Package org.biojava.nbio.alignment.template

Interface GapPenalty

All Known Implementing Classes:
SimpleGapPenalty
public interface GapPenalty
Defines a data structure for the gap penalties used during a sequence alignment routine.
Author:
Mark Chapman

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Interface
    Description
    static enum 
    GapPenalty.Type
    Defines the possible types of gap penalties.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    getExtensionPenalty()
    Returns penalty given when an already open gap elongates by a single element
    int
    getOpenPenalty()
    Returns penalty given when a deletion or insertion gap first opens
    GapPenalty.Type
    getType()
    Returns GapPenalty.Type stored.
    void
    setExtensionPenalty(int gep)
    Sets penalty given when an already open gap elongates by a single element
    void
    setOpenPenalty(int gop)
    Sets penalty given when a deletion or insertion gap first opens

  • Method Details

    • getExtensionPenalty

      int getExtensionPenalty()
      Returns penalty given when an already open gap elongates by a single element
      Returns:
      gap extension penalty

    • getOpenPenalty

      int getOpenPenalty()
      Returns penalty given when a deletion or insertion gap first opens
      Returns:
      gap open penalty

    • getType

      GapPenalty.Type getType()
      Returns GapPenalty.Type stored.
      Returns:
      gap penalty type

    • setExtensionPenalty

      void setExtensionPenalty(int gep)
      Sets penalty given when an already open gap elongates by a single element
      Parameters:
      gep - gap extension penalty

    • setOpenPenalty

      void setOpenPenalty(int gop)
      Sets penalty given when a deletion or insertion gap first opens
      Parameters:
      gop - gap open penalty