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

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

public class ExportableFieldFactory
extends Object

Utility class with factory methods that helps with the creation of exportable fields.

Version:

2.12

Author:

Nicklas

Last modified

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

Constructor Summary

ExportableFieldFactory()

Method Summary

static AnnotationAssayField	annotation(AnnotationType at, Formatter<?> formatter) Create an annotation assay field.
static AnnotationAssayField	annotation(AnnotationType at, String title, Formatter<?> formatter) Create an annotation assay field, overriding the title of the annotation type.
static AssayPropertyField	assayProperty(String property, String title, Type type, Formatter<?> formatter) Create a property assay field.
static SimpleDynamicField	channel(int channel, String title, Formatter<?> formatter) Create a simple dynamic field that exports the channel intensity of the given channel.
static JepDynamicField	extraValue(ExtraValueType extra, String title, Formatter<?> formatter) Create a JEP dynamic field that exports an extra value.
static JepDynamicField	formula(Formula f, String title, Formatter<?> formatter) Create a JEP dynamic field that exports the result of the JEP expression in a formula.
static JepDynamicField	jep(String jep, String title, Formula.AverageMethod averageMethod, Formatter<?> formatter) Deprecated. In 2.15, use jep(String, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter) instead
static JepDynamicField	jep(String jep, String title, Type type, Formula.AverageMethod averageMethod, Formatter<?> formatter) Create a JEP dynamic field.
static SimpleDynamicField	rawData(RawDataProperty property, String title, Formatter<?> formatter) Create a simple dynamic field that exports a raw data value.
static SimpleDynamicField	rawData(String property, String title, Formula.AverageMethod averageMethod, Formatter<?> formatter) Deprecated. In 2.15, use rawData(String, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter) instead
static SimpleDynamicField	rawData(String property, String title, Type type, Formula.AverageMethod averageMethod, Formatter<?> formatter) Create a simple dynamic field that exports a raw data value.
static SimpleDynamicField	reporter(ExtendedProperty property, String title, Formatter<?> formatter) Create a simple dynamic field that exports reporter annotation values.
static DynamicField	reporter(String property, String title, Formula.AverageMethod averageMethod, Formatter<?> formatter) Deprecated. In 2.15, use reporter(String, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter) instead
static DynamicField	reporter(String property, String title, Type type, Formula.AverageMethod averageMethod, Formatter<?> formatter) Create a simple dynamic field that exports reporter annotation values.
static SimpleDynamicField	simple(Expression e, String title, Formula.AverageMethod averageMethod, Formatter<?> formatter) Deprecated. In 2.15, use simple(Expression, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter) instead
static SimpleDynamicField	simple(Expression e, String title, Type type, Formula.AverageMethod averageMethod, Formatter<?> formatter) Create a simple dynamic field.

Methods inherited from class java.lang.Object

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

Constructor Detail

ExportableFieldFactory

public ExportableFieldFactory()

Method Detail

annotation

public static AnnotationAssayField annotation(AnnotationType at,
                                              Formatter<?> formatter)

Create an annotation assay field.

Parameters:

at - The annotation type

formatter - A formatter or null

See Also:

AnnotationAssayField

annotation

public static AnnotationAssayField annotation(AnnotationType at,
                                              String title,
                                              Formatter<?> formatter)

Create an annotation assay field, overriding the title of the annotation type.

Parameters:

at - The annotation type

title - A custom title for the assay field, or null to use the name of the annotation type

formatter - A formatter or null

Since:

2.15

See Also:

AnnotationAssayField

assayProperty

public static AssayPropertyField assayProperty(String property,
                                               String title,
                                               Type type,
                                               Formatter<?> formatter)

Create a property assay field. This field is used to export, for example, name and description, from the bioassay.

Parameters:

property - The property to export, see Metadata.getPropertyValue(net.sf.basedb.core.DbControl, Object, String) for more information about the syntax of this parameter.

title - The column title

formatter - A formatter or null

Returns:

An AssayPropertyField object

Since:

2.15

simple

@Deprecated
public static SimpleDynamicField simple(Expression e,
                                                   String title,
                                                   Formula.AverageMethod averageMethod,
                                                   Formatter<?> formatter)

Deprecated. In 2.15, use simple(Expression, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter) instead

simple

public static SimpleDynamicField simple(Expression e,
                                        String title,
                                        Type type,
                                        Formula.AverageMethod averageMethod,
                                        Formatter<?> formatter)

Create a simple dynamic field.

Parameters:

e - The expression to export

title - The column title

averageMethod - Average method to use or null to use the average method specified by the bioassay set

formatter - A formatter or null

Since:

2.15

See Also:

SimpleDynamicField

jep

@Deprecated
public static JepDynamicField jep(String jep,
                                             String title,
                                             Formula.AverageMethod averageMethod,
                                             Formatter<?> formatter)

Deprecated. In 2.15, use jep(String, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter) instead

jep

public static JepDynamicField jep(String jep,
                                  String title,
                                  Type type,
                                  Formula.AverageMethod averageMethod,
                                  Formatter<?> formatter)

Create a JEP dynamic field.

Parameters:

jep - The JEP expression

title - The column title

type - The data type of the expression

averageMethod - Average method to use or null to use the average method specified by the bioassay set

formatter - A formatter or null

channel

public static SimpleDynamicField channel(int channel,
                                         String title,
                                         Formatter<?> formatter)

Create a simple dynamic field that exports the channel intensity of the given channel. This method uses Dynamic.column(VirtualColumn) and VirtualColumn.channelRaw(int) to generate the expression. It uses the average method specified by the bioassay set.

Parameters:

channel - The channel number

title - The column title. If null, the title is generated as 'intensity' + channel

formatter - A formatter for numeric data or null

rawData

public static SimpleDynamicField rawData(RawDataProperty property,
                                         String title,
                                         Formatter<?> formatter)

Create a simple dynamic field that exports a raw data value. This method uses Dynamic.rawData(String) to generate the expression and uses the average method specified by the raw data property.

Parameters:

property - The raw data property

title - The column title, or null to use the title of the property

formatter - A formatter or null

rawData

@Deprecated
public static SimpleDynamicField rawData(String property,
                                                    String title,
                                                    Formula.AverageMethod averageMethod,
                                                    Formatter<?> formatter)

Deprecated. In 2.15, use rawData(String, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter) instead

rawData

public static SimpleDynamicField rawData(String property,
                                         String title,
                                         Type type,
                                         Formula.AverageMethod averageMethod,
                                         Formatter<?> formatter)

Create a simple dynamic field that exports a raw data value. This method uses Dynamic.rawData(String) to generate the expression.

Parameters:

property - The raw data property

title - The column title, or null to use the property as title

averageMethod - Average method to use or null to use Formula.AverageMethod.NONE

formatter - A formatter or null

Since:

2.15

reporter

public static SimpleDynamicField reporter(ExtendedProperty property,
                                          String title,
                                          Formatter<?> formatter)

Create a simple dynamic field that exports reporter annotation values. This method uses Dynamic.reporter(String) to generate the expression and uses the average method specified by the reporter property.

Parameters:

property - The reporter property

title - The column title, or null to use the title of the property

formatter - A formatter or null

reporter

public static DynamicField reporter(String property,
                                    String title,
                                    Formula.AverageMethod averageMethod,
                                    Formatter<?> formatter)

Deprecated. In 2.15, use reporter(String, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter) instead

reporter

public static DynamicField reporter(String property,
                                    String title,
                                    Type type,
                                    Formula.AverageMethod averageMethod,
                                    Formatter<?> formatter)

Create a simple dynamic field that exports reporter annotation values. This method uses Dynamic.reporter(String) to generate the expression.

Parameters:

property - The reporter property

title - The column title, or null to use the property as title

averageMethod - Average method to use or null to use Formula.AverageMethod.NONE

formatter - A formatter or null

Since:

2.15

formula

public static JepDynamicField formula(Formula f,
                                      String title,
                                      Formatter<?> formatter)

Create a JEP dynamic field that exports the result of the JEP expression in a formula. This method doesn't check the type of the formula or the number of expressions stored in the formula. It just takes the first expression it finds.

Parameters:

f - The formula

title - The column title, or null to use the name of the formula as the title

formatter - A formatter or null

extraValue

public static JepDynamicField extraValue(ExtraValueType extra,
                                         String title,
                                         Formatter<?> formatter)

Create a JEP dynamic field that exports an extra value.

Parameters:

extra - The extra value type

title - The column title, or null to use the name of the formula as the title

formatter - A formatter or null