Package net.sf.basedb.util

Class AnnotationUtil.AnnotatableWrapper

java.lang.Object

net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper

Enclosing class:

AnnotationUtil

static class AnnotationUtil.AnnotatableWrapper
extends Object

This wrapper class is needed because we need to keep track of extracts linked with raw bioassays and derived bioassays until we have loaded the Extracts of a Physical Bioassay.

When we reach a RawBioAssay item or DerivedBioAssay item, we remember the extract on that as we move up towards PhysicalBioAssay. When the PhysicalBioAssay is reached we use the extracts to call PhysicalBioAssay.getAnnotatableParents(int, Collection).

Field Summary

Fields

Modifier and Type	Field	Description
private Set<Extract>	allChildExtractsInChain
private AnnotationUtil.Cache	cache
private AnnotationUtil.AnnotatableWrapper	chain
private Extract	extract
private Set<Integer>	extractsInChain
private Annotatable	item

Constructor Summary

Constructors

Constructor	Description
AnnotatableWrapper(Annotatable item, AnnotationUtil.AnnotatableWrapper chain)
AnnotatableWrapper(Annotatable item, AnnotationUtil.Cache cache)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)	A wrapper is equal to another if they references the same item and chain of extracts.
(package private) Annotatable	getAnnotatable()	The annotatable that we are wrapping.
(package private) Set<AnnotationUtil.AnnotatableWrapper>	getAnnotatableParentWrappers(DbControl dc)	Get all annotatable parents wrapped inside AnnotatableWrapper:s
private static Extract	getExtract(Annotatable item)	Get the extract to use.
int	hashCode()
private Set<Integer>	loadExtracts()	Load extracts in parent chain.
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Details

item

private final Annotatable item

extractsInChain

private final Set<Integer> extractsInChain

allChildExtractsInChain

private Set<Extract> allChildExtractsInChain

chain

private final AnnotationUtil.AnnotatableWrapper chain

cache

private final AnnotationUtil.Cache cache

extract

private final Extract extract

Constructor Details

AnnotatableWrapper

AnnotatableWrapper(Annotatable item,
AnnotationUtil.Cache cache)

AnnotatableWrapper

AnnotatableWrapper(Annotatable item,
AnnotationUtil.AnnotatableWrapper chain)

Method Details

getExtract

private static Extract getExtract(Annotatable item)

Get the extract to use. This method returns:

• If the item is a raw bioassay, RawBioAssay.getParentExtract()
• If the item is a derived bioassay, DerivedBioAssay.getExtract()
• null in all other cases.

getAnnotatable

Annotatable getAnnotatable()

The annotatable that we are wrapping.

loadExtracts

private Set<Integer> loadExtracts()

Load extracts in parent chain. We have to consider this for rawbioassay, derived bioassay and physical bioassay since the annotatable parents to a physical bioassay depends on the extracts we have seen while traversing the path from the raw bioassay and up. After reaching the physical bioassay we can forget about the extracts.

getAnnotatableParentWrappers

Set<AnnotationUtil.AnnotatableWrapper> getAnnotatableParentWrappers(DbControl dc)
                                                             throws BaseException

Get all annotatable parents wrapped inside AnnotatableWrapper:s

Throws:

BaseException

equals

public boolean equals(Object o)

A wrapper is equal to another if they references the same item and chain of extracts.

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object