Package org.biojava.bio.seq
Class SimpleFeatureHolder
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.AbstractFeatureHolder
org.biojava.bio.seq.SimpleFeatureHolder
- All Implemented Interfaces:
Serializable
,FeatureHolder
,Changeable
A no-frills implementation of FeatureHolder.
- Author:
- Matthew Pocock, Thomas Down
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
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Field Summary
Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA
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Constructor Summary
ConstructorsConstructorDescriptionConstruct a new SimpleFeatureHolder with a non-informative schema.SimpleFeatureHolder
(FeatureFilter schema) Construct a new SimpleFeatureHolder with the specified schema. -
Method Summary
Modifier and TypeMethodDescriptionvoid
Add a feature to the featureholderboolean
Check if the feature is present in this holder.int
Count how many features are contained.features()
Iterate over the features in no well defined order.protected List
Returns the list of features in this featureholder.Return a schema-filter for thisFeatureHolder
.void
Remove a feature from this FeatureHolder.Methods inherited from class org.biojava.bio.seq.AbstractFeatureHolder
createFeature, filter, filter
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Constructor Details
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SimpleFeatureHolder
public SimpleFeatureHolder()Construct a new SimpleFeatureHolder with a non-informative schema. -
SimpleFeatureHolder
Construct a new SimpleFeatureHolder with the specified schema.
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Method Details
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getFeatures
Returns the list of features in this featureholder. -
countFeatures
Description copied from interface:FeatureHolder
Count how many features are contained.- Specified by:
countFeatures
in interfaceFeatureHolder
- Returns:
- a positive integer or zero, equal to the number of features contained
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features
Description copied from interface:FeatureHolder
Iterate over the features in no well defined order.- Specified by:
features
in interfaceFeatureHolder
- Returns:
- an Iterator
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addFeature
Add a feature to the featureholder- Throws:
ChangeVetoException
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removeFeature
Description copied from interface:FeatureHolder
Remove a feature from this FeatureHolder.- Specified by:
removeFeature
in interfaceFeatureHolder
- Overrides:
removeFeature
in classAbstractFeatureHolder
- Throws:
ChangeVetoException
- if this FeatureHolder does not support feature removal or if the change was vetoed
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containsFeature
Description copied from interface:FeatureHolder
Check if the feature is present in this holder.- Specified by:
containsFeature
in interfaceFeatureHolder
- Parameters:
f
- the Feature to check- Returns:
- true if f is in this set
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getSchema
Description copied from interface:FeatureHolder
Return a schema-filter for thisFeatureHolder
. This is a filter which allFeature
s immediately contained by thisFeatureHolder
will match. It need not directly match their child features, but it can (and should!) provide information about them usingFeatureFilter.OnlyChildren
filters. In cases where there is no feature hierarchy, this can be indicated by includingFeatureFilter.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, returnFeatureFilter.top_level
.Feature
objects should, as a minimum, returnFeatureFilter.ByParent(new FeatureFilter.ByFeature(this))
.- Specified by:
getSchema
in interfaceFeatureHolder
- Returns:
- the schema filter
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