org.biojavax.bio.seq
Class CompoundRichLocation

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by org.biojavax.bio.seq.SimpleRichLocation
          extended by org.biojavax.bio.seq.CompoundRichLocation
All Implemented Interfaces:
Comparable, Annotatable, Location, Changeable, RichLocation, RichAnnotatable
Direct Known Subclasses:
MultiSourceCompoundRichLocation

public class CompoundRichLocation
extends SimpleRichLocation
implements RichLocation

An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.

Since:
1.5
Author:
Richard Holland, Mark Schreiber

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
protected  List members
           
protected  int size
           
 
Fields inherited from class org.biojavax.bio.seq.SimpleRichLocation
circularLength, 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
protected CompoundRichLocation()
           
  CompoundRichLocation(Collection members)
          Constructs a CompoundRichLocation from the given set of members, with the default term of "join".
  CompoundRichLocation(ComparableTerm term, Collection members)
          Constructs a CompoundRichLocation from the given set of members.
 
Method Summary
 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.
 Location getDecorator(Class decoratorClass)
          Checks the decorator chain for an instance of decoratorClass and return it if found.
static ComparableTerm getJoinTerm()
          Getter for the "join" term
 Set getNoteSet()
          Returns the set of notes associated with this object.
static ComparableTerm getOrderTerm()
          Getter for the "order" term
 RichAnnotation getRichAnnotation()
          Return the associated annotation object.
 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.
 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 setNoteSet(Set notes)
          Clears the notes associated with this object and replaces them with the contents of this set.
 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.biojavax.bio.seq.SimpleRichLocation
getCircularLength, getCrossRef, getFeature, getId, getMax, getMaxPosition, getMin, getMinPosition, getRank, getStrand, 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.biojavax.bio.seq.RichLocation
getCircularLength, getCrossRef, getFeature, getMaxPosition, getMinPosition, getRank, getStrand, getTerm, setPositionResolver, setRank
 
Methods inherited from interface org.biojava.bio.symbol.Location
getMax, getMin
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

Field Detail

members

protected List members

size

protected int size
Constructor Detail

CompoundRichLocation

public CompoundRichLocation(Collection members)
Constructs a CompoundRichLocation 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(). All members must come from the same strand of the same sequence with the same circular length.

Parameters:
members - the members to put into the compound location.
See Also:
RichLocation.Tools

CompoundRichLocation

public CompoundRichLocation(ComparableTerm term,
                            Collection members)
Constructs a CompoundRichLocation 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

CompoundRichLocation

protected CompoundRichLocation()
Method Detail

getJoinTerm

public static ComparableTerm getJoinTerm()
Getter for the "join" term

Returns:
the "join" term

getOrderTerm

public static ComparableTerm getOrderTerm()
Getter for the "order" term

Returns:
the "order" term

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
Overrides:
sort in class SimpleRichLocation

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. Passes the call on to each of its members in turn.

Specified by:
setFeature in interface RichLocation
Overrides:
setFeature in class SimpleRichLocation
Parameters:
feature - the feature.
Throws:
ChangeVetoException

getAnnotation

public Annotation getAnnotation()
Should return the associated annotation object. ALWAYS RETURNS THE EMPTY ANNOTATION

Specified by:
getAnnotation in interface Annotatable
Overrides:
getAnnotation in class SimpleRichLocation
Returns:
an Annotation object, never null

getRichAnnotation

public RichAnnotation getRichAnnotation()
Return the associated annotation object. ALWAYS RETURNS THE EMPTY ANNOTATION

Specified by:
getRichAnnotation in interface RichAnnotatable
Overrides:
getRichAnnotation in class SimpleRichLocation
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. ALWAYS RETURNS THE EMPTY ANNOTATION NOTE SET

Specified by:
getNoteSet in interface RichAnnotatable
Overrides:
getNoteSet in class SimpleRichLocation
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. NOT IMPLEMENTED

Specified by:
setNoteSet in interface RichAnnotatable
Overrides:
setNoteSet in class SimpleRichLocation
Parameters:
notes - the set of Note objects to replace the existing ones with.
Throws:
ChangeVetoException - ALWAYS
See Also:
Note

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

Specified by:
setCircularLength in interface RichLocation
Overrides:
setCircularLength in class SimpleRichLocation
Parameters:
sourceSeqLength - the circular length of this location
Throws:
ChangeVetoException - if it doesn't want to change.

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
Overrides:
blockIterator in class SimpleRichLocation
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. ALWAYS RETURNS FALSE

Specified by:
isContiguous in interface Location
Overrides:
isContiguous in class SimpleRichLocation
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. Recursively applies this call to all members.

Specified by:
contains in interface Location
Overrides:
contains in class SimpleRichLocation
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. ALWAYS RETURNS NULL

Specified by:
getDecorator in interface Location
Overrides:
getDecorator in class SimpleRichLocation
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. ALWAYS RETURNS SELF

Specified by:
newInstance in interface Location
Overrides:
newInstance in class SimpleRichLocation
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. Recursively translates all members of this location.

Specified by:
translate in interface Location
Overrides:
translate in class SimpleRichLocation
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. Recursively applies this call to all members. If passed a Location which is not a RichLocation, it converts it first using RichLocation.Tools.enrich().

Specified by:
contains in interface Location
Overrides:
contains in class SimpleRichLocation
Parameters:
l - the Location to check
Returns:
true if an only if one of the members of this Location wholey contains l.
See Also:
RichLocation.Tools

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. Recursively applies this call to all members.

Specified by:
overlaps in interface Location
Overrides:
overlaps in class SimpleRichLocation
Parameters:
l - the Location to check
Returns:
true if and only if at least on of the members overlaps l

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. If passed a Location which is not a RichLocation, it converts it first using RichLocation.Tools.enrich(). The resulting location may or may not be a compound location. If it is a compound location, its contents will be a set of simple locations. Regions that overlap will be merged into a single location.

Specified by:
union in interface Location
Overrides:
union in class SimpleRichLocation
Parameters:
l - the Location to union with
Returns:
a CompoundLocation if the components of the union cannot be merged else a SimpleRichLocation
See Also:
RichLocation.Tools

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. If passed a Location which is not a RichLocation, it converts it first using RichLocation.Tools.enrich(). The resulting location may or may not be a compound location. If it is a compound location, its contents will be a set of simple locations.

Specified by:
intersection in interface Location
Overrides:
intersection in class SimpleRichLocation
Parameters:
l - the Location to intersect with
Returns:
a CompoundLocation if there is more than one region of intersection that cannot be merged. Else a SimpleRichLocation.

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. Recursively applies this call to all members.

Specified by:
setCrossRefResolver in interface RichLocation
Overrides:
setCrossRefResolver in class SimpleRichLocation
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. This function concatenates the symbols of all its child locations.

The most obvious application of this method to a CompoundRichLocation is the contatenation of the components of a gene with multiple exons.

Specified by:
symbols in interface Location
Overrides:
symbols in class SimpleRichLocation
Parameters:
seq - the SymbolList to process
Returns:
the SymbolList containing the symbols in seq in this range

setTerm

public void setTerm(ComparableTerm term)
             throws ChangeVetoException
Sets the term for this location.

Specified by:
setTerm in interface RichLocation
Overrides:
setTerm in class SimpleRichLocation
Parameters:
term - the term this location should adopt.
Throws:
ChangeVetoException - in case of error.

hashCode

public int hashCode()

Overrides:
hashCode in class SimpleRichLocation

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. Compound locations are only equal to other Locations if all their components are equal.

Specified by:
equals in interface Location
Overrides:
equals in class SimpleRichLocation
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
Overrides:
compareTo in class SimpleRichLocation

toString

public String toString()
Form: "start..end" or just "point" for point locations Form: "term:[location,location...]"

Overrides:
toString in class SimpleRichLocation


Copyright © 2012 BioJava. All Rights Reserved.