngine);
+ presentationMap.put(modelID, renderingEngine);
iframe.pack();
@@ -387,20 +349,22 @@
iframe.setLocation(x, y);
// maximize the frame if the specified property is set
- try {
- String max = props.getProperty("maximizeViewOnCreate");
+
+ final String max = props.getProperty("maximizeViewOnCreate");
- if ((max != null) && Boolean.parseBoolean(max)) {
+ if ((max != null) && Boolean.parseBoolean(max)) {
+ try {
iframe.setMaximum(true);
- } else {
- int w =
view.getVisualProperty(MinimalVisualLexicon.NETWORK_WIDTH).intValue();
- int h =
view.getVisualProperty(MinimalVisualLexicon.NETWORK_HEIGHT).intValue();
- updateNetworkSize(netModelId, w, h);
+ } catch (PropertyVetoException pve) {
+ logger.warn("Could not maximize frame.", pve);
}
- } catch (PropertyVetoException pve) {
- pve.printStackTrace();
+ } else {
+ int w =
view.getVisualProperty(MinimalVisualLexicon.NETWORK_WIDTH).intValue();
+ int h =
view.getVisualProperty(MinimalVisualLexicon.NETWORK_HEIGHT).intValue();
+ updateNetworkSize(modelID, w, h);
}
+
// Display it and add listeners
iframe.setVisible(true);
iframe.addInternalFrameListener(this);
@@ -428,7 +392,7 @@
RowSetMicroListener rsml = new
AbstractNetworkNameListener(view.getModel()) {
@Override
public void updateNetworkName(CyNetwork net, String
name) {
- final String title = net.getCyRow().get("name",
String.class);
+ final String title =
net.getCyRow().get(CyTableEntry.NAME, String.class);
updateNetworkTitle(net.getSUID(), title);
}
};
@@ -477,12 +441,14 @@
}
}
- private void updateNetworkSize(Long networkModelID, int width, int
height) {
- JInternalFrame frame =
presentationContainerMap.get(networkModelID);
+ private void updateNetworkSize(final Long networkModelID, int width,
int height) {
+ final JInternalFrame frame =
presentationContainerMap.get(networkModelID);
- if (frame != null && width > 0 && height > 0) {
+ if(frame == null)
+ return;
+
+ if (width > 0 && height > 0)
frame.setSize(new Dimension(width, height));
- }
}
private void setFocus(Long networkModelID) {
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderFactory.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderFactory.java
2011-04-01 00:00:53 UTC (rev 24640)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderFactory.java
2011-04-01 16:29:46 UTC (rev 24641)
@@ -1,5 +1,7 @@
package org.cytoscape.tableimport.internal;
+import java.io.InputStream;
+
import org.cytoscape.session.CyApplicationManager;
import org.cytoscape.tableimport.internal.util.CytoscapeServices;
import org.cytoscape.util.swing.FileUtil;
@@ -52,4 +54,10 @@
return new TaskIterator(new ImportAttributeTableReaderTask(
this.inputStream, fileFormat));
}
+
+ @Override
+ public void setInputStream(InputStream is, String inputName) {
+ // TODO Auto-generated method stub
+
+ }
}
Modified:
core3/webservice-biomart-client-impl/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportTableTask.java
===================================================================
---
core3/webservice-biomart-client-impl/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportTableTask.java
2011-04-01 00:00:53 UTC (rev 24640)
+++
core3/webservice-biomart-client-impl/trunk/src/main/java/org/cytoscape/io/webservice/biomart/task/ImportTableTask.java
2011-04-01 16:29:46 UTC (rev 24641)
@@ -96,8 +96,7 @@
if (columnNames[0].contains("Query ERROR"))
throw new IOException("BioMart service returns error:
\n" + line);
- final CyTable globalTable = tableFactory.createTable(
- query.getTableName(), key, String.class, true);
+ final CyTable globalTable =
tableFactory.createTable(query.getTableName(), key, String.class, true, true);
// For status report
int recordCount = 0;
@@ -109,7 +108,7 @@
// Search column index of the key
for (int i = 0; i < colSize; i++) {
- globalTable.createColumn(columnNames[i], String.class);
+ globalTable.createColumn(columnNames[i], String.class,
false);
if (columnNames[i].equals(key))
keyIdx = i;
Modified:
core3/webservice-biomart-client-impl/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
===================================================================
---
core3/webservice-biomart-client-impl/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
2011-04-01 00:00:53 UTC (rev 24640)
+++
core3/webservice-biomart-client-impl/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/AttributeImportPanel.java
2011-04-01 16:29:46 UTC (rev 24641)
@@ -36,6 +36,7 @@
import java.awt.Color;
import java.awt.event.ActionEvent;
+import java.util.Collection;
import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
@@ -48,6 +49,7 @@
import javax.swing.JPanel;
import javax.swing.LayoutStyle;
+import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyNode;
@@ -429,9 +431,10 @@
for(CyNetwork network: networks) {
final Map<String, CyTable> tables =
this.tblManager.getTableMap(CyNode.class, network);
final CyTable nodeTable =
tables.get(CyNetwork.DEFAULT_ATTRS);
- final Map<String, Class<?>> columns =
nodeTable.getColumnTypeMap();
- for (String name : columns.keySet())
- attributeComboBox.addItem(name);
+ //final Map<String, Class<?>> columns =
nodeTable.getColumnTypeMap();
+ Collection<CyColumn> columns = nodeTable.getColumns();
+ for (CyColumn col : columns)
+ attributeComboBox.addItem(col.getName());
}
}
Modified:
core3/webservice-biomart-client-impl/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
===================================================================
---
core3/webservice-biomart-client-impl/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
2011-04-01 00:00:53 UTC (rev 24640)
+++
core3/webservice-biomart-client-impl/trunk/src/main/java/org/cytoscape/io/webservice/biomart/ui/BiomartAttrMappingPanel.java
2011-04-01 16:29:46 UTC (rev 24641)
@@ -37,6 +37,7 @@
import java.awt.Window;
import java.awt.event.ActionEvent;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
@@ -56,6 +57,7 @@
import org.cytoscape.io.webservice.biomart.task.ImportAttributeListTask;
import org.cytoscape.io.webservice.biomart.task.ImportFilterTask;
import org.cytoscape.io.webservice.biomart.task.LoadRepositoryResult;
+import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyNode;
@@ -251,8 +253,9 @@
// Use Attributes for mapping
final CyTable defTable = tblManager.getTableMap(CyNode.class,
curNetwork).get(CyNetwork.DEFAULT_ATTRS);
- final Class<?> attrDataType = defTable.getColumnTypeMap().get(
- keyAttrName);
+
+ final CyColumn column = defTable.getColumn(keyAttrName);
+ final Class<?> attrDataType = column.getType();
for (CyNode node : nodes) {
final CyRow row = defTable.getRow(node.getSUID());
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