net.sf.basedb.core
Class Formula

java.lang.Object
  net.sf.basedb.core.BasicItem<D>
      net.sf.basedb.core.OwnedItem<D>
          net.sf.basedb.core.SharedItem<D>
              net.sf.basedb.core.CommonItem<FormulaData>
                  net.sf.basedb.core.Formula

All Implemented Interfaces:

AccessControlled, Controlled, Identifiable, Nameable, Ownable, Registered, Removable, Shareable, Validatable

public class Formula
extends CommonItem<FormulaData>
implements Validatable, Registered

This class represents a formula. Formulas can be used for various things such as calculating the spot intensities from raw data or filtering bioassay sets.

Version:

2.0

Author:

Nicklas

Last modified

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

Nested Class Summary

static class	Formula.AverageMethod The average method used for the values of this formula.
static class	Formula.Parser The parser used to parse the formula.
static class	Formula.Type The type of formula indicats in which situations it can be used.

Field Summary

private Coloring	coloring
static int	MAX_FORMULA_LENGTH The maximum length of the formula that can be stored in the database.
static Item	TYPE The type of item represented by this class.

Fields inherited from interface net.sf.basedb.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

Formula(FormulaData formulaData)

Method Summary

Formula.AverageMethod	getAverageMethod() Get the average method for this formula.
static Formula	getById(DbControl dc, int id) Get a Formula item when you know the ID.
int	getChannels() Get the number of channels required to be able to use this formula.
Coloring	getColoring() Get coloring information for this formula.
Date	getEntryDate() Get the date that the item was registered in the database.
String	getFormula(int index) Get an expression.
List<String>	getFormulas() Get all expressions as an unmodifiable list.
Formula.Type	getFormulaType() Get the type of formula.
static Formula	getNew(DbControl dc) Create a new Formula item.
int	getNumFormulas() Get the number of expression defined by this formula.
Formula.Parser	getParser() Get the parser that converts the formula to an expresion or restriction.
static ItemQuery<Formula>	getQuery() Get a new query object for this class.
static ItemQuery<Formula>	getQuery(Formula.Type type, RawDataType rawDataType, IntensityTransform source) Get a query that return formulas that can be used with the specified raw data type.
RawDataType	getRawDataType() Get the raw data type this formula can be used on.
IntensityTransform	getResultIntensityTransform() Get the spot intensity transformation that this formula generates.
IntensityTransform	getSourceIntensityTransform() Get the intensity transformation that is required on spot data if this formula should generate the correct result.
Item	getType() Get the type of item represented by the object.
Type	getValueType() Get the type of values that this formula produces.
void	setAverageMethod(Formula.AverageMethod averageMethod) Set the average method of the formula.
void	setChannels(int channels) Set the number of channels that are required to use this formula.
void	setFormulas(List<String> formulas) Set the expressions used by this formula.
void	setFormulaType(Formula.Type type) Set the type of the formula.
void	setParser(Formula.Parser parser) Set the parser used to convert the formula to an expression or restriction.
void	setRawDataType(RawDataType rawDataType) Set the raw data type this formula can be used on.
void	setResultIntensityTransform(IntensityTransform transform) Sets the transform that this formula generates.
void	setSourceIntensityTransform(IntensityTransform transform) Sets the transform that is required on spot data if this formula should generate the correct result.
void	setValueType(Type valueType) Set the type of the values that this formula produces.
(package private) void	validate() This method is called on each Validatable item before is saved to the database.
static ItemQuery<Formula>	xgetQuery(Formula.Type type, RawDataType rawDataType) Deprecated. In 2.12. Use getQuery(Type, RawDataType, IntensityTransform) instead

Methods inherited from class net.sf.basedb.core.CommonItem

getDescription, getName, isRemoved, setDescription, setName, setRemoved, toTransferable

Methods inherited from class net.sf.basedb.core.SharedItem

getItemKey, getProjectKey, initPermissions, isShared, onBeforeCommit, setItemKey, setProjectKey, toTransferable

Methods inherited from class net.sf.basedb.core.OwnedItem

getOwner, isOwner, setOwner, takeOwnership, toTransferable

Methods inherited from class net.sf.basedb.core.BasicItem

addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getUsingItems, getVersion, hashCode, hasPermission, isDetached, isInDatabase, isUsed, onAfterCommit, onAfterInsert, onRollback, setDbControl, setProjectDefaults, toString, toTransferable

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface net.sf.basedb.core.Identifiable

getId, getVersion

Methods inherited from interface net.sf.basedb.core.AccessControlled

checkPermission, getPermissions, hasPermission

Methods inherited from interface net.sf.basedb.core.Ownable

getOwner, isOwner, setOwner, takeOwnership

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.CLIENT, getType()

MAX_FORMULA_LENGTH

public static final int MAX_FORMULA_LENGTH

The maximum length of the formula that can be stored in the database. Check the length against this value before calling the setFormulas(List) method to avoid exceptions.

See Also:

Constant Field Values

coloring

private Coloring coloring

Constructor Detail

Formula

Formula(FormulaData formulaData)

Method Detail

getNew

public static Formula getNew(DbControl dc)
                      throws BaseException

Create a new Formula item.

Parameters:

dc - The DbControl which will be used for permission checking and database access

Returns:

The new Formula item

Throws:

BaseException - If there is an error

getById

public static Formula getById(DbControl dc,
                              int id)
                       throws ItemNotFoundException,
                              PermissionDeniedException,
                              BaseException

Get a Formula item when you know the ID.

Parameters:

dc - The DbControl which will be used for permission checking and database access.

id - The ID of the item to load

Returns:

The Formula item

Throws:

ItemNotFoundException - If an item with the specified ID is not found

PermissionDeniedException - If the logged in user doesn't have Permission.READ permission to the item

BaseException - If there is another error

getQuery

public static ItemQuery<Formula> getQuery()

Get a new query object for this class.

Returns:

An ItemQuery object

xgetQuery

public static ItemQuery<Formula> xgetQuery(Formula.Type type,
                                           RawDataType rawDataType)

Deprecated. In 2.12. Use getQuery(Type, RawDataType, IntensityTransform) instead

getQuery

public static ItemQuery<Formula> getQuery(Formula.Type type,
                                          RawDataType rawDataType,
                                          IntensityTransform source)

Get a query that return formulas that can be used with the specified raw data type. The formulas returned are those that match the specified raw data type or are generic for the number of channels.

Parameters:

type - The type of formula to return, or null to return any type

rawDataType - The raw data type the formula should be useful for, or null to not filter on the raw data type

source - Source data intensity transformation that the formula should be useful for. This includes all formulas that has specified the same transformation and those that hasn't specified any transformation at all. If this parameter is null, no filtering on intensity transformation is done.

Returns:

An ItemQuery object

Since:

2.12

getType

public Item getType()

Description copied from interface: Identifiable

Get the type of item represented by the object. The returned value is one of the values defined in the Item enumeration.

Specified by:

getType in interface Identifiable

Returns:

A value indicating the type of item

getEntryDate

public Date getEntryDate()

Description copied from interface: Registered

Get the date that the item was registered in the database.

Specified by:

getEntryDate in interface Registered

Returns:

A date or null if this is not known

validate

void validate()
        throws InvalidDataException,
               BaseException

Description copied from class: BasicItem

This method is called on each Validatable item before is saved to the database. If the subclass overrides this method it should also propagate the call to the superclass, ie. super.validate().

Overrides:

validate in class BasicItem<FormulaData>

Throws:

BaseException - If there is an error

InvalidDataException

See Also:

Formula.Type.validate(Formula)

getAverageMethod

public Formula.AverageMethod getAverageMethod()

Get the average method for this formula.

Returns:

A Formula.AverageMethod object

Since:

2.4

setAverageMethod

public void setAverageMethod(Formula.AverageMethod averageMethod)
                      throws PermissionDeniedException,
                             InvalidDataException

Set the average method of the formula.

Parameters:

averageMethod - A Formula.AverageMethod object, null is not allowed

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

InvalidDataException - If the averageMethod is null

Since:

2.4

getFormulaType

public Formula.Type getFormulaType()

Get the type of formula. The type indicates in which situation the formula can be used.

Returns:

A Type object

setFormulaType

public void setFormulaType(Formula.Type type)
                    throws PermissionDeniedException,
                           InvalidDataException

Set the type of the formula. If the type is locked to a specific value type this is also changed.

Parameters:

type - A Type object, null is not allowed

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

InvalidDataException - If the type is null

getValueType

public Type getValueType()

Get the type of values that this formula produces.

Returns:

A Type object, or null if not known

Since:

2.15

setValueType

public void setValueType(Type valueType)
                  throws PermissionDeniedException,
                         InvalidDataException

Set the type of the values that this formula produces. Note! It is only Formula.Type.COLUMN_EXPRESSION formulas that can have a free value type. Calls to this method are ignored for other formula types.

Parameters:

valueType - A Type object, or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

InvalidDataException

Since:

2.15

getParser

public Formula.Parser getParser()

Get the parser that converts the formula to an expresion or restriction.

Returns:

A Formula.Parser object

setParser

public void setParser(Formula.Parser parser)
               throws PermissionDeniedException

Set the parser used to convert the formula to an expression or restriction.

Parameters:

parser - The Formula.Parser object, null is not allowed

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

InvalidDataException - If the parser is null

getSourceIntensityTransform

public IntensityTransform getSourceIntensityTransform()

Get the intensity transformation that is required on spot data if this formula should generate the correct result.

Returns:

An intensity transform or null if the formula can be used on all types of spot data

Since:

2.12

setSourceIntensityTransform

public void setSourceIntensityTransform(IntensityTransform transform)

Sets the transform that is required on spot data if this formula should generate the correct result.

Parameters:

transform - The required transform or null if the formula works with all kind of data

Since:

2.12

getResultIntensityTransform

public IntensityTransform getResultIntensityTransform()

Get the spot intensity transformation that this formula generates.

Returns:

An intensity transform or null if the formula generates the same kind of data used as source or doesn't generate intensity data at all

Since:

2.12

setResultIntensityTransform

public void setResultIntensityTransform(IntensityTransform transform)

Sets the transform that this formula generates.

Parameters:

transform - An intensity transform or null if the formula generates the same kind of data used as source or doesn't generate intensity data at all

Since:

2.12

getRawDataType

public RawDataType getRawDataType()

Get the raw data type this formula can be used on. A null value indicates that the formula can be used on any raw data type.

Returns:

A RawDataType object

setRawDataType

public void setRawDataType(RawDataType rawDataType)
                    throws PermissionDeniedException

Set the raw data type this formula can be used on. A null value indicates that the formula can be used on any raw data type.

Parameters:

rawDataType - The raw data type, or null

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

getChannels

public int getChannels()

Get the number of channels required to be able to use this formula. A value of 0 indicates that the formula may be used on any number of channels.

Returns:

The number of channels or 0

setChannels

public void setChannels(int channels)
                 throws PermissionDeniedException,
                        InvalidDataException

Set the number of channels that are required to use this formula.

Parameters:

channels - The number of channels or 0

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

InvalidDataException - If the value is negative

getNumFormulas

public int getNumFormulas()

Get the number of expression defined by this formula.

getFormula

public String getFormula(int index)

Get an expression.

Parameters:

index - The index of the expression, starting at 0

Returns:

The expression

setFormulas

public void setFormulas(List<String> formulas)
                 throws InvalidDataException

Set the expressions used by this formula. All expressions must be set at once, they can't be changed individually.

Parameters:

formulas - The list of expressions

Throws:

InvalidDataException

InvalidUseOfNullException - If the list is null or empty or if an individual element in the list is null

PermissionDeniedException - If the logged in user doesn't have write permission

getFormulas

public List<String> getFormulas()

Get all expressions as an unmodifiable list.

Returns:

A list with the expressions

getColoring

public Coloring getColoring()

Get coloring information for this formula.

Returns:

A Coloring object