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
Methods inherited from interface org.biojava.bio.seq.Feature |
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm |
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
java.lang.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