3.2.4: 2013-12-06

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

java.lang.Object
  extended by net.sf.basedb.util.overview.loader.AbstractNodeLoader<I>
      extended by net.sf.basedb.util.overview.loader.BasicItemNodeLoader<PhysicalBioAssay>
          extended by 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: 2012-08-22 13:36:15 +0200 (Wed, 22 Aug 2012) $

Field Summary
 
Fields inherited from class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
ALLOW_ROOT_NODE, allowAsRootNode, DENY_ROOT_NODE, factoryKey, nameGenerator
 
Constructor Summary
PhysicalBioAssayLoader()
           
 
Method Summary
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 Detail

PhysicalBioAssayLoader

public PhysicalBioAssayLoader()
Method Detail

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.

Overrides:
loadPropertyChildNodes in class AbstractNodeLoader<PhysicalBioAssay>

loadForwardChildNodes

protected void loadForwardChildNodes(DbControl dc,
                                     OverviewContext context,
                                     Node bioAssayNode)
Load forward-loading child nodes:

Overrides:
loadForwardChildNodes in class AbstractNodeLoader<PhysicalBioAssay>

loadReverseChildNodes

protected void loadReverseChildNodes(DbControl dc,
                                     OverviewContext context,
                                     Node bioAssayNode)
Load reverse child nodes:

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.


3.2.4: 2013-12-06