net.sf.basedb.util.export.spotdata
Class Base1FieldConverter

java.lang.Object
  net.sf.basedb.util.export.spotdata.AbstractFieldConverter
      net.sf.basedb.util.export.spotdata.StandardFieldConverter
          net.sf.basedb.util.export.spotdata.Base1FieldConverter

All Implemented Interfaces:

ExportableFieldConverter

public class Base1FieldConverter
extends StandardFieldConverter

Exportable field converter that support BASE 1 naming conventions. This implementation rely in most cases on 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.

This class extends the standard field converter and only overrides methods that is used by the Base1PluginExecuter so thatit can work as expected. The major differences are the name of intensity fields and the _xc_ prefix on extra value fields.

Version:

2.15

Author:

Nicklas

Last modified

$Date: 2010-03-22 13:45:37 +0100 (må, 22 mar 2010) $

Constructor Summary

Base1FieldConverter(DbControl dc, BioAssaySet source)
Create a new converter for the given bioassay set.

Method Summary

protected DynamicField	getIntensityField(String fieldName, String exportTitle) 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	getReporterField(String name, boolean required) Convert a reporter field.
DynamicField	getSpotField(String name, boolean required) Convert a spot field.

Methods inherited from class net.sf.basedb.util.export.spotdata.StandardFieldConverter

getAssayField

Methods inherited from class net.sf.basedb.util.export.spotdata.AbstractFieldConverter

getAssayAnnotationField, getAssayPropertyField, getDbControl, getExperimentalFactorField, getExtraValueField, getFormulaField, getRawDataProperty, getReporterProperty, getSnapshotManager, getSource, setSnapshotManager

Methods inherited from class java.lang.Object

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

Constructor Detail

Base1FieldConverter

public Base1FieldConverter(DbControl dc,
                           BioAssaySet source)

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 name,
                                     boolean required)

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.

Specified by:

getReporterField in interface ExportableFieldConverter

Overrides:

getReporterField in class StandardFieldConverter

Parameters:

name - The BASE 1 field name

required - Controls if null is returned or an exception is thrown when a field is not found

Returns:

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

getSpotField

public DynamicField getSpotField(String name,
                                 boolean required)

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.

Specified by:

getSpotField in interface ExportableFieldConverter

Overrides:

getSpotField in class StandardFieldConverter

Parameters:

name - The BASE 1 field name

required - Controls if null is returned or an exception is thrown when a field is not found

Returns:

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

getIntensityField

protected DynamicField getIntensityField(String fieldName,
                                         String exportTitle)

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.

Overrides:

getIntensityField in class AbstractFieldConverter

Parameters:

fieldName - The field name

Returns:

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