Class StandardFieldConverter
java.lang.Object
net.sf.basedb.util.export.spotdata.AbstractFieldConverter
net.sf.basedb.util.export.spotdata.StandardFieldConverter
- All Implemented Interfaces:
ExportableFieldConverter
- Direct Known Subclasses:
AdvancedFieldConverter
,Base1FieldConverter
Default field converter implementation that works mainly by
checking names and/or external id values of formulas, extra
values, experimental factors etc.
- Since:
- 2.15
- Author:
- nicklas
-
Constructor Summary
ConstructorDescriptionStandardFieldConverter
(DbControl dc, BioAssaySet source) Create a new standard field converter. -
Method Summary
Modifier and TypeMethodDescriptiongetAssayField
(String name, boolean required) Find an assay field.getReporterField
(String name, boolean required) Find a reporter dynamic field.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
-
Constructor Details
-
StandardFieldConverter
Create a new standard field converter.- Parameters:
dc
- A DbControl to use for database accesssource
- The source bioassay set
-
-
Method Details
-
getAssayField
Find an assay field. This method will try to locate a field in the following order:- Check if there is an experimental factor with the given name (case-sensitivity depends on the database that is used).
- Check if there is an assay-level annotation type with the given name.
- If name is 'name', 'description' or another static property (case-insensitive) the corresponding assay value is used.
- Parameters:
name
- The name to findrequired
- If TRUE and no field is found this method will throw an ItemNotFoundException- Returns:
- The field or null
-
getReporterField
Find a reporter dynamic field. This method will try to locate a field in the following order:- Check if there is an position extra value with the given name (case-sensitivity depends on the database that is used).
- Check if there is a formula with the given name (case-sensitivity depends on the database that is used).
- If name is 'name', 'externalId', 'description' or another static property (case-insensitive) the corresponding reporter value is used.
- Special case for "External ID" and "Internal ID" to simplify pass-throguh to the BFS importer which expects at least one of those columns.
- Parameters:
name
- The name to findrequired
- If TRUE and no field is found this method will throw an ItemNotFoundException- Returns:
- The field or null
-
getSpotField
Find a spot dynamic field. This method will try to locate a field in the following order:- Check if there is a spot extra value with the given name (case-sensitivity depends on the database that is used).
- Check if there is a formula with the given name (case-sensitivity depends on the database that is used).
- Check if there is a raw data property that matches the name (case-insensitive)
- Special values: Ch 1, Ch2, etc. to get channel intensities (case-insensitive)
- Parameters:
name
- The name to findrequired
- If TRUE and no field is found this method will throw an ItemNotFoundException- Returns:
- The field or null
-