Package org.biojavax.bio.seq

Class SimplePosition

java.lang.Object
org.biojavax.bio.seq.SimplePosition
All Implemented Interfaces:
Position
public class SimplePosition extends Object implements Position
A simple implementation of the Position interface.
Since:
1.5
Author:
Richard Holland

  • Field Summary

    Fields inherited from interface org.biojavax.bio.seq.Position

    BETWEEN_BASES, EMPTY_POSITION, IN_RANGE

  • Constructor Summary

    Constructors
    Modifier
    Constructor
    Description
    protected
    SimplePosition()
     
     
    SimplePosition(boolean fs, boolean fe, int p)
    Constructs a point position, with optionally fuzzy start and end.
     
    SimplePosition(boolean fs, boolean fe, int s, int e, String t)
    Constructs a range position, with optionally fuzzy start and end.
     
    SimplePosition(int p)
    Constructs a point position, with no fuzzy start or end.
     
    SimplePosition(int s, int e)
    Constructs a range position, with no fuzzy start or end.

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    equals(Object o)
    Two positions are equal if they share all parameters in common, eg. fuzzy start+end, start, end, type.
    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.
    Integer
    getId()
    Gets the Hibernate ID.
    int
    getStart()
    Returns the beginning of the range of bases this base could lie in.
    String
    getType()
    Returns the type of this position if it is not a point/single position.
    void
    setId(Integer id)
    Sets the Hibernate ID.
    String
    toString()
    Position
    translate(int distance)
    Takes this position and returns a copy translated by 'distance' bases.

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

  • Constructor Details

    • SimplePosition

      public SimplePosition(int p)
      Constructs a point position, with no fuzzy start or end. (eg. 1, 2, or 3).
      Parameters:
      p - the point position

    • SimplePosition

      public SimplePosition(int s, int e)
      Constructs a range position, with no fuzzy start or end. (eg. 1..2, 2..5, or 3..8).
      Parameters:
      s - the start position
      e - the end position

    • SimplePosition

      public SimplePosition(boolean fs, boolean fe, int p)
      Constructs a point position, with optionally fuzzy start and end. (eg. <1 or 3> or 2 or even <5>).
      Parameters:
      fs - fuzzy start?
      fe - fuzzy end?
      p - the point position

    • SimplePosition

      public SimplePosition(boolean fs, boolean fe, int s, int e, String t)
      Constructs a range position, with optionally fuzzy start and end. (eg. <1.2 or 1^3> or 2.2 or even <5^6>). The type of the range is given, it should normally be one of the two defined in the Position interface, but its up to you.
      Parameters:
      fs - fuzzy start?
      fe - fuzzy end?
      s - the start of the position
      e - the end of the position
      t - the type of the position

    • SimplePosition

      protected SimplePosition()

  • Method Details

    • getFuzzyStart

      public boolean getFuzzyStart()
      Returns true if the position has a fuzzy start.
      Specified by:
      getFuzzyStart in interface Position
      Returns:
      the fuzziness of the start.

    • getFuzzyEnd

      public boolean getFuzzyEnd()
      Returns true if the position has a fuzzy end.
      Specified by:
      getFuzzyEnd in interface Position
      Returns:
      the fuzziness of the end.

    • getStart

      public 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.
      Specified by:
      getStart in interface Position
      Returns:
      the start of this position.

    • getEnd

      public 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.
      Specified by:
      getEnd in interface Position
      Returns:
      the end of this position.

    • getType

      public 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.
      Specified by:
      getType in interface Position
      Returns:
      the type of this position.

    • translate

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

    • equals

      public boolean equals(Object o)
      Two positions are equal if they share all parameters in common, eg. fuzzy start+end, start, end, type.
      Overrides:
      equals in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getId

      public Integer getId()
      Gets the Hibernate ID. Should be used with caution.
      Returns:
      the Hibernate ID, if using Hibernate.

    • setId

      public void setId(Integer id)
      Sets the Hibernate ID. Should be used with caution.
      Parameters:
      id - the Hibernate ID, if using Hibernate.