org.biojava.bio.seq
Class SimpleFeatureRealizer
java.lang.Object
|
+--org.biojava.bio.seq.SimpleFeatureRealizer
- public class SimpleFeatureRealizer
- extends java.lang.Object
- implements FeatureRealizer, java.io.Serializable
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:
- Serialized Form
Field Summary |
static FeatureRealizer |
DEFAULT
Default implementation of FeatureRealizer, which wraps simple
implementations of Feature and StrandedFeature. |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
DEFAULT
public static final FeatureRealizer DEFAULT
- Default implementation of FeatureRealizer, which wraps simple
implementations of Feature and StrandedFeature. This is the
default FeatureRealizer used by SimpleSequence and ViewSequence,
and may also be used by others. When building new FeatureRealizers,
you may wish to use this as a `fallback' realizer, and benefit from
the Feature and StrandedFeature implementations.
SimpleFeatureRealizer
public SimpleFeatureRealizer()
SimpleFeatureRealizer
public SimpleFeatureRealizer(FeatureRealizer fallBack)
addImplementation
public void addImplementation(java.lang.Class template,
java.lang.Class impl)
throws BioException
- 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.
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 interface FeatureRealizer
- Tags copied from interface: FeatureRealizer
- Parameters:
seq
- The sequence to which the feature will be added.template
- A description of the desired feature.parent
- The FeatureHolder which is to be the Feature's
immediate parent.- Throws:
- BioException - If the feature could not be constructed.