org.biojava.nbio.structure.align.seq

Class SmithWaterman3DParameters

java.lang.Object

org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

All Implemented Interfaces:

ConfigStrucAligParams

public class SmithWaterman3DParameters
extends java.lang.Object
implements ConfigStrucAligParams

Constructor Summary

Constructors

Constructor and Description
SmithWaterman3DParameters()

Method Summary

Modifier and Type	Method and Description
java.lang.Short	getGapExtend()
java.lang.Short	getGapOpen()
java.lang.Double	getMaxRmsd()
java.lang.Integer	getMinLen()
java.util.List<java.lang.String>	getUserConfigHelp() The help text for each of these parameters.
java.util.List<java.lang.String>	getUserConfigParameterNames() The labels to be displayed to the user for each parameter
java.util.List<java.lang.String>	getUserConfigParameters() get the list of parameters that the user can change through the user interface.
java.util.List<java.lang.Class>	getUserConfigTypes() Get the data types of the parameters
void	reset() Set the parameters to the default.
void	setGapExtend(java.lang.Short gapExtend)
void	setGapOpen(java.lang.Short gapOpen)
void	setMaxRmsd(java.lang.Double maxRmsd)
void	setMinLen(java.lang.Integer minLen)

Methods inherited from class java.lang.Object

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

Constructor Detail

SmithWaterman3DParameters

public SmithWaterman3DParameters()

Method Detail

getUserConfigHelp

public java.util.List<java.lang.String> getUserConfigHelp()

Description copied from interface: ConfigStrucAligParams

The help text for each of these parameters.

Specified by:

getUserConfigHelp in interface ConfigStrucAligParams

Returns:

help strings

getUserConfigParameterNames

public java.util.List<java.lang.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

getUserConfigParameters

public java.util.List<java.lang.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

getUserConfigTypes

public java.util.List<java.lang.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

reset

public void reset()

Description copied from interface: ConfigStrucAligParams

Set the parameters to the default.

Specified by:

reset in interface ConfigStrucAligParams

getGapExtend

public java.lang.Short getGapExtend()

setGapExtend

public void setGapExtend(java.lang.Short gapExtend)

getGapOpen

public java.lang.Short getGapOpen()

setGapOpen

public void setGapOpen(java.lang.Short gapOpen)

getMaxRmsd

public java.lang.Double getMaxRmsd()

setMaxRmsd

public void setMaxRmsd(java.lang.Double maxRmsd)

getMinLen

public java.lang.Integer getMinLen()

setMinLen

public void setMinLen(java.lang.Integer minLen)