Class FatCatParameters

Method Details

• 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