Author: clopes
Date: 2011-12-09 09:38:49 -0800 (Fri, 09 Dec 2011)
New Revision: 27750
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
Log:
Fixed setting 2.x selection values.
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
2011-12-08 23:32:19 UTC (rev 27749)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
2011-12-09 17:38:49 UTC (rev 27750)
@@ -69,6 +69,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.property.bookmark.Bookmarks;
@@ -371,21 +372,12 @@
continue;
final String netName = net.getId();
- final CyNetworkView[] views =
getNetworkViews(netName);
-
- if (views != null) {
- for (CyNetworkView nv : views) {
- String vsName =
net.getVisualStyle();
-
- if (vsName != null)
- visualStyleMap.put(nv,
vsName);
- }
- }
-
+
+ // Set attribute values that are saved in the
cysession.xml
final CyNetwork cyNet = getNetwork(netName);
if (cyNet != null) {
- // TODO: check if should delete from
network
+ // TODO: check if should delete from
sub-network
// if (net.getHiddenNodes() != null)
// setBooleanNodeAttr(cyNet,
net.getHiddenNodes().getNode().iterator(), "hidden");
// if (net.getHiddenEdges() != null)
@@ -398,6 +390,18 @@
if (net.getSelectedEdges() != null)
setBooleanEdgeAttr(cyNet,
net.getSelectedEdges().getEdge().iterator(), CyNetwork.SELECTED);
}
+
+ // Populate the visual style map
+ final CyNetworkView[] views =
getNetworkViews(netName);
+
+ if (views != null) {
+ for (CyNetworkView nv : views) {
+ String vsName =
net.getVisualStyle();
+
+ if (vsName != null)
+ visualStyleMap.put(nv,
vsName);
+ }
+ }
}
}
@@ -437,7 +441,7 @@
try {
decode = URLDecoder.decode(s, "UTF-8");
- if (decode.endsWith(name)) {
+ if (decode.equals(name)) {
// this is OK since XGMML only ever
reads one network
views = networkViewLookup.get(s);
}
@@ -460,7 +464,7 @@
return null;
}
- if (decode.endsWith("/" + name)) {
+ if (decode.equals(name)) {
return networkLookup.get(s);
}
}
@@ -475,8 +479,16 @@
// create an id map
Map<String, CyNode> nodeMap = new HashMap<String, CyNode>();
- for (CyNode n : net.getNodeList())
-
nodeMap.put(net.getCyRow(n).get(CyRootNetwork.SHARED_NAME, String.class), n);
+ for (CyNode n : net.getNodeList()) {
+ CyRow row = net.getCyRow(n);
+ String name = row.get(CyNetwork.NAME, String.class);
+
+ if (name == null) // try another column...
+ name = row.get(CyRootNetwork.SHARED_NAME,
String.class);
+
+ if (name != null)
+ nodeMap.put(name, n);
+ }
// set attr values based on ids
while (it.hasNext()) {
@@ -484,7 +496,6 @@
String name = nodeObject.getId();
CyNode n = nodeMap.get(name);
- // FIXME this fires too many events
if (n != null)
net.getCyRow(n).set(attrName, true);
else
@@ -499,8 +510,16 @@
// create an id map
Map<String, CyEdge> edgeMap = new HashMap<String, CyEdge>();
- for (CyEdge e : net.getEdgeList())
-
edgeMap.put(net.getCyRow(e).get(CyRootNetwork.SHARED_NAME, String.class), e);
+ for (CyEdge e : net.getEdgeList()){
+ CyRow row = net.getCyRow(e);
+ String name = row.get(CyNetwork.NAME, String.class);
+
+ if (name == null) // try another column...
+ name = row.get(CyRootNetwork.SHARED_NAME,
String.class);
+
+ if (name != null)
+ edgeMap.put(name, e);
+ }
// set attr values based on ids
while (it.hasNext()) {
@@ -508,7 +527,6 @@
String name = edgeObject.getId();
CyEdge e = edgeMap.get(name);
- // FIXME this fires too many events
if (e != null)
net.getCyRow(e).set(attrName, true);
else
--
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