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

Class DerivedBioAssayLoader

java.lang.Object

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

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

net.sf.basedb.util.overview.loader.DerivedBioAssayLoader

All Implemented Interfaces:

NodeLoader<DerivedBioAssay>

public class DerivedBioAssayLoader
extends BasicItemNodeLoader<DerivedBioAssay>

Since:

3.0

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
DerivedBioAssayLoader()

Method Summary

Modifier and Type	Method	Description
Node	createForwardNode(DbControl dc, OverviewContext context, Node parentNode)	Create forward-loading bioassay nodes from a given physical bioassay node or a parent derived bioassay set node.
private Node	createForwardNode(DerivedBioAssay parent, DbControl dc, OverviewContext context, Node parentNode)	Create forward-loading derived bioassay set nodes that have the given derived bioassay set as the parent
private Node	createForwardNode(Extract extract, DbControl dc, OverviewContext context, Node extractNode)
private Node	createForwardNode(PhysicalBioAssay bioAssay, DbControl dc, OverviewContext context, Node bioAssayNode)	Create forward-loading derived bioassay nodes that have the given physical bioassay as the immediate parent (eg. root bioassays).
Node	createReverseNode(DbControl dc, OverviewContext context, Node parentNode)	Create a reverse-loading bioassay node from a cild bioassay node or a raw bioassay node.
private Node	createReverseNode(DerivedBioAssay child, DbControl dc, OverviewContext context, Node childNode)	Create a reverse-loading bioassay node for the bioassay that is the parent to the given child bioassay.
private Node	createReverseNode(RawBioAssay raw, DbControl dc, OverviewContext context, Node rawNode)	Create a reverse-loading bioassay node for the bioassay that is the parent to the given raw bioassay.
Node	createRootNode(DbControl dc, OverviewContext context, DerivedBioAssay item)	Create a root node for the given item.
private Extract	getExtract(DerivedBioAssay bioAssay)	Get the extract that is associated with the current derived bioassay
private Set<Integer>	getExtractChain(DbControl dc, Node node)
protected void	loadForwardChildNodes(DbControl dc, OverviewContext context, Node parentNode)	Loads all child derived bioassay and raw bioassay nodes.
protected void	loadPropertyChildNodes(DbControl dc, OverviewContext context, Node bioAssayNode)	Loads property nodes of a derived bioassay set.
protected void	loadReverseChildNodes(DbControl dc, OverviewContext context, Node bioAssayNode)	Loads the parent bioassay or the parent physical bioassay.

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

DerivedBioAssayLoader

public DerivedBioAssayLoader()

Method Details

createRootNode

public Node createRootNode(DbControl dc,
 OverviewContext context,
 DerivedBioAssay 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<DerivedBioAssay>

Overrides:

createRootNode in class BasicItemNodeLoader<DerivedBioAssay>

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 bioassay nodes from a given physical bioassay node or a parent derived bioassay set node. The returned node is a folder-type node containing item nodes for each bioassay set.

Specified by:

createForwardNode in interface NodeLoader<DerivedBioAssay>

Overrides:

createForwardNode in class AbstractNodeLoader<DerivedBioAssay>

Parameters:

dc - The DbControl to use for database access

context - The overview context

parentNode - The parent node

Returns:

The folder node for the bioassay sets

createReverseNode

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

Create a reverse-loading bioassay node from a cild bioassay node or a raw bioassay node.

Specified by:

createReverseNode in interface NodeLoader<DerivedBioAssay>

Overrides:

createReverseNode in class AbstractNodeLoader<DerivedBioAssay>

Parameters:

dc - The DbControl to use for database access

context - The overview context

parentNode - The child node

Returns:

A bioassay node, or null if the raw bioassay doesn't have a parent bioassay

loadPropertyChildNodes

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

Loads property nodes of a derived bioassay set.

• Annotations: AnnotationLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Data files: DataFileLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Protocol: ProtocolLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Kit: KitLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Hardware: HardwareLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Software: SoftwareLoader.createPropertyNode(DbControl, OverviewContext, Node)

Overrides:

loadPropertyChildNodes in class AbstractNodeLoader<DerivedBioAssay>

loadForwardChildNodes

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

Loads all child derived bioassay and raw bioassay nodes.

Overrides:

loadForwardChildNodes in class AbstractNodeLoader<DerivedBioAssay>

See Also:

• createForwardNode(DbControl, OverviewContext, Node)
• RawBioAssayLoader.createForwardNode(DbControl, OverviewContext, Node)

loadReverseChildNodes

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

Loads the parent bioassay or the parent physical bioassay.

Overrides:

loadReverseChildNodes in class AbstractNodeLoader<DerivedBioAssay>

See Also:

• PhysicalBioAssayLoader.createReverseNode(DbControl, OverviewContext, Node)
• createReverseNode(DbControl, OverviewContext, Node)

createForwardNode

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

Create forward-loading derived bioassay nodes that have the given physical bioassay as the immediate parent (eg. root bioassays).

createForwardNode

private Node createForwardNode(DerivedBioAssay parent,
 DbControl dc,
 OverviewContext context,
 Node parentNode)

Create forward-loading derived bioassay set nodes that have the given derived bioassay set as the parent

createForwardNode

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

createReverseNode

private Node createReverseNode(RawBioAssay raw,
 DbControl dc,
 OverviewContext context,
 Node rawNode)

Create a reverse-loading bioassay node for the bioassay that is the parent to the given raw bioassay.

createReverseNode

private Node createReverseNode(DerivedBioAssay child,
 DbControl dc,
 OverviewContext context,
 Node childNode)

Create a reverse-loading bioassay node for the bioassay that is the parent to the given child bioassay.

getExtract

private Extract getExtract(DerivedBioAssay bioAssay)

Get the extract that is associated with the current derived bioassay

Returns:

The extract or null if none was found

getExtractChain

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