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

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

Deprecated. In 2.15. This implementation is Base1-specific. It has been replaced with Base1FieldConverter

@Deprecated
public class FieldConverter
extends Object

Class for converting string-based spot and reporter names into dynamic field representation suitable for bioassay set exporter. This class is for example used by the Base1PluginExecuter to convert BASE 1 names into BASE 2 expressions. This feature rely in most cases on the use of formulas with the same name as the BASE 1 field. BASE 1 fields that happens to have the same name in BASE 2 doesn't need formulas.

Version:

2.12

Author:

Nicklas

Last modified

$Date: 2010-08-13 12:48:17 +0200 (Fri, 13 Aug 2010) $

Field Summary

private DbControl	dc Deprecated.
private ItemQuery<ExtraValue>	extraQuery Deprecated.
private ItemQuery<Formula>	formulaQuery Deprecated.
private BioAssaySet	source Deprecated.

Constructor Summary

FieldConverter(DbControl dc, BioAssaySet source)
Deprecated. Create a new converter for the given bioassay set.

Method Summary

DynamicField	getExtraValueField(String externalId, ExtraValue.CoordinateType type, String exportTitle) Deprecated. Find an extra value with the given external id and coordinate type and create a dynamic field from it using exportTitle as the title.
DynamicField	getFormulaField(String formulaName, String exportTitle) Deprecated. Find a formula with the given name and create a dynamic field from it using exportTitle as the title.
DynamicField	getIntensityField(String fieldName) Deprecated. Create a dynamic field for spot intensity if the field name has the pattern 'intensityX' where 'X' is a channel number between 1 and the number of channels in the raw data type used by the source bioassay set.
DynamicField	getRawdataProperty(String name, String exportTitle) Deprecated. Find an extended raw data property with the given name and create a dynamic field from it using exportTitle as the title.
DynamicField	getReporterField(String fieldName) Deprecated. Convert a reporter field.
DynamicField	getReporterProperty(String name, String exportTitle) Deprecated. Find an extended reporter property with the given name and create a dynamic field from it using exportTitle as the title.
DynamicField	getSpotField(String fieldName) Deprecated. Convert a spot field.

Methods inherited from class java.lang.Object

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

Field Detail

dc

private final DbControl dc

Deprecated.

source

private final BioAssaySet source

Deprecated.

formulaQuery

private ItemQuery<Formula> formulaQuery

Deprecated.

extraQuery

private ItemQuery<ExtraValue> extraQuery

Deprecated.

Constructor Detail

FieldConverter

public FieldConverter(DbControl dc,
                      BioAssaySet source)

Deprecated.

Create a new converter for the given bioassay set.

Parameters:

dc - A DbControl to use for database access

source - The source bioassay set

Method Detail

getReporterField

public DynamicField getReporterField(String fieldName)

Deprecated.

Convert a reporter field. The conversion is done in steps until a match is found:

• If the field starts with '_xc_' it could be an extra value. We check if there is a position extra value with an external id that is the same as the rest of the field (eg. without the _xc_ prefix).
• Check if a formula that has the exactly the same name as the given field name exists. The formula must be a column expression and it must usable on the raw data type and the intensity transform that the source bioassay set uses.
• Check if an extended reporter property with exactly the same name as the given field name exists.

Parameters:

fieldName - The BASE 1 field name

Returns:

A DynamicField expression or null if the field name can't be converted

getSpotField

public DynamicField getSpotField(String fieldName)

Deprecated.

Convert a spot field. The conversion is done in steps until a match is found:

• If the field starts with '_xc_' it could be an extra value. We check if there is an spot extra value with an external id that is the same as the rest of the field (eg. without the _xc_ prefix).
• Check if a formula that has the exactly the same name as the given field name exists. The formula must be a column expression and it must usable on the raw data type and the intensity transform that the source bioassay set uses.
• Check if a raw data property with exactly the same name as the given field name exists.
• Check if the field name is 'intensityX' where 'X' is a channel number.

Parameters:

fieldName - The BASE 1 field name

Returns:

A DynamicField expression or null if the field name can't be converted

getFormulaField

public DynamicField getFormulaField(String formulaName,
                                    String exportTitle)

Deprecated.

Find a formula with the given name and create a dynamic field from it using exportTitle as the title. The formula must be a Formula.Type.COLUMN_EXPRESSION and be suitable for the RawDataType and IntensityTransform used by the source bioassay set.

Parameters:

formulaName - The name of the formula to look for

exportTitle - The exported title, or null to use the formula name

Returns:

A dynamic field, or null if no formula is found

getExtraValueField

public DynamicField getExtraValueField(String externalId,
                                       ExtraValue.CoordinateType type,
                                       String exportTitle)

Deprecated.

Find an extra value with the given external id and coordinate type and create a dynamic field from it using exportTitle as the title. The extra value must of course be attached to the source bioassay set.

Parameters:

externalId - The external id of the ExtraValueType

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

exportTitle - The exported title or null to use the name (not the external id) of the extra value type

Returns:

A dynamic field, or null if no extra value is found

getReporterProperty

public DynamicField getReporterProperty(String name,
                                        String exportTitle)

Deprecated.

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

Parameters:

name - The name of the extended 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

public DynamicField getRawdataProperty(String name,
                                       String exportTitle)

Deprecated.

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

getIntensityField

public DynamicField getIntensityField(String fieldName)

Deprecated.

Create a dynamic field for spot intensity if the field name has the pattern 'intensityX' 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