Package org.biojava.nbio.alignment

Class SimpleGapPenalty

java.lang.Object
org.biojava.nbio.alignment.SimpleGapPenalty
All Implemented Interfaces:
Serializable, GapPenalty
public class SimpleGapPenalty extends Object implements GapPenalty, Serializable
Implements a data structure for the gap penalties used during a sequence alignment routine.
Author:
Mark Chapman
See Also:

  • Constructor Details

    • 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 Details

    • 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

    • getType

      public GapPenalty.Type getType()
      Description copied from interface: GapPenalty
      Returns GapPenalty.Type stored.
      Specified by:
      getType in interface GapPenalty
      Returns:
      gap penalty type

    • 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