Package org.biojava.nbio.structure.align.multiple.mc

Class MultipleMcParameters

java.lang.Object

org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters

All Implemented Interfaces:

ConfigStrucAligParams

public class MultipleMcParameters
extends Object
implements ConfigStrucAligParams

Contains the parameters to be sent to the MC optimization.

Since:

4.1.0

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor	Description
MultipleMcParameters()	Constructor with DEFAULT values of the parameters.

Method Summary

Modifier and Type	Method	Description
int	getConvergenceSteps()
double	getDistanceCutoff()
double	getGapExtension()
double	getGapOpen()
int	getMinAlignedStructures()
int	getMinBlockLen()
int	getNrThreads()
int	getRandomSeed()
List<String>	getUserConfigHelp()	The help text for each of these parameters.
List<String>	getUserConfigParameterNames()	The labels to be displayed to the user for each parameter
List<String>	getUserConfigParameters()	get the list of parameters that the user can change through the user interface.
List<Class>	getUserConfigTypes()	Get the data types of the parameters
void	reset()	Set the parameters to the default.
void	setConvergenceSteps(Integer convergenceSteps)
void	setDistanceCutoff(Double distanceCutoff)
void	setGapExtension(Double gapExtension)
void	setGapOpen(Double gapOpen)
void	setMinAlignedStructures(Integer minAlignedStructures)
void	setMinBlockLen(Integer minBlockLen)
void	setNrThreads(Integer nrThreads)
void	setRandomSeed(Integer randomSeed)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

MultipleMcParameters

public MultipleMcParameters()

Constructor with DEFAULT values of the parameters.

Method Detail

getUserConfigParameters

public List<String> getUserConfigParameters()

Description copied from interface: ConfigStrucAligParams

get the list of parameters that the user can change through the user interface. Parameter names are the same names as the corresponding Get/Set methods.

Specified by:

getUserConfigParameters in interface ConfigStrucAligParams

Returns:

list of parameters

getUserConfigParameterNames

public List<String> getUserConfigParameterNames()

Description copied from interface: ConfigStrucAligParams

The labels to be displayed to the user for each parameter

Specified by:

getUserConfigParameterNames in interface ConfigStrucAligParams

Returns:

list of parameter names

getUserConfigTypes

public List<Class> getUserConfigTypes()

Description copied from interface: ConfigStrucAligParams

Get the data types of the parameters

Specified by:

getUserConfigTypes in interface ConfigStrucAligParams

Returns:

list of parameter classes

getUserConfigHelp

public List<String> getUserConfigHelp()

Description copied from interface: ConfigStrucAligParams

The help text for each of these parameters.

Specified by:

getUserConfigHelp in interface ConfigStrucAligParams

Returns:

help strings

toString

public String toString()

Overrides:

toString in class Object

reset

public void reset()

Description copied from interface: ConfigStrucAligParams

Set the parameters to the default.

Specified by:

reset in interface ConfigStrucAligParams

getRandomSeed

public int getRandomSeed()

setRandomSeed

public void setRandomSeed(Integer randomSeed)

getMinBlockLen

public int getMinBlockLen()

setMinBlockLen

public void setMinBlockLen(Integer minBlockLen)

getMinAlignedStructures

public int getMinAlignedStructures()

setMinAlignedStructures

public void setMinAlignedStructures(Integer minAlignedStructures)

getGapOpen

public double getGapOpen()

setGapOpen

public void setGapOpen(Double gapOpen)

getGapExtension

public double getGapExtension()

setGapExtension

public void setGapExtension(Double gapExtension)

getConvergenceSteps

public int getConvergenceSteps()

setConvergenceSteps

public void setConvergenceSteps(Integer convergenceSteps)

getNrThreads

public int getNrThreads()

setNrThreads

public void setNrThreads(Integer nrThreads)

getDistanceCutoff

public double getDistanceCutoff()

setDistanceCutoff

public void setDistanceCutoff(Double distanceCutoff)