org.biojava.bio.seq

Interface Feature

All Superinterfaces:

Annotatable, Changeable, FeatureHolder

All Known Subinterfaces:

ComponentFeature, FramedFeature, HomologyFeature, RemoteFeature, RestrictionSite, RichFeature, SimilarityPairFeature, StrandedFeature

All Known Implementing Classes:

ProjectedFeature, SimpleFeature, SimpleFramedFeature, SimpleHomologyFeature, SimpleRemoteFeature, SimpleRestrictionSite, SimpleRichFeature, SimpleSimilarityPairFeature, SimpleStrandedFeature

public interface Feature
extends FeatureHolder, Annotatable

A feature within a sequence, or nested within another feature.

Common operations

 // loop over all features in a sequence
 for(Iterator fi = mySeq.features(); fi.hasNext(); ) {
   Feature f = (Feature) fi.next();
   System.out.println(f.getType() + "\t" + f.getLocation());
 }

 // loop over all features that are children of this one, such as exons in a
 // gene
 for(Iterator cfi = feature.features(); cfi.hasNext(); ) {
   ...

 // extract all stranded features that are directly on a sequence
 FeatureHolder strandedFeatures = mySeq.filter(
   new FeatureFilter.ByClass(StrandedFeature.class),
   false
  );
 for(fi = strandedFeatures.features(); ...

 // find all features with the type property set to "EXON" no matter how
 // far down the feature hierachy they are
 FeatureHolder repeats = mySeq.filter(
   new FeatureFilter.ByType("EXON"),
   true;
 );
 

Description

Features contain annotation and a location. The type of the feature is something like 'Repeat' or 'BetaStrand'. Where the feature has been read from an EMBL or Genbank source the type will be the same as the feature key in the feature table e.g. 'gene', 'CDS', 'repeat_unit', 'misc_feature'. The source of the feature is something like 'genscan', 'repeatmasker' or 'made-up'.

Features are always contained by a parent FeatureHolder, which may either be a Sequence or another Feature. Feature instances should never be constructed directly by client code, and the BioJava core does not contain any publicly accessible implementations of the Feature interface. Instead, you should create a suitable Feature.Template, then pass this to the createFeature method of a Sequence or Feature.

We may need some standardisation for what the fields mean. In particular, we should be compliant where sensible with GFF.

Author:

Matthew Pocock, Thomas Down, Keith James

See Also:

RichFeature

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	Feature.ByLocationComparator ByLocationComparator compares Features by the minimum base position of their Location.
static class	Feature.Template Template class for a plain feature.

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

Modifier and Type	Field and Description
static Feature.ByLocationComparator	byLocationOrder byLocationOrder contains a Feature comparator which compares by the minimum base position of their Location.
static ChangeType	LOCATION The location of this feature is being altered.
static String	PROPERTY_DATA_KEY This is used as a key in the Annotation where it identifies internal data.
static ChangeType	SOURCE The source of this feature has altered
static ChangeType	SOURCETERM The ontological source of this feature has altered
static ChangeType	TYPE The type of this feature has altered.
static ChangeType	TYPETERM The ontological type of this feature has altered.

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

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Method Summary

Methods

Modifier and Type	Method and Description
Iterator	features() Iterate over any child features which are held by this feature.
Location	getLocation() The location of this feature.
FeatureHolder	getParent() Return the FeatureHolder to which this feature has been attached.
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.
Feature.Template	makeTemplate() Create a new Template that could be used to generate a feature identical to this one.
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.

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

containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

PROPERTY_DATA_KEY

static final String PROPERTY_DATA_KEY

This is used as a key in the Annotation where it identifies internal data. This is not printed when the Feature is written to a flatfile. E.g. the original feature's EMBL location string (if it has one) is stored here.

See Also:

Constant Field Values

LOCATION

static final ChangeType LOCATION

The location of this feature is being altered.

TYPE

static final ChangeType TYPE

The type of this feature has altered.

SOURCE

static final ChangeType SOURCE

The source of this feature has altered

TYPETERM

static final ChangeType TYPETERM

The ontological type of this feature has altered.

SOURCETERM

static final ChangeType SOURCETERM

The ontological source of this feature has altered

byLocationOrder

static final Feature.ByLocationComparator byLocationOrder

byLocationOrder contains a Feature comparator which compares by the minimum base position of their Location.

Method Detail

getLocation

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.

Returns:

a Location anchoring this feature

setLocation

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.

Parameters:

loc - the new Location for this feature

Throws:

ChangeVetoException - if the location can't be altered

getType

String getType()

The type of the feature.

Returns:

the type of this sequence

setType

void setType(String type)
             throws ChangeVetoException

Change the type of this feature.

Parameters:

type - new type String

Throws:

ChangeVetoException - if the type can't be altered

getTypeTerm

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.

Since:

1.4

setTypeTerm

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.

Throws:

ChangeVetoException - if changes are not allowed

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

Since:

1.4

getSourceTerm

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.

Since:

1.4

setSourceTerm

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.

Throws:

ChangeVetoException - if changes are not allowed

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

Since:

1.4

getSource

String getSource()

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

Returns:

the source, or generator

setSource

void setSource(String source)
               throws ChangeVetoException

Change the source of the Feature.

Parameters:

source - the new source String

Throws:

ChangeVetoException - if the source can't be altered

getSymbols

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

Returns:

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

getParent

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.

getSequence

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.

Returns:

the ultimate parent Sequence

features

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 FeatureHolder

Returns:

an Iterator

makeTemplate

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.

Returns:

a new Template that would make a feature like this one