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(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.
     
    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
    Two positions are equal if they share all parameters in common, eg. fuzzy start+end, start, end, type.
    int
    Returns the end of the range of bases this base could lie in.
    boolean
    Returns true if the position has a fuzzy end.
    boolean
    Returns true if the position has a fuzzy start.
    Gets the Hibernate ID.
    int
    Returns the beginning of the range of bases this base could lie in.
    Returns the type of this position if it is not a point/single position.
    void
    Sets the Hibernate ID.
    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. invalid input: '<'1 or 3> or 2 or even invalid input: '<'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. invalid input: '<'1.2 or 1^3> or 2.2 or even invalid input: '<'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.