Author: clopes
Date: 2012-04-09 13:58:39 -0700 (Mon, 09 Apr 2012)
New Revision: 28771
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
Log:
XGMML parser: Removes internal node/edge suid-to-index map, since it is no
longer necessary.
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2012-04-09 20:37:10 UTC (rev 28770)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2012-04-09 20:58:39 UTC (rev 28771)
@@ -429,12 +429,10 @@
if (this.getCurrentNetwork() instanceof CySubNetwork &&
this.getParentNetwork() != null) {
// Do not create the element again if the network is a
sub-network!
- Long index = cache.getIndex(oldId);
+ node = cache.getNode(oldId);
- if (index != null) {
- node = this.getRootNetwork().getNode(index);
+ if (node != null) {
((CySubNetwork) this.getCurrentNetwork()).addNode(node);
- node = this.getCurrentNetwork().getNode(index); // in
order to return the correct instance!
}
}
@@ -459,12 +457,10 @@
if (this.getCurrentNetwork() instanceof CySubNetwork &&
this.getParentNetwork() != null) {
// Do not create the element again if the network is a
sub-network and the edge already exists!
- Long index = cache.getIndex(id);
+ edge = cache.getEdge(id);
- if (index != null) {
- edge = this.getRootNetwork().getEdge(index);
+ if (edge != null) {
((CySubNetwork) this.getCurrentNetwork()).addEdge(edge);
- edge = this.getCurrentNetwork().getEdge(index); // in
order to return the correct instance!
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
2012-04-09 20:37:10 UTC (rev 28770)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
2012-04-09 20:58:39 UTC (rev 28771)
@@ -45,8 +45,6 @@
/* Map of new to old element IDs */
private Map<Long, Object> oldIdMap;
- /* Map of old ID to node/edge indexes */
- private Map<Object, Long> indexMap;
/* Maps of XML ID's to elements (the keys should be a Long if reading a
Cy3 session file) */
private Map<Object, CyNetwork> networkByIdMap;
@@ -67,7 +65,6 @@
public void init() {
oldIdMap = new HashMap<Long, Object>();
- indexMap = new HashMap<Object, Long>();
nodeByIdMap = new HashMap<Object, CyNode>();
edgeByIdMap = new HashMap<Object, CyEdge>();
@@ -102,15 +99,11 @@
* @param element A CyNetwork, CyNetworkView, CyNode or CyEdge.
*/
public void cache(Object xgmmlId, CyIdentifiable element) {
- long index = -1;
-
if (xgmmlId != null) {
if (element instanceof CyNode) {
nodeByIdMap.put(xgmmlId, (CyNode) element);
- index = ((CyNode) element).getSUID();
} else if (element instanceof CyEdge) {
edgeByIdMap.put(xgmmlId, (CyEdge) element);
- index = ((CyEdge) element).getSUID();
} else if (element instanceof CyNetwork) {
networkByIdMap.put(xgmmlId, (CyNetwork)
element);
} else if (element instanceof CyNetworkView) {
@@ -118,7 +111,6 @@
}
oldIdMap.put(element.getSUID(), xgmmlId);
- indexMap.put(xgmmlId, index);
}
}
@@ -166,10 +158,6 @@
return null;
}
- public Long getIndex(Object oldId) {
- return indexMap.get(oldId);
- }
-
public CyNetwork getNetwork(Object oldId) {
return networkByIdMap.get(oldId);
}
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