Class SimpleRichLocation
- All Implemented Interfaces:
Comparable
,Annotatable
,Location
,Changeable
,RichLocation
,RichAnnotatable
- Direct Known Subclasses:
CompoundRichLocation
- Since:
- 1.5
- Author:
- Richard Holland, Mark Schreiber, George Waldon
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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
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Field Summary
FieldsFields 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
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Constructor Summary
ConstructorsModifierConstructorDescriptionprotected
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
Modifier and TypeMethodDescriptionReturn an Iterator over the set of maximal contiguous sub-locations.int
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
Checks if this location contains the other.boolean
Checks if this location is equivalent to the other.Should return the associated annotation object.int
Retrieves the circular length of this location.Retrieves the crossref associated with this location.getDecorator
(Class decoratorClass) Checks the decorator chain for an instance ofdecoratorClass and return it if found.Retrieves the feature this location is associated with.getId()
Gets the Hibernate ID.int
getMax()
The maximum position contained.Retrieves the end position of this location.int
getMin()
The minimum position contained.Retrieves the start position of this location.Returns the set of notes associated with this object.int
getRank()
Retrieves the rank associated with this location.Return the associated annotation object.Retrieves the strand associated with this location.getTerm()
Retrieves the term associated with this location.int
hashCode()
Returns a Location that contains all points common to both ranges.boolean
Determine if a Location is contiguous.newInstance
(Location loc) Create a new instance of Location with all of the same decorators as this instance but with the data stored inloc
.boolean
Checks if these two locations overlap, using this location's concept of overlapping.protected Position
protected Position
void
setCircularLength
(int circularLength) Sets the circular length of this location.protected void
setCrossRef
(CrossRef crossRef) void
Sets the cross ref resolver to use when retrieving remote symbols.void
setFeature
(RichFeature feature) Sets the feature this location is associated with.void
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
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.symbols
(SymbolList seq) Return the symbols in a sequence that fall within this range.toString()
Form: "start..end" or just "point" for point locationstranslate
(int dist) Create a location that is a translation of this location.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
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Field Details
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term
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circularLength
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Constructor Details
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SimpleRichLocation
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.
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SimpleRichLocation
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
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SimpleRichLocation
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 locationcrossRef
- a cross reference to another object (null for parent sequence)
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SimpleRichLocation
Creates a new instance of SimpleRichSequenceLocation that points to a range position on the positive strand.- Parameters:
min
- the minimum bound of the locationmax
- the maximum bound of the locationrank
- Rank of location.
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SimpleRichLocation
Creates a new instance of SimpleRichSequenceLocation that points to a range position.- Parameters:
min
- the minimum bound of the locationmax
- the maximum bound of the locationrank
- Rank of location.strand
- the strand of the location
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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 locationmax
- the maximum bound of the locationrank
- Rank of location.strand
- the strand of the locationcrossRef
- a cross reference to another object (null for parent sequence)
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SimpleRichLocation
protected SimpleRichLocation()
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Method Details
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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 interfaceRichLocation
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getFeature
Retrieves the feature this location is associated with. May be null.- Specified by:
getFeature
in interfaceRichLocation
- Returns:
- the feature.
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setFeature
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 interfaceRichLocation
- Parameters:
feature
- the feature.- Throws:
ChangeVetoException
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getCrossRef
Retrieves the crossref associated with this location.- Specified by:
getCrossRef
in interfaceRichLocation
- Returns:
- the crossref.
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setCrossRef
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getAnnotation
Should return the associated annotation object.- Specified by:
getAnnotation
in interfaceAnnotatable
- Returns:
- an Annotation object, never null
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getRichAnnotation
Return the associated annotation object.- Specified by:
getRichAnnotation
in interfaceRichAnnotatable
- Returns:
- a RichAnnotation object, never null
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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 interfaceRichAnnotatable
- Returns:
- set a set of Note objects.
- See Also:
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setNoteSet
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 interfaceRichAnnotatable
- 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:
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getTerm
Retrieves the term associated with this location.- Specified by:
getTerm
in interfaceRichLocation
- Returns:
- the term.
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setTerm
Sets the term for this location.- Specified by:
setTerm
in interfaceRichLocation
- Parameters:
term
- the term this location should adopt.- Throws:
ChangeVetoException
- in case of error.
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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 interfaceRichLocation
- Returns:
- the position.
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setCircularLength
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 interfaceRichLocation
- Parameters:
circularLength
- the circular length of this location- Throws:
ChangeVetoException
- if it doesn't want to change.
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getStrand
Retrieves the strand associated with this location.- Specified by:
getStrand
in interfaceRichLocation
- Returns:
- the strand.
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setStrand
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getRank
Retrieves the rank associated with this location.- Specified by:
getRank
in interfaceRichLocation
- Returns:
- the rank.
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setRank
Sets the rank for this location.- Specified by:
setRank
in interfaceRichLocation
- Parameters:
rank
- the rank this location should adopt.- Throws:
ChangeVetoException
- in case of error.
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getMax
The maximum position contained.WARNING: The location will not contain every point between
getMin()
andgetMax()
ifisContiguous()
is false. IfisContiguous()
does return false you should use theIterator
returned byblockIterator()
to iterate over the minimum set of contiguous blocks that make up thisLocation
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getMin
The minimum position contained.WARNING: The location will not contain every point between
getMin()
andgetMax()
ifisContiguous()
is false. IfisContiguous()
does return false you should use theIterator
returned byblockIterator()
to iterate over the minimum set of contiguous blocks that make up thisLocation
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getMinPosition
Retrieves the start position of this location.- Specified by:
getMinPosition
in interfaceRichLocation
- Returns:
- the position.
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setMinPosition
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getMaxPosition
Retrieves the end position of this location.- Specified by:
getMaxPosition
in interfaceRichLocation
- Returns:
- the position.
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setMaxPosition
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setPositionResolver
Sets the resolver to use when working out actual base coordinates from fuzzy positions.- Specified by:
setPositionResolver
in interfaceRichLocation
- Parameters:
p
- the position resolver to use.
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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 interfaceLocation
- Returns:
- an Iterator over Location objects that are the maximally contiguous set of locations contained within this location
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isContiguous
Determine if a Location is contiguous.- Specified by:
isContiguous
in interfaceLocation
- Returns:
true
if and only if this Location contains every point frommin
tomax
inclusive.
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contains
Checks if this location contains a point. -
getDecorator
Checks the decorator chain for an instance ofdecoratorClass 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 interfaceLocation
- Parameters:
decoratorClass
- the Class to check- Returns:
- a Location if an instance of this class is present in the decorator chain and null otherwise.
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newInstance
Create a new instance of Location with all of the same decorators as this instance but with the data stored inloc
.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 decoratesloc
.- Specified by:
newInstance
in interfaceLocation
- Parameters:
loc
- the Location to use as template- Returns:
- a Location instance based on loc with the same decorators as the current instance
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translate
Create a location that is a translation of this location. -
contains
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.
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overlaps
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.
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union
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. -
intersection
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 interfaceLocation
- 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
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posmin
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posmax
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setCrossRefResolver
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 interfaceRichLocation
- Parameters:
r
- the resolver to use.
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symbols
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. -
hashCode
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equals
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) invalid input: '&'invalid input: '&' 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.
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compareTo
Locations are sorted first by rank, then crossref, then strand, then term, then min, then max.- Specified by:
compareTo
in interfaceComparable
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toString
Form: "start..end" or just "point" for point locations -
getId
Gets the Hibernate ID. Should be used with caution.- Returns:
- the Hibernate ID, if using Hibernate.
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setId
Sets the Hibernate ID. Should be used with caution.- Parameters:
id
- the Hibernate ID, if using Hibernate.
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