Package org.biojava.bio.seq
Interface ComponentFeature
- All Superinterfaces:
Annotatable,Changeable,Feature,FeatureHolder,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 ClassesModifier and TypeInterfaceDescriptionstatic classTemplate for constructing a new ComponentFeature.Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarderNested classes/interfaces inherited from interface org.biojava.bio.seq.Feature
Feature.ByLocationComparatorNested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolderNested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand -
Field Summary
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATIONFields inherited from interface org.biojava.bio.seq.Feature
byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERMFields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMAFields inherited from interface org.biojava.bio.seq.StrandedFeature
NEGATIVE, POSITIVE, STRAND, UNKNOWN -
Method Summary
Modifier and TypeMethodDescriptionReturn a location which identifies a portion of the component sequence which is to be included in the assembly.Get the sequence object which provides a component of this feature's parent sequence.Get the name of the component sequence.booleanDetermine if the sequence references by this ComponentFeature is available in this context.Methods inherited from interface org.biojava.bio.Annotatable
getAnnotationMethods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListenerMethods inherited from interface org.biojava.bio.seq.Feature
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTermMethods inherited from interface org.biojava.bio.seq.FeatureHolder
containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeatureMethods inherited from interface org.biojava.bio.seq.StrandedFeature
getStrand, getSymbols, setStrand
-
Method Details
-
getComponentSequence
Get the sequence object which provides a component of this feature's parent sequence.- Returns:
- A sequence.
-
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
Get the name of the component sequence. In general, this should be equivalent togetComponentSequence().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-informativeSymbolList(in a DNA context, a list of Ns).- Since:
- 1.2
-