Author: mes
Date: 2011-03-08 15:27:00 -0800 (Tue, 08 Mar 2011)
New Revision: 24342
Modified:
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/CyNodeImpl.java
Log:
added better support for groups/metanodes based on mini retreat discussion
Modified:
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
===================================================================
---
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2011-03-08 23:26:51 UTC (rev 24341)
+++
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2011-03-08 23:27:00 UTC (rev 24342)
@@ -128,10 +128,6 @@
String.class, true);
nodeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyNetwork.SELECTED,
Boolean.class, true);
-
nodeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyNode.NESTED_NETWORK_ATTR,
-
String.class, true);
-
nodeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn(CyNode.HAS_NESTED_NETWORK_ATTR,
-
Boolean.class, true);
edgeAttrMgr = new HashMap<String, CyTable>();
edgeAttrMgr.put(CyNetwork.DEFAULT_ATTRS,
@@ -835,6 +831,22 @@
/**
* {@inheritDoc}
*/
+ public CySubNetwork addSubNetwork(final Iterable<CyNode> nodes, final
Iterable<CyEdge> edges) {
+ // Only addSubNetwork() modifies the internal state of
ArrayGraph (this object),
+ // so because it's synchronized, we don't need to synchronize
this method.
+ final CySubNetwork sub = addSubNetwork();
+ if ( nodes != null )
+ for ( CyNode n : nodes )
+ sub.addNode(n);
+ if ( edges != null )
+ for ( CyEdge e : edges )
+ sub.addEdge(e);
+ return sub;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
public synchronized CySubNetwork addSubNetwork() {
final int newId = ++numSubNetworks;
final ArraySubGraph sub = new
ArraySubGraph(this,newId,eventHelper);
@@ -902,4 +914,11 @@
public CyTable getDefaultEdgeTable() {
return edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS);
}
+
+ /**
+ * {@inheritDoc}
+ */
+ public synchronized boolean containsNetwork(final CyNetwork net) {
+ return subNetworks.contains(net);
+ }
}
Modified:
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
===================================================================
---
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
2011-03-08 23:26:51 UTC (rev 24341)
+++
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
2011-03-08 23:27:00 UTC (rev 24342)
@@ -307,12 +307,13 @@
if (!parent.containsEdge(edge))
throw new IllegalArgumentException("edge is not
contained in parent network!");
- if (!containsNode(edge.getSource()))
- throw new IllegalArgumentException("source node
of edge is not contained in network!");
+ // This will:
+ // -- add the node if it doesn't already exist
+ // -- do nothing if the node does exist
+ // -- throw an exception if the node isn't part of the
root network
+ addNode(edge.getSource());
+ addNode(edge.getTarget());
- if (!containsNode(edge.getTarget()))
- throw new IllegalArgumentException("target node
of edge is not contained in network!");
-
// add edge
internalEdgeCount++;
edgeSet.add(edge);
Modified:
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/CyNodeImpl.java
===================================================================
---
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/CyNodeImpl.java
2011-03-08 23:26:51 UTC (rev 24341)
+++
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/CyNodeImpl.java
2011-03-08 23:27:00 UTC (rev 24342)
@@ -51,8 +51,6 @@
index = ind;
nestedNet = null;
this.eventHelper = eventHelper;
-
- getCyRow().set(HAS_NESTED_NETWORK_ATTR, Boolean.valueOf(false));
}
/**
@@ -74,27 +72,24 @@
return "Node suid: " + getSUID() + " index: " + index;
}
- public synchronized CyNetwork getNestedNetwork() {
+ public synchronized CyNetwork getNetwork() {
return nestedNet;
}
- public synchronized void setNestedNetwork(final CyNetwork n) {
- if (n == nestedNet)
- return;
+ public void setNetwork(final CyNetwork n) {
+ final CyNetwork orig;
+
+ synchronized (this) {
+ orig = nestedNet;
+ if (n == nestedNet)
+ return;
+ else
+ nestedNet = n;
+ }
+ if (orig != null)
+ eventHelper.fireSynchronousEvent(new
UnsetNestedNetworkEvent(this, orig));
if (nestedNet != null)
- eventHelper.fireSynchronousEvent(new
UnsetNestedNetworkEvent(this, nestedNet));
- if (n != null)
- eventHelper.fireSynchronousEvent(new
SetNestedNetworkEvent(this, n));
- nestedNet = n;
-
- final CyRow row = getCyRow();
- if (n == null) {
- row.set(NESTED_NETWORK_ATTR, null);
- row.set(HAS_NESTED_NETWORK_ATTR,
Boolean.valueOf(false));
- } else {
- row.set(NESTED_NETWORK_ATTR,
Long.valueOf(n.getSUID()).toString());
- row.set(HAS_NESTED_NETWORK_ATTR, Boolean.valueOf(true));
- }
+ eventHelper.fireSynchronousEvent(new
SetNestedNetworkEvent(this, nestedNet));
}
}
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