Class SimpleGapPenalty

  • All Implemented Interfaces:
    java.io.Serializable, GapPenalty

    public class SimpleGapPenalty
    extends java.lang.Object
    implements GapPenalty, java.io.Serializable
    Implements a data structure for the gap penalties used during a sequence alignment routine.
    Author:
    Mark Chapman
    See Also:
    Serialized Form
    • Constructor Detail

      • SimpleGapPenalty

        public SimpleGapPenalty()
        Creates a new set of gap penalties using the defaults.
      • SimpleGapPenalty

        public SimpleGapPenalty​(int gop,
                                int gep)
        Creates a new set of gap penalties.
        Parameters:
        gop - the gap open penalty; should be nonnegative
        gep - the gap extension penalty; should be nonnegative
    • Method Detail

      • setDefaultExtensionPenalty

        public static void setDefaultExtensionPenalty​(int gep)
        Sets the default gap extension penalty.
        Parameters:
        gep - the default gap extension penalty
      • setDefaultOpenPenalty

        public static void setDefaultOpenPenalty​(int gop)
        Sets the default gap open penalty.
        Parameters:
        gop - the default gap open penalty
      • getExtensionPenalty

        public int getExtensionPenalty()
        Returns the negative of the extension penalty passed to the constructor.
        Specified by:
        getExtensionPenalty in interface GapPenalty
        Returns:
        gap extension penalty
      • getOpenPenalty

        public int getOpenPenalty()
        Returns the negative of the opening penalty passed to the constructor.
        Specified by:
        getOpenPenalty in interface GapPenalty
        Returns:
        gap open penalty
      • setExtensionPenalty

        public void setExtensionPenalty​(int gep)
        Description copied from interface: GapPenalty
        Sets penalty given when an already open gap elongates by a single element
        Specified by:
        setExtensionPenalty in interface GapPenalty
        Parameters:
        gep - Should be nonnegative
      • setOpenPenalty

        public void setOpenPenalty​(int gop)
        Description copied from interface: GapPenalty
        Sets penalty given when a deletion or insertion gap first opens
        Specified by:
        setOpenPenalty in interface GapPenalty
        Parameters:
        gop - Should be nonnegative