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
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
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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
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
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Constructor Summary
ConstructorsConstructorDescriptionConstructs 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 TypeMethodDescriptionint
Retrieves the circular length of this location.Retrieves the crossref associated with this location.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.Retrieves the strand associated with this location.void
setCircularLength
(int sourceSeqLength) Sets the circular length of this 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
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Constructor Details
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MultiSourceCompoundRichLocation
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:
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MultiSourceCompoundRichLocation
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:
-
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Method Details
-
getCrossRef
Retrieves the crossref associated with this location. ALWAYS RETURNS NULL- Specified by:
getCrossRef
in interfaceRichLocation
- Overrides:
getCrossRef
in classSimpleRichLocation
- Returns:
- the crossref.
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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. ALWAYS RETURNS ZERO- Specified by:
getCircularLength
in interfaceRichLocation
- Overrides:
getCircularLength
in classSimpleRichLocation
- Returns:
- the position.
-
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. RECURSIVELY APPLIES CALL TO ALL MEMBERS NOT IMPLEMENTED- Specified by:
setCircularLength
in interfaceRichLocation
- Overrides:
setCircularLength
in classCompoundRichLocation
- Parameters:
sourceSeqLength
- the circular length of this location- Throws:
ChangeVetoException
- ALWAYS
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getStrand
Retrieves the strand associated with this location.- Specified by:
getStrand
in interfaceRichLocation
- Overrides:
getStrand
in classSimpleRichLocation
- Returns:
- the strand.
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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
ALWAYS RETURNS ONE- Specified by:
getMin
in interfaceLocation
- Overrides:
getMin
in classSimpleRichLocation
- Returns:
- the minimum position contained
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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
ALWAYS RETURNS COMBINED LENGTH OF MEMBERS- Specified by:
getMax
in interfaceLocation
- Overrides:
getMax
in classSimpleRichLocation
- Returns:
- the maximum position contained
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getMinPosition
Retrieves the start position of this location. ALWAYS RETURNS A POINT POSITION AT POINT 1- Specified by:
getMinPosition
in interfaceRichLocation
- Overrides:
getMinPosition
in classSimpleRichLocation
- Returns:
- the position.
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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 interfaceRichLocation
- Overrides:
getMaxPosition
in classSimpleRichLocation
- Returns:
- the position.
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translate
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 interfaceLocation
- Overrides:
translate
in classCompoundRichLocation
- Parameters:
dist
- the distance to translate (to the right)
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