Author: clopes
Date: 2012-05-04 09:49:06 -0700 (Fri, 04 May 2012)
New Revision: 29105
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
Log:
Fixes #948 : The node/edge hidden state is not restored from 2.x session files
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
2012-05-04 01:36:59 UTC (rev 29104)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
2012-05-04 16:49:06 UTC (rev 29105)
@@ -86,6 +86,7 @@
import org.cytoscape.property.SimpleCyProperty;
import org.cytoscape.property.bookmark.Bookmarks;
import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.View;
import org.cytoscape.view.presentation.property.BasicVisualLexicon;
import org.cytoscape.work.TaskMonitor;
@@ -320,21 +321,16 @@
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
-// // should not be registered, because
they are probably 2.x groups.
- networks.add(net);
-
- if (i == 0 && createView) {
- // Create a network view for
the first network only,
- // which is supposed to be the
top-level one
- CyNetworkView view =
reader.buildCyNetworkView(net);
- networkViewLookup.put(netName,
view);
- networkViews.add(view);
- cache.cache(netName, view);
- }
-// }
+ networks.add(net);
+
+ if (i == 0 && createView) {
+ // Create a network view for the first
network only,
+ // which is supposed to be the
top-level one
+ CyNetworkView view =
reader.buildCyNetworkView(net);
+ networkViewLookup.put(netName, view);
+ networkViews.add(view);
+ cache.cache(netName, view);
+ }
}
}
@@ -524,26 +520,53 @@
continue;
final String netName = net.getId();
-
- // Set attribute values that are saved in the
cysession.xml
- final CyNetwork cyNet = getNetwork(netName);
-
- if (cyNet != null) {
- // TODO: disabled due to timing
conflicts with Ding (The VIEW tables are not created yet).
-// if (net.getHiddenNodes() != null)
-// setBooleanNodeAttr(cyNet,
net.getHiddenNodes().getNode(), "hidden", "VIEW");
-// if (net.getHiddenEdges() != null)
-// setBooleanEdgeAttr(cyNet,
net.getHiddenEdges().getEdge(), "hidden", "VIEW");
- }
-
- // Populate the visual style map
final CyNetworkView view =
getNetworkView(netName);
if (view != null) {
+ // Populate the visual style map
String vsName = net.getVisualStyle();
if (vsName != null)
visualStyleMap.put(view,
vsName);
+
+ // Convert 2.x hidden state
(cysession.xml) to 3.x visual properties
+ if (net.getHiddenEdges() != null) {
+ for (final Edge edgeObject :
net.getHiddenEdges().getEdge()) {
+ final String name =
edgeObject.getId();
+ final CyEdge e =
cache.getEdge(name);
+
+ if (e != null) {
+ final
View<CyEdge> ev = view.getEdgeView(e);
+
+ if (ev != null)
+
ev.setVisualProperty(BasicVisualLexicon.EDGE_VISIBLE, false);
+ else
+
logger.error("Cannot restore hidden state of edge \"" + name
+
+ "\": Edge view not found.");
+ } else {
+
logger.error("Cannot restore hidden state of edge \"" + name + "\": Edge not
found.");
+ }
+ }
+ }
+
+ if (net.getHiddenNodes() != null) {
+ for (final Node nodeObject :
net.getHiddenNodes().getNode()) {
+ final String name =
nodeObject.getId();
+ final CyNode n =
cache.getNodeByName(name);
+
+ if (n != null) {
+ final
View<CyNode> nv = view.getNodeView(n);
+
+ if (nv != null)
+
nv.setVisualProperty(BasicVisualLexicon.NODE_VISIBLE, false);
+ else
+
logger.error("Cannot restore hidden state of node \"" + name
+
+ "\": Node view not found.");
+ } else {
+
logger.error("Cannot restore hidden state of node \"" + name + "\": Node not
found.");
+ }
+ }
+ }
}
}
}
@@ -595,25 +618,6 @@
return view;
}
- private CyNetwork getNetwork(final String name) {
- for (String s : networkLookup.keySet()) {
- String decode = s;
-
- try {
- decode = URLDecoder.decode(s, "UTF-8");
- } catch (UnsupportedEncodingException e) {
- e.printStackTrace();
- return null;
- }
-
- if (decode.equals(name)) {
- return networkLookup.get(s);
- }
- }
-
- return null;
- }
-
private void setBooleanNodeAttr(final CyNetwork net, final List<Node>
nodes, final String attrName,
final String tableName) {
if (net != null && nodes != null) {
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