net.sf.basedb.util.export.spotdata
Class AbstractFieldConverter

java.lang.Object
  net.sf.basedb.util.export.spotdata.AbstractFieldConverter

All Implemented Interfaces:

ExportableFieldConverter

Direct Known Subclasses:

StandardFieldConverter

public abstract class AbstractFieldConverter
extends Object
implements ExportableFieldConverter

Abstract helper class for implementing ExportableFieldConverter. It contains a lot of helper method for locating formulas, extra values, experimental factors, etc.

Since:

2.15

Author:

nicklas

Field Summary

private ItemQuery<AnnotationType>	assayAnnotationQuery
private DbControl	dc
private ItemQuery<ExtraValue>	extraQuery
private ItemQuery<AnnotationType>	factorQuery
private ItemQuery<Formula>	formulaQuery
private SnapshotManager	snapshotManager
private BioAssaySet	source

Constructor Summary

protected

AbstractFieldConverter(DbControl dc, BioAssaySet source) Creates a new field converter to be used with a specific bioassay set source.

Method Summary

protected AnnotationAssayField	getAssayAnnotationField(String name, String exportTitle) Get an assay annotation field.
protected AssayPropertyField	getAssayPropertyField(String name, String exportTitle) Get a static assay property field, such as name, description or id.
protected DbControl	getDbControl() Get the DbControl to use for database access.
protected AnnotationAssayField	getExperimentalFactorField(String name, String exportTitle) Get an experimental factor assay field.
protected DynamicField	getExtraValueField(String name, ExtraValue.CoordinateType type, String exportTitle) Get an extra value dynamic field.
protected DynamicField	getFormulaField(String name, String exportTitle) Get a formula dynamic field.
protected DynamicField	getIntensityField(String fieldName, String exportTitle) Create a dynamic field for spot intensity if the field name has the pattern 'Ch X' where 'X' is a channel number between 1 and the number of channels in the raw data type used by the source bioassay set.
protected DynamicField	getRawDataProperty(String name, String exportTitle) Find an extended raw data property with the given name and create a dynamic field from it using exportTitle as the title.
protected DynamicField	getReporterProperty(String name, String exportTitle) Get a static or extended reporter property field, such as name, description or id.
SnapshotManager	getSnapshotManager() Get the snapshot manager to use with annotation-based fields.
protected BioAssaySet	getSource() Get the source bioassay set.
void	setSnapshotManager(SnapshotManager snapshotManager) Set a snapshot manager that should be used with annotation-based fields.

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.sf.basedb.util.export.spotdata.ExportableFieldConverter

getAssayField, getReporterField, getSpotField

Field Detail

dc

private final DbControl dc

source

private final BioAssaySet source

snapshotManager

private SnapshotManager snapshotManager

factorQuery

private ItemQuery<AnnotationType> factorQuery

assayAnnotationQuery

private ItemQuery<AnnotationType> assayAnnotationQuery

extraQuery

private ItemQuery<ExtraValue> extraQuery

formulaQuery

private ItemQuery<Formula> formulaQuery

Constructor Detail

AbstractFieldConverter

protected AbstractFieldConverter(DbControl dc,
                                 BioAssaySet source)

Creates a new field converter to be used with a specific bioassay set source.

Parameters:

dc - A DbControl to use for database access

source - The source bioassay set

Method Detail

getDbControl

protected DbControl getDbControl()

Get the DbControl to use for database access.

getSource

protected BioAssaySet getSource()

Get the source bioassay set.

setSnapshotManager

public void setSnapshotManager(SnapshotManager snapshotManager)

Set a snapshot manager that should be used with annotation-based fields. If no snapshot manager is provided, a new manager will automatically be created if needed.

Parameters:

snapshotManager - The snapshot manager to use

getSnapshotManager

public SnapshotManager getSnapshotManager()

Get the snapshot manager to use with annotation-based fields. If no snapshot manager has been configured a new one is automatically created.

Returns:

A snapshot manager object

getAssayPropertyField

protected AssayPropertyField getAssayPropertyField(String name,
                                                   String exportTitle)

Get a static assay property field, such as name, description or id. Property lookup is not case-sensitive. Eg. both 'name' and 'Name' will match.

Parameters:

name - The property name

exportTitle - The title as it should be in the exported file

Returns:

An AssayPropertyField or null if not found

getExperimentalFactorField

protected AnnotationAssayField getExperimentalFactorField(String name,
                                                          String exportTitle)

Get an experimental factor assay field. A database query is used to locate an experimental factor for the experiment that has the given name or external id. Depending on the underlying database, the lookup may be case-sensitive or case-insensitive. If more than one experimental factor is found an exception is thrown.

Parameters:

name - The name or external id of the experimental factor to find

exportTitle - The title as it should be in the exported file or null to use the name of the experimental factor

Returns:

An AnnotationAssayField or null if no experimental factor is found

getAssayAnnotationField

protected AnnotationAssayField getAssayAnnotationField(String name,
                                                       String exportTitle)

Get an assay annotation field. A database query is used to locate an annotation type that has been used on at least one assay in the bioassay set. Depending on the underlying database, the lookup may be case-sensitive or case-insensitive. If more than one annotation type is found an exception is thrown.

Parameters:

name - The name or external id of the annotation type to find

exportTitle - The title as it should be in the exported file or null to use the name of the annotation type

Returns:

An AnnotationAssayField or null if no annotation type is found

getReporterProperty

protected DynamicField getReporterProperty(String name,
                                           String exportTitle)

Get a static or extended reporter property field, such as name, description or id. Property lookup is not case-sensitive. Eg. both 'name' and 'Name' will match.

Parameters:

name - The name of the reporter property

exportTitle - The exported title or null to use the title of the extended property (which can be different from the name)

Returns:

A dynamic field, or null if no reporter property is found

getRawDataProperty

protected DynamicField getRawDataProperty(String name,
                                          String exportTitle)

Find an extended raw data property with the given name and create a dynamic field from it using exportTitle as the title.

Parameters:

name - The name of the extended raw data property

exportTitle - The exported title or null to use the title of the extended property (which can be different from the name)

Returns:

A dynamic field, or null if no raw data property is found

getExtraValueField

protected DynamicField getExtraValueField(String name,
                                          ExtraValue.CoordinateType type,
                                          String exportTitle)

Get an extra value dynamic field. A database query is used to locate an extra value for the bioassay set that has the given name or external id. Depending on the underlying database, the lookup may be case-sensitive or case-insensitive. If more than one extra value is found an exception is thrown.

Parameters:

name - The name or external id of the experimental factor to find

type - The coordinate type of the extra value (eg. POSITION for reporter extra values, and SPOT for spot extra values)

exportTitle - The title as it should be in the exported file or null to use the name of the extra value

Returns:

A DynamicField or null if no extra value is found

getFormulaField

protected DynamicField getFormulaField(String name,
                                       String exportTitle)

Get a formula dynamic field. A database query is used to locate the formula which must be a Formula.Type.COLUMN_EXPRESSION and be suitable for the RawDataType and IntensityTransform used by the source bioassay set. Depending on the underlying database, the lookup may be case-sensitive or case-insensitive. If more than one formula is found an exception is thrown.

Parameters:

name - The name of the formula to find

exportTitle - The title as it should be in the exported file or null to use the name of the formula

Returns:

A DynamicField or null if no extra value is found

getIntensityField

protected DynamicField getIntensityField(String fieldName,
                                         String exportTitle)

Create a dynamic field for spot intensity if the field name has the pattern 'Ch X' where 'X' is a channel number between 1 and the number of channels in the raw data type used by the source bioassay set.

Parameters:

fieldName - The field name

Returns:

A dynamic field, or null if the name doesn't match the pattern