Author: ruschein
Date: 2011-08-04 08:19:56 -0700 (Thu, 04 Aug 2011)
New Revision: 26375
Modified:
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java
Log:
Closes Redmine bug #341.
Modified:
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java
===================================================================
---
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java
2011-08-04 15:15:42 UTC (rev 26374)
+++
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java
2011-08-04 15:19:56 UTC (rev 26375)
@@ -1,49 +1,41 @@
-
/*
- Copyright (c) 2008, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2008, 2011, The Cytoscape Consortium (www.cytoscape.org)
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
package org.cytoscape.model.internal;
import org.cytoscape.model.CyEdge;
+
/**
* Element of the edge linked list used in {@link ArrayGraph}.
* You should only touch this if you know what you're doing.
*/
-class EdgePointer {
-
+final class EdgePointer {
final CyEdge cyEdge;
final int index;
final boolean directed;
@@ -60,7 +52,7 @@
source = s;
target = t;
directed = dir;
- cyEdge = edge;
+ cyEdge = edge;
nextOutEdge[0] = null;
prevOutEdge[0] = null;
@@ -81,11 +73,11 @@
prevInEdge = expandEdgePointerArray(prevInEdge, x);
}
- static EdgePointer[] expandEdgePointerArray(final EdgePointer[] np, final
int n) {
- final EdgePointer[] nnp = new EdgePointer[n+1];
- System.arraycopy(np,0,nnp,0,np.length);
- return nnp;
- }
+ static EdgePointer[] expandEdgePointerArray(final EdgePointer[] np,
final int n) {
+ final EdgePointer[] nnp = new EdgePointer[n+1];
+ System.arraycopy(np,0,nnp,0,np.length);
+ return nnp;
+ }
void insert(final int inId) {
nextOutEdge[inId] = source.firstOutEdge[inId];
@@ -102,62 +94,61 @@
target.firstInEdge[inId] = this;
- if (directed) {
- source.outDegree[inId]++;
- target.inDegree[inId]++;
- } else {
- source.undDegree[inId]++;
- target.undDegree[inId]++;
- }
+ if (directed) {
+ source.outDegree[inId]++;
+ target.inDegree[inId]++;
+ } else {
+ source.undDegree[inId]++;
+ target.undDegree[inId]++;
+ }
- // Self-edge
- if (source == target) {
- if (directed) {
- source.selfEdges[inId]++;
- } else {
- source.undDegree[inId]--;
- }
- }
+ // Self-edge
+ if (source == target) {
+ if (directed) {
+ source.selfEdges[inId]++;
+ } else {
+ source.undDegree[inId]--;
+ }
+ }
}
void remove(final int inId) {
- if (prevOutEdge[inId] != null)
- prevOutEdge[inId].nextOutEdge[inId] = nextOutEdge[inId];
- else
- source.firstOutEdge[inId] = nextOutEdge[inId];
+ if (prevOutEdge[inId] != null)
+ prevOutEdge[inId].nextOutEdge[inId] = nextOutEdge[inId];
+ else
+ source.firstOutEdge[inId] = nextOutEdge[inId];
- if (nextOutEdge[inId] != null)
- nextOutEdge[inId].prevOutEdge[inId] = prevOutEdge[inId];
+ if (nextOutEdge[inId] != null)
+ nextOutEdge[inId].prevOutEdge[inId] = prevOutEdge[inId];
- if (prevInEdge[inId] != null)
- prevInEdge[inId].nextInEdge[inId] = nextInEdge[inId];
- else
- target.firstInEdge[inId] = nextInEdge[inId];
+ if (prevInEdge[inId] != null)
+ prevInEdge[inId].nextInEdge[inId] = nextInEdge[inId];
+ else
+ target.firstInEdge[inId] = nextInEdge[inId];
- if (nextInEdge[inId] != null)
- nextInEdge[inId].prevInEdge[inId] = prevInEdge[inId];
+ if (nextInEdge[inId] != null)
+ nextInEdge[inId].prevInEdge[inId] = prevInEdge[inId];
- if (directed) {
- source.outDegree[inId]--;
- target.inDegree[inId]--;
- } else {
- source.undDegree[inId]--;
- target.undDegree[inId]--;
- }
+ if (directed) {
+ source.outDegree[inId]--;
+ target.inDegree[inId]--;
+ } else {
+ source.undDegree[inId]--;
+ target.undDegree[inId]--;
+ }
// Self-edge.
- if (source == target) {
- // TODO are these correct?
- if (directed) {
- source.selfEdges[inId]++;
- } else {
- source.undDegree[inId]++;
- }
- }
+ if (source == target) {
+ if (directed) {
+ source.selfEdges[inId]--;
+ } else {
+ source.undDegree[inId]--;
+ }
+ }
- nextOutEdge[inId] = null; // ?? wasn't here in DynamicGraph
- prevOutEdge[inId] = null;
- nextInEdge[inId] = null;
- prevInEdge[inId] = null;
+ nextOutEdge[inId] = null; // ?? wasn't here in DynamicGraph
+ prevOutEdge[inId] = null;
+ nextInEdge[inId] = null;
+ prevInEdge[inId] = null;
}
}
Modified:
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java
===================================================================
---
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java
2011-08-04 15:15:42 UTC (rev 26374)
+++
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java
2011-08-04 15:19:56 UTC (rev 26375)
@@ -1,48 +1,41 @@
-
/*
- Copyright (c) 2008, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2008, 2011, The Cytoscape Consortium (www.cytoscape.org)
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
package org.cytoscape.model.internal;
import org.cytoscape.model.CyNode;
+
/**
* Element of the edge linked list used in {@link ArrayGraph}.
- * You should only touch this if you know what you're doing.
+ * You should only touch this if you know what you're doing!
*/
-class NodePointer {
+final class NodePointer {
final CyNode cyNode;
final int index;
NodePointer[] nextNode = new NodePointer[1];
@@ -64,7 +57,7 @@
NodePointer(final int nodeIndex, final CyNode cyn) {
index = nodeIndex;
- cyNode = cyn;
+ cyNode = cyn;
outDegree[0] = 0;
inDegree[0] = 0;
@@ -91,17 +84,17 @@
selfEdges = expandIntArray(selfEdges, x);
}
- static NodePointer[] expandNodePointerArray(final NodePointer[] np, final
int n) {
- final NodePointer[] nnp = new NodePointer[n+1];
- System.arraycopy(np,0,nnp,0,np.length);
- return nnp;
- }
+ static NodePointer[] expandNodePointerArray(final NodePointer[] np,
final int n) {
+ final NodePointer[] nnp = new NodePointer[n+1];
+ System.arraycopy(np,0,nnp,0,np.length);
+ return nnp;
+ }
- static int[] expandIntArray(final int[] np, final int n) {
- final int[] nnp = new int[n+1];
- System.arraycopy(np,0,nnp,0,np.length);
- return nnp;
- }
+ static int[] expandIntArray(final int[] np, final int n) {
+ final int[] nnp = new int[n+1];
+ System.arraycopy(np,0,nnp,0,np.length);
+ return nnp;
+ }
NodePointer insert(final NodePointer next, final int inId) {
nextNode[inId] = next;
@@ -109,23 +102,23 @@
next.prevNode[inId] = this;
// return instead of:
// next = this;
- return this;
+ return this;
}
NodePointer remove(final NodePointer first, final int inId) {
- NodePointer ret = first;
- if (prevNode[inId] != null)
- prevNode[inId].nextNode[inId] = nextNode[inId];
- else
- ret = nextNode[inId];
+ NodePointer ret = first;
+ if (prevNode[inId] != null)
+ prevNode[inId].nextNode[inId] = nextNode[inId];
+ else
+ ret = nextNode[inId];
- if (nextNode[inId] != null)
- nextNode[inId].prevNode[inId] = prevNode[inId];
+ if (nextNode[inId] != null)
+ nextNode[inId].prevNode[inId] = prevNode[inId];
- nextNode[inId] = null; // ??
- prevNode[inId] = null;
- firstOutEdge[inId] = null;
- firstInEdge[inId] = null;
+ nextNode[inId] = null; // ??
+ prevNode[inId] = null;
+ firstOutEdge[inId] = null;
+ firstInEdge[inId] = null;
return ret;
}
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