org.biojava.bio.seq

Interface ComponentFeature

All Superinterfaces:

Annotatable, Changeable, Feature, FeatureHolder, StrandedFeature

public interface ComponentFeature
extends StrandedFeature

Feature which represents a component in an assembly (contig). This implies that a portion (possibly all) of the associated componentSequence is included in this feature's parent sequence.

There are important invariants which apply to all ComponentFeatures. The Location returned by getLocation() must contain the same number of unique point locations as that returned by getComponentLocation().

In BioJava 1.2, two extra properties were added to ComponentFeature to support the use of these features in environments were it it necessary to represent an assembly built from sequences which are not currently available. Widespread use of such sequences is not encouraged, but it is recognized that they are useful as intermediate objects for data integration applications.

Since:

1.1

Author:

Thomas Down

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	ComponentFeature.Template Template for constructing a new ComponentFeature.

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.biojava.bio.seq.StrandedFeature

NEGATIVE, POSITIVE, STRAND, UNKNOWN

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

Method Summary

Methods

Modifier and Type	Method and Description
Location	getComponentLocation() Return a location which identifies a portion of the component sequence which is to be included in the assembly.
Sequence	getComponentSequence() Get the sequence object which provides a component of this feature's parent sequence.
String	getComponentSequenceName() Get the name of the component sequence.
boolean	isComponentResolvable() Determine if the sequence references by this ComponentFeature is available in this context.

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

getStrand, getSymbols, setStrand

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

features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm

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

Method Detail

getComponentSequence

Sequence getComponentSequence()

Get the sequence object which provides a component of this feature's parent sequence.

Returns:

A sequence.

getComponentLocation

Location getComponentLocation()

Return a location which identifies a portion of the component sequence which is to be included in the assembly.

Returns:

A location within the component sequence.

getComponentSequenceName

String getComponentSequenceName()

Get the name of the component sequence. In general, this should be equivalent to getComponentSequence().getName(). However, it may still be defined for un-resolveable components.

Since:

1.2

isComponentResolvable

boolean isComponentResolvable()

Determine if the sequence references by this ComponentFeature is available in this context. If not, calls to getComponentSequence will fail, and getSymbols will return a non-informative SymbolList (in a DNA context, a list of Ns).

Since:

1.2