Author: clopes
Date: 2011-12-02 16:02:50 -0800 (Fri, 02 Dec 2011)
New Revision: 27684
Modified:
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CyActivator.java
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
Log:
Added changes to make it possible to save networks without views and
CyRootNetwork tables.
Modified:
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CyActivator.java
2011-12-02 23:59:40 UTC (rev 27683)
+++
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CyActivator.java
2011-12-03 00:02:50 UTC (rev 27684)
@@ -1,32 +1,22 @@
-
-
-
-
package org.cytoscape.session.internal;
-import org.cytoscape.view.vizmap.VisualMappingManager;
+import java.util.Properties;
+
import org.cytoscape.event.CyEventHelper;
-import org.cytoscape.model.CyTableManager;
-import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyNetworkTableManager;
-
-import org.cytoscape.session.internal.CySessionManagerImpl;
-import org.cytoscape.session.internal.CyNetworkNamingImpl;
-
-import org.cytoscape.session.CySessionManager;
-import org.cytoscape.session.CyNetworkNaming;
-
+import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.property.CyProperty;
-
+import org.cytoscape.service.util.AbstractCyActivator;
+import org.cytoscape.session.CyNetworkNaming;
+import org.cytoscape.session.CySessionManager;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.vizmap.VisualMappingManager;
import org.osgi.framework.BundleContext;
-import org.cytoscape.service.util.AbstractCyActivator;
-import java.util.Properties;
-
-
public class CyActivator extends AbstractCyActivator {
public CyActivator() {
super();
@@ -40,9 +30,10 @@
VisualMappingManager visualMappingManagerServiceRef =
getService(bc,VisualMappingManager.class);
CyNetworkViewManager cyNetworkViewManagerServiceRef =
getService(bc,CyNetworkViewManager.class);
CyNetworkTableManager cyNetworkTableManagerServiceRef =
getService(bc,CyNetworkTableManager.class);
+ CyRootNetworkManager cyRootNetworkManagerServiceRef =
getService(bc,CyRootNetworkManager.class);
CyNetworkNamingImpl cyNetworkNaming = new
CyNetworkNamingImpl(cyNetworkManagerServiceRef);
- CySessionManagerImpl cySessionManager = new
CySessionManagerImpl(cyEventHelperServiceRef,cyNetworkManagerServiceRef,cyTableManagerServiceRef,cyNetworkTableManagerServiceRef,visualMappingManagerServiceRef,cyNetworkViewManagerServiceRef);
+ CySessionManagerImpl cySessionManager = new
CySessionManagerImpl(cyEventHelperServiceRef,cyNetworkManagerServiceRef,cyTableManagerServiceRef,cyNetworkTableManagerServiceRef,visualMappingManagerServiceRef,cyNetworkViewManagerServiceRef,cyRootNetworkManagerServiceRef);
registerService(bc,cyNetworkNaming,CyNetworkNaming.class, new
Properties());
registerService(bc,cySessionManager,CySessionManager.class, new
Properties());
Modified:
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
===================================================================
---
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
2011-12-02 23:59:40 UTC (rev 27683)
+++
core3/impl/trunk/session-impl/src/main/java/org/cytoscape/session/internal/CySessionManagerImpl.java
2011-12-03 00:02:50 UTC (rev 27684)
@@ -37,15 +37,17 @@
import java.io.File;
import java.math.BigInteger;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Properties;
import java.util.Set;
-import java.util.Map.Entry;
import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
@@ -56,6 +58,8 @@
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyTableManager;
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.bookmark.Bookmarks;
import org.cytoscape.property.session.Cysession;
@@ -91,6 +95,7 @@
private final CyNetworkTableManager netTblMgr;
private final VisualMappingManager vmMgr;
private final CyNetworkViewManager nvMgr;
+ private final CyRootNetworkManager rootNetMgr;
private final Map<CyProperty<?>, Map<String, String>> sessionProperties;
@@ -101,13 +106,15 @@
final
CyTableManager tblMgr,
final
CyNetworkTableManager netTblMgr,
final
VisualMappingManager vmMgr,
- final
CyNetworkViewManager nvMgr) {
+ final
CyNetworkViewManager nvMgr,
+ final
CyRootNetworkManager rootNetMgr) {
this.cyEventHelper = cyEventHelper;
this.netMgr = netMgr;
this.tblMgr = tblMgr;
this.netTblMgr = netTblMgr;
this.vmMgr = vmMgr;
this.nvMgr = nvMgr;
+ this.rootNetMgr = rootNetMgr;
sessionProperties = new HashMap<CyProperty<?>, Map<String,
String>>();
}
@@ -119,6 +126,7 @@
cyEventHelper.fireEvent(savingEvent);
CysessionFactory cysessFactory = new CysessionFactory(netMgr,
nvMgr, vmMgr);
+ Set<CyNetwork> networks = netMgr.getNetworkSet();
Set<CyNetworkView> netViews = nvMgr.getNetworkViewSet();
// Visual Styles Map
@@ -143,24 +151,48 @@
Properties props = getProperties();
Bookmarks bkmarks = getBookmarks();
- Set<CyTableMetadata> metadata = buildMetadata(tables, netViews);
+ Set<CyTableMetadata> metadata = buildMetadata(tables, networks);
// Build the session
CySession sess = new
CySession.Builder().cytoscapeProperties(props).bookmarks(bkmarks).cysession(cysess)
-
.pluginFileListMap(pluginMap).tables(metadata).networkViews(netViews).visualStyles(styles)
- .viewVisualStyleMap(stylesMap).build();
+
.pluginFileListMap(pluginMap).tables(metadata).networks(networks).networkViews(netViews)
+
.visualStyles(styles).viewVisualStyleMap(stylesMap).build();
return sess;
}
- private Set<CyTableMetadata> buildMetadata(Set<CyTable> tables,
Set<CyNetworkView> netViews) {
+ @SuppressWarnings("unchecked")
+ private static Class<? extends CyTableEntry>[] TYPES = new Class[] {
CyNetwork.class, CyNode.class, CyEdge.class };
+
+ private Set<CyTableMetadata> buildMetadata(Set<CyTable> tables,
Set<CyNetwork> networks) {
Set<CyTableMetadata> result = new HashSet<CyTableMetadata>();
+ // Clone the networks and tables to add the root-networks
without changing the original sets:
+ Set<CyNetwork> allNetworks = new HashSet<CyNetwork>(networks);
+ Set<CyTable> allTables = new HashSet<CyTable>(tables);
+
+ // Add the root-networks, which are not included in the
original networks set:
+ for (CyNetwork network : networks) {
+ if (!(network instanceof CyRootNetwork)) {
+ CyRootNetwork rootNet =
rootNetMgr.getRootNetwork(network);
+
+ if (!allNetworks.contains(rootNet)) {
+ allNetworks.add(rootNet);
+
+ for (Class<? extends CyTableEntry> type
: TYPES) {
+ Map<String, CyTable> tableMap =
netTblMgr.getTables(rootNet, type);
+
allTables.addAll(tableMap.values());
+ }
+ }
+ }
+ }
+
// Figure out which tables aren't associated with networks
- Map<CyTable, Set<CyTableMetadata>> networkTables =
getNetworkTables(netViews);
+ Map<CyTable, Set<CyTableMetadata>> networkTables =
getNetworkTables(allNetworks);
// Merge network/global metadata into a single set
- for (CyTable table : tables) {
+ for (CyTable table : allTables) {
Set<CyTableMetadata> metadataSet =
networkTables.get(table);
+
if (metadataSet == null || metadataSet.size() == 0) {
result.add(new
CyTableMetadataImpl.CyTableMetadataBuilder().setCyTable(table));
} else {
@@ -169,26 +201,26 @@
}
}
}
+
return result;
}
- @SuppressWarnings("unchecked")
- private static Class<? extends CyTableEntry>[] TYPES = new Class[] {
CyNetwork.class, CyNode.class, CyEdge.class };
-
- private Map<CyTable, Set<CyTableMetadata>>
getNetworkTables(Set<CyNetworkView> views) {
+ private Map<CyTable, Set<CyTableMetadata>> getNetworkTables(final
Set<CyNetwork> networks) {
Map<CyTable, Set<CyTableMetadata>> result = new
HashMap<CyTable, Set<CyTableMetadata>>();
- for (CyNetworkView view : views) {
- CyNetwork network = view.getModel();
+
+ for (CyNetwork network : networks) {
for (Class<? extends CyTableEntry> type : TYPES) {
Map<String, CyTable> tableMap =
netTblMgr.getTables(network, type);
+
for (Entry<String, CyTable> entry :
tableMap.entrySet()) {
CyTable table = entry.getValue();
+ Set<CyTableMetadata> metadataSet =
result.get(table);
- Set<CyTableMetadata> metadataSet =
result.get(table);
if (metadataSet == null) {
metadataSet = new
HashSet<CyTableMetadata>();
result.put(table, metadataSet);
}
+
String namespace = entry.getKey();
metadataSet.add(new
CyTableMetadataImpl.CyTableMetadataBuilder()
.setCyTable(table)
@@ -199,6 +231,7 @@
}
}
}
+
return result ;
}
@@ -224,11 +257,12 @@
} else {
logger.debug("Restoring the session...");
restoreNetworks(sess);
+ restoreNetworkViews(sess);
restoreTables(sess);
restoreVisualStyles(sess);
- restoreSelection(sess);
+// restoreSelection(sess);
}
-
+
currentSession = sess;
currentFileName = fileName;
@@ -239,6 +273,7 @@
// Register global tables
for (CyTableMetadata metadata : sess.getTables()) {
CyNetwork network = metadata.getCyNetwork();
+
if (network == null) {
tblMgr.addTable(metadata.getCyTable());
}
@@ -292,13 +327,24 @@
private void restoreNetworks(CySession sess) {
logger.debug("Restoring networks...");
- Set<CyNetworkView> netViews = sess.getNetworkViews();
+ Set<CyNetwork> networks = sess.getNetworks();
- for (CyNetworkView nv : netViews) {
- netMgr.addNetwork(nv.getModel());
- nvMgr.addNetworkView(nv);
+ for (CyNetwork n : networks) {
+ netMgr.addNetwork(n);
}
}
+
+ private void restoreNetworkViews(CySession sess) {
+ logger.debug("Restoring network views...");
+ Set<CyNetworkView> netViews = sess.getNetworkViews();
+
+ if (netViews != null) {
+ for (CyNetworkView nv : netViews) {
+ if (nv != null)
+ nvMgr.addNetworkView(nv);
+ }
+ }
+ }
private void restoreVisualStyles(final CySession sess) {
logger.debug("Restoring visual styles...");
@@ -369,63 +415,63 @@
}
if (version < 3.0) {
- logger.debug("Restoring node/edge selection...");
+// logger.debug("Restoring node/edge selection...");
+//
+// // First create network_title -> element_name lookup
maps
+// final Map<String, Set<String>> selectedNodesMap = new
HashMap<String, Set<String>>();
+// final Map<String, Set<String>> selectedEdgesMap = new
HashMap<String, Set<String>>();
+// final List<Network> networks =
cysess.getNetworkTree().getNetwork();
+//
+// for (Network net : networks) {
+// String netTitle = net.getId();
+//
+// if (net.getSelectedNodes() != null) {
+// // Store selected node names for future
reference
+// Set<String> selectedNodes = new
HashSet<String>();
+// selectedNodesMap.put(netTitle,
selectedNodes);
+//
+// for (Node n :
net.getSelectedNodes().getNode()) {
+// selectedNodes.add(n.getId());
+// }
+// }
+//
+// if (net.getSelectedEdges() != null) {
+// // Store selected edge names for future
reference
+// Set<String> selectedEdges = new
HashSet<String>();
+// selectedEdgesMap.put(netTitle,
selectedEdges);
+//
+// for (Edge e :
net.getSelectedEdges().getEdge()) {
+// selectedEdges.add(e.getId());
+// }
+// }
+// }
- // First create network_title -> element_name lookup
maps
- final Map<String, Set<String>> selectedNodesMap = new
HashMap<String, Set<String>>();
- final Map<String, Set<String>> selectedEdgesMap = new
HashMap<String, Set<String>>();
- final List<Network> networks =
cysess.getNetworkTree().getNetwork();
-
- for (Network net : networks) {
- String netTitle = net.getId();
-
- if (net.getSelectedNodes() != null) {
- // Store selected node names for future
reference
- Set<String> selectedNodes = new
HashSet<String>();
- selectedNodesMap.put(netTitle,
selectedNodes);
-
- for (Node n :
net.getSelectedNodes().getNode()) {
- selectedNodes.add(n.getId());
- }
- }
-
- if (net.getSelectedEdges() != null) {
- // Store selected edge names for future
reference
- Set<String> selectedEdges = new
HashSet<String>();
- selectedEdgesMap.put(netTitle,
selectedEdges);
-
- for (Edge e :
net.getSelectedEdges().getEdge()) {
- selectedEdges.add(e.getId());
- }
- }
- }
-
// Now iterate through all CyNodes/Edges and select the
ones that are found in the lookup maps
- Set<CyNetwork> cyNetworks = netMgr.getNetworkSet();
-
- if (cyNetworks != null) {
- for (CyNetwork cyNet : cyNetworks) {
- String netTitle =
cyNet.getCyRow().get(CyNetwork.NAME, String.class);
-
-
selectElementsByName(cyNet.getNodeList(), selectedNodesMap.get(netTitle));
-
selectElementsByName(cyNet.getEdgeList(), selectedEdgesMap.get(netTitle));
- }
- }
+// Set<CyNetwork> cyNetworks = netMgr.getNetworkSet();
+//
+// if (cyNetworks != null) {
+// for (CyNetwork cyNet : cyNetworks) {
+// String netTitle =
cyNet.getCyRow().get(CyNetwork.NAME, String.class);
+//
+//
selectElementsByName(cyNet.getNodeList(), selectedNodesMap.get(netTitle));
+//
selectElementsByName(cyNet.getEdgeList(), selectedEdgesMap.get(netTitle));
+// }
+// }
}
}
- private <T extends CyTableEntry> void selectElementsByName(List<T>
entries, Set<String> names) {
- if (entries != null && names != null) {
- for (T entry : entries) {
- CyRow row = entry.getCyRow();
+// private <T extends CyTableEntry> void selectElementsByName(List<T>
entries, Set<String> names) {
+// if (entries != null && names != null) {
+// for (T entry : entries) {
+// CyRow row = entry.getCyRow();
+//
+// if (names.contains(row.get(CyNetwork.NAME,
String.class))) {
+// row.set(CyNetwork.SELECTED, true);
+// }
+// }
+// }
+// }
- if (names.contains(row.get(CyNetwork.NAME,
String.class))) {
- row.set(CyNetwork.SELECTED, true);
- }
- }
- }
- }
-
private void disposeCurrentSession(boolean removeVisualStyles) {
logger.debug("Disposing current session...");
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