org.biojavax.bio.seq

Class SimpleRichFeature

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.seq.SimpleRichFeature

All Implemented Interfaces:

Comparable, Annotatable, Feature, FeatureHolder, StrandedFeature, Changeable, RichFeature, RichFeatureRelationshipHolder, RankedCrossRefable, RichAnnotatable

public class SimpleRichFeature
extends AbstractChangeable
implements RichFeature

A simple implementation of RichFeature.

Since:

1.5

Author:

Richard Holland, Mark Schreiber, Bubba Puryear, George Waldon

Nested Class Summary

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

RichFeature.Template, RichFeature.Tools

Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature

StrandedFeature.Strand

Nested classes/interfaces inherited from interface org.biojava.bio.seq.Feature

Feature.ByLocationComparator

Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder

FeatureHolder.EmptyFeatureHolder

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

Annotatable.AnnotationForwarder

Field Summary

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

CROSSREF, LOCATION, NAME, PARENT, RANK, RELATION, SOURCETERM, TYPETERM

Fields inherited from interface org.biojava.bio.seq.StrandedFeature

NEGATIVE, POSITIVE, STRAND, UNKNOWN

Fields inherited from interface org.biojava.bio.seq.Feature

byLocationOrder, PROPERTY_DATA_KEY, SOURCE, TYPE

Fields inherited from interface org.biojava.bio.seq.FeatureHolder

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SimpleRichFeature()
	SimpleRichFeature(FeatureHolder parent, Feature.Template templ) Creates a new instance of SimpleRichFeature based on a template.

Method Summary

Modifier and Type	Method and Description
void	addFeatureRelationship(RichFeatureRelationship relationship) Adds a relationship to this feature holder.
void	addRankedCrossRef(RankedCrossRef crossref) Adds a ranked cross reference to the existing set.
int	compareTo(Object o) Features are sorted first by rank, then parent, type, and source.
boolean	containsFeature(Feature f) Check if the feature is present in this holder.
int	countFeatures() Count how many features are contained.
Feature	createFeature(Feature.Template ft) Create a new Feature, and add it to this FeatureHolder.
boolean	equals(Object o) Features are equal when they have the same rank, parent, type, and source.
Iterator	features() Iterate over any child features which are held by this feature.
FeatureHolder	filter(FeatureFilter filter) Query this set of features using a supplied FeatureFilter.
FeatureHolder	filter(FeatureFilter fc, boolean recurse) Return a new FeatureHolder that contains all of the children of this one that passed the filter fc.
Annotation	getAnnotation() Should return the associated annotation object.
Set<RichFeatureRelationship>	getFeatureRelationshipSet() Returns the set of relationships held in this feature holder.
Integer	getId() Gets the Hibernate ID.
Location	getLocation() The location of this feature.
String	getName() Returns the name of this feature.
Set	getNoteSet() Returns the set of notes associated with this object.
FeatureHolder	getParent() Return the FeatureHolder to which this feature has been attached.
int	getRank() Returns the rank of this feature.
Set<RankedCrossRef>	getRankedCrossRefs() Returns the set of all ranked cross references associated with an object.
RichAnnotation	getRichAnnotation() Return the associated annotation object.
FeatureFilter	getSchema() Return a schema-filter for this FeatureHolder.
Sequence	getSequence() Return the Sequence object to which this feature is (ultimately) attached.
String	getSource() The source of the feature.
Term	getSourceTerm() An ontology term defining the source of this feature.
StrandedFeature.Strand	getStrand() Retrieve the strand that this feature lies upon.
SymbolList	getSymbols() Return a list of symbols that are contained in this feature.
String	getType() The type of the feature.
Term	getTypeTerm() An ontology term defining the type of feature.
int	hashCode()
Feature.Template	makeTemplate() Create a new Template that could be used to generate a feature identical to this one.
void	removeFeature(Feature f) Remove a feature from this FeatureHolder.
void	removeFeatureRelationship(RichFeatureRelationship relationship) Removes a relationship from this feature holder.
void	removeRankedCrossRef(RankedCrossRef crossref) Removes a ranked cross reference from the existing set.
void	setFeatureRelationshipSet(Set<RichFeatureRelationship> relationships) Clears the relations from this feature holder and replaces them with a new set.
void	setId(Integer id) Sets the Hibernate ID.
void	setLocation(Location loc) The new location for this feature.
void	setName(String name) Sets the name of this feature.
void	setNoteSet(Set notes) Clears the notes associated with this object and replaces them with the contents of this set.
void	setParent(FeatureHolder parent) Sets the parent of this feature.
void	setRank(int rank) Sets the rank of this feature.
void	setRankedCrossRefs(Set crossrefs) Sets the ranked cross references associated with an object.
void	setSource(String source) Change the source of the Feature.
void	setSourceTerm(Term t) Set the source ontology-term for this feature.
void	setStrand(StrandedFeature.Strand strand) Set the strand that this feature lies upon.
void	setType(String type) Change the type of this feature.
void	setTypeTerm(Term t) Set the type ontology-term for this feature.
String	toString() Form: "(#rank) parent:type,source(location)"

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

Constructor Detail

SimpleRichFeature

public SimpleRichFeature(FeatureHolder parent,
                         Feature.Template templ)
                  throws ChangeVetoException,
                         InvalidTermException

Creates a new instance of SimpleRichFeature based on a template.

Parameters:

parent - The parent feature holder.

templ - The template to construct the feature from.

Throws:

ChangeVetoException - if we don't want to be like the template.

InvalidTermException - if any of the template terms are bad.

SimpleRichFeature

protected SimpleRichFeature()

Method Detail

makeTemplate

public Feature.Template makeTemplate()

Create a new Template that could be used to generate a feature identical to this one. The fields of the template can be edited without changing the feature.

Specified by:

makeTemplate in interface Feature

Returns:

a new Template that would make a feature like this one

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

setName

public void setName(String name)
             throws ChangeVetoException

Sets the name of this feature.

Specified by:

setName in interface RichFeature

Parameters:

name - the name the feature should identify itself with.

Throws:

ChangeVetoException - if the new value is unacceptable.

getName

public String getName()

Returns the name of this feature.

Specified by:

getName in interface RichFeature

Returns:

the name.

setRank

public void setRank(int rank)
             throws ChangeVetoException

Sets the rank of this feature.

Specified by:

setRank in interface RichFeature

Parameters:

rank - the rank the feature should identify itself with.

Throws:

ChangeVetoException - if the new value is unacceptable.

getRank

public int getRank()

Returns the rank of this feature.

Specified by:

getRank in interface RichFeature

Returns:

the rank.

getSequence

public Sequence getSequence()

Return the Sequence object to which this feature is (ultimately) attached. For top level features, this will be equal to the FeatureHolder returned by getParent.

Specified by:

getSequence in interface Feature

Returns:

the ultimate parent Sequence

getSource

public String getSource()

The source of the feature. This may be a program or process.

Specified by:

getSource in interface Feature

Returns:

the source, or generator

setSource

public void setSource(String source)
               throws ChangeVetoException

Change the source of the Feature.

Specified by:

setSource in interface Feature

Parameters:

source - the new source String

Throws:

ChangeVetoException - if the source can't be altered

getSourceTerm

public Term getSourceTerm()

An ontology term defining the source of this feature. This is optional, and will default to OntoTools.ANY in implementations which aren't ontology aware.

Specified by:

getSourceTerm in interface Feature

setSourceTerm

public void setSourceTerm(Term t)
                   throws ChangeVetoException,
                          InvalidTermException

Set the source ontology-term for this feature. If this succeeds, it will generally also change the source name.

Specified by:

setSourceTerm in interface Feature

Throws:

ChangeVetoException - if changes are not allowed

InvalidTermException - if the specified term is not an acceptable type for this feature.

getType

public String getType()

The type of the feature.

Specified by:

getType in interface Feature

Returns:

the type of this sequence

setType

public void setType(String type)
             throws ChangeVetoException

Change the type of this feature.

Specified by:

setType in interface Feature

Parameters:

type - new type String

Throws:

ChangeVetoException - if the type can't be altered

getTypeTerm

public Term getTypeTerm()

An ontology term defining the type of feature. This is optional, and will default to OntoTools.ANY in implementations which aren't ontology aware.

Specified by:

getTypeTerm in interface Feature

setTypeTerm

public void setTypeTerm(Term t)
                 throws ChangeVetoException,
                        InvalidTermException

Set the type ontology-term for this feature. If this succeeds, it will generally also change the source name.

Specified by:

setTypeTerm in interface Feature

Throws:

ChangeVetoException - if changes are not allowed

InvalidTermException - if the specified term is not an acceptable type for this feature.

getSymbols

public SymbolList getSymbols()

Return a list of symbols that are contained in this feature.

The symbols may not be contiguous in the original sequence, but they will be concatenated together in the resulting SymbolList.

The order of the Symbols within the resulting symbol list will be according to the concept of ordering within the location object.

If the feature is on the negative strand then the SymbolList will be reverse-complemented as appropriate.

Specified by:

getSymbols in interface Feature

Specified by:

getSymbols in interface StrandedFeature

Returns:

a SymbolList containing each symbol of the parent sequence contained within this feature in the order they appear in the parent

getLocation

public Location getLocation()

The location of this feature.

The location may be complicated, or simply a range. The annotation is assumed to apply to all the region contained within the location.

Specified by:

getLocation in interface Feature

Returns:

a Location anchoring this feature

setLocation

public void setLocation(Location loc)
                 throws ChangeVetoException

The new location for this feature.

The location may be complicated or simply a range. The annotation is assumed to apply to the entire region contained within the location. Any values returned from methods that rely on the old location must not be affected.

Specified by:

setLocation in interface Feature

Parameters:

loc - the new Location for this feature

Throws:

ChangeVetoException - if the location can't be altered

getParent

public FeatureHolder getParent()

Return the FeatureHolder to which this feature has been attached. This will be a Sequence object for top level features, and a Feature object for features further down the tree.

Specified by:

getParent in interface Feature

setParent

public void setParent(FeatureHolder parent)
               throws ChangeVetoException

Sets the parent of this feature.

Specified by:

setParent in interface RichFeature

Parameters:

parent - the parent the feature should identify itself with.

Throws:

ChangeVetoException - if the new value is unacceptable.

getRankedCrossRefs

public Set<RankedCrossRef> getRankedCrossRefs()

Returns the set of all ranked cross references associated with an object. 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:

getRankedCrossRefs in interface RankedCrossRefable

Returns:

a set of RankedCrossRef objects.

setRankedCrossRefs

public void setRankedCrossRefs(Set crossrefs)
                        throws ChangeVetoException

Sets the ranked cross references associated with an object. Null will throw an exception but the empty set is fine. 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:

setRankedCrossRefs in interface RankedCrossRefable

Parameters:

crossrefs - a set of RankedCrossRef objects.

Throws:

ChangeVetoException - if the set was null or any of its contents were not RankedCrossRef objects.

addRankedCrossRef

public void addRankedCrossRef(RankedCrossRef crossref)
                       throws ChangeVetoException

Adds a ranked cross reference to the existing set. If already present, this call is ignored. Null values are not acceptable.

Specified by:

addRankedCrossRef in interface RankedCrossRefable

Parameters:

crossref - the ranked cross reference to add.

Throws:

ChangeVetoException - if the parameter is null.

removeRankedCrossRef

public void removeRankedCrossRef(RankedCrossRef crossref)
                          throws ChangeVetoException

Removes a ranked cross reference from the existing set. If not present, this call is ignored. Null values are not acceptable.

Specified by:

removeRankedCrossRef in interface RankedCrossRefable

Parameters:

crossref - the ranked cross reference to remove.

Throws:

ChangeVetoException - if the parameter is null.

getFeatureRelationshipSet

public Set<RichFeatureRelationship> getFeatureRelationshipSet()

Returns the set of relationships held in this feature holder. 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:

getFeatureRelationshipSet in interface RichFeatureRelationshipHolder

Returns:

a set of RichFeatureRelationship objects.

setFeatureRelationshipSet

public void setFeatureRelationshipSet(Set<RichFeatureRelationship> relationships)
                               throws ChangeVetoException

Clears the relations from this feature holder and replaces them with a new set. 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:

setFeatureRelationshipSet in interface RichFeatureRelationshipHolder

Parameters:

relationships - the new set of features this holder should have. The set must contain only RichFeatureRelationship objects.

Throws:

ChangeVetoException - if the new set could not be installed.

addFeatureRelationship

public void addFeatureRelationship(RichFeatureRelationship relationship)
                            throws ChangeVetoException

Adds a relationship to this feature holder.

Specified by:

addFeatureRelationship in interface RichFeatureRelationshipHolder

Parameters:

relationship - the relationship to add.

Throws:

ChangeVetoException - if the relationship is unacceptable.

removeFeatureRelationship

public void removeFeatureRelationship(RichFeatureRelationship relationship)
                               throws ChangeVetoException

Removes a relationship from this feature holder.

Specified by:

removeFeatureRelationship in interface RichFeatureRelationshipHolder

Parameters:

relationship - the relationship to remove.

Throws:

ChangeVetoException - if it cannot be removed.

containsFeature

public boolean containsFeature(Feature f)

Check if the feature is present in this holder.

Specified by:

containsFeature in interface FeatureHolder

Parameters:

f - the Feature to check

Returns:

true if f is in this set

countFeatures

public int countFeatures()

Count how many features are contained.

Specified by:

countFeatures in interface FeatureHolder

Returns:

a positive integer or zero, equal to the number of features contained

createFeature

public Feature createFeature(Feature.Template ft)
                      throws BioException,
                             ChangeVetoException

Create a new Feature, and add it to this FeatureHolder. This method will generally only work on Sequences, and on some Features which have been attached to Sequences.

Specified by:

createFeature in interface FeatureHolder

Throws:

BioException - if something went wrong during creating the feature

ChangeVetoException - if this FeatureHolder does not support creation of new features, or if the change was vetoed

features

public Iterator features()

Iterate over any child features which are held by this feature. The order of iteration MAY be significant for some types of Feature.

Specified by:

features in interface Feature

Specified by:

features in interface FeatureHolder

Returns:

an Iterator

filter

public FeatureHolder filter(FeatureFilter filter)

Query this set of features using a supplied FeatureFilter.

Specified by:

filter in interface FeatureHolder

Parameters:

filter - the FeatureFilter to apply.

Returns:

all features in this container which match filter.

filter

public FeatureHolder filter(FeatureFilter fc,
                            boolean recurse)

Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. This method is scheduled for deprecation. Use the 1-arg filter instead.

Specified by:

filter in interface FeatureHolder

Parameters:

fc - the FeatureFilter to apply

recurse - true if all features-of-features should be scanned, and a single flat collection of features returned, or false if just immediate children should be filtered.

getSchema

public FeatureFilter getSchema()

Return a schema-filter for this FeatureHolder. This is a filter which all Features immediately contained by this FeatureHolder will match. It need not directly match their child features, but it can (and should!) provide information about them using FeatureFilter.OnlyChildren filters. In cases where there is no feature hierarchy, this can be indicated by including FeatureFilter.leaf in the schema filter.

For the truly non-informative case, it is possible to return FeatureFilter.all. However, it is almost always possible to provide slightly more information that this. For example, Sequence objects should, at a minimum, return FeatureFilter.top_level. Feature objects should, as a minimum, return FeatureFilter.ByParent(new FeatureFilter.ByFeature(this)).

Specified by:

getSchema in interface FeatureHolder

Returns:

the schema filter

removeFeature

public void removeFeature(Feature f)
                   throws ChangeVetoException,
                          BioException

Remove a feature from this FeatureHolder.

Specified by:

removeFeature in interface FeatureHolder

Throws:

ChangeVetoException - if this FeatureHolder does not support feature removal or if the change was vetoed

BioException - if there was an error removing the feature

setStrand

public void setStrand(StrandedFeature.Strand strand)
               throws ChangeVetoException

Set the strand that this feature lies upon.

This will be one of StrandedFeature.POSITIVE or NEGATIVE. NOT IMPLEMENTED.

Specified by:

setStrand in interface StrandedFeature

Parameters:

strand - a Strand.

Throws:

ChangeVetoException - if the strand may not be changed.

getStrand

public StrandedFeature.Strand getStrand()

Retrieve the strand that this feature lies upon.

This will be one of StrandedFeature.POSITIVE or NEGATIVE.

Specified by:

getStrand in interface StrandedFeature

Returns:

one of the Strand constants

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Features are equal when they have the same rank, parent, type, and source. Features which are not instance of RichFeature are given a rank of zero.

Overrides:

equals in class Object

compareTo

public int compareTo(Object o)

Features are sorted first by rank, then parent, type, and source. If both parents are not comparable then this part of the sorting is skipped. Features which are not instance of RichFeature are given a rank of zero.

Specified by:

compareTo in interface Comparable

toString

public String toString()

Form: "(#rank) parent:type,source(location)"

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.