org.biojava.nbio.structure.symmetry.internal

Class CESymmParameters

java.lang.Object

org.biojava.nbio.structure.align.ce.CeParameters

org.biojava.nbio.structure.symmetry.internal.CESymmParameters

All Implemented Interfaces:

ConfigStrucAligParams

public class CESymmParameters
extends CeParameters

Provides parameters to CeSymm.

Since:

4.1.1

Author:

Spencer Bliven, Aleix Lafita

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CESymmParameters.OrderDetectorMethod
static class	CESymmParameters.RefineMethod
static class	CESymmParameters.SymmetryType The internal symmetry detection can be divided into two types: CLOSE: includes the circular and dihedral symmetries, and OPEN: includes the helical and protein repeats symmetries.

Nested classes/interfaces inherited from class org.biojava.nbio.structure.align.ce.CeParameters

CeParameters.ScoringStrategy

Field Summary

Fields

Modifier and Type	Field and Description
static double	DEFAULT_SYMMETRY_THRESHOLD

Fields inherited from class org.biojava.nbio.structure.align.ce.CeParameters

DEFAULT_GAP_EXTENSION, DEFAULT_GAP_OPEN, DEFAULT_oRmsdThr, DEFAULT_SUBSTITUTION_MATRIX, DISTANCE_INCREMENT, distanceIncrement, gapExtension, gapOpen, maxGapSize, maxNrIterationsForOptimization, maxOptRMSD, oRmsdThr, rmsdThr, rmsdThrJoin, scoringStrategy, seqWeight, showAFPRanges, sideChainScoringType, substitutionMatrix, winSize

Constructor Summary

Constructors

Constructor and Description
CESymmParameters()
CESymmParameters(CESymmParameters o)

Method Summary

Modifier and Type	Method and Description
CESymmParameters	clone()
double	getDistanceCutoff()
int	getMaxSymmOrder()
int	getMinCoreLength()
boolean	getOptimization()
int	getOptimizationSteps()
CESymmParameters.OrderDetectorMethod	getOrderDetectorMethod()
double	getRefinedScoreThreshold()
CESymmParameters.RefineMethod	getRefineMethod()
int	getRndSeed()
int	getSSEThreshold()
int	getSymmLevels()
CESymmParameters.SymmetryType	getSymmType()
double	getUnrefinedScoreThreshold()
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
int	getUserOrder()
boolean	isGaps()
void	reset() Set the parameters to the default.
void	setDistanceCutoff(Double distanceCutoff)
void	setGaps(Boolean gaps)
void	setMaxSymmOrder(Integer maxSymmOrder)
void	setMinCoreLength(Integer minCoreLength)
void	setOptimization(Boolean optimization)
void	setOptimizationSteps(Integer optimizationSteps)
void	setOrderDetectorMethod(CESymmParameters.OrderDetectorMethod orderDetectorMethod)
void	setRefinedScoreThreshold(Double refinedScoreThreshold)
void	setRefineMethod(CESymmParameters.RefineMethod refineMethod)
void	setRefineResult(boolean doRefine) Deprecated.
void	setRndSeed(Integer seed)
void	setSSEThreshold(Integer sseThreshold)
void	setSymmLevels(Integer symmLevels)
void	setSymmType(CESymmParameters.SymmetryType type)
void	setUnrefinedScoreThreshold(Double unrefinedScoreThreshold)
void	setUserOrder(Integer userOrder)
String	toString()

Methods inherited from class org.biojava.nbio.structure.align.ce.CeParameters

getDistanceIncrement, getGapExtension, getGapOpen, getMaxGapSize, getMaxNrIterationsForOptimization, getMaxOptRMSD, getORmsdThr, getRmsdThr, getRmsdThrJoin, getScoringStrategy, getSeqWeight, getSubstitutionMatrix, getWinSize, isOptimizeAlignment, isShowAFPRanges, setDistanceIncrement, setGapExtension, setGapOpen, setMaxGapSize, setMaxNrIterationsForOptimization, setMaxOptRMSD, setOptimizeAlignment, setORmsdThr, setRmsdThr, setRmsdThrJoin, setScoringStrategy, setSeqWeight, setShowAFPRanges, setSubstitutionMatrix, setWinSize

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_SYMMETRY_THRESHOLD

public static final double DEFAULT_SYMMETRY_THRESHOLD

See Also:

Constant Field Values

Constructor Detail

CESymmParameters

public CESymmParameters()

CESymmParameters

public CESymmParameters(CESymmParameters o)

Method Detail

clone

public CESymmParameters clone()

Overrides:

clone in class Object

reset

public void reset()

Description copied from interface: ConfigStrucAligParams

Set the parameters to the default.

Specified by:

reset in interface ConfigStrucAligParams

Overrides:

reset in class CeParameters

getUserConfigHelp

public List<String> getUserConfigHelp()

Description copied from interface: ConfigStrucAligParams

The help text for each of these parameters.

Specified by:

getUserConfigHelp in interface ConfigStrucAligParams

Overrides:

getUserConfigHelp in class CeParameters

Returns:

help strings

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

Overrides:

getUserConfigParameters in class CeParameters

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

Overrides:

getUserConfigParameterNames in class CeParameters

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

Overrides:

getUserConfigTypes in class CeParameters

Returns:

list of parameter classes

getRefineMethod

public CESymmParameters.RefineMethod getRefineMethod()

setRefineMethod

public void setRefineMethod(CESymmParameters.RefineMethod refineMethod)

setRefineResult

@Deprecated
public void setRefineResult(boolean doRefine)

Deprecated.

getOrderDetectorMethod

public CESymmParameters.OrderDetectorMethod getOrderDetectorMethod()

setOrderDetectorMethod

public void setOrderDetectorMethod(CESymmParameters.OrderDetectorMethod orderDetectorMethod)

setUserOrder

public void setUserOrder(Integer userOrder)

getUserOrder

public int getUserOrder()

setMaxSymmOrder

public void setMaxSymmOrder(Integer maxSymmOrder)

getMaxSymmOrder

public int getMaxSymmOrder()

getSymmType

public CESymmParameters.SymmetryType getSymmType()

setSymmType

public void setSymmType(CESymmParameters.SymmetryType type)

getOptimization

public boolean getOptimization()

setOptimization

public void setOptimization(Boolean optimization)

getRndSeed

public int getRndSeed()

setRndSeed

public void setRndSeed(Integer seed)

getSymmLevels

public int getSymmLevels()

setSymmLevels

public void setSymmLevels(Integer symmLevels)

getUnrefinedScoreThreshold

public double getUnrefinedScoreThreshold()

setUnrefinedScoreThreshold

public void setUnrefinedScoreThreshold(Double unrefinedScoreThreshold)

getRefinedScoreThreshold

public double getRefinedScoreThreshold()

setRefinedScoreThreshold

public void setRefinedScoreThreshold(Double refinedScoreThreshold)

getSSEThreshold

public int getSSEThreshold()

setSSEThreshold

public void setSSEThreshold(Integer sseThreshold)

getMinCoreLength

public int getMinCoreLength()

setMinCoreLength

public void setMinCoreLength(Integer minCoreLength)

getDistanceCutoff

public double getDistanceCutoff()

setDistanceCutoff

public void setDistanceCutoff(Double distanceCutoff)

isGaps

public boolean isGaps()

setGaps

public void setGaps(Boolean gaps)

getOptimizationSteps

public int getOptimizationSteps()

setOptimizationSteps

public void setOptimizationSteps(Integer optimizationSteps)

toString

public String toString()

Overrides:

toString in class CeParameters