Package org.biojava.nbio.core.sequence.location

Class SimplePoint

java.lang.Object
org.biojava.nbio.core.sequence.location.SimplePoint
All Implemented Interfaces:
Serializable, Comparable<Point>, Point
Direct Known Subclasses:
FuzzyPoint
public class SimplePoint extends Object implements Serializable, Point
Basic implementation of the Point interface.
Author:
ayates
See Also:

  • Nested Class Summary

    Nested classes/interfaces inherited from interface org.biojava.nbio.core.sequence.location.template.Point

    Point.Resolver<T extends Point>

  • Constructor Summary

    Constructors
    Modifier
    Constructor
    Description
    protected
    SimplePoint()
     
     
    SimplePoint(int position)
     
     
    SimplePoint(int position, boolean unknown, boolean uncertain)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    Point
    clonePoint()
    Returns a copy of this point
    int
    compareTo(Point o)
     
    boolean
    equals(Object obj)
     
    Integer
    getPosition()
    Returns the position held by this object
    int
    hashCode()
     
    boolean
    isHigher(Point point)
    Returns true if the point is higher in value to the current point
    boolean
    isLower(Point point)
    Returns true if the current point is at a lower position than the point given.
    boolean
    isUncertain()
    Returns a true if the exact point is unknown.
    boolean
    isUnknown()
    Returns true if the current position is unknown but is beyond the position encoded for.
    Point
    offset(int distance)
    Returns a new point offset by the given distance
    Point
    reverse(int length)
    Returns the equivalent position on the reverse strand
    protected int
    reverse(int position, int length)
     
    protected void
    setPosition(int position)
     
    protected void
    setUncertain(boolean uncertain)
     
    protected void
    setUnknown(boolean unknown)
     
    String
    toString()
     

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • SimplePoint

      protected SimplePoint()

    • SimplePoint

      public SimplePoint(int position)

    • SimplePoint

      public SimplePoint(int position, boolean unknown, boolean uncertain)

  • Method Details

    • getPosition

      public Integer getPosition()
      Description copied from interface: Point
      Returns the position held by this object
      Specified by:
      getPosition in interface Point

    • setPosition

      protected void setPosition(int position)

    • isUnknown

      public boolean isUnknown()
      Description copied from interface: Point
      Returns true if the current position is unknown but is beyond the position encoded for. This is the same as the position 
      >80
      as encoded by UniProt.
      Specified by:
      isUnknown in interface Point

    • setUnknown

      protected void setUnknown(boolean unknown)

    • isUncertain

      public boolean isUncertain()
      Description copied from interface: Point
      Returns a true if the exact point is unknown. Equivalent position from UniProt is 
      ?80
      .
      Specified by:
      isUncertain in interface Point

    • setUncertain

      protected void setUncertain(boolean uncertain)

    • reverse

      public Point reverse(int length)
      Description copied from interface: Point
      Returns the equivalent position on the reverse strand
      Specified by:
      reverse in interface Point
      Parameters:
      length - Length of the sequence to translate to

    • offset

      public Point offset(int distance)
      Description copied from interface: Point
      Returns a new point offset by the given distance
      Specified by:
      offset in interface Point

    • reverse

      protected int reverse(int position, int length)

    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • compareTo

      public int compareTo(Point o)
      Specified by:
      compareTo in interface Comparable<Point>

    • isLower

      public boolean isLower(Point point)
      Description copied from interface: Point
      Returns true if the current point is at a lower position than the point given.
      Specified by:
      isLower in interface Point

    • isHigher

      public boolean isHigher(Point point)
      Description copied from interface: Point
      Returns true if the point is higher in value to the current point
      Specified by:
      isHigher in interface Point

    • clonePoint

      public Point clonePoint()
      Description copied from interface: Point
      Returns a copy of this point
      Specified by:
      clonePoint in interface Point