ConfigStrucAligParams
public class CESymmParameters extends CeParameters
CeSymm
.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.
|
CeParameters.ScoringStrategy
Modifier and Type | Field | Description |
---|---|---|
static double |
DEFAULT_SYMMETRY_THRESHOLD |
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 | Description |
---|---|
CESymmParameters() |
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() |
|
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() |
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
public static final double DEFAULT_SYMMETRY_THRESHOLD
public CESymmParameters clone()
clone
in class java.lang.Object
public void reset()
ConfigStrucAligParams
reset
in interface ConfigStrucAligParams
reset
in class CeParameters
public java.util.List<java.lang.String> getUserConfigHelp()
ConfigStrucAligParams
getUserConfigHelp
in interface ConfigStrucAligParams
getUserConfigHelp
in class CeParameters
public java.util.List<java.lang.String> getUserConfigParameters()
ConfigStrucAligParams
getUserConfigParameters
in interface ConfigStrucAligParams
getUserConfigParameters
in class CeParameters
public java.util.List<java.lang.String> getUserConfigParameterNames()
ConfigStrucAligParams
getUserConfigParameterNames
in interface ConfigStrucAligParams
getUserConfigParameterNames
in class CeParameters
public java.util.List<java.lang.Class> getUserConfigTypes()
ConfigStrucAligParams
getUserConfigTypes
in interface ConfigStrucAligParams
getUserConfigTypes
in class CeParameters
public CESymmParameters.RefineMethod getRefineMethod()
public void setRefineMethod(CESymmParameters.RefineMethod refineMethod)
@Deprecated public void setRefineResult(boolean doRefine)
public CESymmParameters.OrderDetectorMethod getOrderDetectorMethod()
public void setOrderDetectorMethod(CESymmParameters.OrderDetectorMethod orderDetectorMethod)
public void setUserOrder(java.lang.Integer userOrder)
public int getUserOrder()
public void setMaxSymmOrder(java.lang.Integer maxSymmOrder)
public int getMaxSymmOrder()
public CESymmParameters.SymmetryType getSymmType()
public void setSymmType(CESymmParameters.SymmetryType type)
public boolean getOptimization()
public void setOptimization(java.lang.Boolean optimization)
public int getRndSeed()
public void setRndSeed(java.lang.Integer seed)
public int getSymmLevels()
public void setSymmLevels(java.lang.Integer symmLevels)
public double getUnrefinedScoreThreshold()
public void setUnrefinedScoreThreshold(java.lang.Double unrefinedScoreThreshold)
public double getRefinedScoreThreshold()
public void setRefinedScoreThreshold(java.lang.Double refinedScoreThreshold)
public int getSSEThreshold()
public void setSSEThreshold(java.lang.Integer sseThreshold)
public int getMinCoreLength()
public void setMinCoreLength(java.lang.Integer minCoreLength)
public double getDistanceCutoff()
public void setDistanceCutoff(java.lang.Double distanceCutoff)
public boolean isGaps()
public void setGaps(java.lang.Boolean gaps)
public int getOptimizationSteps()
public void setOptimizationSteps(java.lang.Integer optimizationSteps)
public java.lang.String toString()
toString
in class CeParameters