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
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) $
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Constructor Summary
ConstructorDescriptionBase1FieldConverter
(DbControl dc, BioAssaySet source) Create a new converter for the given bioassay set. -
Method Summary
Modifier and TypeMethodDescriptionprotected 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.getReporterField
(String name, boolean required) Convert a reporter field.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
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Constructor Details
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Base1FieldConverter
Create a new converter for the given bioassay set.- Parameters:
dc
- A DbControl to use for database accesssource
- The source bioassay set
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Method Details
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getReporterField
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 interfaceExportableFieldConverter
- Overrides:
getReporterField
in classStandardFieldConverter
- Parameters:
name
- The BASE 1 field namerequired
- 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
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getSpotField
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 interfaceExportableFieldConverter
- Overrides:
getSpotField
in classStandardFieldConverter
- Parameters:
name
- The BASE 1 field namerequired
- 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
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getIntensityField
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 classAbstractFieldConverter
- Parameters:
fieldName
- The field name- Returns:
- A dynamic field, or null if the name doesn't match the pattern
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