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

Fields
Modifier and Type	Field and Description
`static double`	`DEFAULT_SYMMETRY_THRESHOLD`

Constructor Summary

Constructors
Constructor and Description

CESymmParameters()

Constructors
Constructor and Description
`CESymmParameters()`

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
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()`
`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
`int`	`getUserOrder()`
`boolean`	`isGaps()`
`void`	`reset()` Set the parameters to the default.
`void`	`setDistanceCutoff(java.lang.Double distanceCutoff)`
`void`	`setGaps(java.lang.Boolean gaps)`
`void`	`setMaxSymmOrder(java.lang.Integer maxSymmOrder)`
`void`	`setMinCoreLength(java.lang.Integer minCoreLength)`
`void`	`setOptimization(java.lang.Boolean optimization)`
`void`	`setOptimizationSteps(java.lang.Integer optimizationSteps)`
`void`	`setOrderDetectorMethod(CESymmParameters.OrderDetectorMethod orderDetectorMethod)`
`void`	`setRefinedScoreThreshold(java.lang.Double refinedScoreThreshold)`
`void`	`setRefineMethod(CESymmParameters.RefineMethod refineMethod)`
`void`	`setRefineResult(boolean doRefine)` Deprecated.
`void`	`setRndSeed(java.lang.Integer seed)`
`void`	`setSSEThreshold(java.lang.Integer sseThreshold)`
`void`	`setSymmLevels(java.lang.Integer symmLevels)`
`void`	`setSymmType(CESymmParameters.SymmetryType type)`
`void`	`setUnrefinedScoreThreshold(java.lang.Double unrefinedScoreThreshold)`
`void`	`setUserOrder(java.lang.Integer userOrder)`
`java.lang.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 Detail
- DEFAULT_SYMMETRY_THRESHOLD
```
public static final double DEFAULT_SYMMETRY_THRESHOLD
```
  See Also:
  
  Constant Field Values

Constructor Detail
- CESymmParameters
```
public CESymmParameters()
```

Method Detail

clone
```
public CESymmParameters clone()
```
Overrides:

clone in class java.lang.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 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

Overrides:

getUserConfigHelp in class CeParameters

Returns:

help strings

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

Overrides:

getUserConfigParameters in class CeParameters

Returns:

list of parameters

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

Overrides:

getUserConfigParameterNames in class CeParameters

Returns:

list of parameter names

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

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(java.lang.Integer userOrder)

getUserOrder
```
public int getUserOrder()
```

setMaxSymmOrder

public void setMaxSymmOrder(java.lang.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(java.lang.Boolean optimization)

getRndSeed
```
public int getRndSeed()
```

setRndSeed

public void setRndSeed(java.lang.Integer seed)

getSymmLevels
```
public int getSymmLevels()
```

setSymmLevels

public void setSymmLevels(java.lang.Integer symmLevels)

getUnrefinedScoreThreshold

public double getUnrefinedScoreThreshold()

setUnrefinedScoreThreshold

public void setUnrefinedScoreThreshold(java.lang.Double unrefinedScoreThreshold)

getRefinedScoreThreshold

public double getRefinedScoreThreshold()

setRefinedScoreThreshold

public void setRefinedScoreThreshold(java.lang.Double refinedScoreThreshold)

getSSEThreshold
```
public int getSSEThreshold()
```

setSSEThreshold

public void setSSEThreshold(java.lang.Integer sseThreshold)

getMinCoreLength
```
public int getMinCoreLength()
```

setMinCoreLength

public void setMinCoreLength(java.lang.Integer minCoreLength)

getDistanceCutoff
```
public double getDistanceCutoff()
```

setDistanceCutoff

public void setDistanceCutoff(java.lang.Double distanceCutoff)

isGaps
```
public boolean isGaps()
```

setGaps

public void setGaps(java.lang.Boolean gaps)

getOptimizationSteps
```
public int getOptimizationSteps()
```

setOptimizationSteps

public void setOptimizationSteps(java.lang.Integer optimizationSteps)

toString
```
public java.lang.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 Detail

DEFAULT_SYMMETRY_THRESHOLD

Constructor Detail

CESymmParameters

Method Detail

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