Author: clopes
Date: 2011-07-07 13:30:01 -0700 (Thu, 07 Jul 2011)
New Revision: 26101
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/BioLayoutKKAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
Log:
fixes #121 - Layout --> Settings --> pick Edge-weighted force directed
(BiolLayout)/Spring Embeded, got very wise dialog box
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
2011-07-07 19:43:54 UTC (rev 26100)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2011-07-07 20:30:01 UTC (rev 26101)
@@ -31,17 +31,10 @@
package csplugins.layout.algorithms.bioLayout;
-import java.awt.Dimension;
-import java.util.ArrayList;
-
import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
-import org.cytoscape.view.layout.LayoutEdge;
-import org.cytoscape.view.layout.LayoutNode;
-import org.cytoscape.view.layout.LayoutPartition;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
-import org.cytoscape.work.TunableValidator.ValidationState;
import org.cytoscape.work.undo.UndoSupport;
@@ -64,18 +57,18 @@
/**
* Sets the number of iterations for each update
*/
- @Tunable(description="Number of iterations before updating display (0:
update only at end)", groups="Algorithm settings")
+ @Tunable(description="Number of iterations before updating display (0:
update only at end)")
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",
groups="Algorithm settings")
+ @Tunable(description="Divisor to calculate the attraction force")
public double attraction_multiplier = .03;
- @Tunable(description="Multiplier to calculate the repulsion force",
groups="Algorithm settings")
+ @Tunable(description="Multiplier to calculate the repulsion force")
public double repulsion_multiplier = 0.04;
- @Tunable(description="Multiplier to calculate the gravity force",
groups="Algorithm settings")
+ @Tunable(description="Multiplier to calculate the gravity force")
public double gravity_multiplier = 1;
/**
@@ -83,33 +76,33 @@
* gets applied when two vertices are very close
* to each other.
*/
- @Tunable(description="Constant force applied to avoid conflicts",
groups="Algorithm settings")
+ @Tunable(description="Constant force applied to avoid conflicts")
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", groups="Algorithm settings")
+ @Tunable(description="Percent of graph used for node repulsion
calculations")
public double max_distance_factor = 20;
/**
* The spread factor -- used to give extra space to expand
*/
- @Tunable(description="Amount of extra room for layout",
groups="Algorithm settings")
+ @Tunable(description="Amount of extra room for layout")
public double spread_factor = 2;
/**
* The initial temperature factor. This will get damped
* out through the iterations
*/
- @Tunable(description="Initial temperature", groups="Algorithm settings")
+ @Tunable(description="Initial temperature")
public double temperature = 80;
/**
* The number of iterations to run.
*/
- @Tunable(description="Number of iterations", groups="Algorithm
settings")
+ @Tunable(description="Number of iterations")
public int nIterations = 500;
@Tunable(description="Don't partition graph before layout",
groups="Standard settings")
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
2011-07-07 19:43:54 UTC (rev 26100)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2011-07-07 20:30:01 UTC (rev 26101)
@@ -32,11 +32,9 @@
package csplugins.layout.algorithms.bioLayout;
import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
-
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
-import org.cytoscape.work.TunableValidator.ValidationState;
import org.cytoscape.work.undo.UndoSupport;
@@ -63,18 +61,18 @@
/**
* The average number of iterations per Node
*/
- @Tunable(description="Average number of iteratations for each node",
groups="Algorithm settings")
+ @Tunable(description="Average number of iteratations for each node")
public double m_averageIterationsPerNode = 40;
- @Tunable(description="Spring strength", groups="Algorithm settings")
+ @Tunable(description="Spring strength")
public double m_nodeDistanceStrengthConstant=15.0;
- @Tunable(description="Spring rest length", groups="Algorithm settings")
+ @Tunable(description="Spring rest length")
public double m_nodeDistanceRestLengthConstant=45.0;
//private double[] m_nodeDistanceSpringScalars;
- @Tunable(description="Strength of a 'disconnected' spring",
groups="Algorithm settings")
+ @Tunable(description="Strength of a 'disconnected' spring")
public double m_disconnectedNodeDistanceSpringStrength=0.05;
- @Tunable(description="Rest length of a 'disconnected' spring",
groups="Algorithm settings")
+ @Tunable(description="Rest length of a 'disconnected' spring")
public double m_disconnectedNodeDistanceSpringRestLength=2000.0;
- @Tunable(description="Strength to apply to avoid collisions",
groups="Algorithm settings")
+ @Tunable(description="Strength to apply to avoid collisions")
public double m_anticollisionSpringStrength;
@Tunable(description="Don't partition graph before layout",
groups="Standard settings")
public boolean singlePartition;
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
2011-07-07 19:43:54 UTC (rev 26100)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
2011-07-07 20:30:01 UTC (rev 26101)
@@ -32,7 +32,7 @@
public double sizeFactor = 100;
@Tunable(description="Cooling factor")
public double coolingFactor = 2;
- @Tunable(description="Don't partition graph before layout",
groups="Standard settings")
+ @Tunable(description="Don't partition graph before layout",
groups="Standard settings")
public boolean singlePartition;
/**
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