Author: clopes
Date: 2012-02-14 14:10:59 -0800 (Tue, 14 Feb 2012)
New Revision: 28269
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CyActivator.java
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DropNetworkViewTask.java
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DropNetworkViewTaskFactoryImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderFactoryImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/CyTableMetadataImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdge.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNode.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/session/VirtualColumnSerializer.java
Log:
fixes #685 : Node and Edge "name" columns are null in sub-networks
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CyActivator.java
2012-02-14 20:50:53 UTC (rev 28268)
+++
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CyActivator.java
2012-02-14 22:10:59 UTC (rev 28269)
@@ -8,6 +8,7 @@
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.task.creation.NewEmptyNetworkViewFactory;
import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.editor.internal.DropNetworkViewTaskFactoryImpl;
import org.cytoscape.editor.internal.DropNodeViewTaskFactoryImpl;
@@ -47,12 +48,11 @@
CySwingApplication cySwingApplicationServiceRef =
getService(bc,CySwingApplication.class);
CyNetworkManager cyNetworkManagerServiceRef =
getService(bc,CyNetworkManager.class);
+ CyRootNetworkManager cyRootNetworkManagerServiceRef =
getService(bc,CyRootNetworkManager.class);
NewEmptyNetworkViewFactory newEmptyNetworkViewFactoryServiceRef
= getService(bc,NewEmptyNetworkViewFactory.class);
CyEventHelper cyEventHelperServiceRef =
getService(bc,CyEventHelper.class);
-
VisualMappingManager vmm =
getService(bc,VisualMappingManager.class);
-
ImageIcon nodeIcon = new
ImageIcon(getClass().getResource("/images/node.png"));
ImageIcon edgeIcon = new
ImageIcon(getClass().getResource("/images/edge.png"));
ImageIcon netIcon = new
ImageIcon(getClass().getResource("/images/network.png"));
@@ -87,7 +87,7 @@
ShapePalette shapePalette = new
ShapePalette(cySwingApplicationServiceRef);
SIFInterpreterTaskFactory sifInterpreterTaskFactory = new
SIFInterpreterTaskFactory();
- DropNetworkViewTaskFactoryImpl dropNetworkViewTaskFactory = new
DropNetworkViewTaskFactoryImpl(cyEventHelperServiceRef, vmm);
+ DropNetworkViewTaskFactoryImpl dropNetworkViewTaskFactory = new
DropNetworkViewTaskFactoryImpl(cyEventHelperServiceRef, vmm,
cyRootNetworkManagerServiceRef);
DropNodeViewTaskFactoryImpl dropNodeViewTaskFactory = new
DropNodeViewTaskFactoryImpl(cyNetworkManagerServiceRef);
EditorCytoPanelComponent editorCytoPanelComponent = new
EditorCytoPanelComponent(shapePalette);
CurrentNetworkViewListener currentNetworkViewListener = new
CurrentNetworkViewListener(cySwingApplicationServiceRef,editorCytoPanelComponent);
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DropNetworkViewTask.java
===================================================================
---
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DropNetworkViewTask.java
2012-02-14 20:50:53 UTC (rev 28268)
+++
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DropNetworkViewTask.java
2012-02-14 22:10:59 UTC (rev 28269)
@@ -1,46 +1,47 @@
package org.cytoscape.editor.internal;
+import java.awt.datatransfer.Transferable;
import java.awt.geom.Point2D;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.Transferable;
+import javax.swing.JOptionPane;
+
+import org.cytoscape.dnd.DropUtil;
+import org.cytoscape.editor.internal.gui.ShapePalette;
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.task.AbstractNetworkViewTask;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
+import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.TaskMonitor;
-
-import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-
-import org.cytoscape.dnd.DropUtil;
-import org.cytoscape.editor.internal.gui.ShapePalette;
-import org.cytoscape.event.CyEventHelper;
-
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import org.cytoscape.view.vizmap.VisualMappingManager;
-import org.cytoscape.view.vizmap.VisualStyle;
-import javax.swing.JOptionPane;
public class DropNetworkViewTask extends AbstractNetworkViewTask {
+ private final VisualMappingManager vmm;
+ private final CyRootNetworkManager rnm;
private final Transferable t;
private final Point2D xformPt;
private final CyEventHelper eh;
private static int new_node_index =1;
- private VisualMappingManager vmm;
private static final Logger logger =
LoggerFactory.getLogger(DropNetworkViewTask.class);
- public DropNetworkViewTask(VisualMappingManager vmm, CyNetworkView
view, Transferable t, Point2D xformPt, CyEventHelper eh) {
+ public DropNetworkViewTask(final VisualMappingManager vmm, final
CyRootNetworkManager rnm, final CyNetworkView view,
+ final Transferable t, final Point2D xformPt, final
CyEventHelper eh) {
super(view);
+ this.vmm = vmm;
+ this.rnm = rnm;
this.t = t;
this.xformPt = xformPt;
this.eh = eh;
- this.vmm = vmm;
}
@Override
@@ -58,13 +59,13 @@
if (ShapePalette.specifyIdentifier){
nodeName = JOptionPane.showInputDialog("Please specify
a name");
- }
- else {
+ } else {
nodeName = "Node_"+ new_node_index;
new_node_index++;
}
- net.getRow(n).set("name", nodeName);
+ net.getRow(n).set(CyNode.NAME, nodeName);
+ rnm.getRootNetwork(net).getRow(n).set(CyNode.NAME, nodeName);
eh.flushPayloadEvents();
View<CyNode> nv = view.getNodeView(n);
@@ -75,6 +76,5 @@
// Apply visual style
VisualStyle vs = vmm.getVisualStyle(view);
vs.apply(view);
-
}
}
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DropNetworkViewTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DropNetworkViewTaskFactoryImpl.java
2012-02-14 20:50:53 UTC (rev 28268)
+++
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DropNetworkViewTaskFactoryImpl.java
2012-02-14 22:10:59 UTC (rev 28269)
@@ -6,6 +6,7 @@
import org.cytoscape.dnd.DropNetworkViewTaskFactory;
import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.TaskIterator;
@@ -18,10 +19,12 @@
private Point2D xformPt;
private final CyEventHelper eh;
private final VisualMappingManager vmm;
+ final CyRootNetworkManager rnm;
- public DropNetworkViewTaskFactoryImpl(CyEventHelper eh,
VisualMappingManager vmm) {
+ public DropNetworkViewTaskFactoryImpl(CyEventHelper eh,
VisualMappingManager vmm, CyRootNetworkManager rnm) {
this.eh = eh;
this.vmm = vmm;
+ this.rnm = rnm;
}
public void setNetworkView(CyNetworkView view) {
@@ -35,6 +38,6 @@
}
public TaskIterator createTaskIterator() {
- return new TaskIterator(new DropNetworkViewTask(vmm, view, t,
xformPt, eh));
+ return new TaskIterator(new DropNetworkViewTask(vmm, rnm, view,
t, xformPt, eh));
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
2012-02-14 20:50:53 UTC (rev 28268)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
2012-02-14 22:10:59 UTC (rev 28269)
@@ -132,7 +132,7 @@
VisualMappingFunctionFactory continuousMappingFactoryServiceRef
= getService(bc,VisualMappingFunctionFactory.class,"(mapping.type=continuous)");
VisualMappingFunctionFactory
passthroughMappingFactoryServiceRef =
getService(bc,VisualMappingFunctionFactory.class,"(mapping.type=passthrough)");
EquationCompiler equationCompilerServiceRef =
getService(bc,EquationCompiler.class);
- CyRootNetworkManager cyRootNetworkFactoryServiceRef =
getService(bc,CyRootNetworkManager.class);
+ CyRootNetworkManager cyRootNetworkManagerServiceRef =
getService(bc,CyRootNetworkManager.class);
StreamUtilImpl streamUtil = new
StreamUtilImpl(cyPropertyServiceRef);
BasicCyFileFilter expressionFilter = new BasicCyFileFilter(new
String[]{"pvals"}, new String[]{"text/plain"},"Cytoscape Expression Matrix
(.pvals) File", DataCategory.TABLE, streamUtil);
@@ -175,20 +175,20 @@
CalculatorConverterFactory calculatorConverterFactory = new
CalculatorConverterFactory();
ReadUtils readUtil = new ReadUtils(streamUtil);
ExpressionReaderFactory expressionReaderFactory = new
ExpressionReaderFactory(expressionFilter,cyTableFactoryServiceRef,cyTableManagerServiceRef);
- CyAttributesReaderFactory attrsDataReaderFactory = new
CyAttributesReaderFactory(attrsFilter,cyTableFactoryServiceRef,cyApplicationManagerServiceRef,cyNetworkManagerServiceRef,cyTableManagerServiceRef,cyRootNetworkFactoryServiceRef);
+ CyAttributesReaderFactory attrsDataReaderFactory = new
CyAttributesReaderFactory(attrsFilter,cyTableFactoryServiceRef,cyApplicationManagerServiceRef,cyNetworkManagerServiceRef,cyTableManagerServiceRef,cyRootNetworkManagerServiceRef);
SIFNetworkReaderFactory sifNetworkViewReaderFactory = new
SIFNetworkReaderFactory(sifFilter,cyLayoutsServiceRef,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,cyEventHelperRef);
UnrecognizedVisualPropertyManager
unrecognizedVisualPropertyManager = new
UnrecognizedVisualPropertyManager(cyTableFactoryServiceRef,cyTableManagerServiceRef);
GMLNetworkReaderFactory gmlNetworkViewReaderFactory = new
GMLNetworkReaderFactory(gmlFilter,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,renderingEngineManagerServiceRef,unrecognizedVisualPropertyManager);
ReadCache readCache = new ReadCache();
- ReadDataManager readDataManager = new
ReadDataManager(readCache,equationCompilerServiceRef,cyNetworkFactoryServiceRef,cyRootNetworkFactoryServiceRef);
+ ReadDataManager readDataManager = new
ReadDataManager(readCache,equationCompilerServiceRef,cyNetworkFactoryServiceRef,cyRootNetworkManagerServiceRef);
HandlerFactory handlerFactory = new
HandlerFactory(readDataManager);
XGMMLParser xgmmlParser = new
XGMMLParser(handlerFactory,readDataManager);
- XGMMLNetworkReaderFactory xgmmlNetworkReaderFactory = new
XGMMLNetworkReaderFactory(xgmmlFilter,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,cyRootNetworkFactoryServiceRef,renderingEngineManagerServiceRef,readDataManager,xgmmlParser,unrecognizedVisualPropertyManager);
+ XGMMLNetworkReaderFactory xgmmlNetworkReaderFactory = new
XGMMLNetworkReaderFactory(xgmmlFilter,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,cyRootNetworkManagerServiceRef,renderingEngineManagerServiceRef,readDataManager,xgmmlParser,unrecognizedVisualPropertyManager);
XGMMLNetworkViewReaderFactory xgmmlNetworkViewReaderFactory =
new
XGMMLNetworkViewReaderFactory(xgmmlViewFilter,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,renderingEngineManagerServiceRef,readDataManager,xgmmlParser,unrecognizedVisualPropertyManager);
CSVCyReaderFactory sessionTableReaderFactory = new
CSVCyReaderFactory(sessionTableFilter,true,true,cyTableFactoryServiceRef,compilerServiceRef,cyTableManagerServiceRef);
- Cy3SessionReaderFactoryImpl cy3SessionReaderFactory = new
Cy3SessionReaderFactoryImpl(cys3Filter,readCache,cyNetworkReaderManager,cyPropertyReaderManager,vizmapReaderManager,sessionTableReaderFactory,cyNetworkTableManagerServiceRef);
- Cy2SessionReaderFactoryImpl cy2SessionReaderFactory = new
Cy2SessionReaderFactoryImpl(cys2Filter,readCache,cyNetworkReaderManager,cyPropertyReaderManager,vizmapReaderManager,cyRootNetworkFactoryServiceRef);
+ Cy3SessionReaderFactoryImpl cy3SessionReaderFactory = new
Cy3SessionReaderFactoryImpl(cys3Filter,readCache,cyNetworkReaderManager,cyPropertyReaderManager,vizmapReaderManager,sessionTableReaderFactory,cyNetworkTableManagerServiceRef,cyRootNetworkManagerServiceRef);
+ Cy2SessionReaderFactoryImpl cy2SessionReaderFactory = new
Cy2SessionReaderFactoryImpl(cys2Filter,readCache,cyNetworkReaderManager,cyPropertyReaderManager,vizmapReaderManager,cyRootNetworkManagerServiceRef);
CysessionReaderFactory cysessionReaderFactory = new
CysessionReaderFactory(cysessionFilter);
BookmarkReaderFactory bookmarkReaderFactory = new
BookmarkReaderFactory(bookmarksFilter);
PropertiesReaderFactory propertiesReaderFactory = new
PropertiesReaderFactory(propertiesFilter);
@@ -201,14 +201,14 @@
PSWriterFactory psWriterFactory = new PSWriterFactory(psFilter);
SVGWriterFactory svgWriterFactory = new
SVGWriterFactory(svgFilter);
SifNetworkWriterFactory sifNetworkViewWriterFactory = new
SifNetworkWriterFactory(sifFilter);
- XGMMLNetworkViewWriterFactory xgmmlNetworkViewWriterFactory =
new
XGMMLNetworkViewWriterFactory(xgmmlFilter,renderingEngineManagerServiceRef,unrecognizedVisualPropertyManager,cyNetworkManagerServiceRef,cyRootNetworkFactoryServiceRef);
+ XGMMLNetworkViewWriterFactory xgmmlNetworkViewWriterFactory =
new
XGMMLNetworkViewWriterFactory(xgmmlFilter,renderingEngineManagerServiceRef,unrecognizedVisualPropertyManager,cyNetworkManagerServiceRef,cyRootNetworkManagerServiceRef);
CysessionWriterFactoryImpl cysessionWriterFactory = new
CysessionWriterFactoryImpl(cysessionFilter);
BookmarksWriterFactoryImpl bookmarksWriterFactory = new
BookmarksWriterFactoryImpl(bookmarksFilter);
PropertiesWriterFactoryImpl propertiesWriterFactory = new
PropertiesWriterFactoryImpl(propertiesFilter);
CSVTableWriterFactory csvTableWriterFactory = new
CSVTableWriterFactory(csvFilter,false,false);
CSVTableWriterFactory sessionTableWriterFactory = new
CSVTableWriterFactory(sessionTableFilter,true,true);
VizmapWriterFactoryImpl vizmapWriterFactory = new
VizmapWriterFactoryImpl(vizmapXMLFilter,visualStyleSerializer);
- SessionWriterFactoryImpl sessionWriterFactory = new
SessionWriterFactoryImpl(cys3Filter,xgmmlFilter,bookmarksFilter,propertiesFilter,sessionTableFilter,vizmapXMLFilter,networkViewWriterManager,cyRootNetworkFactoryServiceRef,propertyWriterManager,tableWriterManager,vizmapWriterManager);
+ SessionWriterFactoryImpl sessionWriterFactory = new
SessionWriterFactoryImpl(cys3Filter,xgmmlFilter,bookmarksFilter,propertiesFilter,sessionTableFilter,vizmapXMLFilter,networkViewWriterManager,cyRootNetworkManagerServiceRef,propertyWriterManager,tableWriterManager,vizmapWriterManager);
RecentlyOpenedTrackerImpl recentlyOpenedTracker = new
RecentlyOpenedTrackerImpl("tracker.recent.sessions",cyApplicationConfigurationServiceRef);
registerService(bc,cyNetworkReaderManager,CyNetworkReaderManager.class, new
Properties());
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderFactoryImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderFactoryImpl.java
2012-02-14 20:50:53 UTC (rev 28268)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderFactoryImpl.java
2012-02-14 22:10:59 UTC (rev 28269)
@@ -37,6 +37,7 @@
import org.cytoscape.io.read.InputStreamTaskFactory;
import org.cytoscape.io.read.VizmapReaderManager;
import org.cytoscape.model.CyNetworkTableManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.work.TaskIterator;
public class Cy3SessionReaderFactoryImpl implements InputStreamTaskFactory {
@@ -47,7 +48,8 @@
private final CyPropertyReaderManager propertyReaderMgr;
private final VizmapReaderManager vizmapReaderMgr;
private final CSVCyReaderFactory csvCyReaderFactory;
- private final CyNetworkTableManager networkTableManager;
+ private final CyNetworkTableManager networkTableMgr;
+ private final CyRootNetworkManager rootNetworkMgr;
private InputStream inputStream;
private String inputName;
@@ -58,14 +60,16 @@
final CyPropertyReaderManager propertyReaderMgr,
final VizmapReaderManager vizmapReaderMgr,
final CSVCyReaderFactory csvCyReaderFactory,
-
final CyNetworkTableManager networkTableManager) {
+
final CyNetworkTableManager networkTableMgr,
+
final CyRootNetworkManager rootNetworkMgr) {
this.filter = filter;
this.cache = cache;
this.networkReaderMgr = networkReaderMgr;
this.propertyReaderMgr = propertyReaderMgr;
this.vizmapReaderMgr = vizmapReaderMgr;
this.csvCyReaderFactory = csvCyReaderFactory;
- this.networkTableManager = networkTableManager;
+ this.networkTableMgr = networkTableMgr;
+ this.rootNetworkMgr = rootNetworkMgr;
}
@Override
@@ -83,6 +87,6 @@
@Override
public TaskIterator createTaskIterator() {
return new TaskIterator(new Cy3SessionReaderImpl(inputStream,
cache, networkReaderMgr, propertyReaderMgr,
- vizmapReaderMgr, csvCyReaderFactory,
networkTableManager));
+ vizmapReaderMgr, csvCyReaderFactory,
networkTableMgr, rootNetworkMgr));
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
2012-02-14 20:50:53 UTC (rev 28268)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
2012-02-14 22:10:59 UTC (rev 28269)
@@ -49,6 +49,7 @@
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@@ -79,6 +80,8 @@
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyTableMetadata;
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.property.CyProperty;
import org.cytoscape.property.SimpleCyProperty;
import org.cytoscape.property.bookmark.Bookmarks;
@@ -98,14 +101,15 @@
public static final Pattern GLOBAL_TABLE_PATTERN =
Pattern.compile(".*/(global/(\\d+)-([^/]+)[.]cytable)");
public static final Pattern PROPERTIES_PATTERN =
Pattern.compile(".*/"+PROPERTIES_FOLDER+"?(([^/]+)[.](props|properties))");
- private final Map<Long/*network_suid*/, CyNetwork> networkLookup = new
HashMap<Long, CyNetwork>();
+ private final Map<Long/*network_suid*/, CyNetwork> networkLookup = new
LinkedHashMap<Long, CyNetwork>();
private final Map<Long/*old_network_id*/, Set<CyTableMetadataBuilder>>
networkTableMap = new HashMap<Long, Set<CyTableMetadataBuilder>>();
private final CyNetworkReaderManager networkReaderMgr;
private final CyPropertyReaderManager propertyReaderMgr;
private final VizmapReaderManager vizmapReaderMgr;
private final CSVCyReaderFactory csvCyReaderFactory;
- private final CyNetworkTableManager networkTableManager;
+ private final CyNetworkTableManager networkTableMgr;
+ private final CyRootNetworkManager rootNetworkMgr;
private Map<String, CyTable> filenameTableMap;
private Map<CyTableMetadataBuilder, String> builderFilenameMap;
@@ -120,7 +124,8 @@
final
CyPropertyReaderManager propertyReaderMgr,
final
VizmapReaderManager vizmapReaderMgr,
final
CSVCyReaderFactory csvCyReaderFactory,
- final
CyNetworkTableManager networkTableManager) {
+ final
CyNetworkTableManager networkTableMgr,
+ final
CyRootNetworkManager rootNetworkMgr) {
super(sourceInputStream, cache);
if (networkReaderMgr == null) throw new
NullPointerException("network reader manager is null!");
@@ -135,8 +140,11 @@
if (csvCyReaderFactory == null) throw new
NullPointerException("table reader manager is null!");
this.csvCyReaderFactory = csvCyReaderFactory;
- if (networkTableManager == null) throw new
NullPointerException("network table manager is null!");
- this.networkTableManager = networkTableManager;
+ if (networkTableMgr == null) throw new
NullPointerException("network table manager is null!");
+ this.networkTableMgr = networkTableMgr;
+
+ if (rootNetworkMgr == null) throw new
NullPointerException("root network manager is null!");
+ this.rootNetworkMgr = rootNetworkMgr;
filenameTableMap = new HashMap<String, CyTable>();
builderFilenameMap = new HashMap<CyTableMetadataBuilder,
String>();
@@ -283,8 +291,14 @@
CyNetwork[] netArray = reader.getNetworks();
for (CyNetwork net : netArray) {
+ // Add its root-network to the lookup map first
+ CyRootNetwork rootNet =
rootNetworkMgr.getRootNetwork(net);
+
+ if (!networkLookup.containsKey(rootNet.getSUID()));
+ networkLookup.put(rootNet.getSUID(), rootNet);
+
networkLookup.put(net.getSUID(), net);
- networks.add(net);
+ networks.add(net); // Note: do NOT add the root-network
to this set!
}
}
@@ -466,7 +480,7 @@
return; // TODO: disabled due to timing conflicts with
Ding (The VIEW tables are not created yet).
}
- Map<String, CyTable> tableMap =
networkTableManager.getTables(network, type);
+ Map<String, CyTable> tableMap =
networkTableMgr.getTables(network, type);
CyTable targetTable = tableMap.get(namespace);
CyTable sourceTable = builder.getTable();
mergeTables(sourceTable, targetTable, type);
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/CyTableMetadataImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/CyTableMetadataImpl.java
2012-02-14 20:50:53 UTC (rev 28268)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/CyTableMetadataImpl.java
2012-02-14 22:10:59 UTC (rev 28269)
@@ -87,5 +87,11 @@
public Class<?> getType() {
return type;
}
+
+ @Override
+ public String toString() {
+ return "CyTableMetadataBuilder [type=" + type + ",
namespace=" + namespace + ", table=" + table
+ + ", network=" + network + "]";
+ }
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdge.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdge.java
2012-02-14 20:50:53 UTC (rev 28268)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdge.java
2012-02-14 22:10:59 UTC (rev 28269)
@@ -30,6 +30,7 @@
import org.cytoscape.io.internal.read.xgmml.ParseState;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
@@ -96,7 +97,19 @@
label = String.format("%s (%s) %s", sourceId,
(directed ? "directed" : "undirected"), targetId);
if (sourceNode != null && targetNode != null) {
- manager.createEdge(sourceNode, targetNode, id,
label, interaction, directed);
+ final CyEdge edge =
manager.createEdge(sourceNode, targetNode, id, label, directed);
+
+ if (!manager.isSessionFormat() ||
manager.getDocumentVersion() < 3.0) {
+ CyRow row =
manager.getCurrentNetwork().getRow(edge);
+ row.set(CyEdge.NAME, label);
+ row.set(CyEdge.INTERACTION,
interaction);
+
+ if (manager.getRootNetwork() != null &&
manager.getCurrentNetwork() != manager.getRootNetwork()) {
+ row =
manager.getRootNetwork().getRow(edge);
+ row.set(CyEdge.NAME, label);
+ row.set(CyEdge.INTERACTION,
interaction);
+ }
+ }
} else {
throw new SAXException("Cannot create edge from
XGMML (id=" + id + " label=" + label + " source=" +
sourceId + " target=" + targetId + "): source or target node not found");
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNode.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNode.java
2012-02-14 20:50:53 UTC (rev 28268)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNode.java
2012-02-14 22:10:59 UTC (rev 28269)
@@ -30,6 +30,7 @@
import org.cytoscape.io.internal.read.xgmml.ParseState;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
import org.cytoscape.model.subnetwork.CySubNetwork;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
@@ -51,6 +52,14 @@
label = atts.getValue("name"); // For backwards
compatibility
node = manager.createNode(id, label);
+
+ if ( label != null && (!manager.isSessionFormat() ||
manager.getDocumentVersion() < 3.0) ) {
+
manager.getCurrentNetwork().getRow(node).set(CyNode.NAME, label);
+
+ if (manager.getRootNetwork() != null &&
manager.getCurrentNetwork() != manager.getRootNetwork()) {
+
manager.getRootNetwork().getRow(node).set(CyNode.NAME, label);
+ }
+ }
} else {
// Try to get the node from the internal cache
final Long id = AttributeValueUtil.getIdFromXLink(href);
@@ -58,7 +67,6 @@
if (node != null) {
CyNetwork net = manager.getCurrentNetwork();
- label =
manager.getRootNetwork().getRow(node).get(CyNode.NAME, String.class);
if (net instanceof CySubNetwork)
((CySubNetwork) net).addNode(node);
@@ -71,14 +79,6 @@
}
}
- if ( label != null && (!manager.isSessionFormat() ||
manager.getDocumentVersion() < 3.0) ) {
-
manager.getCurrentNetwork().getRow(node).set(CyNode.NAME, label);
-
- if (manager.getRootNetwork() != null &&
manager.getCurrentNetwork() != manager.getRootNetwork()) {
-
manager.getRootNetwork().getRow(node).set(CyNode.NAME, label);
- }
- }
-
return current;
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2012-02-14 20:50:53 UTC (rev 28268)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2012-02-14 22:10:59 UTC (rev 28269)
@@ -430,8 +430,7 @@
return node;
}
- protected CyEdge createEdge(CyNode source, CyNode target, Object id,
String label, String interaction,
- boolean directed) {
+ protected CyEdge createEdge(final CyNode source, final CyNode target,
Object id, String label, boolean directed) {
CyEdge edge = null;
if (id == null) id = label;
@@ -477,14 +476,6 @@
edge = net.addEdge(actualSrc, actualTgt, directed);
this.currentEdge = edge;
this.currentRow = net.getRow(edge);
-
- if (getDocumentVersion() < 3.0 || !isSessionFormat()) {
- CyRow row = net.getRow(edge);
- row.set(CyEdge.NAME, label);
-
- if (interaction != null)
- row.set(CyEdge.INTERACTION,
interaction);
- }
}
// Add to internal cache:
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/session/VirtualColumnSerializer.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/session/VirtualColumnSerializer.java
2012-02-14 20:50:53 UTC (rev 28268)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/session/VirtualColumnSerializer.java
2012-02-14 22:10:59 UTC (rev 28269)
@@ -100,4 +100,10 @@
String.valueOf(isImmutable));
}
+
+ @Override
+ public String toString() {
+ return "VirtualColumnSerializer [name=" + name + ",
sourceTable=" + sourceTable + ", targetTable="
+ + targetTable + ", sourceColumn=" +
sourceColumn + "]";
+ }
}
\ No newline at end of file
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