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

Class PhysicalBioAssayLoader

java.lang.Object

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

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

net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader

All Implemented Interfaces:

NodeLoader<PhysicalBioAssay>

public class PhysicalBioAssayLoader
extends BasicItemNodeLoader<PhysicalBioAssay>

Node loader implementation for physical bioassays. There are two forward-loading directions:

1. Extract:s -> PhysicalBioAssay:s -> DerivedBioAssay:s.
2. ArraySlide:s -> PhysicalBioAssay:s -> DerivedBioAssay:s

The reverse-loading direction starts with a derived bioassay set and moves to both extracts and array slide.

Version:

2.10

Author:

Nicklas

Last modified

$Date: 2015-11-09 08:33:52 +0100 (må, 09 nov 2015) $

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
PhysicalBioAssayLoader()

Method Summary

Modifier and Type	Method	Description
private Node	createForwardNode(ArraySlide slide, DbControl dc, OverviewContext context, Node parentNode)	Create a forward-loading bioassay node from an array slide.
Node	createForwardNode(DbControl dc, OverviewContext context, Node parentNode)	Create forward-loading physical bioassay nodes from either an extract or an array slide node.
private Node	createForwardNode(Extract extract, DbControl dc, OverviewContext context, Node parentNode, boolean onlyPushAnnotationTypes)	Create forward-loading bioassay nodes for the bioassays that has a given extract as a source.
Node	createPropertyNode(DbControl dc, OverviewContext context, Node parentNode)	A property node is created when moving in the reverse direction so that we can load child physical bioassays with the ItemSubtype.getPushAnnotations() flag set.
Node	createReverseNode(DbControl dc, OverviewContext context, Node derivedBioAssayNode)	Create a reverse-loading bioassay node from the derived bioassay node.
protected void	loadForwardChildNodes(DbControl dc, OverviewContext context, Node bioAssayNode)	Load forward-loading child nodes: Derived bioassay sets (root): DerivedBioAssayLoader.createForwardNode(DbControl, OverviewContext, Node) Array slide in reverse direction (if the parent node is an extract): ArraySlideLoader.createReverseNode(DbControl, OverviewContext, Node) Extracts in reverse direction (if the parent node is the array slide): ExtractLoader.createReverseNode(DbControl, OverviewContext, Node)
protected void	loadPropertyChildNodes(DbControl dc, OverviewContext context, Node bioAssayNode)	Loads property nodes of a physical bioassay.
protected void	loadReverseChildNodes(DbControl dc, OverviewContext context, Node bioAssayNode)	Load reverse child nodes: Extracts: ExtractLoader.createReverseNode(DbControl, OverviewContext, Node) Array slide: ArraySlideLoader.createReverseNode(DbControl, OverviewContext, Node)

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

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

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

loadChildNodes, loadChildNodesOfFolderNode, loadChildNodesOfItemNode

Methods inherited from class java.lang.Object

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

Constructor Details

PhysicalBioAssayLoader

public PhysicalBioAssayLoader()

Method Details

createForwardNode

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

Create forward-loading physical bioassay nodes from either an extract or an array slide node. The returned node is either folder-type node containing nodes for each bioassay that has been created from the extract or an item node with the bioassay on the array slide.

Specified by:

createForwardNode in interface NodeLoader<PhysicalBioAssay>

Overrides:

createForwardNode in class AbstractNodeLoader<PhysicalBioAssay>

Parameters:

dc - The DbControl to use for database access

context - The overview context

parentNode - The parent node

Returns:

The folder node with the bioassays, or the item node (can be null)

createReverseNode

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

Create a reverse-loading bioassay node from the derived bioassay node.

Specified by:

createReverseNode in interface NodeLoader<PhysicalBioAssay>

Overrides:

createReverseNode in class AbstractNodeLoader<PhysicalBioAssay>

Parameters:

dc - The DbControl to use for database access

context - The overview context

derivedBioAssayNode - The child node

Returns:

A bioassay node

createPropertyNode

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

A property node is created when moving in the reverse direction so that we can load child physical bioassays with the ItemSubtype.getPushAnnotations() flag set. The parent node should be an extract node.

Specified by:

createPropertyNode in interface NodeLoader<PhysicalBioAssay>

Overrides:

createPropertyNode in class AbstractNodeLoader<PhysicalBioAssay>

Parameters:

dc - The DbControl to use for database access

context - The overview context

parentNode - The parent node

Returns:

A node (may be a folder-type node with many subnodes), or null

Since:

3.1

loadPropertyChildNodes

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

Loads property nodes of a physical bioassay.

• Annotations: AnnotationLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Protocol: ProtocolLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Kit: KitLoader.createPropertyNode(DbControl, OverviewContext, Node)
• Hardware: HardwareLoader.createPropertyNode(DbControl, OverviewContext, Node)

Overrides:

loadPropertyChildNodes in class AbstractNodeLoader<PhysicalBioAssay>

loadForwardChildNodes

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

Load forward-loading child nodes:

• Derived bioassay sets (root): DerivedBioAssayLoader.createForwardNode(DbControl, OverviewContext, Node)
• Array slide in reverse direction (if the parent node is an extract): ArraySlideLoader.createReverseNode(DbControl, OverviewContext, Node)
• Extracts in reverse direction (if the parent node is the array slide): ExtractLoader.createReverseNode(DbControl, OverviewContext, Node)

Overrides:

loadForwardChildNodes in class AbstractNodeLoader<PhysicalBioAssay>

loadReverseChildNodes

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

Load reverse child nodes:

• Extracts: ExtractLoader.createReverseNode(DbControl, OverviewContext, Node)
• Array slide: ArraySlideLoader.createReverseNode(DbControl, OverviewContext, Node)

Overrides:

loadReverseChildNodes in class AbstractNodeLoader<PhysicalBioAssay>

createForwardNode

private Node createForwardNode(Extract extract,
 DbControl dc,
 OverviewContext context,
 Node parentNode,
 boolean onlyPushAnnotationTypes)

Create forward-loading bioassay nodes for the bioassays that has a given extract as a source.

createForwardNode

private Node createForwardNode(ArraySlide slide,
 DbControl dc,
 OverviewContext context,
 Node parentNode)

Create a forward-loading bioassay node from an array slide.