org.biojava.bio.structure.align.fatcat.calc
Class FatCatParameters

java.lang.Object
  extended by org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
All Implemented Interfaces:
ConfigStrucAligParams

public class FatCatParameters
extends Object
implements ConfigStrucAligParams


Field Summary
static int DEFAULT_FRAGLEN
           
 
Constructor Summary
FatCatParameters()
           
 
Method Summary
 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
 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 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