Class CeParameters

Method Details

• toString

  public String toString()

  Overrides:

  toString in class Object

• reset

  public void reset()

  Description copied from interface: ConfigStrucAligParams

  Set the parameters to the default.

  Specified by:

  reset in interface ConfigStrucAligParams

• getWinSize

  public Integer getWinSize()

  The window size to look at

  Returns:

  window size

• setWinSize

  public void setWinSize(Integer winSize)

• getRmsdThr

  public Double getRmsdThr()

  RMSD Threshold

  Returns:

  RMSD threshold

• setRmsdThr

  public void setRmsdThr(Double rmsdThr)

• getRmsdThrJoin

  public Double getRmsdThrJoin()

  RMSD threshold for joining of AFPs

  Returns:

  rmsd threshold

• setRmsdThrJoin

  public void setRmsdThrJoin(Double rmsdThrJoin)

• getScoringStrategy

  public CeParameters.ScoringStrategy getScoringStrategy()

• setScoringStrategy

  public void setScoringStrategy(CeParameters.ScoringStrategy scoringStrategy)

  Set the scoring strategy to use. 0 is default CE scoring scheme. 1 uses Side chain orientation.

  Parameters:

  scoringStrategy -

• setMaxGapSize

  public void setMaxGapSize(Integer maxGapSize)

  Set the Max gap size parameter. Default 30. For unlimited gaps set to -1

  Parameters:

  maxGapSize -

• getMaxGapSize

  public Integer getMaxGapSize()

  the Max gap size parameter G . default is 30, which was described to obtained empirically in the CE paper. the larger the max gap size, the longer the compute time, but in same cases drastically improved results. Set to -1 for unlimited gap size.

  Returns:

  max gap size parameter

• 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

• 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

• 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

• 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

• isShowAFPRanges

  public boolean isShowAFPRanges()

  Returns:

  whether information about AFPs should be printed

• setShowAFPRanges

  public void setShowAFPRanges(boolean showAFPRanges)

• setMaxOptRMSD

  public void setMaxOptRMSD(Double param)

  set the maximum RMSD cutoff to be applied during alignment optimization. (default: 99 = unlimited)

  Parameters:

  param - maxOptRMSD

• getMaxOptRMSD

  public Double getMaxOptRMSD()

  Returns the maximum RMSD cutoff to be applied during alignment optimization (default: 99 = unlimited)

  Returns:

  maxOptRMSD

• getGapOpen

  public Double getGapOpen()

• setGapOpen

  public void setGapOpen(Double gapOpen)

• getGapExtension

  public Double getGapExtension()

• setGapExtension

  public void setGapExtension(Double gapExtension)

• getDistanceIncrement

  public Double getDistanceIncrement()

• setDistanceIncrement

  public void setDistanceIncrement(Double distanceIncrement)

• getORmsdThr

  public Double getORmsdThr()

  Get the Original RMSD threshold from which the alignment optimization is started

  Returns:

  oRMSDThreshold

• setORmsdThr

  public void setORmsdThr(Double oRmsdThr)

  Set the Original RMSD threshold from which the alignment optimization is started

  Parameters:

  oRmsdThr - the threshold

• getMaxNrIterationsForOptimization

  public int getMaxNrIterationsForOptimization()

  Get the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited

  Parameters:

  maxNrIterationsForOptimization -

• setMaxNrIterationsForOptimization

  public void setMaxNrIterationsForOptimization(int maxNrIterationsForOptimization)

  Set the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited

  Parameters:

  maxNrIterationsForOptimization -

• getSeqWeight

  public double getSeqWeight()

  Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much. By default this is set to 0, meaning no contribution of the sequence alignment score.

  Returns:

  seqWeight the weight factor (default 0)

• setSeqWeight

  public void setSeqWeight(double seqWeight)

  Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much. By default this is set to 0, meaning no contribution of the sequence alignment score.

  Parameters:

  seqWeight - the weight factor (default 0)

• getSubstitutionMatrix

  public SubstitutionMatrix<AminoAcidCompound> getSubstitutionMatrix()

  Sets the substitution matrix to be used for influencing the alignment with sequence conservation information. Default: SDM matrix (Prlic et al 2000)

  Returns:

  substitutionMatrix

• setSubstitutionMatrix

  public void setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound> substitutionMatrix)

  Sets the substitution matrix to be used for influencing the alignment with sequence conservation information. Default: SDM matrix (Prlic et al 2000)

  Parameters:

  substitutionMatrix -