Package org.biojava.bio.seq
Class SimpleFeatureRealizer
java.lang.Object
org.biojava.bio.seq.SimpleFeatureRealizer
- All Implemented Interfaces:
Serializable
,FeatureRealizer
FeatureRealizer which uses a lookup table to map template classes
to implementations. Optionally, this implementation can fall back
on another FeatureRealizer if it fails.
When searching for a Feature implementation to match a specific Feature.Template class, the following search order is used:
- Mappings added to this SimpleFeatureRealizer, in reverse order of addition.
- Any mappings known to the fallback realizer, if one is installed.
- If no mapping can be found, a BioException is thrown.
- Author:
- Thomas Down
- See Also:
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addImplementation
(Class template, Class impl) Install a new mapping from a class of Feature.Template to a class of Feature implementations.realizeFeature
(Sequence seq, FeatureHolder parent, Feature.Template temp) Install a feature on the specified sequence.
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Constructor Details
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SimpleFeatureRealizer
public SimpleFeatureRealizer() -
SimpleFeatureRealizer
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Method Details
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addImplementation
Install a new mapping from a class of Feature.Template to a class of Feature implementations. The implementation class MUST have a public constructor of the form (Sequence, FeatureHolder, Feature.Template).A newly added implementation takes precendence over any existing implementations if a template can be realized by more than one implementation.
- Parameters:
template
- The class of templates to implement.impl
- A class of Feature which can be used to implement these templates.- Throws:
BioException
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realizeFeature
public Feature realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template temp) throws BioException Description copied from interface:FeatureRealizer
Install a feature on the specified sequence.- Specified by:
realizeFeature
in interfaceFeatureRealizer
- Parameters:
seq
- The sequence to which the feature will be added.parent
- The FeatureHolder which is to be the Feature's immediate parent.temp
- A description of the desired feature.- Returns:
- A newly constructed feature, to be added to the sequence.
- Throws:
BioException
- If the feature could not be constructed.
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