Author: ruschein
Date: 2010-08-03 15:01:09 -0700 (Tue, 03 Aug 2010)
New Revision: 21156
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
Log:
Updated to track changes in Tunable.
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
2010-08-03 22:00:54 UTC (rev 21155)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
2010-08-03 22:01:09 UTC (rev 21156)
@@ -82,7 +82,7 @@
/**
* Whether or not to initialize by randomizing all points
*/
- @Tunable(description="Randomize graph before layout", group="Standard
settings")
+ @Tunable(description="Randomize graph before layout", groups="Standard
settings")
public boolean randomize = true;
/**
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2010-08-03 22:00:54 UTC (rev 21155)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2010-08-03 22:01:09 UTC (rev 21156)
@@ -60,20 +60,20 @@
/**
* Sets the number of iterations for each update
*/
- @Tunable(description="Number of iterations before updating display (0:
update only at end)", group="Algorithm settings")
+ @Tunable(description="Number of iterations before updating display (0:
update only at end)", groups="Algorithm settings")
public static int update_iterations = 0; // 0 means we only update at
the end
/**
* The multipliers and computed result for the
* attraction and repulsion values.
*/
- @Tunable(description="Divisor to calculate the attraction force",
group="Algorithm settings")
+ @Tunable(description="Divisor to calculate the attraction force",
groups="Algorithm settings")
public double attraction_multiplier = .03;
private double attraction_constant;
- @Tunable(description="Multiplier to calculate the repulsion force",
group="Algorithm settings")
+ @Tunable(description="Multiplier to calculate the repulsion force",
groups="Algorithm settings")
public double repulsion_multiplier = 0.04;
private double repulsion_constant;
- @Tunable(description="Multiplier to calculate the gravity force",
group="Algorithm settings")
+ @Tunable(description="Multiplier to calculate the gravity force",
groups="Algorithm settings")
public double gravity_multiplier = 1;
private double gravity_constant;
@@ -82,14 +82,14 @@
* gets applied when two vertices are very close
* to each other.
*/
- @Tunable(description="Constant force applied to avoid conflicts",
group="Algorithm settings")
+ @Tunable(description="Constant force applied to avoid conflicts",
groups="Algorithm settings")
public double conflict_avoidance = 20;
/**
* max_distance_factor is the portion of the graph
* beyond which repulsive forces will not operate.
*/
- @Tunable(description="Percent of graph used for node repulsion
calculations", group="Algorithm settings")
+ @Tunable(description="Percent of graph used for node repulsion
calculations", groups="Algorithm settings")
public double max_distance_factor = 20;
/**
@@ -111,20 +111,20 @@
/**
* The spread factor -- used to give extra space to expand
*/
- @Tunable(description="Amount of extra room for layout",
group="Algorithm settings")
+ @Tunable(description="Amount of extra room for layout",
groups="Algorithm settings")
public double spread_factor = 2;
/**
* The initial temperature factor. This will get damped
* out through the iterations
*/
- @Tunable(description="Initial temperature", group="Algorithm settings")
+ @Tunable(description="Initial temperature", groups="Algorithm settings")
public double temperature = 80;
/**
* The number of iterations to run.
*/
- @Tunable(description="Number of iterations", group="Algorithm settings")
+ @Tunable(description="Number of iterations", groups="Algorithm
settings")
public int nIterations = 500;
/**
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2010-08-03 22:00:54 UTC (rev 21155)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2010-08-03 22:01:09 UTC (rev 21156)
@@ -75,24 +75,24 @@
/**
* The total number of layout passes
*/
- @Tunable(description="Number of layout passes", group="Algorithm
settings")
+ @Tunable(description="Number of layout passes", groups="Algorithm
settings")
public int m_numLayoutPasses = 10;
/**
* The average number of iterations per Node
*/
- @Tunable(description="Average number of iteratations for each node",
group="Algorithm settings")
+ @Tunable(description="Average number of iteratations for each node",
groups="Algorithm settings")
public double m_averageIterationsPerNode = 40;
- @Tunable(description="Spring strength", group="Algorithm settings")
+ @Tunable(description="Spring strength", groups="Algorithm settings")
public double m_nodeDistanceStrengthConstant=15.0;
- @Tunable(description="Spring rest length", group="Algorithm settings")
+ @Tunable(description="Spring rest length", groups="Algorithm settings")
public double m_nodeDistanceRestLengthConstant=45.0;
private double[] m_nodeDistanceSpringScalars;
- @Tunable(description="Strength of a 'disconnected' spring",
group="Algorithm settings")
+ @Tunable(description="Strength of a 'disconnected' spring",
groups="Algorithm settings")
public double m_disconnectedNodeDistanceSpringStrength=0.05;
- @Tunable(description="Rest length of a 'disconnected' spring",
group="Algorithm settings")
+ @Tunable(description="Rest length of a 'disconnected' spring",
groups="Algorithm settings")
public double m_disconnectedNodeDistanceSpringRestLength=2000.0;
- @Tunable(description="Strength to apply to avoid collisions",
group="Algorithm settings")
+ @Tunable(description="Strength to apply to avoid collisions",
groups="Algorithm settings")
public double m_anticollisionSpringStrength;
private double[] m_anticollisionSpringScalars;
@@ -105,7 +105,7 @@
/**
* Current layout pass
*/
- @Tunable(description="Number of layout passes", group="Algorithm
settings")
+ @Tunable(description="Number of layout passes", groups="Algorithm
settings")
public int m_layoutPass = 2;
/**
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