Class FatCatParameters
- java.lang.Object
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- org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters
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- All Implemented Interfaces:
ConfigStrucAligParams
public class FatCatParameters extends Object implements ConfigStrucAligParams
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Field Summary
Fields Modifier and Type Field Description static int
DEFAULT_FRAGLEN
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Constructor Summary
Constructors Constructor Description FatCatParameters()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
getAfpDisCut()
double
getAfpDisCut0()
double
getBadRmsd()
Double
getDisCut()
Get the distance cutoff used during AFP chain connectivity checksdouble
getDisFilter()
double
getDisSmooth()
Integer
getFragLen()
int
getFragLenSq()
double
getFragScore()
double
getGapCreate()
double
getGapExtend()
int
getMaxGap()
int
getMaxGapFrag()
double
getMaxPenalty()
Integer
getMaxTra()
get the maximum number of Twists that are allowed...int
getMisCut()
double
getMisScore()
double
getResScore()
Double
getRmsdCut()
The cutoff to be used during AFP detectionint
getSparse()
double
getTorsionPenalty()
List<String>
getUserConfigHelp()
The help text for each of these parameters.List<String>
getUserConfigParameterNames()
The labels to be displayed to the user for each parameterList<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 parametersboolean
isOptimizeAlignment()
Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.void
reset()
Set the parameters to the default.void
setAfpDisCut(double afpDisCut)
void
setAfpDisCut0(double afpDisCut0)
void
setBadRmsd(double badRmsd)
void
setDisCut(Double disCut)
void
setDisFilter(double disFilter)
void
setDisSmooth(double disSmooth)
void
setFragLen(Integer fragLen)
void
setFragLenSq(int fragLenSq)
void
setFragScore(double fragScore)
void
setGapCreate(double gapCreate)
void
setGapExtend(double gapExtend)
void
setMaxGap(int maxGap)
void
setMaxGapFrag(int maxGapFrag)
void
setMaxPenalty(double maxPenalty)
void
setMaxTra(Integer maxTra)
set the maximum number of Twists that are allowed...void
setMisCut(int misCut)
void
setMisScore(double misScore)
void
setOptimizeAlignment(boolean optimizeAlignment)
Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.void
setResScore(double resScore)
void
setRmsdCut(Double rmsdCut)
The cutoff to be used during AFP detectionvoid
setSparse(int sparse)
void
setTorsionPenalty(double torsionPenalty)
String
toString()
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Field Detail
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DEFAULT_FRAGLEN
public static final int DEFAULT_FRAGLEN
- See Also:
- Constant Field Values
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Constructor Detail
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FatCatParameters
public FatCatParameters()
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Method Detail
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reset
public void reset()
Description copied from interface:ConfigStrucAligParams
Set the parameters to the default.- Specified by:
reset
in interfaceConfigStrucAligParams
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getFragLen
public Integer getFragLen()
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setFragLen
public void setFragLen(Integer fragLen)
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getFragLenSq
public int getFragLenSq()
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setFragLenSq
public void setFragLenSq(int fragLenSq)
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getRmsdCut
public Double getRmsdCut()
The cutoff to be used during AFP detection- Returns:
- rmsdCut parameter
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setRmsdCut
public void setRmsdCut(Double rmsdCut)
The cutoff to be used during AFP detection- Parameters:
rmsdCut
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getDisCut
public Double getDisCut()
Get the distance cutoff used during AFP chain connectivity checks- Returns:
- distance Cutoff
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getAfpDisCut
public double getAfpDisCut()
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setAfpDisCut
public void setAfpDisCut(double afpDisCut)
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getAfpDisCut0
public double getAfpDisCut0()
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setAfpDisCut0
public void setAfpDisCut0(double afpDisCut0)
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getDisSmooth
public double getDisSmooth()
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setDisSmooth
public void setDisSmooth(double disSmooth)
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getMisCut
public int getMisCut()
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setMisCut
public void setMisCut(int misCut)
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getMaxGap
public int getMaxGap()
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setMaxGap
public void setMaxGap(int maxGap)
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getMaxGapFrag
public int getMaxGapFrag()
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setMaxGapFrag
public void setMaxGapFrag(int maxGapFrag)
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getDisFilter
public double getDisFilter()
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setDisFilter
public void setDisFilter(double disFilter)
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getBadRmsd
public double getBadRmsd()
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setBadRmsd
public void setBadRmsd(double badRmsd)
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getMaxTra
public Integer getMaxTra()
get the maximum number of Twists that are allowed...- Returns:
- max nr of allowed twists
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setMaxTra
public void setMaxTra(Integer maxTra)
set the maximum number of Twists that are allowed...- Parameters:
maxTra
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getGapCreate
public double getGapCreate()
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setGapCreate
public void setGapCreate(double gapCreate)
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getGapExtend
public double getGapExtend()
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setGapExtend
public void setGapExtend(double gapExtend)
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getMisScore
public double getMisScore()
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setMisScore
public void setMisScore(double misScore)
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getTorsionPenalty
public double getTorsionPenalty()
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setTorsionPenalty
public void setTorsionPenalty(double torsionPenalty)
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getMaxPenalty
public double getMaxPenalty()
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setMaxPenalty
public void setMaxPenalty(double maxPenalty)
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getResScore
public double getResScore()
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setResScore
public void setResScore(double resScore)
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getFragScore
public double getFragScore()
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setFragScore
public void setFragScore(double fragScore)
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getSparse
public int getSparse()
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setSparse
public void setSparse(int sparse)
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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
- Returns:
- help strings
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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
- Returns:
- list of parameter names
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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
- Returns:
- list of parameters
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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
- Returns:
- list of parameter classes
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isOptimizeAlignment
public boolean isOptimizeAlignment()
Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result. NB: Not implemented in jFatCat- Returns:
- optimizeAlignment
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setOptimizeAlignment
public void setOptimizeAlignment(boolean optimizeAlignment)
Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result. NB: Not implemented in jFatCat- Parameters:
optimizeAlignment
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