Author: scooter
Date: 2012-08-24 14:54:43 -0700 (Fri, 24 Aug 2012)
New Revision: 30274
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/GroupUtil.java
Log:
Since XGMML doesn't export root network attributes, move values to
CySubNetwork
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/GroupUtil.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/GroupUtil.java
2012-08-24 21:51:08 UTC (rev 30273)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/GroupUtil.java
2012-08-24 21:54:43 UTC (rev 30274)
@@ -73,16 +73,17 @@
externalEdgeSUIDs.add(edge.getSUID());
}
- // We need to use the root network to get the
row because the group might be expanded
- CyRow groupNodeRow =
rootNetwork.getRow(groupNode, CyNetwork.HIDDEN_ATTRS);
+ // We need to use the sub network to get the
row because the group might be expanded
+ final CyNetwork netPointer =
groupNode.getNetworkPointer();
+ final CyRow snRow =
netPointer.getRow(netPointer, CyNetwork.HIDDEN_ATTRS);
// Make sure our column exists
- CyTable hiddenNodeTable =
groupNodeRow.getTable();
- if
(hiddenNodeTable.getColumn(EXTERNAL_EDGE_ATTRIBUTE) == null) {
-
hiddenNodeTable.createListColumn(EXTERNAL_EDGE_ATTRIBUTE, Long.class, false);
+ CyTable groupNetTable = snRow.getTable();
+ if
(groupNetTable.getColumn(EXTERNAL_EDGE_ATTRIBUTE) == null) {
+
groupNetTable.createListColumn(EXTERNAL_EDGE_ATTRIBUTE, Long.class, false);
}
- groupNodeRow.set(EXTERNAL_EDGE_ATTRIBUTE,
externalEdgeSUIDs);
+ snRow.set(EXTERNAL_EDGE_ATTRIBUTE,
externalEdgeSUIDs);
}
}
}
@@ -113,9 +114,9 @@
// Retrieve the internal nodes and edges
final CyRow dnRow = net.getRow(n,
CyNetwork.DEFAULT_ATTRS);
final CyRow hnRow = net.getRow(n,
CyNetwork.HIDDEN_ATTRS);
- final CyRow rnRow = rootNet.getRow(n,
CyNetwork.HIDDEN_ATTRS);
+ final CyRow snRow = netPointer.getRow(netPointer,
CyNetwork.HIDDEN_ATTRS);
if (!dnRow.isSet(GROUP_STATE_ATTRIBUTE) &&
!hnRow.isSet(GROUP_STATE_ATTRIBUTE)
- && !hnRow.isSet(GROUP_COLLAPSED_ATTRIBUTE))
+ && !snRow.isSet(GROUP_COLLAPSED_ATTRIBUTE))
return;
boolean collapsed = false;
@@ -132,13 +133,19 @@
}
// Check to make sure the column exists
- if
(hnRow.getTable().getColumn(GROUP_COLLAPSED_ATTRIBUTE) == null) {
-
hnRow.getTable().createColumn(GROUP_COLLAPSED_ATTRIBUTE, Boolean.class, false);
+ if
(snRow.getTable().getColumn(GROUP_COLLAPSED_ATTRIBUTE) == null) {
+ CyTable snTable = snRow.getTable();
+
snTable.createListColumn(GROUP_COLLAPSED_ATTRIBUTE, String.class, false);
}
- if (!hnRow.isSet(GROUP_COLLAPSED_ATTRIBUTE)) {
- // This is a 2.x group. We need to recreate
the 3.x structure
- hnRow.set(GROUP_COLLAPSED_ATTRIBUTE, collapsed);
+ // If we're a Cy2 import, create the Cy3 structure
+ if (cy2group) {
+ String netName = net.getRow(net).get(CyNetwork.NAME,
String.class);
+ if (netName == null) netName = "(null)"; // Handle the
unnamed network
+
+ List<String> list = new ArrayList<String>();
+ list.add(netName+":"+collapsed);
+ snRow.set(GROUP_COLLAPSED_ATTRIBUTE, list);
}
// Create the group
@@ -146,8 +153,8 @@
// Add in the missing external edges if we're collapsed
// CyRow groupNodeRow = net.getRow(n,
CyNetwork.HIDDEN_ATTRS);
- if (rnRow.isSet(EXTERNAL_EDGE_ATTRIBUTE)) {
- List<Long> externalIDs =
rnRow.getList(EXTERNAL_EDGE_ATTRIBUTE, Long.class);
+ if (snRow.isSet(EXTERNAL_EDGE_ATTRIBUTE)) {
+ List<Long> externalIDs =
snRow.getList(EXTERNAL_EDGE_ATTRIBUTE, Long.class);
List<CyEdge> externalEdges = new
ArrayList<CyEdge>();
for (Long suid: externalIDs) {
@@ -196,7 +203,7 @@
public void updateGroupNodes(final CyNetworkView view) {
if (view == null) return;
-
+
CyNetwork network = view.getModel();
Set<CyGroup> groupSet = groupMgr.getGroupSet(network);
--
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