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

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

All Implemented Interfaces:

ExportableFieldConverter

public class AdvancedFieldConverter
extends StandardFieldConverter

Field converter implementation that gives more detailed control how fields are converted and used in the export. The implementation builds on the StandardFieldConverter which is used as a fallback. The advanced options can be accessed by using formula-like field "names" as shown below. In most cases the "title" parameter is optional. If not given, the name is used as the title.

• =property("name", ["title"]): Lookup a static property with the given name. Can be used on assay, reporter and spot (=raw data properties) fields.
• =factor("name" [,"title"]): Lookup an experimental factor with the given name or external id. Can be used in getAssayField(String, boolean).
• =annotation("name" [,"title"]): Lookup an assay annotation with the given name or external id. Can be used in getAssayField(String, boolean).
• =xtra("name" [,"title"]): Lookup an extra value with the given name or external id. Can be used in getReporterField(String, boolean) and getSpotField(String, boolean).
• =formula("name" [,"title"]): Lookup a formula with the given name. Can be used in getReporterField(String, boolean) and getSpotField(String, boolean).
• =jep("jep expression", "title" [,"datatype"]): Use the given JEP formula to calculate the exported value. Can be used in getReporterField(String, boolean) and getSpotField(String, boolean). The "title" is required. The "datatype" is optional. If not given "string" will be used. Valid values are constants from the Type enumeration (case-insensitive).

Field names that doesn't start with an equal character (=) are passed on to the StandardFieldConverter.

Since:

2.16

Author:

Nicklas

Last modified

$Date: 2010-08-05 13:16:18 +0200 (Thu, 05 Aug 2010) $

Field Summary

private Map<String,Pattern>

patterns

Constructor Summary

AdvancedFieldConverter(DbControl dc, BioAssaySet source)
Create a new advanced field converter.

Method Summary

protected AssayField	getAdvancedAssayField(String expression, boolean required) Convert an expression to an assay field.
protected DynamicField	getAdvancedReporterField(String expression, boolean required) Convert an expression to a reporter field.
protected DynamicField	getAdvancedSpotField(String expression, boolean required) Convert an expression to a spot field.
AssayField	getAssayField(String name, boolean required) Find an assay field.
private Pattern	getPattern(String function, int requiredParameters, int optionalParameters)
DynamicField	getReporterField(String name, boolean required) Find a reporter dynamic field.
DynamicField	getSpotField(String name, boolean required) Find a spot dynamic field.

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

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

Methods inherited from class java.lang.Object

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

Field Detail

patterns

private Map<String,Pattern> patterns

Constructor Detail

AdvancedFieldConverter

public AdvancedFieldConverter(DbControl dc,
                              BioAssaySet source)

Create a new advanced field converter.

Parameters:

dc - A DbControl to use for database access

source - The source bioassay set

Method Detail

getAssayField

public AssayField getAssayField(String name,
                                boolean required)

Description copied from class: StandardFieldConverter

Find an assay field. This method will try to locate a field in the following order:

1. Check if there is an experimental factor with the given name (case-sensitivity depends on the database that is used).
2. Check if there is an assay-level annotation type with the given name.
3. If name is 'name', 'description' or another static property (case-insensitive) the corresponding assay value is used.

Specified by:

getAssayField in interface ExportableFieldConverter

Overrides:

getAssayField in class StandardFieldConverter

Parameters:

name - The name to find

required - If TRUE and no field is found this method will throw an ItemNotFoundException

Returns:

The field or null

getReporterField

public DynamicField getReporterField(String name,
                                     boolean required)

Description copied from class: StandardFieldConverter

Find a reporter dynamic field. This method will try to locate a field in the following order:

1. Check if there is an position extra value with the given name (case-sensitivity depends on the database that is used).
2. Check if there is a formula with the given name (case-sensitivity depends on the database that is used).
3. If name is 'name', 'externalId', 'description' or another static property (case-insensitive) the corresponding reporter value is used.
4. Special case for "External ID" and "Internal ID" to simplify pass-throguh to the BFS importer which expects at least one of those columns.

Specified by:

getReporterField in interface ExportableFieldConverter

Overrides:

getReporterField in class StandardFieldConverter

Parameters:

name - The name to find

required - If TRUE and no field is found this method will throw an ItemNotFoundException

Returns:

The field or null

getSpotField

public DynamicField getSpotField(String name,
                                 boolean required)

Description copied from class: StandardFieldConverter

Find a spot dynamic field. This method will try to locate a field in the following order:

1. Check if there is a spot extra value with the given name (case-sensitivity depends on the database that is used).
2. Check if there is a formula with the given name (case-sensitivity depends on the database that is used).
3. Check if there is a raw data property that matches the name (case-insensitive)
4. Special values: Ch 1, Ch2, etc. to get channel intensities (case-insensitive)

Specified by:

getSpotField in interface ExportableFieldConverter

Overrides:

getSpotField in class StandardFieldConverter

Parameters:

name - The name to find

required - If TRUE and no field is found this method will throw an ItemNotFoundException

Returns:

The field or null

getAdvancedAssayField

protected AssayField getAdvancedAssayField(String expression,
                                           boolean required)

Convert an expression to an assay field. Supported expressions are listed below. The "title" parameter is optional in all cases.

• =property("name" [,"title"]): Get the value of the property with the given name.
• =factor("name" [,"title"]): Get the value of the experimental factor with the given name or external id.
• =annotation("name" [,"title"]): Get the value of the assay annotation with the given name or external id.

getAdvancedReporterField

protected DynamicField getAdvancedReporterField(String expression,
                                                boolean required)

Convert an expression to a reporter field. Supported expressions are listed below. The "title" parameter is optional in the "jep" expression.

• =property("name" [,"title"]): Get the value of the reporter property with the given name.
• =formula("name" [,"title"]): Get the value of the formula with the given name. The formula should only use properties that are related to the reporter and it's position.
• =xtra("name" [,"title"]): Get the value of the extra value with the given name or external id. The extra value should be a position-based extra value.
• =jep("expression", "title" [,"datatype"]): Calculate the value using the given JEP expression. A title is required. The datatype is optional (default is STRING). Valid datatypes are those defined by the Type enumeration.

getAdvancedSpotField

protected DynamicField getAdvancedSpotField(String expression,
                                            boolean required)

Convert an expression to a spot field. Supported expressions are listed below. The "title" parameter is optional in the "jep" expression.

• =property("name" [,"title"]): Get the value of the raw data property with the given name.
• =formula("name" [,"title"]): Get the value of the formula with the given name. The formula should only use properties that are related to the spot and raw data.
• =xtra("name" [,"title"]): Get the value of the extra value with the given name or external id. The extra value should be a spot-based extra value.
• =jep("expression", "title" [,"datatype"]): Calculate the value using the given JEP expression. A title is required. The datatype is optional (default is STRING). Valid datatypes are those defined by the Type enumeration.

getPattern

private Pattern getPattern(String function,
                           int requiredParameters,
                           int optionalParameters)