org.biojava3.core.sequence.location
Class SimplePoint

java.lang.Object
  extended by org.biojava3.core.sequence.location.SimplePoint
All Implemented Interfaces:
Comparable<Point>, Point
Direct Known Subclasses:
FuzzyPoint

public class SimplePoint
extends Object
implements Point

Basic implementation of the Point interface.

Author:
ayates

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava3.core.sequence.location.template.Point
Point.Resolver<T extends Point>
 
Constructor Summary
protected SimplePoint()
           
  SimplePoint(int position)
           
  SimplePoint(int position, boolean unknown, boolean uncertain)
           
 
Method Summary
 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 Detail

SimplePoint

protected SimplePoint()

SimplePoint

public SimplePoint(int position)

SimplePoint

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

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