Author: abeld
Date: 2009-07-09 10:22:45 -0700 (Thu, 09 Jul 2009)
New Revision: 17287
Modified:
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Graph.java
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
Log:
small bugfixes, mostly to fix porting errors
Modified:
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
===================================================================
---
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2009-07-09 17:21:53 UTC (rev 17286)
+++
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2009-07-09 17:22:45 UTC (rev 17287)
@@ -75,7 +75,8 @@
/**
* The total number of layout passes
*/
- private int m_numLayoutPasses;
+ @Tunable(description="Number of layout passes", group="Algorithm
settings")
+ public int m_numLayoutPasses = 10;
/**
* The average number of iterations per Node
@@ -83,14 +84,14 @@
@Tunable(description="Average number of iteratations for each node",
group="Algorithm settings")
public double m_averageIterationsPerNode = 40;
@Tunable(description="Spring strength", group="Algorithm settings")
- public double m_nodeDistanceStrengthConstant;
+ public double m_nodeDistanceStrengthConstant=15.0;
@Tunable(description="Spring rest length", group="Algorithm settings")
- public double m_nodeDistanceRestLengthConstant;
+ public double m_nodeDistanceRestLengthConstant=45.0;
private double[] m_nodeDistanceSpringScalars;
@Tunable(description="Strength of a 'disconnected' spring",
group="Algorithm settings")
- public double m_disconnectedNodeDistanceSpringStrength;
+ public double m_disconnectedNodeDistanceSpringStrength=0.05;
@Tunable(description="Rest length of a 'disconnected' spring",
group="Algorithm settings")
- public double m_disconnectedNodeDistanceSpringRestLength;
+ public double m_disconnectedNodeDistanceSpringRestLength=2000.0;
@Tunable(description="Strength to apply to avoid collisions",
group="Algorithm settings")
public double m_anticollisionSpringStrength;
private double[] m_anticollisionSpringScalars;
Modified:
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Graph.java
===================================================================
---
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Graph.java
2009-07-09 17:21:53 UTC (rev 17286)
+++
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/Graph.java
2009-07-09 17:22:45 UTC (rev 17287)
@@ -254,7 +254,7 @@
int edgeFrom = a_edge[x].getFrom();
int edgeTo = a_edge[x].getTo();
- if ((edgeFrom < 0) || (edgeTo >= nodecount) || (edgeTo
< 0) || (edgeTo >= nodecount)) {
+ if ((edgeFrom < 0) || (edgeFrom >= nodecount) ||
(edgeTo < 0) || (edgeTo >= nodecount)) {
throw new IllegalArgumentException("Edge
refered to node outside of valid range: "
+ "From=" +
edgeFrom + " To=" + edgeTo
+ " with
nodecount=" + nodecount + "\n");
Modified:
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
===================================================================
---
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2009-07-09 17:21:53 UTC (rev 17286)
+++
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2009-07-09 17:22:45 UTC (rev 17287)
@@ -759,7 +759,8 @@
if (node.nodeView != null) {
View<CyNode> currentView = node.nodeView;
- //currentView.setOffset(node.getXPos(),
node.getYPos()); // FIXME
+
currentView.setVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION,
Double.valueOf((double)node.getXPos()));
+
currentView.setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION,
Double.valueOf((double)node.getYPos()));
}
}
--~--~---------~--~----~------------~-------~--~----~
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected]
To unsubscribe from this group, send email to
[email protected]
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en
-~----------~----~----~----~------~----~------~--~---
