net.sf.basedb.util
Class BioAssaySetUtil

java.lang.Object
  net.sf.basedb.util.BioAssaySetUtil

public class BioAssaySetUtil
extends Object

This is a utility class for BioAssaySet.

Version:

2.0

Author:

Johan

Last modified

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

Constructor Summary

BioAssaySetUtil()

Method Summary

static Expression	createJepExpression(DbControl dc, BioAssaySet bioAssaySet, String formula, boolean allowRawIfMultipleMappings) Deprecated. In 2.15, use createJepExpression(DbControl, String, DynamicQuery) instead. The 'allowRawIfMultipleMappings' parameter is replaced with an option on the spot query: DynamicSpotQuery.setDisableRawJoinOnMergedData(boolean) (it has no meaning on other queries)
static Expression	createJepExpression(DbControl dc, String formula, DynamicQuery query) 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) Deprecated. In 2.15, use createJepRestriction(DbControl, String, DynamicQuery) instead. The 'allowRawIfMultipleMappings' parameter is replaced with an option on the spot query: DynamicSpotQuery.setDisableRawJoinOnMergedData(boolean) (it has no meaning on other queries)
static Restriction	createJepRestriction(DbControl dc, String formula, DynamicQuery query) 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) Deprecated. In BASE 2.14 due to performance problems, use getAnnotationValues(DbControl, SnapshotManager, BioAssay, AnnotationType) instead
static Set<?>	getAnnotationValues(DbControl dc, SnapshotManager snapshotManager, BioAssay bioAssay, AnnotationType annotationType) Find the annotation values for a given annotation type on a bioassay.
static Set<Object>	getParentProperties(DbControl dc, BioAssay bioAssay, Metadata.PropertyPath<RawBioAssay,?> property) Find the values of parent properties for a given bioassay.
static Set<Object>	getParentProperties(DbControl dc, BioAssay bioAssay, String property) Deprecated. In 2.15, use getParentProperties(DbControl, BioAssay, Metadata.PropertyPath) instead

Methods inherited from class java.lang.Object

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

Constructor Detail

BioAssaySetUtil

public BioAssaySetUtil()

Method Detail

getAnnotationValues

public static Set<?> getAnnotationValues(DbControl dc,
                                         BioAssay bioAssay,
                                         AnnotationType annotationType)

Deprecated. In BASE 2.14 due to performance problems, use getAnnotationValues(DbControl, SnapshotManager, BioAssay, AnnotationType) instead

Find the annotation values for a given annotation type on a bioassay. This method will only check annotations, primary and inherited, on the raw bioassays that the bioassay is a child of.

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.

Parameters:

dc - The DbControl for database access

bioAssay - The bioassay to get the annotations for

annotationType - The annotation type of the annotations

Returns:

A set containing all values

getAnnotationValues

public static Set<?> getAnnotationValues(DbControl dc,
                                         SnapshotManager snapshotManager,
                                         BioAssay bioAssay,
                                         AnnotationType annotationType)

Find the annotation values for a given annotation type on a bioassay. This method will only check annotations, primary and inherited, on the raw bioassays that the bioassay is a child of.

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.

Parameters:

dc - The DbControl for database access

snapshotManager - A snapshot manager that is used for loading the annotations from either the database or the file cache (if null, an internal, non-reusable snapshot manager is used)

bioAssay - The bioassay to get the annotations for

annotationType - The annotation type of the annotations

Returns:

A set containing all values

Since:

2.14

getParentProperties

@Deprecated
public static Set<Object> getParentProperties(DbControl dc,
                                                         BioAssay bioAssay,
                                                         String property)

Deprecated. In 2.15, use getParentProperties(DbControl, BioAssay, Metadata.PropertyPath) instead

getParentProperties

public static Set<Object> getParentProperties(DbControl dc,
                                              BioAssay bioAssay,
                                              Metadata.PropertyPath<RawBioAssay,?> property)

Find the values of parent properties for a given bioassay. This method starts by loading all raw bioassays that are parents to the bioassay. For each raw bioassay it uses the Metadata.PropertyPath object 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 paths:

• spots: to get the number of spots in the raw bioassay
• software.name: to get the name of the software used to analyse the image files
• scan.hybridization.creationEvent.eventDate: to get the date when the hybridization was created

Parameters:

dc - The DbControl for database access

bioAssay - The bioassay to get the annotations for

property - The property to get the value for

Returns:

A set containing all values

createJepRestriction

@Deprecated
public static Restriction createJepRestriction(DbControl dc,
                                                          BioAssaySet bioAssaySet,
                                                          String formula,
                                                          boolean allowRawIfMultipleMappings)
                                        throws InvalidDataException,
                                               BaseException

Deprecated. In 2.15, use createJepRestriction(DbControl, String, DynamicQuery) instead. The 'allowRawIfMultipleMappings' parameter is replaced with an option on the spot query: DynamicSpotQuery.setDisableRawJoinOnMergedData(boolean) (it has no meaning on other queries)

Throws:

InvalidDataException

BaseException

createJepRestriction

public static Restriction createJepRestriction(DbControl dc,
                                               String formula,
                                               DynamicQuery query)

Parse a JEP expression and create a restrictions that is suitable to be used in a dynamic query. In addition to the standard functions defined by JEP (see Jep.getFunctions()) this method can use additional functions. The extra functions are defined by the query. See DynamicQuery.getJepFunctions(DbControl, boolean) and it's subclasses for detailed information. Here are some useful functions:

• all functions defined by the createJepExpression(DbControl, String, DynamicQuery) method
• inList(list): Checks if the reporter is included in the specified list
• notInList(list): Checks if the reporter isn't included in the specified list

Parameters:

dc - DbControl to use when accessing the database.

formula - The formula to parse. Must not be null.

query - The query where the restriction will be used, it is not recommended to use the expression in a different query since it may generate incorrect SQL

Returns:

A restriction to be used on a query.

Throws:

InvalidDataException - If any of required parameters are null.

BaseException - If creating the restriction fails.

See Also:

Jep

createJepExpression

@Deprecated
public static Expression createJepExpression(DbControl dc,
                                                        BioAssaySet bioAssaySet,
                                                        String formula,
                                                        boolean allowRawIfMultipleMappings)
                                      throws InvalidDataException,
                                             BaseException

Deprecated. In 2.15, use createJepExpression(DbControl, String, DynamicQuery) instead. The 'allowRawIfMultipleMappings' parameter is replaced with an option on the spot query: DynamicSpotQuery.setDisableRawJoinOnMergedData(boolean) (it has no meaning on other queries)

Throws:

InvalidDataException

BaseException

createJepExpression

public static Expression createJepExpression(DbControl dc,
                                             String formula,
                                             DynamicQuery query)

Parse a JEP expression and create a restrictions that is suitable to be used in a dynamic query. In addition to the standard functions defined by JEP (see Jep.getFunctions()) this method can use additional functions. The extra functions are defined by the query. See DynamicQuery.getJepFunctions(DbControl, boolean) and it's subclasses for detailed information. Here are some useful functions:

• raw(property): The value of the specified raw data property. The use of this function can be denied if the bioassayset contains merged spot data. The DynamicSpotQuery.setDisableRawJoinOnMergedData(boolean) flag controls this.
• rep(property): The value of the specified reporter property
• pos(): The position of a spot. Note that this is not the same as raw(position)
• ch(n): The intensity in channel n (un-transformed)
• rawCh(n): The possibly transformed intensity in channel n
• score(list): The score of the ReporterData in the specified ReporterList (numeric or external ID)
• xtra(extraValue): The value of the specified ExtraValue (numeric ID or the external ID of the ExtraValueType)

Parameters:

dc - The DbControl to use when accessing the database.

formula - The formula that should be parsed. Must not be null.

query - The query where the expression will be used, it is not recommended to use the expression in a different query since it may generate incorrect SQL

Returns:

An expression to be used with a query.

Throws:

InvalidDataException - If any of required parameters are null.

BaseException - If creating the expression fails.

Since:

2.15

See Also:

Jep