RichObjectFactory (biojava-legacy 1.9.3 API)

java.lang.Object
- org.biojavax.RichObjectFactory

```
public class RichObjectFactory
extends Object
```
Runs a service that builds rich objects, and provides some default values for things like default ontology, default namespace, etc.

Since:

1.5

Author:

Richard Holland

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`clearLRUCache()` Removes all objects from the LRU cache.
`static void`	`clearLRUCache(Class clazz)` Removes all objects of the specified class from the LRU cache.
`static CrossReferenceResolver`	`getDefaultCrossReferenceResolver()` Returns the default cross ref resolver object.
`static Namespace`	`getDefaultNamespace()` Returns the default namespace object.
`static ComparableOntology`	`getDefaultOntology()` Returns the default ontology object.
`static PositionResolver`	`getDefaultPositionResolver()` Returns the default position resolver object.
`static RichSequenceHandler`	`getDefaultRichSequenceHandler()` Returns the default sequence resolver object.
`static Object`	`getObject(Class clazz, Object[] params)` Delegates to a RichObjectBuilder to construct/retrieve the object, and returns it.
`static void`	`setApplicationClass(Class theBiojavaClass, Class theApplicationClass)` Allow application to override the default biojava class created in getObject - subclass restriction is checked in the builder.
`static void`	`setDefaultCrossReferenceResolver(CrossReferenceResolver crr)` Sets the default crossref resolver to use when resolving remote entries.
`static void`	`setDefaultNamespaceName(String name)` Sets the default namespace name to use when loading sequences.
`static void`	`setDefaultOntologyName(String name)` Sets the default ontology name to use when loading sequences.
`static void`	`setDefaultPositionResolver(PositionResolver pr)` Sets the default position resolver to use when creating new rich feature locations.
`static void`	`setDefaultRichSequenceHandler(RichSequenceHandler rsh)` Sets the default sequence handler to use when performing sequence manipulation.
`static void`	`setLRUCacheSize(Class clazz, int size)` Sets the size of the LRU cache.
`static void`	`setLRUCacheSize(int size)` Sets the size of the LRU cache.
`static void`	`setRichObjectBuilder(RichObjectBuilder b)` Sets the builder to use when instantiating new Rich objects.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Method Detail
  - setRichObjectBuilder
```
public static void setRichObjectBuilder(RichObjectBuilder b)
```
    Sets the builder to use when instantiating new Rich objects. The basic, default, one is a SimpleRichObjectBuilder, which just calls the constructor. Another useful one is BioSQLRichObjectBuilder, which attempts to load objects from the database. The latter is required if you are working with Hibernate as it will not work without it.
    
    Parameters:
    
    b - the builder to use.
    
    See Also:
    
    SimpleRichObjectBuilder, BioSQLRichObjectBuilder
  - getObject
```
public static Object getObject(Class clazz,
                               Object[] params)
```
    Delegates to a RichObjectBuilder to construct/retrieve the object, and returns it. To increase efficiency, it keeps a list of recently requested objects. If it receives further requests for the same object, it returns them from the cache. The size of the cache can be altered using setLRUCacheSize(). The default cache size is 20 objects for each type of class requested.
    
    Parameters:
    
    clazz - the class to build
    
    params - the parameters to pass to the class' constructor
    
    Returns:
    
    the instantiated object
  - setApplicationClass
```
public static final void setApplicationClass(Class theBiojavaClass,
                                             Class theApplicationClass)
```
    Allow application to override the default biojava class created in getObject - subclass restriction is checked in the builder.
    
    Parameters:
    
    theBiojavaClass - one of the well-known builder classes: SimpleNamespace, SimpleComparableOntology, SimpleNCBITaxon, SimpleCrossRef, or SimpleDocRef
    
    theApplicationClass - - a subclass of theBiojavaClass
  - clearLRUCache
```
public static void clearLRUCache()
```
    Removes all objects from the LRU cache.
  - clearLRUCache
```
public static void clearLRUCache(Class clazz)
```
    Removes all objects of the specified class from the LRU cache.
    
    Parameters:
    
    clazz - The class of the objects to remove.
  - setLRUCacheSize
```
public static void setLRUCacheSize(int size)
```
    Sets the size of the LRU cache. This is the size per class of object requested, so if you set it to 20 and request 3 different types of object, you will get 20*3=60 entries in the cache. The default cache size is 20. Setting this value will undo any previous changes made using the setLRUCacheSize(Class,int) method below, but will not override future ones.
    
    Parameters:
    
    size - the size of the cache.
  - setLRUCacheSize
```
public static void setLRUCacheSize(Class clazz,
                                   int size)
```
    Sets the size of the LRU cache. This is the size for the specific class of object requested, so does not affect the size of caches of other objects. If this method is not called, then the cache size defaults to 20, or whatever value was passed to setLRUCacheSize(int) above.
    
    Parameters:
    
    size - the size of the cache.
  - setDefaultNamespaceName
```
public static void setDefaultNamespaceName(String name)
```
    Sets the default namespace name to use when loading sequences. Defaults to "lcl".
    
    Parameters:
    
    name - the namespace name to use.
  - setDefaultOntologyName
```
public static void setDefaultOntologyName(String name)
```
    Sets the default ontology name to use when loading sequences. Defaults to "biojavax".
    
    Parameters:
    
    name - the ontology name to use.
  - setDefaultPositionResolver
```
public static void setDefaultPositionResolver(PositionResolver pr)
```
    Sets the default position resolver to use when creating new rich feature locations. Defaults to the AverageResolver
    
    Parameters:
    
    pr - the position resolver to use.
    
    See Also:
    
    PositionResolver, PositionResolver.AverageResolver, RichLocation
  - setDefaultCrossReferenceResolver
```
public static void setDefaultCrossReferenceResolver(CrossReferenceResolver crr)
```
    Sets the default crossref resolver to use when resolving remote entries. Defaults to the DummyCrossReferenceResolver.
    
    Parameters:
    
    crr - the resolver to use.
    
    See Also:
    
    CrossReferenceResolver, DummyCrossReferenceResolver
  - setDefaultRichSequenceHandler
```
public static void setDefaultRichSequenceHandler(RichSequenceHandler rsh)
```
    Sets the default sequence handler to use when performing sequence manipulation. Defaults to the DummyRichSequenceHandler.
    
    Parameters:
    
    rsh - the resolver to use.
    
    See Also:
    
    RichSequenceHandler, DummyRichSequenceHandler
  - getDefaultNamespace
```
public static Namespace getDefaultNamespace()
```
    Returns the default namespace object. Defaults to "lcl".
    
    Returns:
    
    the default namespace.
  - getDefaultOntology
```
public static ComparableOntology getDefaultOntology()
```
    Returns the default ontology object. Defaults to "biojavax".
    
    Returns:
    
    the default ontology.
  - getDefaultPositionResolver
```
public static PositionResolver getDefaultPositionResolver()
```
    Returns the default position resolver object. Defaults to PositionResolver.AverageResolver
    
    Returns:
    
    the default position resolver.
    
    See Also:
    
    PositionResolver.AverageResolver
  - getDefaultCrossReferenceResolver
```
public static CrossReferenceResolver getDefaultCrossReferenceResolver()
```
    Returns the default cross ref resolver object. Defaults to DummyCrossReferenceResolver
    
    Returns:
    
    the default resolver.
    
    See Also:
    
    DummyCrossReferenceResolver
  - getDefaultRichSequenceHandler
```
public static RichSequenceHandler getDefaultRichSequenceHandler()
```
    Returns the default sequence resolver object. Defaults to DummyRichSequenceHandler.
    
    Returns:
    
    the default resolver.
    
    See Also:
    
    DummyRichSequenceHandler

Class RichObjectFactory

Method Summary

Methods inherited from class java.lang.Object

Method Detail

setRichObjectBuilder

getObject

setApplicationClass

clearLRUCache

clearLRUCache

setLRUCacheSize

setLRUCacheSize

setDefaultNamespaceName

setDefaultOntologyName

setDefaultPositionResolver

setDefaultCrossReferenceResolver

setDefaultRichSequenceHandler

getDefaultNamespace

getDefaultOntology

getDefaultPositionResolver

getDefaultCrossReferenceResolver

getDefaultRichSequenceHandler