org.biojavax.bio.seq

Class SimpleRichLocation

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.seq.SimpleRichLocation

All Implemented Interfaces:

Comparable, Annotatable, Location, Changeable, RichLocation, RichAnnotatable

Direct Known Subclasses:

CompoundRichLocation

public class SimpleRichLocation
extends AbstractChangeable
implements RichLocation

A simple implementation of RichLocation.

Since:

1.5

Author:

Richard Holland, Mark Schreiber, George Waldon

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojavax.bio.seq.RichLocation

RichLocation.Strand, RichLocation.Tools

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

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field and Description
protected int	circularLength
protected ComparableTerm	term

Fields inherited from interface org.biojavax.bio.seq.RichLocation

CIRCULAR, EMPTY_LOCATION, FEATURE, NOTE, RANK, TERM

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

empty, full, naturalOrder

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SimpleRichLocation()
	SimpleRichLocation(Position pos, int rank) Creates a new instance of SimpleRichSequenceLocation that points to a single position on the positive strand.
	SimpleRichLocation(Position pos, int rank, RichLocation.Strand strand) Creates a new instance of SimpleRichSequenceLocation that points to a single position.
	SimpleRichLocation(Position pos, int rank, RichLocation.Strand strand, CrossRef crossRef) Creates a new instance of SimpleRichSequenceLocation that points to a single position on another sequence.
	SimpleRichLocation(Position min, Position max, int rank) Creates a new instance of SimpleRichSequenceLocation that points to a range position on the positive strand.
	SimpleRichLocation(Position min, Position max, int rank, RichLocation.Strand strand) Creates a new instance of SimpleRichSequenceLocation that points to a range position.
	SimpleRichLocation(Position min, Position max, int rank, RichLocation.Strand strand, CrossRef crossRef) Creates a new instance of SimpleRichSequenceLocation that points to a range position on another sequence.

Method Summary

Methods

Modifier and Type	Method and Description
Iterator	blockIterator() Return an Iterator over the set of maximal contiguous sub-locations.
int	compareTo(Object o) Locations are sorted first by rank, then crossref, then strand, then term, then min, then max.
boolean	contains(int p) Checks if this location contains a point.
boolean	contains(Location l) Checks if this location contains the other.
boolean	equals(Object o) Checks if this location is equivalent to the other.
Annotation	getAnnotation() Should return the associated annotation object.
int	getCircularLength() Retrieves the circular length of this location.
CrossRef	getCrossRef() Retrieves the crossref associated with this location.
Location	getDecorator(Class decoratorClass) Checks the decorator chain for an instance of decoratorClass and return it if found.
RichFeature	getFeature() Retrieves the feature this location is associated with.
Integer	getId() Gets the Hibernate ID.
int	getMax() The maximum position contained.
Position	getMaxPosition() Retrieves the end position of this location.
int	getMin() The minimum position contained.
Position	getMinPosition() Retrieves the start position of this location.
Set	getNoteSet() Returns the set of notes associated with this object.
int	getRank() Retrieves the rank associated with this location.
RichAnnotation	getRichAnnotation() Return the associated annotation object.
RichLocation.Strand	getStrand() Retrieves the strand associated with this location.
ComparableTerm	getTerm() Retrieves the term associated with this location.
int	hashCode()
Location	intersection(Location l) Returns a Location that contains all points common to both ranges.
boolean	isContiguous() Determine if a Location is contiguous.
Location	newInstance(Location loc) Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.
boolean	overlaps(Location l) Checks if these two locations overlap, using this location's concept of overlapping.
protected Position	posmax(Position a, Position b)
protected Position	posmin(Position a, Position b)
void	setCircularLength(int circularLength) Sets the circular length of this location.
protected void	setCrossRef(CrossRef crossRef)
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	setId(Integer id) Sets the Hibernate ID.
protected void	setMaxPosition(Position max)
protected void	setMinPosition(Position min)
void	setNoteSet(Set notes) Clears the notes associated with this object and replaces them with the contents of this set.
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.
protected void	setStrand(RichLocation.Strand strand)
void	setTerm(ComparableTerm term) Sets the term for this location.
void	sort() Sorts the member locations of a compound location.
SymbolList	symbols(SymbolList seq) Return the symbols in a sequence that fall within this range.
String	toString() Form: "start..end" or just "point" for point locations
Location	translate(int dist) Create a location that is a translation of this location.
Location	union(Location l) Return a Location containing all points in either ranges.

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

term

protected ComparableTerm term

circularLength

protected int circularLength

Constructor Detail

SimpleRichLocation

public SimpleRichLocation(Position pos,
                  int rank)

Creates a new instance of SimpleRichSequenceLocation that points to a single position on the positive strand.

Parameters:

pos - the location position (a point).

rank - Rank of location.

SimpleRichLocation

public SimpleRichLocation(Position pos,
                  int rank,
                  RichLocation.Strand strand)

Creates a new instance of SimpleRichSequenceLocation that points to a single position.

Parameters:

pos - the location position (a point).

rank - Rank of location.

strand - The strand of the location

SimpleRichLocation

public SimpleRichLocation(Position pos,
                  int rank,
                  RichLocation.Strand strand,
                  CrossRef crossRef)

Creates a new instance of SimpleRichSequenceLocation that points to a single position on another sequence.

Parameters:

pos - the location position (a point).

rank - Rank of location.

strand - the strand of the location

crossRef - a cross reference to another object (null for parent sequence)

SimpleRichLocation

public SimpleRichLocation(Position min,
                  Position max,
                  int rank)

Creates a new instance of SimpleRichSequenceLocation that points to a range position on the positive strand.

Parameters:

min - the minimum bound of the location

max - the maximum bound of the location

rank - Rank of location.

SimpleRichLocation

public SimpleRichLocation(Position min,
                  Position max,
                  int rank,
                  RichLocation.Strand strand)

Creates a new instance of SimpleRichSequenceLocation that points to a range position.

Parameters:

min - the minimum bound of the location

max - the maximum bound of the location

rank - Rank of location.

strand - the strand of the location

SimpleRichLocation

public SimpleRichLocation(Position min,
                  Position max,
                  int rank,
                  RichLocation.Strand strand,
                  CrossRef crossRef)

Creates a new instance of SimpleRichSequenceLocation that points to a range position on another sequence.

Parameters:

min - the minimum bound of the location

max - the maximum bound of the location

rank - Rank of location.

strand - the strand of the location

crossRef - a cross reference to another object (null for parent sequence)

SimpleRichLocation

protected SimpleRichLocation()

Method Detail

sort

public 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.

Specified by:

sort in interface RichLocation

getFeature

public RichFeature getFeature()

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

Specified by:

getFeature in interface RichLocation

Returns:

the feature.

setFeature

public 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.

Specified by:

setFeature in interface RichLocation

Parameters:

feature - the feature.

Throws:

ChangeVetoException

getCrossRef

public CrossRef getCrossRef()

Retrieves the crossref associated with this location.

Specified by:

getCrossRef in interface RichLocation

Returns:

the crossref.

setCrossRef

protected void setCrossRef(CrossRef crossRef)

getAnnotation

public Annotation getAnnotation()

Should return the associated annotation object.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation object, never null

getRichAnnotation

public RichAnnotation getRichAnnotation()

Return the associated annotation object.

Specified by:

getRichAnnotation in interface RichAnnotatable

Returns:

a RichAnnotation object, never null

getNoteSet

public Set getNoteSet()

Returns the set of notes associated with this object. Would normally delegate call to internal RichAnnotation instance. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

Specified by:

getNoteSet in interface RichAnnotatable

Returns:

set a set of Note objects.

See Also:

Note

setNoteSet

public void setNoteSet(Set notes)
                throws ChangeVetoException

Clears the notes associated with this object and replaces them with the contents of this set. Would normally delegate call to internal RichAnnotation instance. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

Specified by:

setNoteSet in interface RichAnnotatable

Parameters:

notes - the set of Note objects to replace the existing ones with.

Throws:

ChangeVetoException - if the set is null or contains any objects that are not Note objects.

See Also:

Note

getTerm

public ComparableTerm getTerm()

Retrieves the term associated with this location.

Specified by:

getTerm in interface RichLocation

Returns:

the term.

setTerm

public void setTerm(ComparableTerm term)
             throws ChangeVetoException

Sets the term for this location.

Specified by:

setTerm in interface RichLocation

Parameters:

term - the term this location should adopt.

Throws:

ChangeVetoException - in case of error.

getCircularLength

public 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.

Specified by:

getCircularLength in interface RichLocation

Returns:

the position.

setCircularLength

public void setCircularLength(int circularLength)
                       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.

Specified by:

setCircularLength in interface RichLocation

Parameters:

circularLength - the circular length of this location

Throws:

ChangeVetoException - if it doesn't want to change.

getStrand

public RichLocation.Strand getStrand()

Retrieves the strand associated with this location.

Specified by:

getStrand in interface RichLocation

Returns:

the strand.

setStrand

protected void setStrand(RichLocation.Strand strand)

getRank

public int getRank()

Retrieves the rank associated with this location.

Specified by:

getRank in interface RichLocation

Returns:

the rank.

setRank

public void setRank(int rank)
             throws ChangeVetoException

Sets the rank for this location.

Specified by:

setRank in interface RichLocation

Parameters:

rank - the rank this location should adopt.

Throws:

ChangeVetoException - in case of error.

getMax

public int getMax()

The maximum position contained.

WARNING: The location will not contain every point between getMin() and getMax() if isContiguous() is false. If isContiguous() does return false you should use the Iterator returned by blockIterator() to iterate over the minimum set of contiguous blocks that make up this Location

Specified by:

getMax in interface Location

Returns:

the maximum position contained

getMin

public int getMin()

The minimum position contained.

WARNING: The location will not contain every point between getMin() and getMax() if isContiguous() is false. If isContiguous() does return false you should use the Iterator returned by blockIterator() to iterate over the minimum set of contiguous blocks that make up this Location

Specified by:

getMin in interface Location

Returns:

the minimum position contained

getMinPosition

public Position getMinPosition()

Retrieves the start position of this location.

Specified by:

getMinPosition in interface RichLocation

Returns:

the position.

setMinPosition

protected void setMinPosition(Position min)

getMaxPosition

public Position getMaxPosition()

Retrieves the end position of this location.

Specified by:

getMaxPosition in interface RichLocation

Returns:

the position.

setMaxPosition

protected void setMaxPosition(Position max)

setPositionResolver

public void setPositionResolver(PositionResolver p)

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

Specified by:

setPositionResolver in interface RichLocation

Parameters:

p - the position resolver to use.

blockIterator

public Iterator blockIterator()

Return an Iterator over the set of maximal contiguous sub-locations.

Given any location, it can be considered to contain zero or more maximal contiguous blocks of width 1 or greater. The empty location is composed from nothing. A contiguous location is composed from itself. A non-contiguous location is composed from contiguous blocks seperated by gaps.

This method should return an Iterator over these maximally contiguous blocks starting with the left-most block, and finishing at the right-most block.

Specified by:

blockIterator in interface Location

Returns:

an Iterator over Location objects that are the maximally contiguous set of locations contained within this location

isContiguous

public boolean isContiguous()

Determine if a Location is contiguous.

Specified by:

isContiguous in interface Location

Returns:

true if and only if this Location contains every point from min to max inclusive.

contains

public boolean contains(int p)

Checks if this location contains a point.

Specified by:

contains in interface Location

Parameters:

p - the point to check

Returns:

true if this contains p, otherwise false

getDecorator

public Location getDecorator(Class decoratorClass)

Checks the decorator chain for an instance of decoratorClass and return it if found.

The default behavior is to return null. If the current object is a decorator and is an instance of decoratorClass it should return itself. Otherwise, the decorator should chain this method onto the instance it wraps.

Specified by:

getDecorator in interface Location

Parameters:

decoratorClass - the Class to check

Returns:

a Location if an instance of this class is present in the decorator chain and null otherwise.

newInstance

public Location newInstance(Location loc)

Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.

The default behavior is to return loc unchanged. If the class is a location decorator then it should instantiate an instance of the same type that decorates loc.

Specified by:

newInstance in interface Location

Parameters:

loc - the Location to use as template

Returns:

a Location instance based on loc with the same decorators as the current instance

translate

public Location translate(int dist)

Create a location that is a translation of this location.

Specified by:

translate in interface Location

Parameters:

dist - the distance to translate (to the right)

contains

public boolean contains(Location l)

Checks if this location contains the other.

Abstractly, a location contains another if every point in the other location is contained within this one. A location contains another location if it overlaps it, and the coordinates enclose those of the other location at both ends, and they fall on the same strand.

Specified by:

contains in interface Location

Parameters:

l - the Location to check

Returns:

true if this contains l, otherwise false

overlaps

public boolean overlaps(Location l)

Checks if these two locations overlap, using this location's concept of overlapping.

Abstractly, two locations overlap if they both contain any point. A location overlaps another location if it is on the same sequence, and the coordinates overlap, and both are of the same circularity.

Specified by:

overlaps in interface Location

Parameters:

l - the Location to check

Returns:

true if they overlap, otherwise false

union

public Location union(Location l)

Return a Location containing all points in either ranges. A merged SimpleRichLocation is returned if the two locations overlap and are on the same strand. Otherwise, a CompoundRichLocation is returned containing the two locations as members.

Specified by:

union in interface Location

Parameters:

l - the Location to union with

Returns:

a Location representing the union

intersection

public Location intersection(Location l)

Returns a Location that contains all points common to both ranges. If the locations overlap and are on the same strand, the intersection is returned. If they overlap but are on different strands, a CompoundRichLocation of the overlapping portions is returned. If they do not overlap, the empty sequence is returned.

Specified by:

intersection in interface Location

Parameters:

l - the Location to intersect with

Returns:

a Location containing all points common to both, or the empty range if there are no such points

posmin

protected Position posmin(Position a,
              Position b)

posmax

protected Position posmax(Position a,
              Position b)

setCrossRefResolver

public 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.

Specified by:

setCrossRefResolver in interface RichLocation

Parameters:

r - the resolver to use.

symbols

public SymbolList symbols(SymbolList seq)

Return the symbols in a sequence that fall within this range. If the location is circular but the sequence is not, or they are both circular but of different circular lengths, an exception is thrown. The symbol list passed in is the sequence used to obtain symbols if the cross reference for this location has not been set. If the cross reference has been set, then the symbol list passed in is only used if it has the same accession, namespace and version as the cross reference on this location. Otherwise, the cross referenced symbol list is looked up and used instead.

Specified by:

symbols in interface Location

Parameters:

seq - the SymbolList to process

Returns:

the SymbolList containing the symbols in seq in this range

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Checks if this location is equivalent to the other.

Abstractly, a location is equal to another if for every point in one it is also in the other. This is equivalent to a.contains(b) && b.contains(a). You should call LocationTools.areEqual after casting l to Location. Locations are equal if their term, min, max, strand, and crossref are the same, and if their rank is the same too.

Specified by:

equals in interface Location

Overrides:

equals in class Object

Parameters:

o - the Object to check

Returns:

true if this equals l, otherwise false

compareTo

public int compareTo(Object o)

Locations are sorted first by rank, then crossref, then strand, then term, then min, then max.

Specified by:

compareTo in interface Comparable

toString

public String toString()

Form: "start..end" or just "point" for point locations

Overrides:

toString in class Object

getId

public Integer getId()

Gets the Hibernate ID. Should be used with caution.

Returns:

the Hibernate ID, if using Hibernate.

setId

public void setId(Integer id)

Sets the Hibernate ID. Should be used with caution.

Parameters:

id - the Hibernate ID, if using Hibernate.