uk.ac.roslin.ensembl.model

Class Coordinate

java.lang.Object

uk.ac.roslin.ensembl.model.Coordinate

All Implemented Interfaces:

Serializable, Comparable<Coordinate>

public class Coordinate
extends Object
implements Comparable<Coordinate>, Serializable

In general a Coordinate must have a non-null non-zero value for both start and end. DNA coordinate systems are complicated by the absence of zero (i.e. ...-3,-2,-1,+1,+2,+3...).

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Coordinate.Strand Public enumeration of the two alternate Strands, FORWARD and REVERSE.

Constructor Summary

Constructors

Constructor and Description
Coordinate() Parameterless constructor.
Coordinate(Integer begin, Integer stop) Utility constructor that takes start and stop integer positions with no defined Strand.
Coordinate(Integer begin, Integer stop, Coordinate.Strand _strand) Full constructor that takes start and stop integer positions and a specified Strand (FORWARD_STRAND, REVERSE_STRAND, otherwise NULL).
Coordinate(Integer begin, Integer stop, Integer strandID) Utility constructor that takes start and stop integer positions and an Integer defining the Strand to be used (FORWARD_STRAND for '+1' and REVERSE_STRAND for '-1' - otherwise NULL).

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(Coordinate o) Implements compareTo(another Coordinate) method for the Comparable interface.
Boolean	containsPoint(Integer point)
Integer	getEnd()
Integer	getLength() Returns the length of this Coordinate - taking into consideration whether the range spans the 'absent' Zero.
Coordinate	getOverlap(Coordinate test) Returns the overlap extent (as a Coordinate) between this Coordinate and a test Coordinate.
Integer	getStart()
Coordinate.Strand	getStrand()
Integer	getStrandInt()
Boolean	liesWithinCoordinate(Coordinate test) Tests whether this Coordinate lies TOTALLY within the range of another test Coordinate.
Boolean	overlaps(Coordinate test) Returns whether this Coordinate overlaps with the extent of a test Coordinate.
void	setEnd(Integer e) public setter for the End of the Coordinate, will swap start and end if new end is less than start.
void	setStart(Integer b) public setter for the start of the Coordinate, will swap start and end if new start is more than the end.
void	setStrand(Coordinate.Strand s)
void	setStrandInt(Integer s) Utility method to set the Strand using an Integer (FORWARD_STRAND for '+1' and REVERSE_STRAND for '-1' - otherwise NULL).
void	setValues(Integer b, Integer e) public setter for the start and end of the Coordinate, will swap start and end if end is less than start.
String	toShortString() Returns String representation in format '1 - 2345' etc.
String	toString() Returns String representation in of format '1 - 5987 REVERSE_STRAND', '1 - 5987 FORWARD_STRAND', '1 - 5987 UNSPECIFIED_STRAND' etc.

Methods inherited from class java.lang.Object

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

Constructor Detail

Coordinate

public Coordinate()

Parameterless constructor. Only to be used by for Mybatis (object mapping API) etc. In general a Coordinate must have a non null non zero value for both start and end.

Coordinate

public Coordinate(Integer begin,
          Integer stop)

Utility constructor that takes start and stop integer positions with no defined Strand. ZERO and null locations are disallowed and will throw IllegalArgument RuntimeExceptions.

Parameters:

begin -

stop -

Coordinate

public Coordinate(Integer begin,
          Integer stop,
          Integer strandID)

Utility constructor that takes start and stop integer positions and an Integer defining the Strand to be used (FORWARD_STRAND for '+1' and REVERSE_STRAND for '-1' - otherwise NULL). ZERO and null locations are disallowed and will throw IllegalArgument RuntimeExceptions.

Parameters:

begin -

stop -

strandID -

Coordinate

public Coordinate(Integer begin,
          Integer stop,
          Coordinate.Strand _strand)

Full constructor that takes start and stop integer positions and a specified Strand (FORWARD_STRAND, REVERSE_STRAND, otherwise NULL). ZERO and null locations are disallowed and will throw IllegalArgument RuntimeExceptions.

Parameters:

begin -

stop -

_strand -

Method Detail

toString

public String toString()

Returns String representation in of format '1 - 5987 REVERSE_STRAND', '1 - 5987 FORWARD_STRAND', '1 - 5987 UNSPECIFIED_STRAND' etc.

Overrides:

toString in class Object

Returns:

String representation of this Coordinate as 'start - stop (Strand)'

toShortString

public String toShortString()

Returns String representation in format '1 - 2345' etc.

Returns:

String representation of this Coordinate as 'start - stop'

getStart

public Integer getStart()

getEnd

public Integer getEnd()

getStrand

public Coordinate.Strand getStrand()

setStart

public void setStart(Integer b)
              throws IllegalArgumentException

public setter for the start of the Coordinate, will swap start and end if new start is more than the end. Use of ZERO (0) or null is disallowed and will throw an IllegalArgument RuntimeException.

Parameters:

b -

Throws:

IllegalArgumentException

setEnd

public void setEnd(Integer e)
            throws IllegalArgumentException

public setter for the End of the Coordinate, will swap start and end if new end is less than start. Use of ZERO (0) or null is disallowed and will throw an IllegalArgument RuntimeException.

Parameters:

e -

Throws:

IllegalArgumentException

setValues

public void setValues(Integer b,
             Integer e)

public setter for the start and end of the Coordinate, will swap start and end if end is less than start. Use of ZERO (0) or null is disallowed and will throw an IllegalArgument RuntimeException.

Parameters:

b -

e -

setStrand

public void setStrand(Coordinate.Strand s)

setStrandInt

public void setStrandInt(Integer s)

Utility method to set the Strand using an Integer (FORWARD_STRAND for '+1' and REVERSE_STRAND for '-1' - otherwise NULL).

Parameters:

s -

getStrandInt

public Integer getStrandInt()

getLength

public Integer getLength()

Returns the length of this Coordinate - taking into consideration whether the range spans the 'absent' Zero.

Returns:

span length of the coordinate

compareTo

public int compareTo(Coordinate o)

Implements compareTo(another Coordinate) method for the Comparable interface. It orders Coordinate objects by the plus strand start, or the plus strand end if the starts are identical. If two Coordinates start at the same position, the the longer one is put first, this has consequences for getting the end coordinate of a set. Zero (0) != Identity because the comparison doesn't consider the strand, just the order. NB. Take care with Integer comparisons.

Specified by:

compareTo in interface Comparable<Coordinate>

Parameters:

o - the compared other Coordinate

Returns:

-1 if this object is upstream of 'o', 1 if downstream of 'o', 0 if coincident or not comparable

liesWithinCoordinate

public Boolean liesWithinCoordinate(Coordinate test)

Tests whether this Coordinate lies TOTALLY within the range of another test Coordinate.

Parameters:

test -

Returns:

Boolean

overlaps

public Boolean overlaps(Coordinate test)

Returns whether this Coordinate overlaps with the extent of a test Coordinate.

Parameters:

test -

Returns:

Boolean

getOverlap

public Coordinate getOverlap(Coordinate test)

Returns the overlap extent (as a Coordinate) between this Coordinate and a test Coordinate.

Parameters:

test -

Returns:

Coordinate

containsPoint

public Boolean containsPoint(Integer point)