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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.seq.AbstractFeatureHolder
org.biojava.bio.seq.SimpleFeatureHolder
public class SimpleFeatureHolder
A no-frills implementation of FeatureHolder.
RichFeatureRelationshipHolder
,
Serialized FormNested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder |
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FeatureHolder.EmptyFeatureHolder |
Field Summary |
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Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
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EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA |
Constructor Summary | |
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SimpleFeatureHolder()
Construct a new SimpleFeatureHolder with a non-informative schema. |
|
SimpleFeatureHolder(FeatureFilter schema)
Construct a new SimpleFeatureHolder with the specified schema. |
Method Summary | |
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void |
addFeature(Feature f)
Add a feature to the featureholder |
boolean |
containsFeature(Feature f)
Check if the feature is present in this holder. |
int |
countFeatures()
Count how many features are contained. |
Iterator |
features()
Iterate over the features in no well defined order. |
protected List |
getFeatures()
Returns the list of features in this featureholder. |
FeatureFilter |
getSchema()
Return a schema-filter for this FeatureHolder . |
void |
removeFeature(Feature f)
Remove a feature from this FeatureHolder. |
Methods inherited from class org.biojava.bio.seq.AbstractFeatureHolder |
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createFeature, filter, filter |
Methods inherited from class org.biojava.utils.AbstractChangeable |
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addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Constructor Detail |
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public SimpleFeatureHolder()
public SimpleFeatureHolder(FeatureFilter schema)
Method Detail |
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protected List getFeatures()
public int countFeatures()
FeatureHolder
countFeatures
in interface FeatureHolder
public Iterator features()
FeatureHolder
features
in interface FeatureHolder
public void addFeature(Feature f) throws ChangeVetoException
ChangeVetoException
public void removeFeature(Feature f) throws ChangeVetoException
FeatureHolder
removeFeature
in interface FeatureHolder
removeFeature
in class AbstractFeatureHolder
ChangeVetoException
- if this FeatureHolder does not support
feature removal or if the change was vetoedpublic boolean containsFeature(Feature f)
FeatureHolder
containsFeature
in interface FeatureHolder
f
- the Feature to check
public FeatureFilter getSchema()
FeatureHolder
FeatureHolder
. This is a filter
which all Feature
s immediately contained by this FeatureHolder
will match. It need not directly match their child features, but it can (and should!) provide
information about them using FeatureFilter.OnlyChildren
filters. In cases where there
is no feature hierarchy, this can be indicated by including FeatureFilter.leaf
in
the schema filter.
For the truly non-informative case, it is possible to return FeatureFilter.all
. However,
it is almost always possible to provide slightly more information that this. For example, Sequence
objects should, at a minimum, return FeatureFilter.top_level
. Feature
objects
should, as a minimum, return FeatureFilter.ByParent(new FeatureFilter.ByFeature(this))
.
getSchema
in interface FeatureHolder
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