uk.ac.man.bioinf.sequence.geom
Class SequenceAlignmentPoint

java.lang.Object
  |
  +--uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint

All Implemented Interfaces:

Cloneable, Comparable

public class SequenceAlignmentPoint

extends Object

implements Cloneable, Comparable

SequenceAlignmentPoint.java Represents a point in an alignment, where X is the position in a sequence, and Y is the index of the sequence in the alignment. No checking is currently written into this object for the validity of the point, and the opportunity to use listeners is not seized (although this can easily be added later). Created: Mon Mar 27 11:16:19 2000

Version:

$Id: SequenceAlignmentPoint.java,v 1.9 2001/04/11 17:04:43 lord Exp $

Author:

J Selley

Constructor Summary

SequenceAlignmentPoint()

SequenceAlignmentPoint(int x, int y)

SequenceAlignmentPoint(SequenceAlignmentPoint point)

Method Summary

Object	clone()
int	compareTo(Object obj) Compares this point to another.
boolean	equals(Object obj) Ascertains the equality of a given point to this object.
SequenceAlignmentPoint	getLocation() Returns the location in the sequence alignment, represented by this object.
int	getX() Returns the X index of the point.
int	getY() Returns the Y index of the point.
SequenceAlignmentPoint	move(int x, int y) Allows the moving of a point to a new position.
SequenceAlignmentPoint	setLocation(int x, int y) Sets the location of the point.
SequenceAlignmentPoint	setLocation(SequenceAlignmentPoint point) Sets the location of the point.
SequenceAlignmentPoint	setX(int x)
SequenceAlignmentPoint	setY(int y)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceAlignmentPoint

public SequenceAlignmentPoint()

SequenceAlignmentPoint

public SequenceAlignmentPoint(int x,
                              int y)

SequenceAlignmentPoint

public SequenceAlignmentPoint(SequenceAlignmentPoint point)

Method Detail

equals

public boolean equals(Object obj)

Ascertains the equality of a given point to this object. Overrides the method in Object.

Overrides:

equals in class Object

Parameters:

obj - the point

Returns:

the equality of the objects

compareTo

public int compareTo(Object obj)

Compares this point to another. Points are compared by comparing first the value of getX(), and then getY(). If obj is not a SequenceAlignmentPoint an exception is thrown.

Specified by:

compareTo in interface Comparable

setX

public SequenceAlignmentPoint setX(int x)

setY

public SequenceAlignmentPoint setY(int y)

setLocation

public SequenceAlignmentPoint setLocation(int x,
                                          int y)

Sets the location of the point. This method can be further expanded if listeners are appropriate, and to include error checking.

Parameters:

x - the x position of the point

y - the y position of the point

setLocation

public SequenceAlignmentPoint setLocation(SequenceAlignmentPoint point)

Sets the location of the point. This method will allow a point to be duplicated. Calls setLocation(int, int) to save on correction procedures.

Parameters:

point - the point in a sequence alignment

move

public SequenceAlignmentPoint move(int x,
                                   int y)

Allows the moving of a point to a new position.

Parameters:

x - the X index

y - the Y index

getLocation

public SequenceAlignmentPoint getLocation()

Returns the location in the sequence alignment, represented by this object.

Returns:

the location represented by this point

getX

public int getX()

Returns the X index of the point.

Returns:

the X index

getY

public int getY()

Returns the Y index of the point.

Returns:

the Y index

clone

public Object clone()
             throws CloneNotSupportedException

Overrides:

clone in class Object

CloneNotSupportedException

toString

public String toString()

Overrides:

toString in class Object