Author: mes
Date: 2012-01-20 10:20:24 -0800 (Fri, 20 Jan 2012)
New Revision: 28065
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java
Log:
This change improves memory consumption for subnetworks by about 20%.
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
2012-01-20 01:26:36 UTC (rev 28064)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
2012-01-20 18:20:24 UTC (rev 28065)
@@ -76,8 +76,6 @@
private int internalNodeCount;
private int internalEdgeCount;
private NodePointer inFirstNode;
- private Set<CyNode> nodeSet;
- private Set<CyEdge> edgeSet;
private boolean fireAddedNodesAndEdgesEvents;
private final Map<String,CyTable> netTables;
@@ -103,9 +101,6 @@
this.edgeTables = edgeTables;
this.tableMgr = tableMgr;
- nodeSet = new HashSet<CyNode>(20000);
- edgeSet = new HashSet<CyEdge>(20000);
-
internalNodeCount = 0;
internalEdgeCount = 0;
fireAddedNodesAndEdgesEvents = false;
@@ -181,7 +176,6 @@
ret = parent.nodeAdd();
updateNode(ret);
internalNodeCount++;
- nodeSet.add(ret);
}
if (fireAddedNodesAndEdgesEvents)
@@ -201,7 +195,6 @@
ret = parent.edgeAdd(source, target, isDirected, this);
updateEdge(ret);
internalEdgeCount++;
- edgeSet.add(ret);
}
if (fireAddedNodesAndEdgesEvents)
@@ -243,14 +236,24 @@
* {@inheritDoc}
*/
public boolean containsNode(final CyNode node) {
- return parent.containsNode(node) && nodeSet.contains(node);
+ if ( parent.containsNode(node) ) {
+ final NodePointer np = parent.getNodePointer(node);
+ return np.isSet(internalId);
+ } else {
+ return false;
+ }
}
/**
* {@inheritDoc}
*/
public boolean containsEdge(final CyEdge edge) {
- return parent.containsEdge(edge) && edgeSet.contains(edge);
+ if ( parent.containsEdge(edge) ) {
+ final EdgePointer np = parent.getEdgePointer(edge);
+ return np.isSet(internalId);
+ } else {
+ return false;
+ }
}
/**
@@ -270,7 +273,8 @@
return null;
// make sure the subnetwork still contains the node
- if ( nodeSet.contains(n) )
+ final NodePointer np = parent.getNodePointer(n);
+ if ( np.isSet(internalId) )
return n;
else
return null;
@@ -286,7 +290,8 @@
return null;
// make sure the subnetwork still contains the edge
- if ( edgeSet.contains(e) )
+ final EdgePointer ep = parent.getEdgePointer(e);
+ if ( ep.isSet(internalId) )
return e;
else
return null;
@@ -337,7 +342,6 @@
// add node
internalNodeCount++;
- nodeSet.add(node);
updateNode(node);
copyDefaultAttrs(parent.getRow(node),
this.getRow(node));
}
@@ -375,7 +379,6 @@
// add edge
internalEdgeCount++;
- edgeSet.add(edge);
updateEdge(edge);
copyDefaultAttrs(parent.getRow(edge),
this.getRow(edge));
copyDefaultEdgeAttrs(parent.getRow(edge),
this.getRow(edge));
@@ -410,7 +413,6 @@
inFirstNode =
node.remove(inFirstNode,internalId);
internalNodeCount--;
- nodeSet.remove(n);
}
}
@@ -452,7 +454,6 @@
e.remove(internalId);
internalEdgeCount--;
- edgeSet.remove(edge);
}
return true;
}
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java
2012-01-20 01:26:36 UTC (rev 28064)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java
2012-01-20 18:20:24 UTC (rev 28065)
@@ -29,6 +29,7 @@
import org.cytoscape.model.CyEdge;
+import java.util.Arrays;
/**
@@ -48,6 +49,8 @@
EdgePointer[] nextInEdge = new
EdgePointer[NodePointer.INITIAL_ALLOCATION];
EdgePointer[] prevInEdge = new
EdgePointer[NodePointer.INITIAL_ALLOCATION];
+ boolean[] includes = new boolean[NodePointer.INITIAL_ALLOCATION];
+
EdgePointer(final NodePointer s, final NodePointer t, final boolean
dir, final int ind, final CyEdge edge) {
index = ind;
source = s;
@@ -60,6 +63,8 @@
nextInEdge[0] = null;
prevInEdge[0] = null;
+
+ Arrays.fill(includes,false);
}
void expandTo(final int z) {
@@ -72,6 +77,7 @@
prevOutEdge = expandEdgePointerArray(prevOutEdge, x);
nextInEdge = expandEdgePointerArray(nextInEdge, x);
prevInEdge = expandEdgePointerArray(prevInEdge, x);
+ includes = NodePointer.expandBooleanArray(includes,x);
}
static EdgePointer[] expandEdgePointerArray(final EdgePointer[] np,
final int n) {
@@ -81,6 +87,8 @@
}
void insert(final int inId) {
+ includes[inId] = true;
+
nextOutEdge[inId] = source.firstOutEdge[inId];
if (source.firstOutEdge[inId] != null)
@@ -114,6 +122,8 @@
}
void remove(final int inId) {
+ includes[inId] = false;
+
if (prevOutEdge[inId] != null)
prevOutEdge[inId].nextOutEdge[inId] = nextOutEdge[inId];
else
@@ -152,4 +162,10 @@
nextInEdge[inId] = null;
prevInEdge[inId] = null;
}
+
+ boolean isSet(final int inId) {
+ return ( inId >= 0 &&
+ inId < includes.length &&
+ includes[inId] );
+ }
}
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java
2012-01-20 01:26:36 UTC (rev 28064)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java
2012-01-20 18:20:24 UTC (rev 28065)
@@ -29,6 +29,7 @@
import org.cytoscape.model.CyNode;
+import java.util.Arrays;
/**
@@ -60,6 +61,10 @@
// The number of directed self-edges on this node.
int[] selfEdges = new int[INITIAL_ALLOCATION];
+ // Whether the node pointer is included in the subnetwork
+ // specified by the index of the array.
+ boolean[] includes = new boolean[INITIAL_ALLOCATION];
+
NodePointer(final int nodeIndex, final CyNode cyn) {
index = nodeIndex;
cyNode = cyn;
@@ -71,6 +76,8 @@
firstOutEdge[0] = null;
firstInEdge[0] = null;
+
+ Arrays.fill(includes,false);
}
void expandTo(final int z) {
@@ -87,6 +94,7 @@
inDegree = expandIntArray(inDegree, x);
undDegree = expandIntArray(undDegree, x);
selfEdges = expandIntArray(selfEdges, x);
+ includes = expandBooleanArray(includes, x);
}
static NodePointer[] expandNodePointerArray(final NodePointer[] np,
final int n) {
@@ -101,7 +109,15 @@
return nnp;
}
+ static boolean[] expandBooleanArray(final boolean[] np, final int n) {
+ final boolean[] nnp = new boolean[n+1];
+ System.arraycopy(np,0,nnp,0,np.length);
+ return nnp;
+ }
+
NodePointer insert(final NodePointer next, final int inId) {
+ includes[inId] = true;
+
nextNode[inId] = next;
if (next != null)
next.prevNode[inId] = this;
@@ -111,6 +127,8 @@
}
NodePointer remove(final NodePointer first, final int inId) {
+ includes[inId] = false;
+
NodePointer ret = first;
if (prevNode[inId] != null)
prevNode[inId].nextNode[inId] = nextNode[inId];
@@ -127,4 +145,10 @@
return ret;
}
+
+ boolean isSet(final int inId) {
+ return ( inId >= 0 &&
+ inId < includes.length &&
+ includes[inId] );
+ }
}
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