Package org.biojavax.bio.seq

Interface Position

  • All Known Implementing Classes:
    SimplePosition
    public interface Position
    Holds info about base positions.
    Since:
    1.5
    Author:
    Richard Holland

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String BETWEEN_BASES
      A symbol representing a position that falls in between two bases, eg.
      static Position EMPTY_POSITION
      The empty position lies nowhere.
      static java.lang.String IN_RANGE
      A symbol representing a position that occupies a single base somewhere in a range, eg.

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      int getEnd()
      Returns the end of the range of bases this base could lie in.
      boolean getFuzzyEnd()
      Returns true if the position has a fuzzy end.
      boolean getFuzzyStart()
      Returns true if the position has a fuzzy start.
      int getStart()
      Returns the beginning of the range of bases this base could lie in.
      java.lang.String getType()
      Returns the type of this position if it is not a point/single position.
      Position translate​(int distance)
      Takes this position and returns a copy translated by 'distance' bases.

    • Field Detail

      • EMPTY_POSITION

        static final Position EMPTY_POSITION
        The empty position lies nowhere.

      • BETWEEN_BASES

        static final java.lang.String BETWEEN_BASES
        A symbol representing a position that falls in between two bases, eg. 2^3 falls somewhere in the gap between 2 and 3.
        See Also:
        Constant Field Values

      • IN_RANGE

        static final java.lang.String IN_RANGE
        A symbol representing a position that occupies a single base somewhere in a range, eg. 5.10 falls on some base between 5 and 10.
        See Also:
        Constant Field Values

    • Method Detail

      • getFuzzyStart

        boolean getFuzzyStart()
        Returns true if the position has a fuzzy start.
        Returns:
        the fuzziness of the start.

      • getFuzzyEnd

        boolean getFuzzyEnd()
        Returns true if the position has a fuzzy end.
        Returns:
        the fuzziness of the end.

      • getStart

        int getStart()
        Returns the beginning of the range of bases this base could lie in. If this position is a single position, then start=end.
        Returns:
        the start of this position.

      • getEnd

        int getEnd()
        Returns the end of the range of bases this base could lie in. If this position is a single position, then start=end.
        Returns:
        the end of this position.

      • translate

        Position translate​(int distance)
        Takes this position and returns a copy translated by 'distance' bases.
        Parameters:
        distance - the distance to translate it.
        Returns:
        the translated position.

      • getType

        java.lang.String getType()
        Returns the type of this position if it is not a point/single position. Types are usually BETWEEN_BASES or IN_RANGE but could be any string value.
        Returns:
        the type of this position.