Package net.sf.basedb.core

Class FeatureBatcher

java.lang.Object

net.sf.basedb.core.AbstractBatcher

net.sf.basedb.core.BasicBatcher<FeatureData>

net.sf.basedb.core.FeatureBatcher

All Implemented Interfaces:

AutoCloseable, AccessControlled, Batcher

public class FeatureBatcher
extends BasicBatcher<FeatureData>

Batcher class for Features or AffyFeatures. A single instance can be used for features belonging to a single ArrayDesign.

Create new FeatureData objects with either newFeature(ArrayDesignBlock, ReporterData) or newFeature(ArrayDesignBlock, Well). Use the latter method if the array desing is connected to plates.

Depending on the FeatureIdentificationMethod used by the array design, you must set different properties on the FeatureData object.

• NONE: Not supported
• COORDINATES: FeatureData.setRow(int) and FeatureData.setColumn(int)
• POSITION: FeatureData.setPosition(int)
• FEATURE_ID: FeatureData.setExternalId(String)

For all methods, each feature that is inserted must have a unqiue value. For example, there can't be two features with the same external ID if the FEATURE_ID method is used. Values for the methods that are not used can still be set and saved to the database, but the uniqueness is not checked. The position number will be auto-generated (and overwritten) if the identification method is not POSITION.

Version:

2.0

Author:

Enell, Nicklas

Last modified

$Date$

Field Summary

Fields

Modifier and Type	Field	Description
private final ArrayDesign	arrayDesign	The array design this batcher adds features to.
private final ArrayDesignData	arrayDesignData	Just a copy of the data object for the array design.
private int	currentPosition	Keeps track of the position number.
private Set	featureIds	Holds identification of already inserted features.
private final FeatureIdentificationMethod	fiMethod

Fields inherited from class net.sf.basedb.core.BasicBatcher

debugEnabled, logParam

Fields inherited from class net.sf.basedb.core.AbstractBatcher

debugSqlEnabled, logSql

Constructor Summary

Constructors

Constructor	Description
FeatureBatcher(DbControl dc, ArrayDesign arrayDesign)

Method Summary

Modifier and Type	Method	Description
void	delete(int id)	Always throws a PermissionDeniedException, since a feature cannot be modifed once it has been created.
(package private) void	deleteAll()	Delete all features belonging to this array design.
ArrayDesign	getArrayDesign()	Get the array design this batcher is used for.
(package private) static FeatureBatcher	getNew(DbControl dc, ArrayDesign arrayDesign)	Create a new batcher for regular features.
(package private) PluginPermission	getPluginPermissions()
Item	getType()	Get the type of item supported by the batcher.
(package private) void	initPermissions(int granted, int denied)	Grant read permission if the logged in user has read permission to the array design.
void	insert(FeatureData data)	Set the position number and add the feature to the insert queue.
FeatureData	newFeature(ArrayDesignBlock adb, ReporterData reporter)	Create a new feature.
FeatureData	newFeature(ArrayDesignBlock adb, Well well)	Create a new feature.
(package private) void	onBeforeClose()	Set the hasFeature flag on the array design if features has been added.
void	update(FeatureData data)	Always throws a PermissionDeniedException, since a feature cannot be modifed once it has been created.
void	validate(FeatureData data)	Validate all properties for the feature object: The data object is not null An array design block has been specfied The position number is > 0 The external id is not null or too long The feature identification is unique The data object belongs to the correct array design The reporter match the well's reporter if a well has been specified

Methods inherited from class net.sf.basedb.core.BasicBatcher

checkPermission, delete, flush, flushDelete, flushInsert, flushUpdate, getPermissions, getPropertyValue, getTotalInsertCount, hasPermission, onBeforeCommit, setPropertyValue

Methods inherited from class net.sf.basedb.core.AbstractBatcher

analyzeTable, close, getBatchSize, getDbControl, getSessionControl, isClosed, setBatchSize, setDbControl, updateLastAccess

Methods inherited from class java.lang.Object

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

Field Details

arrayDesign

private final ArrayDesign arrayDesign

The array design this batcher adds features to.

arrayDesignData

private final ArrayDesignData arrayDesignData

Just a copy of the data object for the array design.

fiMethod

private final FeatureIdentificationMethod fiMethod

featureIds

private Set featureIds

Holds identification of already inserted features.

currentPosition

private int currentPosition

Keeps track of the position number.

Constructor Details

FeatureBatcher

FeatureBatcher(DbControl dc,
 ArrayDesign arrayDesign)
        throws BaseException

Throws:

BaseException

Method Details

getNew

static FeatureBatcher getNew(DbControl dc,
 ArrayDesign arrayDesign)
                      throws DatabaseException,
BaseException

Create a new batcher for regular features.

Parameters:

dc - The DbControl to use for database access and permission checking

arrayDesign - The array design this batcher should add features to

Throws:

BaseException - If there is an error

DatabaseException

See Also:

• ArrayDesign.getFeatureBatcher(FeatureIdentificationMethod, Job)

getType

public Item getType()

Description copied from class: BasicBatcher

Get the type of item supported by the batcher. The returned value is one of the values defined in the Item enumeration.

Specified by:

getType in class BasicBatcher<FeatureData>

Returns:

A value indicating the type of item

See Also:

• Item

validate

public void validate(FeatureData data)
              throws InvalidDataException

Validate all properties for the feature object:

• The data object is not null
• An array design block has been specfied
• The position number is > 0
• The external id is not null or too long
• The feature identification is unique
• The data object belongs to the correct array design
• The reporter match the well's reporter if a well has been specified

Specified by:

validate in class BasicBatcher<FeatureData>

Parameters:

data - Data object to validate

Throws:

InvalidDataException - If the data object is invalid

insert

public void insert(FeatureData data)
            throws BaseException

Set the position number and add the feature to the insert queue.

Overrides:

insert in class BasicBatcher<FeatureData>

Parameters:

data - Data object to be inserted

Throws:

InvalidDataException - If the data is null or it doesn't validate against the BasicBatcher.validate(BatchableData) method

PermissionDeniedException - If the logged in user doesn't have create permission

BaseException - If there is another error

update

public void update(FeatureData data)
            throws BaseException

Always throws a PermissionDeniedException, since a feature cannot be modifed once it has been created.

Overrides:

update in class BasicBatcher<FeatureData>

Parameters:

data - Data object to be updated

Throws:

InvalidDataException - If the data is null or it doesn't validate against the BasicBatcher.validate(BatchableData) method

PermissionDeniedException - If the logged in user doesn't have write permission

BaseException - If there is another error

delete

public void delete(int id)
            throws BaseException

Always throws a PermissionDeniedException, since a feature cannot be modifed once it has been created.

Overrides:

delete in class BasicBatcher<FeatureData>

Parameters:

id - Id of the object to be deleted

Throws:

PermissionDeniedException - If the logged in user doesn't have delete permission

BaseException - If there is another error

See Also:

• deleteAll()

initPermissions

void initPermissions(int granted,
 int denied)
              throws BaseException

Grant read permission if the logged in user has read permission to the array design. Grant write, delete and create permission if the logged in user has write permission to the array design.

Overrides:

initPermissions in class BasicBatcher<FeatureData>

Parameters:

granted - Permissions that have been granted by the subclass

denied - Permissions that have been denied by the subclass

Throws:

BaseException - If the permissions couldn't be initialised

getPluginPermissions

PluginPermission getPluginPermissions()

Overrides:

getPluginPermissions in class BasicBatcher<FeatureData>

onBeforeClose

void onBeforeClose()
            throws BaseException

Set the hasFeature flag on the array design if features has been added.

Overrides:

onBeforeClose in class BasicBatcher<FeatureData>

Throws:

BaseException

getArrayDesign

public ArrayDesign getArrayDesign()

Get the array design this batcher is used for.

Returns:

An ArrayDesign

newFeature

public FeatureData newFeature(ArrayDesignBlock adb,
 Well well)
                       throws BaseException

Create a new feature.

Parameters:

adb - The array design of the feature.

well - The well of the feature. Null is not allowed. The plate of the well must have a position on the ArrayDesign of the current FeatureBatcher.

Returns:

A feature data object

Throws:

BaseException - If there is an error

newFeature

public FeatureData newFeature(ArrayDesignBlock adb,
 ReporterData reporter)
                       throws BaseException

Create a new feature.

Returns:

A feature data object

Throws:

BaseException - If there is an error

deleteAll

void deleteAll()
        throws BaseException

Delete all features belonging to this array design.

Throws:

BaseException