Package org.biojavax.bio.seq

Interface RichLocation

All Superinterfaces:

Annotatable, Changeable, Comparable, Location, RichAnnotatable

All Known Implementing Classes:

CompoundRichLocation, EmptyRichLocation, MultiSourceCompoundRichLocation, SimpleRichLocation

public interface RichLocation
extends Location, RichAnnotatable, Comparable

Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases. Also includes strands.

Since:

1.5

Author:

Richard Holland, George Waldon - bug fix

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	RichLocation.Strand	This class represents a strand on which a location may lie.
static class	RichLocation.Tools	Some useful tools for working with Locations.

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field	Description
static ChangeType	CIRCULAR
static RichLocation	EMPTY_LOCATION	The empty location matches nothing.
static ChangeType	FEATURE
static ChangeType	NOTE
static ChangeType	RANK
static ChangeType	TERM

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Fields inherited from interface org.biojava.bio.symbol.Location

empty, full, naturalOrder

Method Summary

Modifier and Type	Method	Description
int	getCircularLength()	Retrieves the circular length of this location.
CrossRef	getCrossRef()	Retrieves the crossref associated with this location.
RichFeature	getFeature()	Retrieves the feature this location is associated with.
Position	getMaxPosition()	Retrieves the end position of this location.
Position	getMinPosition()	Retrieves the start position of this location.
int	getRank()	Retrieves the rank associated with this location.
RichLocation.Strand	getStrand()	Retrieves the strand associated with this location.
ComparableTerm	getTerm()	Retrieves the term associated with this location.
void	setCircularLength(int sourceSeqLength)	Sets the circular length of this location.
void	setCrossRefResolver(CrossReferenceResolver r)	Sets the cross ref resolver to use when retrieving remote symbols.
void	setFeature(RichFeature feature)	Sets the feature this location is associated with.
void	setPositionResolver(PositionResolver p)	Sets the resolver to use when working out actual base coordinates from fuzzy positions.
void	setRank(int rank)	Sets the rank for this location.
void	setTerm(ComparableTerm term)	Sets the term for this location.
void	sort()	Sorts the member locations of a compound location.

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface org.biojava.bio.symbol.Location

blockIterator, contains, contains, equals, getDecorator, getMax, getMin, intersection, isContiguous, newInstance, overlaps, symbols, translate, union

Methods inherited from interface org.biojavax.RichAnnotatable

getNoteSet, getRichAnnotation, setNoteSet

Field Detail

NOTE

static final ChangeType NOTE

TERM

static final ChangeType TERM

RANK

static final ChangeType RANK

CIRCULAR

static final ChangeType CIRCULAR

FEATURE

static final ChangeType FEATURE

EMPTY_LOCATION

static final RichLocation EMPTY_LOCATION

The empty location matches nothing.

Method Detail

sort

void sort()

Sorts the member locations of a compound location. Does nothing for non-compound locations. Sorting depends on the compareTo() method of the member locations - usually they will be sorted by their start position. This might be useful when used with the location returned by a union or intersection, or when setting the term of a compound location to ORDER_TERM.

getFeature

RichFeature getFeature()

Retrieves the feature this location is associated with. May be null.

Returns:

the feature.

setFeature

void setFeature(RichFeature feature)
         throws ChangeVetoException

Sets the feature this location is associated with. If null, that's fine, but you won't be able to persist it to the database until you give it a not-null value.

Parameters:

feature - the feature.

Throws:

ChangeVetoException

getCrossRef

CrossRef getCrossRef()

Retrieves the crossref associated with this location.

Returns:

the crossref.

getTerm

ComparableTerm getTerm()

Retrieves the term associated with this location.

Returns:

the term.

setTerm

void setTerm(ComparableTerm term)
      throws ChangeVetoException

Sets the term for this location.

Parameters:

term - the term this location should adopt.

Throws:

ChangeVetoException - in case of error.

getStrand

RichLocation.Strand getStrand()

Retrieves the strand associated with this location.

Returns:

the strand.

getRank

int getRank()

Retrieves the rank associated with this location.

Returns:

the rank.

setRank

void setRank(int rank)
      throws ChangeVetoException

Sets the rank for this location.

Parameters:

rank - the rank this location should adopt.

Throws:

ChangeVetoException - in case of error.

getMinPosition

Position getMinPosition()

Retrieves the start position of this location.

Returns:

the position.

getMaxPosition

Position getMaxPosition()

Retrieves the end position of this location.

Returns:

the position.

setPositionResolver

void setPositionResolver(PositionResolver p)

Sets the resolver to use when working out actual base coordinates from fuzzy positions.

Parameters:

p - the position resolver to use.

getCircularLength

int getCircularLength()

Retrieves the circular length of this location. If it is 0, the location is not circular. If it is not zero, then the number refers to the wrapping length of the location. eg. 100 would signify that a position of 112 would actually be a position of 112-100 = 12.

Returns:

the position.

setCircularLength

void setCircularLength(int sourceSeqLength)
                throws ChangeVetoException

Sets the circular length of this location. If it is 0, the location is not circular. If it is not zero, then the number refers to the wrapping length of the location. eg. 100 would signify that a position of 112 would actually be a position of 112-100 = 12.

Parameters:

sourceSeqLength - the circular length of this location

Throws:

ChangeVetoException - if it doesn't want to change.

setCrossRefResolver

void setCrossRefResolver(CrossReferenceResolver r)

Sets the cross ref resolver to use when retrieving remote symbols. If none is given, then the default from RichObjectFactory.getDefaultCrossRefResolver() is used.

Parameters:

r - the resolver to use.