Package org.biojava.nbio.structure.align.ce

Class CeUserArgumentProcessor.CeStartupParams

java.lang.Object
org.biojava.nbio.structure.align.ce.StartupParameters
org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
Direct Known Subclasses:
CeCPUserArgumentProcessor.CeCPStartupParams
Enclosing class:
CeUserArgumentProcessor
protected static class CeUserArgumentProcessor.CeStartupParams extends StartupParameters

  • Field Details

    • maxGapSize

      protected int maxGapSize

    • winSize

      protected int winSize

    • scoringStrategy

      protected CeParameters.ScoringStrategy scoringStrategy

    • maxOptRMSD

      protected double maxOptRMSD

    • gapOpen

      protected double gapOpen

    • gapExtension

      protected double gapExtension

    • showAFPRanges

      protected boolean showAFPRanges

  • Constructor Details

    • CeStartupParams

      public CeStartupParams()

  • Method Details

    • getWinSize

      public int getWinSize()

    • setWinSize

      public void setWinSize(int winSize)

    • getScoringStrategy

      public CeParameters.ScoringStrategy getScoringStrategy()

    • setScoringStrategy

      public void setScoringStrategy(CeParameters.ScoringStrategy scoringStrategy)

    • getGapOpen

      public double getGapOpen()

    • setGapOpen

      public void setGapOpen(double gapOpen)

    • getGapExtension

      public double getGapExtension()

    • setGapExtension

      public void setGapExtension(double gapExtension)

    • getMaxGapSize

      public int getMaxGapSize()
      CE specific parameter: set the Max gap size parameter G (during AFP extension). Default: 30
      Returns:
      the maximum gap size G parameter.

    • setMaxGapSize

      public void setMaxGapSize(int maxGapSize)
      CE specific parameter: set the Max gap size parameter G (during AFP extension). Default: 30
      Parameters:
      maxGapSize -

    • isShowAFPRanges

      public boolean isShowAFPRanges()

    • setShowAFPRanges

      public void setShowAFPRanges(boolean showAFP)

    • getMaxOptRMSD

      public Double getMaxOptRMSD()
      (jCE specific): maximum RMSD that shall be calculated for the alignment.
      Returns:
      maxOptRMSD parameter

    • setMaxOptRMSD

      public void setMaxOptRMSD(Double maxOptRMSD)
      (jCE specific): maximum RMSD that shall be calculated for the alignment.
      Parameters:
      maxOptRMSD - max RMSD to calculate

    • toString

      public String toString()
      Overrides:
      toString in class StartupParameters