methods.clustering
Class MCLParameters

java.lang.Object
  extended by methods.clustering.MCLParameters

public class MCLParameters
extends Object

Represents a set of parameters for MCL clustering.

The inflation coefficient is the most important parameter and affects the granularity of the clustering. For a more detailed description of all parameters consult the MCL manual at http://micans.org/mcl/

Author:
Jan Krumsiek

Constructor Summary
MCLParameters()
          Creates a set of MCL parameters with default settings.
 
Method Summary
protected  String getCommandLineParameters()
          Assemble command line parameters, directly used in command call
 void setInflation(float i)
          Set the inflation coefficient
 void setP(float p)
          Set the pruning number
 void setPct(float pct)
          Set mass percentage below which to apply recovery
 void setR(float r)
          Set the recover number
 void setS(float s)
          Set the selection number
 void setScheme(int scheme)
          Sets a scheme for the parameters p,s,r and pct.
 void setTimeout(int timeoutSeconds)
          Set the timeout (in seconds) after which the mcl call will be terminated.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MCLParameters

public MCLParameters()
Creates a set of MCL parameters with default settings. By default the inflation coefficient is 2.0, all other parameters are not set. No timeout value is set (see also: setTimeout(int))

Method Detail

setInflation

public void setInflation(float i)
Set the inflation coefficient

Parameters:
i - inflation coefficient

setP

public void setP(float p)
Set the pruning number

Parameters:
p - pruning number

setS

public void setS(float s)
Set the selection number

Parameters:
s - selection number

setR

public void setR(float r)
Set the recover number

Parameters:
r - recover number

setPct

public void setPct(float pct)
Set mass percentage below which to apply recovery

Parameters:
pct - mass percentage

setTimeout

public void setTimeout(int timeoutSeconds)
Set the timeout (in seconds) after which the mcl call will be terminated. This setting can be used to avoid too long or non-converging calculations.

Parameters:
timeoutSeconds -

setScheme

public void setScheme(int scheme)
Sets a scheme for the parameters p,s,r and pct. Any values set for these parameters will be unset.

Parameters:
scheme - scheme to be used

getCommandLineParameters

protected String getCommandLineParameters()
Assemble command line parameters, directly used in command call

Returns:
command line parameters string