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

Description

static enum

CESymmParameters.OrderDetectorMethod

static enum

CESymmParameters.RefineMethod

static enum

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

Description

static final 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

Description

CESymmParameters()
Method Summary

Modifier and Type

Method

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, isShowAFPRanges, setDistanceIncrement, setGapExtension, setGapOpen, setMaxGapSize, setMaxNrIterationsForOptimization, setMaxOptRMSD, 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 Details
- DEFAULT_SYMMETRY_THRESHOLD
  
  public static final double DEFAULT_SYMMETRY_THRESHOLD
  See Also:
  
  Constant Field Values
Constructor Details
- CESymmParameters
  
  public CESymmParameters()
Method Details
- 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

Class CESymmParameters

Nested Class Summary

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

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Details

DEFAULT_SYMMETRY_THRESHOLD

Constructor Details

CESymmParameters

Method Details

clone

reset

getUserConfigHelp

getUserConfigParameters

getUserConfigParameterNames

getUserConfigTypes

getRefineMethod

setRefineMethod

setRefineResult

getOrderDetectorMethod

setOrderDetectorMethod

setUserOrder

getUserOrder

setMaxSymmOrder

getMaxSymmOrder

getSymmType

setSymmType

getOptimization

setOptimization

getRndSeed

setRndSeed

getSymmLevels

setSymmLevels

getUnrefinedScoreThreshold

setUnrefinedScoreThreshold

getRefinedScoreThreshold

setRefinedScoreThreshold

getSSEThreshold

setSSEThreshold

getMinCoreLength

setMinCoreLength

getDistanceCutoff

setDistanceCutoff

isGaps

setGaps

getOptimizationSteps

setOptimizationSteps

toString