java.lang.Object
- org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters

All Implemented Interfaces:: ConfigStrucAligParams

public class FatCatParameters
extends Object
implements ConfigStrucAligParams

Field Summary

Fields
Modifier and Type Field Description

static int DEFAULT_FRAGLEN

Constructor Summary

Constructors
Constructor Description

FatCatParameters()

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 checks
`double`	`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 detection
`int`	`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 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
`boolean`	`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 detection
`void`	`setSparse(int sparse)`
`void`	`setTorsionPenalty(double torsionPenalty)`
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - DEFAULT_FRAGLEN
```
public static final int DEFAULT_FRAGLEN
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - FatCatParameters
```
public FatCatParameters()
```
- Method Detail
  - reset
```
public void reset()
```
    Description copied from interface: ConfigStrucAligParams
    
    Set the parameters to the default.
    
    Specified by:
    
    reset in interface ConfigStrucAligParams
  - getFragLen
```
public Integer getFragLen()
```
  - setFragLen
```
public void setFragLen(Integer fragLen)
```
  - getFragLenSq
```
public int getFragLenSq()
```
  - setFragLenSq
```
public void setFragLenSq(int fragLenSq)
```
  - getRmsdCut
```
public Double getRmsdCut()
```
    The cutoff to be used during AFP detection
    
    Returns:
    
    rmsdCut parameter
  - setRmsdCut
```
public void setRmsdCut(Double rmsdCut)
```
    The cutoff to be used during AFP detection
    
    Parameters:
    
    rmsdCut -
  - getDisCut
```
public Double getDisCut()
```
    Get the distance cutoff used during AFP chain connectivity checks
    
    Returns:
    
    distance Cutoff
  - setDisCut
```
public void setDisCut(Double disCut)
```
  - getAfpDisCut
```
public double getAfpDisCut()
```
  - setAfpDisCut
```
public void setAfpDisCut(double afpDisCut)
```
  - getAfpDisCut0
```
public double getAfpDisCut0()
```
  - setAfpDisCut0
```
public void setAfpDisCut0(double afpDisCut0)
```
  - getDisSmooth
```
public double getDisSmooth()
```
  - setDisSmooth
```
public void setDisSmooth(double disSmooth)
```
  - getMisCut
```
public int getMisCut()
```
  - setMisCut
```
public void setMisCut(int misCut)
```
  - getMaxGap
```
public int getMaxGap()
```
  - setMaxGap
```
public void setMaxGap(int maxGap)
```
  - getMaxGapFrag
```
public int getMaxGapFrag()
```
  - setMaxGapFrag
```
public void setMaxGapFrag(int maxGapFrag)
```
  - getDisFilter
```
public double getDisFilter()
```
  - setDisFilter
```
public void setDisFilter(double disFilter)
```
  - getBadRmsd
```
public double getBadRmsd()
```
  - setBadRmsd
```
public void setBadRmsd(double badRmsd)
```
  - getMaxTra
```
public Integer getMaxTra()
```
    get the maximum number of Twists that are allowed...
    
    Returns:
    
    max nr of allowed twists
  - setMaxTra
```
public void setMaxTra(Integer maxTra)
```
    set the maximum number of Twists that are allowed...
    
    Parameters:
    
    maxTra -
  - getGapCreate
```
public double getGapCreate()
```
  - setGapCreate
```
public void setGapCreate(double gapCreate)
```
  - getGapExtend
```
public double getGapExtend()
```
  - setGapExtend
```
public void setGapExtend(double gapExtend)
```
  - getMisScore
```
public double getMisScore()
```
  - setMisScore
```
public void setMisScore(double misScore)
```
  - getTorsionPenalty
```
public double getTorsionPenalty()
```
  - setTorsionPenalty
```
public void setTorsionPenalty(double torsionPenalty)
```
  - getMaxPenalty
```
public double getMaxPenalty()
```
  - setMaxPenalty
```
public void setMaxPenalty(double maxPenalty)
```
  - getResScore
```
public double getResScore()
```
  - setResScore
```
public void setResScore(double resScore)
```
  - getFragScore
```
public double getFragScore()
```
  - setFragScore
```
public void setFragScore(double fragScore)
```
  - getSparse
```
public int getSparse()
```
  - setSparse
```
public void setSparse(int sparse)
```
  - getUserConfigHelp
```
public List<String> getUserConfigHelp()
```
    Description copied from interface: ConfigStrucAligParams
    
    The help text for each of these parameters.
    
    Specified by:
    
    getUserConfigHelp in interface ConfigStrucAligParams
    
    Returns:
    
    help strings
  - 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
    
    Returns:
    
    list of parameter names
  - 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
    
    Returns:
    
    list of parameters
  - getUserConfigTypes
```
public List<Class> getUserConfigTypes()
```
    Description copied from interface: ConfigStrucAligParams
    
    Get the data types of the parameters
    
    Specified by:
    
    getUserConfigTypes in interface ConfigStrucAligParams
    
    Returns:
    
    list of parameter classes
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - 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
  - 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 -

Class FatCatParameters

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_FRAGLEN

Constructor Detail

FatCatParameters

Method Detail

reset

getFragLen

setFragLen

getFragLenSq

setFragLenSq

getRmsdCut

setRmsdCut

getDisCut

setDisCut

getAfpDisCut

setAfpDisCut

getAfpDisCut0

setAfpDisCut0

getDisSmooth

setDisSmooth

getMisCut

setMisCut

getMaxGap

setMaxGap

getMaxGapFrag

setMaxGapFrag

getDisFilter

setDisFilter

getBadRmsd

setBadRmsd

getMaxTra

setMaxTra

getGapCreate

setGapCreate

getGapExtend

setGapExtend

getMisScore

setMisScore

getTorsionPenalty

setTorsionPenalty

getMaxPenalty

setMaxPenalty

getResScore

setResScore

getFragScore

setFragScore

getSparse

setSparse

getUserConfigHelp

getUserConfigParameterNames

getUserConfigParameters

getUserConfigTypes

toString

isOptimizeAlignment

setOptimizeAlignment