Author: scooter
Date: 2012-04-05 12:40:32 -0700 (Thu, 05 Apr 2012)
New Revision: 28744
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayoutTask.java
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/ISOMLayoutTask.java
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/Layout.java
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
Log:
More changes to remove getIndex and replace it with getSUID
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayoutTask.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayoutTask.java
2012-04-05 19:39:09 UTC (rev 28743)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayoutTask.java
2012-04-05 19:40:32 UTC (rev 28744)
@@ -151,8 +151,8 @@
// FIXME: this code was originally comparing
node1.getIdentifier() to node2.getIdentifier()
// I'm not sure that comparing the indices of
the nodes gets the same effect
// on the other hand, nodes don't have a
human-readable uid in 3.0
- Long a = Long.valueOf(node1.getIndex());
- Long b = Long.valueOf(node2.getIndex());
+ Long a = node1.getSUID();
+ Long b = node2.getSUID();
return a.compareTo(b);
}
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/ISOMLayoutTask.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/ISOMLayoutTask.java
2012-04-05 19:39:09 UTC (rev 28743)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/ISOMLayoutTask.java
2012-04-05 19:40:32 UTC (rev 28744)
@@ -77,7 +77,7 @@
while (nodeIter.hasNext()) {
LayoutNode node = (LayoutNode) nodeIter.next();
- long rootGraphIndex = node.getNode().getIndex();
+ long rootGraphIndex = node.getNode().getSUID();
nodeIndexToLayoutIndex.put(rootGraphIndex,
node.getIndex());
@@ -111,7 +111,7 @@
Iterator nodeIter = partition.nodeIterator();
while (nodeIter.hasNext()) {
- long nodeIndex = ((LayoutNode)
nodeIter.next()).getNode().getIndex();
+ long nodeIndex = ((LayoutNode)
nodeIter.next()).getNode().getSUID();
ISOMVertexData ivd = getISOMVertexData(nodeIndex);
ivd.distance = 0;
ivd.visited = false;
@@ -263,7 +263,7 @@
long [] neighbors = new long[neighborList.size()];
int offset = 0;
for (CyNode n: neighborList){
- neighbors[offset++]=n.getIndex();
+ neighbors[offset++]=n.getSUID();
}
return neighbors;
}
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/Layout.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/Layout.java
2012-04-05 19:39:09 UTC (rev 28743)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/Layout.java
2012-04-05 19:40:32 UTC (rev 28744)
@@ -107,7 +107,7 @@
*
* @return DOCUMENT ME!
*/
- public boolean setX(long node, double x) {
+ public boolean setX(Long node, double x) {
if (nodeXMap.containsKey(node))
return false;
@@ -123,7 +123,7 @@
*
* @return DOCUMENT ME!
*/
- public boolean setY(long node, double y) {
+ public boolean setY(Long node, double y) {
if (nodeYMap.containsKey(node))
return false;
@@ -140,7 +140,7 @@
* @return DOCUMENT ME!
*/
public boolean setX(CyNode node, double x) {
- return setX(node.getIndex(), x);
+ return setX(node.getSUID(), x);
}
/**
@@ -152,7 +152,7 @@
* @return DOCUMENT ME!
*/
public boolean setY(CyNode node, double y) {
- return setY(node.getIndex(), y);
+ return setY(node.getSUID(), y);
}
/**
@@ -164,7 +164,7 @@
* @return DOCUMENT ME!
*/
public boolean setX(View<CyNode> node, double x) {
- return setX(node.getModel().getIndex(), x);
+ return setX(node.getModel().getSUID(), x);
}
/**
@@ -176,7 +176,7 @@
* @return DOCUMENT ME!
*/
public boolean setY(View<CyNode> node, double y) {
- return setY(node.getModel().getIndex(), y);
+ return setY(node.getModel().getSUID(), y);
}
// get
@@ -187,7 +187,7 @@
*
* @return DOCUMENT ME!
*/
- public double getX(long node) {
+ public double getX(Long node) {
return nodeXMap.get(node);
}
@@ -198,7 +198,7 @@
*
* @return DOCUMENT ME!
*/
- public double getY(long node) {
+ public double getY(Long node) {
return nodeYMap.get(node);
}
@@ -210,7 +210,7 @@
* @return DOCUMENT ME!
*/
public double getX(CyNode node) {
- return nodeXMap.get(node.getIndex());
+ return nodeXMap.get(node.getSUID());
}
/**
@@ -221,7 +221,7 @@
* @return DOCUMENT ME!
*/
public double getY(CyNode node) {
- return nodeYMap.get(node.getIndex());
+ return nodeYMap.get(node.getSUID());
}
/**
@@ -232,7 +232,7 @@
* @return DOCUMENT ME!
*/
public double getX(View<CyNode> node) {
- return nodeXMap.get(node.getModel().getIndex());
+ return nodeXMap.get(node.getModel().getSUID());
}
/**
@@ -243,6 +243,6 @@
* @return DOCUMENT ME!
*/
public double getY(View<CyNode> node) {
- return nodeYMap.get(node.getModel().getIndex());
+ return nodeYMap.get(node.getModel().getSUID());
}
}
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
2012-04-05 19:39:09 UTC (rev 28743)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
2012-04-05 19:40:32 UTC (rev 28744)
@@ -104,13 +104,13 @@
if (numSelectedNodes > 1) {
for (CyNode n:
CyTableUtil.getNodesInState(network,"selected",true)){
- index2NodeView.put(n.getIndex(),
networkView.getNodeView(n));
+ index2NodeView.put(n.getSUID(),
networkView.getNodeView(n));
}
} else {
for (View<CyNode> nv: networkView.getNodeViews()){
if (cancelled)
return;
- index2NodeView.put(nv.getModel().getIndex(), nv);
+ index2NodeView.put(nv.getModel().getSUID(), nv);
}
}
@@ -124,8 +124,8 @@
for (View<CyEdge> ev: networkView.getEdgeViews()){
// FIXME: much better would be to query adjacent edges of
selected nodes...
- Long edgeFrom = ev.getModel().getSource().getIndex();
- Long edgeTo = ev.getModel().getTarget().getIndex();
+ Long edgeFrom = ev.getModel().getSource().getSUID();
+ Long edgeTo = ev.getModel().getTarget().getSUID();
if ((edgeFrom == null) || (edgeTo == null)) {
// Must be from an unselected node
@@ -509,8 +509,8 @@
/* Map edges to edge views in order to map dummy nodes to edge
bends properly */
for (View<CyEdge>ev: networkView.getEdgeViews()){
- Long edgeFrom = ev.getModel().getSource().getIndex();
- Long edgeTo = ev.getModel().getTarget().getIndex();
+ Long edgeFrom = ev.getModel().getSource().getSUID();
+ Long edgeTo = ev.getModel().getTarget().getSUID();
if ((edgeFrom == null) || (edgeTo == null)) {
// Must be from an unselected node
@@ -559,8 +559,8 @@
View<CyEdge> ev =
myEdges2EdgeViews[cI[node.graphIndex]].get(theEdge);
if (ev != null) {
- long source =
ev.getModel().getSource().getIndex();
- long target =
ev.getModel().getTarget().getIndex();
+ long source =
ev.getModel().getSource().getSUID();
+ long target =
ev.getModel().getTarget().getSUID();
double k =
(getYPositionOf(index2NodeView, target) - getYPositionOf(index2NodeView,
source)) / (
getXPositionOf(index2NodeView, target) - getXPositionOf(index2NodeView,
source));
--
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