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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
A feature within a sequence, or nested within another feature.
Features contain annotation and a location. The type of the feature is something like 'Repeat' or 'BetaStrand'. 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 publically 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.
Inner Class Summary | |
static class |
Feature.Template
Template class for a plain feature. |
Inner classes inherited from class org.biojava.bio.seq.FeatureHolder |
FeatureHolder.EmptyFeatureHolder |
Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
EMPTY_FEATURE_HOLDER |
Method Summary | |
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. |
java.lang.String |
getSource()
The source of the feature. |
SymbolList |
getSymbols()
Return a list of symbols that are contained in this feature. |
java.lang.String |
getType()
The type of the feature. |
Methods inherited from interface org.biojava.bio.seq.FeatureHolder |
countFeatures,
createFeature,
features,
filter,
removeFeature |
Methods inherited from interface org.biojava.bio.Annotatable |
getAnnotation |
Method Detail |
public Location getLocation()
The location may be complicated, or simply a range. The annotation is assumed to apply to all the region contained within the location.
public java.lang.String getType()
public java.lang.String getSource()
public SymbolList getSymbols()
The symbols may not be contiguous in the original sequence, but they will be concatinated 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.
public FeatureHolder getParent()
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.public Sequence getSequence()
Sequence
object to which this feature
is (ultimately) attached. For top level features, this will be
equal to the FeatureHolder
returned by getParent
.
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