Package org.biojavax.bio.seq

Class MultiSourceCompoundRichLocation

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.seq.SimpleRichLocation

org.biojavax.bio.seq.CompoundRichLocation

org.biojavax.bio.seq.MultiSourceCompoundRichLocation

All Implemented Interfaces:

Comparable, Annotatable, Location, Changeable, RichLocation, RichAnnotatable

public class MultiSourceCompoundRichLocation
extends CompoundRichLocation
implements RichLocation

An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.

Since:

1.5

Author:

Richard Holland, Mark Schreiber

Nested Class Summary

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

Annotatable.AnnotationForwarder

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

RichLocation.Strand, RichLocation.Tools

Field Summary

Fields inherited from class org.biojavax.bio.seq.CompoundRichLocation

members, size

Fields inherited from class org.biojavax.bio.seq.SimpleRichLocation

circularLength, term

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

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

empty, full, naturalOrder

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

CIRCULAR, EMPTY_LOCATION, FEATURE, NOTE, RANK, TERM

Constructor Summary

Constructors

Constructor	Description
MultiSourceCompoundRichLocation(Collection members)	Constructs a MultiSourceCompoundRichLocation from the given set of members, with the default term of "join".
MultiSourceCompoundRichLocation(ComparableTerm term, Collection members)	Constructs a MultiSourceCompoundRichLocation from the given set of members.

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.
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.
RichLocation.Strand	getStrand()	Retrieves the strand associated with this location.
void	setCircularLength(int sourceSeqLength)	Sets the circular length of this location.
Location	translate(int dist)	Create a location that is a translation of this location.

Methods inherited from class org.biojavax.bio.seq.CompoundRichLocation

blockIterator, compareTo, contains, contains, equals, getAnnotation, getDecorator, getJoinTerm, getNoteSet, getOrderTerm, getRichAnnotation, hashCode, intersection, isContiguous, newInstance, overlaps, setCrossRefResolver, setFeature, setNoteSet, setTerm, sort, symbols, toString, union

Methods inherited from class org.biojavax.bio.seq.SimpleRichLocation

getFeature, getId, getRank, getTerm, posmax, posmin, setCrossRef, setId, setMaxPosition, setMinPosition, setPositionResolver, setRank, setStrand

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.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, intersection, isContiguous, newInstance, overlaps, symbols, union

Methods inherited from interface org.biojavax.RichAnnotatable

getNoteSet, getRichAnnotation, setNoteSet

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

getFeature, getRank, getTerm, setCrossRefResolver, setFeature, setPositionResolver, setRank, setTerm, sort

Constructor Detail

MultiSourceCompoundRichLocation

public MultiSourceCompoundRichLocation(Collection members)

Constructs a MultiSourceCompoundRichLocation from the given set of members, with the default term of "join". Note that you really shouldn't use this if you are unsure if your members set contains overlapping members. Use RichLocation.Tools.construct() instead. The members collection must only contain Location instances. Any that are not RichLocations will be converted using RichLocation.Tools.enrich().

Parameters:

members - the members to put into the compound location.

See Also:

RichLocation.Tools

MultiSourceCompoundRichLocation

public MultiSourceCompoundRichLocation(ComparableTerm term,
                                       Collection members)

Constructs a MultiSourceCompoundRichLocation from the given set of members. Note that you really shouldn't use this if you are unsure if your members set contains overlapping members. Use RichLocation.Tools.construct(members) instead. The members collection must only contain Location instances. Any that are not RichLocations will be converted using RichLocation.Tools.enrich().

Parameters:

term - the term to use when describing the group of members.

members - the members to put into the compound location.

See Also:

RichLocation.Tools

Method Detail

getCrossRef

public CrossRef getCrossRef()

Retrieves the crossref associated with this location. ALWAYS RETURNS NULL

Specified by:

getCrossRef in interface RichLocation

Overrides:

getCrossRef in class SimpleRichLocation

Returns:

the crossref.

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. ALWAYS RETURNS ZERO

Specified by:

getCircularLength in interface RichLocation

Overrides:

getCircularLength in class SimpleRichLocation

Returns:

the position.

setCircularLength

public 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. RECURSIVELY APPLIES CALL TO ALL MEMBERS NOT IMPLEMENTED

Specified by:

setCircularLength in interface RichLocation

Overrides:

setCircularLength in class CompoundRichLocation

Parameters:

sourceSeqLength - the circular length of this location

Throws:

ChangeVetoException - ALWAYS

getStrand

public RichLocation.Strand getStrand()

Retrieves the strand associated with this location.

Specified by:

getStrand in interface RichLocation

Overrides:

getStrand in class SimpleRichLocation

Returns:

the strand.

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 ALWAYS RETURNS ONE

Specified by:

getMin in interface Location

Overrides:

getMin in class SimpleRichLocation

Returns:

the minimum position contained

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 ALWAYS RETURNS COMBINED LENGTH OF MEMBERS

Specified by:

getMax in interface Location

Overrides:

getMax in class SimpleRichLocation

Returns:

the maximum position contained

getMinPosition

public Position getMinPosition()

Retrieves the start position of this location. ALWAYS RETURNS A POINT POSITION AT POINT 1

Specified by:

getMinPosition in interface RichLocation

Overrides:

getMinPosition in class SimpleRichLocation

Returns:

the position.

getMaxPosition

public Position getMaxPosition()

Retrieves the end position of this location. ALWAYS RETURNS A POINT POSITION AT POINT EQUIVALENT TO COMBINED LENGTH OF MEMBERS

Specified by:

getMaxPosition in interface RichLocation

Overrides:

getMaxPosition in class SimpleRichLocation

Returns:

the position.

translate

public Location translate(int dist)

Create a location that is a translation of this location. Recursively translates all members of this location. Recursively translates all members of this location.

Specified by:

translate in interface Location

Overrides:

translate in class CompoundRichLocation

Parameters:

dist - the distance to translate (to the right)