Author: clopes
Date: 2012-01-24 12:53:23 -0800 (Tue, 24 Jan 2012)
New Revision: 28091
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
Log:
Fixed subnetwork serialization: The base-network must be the first XGMML
subgraph element; XLINK for network pointers located in another root-network
had the wrong network file name.
Session reader: Fixed NPE that could happen when merging network tables.
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
2012-01-24 19:45:11 UTC (rev 28090)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderImpl.java
2012-01-24 20:53:23 UTC (rev 28091)
@@ -470,12 +470,14 @@
if (keyName.equals(targetKey.getName())) {
for (CyRow sourceRow : source.getAllRows()) {
Long key = sourceRow.get(keyName, Long.class);
+ Long mappedKey = null;
- if (mappings != null) {
- key = mappings.get(""+key);
- }
+ if (mappings != null)
+ mappedKey = mappings.get(""+key);
+ if (mappedKey == null)
+ mappedKey = key;
- CyRow targetRow = target.getRow(key);
+ CyRow targetRow = target.getRow(mappedKey);
mergeRow(keyName, sourceRow, targetRow);
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2012-01-24 19:45:11 UTC (rev 28090)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2012-01-24 20:53:23 UTC (rev 28091)
@@ -38,6 +38,7 @@
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
@@ -454,28 +455,21 @@
// Write a nested graph element
writeElement("<att>\n");
depth++;
-
- if (sameRoot &&
!networkMap.containsKey(netPointer)) {
- // New sub-network...
-
writeSubGraph(netPointer);
- } else {
- // This sub-network has
already been written or belongs to another XGMML file...
- String href = "#" +
netPointer.getSUID();
- if (!sameRoot) {
- // This XGMML
file will be saved as part of a CYS file,
- // and the
sub-network does NOT belong to the same root-network
- CyNetwork
baseNet = netPointerRoot.getBaseNetwork();
- // ...So add
the other base-network's file name to the XLink URI
- String fileName
= SessionUtil.getXGMMLFilename(baseNet);
- href = fileName
+ href;
- }
-
- writeElement("<graph");
-
writeAttributePair("xlink:href", href);
- write("/>\n");
+ // This sub-network has already
been written or belongs to another XGMML file...
+ String href = "#" +
netPointer.getSUID();
+
+ if (!sameRoot) {
+ // This XGMML file will
be saved as part of a CYS file,
+ // and the sub-network
does NOT belong to the same root-network
+ // ...So add the other
root-network's file name to the XLink URI
+ String fileName =
SessionUtil.getXGMMLFilename(netPointerRoot);
+ href = fileName + href;
}
+ writeElement("<graph");
+
writeAttributePair("xlink:href", href);
+ write("/>\n");
depth--;
writeElement("</att>\n");
}
@@ -993,8 +987,10 @@
*/
private Set<CySubNetwork> getRegisteredSubNetworks(CyRootNetwork
rootNetwork) {
List<CySubNetwork> subNetList = rootNetwork.getSubNetworkList();
- Set<CySubNetwork> registeredSubNetSet = new
HashSet<CySubNetwork>();
+ Set<CySubNetwork> registeredSubNetSet = new
LinkedHashSet<CySubNetwork>();
+ registeredSubNetSet.add(rootNetwork.getBaseNetwork()); // The
base network must be the first one!
+
for (CySubNetwork sn : subNetList) {
if (networkManager.networkExists(sn.getSUID()))
registeredSubNetSet.add(sn);
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