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java.lang.Objectnet.sf.basedb.util.BioAssaySetUtil
public class BioAssaySetUtil
This is a utility class for BioAssaySet
.
Constructor Summary | |
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BioAssaySetUtil()
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Method Summary | |
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static Expression |
createJepExpression(DbControl dc,
BioAssaySet bioAssaySet,
String formula,
boolean allowRawIfMultipleMappings)
Parse a JEP expression and create a restrictions that is suitable to be used in a dynamic query. |
static Restriction |
createJepRestriction(DbControl dc,
BioAssaySet bioAssaySet,
String formula,
boolean allowRawIfMultipleMappings)
Parse a JEP expression and create a restrictions that is suitable to be used in a dynamic query. |
static Set<?> |
getAnnotationValues(DbControl dc,
BioAssay bioAssay,
AnnotationType annotationType)
Find the annotation values for a given annotation type on a bioassay. |
static Set<Object> |
getParentProperties(DbControl dc,
BioAssay bioAssay,
String property)
Find the values of parent properties for a given bioassay. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public BioAssaySetUtil()
Method Detail |
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public static Set<?> getAnnotationValues(DbControl dc, BioAssay bioAssay, AnnotationType annotationType)
Since a bioassay may have more than one parent raw bioassay and each annotation may have multiple values it is possible that the set contains multiple values. Each value is only present once regardless of how many times it appears in the annotations.
dc
- The DbControl for database accessbioAssay
- The bioassay to get the annotations forannotationType
- The annotation type of the annotations
public static Set<Object> getParentProperties(DbControl dc, BioAssay bioAssay, String property)
Metadata.getPropertyValue(DbControl, Object, String)
method to find the value of the given property for that raw bioassay.
Since a bioassay may have more than one parent raw bioassay and it is possible that the set contains multiple values. Each value is only present once regardless of how many times it appears among the parents.
Examples of property values:
dc
- The DbControl for database accessbioAssay
- The bioassay to get the annotations forproperty
- The property to get the value for
public static Restriction createJepRestriction(DbControl dc, BioAssaySet bioAssaySet, String formula, boolean allowRawIfMultipleMappings) throws InvalidDataException, BaseException
Jep.getFunctions()
) this method defines the following functions:
createJepExpression(DbControl, BioAssaySet,
String, boolean)
method
dc
- DbControl to use when accessing the database.bioAssaySet
- The current bioassay set. Must not be null.formula
- The formula to parse. Must not be null.allowRawIfMultipleMappings
- TRUE if 'raw' function with merged data, FALSE otherwise.
InvalidDataException
- If any of required parameters are null.
BaseException
- If creating the restriction fails.Jep
public static Expression createJepExpression(DbControl dc, BioAssaySet bioAssaySet, String formula, boolean allowRawIfMultipleMappings) throws InvalidDataException, BaseException
Jep.getFunctions()
) this method defines the following functions:
allowRawIfMultipleMappings
parameter controls
this.
ReporterData
in the
specified ReporterList
(numeric or external ID)
ExtraValue
(numeric ID or the external ID of the ExtraValueType
)
dc
- The DbControl to use when accessing the database.bioAssaySet
- The bioassay set this expression should be used with. Must not be null.formula
- The formula that should be parsed. Must not be null.allowRawIfMultipleMappings
- TRUE if 'raw' function with merged data, FALSE otherwise.
InvalidDataException
- If any of required parameters are null.
BaseException
- If creating the expression fails.Jep
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