Class CESymmParameters
- java.lang.Object
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- org.biojava.nbio.structure.align.ce.CeParameters
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- org.biojava.nbio.structure.symmetry.internal.CESymmParameters
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- All Implemented Interfaces:
ConfigStrucAligParams
public class CESymmParameters extends CeParameters
Provides parameters toCeSymm
.- Since:
- 4.1.1
- Author:
- Spencer Bliven, Aleix Lafita
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Nested Class Summary
Nested Classes Modifier and Type Class 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
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Field Summary
Fields Modifier and Type Field Description static double
DEFAULT_SYMMETRY_THRESHOLD
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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
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Constructor Summary
Constructors Constructor Description CESymmParameters()
CESymmParameters(CESymmParameters o)
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Method Summary
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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
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Field Detail
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DEFAULT_SYMMETRY_THRESHOLD
public static final double DEFAULT_SYMMETRY_THRESHOLD
- See Also:
- Constant Field Values
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Constructor Detail
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CESymmParameters
public CESymmParameters()
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CESymmParameters
public CESymmParameters(CESymmParameters o)
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Method Detail
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clone
public CESymmParameters clone()
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reset
public void reset()
Description copied from interface:ConfigStrucAligParams
Set the parameters to the default.- Specified by:
reset
in interfaceConfigStrucAligParams
- Overrides:
reset
in classCeParameters
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getUserConfigHelp
public List<String> getUserConfigHelp()
Description copied from interface:ConfigStrucAligParams
The help text for each of these parameters.- Specified by:
getUserConfigHelp
in interfaceConfigStrucAligParams
- Overrides:
getUserConfigHelp
in classCeParameters
- Returns:
- help strings
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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 interfaceConfigStrucAligParams
- Overrides:
getUserConfigParameters
in classCeParameters
- Returns:
- list of parameters
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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 interfaceConfigStrucAligParams
- Overrides:
getUserConfigParameterNames
in classCeParameters
- Returns:
- list of parameter names
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getUserConfigTypes
public List<Class> getUserConfigTypes()
Description copied from interface:ConfigStrucAligParams
Get the data types of the parameters- Specified by:
getUserConfigTypes
in interfaceConfigStrucAligParams
- Overrides:
getUserConfigTypes
in classCeParameters
- Returns:
- list of parameter classes
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getRefineMethod
public CESymmParameters.RefineMethod getRefineMethod()
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setRefineMethod
public void setRefineMethod(CESymmParameters.RefineMethod refineMethod)
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setRefineResult
@Deprecated public void setRefineResult(boolean doRefine)
Deprecated.
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getOrderDetectorMethod
public CESymmParameters.OrderDetectorMethod getOrderDetectorMethod()
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setOrderDetectorMethod
public void setOrderDetectorMethod(CESymmParameters.OrderDetectorMethod orderDetectorMethod)
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setUserOrder
public void setUserOrder(Integer userOrder)
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getUserOrder
public int getUserOrder()
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setMaxSymmOrder
public void setMaxSymmOrder(Integer maxSymmOrder)
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getMaxSymmOrder
public int getMaxSymmOrder()
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getSymmType
public CESymmParameters.SymmetryType getSymmType()
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setSymmType
public void setSymmType(CESymmParameters.SymmetryType type)
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getOptimization
public boolean getOptimization()
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setOptimization
public void setOptimization(Boolean optimization)
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getRndSeed
public int getRndSeed()
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setRndSeed
public void setRndSeed(Integer seed)
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getSymmLevels
public int getSymmLevels()
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setSymmLevels
public void setSymmLevels(Integer symmLevels)
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getUnrefinedScoreThreshold
public double getUnrefinedScoreThreshold()
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setUnrefinedScoreThreshold
public void setUnrefinedScoreThreshold(Double unrefinedScoreThreshold)
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getRefinedScoreThreshold
public double getRefinedScoreThreshold()
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setRefinedScoreThreshold
public void setRefinedScoreThreshold(Double refinedScoreThreshold)
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getSSEThreshold
public int getSSEThreshold()
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setSSEThreshold
public void setSSEThreshold(Integer sseThreshold)
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getMinCoreLength
public int getMinCoreLength()
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setMinCoreLength
public void setMinCoreLength(Integer minCoreLength)
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getDistanceCutoff
public double getDistanceCutoff()
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setDistanceCutoff
public void setDistanceCutoff(Double distanceCutoff)
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isGaps
public boolean isGaps()
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getOptimizationSteps
public int getOptimizationSteps()
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setOptimizationSteps
public void setOptimizationSteps(Integer optimizationSteps)
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toString
public String toString()
- Overrides:
toString
in classCeParameters
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