org.biojavax

Interface RankedDocRef

All Superinterfaces:

Changeable, Comparable

All Known Implementing Classes:

SimpleRankedDocRef

public interface RankedDocRef
extends Comparable, Changeable

Represents a documentary reference. Relates to the bioentryreference table in BioSQL.

Since:

1.5

Author:

Richard Holland, gwaldon

See Also:

DocRef

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	LOCATION
static ChangeType	RANK

Method Summary

Modifier and Type	Method and Description
DocRef	getDocumentReference() Represents a reference to a document.
Integer	getEnd() The end position in the sequence that this reference is referred to from.
RichLocation	getLocation() If this object was constructed using a location instead of two integers, then this method will return that location.
int	getRank() The rank of this reference.
Integer	getStart() The start position in the sequence that this reference is referred to from.
void	setLocation(RichLocation location) Set the location of this reference.
void	setRank(int rank) Set the rank of this reference.

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

RANK

static final ChangeType RANK

LOCATION

static final ChangeType LOCATION

Method Detail

getDocumentReference

DocRef getDocumentReference()

Represents a reference to a document. This value is intended to be set by the constructor of the implementing class.

Returns:

the document reference.

getStart

Integer getStart()

The start position in the sequence that this reference is referred to from. This value is intended to be set by the constructor of the implementing class. The position returned is from 1 to the length of the sequence.

Returns:

the start position.

getEnd

Integer getEnd()

The end position in the sequence that this reference is referred to from. This value is intended to be set by the constructor of the implementing class. The position returned is from 1 to the length of the sequence.

Returns:

the end position.

getLocation

RichLocation getLocation()

If this object was constructed using a location instead of two integers, then this method will return that location. The getStart() and getEnd() methods will then return the min and max of that location, using the default location position resolver to resolve them to exact positions. If this object was constructed using two integers, then this method will return a simple location whose min and max correspond to those integers.

Returns:

the location of this reference on the sequence.

setLocation

void setLocation(RichLocation location)
          throws ChangeVetoException

Set the location of this reference.

Parameters:

location - the location to use.

Throws:

ChangeVetoException - if the new location is unacceptable.

getRank

int getRank()

The rank of this reference. This value is intended to be set by the constructor of the implementing class.

Returns:

the rank.

setRank

void setRank(int rank)
      throws ChangeVetoException

Set the rank of this reference.

Parameters:

rank - the rank to use.

Throws:

ChangeVetoException - if the new rank is unacceptable.