Author: clopes
Date: 2012-02-10 12:37:43 -0800 (Fri, 10 Feb 2012)
New Revision: 28236
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
Log:
Partial fix for bug #674 (Node/edge selection is not restored correctly when
opening 2.x sessions): node selection is correctly restored now, but not the
selected edges.
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
2012-02-10 17:58:01 UTC (rev 28235)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
2012-02-10 20:37:43 UTC (rev 28236)
@@ -49,7 +49,6 @@
import java.net.URLDecoder;
import java.util.ArrayList;
import java.util.HashMap;
-import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Properties;
@@ -116,10 +115,10 @@
protected Cysession cysession;
private final Map<String, CyNetwork> networkLookup = new
HashMap<String, CyNetwork>();
private final Map<String, CyNetworkView> networkViewLookup = new
HashMap<String, CyNetworkView>();
+ private final Map<String, List<Node>> nodeSelectionLookup = new
HashMap<String, List<Node>>();
+ private final Map<String, List<Edge>> edgeSelectionLookup = new
HashMap<String, List<Edge>>();
private Map<String, String> xgmmlEntries;
- /**
- */
public Cy2SessionReaderImpl(final InputStream sourceInputStream,
final ReadCache
cache,
final
CyNetworkReaderManager networkReaderMgr,
@@ -294,6 +293,7 @@
topNetwork = netArray[0];
for (int i = 0; i < netArray.length; i++) {
+ // Process each CyNetwork
CyNetwork net = netArray[i];
String netName =
net.getRow(net).get(CyNetwork.NAME, String.class);
networkLookup.put(netName, net);
@@ -308,6 +308,15 @@
row.set(CY2_PARENT_NETWORK_COLUMN,
parent.getSUID());
}
+ // Restore node/edge selection
+ List<Node> selNodes =
nodeSelectionLookup.get(netName);
+ List<Edge> selEdges =
edgeSelectionLookup.get(netName);
+
+ if (selNodes != null)
+ setBooleanNodeAttr(net, selNodes,
SELECTED, DEFAULT_ATTRS);
+ if (selEdges != null)
+ setBooleanEdgeAttr(net, selEdges,
SELECTED, DEFAULT_ATTRS);
+
// TODO: handle 2.x groups
// if (i == 0) {
// // Sub-networks (other than the
base-network) generated from the same 2.x XGMML file
@@ -422,6 +431,30 @@
cysession = (Cysession) reader.getProperty();
if (cysession != null) {
+ // Create map of selected elements:
+ // Network attributes and visual styles
+ if (cysession.getNetworkTree() != null) {
+ for (final Network net :
cysession.getNetworkTree().getNetwork()) {
+ // We no longer have the concept of one
top-level network root,
+ // so let's ignore a network with that
name.
+ if (net.getId().equals(NETWORK_ROOT))
+ continue;
+
+ final String netName = net.getId();
+ List<Node> selNodes = null;
+ List<Edge> selEdges = null;
+
+ if (net.getSelectedNodes() != null)
+ selNodes =
net.getSelectedNodes().getNode();
+ if (net.getSelectedEdges() != null)
+ selEdges =
net.getSelectedEdges().getEdge();
+
+ nodeSelectionLookup.put(netName,
selNodes);
+ edgeSelectionLookup.put(netName,
selEdges);
+ }
+ }
+
+
// Convert the old cysession to core the required 3.0
core plugin files:
// Actually we just need to extract the "networkFrames"
and "cytopanels" data from the Cysession object
// and write an XML file that will be parsed by
swing-application.
@@ -493,17 +526,11 @@
final CyNetwork cyNet = getNetwork(netName);
if (cyNet != null) {
- // From Cytoscape 3.0, the selection
and hidden attributes are stored inside CyTables.
- if (net.getSelectedNodes() != null)
- setBooleanNodeAttr(cyNet,
net.getSelectedNodes().getNode().iterator(), SELECTED, DEFAULT_ATTRS);
- if (net.getSelectedEdges() != null)
- setBooleanEdgeAttr(cyNet,
net.getSelectedEdges().getEdge().iterator(), SELECTED, DEFAULT_ATTRS);
-
// TODO: disabled due to timing
conflicts with Ding (The VIEW tables are not created yet).
// if (net.getHiddenNodes() != null)
-// setBooleanNodeAttr(cyNet,
net.getHiddenNodes().getNode().iterator(), "hidden", "VIEW");
+// setBooleanNodeAttr(cyNet,
net.getHiddenNodes().getNode(), "hidden", "VIEW");
// if (net.getHiddenEdges() != null)
-// setBooleanEdgeAttr(cyNet,
net.getHiddenEdges().getEdge().iterator(), "hidden", "VIEW");
+// setBooleanEdgeAttr(cyNet,
net.getHiddenEdges().getEdge(), "hidden", "VIEW");
}
// Populate the visual style map
@@ -584,38 +611,37 @@
return null;
}
- private void setBooleanNodeAttr(final CyNetwork net, Iterator<?> it,
final String attrName, final String tableName) {
- if (it == null)
- return;
+ private void setBooleanNodeAttr(final CyNetwork net, final List<Node>
nodes, final String attrName,
+ final String tableName) {
+ if (net != null && nodes != null) {
+ // set attr values based on ids
+ for (final Node nodeObject : nodes) {
+ String name = nodeObject.getId();
+ // The XGMML node "id" is only used internally,
by the XGMML parser--the name is the real ID.
+ CyNode n = cache.getNodeByName(name);
- // set attr values based on ids
- while (it.hasNext()) {
- final Node nodeObject = (Node) it.next();
- String name = nodeObject.getId();
- CyNode n = cache.getNodeByName(name); // The XGMML node
"id" is only used internally, by the XGMML parser.
-
- if (n != null)
- net.getRow(n, tableName).set(attrName, true);
- else
- logger.error("Cannot restore boolean node attr
\"" + name + "\": node not found.");
+ if (n != null)
+ net.getRow(n, tableName).set(attrName,
true);
+ else
+ logger.error("Cannot restore boolean
node attr \"" + name + "\": node not found.");
+ }
}
}
- private void setBooleanEdgeAttr(final CyNetwork net, final Iterator<?>
it, final String attrName,
+ private void setBooleanEdgeAttr(final CyNetwork net, final List<Edge>
edges, final String attrName,
final String tableName) {
- if (it == null)
- return;
+ if (net != null && edges != null) {
+ // set attr values based on ids
+ for (final Edge edgeObject : edges) {
+ String name = edgeObject.getId();
+ // In 2.x, XGMML edge elements have no "id"
attribute--the label is the id.
+ CyEdge e = cache.getEdge(name);
- // set attr values based on ids
- while (it.hasNext()) {
- final Edge edgeObject = (Edge) it.next();
- String name = edgeObject.getId();
- CyEdge e = cache.getEdge(name); // In 2.x, XGMML edge
elements have no "id" attribute--the label is the id.
-
- if (e != null)
- net.getRow(e, tableName).set(attrName, true);
- else
- logger.error("Cannot restore boolean edge attr
\"" + name + "\": node not found.");
+ if (e != null)
+ net.getRow(e, tableName).set(attrName,
true);
+ else
+ logger.error("Cannot restore boolean
edge attr \"" + name + "\": node not found.");
+ }
}
}
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