Author: clopes
Date: 2011-12-06 11:17:14 -0800 (Tue, 06 Dec 2011)
New Revision: 27706
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraph.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraphDone.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNodeGraph.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
Log:
Fixed XGMML parser exception when creating edges whose source or target nodes
are written under a parent graph tag.
It also fixes the missing "name" (default table) values in sub-networks
restored from 2.x session files.
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraph.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraph.java
2011-12-06 18:28:30 UTC (rev 27705)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraph.java
2011-12-06 19:17:14 UTC (rev 27706)
@@ -110,6 +110,8 @@
if (!(net instanceof CyRootNetwork))
manager.addNetwork(oldId, net);
+
+ manager.getNetworkStack().push(net);
}
/**
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraphDone.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraphDone.java
2011-12-06 18:28:30 UTC (rev 27705)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleGraphDone.java
2011-12-06 19:17:14 UTC (rev 27706)
@@ -19,6 +19,14 @@
@Override
public ParseState handle(String tag, Attributes atts, ParseState
current) throws SAXException {
+ // In order to handle sub-graphs correctly
+ if (!manager.getNetworkStack().isEmpty())
+ manager.getNetworkStack().pop();
+
+ final CyNetwork currentNet =
manager.getNetworkStack().isEmpty() ? null : manager.getNetworkStack().peek();
+ manager.setCurrentNetwork(currentNet);
+
+ // End of document
if (++manager.graphDoneCount != manager.graphCount)
return current;
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNodeGraph.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNodeGraph.java
2011-12-06 18:28:30 UTC (rev 27705)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNodeGraph.java
2011-12-06 19:17:14 UTC (rev 27706)
@@ -15,6 +15,7 @@
@Override
public ParseState handle(String tag, Attributes atts, ParseState current)
throws SAXException {
ParseState state = current;
+ manager.graphCount++;
final CyNode node = manager.currentNode;
final String href = atts.getValue(ReadDataManager.XLINK,
"href");
@@ -22,7 +23,7 @@
if (href != null) {
// The network has already been created
- netId = href.replaceAll(".*#", "");
+ netId = AttributeValueUtil.getIdFromXLink(href);
} else {
netId = atts.getValue("id");
// Create network
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
2011-12-06 18:28:30 UTC (rev 27705)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2011-12-06 19:17:14 UTC (rev 27706)
@@ -16,6 +16,7 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.Stack;
import org.cytoscape.equations.Equation;
import org.cytoscape.equations.EquationCompiler;
@@ -59,6 +60,7 @@
private Map<String, CyEdge> edgeIdMap;
/* Map of XML ID's to networks */
private Map<String, CyNetwork> networkIdMap;
+ private Stack<CyNetwork> networkStack;
private Map<CyNetwork, Set<String>> nodeLinkMap;
private Map<CyNetwork, Set<String>> edgeLinkMap;
@@ -148,6 +150,7 @@
nodeIdMap = new HashMap<String, CyNode>();
edgeIdMap = new HashMap<String, CyEdge>();
networkIdMap = new HashMap<String, CyNetwork>();
+ networkStack = new Stack<CyNetwork>();
nodeLinkMap = new HashMap<CyNetwork, Set<String>>();
edgeLinkMap = new HashMap<CyNetwork, Set<String>>();
@@ -375,6 +378,10 @@
return this.currentNetwork;
}
+ protected Stack<CyNetwork> getNetworkStack() {
+ return networkStack;
+ }
+
protected CyRootNetwork createRootNetwork() {
final CyNetwork baseNet = networkFactory.createNetwork();
final CyRootNetwork rootNetwork =
rootNetworkManager.getRootNetwork(baseNet);
@@ -400,6 +407,7 @@
if (index != null) {
node = this.getParentNetwork().getNode(index);
((CySubNetwork) this.getCurrentNetwork()).addNode(node);
+ node = this.getCurrentNetwork().getNode(index); // in
order to return the correct instance!
}
}
@@ -419,18 +427,41 @@
CyEdge edge = null;
if (this.getCurrentNetwork() instanceof CySubNetwork &&
this.getParentNetwork() != null) {
- // Do not create the element again if the network is a
sub-network!
+ // Do not create the element again if the network is a
sub-network and the edge already exists!
Integer index = this.getIndex(id);
if (index != null) {
edge = this.getParentNetwork().getEdge(index);
((CySubNetwork) this.getCurrentNetwork()).addEdge(edge);
+ edge = this.getCurrentNetwork().getEdge(index); // in
order to return the correct instance!
}
}
if (edge == null) {
// OK, create it
- edge = this.getCurrentNetwork().addEdge(source, target,
directed);
+ CyNetwork net = getCurrentNetwork();
+ // But first get the actual source/target instances from the
current network,
+ // because both node instances have to belong to the same root
or sub-network.
+ CyNode actualSrc = net.getNode(source.getIndex());
+ CyNode actualTgt = net.getNode(target.getIndex());
+
+ if (actualSrc == null || actualTgt == null) {
+ if ((getDocumentVersion() < 3.0 ||
!isSessionFormat()) && (net == getRootNetwork().getBaseNetwork())) {
+ // The nodes might have been added to the root
network only, but not the base one in this case,
+ // because the root-graph element of old and
generic XGMML formats are handled as base-network in 3.0
+ // (3.0 session XGMML has the root-graph as the
CyRootNetwork, though).
+ if (actualSrc == null) {
+ ((CySubNetwork) net).addNode(source);
+ actualSrc =
net.getNode(source.getIndex());
+ }
+ if (actualTgt == null) {
+ ((CySubNetwork) net).addNode(target);
+ actualTgt =
net.getNode(target.getIndex());
+ }
+ }
+ }
+
+ edge = this.getCurrentNetwork().addEdge(actualSrc,
actualTgt, directed);
}
// Add to internal cache
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
