Package net.sf.basedb.util.overview.loader

Class RawBioAssayLoader

java.lang.Object

net.sf.basedb.util.overview.loader.AbstractNodeLoader<I>

net.sf.basedb.util.overview.loader.BasicItemNodeLoader<RawBioAssay>

net.sf.basedb.util.overview.loader.RawBioAssayLoader

All Implemented Interfaces:

NodeLoader<RawBioAssay>

public class RawBioAssayLoader
extends BasicItemNodeLoader<RawBioAssay>

Node loader implementation for raw bioassays. The forward-loading direction goes from DerivedBioAssay:s -> RawBioAssay:s -> Experiment:s. The reverse-loading direction is the opposite direction.

Version:

2.10

Author:

Nicklas

Last modified

$Date: 2018-06-04 08:42:46 +0200 (må, 04 jun 2018) $

Field Summary

Fields inherited from class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

ALLOW_ROOT_NODE, allowAsRootNode, DENY_ROOT_NODE, factoryKey, nameGenerator

Constructor Summary

Constructors

Constructor	Description
RawBioAssayLoader()

Method Summary

Modifier and Type	Method	Description
Node	createForwardNode(DbControl dc, OverviewContext context, Node parentNode)	Create forward-loading raw bioassay nodes from a given parent derived bioassay or extract node.
private Node	createForwardNode(DerivedBioAssay bioAssay, DbControl dc, OverviewContext context, Node bioAssayNode)
private Node	createForwardNode(Extract extract, DbControl dc, OverviewContext context, Node extractNode)
Node	createReverseNode(DbControl dc, OverviewContext context, Node experimentNode)	Create a reverse-loading raw bioassay nodes from a given experiment node.
Node	createRootNode(DbControl dc, OverviewContext context, RawBioAssay item)	Create a root node for the given item.
private Extract	getExtract(RawBioAssay bioAssay)	Get the extract that is associated with the current raw bioassay
private Set<Integer>	getExtractChain(DbControl dc, Node node)
protected void	loadForwardChildNodes(DbControl dc, OverviewContext context, Node rawBioAssayNode)	Loads all experiment nodes where the given raw bioassay is used.
protected void	loadPropertyChildNodes(DbControl dc, OverviewContext context, Node rawBioAssayNode)	Load property nodes for a raw bioassay: Annotations: AnnotationLoader.createPropertyNode(DbControl, OverviewContext, Node) Data files: DataFileLoader.createPropertyNode(DbControl, OverviewContext, Node) Platform: PlatformLoader.createPropertyNode(DbControl, OverviewContext, Node) Protocol: ProtocolLoader.createPropertyNode(DbControl, OverviewContext, Node) Software: SoftwareLoader.createPropertyNode(DbControl, OverviewContext, Node) Array design: ArrayDesignLoader.createPropertyNode(DbControl, OverviewContext, Node)
protected void	loadReverseChildNodes(DbControl dc, OverviewContext context, Node rawBioAssayNode)	Loads the derived bioassay node that this raw bioassay is created from.

Methods inherited from class net.sf.basedb.util.overview.loader.BasicItemNodeLoader

createItemNode, getNodeFactory, getNodeFactory, getNodeLoader, getNodeLoaderFactory, getNodeNameGenerator, getNodeValidator, getNodeValidatorFactory, postValidateFolder

Methods inherited from class net.sf.basedb.util.overview.loader.AbstractNodeLoader

createPropertyNode, loadChildNodes, loadChildNodesOfFolderNode, loadChildNodesOfItemNode

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

RawBioAssayLoader

public RawBioAssayLoader()

Method Details

createRootNode

public Node createRootNode(DbControl dc,
 OverviewContext context,
 RawBioAssay item)

Description copied from interface: NodeLoader

Create a root node for the given item. A root node is a node with no parent. Typically, the direction of the created node is ChildNodeDirection.ALL so that both forward and reverse child nodes are loaded.

Specified by:

createRootNode in interface NodeLoader<RawBioAssay>

Overrides:

createRootNode in class BasicItemNodeLoader<RawBioAssay>

Parameters:

dc - The DbControl to use for database access

context - The overview context

item - The root item

Returns:

A root node

createForwardNode

public Node createForwardNode(DbControl dc,
 OverviewContext context,
 Node parentNode)

Create forward-loading raw bioassay nodes from a given parent derived bioassay or extract node. The returned node is a folder-type node containing item nodes for each raw bioassay. If the parent item is an extract only raw bioassays which doesn't have a parent derived bioassay are loaded.

Specified by:

createForwardNode in interface NodeLoader<RawBioAssay>

Overrides:

createForwardNode in class AbstractNodeLoader<RawBioAssay>

Parameters:

dc - The DbControl to use for database access

context - The overview context

parentNode - The parent node

Returns:

The folder node for the raw bioassays

createReverseNode

public Node createReverseNode(DbControl dc,
 OverviewContext context,
 Node experimentNode)

Create a reverse-loading raw bioassay nodes from a given experiment node. The returned node is a folder-type node containing nodes for each raw bioassay is part of the experiment.

Specified by:

createReverseNode in interface NodeLoader<RawBioAssay>

Overrides:

createReverseNode in class AbstractNodeLoader<RawBioAssay>

Parameters:

dc - The DbControl to use for database access

context - The overview context

experimentNode - The child node

Returns:

The folder node for the raw bioassays

loadPropertyChildNodes

protected void loadPropertyChildNodes(DbControl dc,
 OverviewContext context,
 Node rawBioAssayNode)

Load property nodes for a raw bioassay:

• Annotations: AnnotationLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Data files: DataFileLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Platform: PlatformLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Protocol: ProtocolLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Software: SoftwareLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Array design: ArrayDesignLoader.createPropertyNode(DbControl, OverviewContext, Node)

Overrides:

loadPropertyChildNodes in class AbstractNodeLoader<RawBioAssay>

loadForwardChildNodes

protected void loadForwardChildNodes(DbControl dc,
 OverviewContext context,
 Node rawBioAssayNode)

Loads all experiment nodes where the given raw bioassay is used.

Overrides:

loadForwardChildNodes in class AbstractNodeLoader<RawBioAssay>

See Also:

• ExperimentLoader.createForwardNode(DbControl, OverviewContext, Node)

loadReverseChildNodes

protected void loadReverseChildNodes(DbControl dc,
 OverviewContext context,
 Node rawBioAssayNode)

Loads the derived bioassay node that this raw bioassay is created from.

Overrides:

loadReverseChildNodes in class AbstractNodeLoader<RawBioAssay>

See Also:

• DerivedBioAssayLoader.createReverseNode(DbControl, OverviewContext, Node)

createForwardNode

private Node createForwardNode(DerivedBioAssay bioAssay,
 DbControl dc,
 OverviewContext context,
 Node bioAssayNode)

createForwardNode

private Node createForwardNode(Extract extract,
 DbControl dc,
 OverviewContext context,
 Node extractNode)

getExtract

private Extract getExtract(RawBioAssay bioAssay)

Get the extract that is associated with the current raw bioassay

Returns:

The extract or null if none was found

getExtractChain

private Set<Integer> getExtractChain(DbControl dc,
 Node node)