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java.lang.Object | +--org.biojava.bridge.Biocorba.Seqcore.FeatureAdapter
Inner classes inherited from class org.biojava.bio.seq.Feature |
Feature.Template |
Inner classes inherited from class org.biojava.bio.seq.FeatureHolder |
FeatureHolder.EmptyFeatureHolder |
Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
EMPTY_FEATURE_HOLDER |
Constructor Summary | |
FeatureAdapter(SequenceAdapter parent,
SeqFeature seqFeature)
|
Method Summary | |
int |
countFeatures()
Count how many features are contained. |
Feature |
createFeature(Feature.Template template)
Create a new Feature, and add it to this FeatureHolder. |
java.util.Iterator |
features()
Iterate over the features in no well defined order. |
FeatureHolder |
filter(FeatureFilter fc,
boolean recurse)
Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. |
Annotation |
getAnnotation()
Should return the associated annotation object. |
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. |
void |
removeFeature(Feature f)
Remove a feature from this FeatureHolder. |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
Constructor Detail |
public FeatureAdapter(SequenceAdapter parent, SeqFeature seqFeature)
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 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 java.lang.String getSource()
public java.lang.String getType()
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
.public int countFeatures()
public java.util.Iterator features()
public FeatureHolder filter(FeatureFilter fc, boolean recurse)
fc
- the FeatureFilter to applyrecurse
- true if all features-of-features should be scanned, and a
single flat collection of features returned, or false if
just immediate children should be filtered.public Annotation getAnnotation()
public Feature createFeature(Feature.Template template)
public void removeFeature(Feature f)
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