org.biojava.bio.seq.impl
Class SimpleFeature

java.lang.Object
  org.biojava.utils.AbstractChangeable
      org.biojava.bio.seq.impl.SimpleFeature

All Implemented Interfaces:

Serializable, Annotatable, Feature, FeatureHolder, RealizingFeatureHolder, Changeable

Direct Known Subclasses:

SimpleStrandedFeature

public class SimpleFeature
extends AbstractChangeable
implements Feature, RealizingFeatureHolder, Serializable

A no-frills implementation of a feature.

Author:

Matthew Pocock, Thomas Down, Kalle N�slund, Paul Seed, Len Trigg

See Also:

SimpleRichFeature, Serialized Form

Nested Class Summary

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

Feature.ByLocationComparator, Feature.Template

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

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

FeatureHolder.EmptyFeatureHolder

Field Summary

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

byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERM

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

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

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

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Constructor Summary

SimpleFeature(Sequence sourceSeq, FeatureHolder parent, Feature.Template template)
Create a SimpleFeature on the given sequence.

Method Summary

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 temp) Create a new Feature, and add it to this FeatureHolder.
boolean	equals(Object o)
protected boolean	featureHolderAllocated() A utility function to find out if the feature holder delegate has been instantiated yet.
Iterator	features() Iterate over any child features which are held by this feature.
protected void	fillTemplate(Feature.Template ft)
FeatureHolder	filter(FeatureFilter ff) Query this set of features using a supplied FeatureFilter.
FeatureHolder	filter(FeatureFilter ff, 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.
protected ChangeSupport	getChangeSupport(ChangeType ct) Called to retrieve the ChangeSupport for this object.
protected SimpleFeatureHolder	getFeatureHolder() A utility function to retrieve the feature holder delegate, creating it if necessary.
Location	getLocation() The location of this feature.
FeatureHolder	getParent() Return the FeatureHolder to which this feature has been attached.
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.
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.
Feature	realizeFeature(FeatureHolder fh, Feature.Template templ) Realize a feature template.
void	removeFeature(Feature f) Remove a feature from this FeatureHolder.
void	setLocation(Location loc) The new location for this feature.
void	setSource(String source) Change the source of the Feature.
void	setSourceTerm(Term t) Set the source ontology-term for this feature.
void	setType(String type) Change the type of this feature.
void	setTypeTerm(Term t) Set the type ontology-term for this feature.
String	toString()

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, 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

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

SimpleFeature

public SimpleFeature(Sequence sourceSeq,
                     FeatureHolder parent,
                     Feature.Template template)

Create a SimpleFeature on the given sequence. The feature is created underneath the parent FeatureHolder and populated directly from the template fields. However, if the template annotation is the Annotation.EMPTY_ANNOTATION, an empty SimpleAnnotation is attached to the feature instead.

Parameters:

sourceSeq - the source sequence

parent - the parent sequence or feature

template - the template for the feature

Method Detail

getFeatureHolder

protected SimpleFeatureHolder getFeatureHolder()

A utility function to retrieve the feature holder delegate, creating it if necessary.

Returns:

the FeatureHolder delegate

featureHolderAllocated

protected boolean featureHolderAllocated()

A utility function to find out if the feature holder delegate has been instantiated yet. If it has not, we may avoid instantiating it by returning some pre-canned result.

Returns:

true if the feature holder delegate has been created and false otherwise

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object.

Your implementation of this method should have the following structure:

 ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
 

It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

Overrides:

getChangeSupport in class AbstractChangeable

getLocation

public Location getLocation()

Description copied from interface: Feature

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

Description copied from interface: Feature

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

getTypeTerm

public Term getTypeTerm()

Description copied from interface: Feature

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

getType

public String getType()

Description copied from interface: Feature

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

Description copied from interface: Feature

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

setTypeTerm

public void setTypeTerm(Term t)
                 throws ChangeVetoException

Description copied from interface: Feature

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

getSource

public String getSource()

Description copied from interface: Feature

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

Specified by:

getSource in interface Feature

Returns:

the source, or generator

getSourceTerm

public Term getSourceTerm()

Description copied from interface: Feature

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

getParent

public FeatureHolder getParent()

Description copied from interface: Feature

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

setSource

public void setSource(String source)
               throws ChangeVetoException

Description copied from interface: Feature

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

setSourceTerm

public void setSourceTerm(Term t)
                   throws ChangeVetoException

Description copied from interface: Feature

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

getSequence

public Sequence getSequence()

Description copied from interface: Feature

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

getAnnotation

public Annotation getAnnotation()

Description copied from interface: Annotatable

Should return the associated annotation object.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation object, never null

getSymbols

public SymbolList getSymbols()

Description copied from interface: Feature

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 location is modified then this does not modify any SymbolList produced by earlier invocations of this method.

Specified by:

getSymbols in interface Feature

Returns:

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

countFeatures

public int countFeatures()

Description copied from interface: FeatureHolder

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

features

public Iterator features()

Description copied from interface: Feature

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

removeFeature

public void removeFeature(Feature f)
                   throws ChangeVetoException

Description copied from interface: FeatureHolder

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

containsFeature

public boolean containsFeature(Feature f)

Description copied from interface: FeatureHolder

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

filter

public FeatureHolder filter(FeatureFilter ff)

Description copied from interface: FeatureHolder

Query this set of features using a supplied FeatureFilter.

Specified by:

filter in interface FeatureHolder

Parameters:

ff - the FeatureFilter to apply.

Returns:

all features in this container which match filter.

filter

public FeatureHolder filter(FeatureFilter ff,
                            boolean recurse)

Description copied from interface: FeatureHolder

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:

ff - 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.

makeTemplate

public Feature.Template makeTemplate()

Description copied from interface: Feature

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

fillTemplate

protected void fillTemplate(Feature.Template ft)

toString

public String toString()

Overrides:

toString in class Object

realizeFeature

public Feature realizeFeature(FeatureHolder fh,
                              Feature.Template templ)
                       throws BioException

Description copied from interface: RealizingFeatureHolder

Realize a feature template. This will be a template which has been passed to the createFeature method of either this FeatureHolder or one of our child Features.

Specified by:

realizeFeature in interface RealizingFeatureHolder

Throws:

BioException

createFeature

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

Description copied from interface: FeatureHolder

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

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

getSchema

public FeatureFilter getSchema()

Description copied from interface: FeatureHolder

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