Package org.biojava.nbio.structure.align.fatcat.calc

Class FatCatParameters

java.lang.Object

org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

All Implemented Interfaces:

ConfigStrucAligParams

public class FatCatParameters
extends Object
implements ConfigStrucAligParams

Field Summary

Fields

Modifier and Type	Field	Description
static final int	DEFAULT_FRAGLEN

Constructor Summary

Constructors

Constructor	Description
FatCatParameters()

Method Summary

Modifier and Type	Method	Description
double	getAfpDisCut()
double	getAfpDisCut0()
double	getBadRmsd()
Double	getDisCut()	Get the distance cutoff used during AFP chain connectivity checks
double	getDisFilter()
double	getDisSmooth()
Integer	getFragLen()
int	getFragLenSq()
double	getFragScore()
double	getGapCreate()
double	getGapExtend()
int	getMaxGap()
int	getMaxGapFrag()
double	getMaxPenalty()
Integer	getMaxTra()	get the maximum number of Twists that are allowed...
int	getMisCut()
double	getMisScore()
double	getResScore()
Double	getRmsdCut()	The cutoff to be used during AFP detection
int	getSparse()
double	getTorsionPenalty()
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
boolean	isOptimizeAlignment()	Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.
void	reset()	Set the parameters to the default.
void	setAfpDisCut(double afpDisCut)
void	setAfpDisCut0(double afpDisCut0)
void	setBadRmsd(double badRmsd)
void	setDisCut(Double disCut)
void	setDisFilter(double disFilter)
void	setDisSmooth(double disSmooth)
void	setFragLen(Integer fragLen)
void	setFragLenSq(int fragLenSq)
void	setFragScore(double fragScore)
void	setGapCreate(double gapCreate)
void	setGapExtend(double gapExtend)
void	setMaxGap(int maxGap)
void	setMaxGapFrag(int maxGapFrag)
void	setMaxPenalty(double maxPenalty)
void	setMaxTra(Integer maxTra)	set the maximum number of Twists that are allowed...
void	setMisCut(int misCut)
void	setMisScore(double misScore)
void	setOptimizeAlignment(boolean optimizeAlignment)	Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.
void	setResScore(double resScore)
void	setRmsdCut(Double rmsdCut)	The cutoff to be used during AFP detection
void	setSparse(int sparse)
void	setTorsionPenalty(double torsionPenalty)
String	toString()

Methods inherited from class java.lang.Object

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

Field Details

DEFAULT_FRAGLEN

public static final int DEFAULT_FRAGLEN

See Also:

• Constant Field Values

Constructor Details

FatCatParameters

public FatCatParameters()

Method Details

reset

public void reset()

Description copied from interface: ConfigStrucAligParams

Set the parameters to the default.

Specified by:

reset in interface ConfigStrucAligParams

getFragLen

public Integer getFragLen()

setFragLen

public void setFragLen(Integer fragLen)

getFragLenSq

public int getFragLenSq()

setFragLenSq

public void setFragLenSq(int fragLenSq)

getRmsdCut

public Double getRmsdCut()

The cutoff to be used during AFP detection

Returns:

rmsdCut parameter

setRmsdCut

public void setRmsdCut(Double rmsdCut)

The cutoff to be used during AFP detection

Parameters:

rmsdCut -

getDisCut

public Double getDisCut()

Get the distance cutoff used during AFP chain connectivity checks

Returns:

distance Cutoff

setDisCut

public void setDisCut(Double disCut)

getAfpDisCut

public double getAfpDisCut()

setAfpDisCut

public void setAfpDisCut(double afpDisCut)

getAfpDisCut0

public double getAfpDisCut0()

setAfpDisCut0

public void setAfpDisCut0(double afpDisCut0)

getDisSmooth

public double getDisSmooth()

setDisSmooth

public void setDisSmooth(double disSmooth)

getMisCut

public int getMisCut()

setMisCut

public void setMisCut(int misCut)

getMaxGap

public int getMaxGap()

setMaxGap

public void setMaxGap(int maxGap)

getMaxGapFrag

public int getMaxGapFrag()

setMaxGapFrag

public void setMaxGapFrag(int maxGapFrag)

getDisFilter

public double getDisFilter()

setDisFilter

public void setDisFilter(double disFilter)

getBadRmsd

public double getBadRmsd()

setBadRmsd

public void setBadRmsd(double badRmsd)

getMaxTra

public Integer getMaxTra()

get the maximum number of Twists that are allowed...

Returns:

max nr of allowed twists

setMaxTra

public void setMaxTra(Integer maxTra)

set the maximum number of Twists that are allowed...

Parameters:

maxTra -

getGapCreate

public double getGapCreate()

setGapCreate

public void setGapCreate(double gapCreate)

getGapExtend

public double getGapExtend()

setGapExtend

public void setGapExtend(double gapExtend)

getMisScore

public double getMisScore()

setMisScore

public void setMisScore(double misScore)

getTorsionPenalty

public double getTorsionPenalty()

setTorsionPenalty

public void setTorsionPenalty(double torsionPenalty)

getMaxPenalty

public double getMaxPenalty()

setMaxPenalty

public void setMaxPenalty(double maxPenalty)

getResScore

public double getResScore()

setResScore

public void setResScore(double resScore)

getFragScore

public double getFragScore()

setFragScore

public void setFragScore(double fragScore)

getSparse

public int getSparse()

setSparse

public void setSparse(int sparse)

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

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

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

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

toString

public String toString()

Overrides:

toString in class Object

isOptimizeAlignment

public boolean isOptimizeAlignment()

Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result. NB: Not implemented in jFatCat

Returns:

optimizeAlignment

setOptimizeAlignment

public void setOptimizeAlignment(boolean optimizeAlignment)

Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result. NB: Not implemented in jFatCat

Parameters:

optimizeAlignment -