|
2.17.2: 2011-06-17 | ||||||||
PREV NEXT | FRAMES NO FRAMES |
About
interface, which
complements all getter methods with setter methods.About
interface.About
object.
ABS(<value>)
.
Abs
function
to a Query API Expression
.ProgressReporter
interface.Quantity
object representing absorbed dose.
AbstractAnalysisPlugin
.
DbControl
object.DataFileValidator
interface.DbEngine
methods.EntityQuery
interface.ImmediateDownloadExporter
interface.AbstractExporterPlugin
.
ExportableFieldConverter
.FileUnpacker
interface.HqlQuery
interface.IOSupport
interface and don't want to be visible as
standalone plug-ins.JepConversionFunction
interface.AbstractPlugin
.
Query
interface.SqlQuery
interface.Quantity
object representing acceleration.
AccountExpiredException
.
ExtensionPoint
by an Extension
.Action
:s.Registry.useExtensions(ClientContext, ExtensionsFilter, String...)
.ProjectData
object of the active project.
ArrayDesignBlock
to the array design.
Batcher
to the batcher queue.
Add
function
to a Query API Expression
.<script>
tag.
Class.hbm.xml
where class
is the name of each class.
<link>
tag.
Role
to a user.
Role
item representing adminstrators.
Affymetrix
platform.
ExtensionsControl.enableExtensionPoint(String, boolean)
,
ExtensionsControl.enableExtension(String, boolean)
, or
ExtensionsControl.enableAllInFile(String, boolean)
.
SocketSignalReceiver
.org.json.simple.*
package. See
http://code.google.com/p/json-simple/ for more information and
documentation.property(alias, null)
.
align
attribute
ANY (subquery)
.
Set
:s all contain
the same permissions.
AlreadyLoggedInException
.
DbEngine.getAnalyzeTableSql(String, String, String)
for that table.
Restriction
.Quantity
object representing angle.
CommonData
class and implements the
AnnotatableData
interface.Annotatable
interface.AnnotationBetweenRestriction.AnnotationBetweenRestriction(String, AnnotationType, Object, Object, boolean)
instead with alias=null
AnnotationInRestriction.AnnotationInRestriction(String, AnnotationType, boolean, Object[])
instead with alias=null
AnnotationSet.getItem()
to hit the database
when the item is known beforehand.
annotation operator value
.AnnotationSimpleRestriction.AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, boolean)
instead with alias=null
annotation operator value
.
AnnotationSimpleRestriction.AnnotationSimpleRestriction(String, int, Type, Operator, Object, boolean)
instead with alias=null
valueType
.
valueType
.
AnnotationType
.RawBioAssay.getArrayNum()
property
until we have loaded the Labeled Extracts of a Hybridization.ANY (subquery)
.
Pinger
is an object that is used to protect another
object from timing out by automatically pinging it.Quantity
object representing area.
ArrayDesign
Provides services to access limited
functionality in this class.Iterator
interface
for an array of objects.ArrayIterator
object.
FileUpload.checkBoundary(byte[], int, byte[], int)
method finds that the line matches the boundary, FALSE otherwise.
FileUpload.checkBoundary(byte[], int, byte[], int)
method finds that the line matches the boundary + two extra dashes (--), FALSE otherwise.
InvalidPasswordException
is thrown.
AuthenticationException
object
AuthenticationException
object
Authenticator.authenticate(String,String)
method and contains information about the authenticated
user.AuthenticationInformation
object without
extra information.
AuthenticationInformation
object with extra
information.
ContextUtil.ContextResult
:s by checking each plug-ins ability to
import a given file.AnnotationSet.autoInherit(DbControl, Collection, SnapshotManager, boolean)
instead since it has better performance
AutoJoiner
is an object that automatically joins
other tables in query depending on other query elements.BaseException
object.
BaseException
object with the specified
message
BaseException
object with the
specified message
BaseException
object acting as a
wrapper for another exception that caused the error.
BaseException
object where the
cause is an SQLException.
BaseFileImporter
.BaseFileInfo.BaseFileInfo(FileWrapper)
instead
BasicItem
parent item.BasicItem
.BasicItem
:s.BasicItem
node loaders.BasicItem
node validators.BasicItem
:s.DbControl
is
closed and will be flushed when commit is called.
ExtensionsControl.enableExtensionPoint(String, boolean)
,
ExtensionsControl.enableExtension(String, boolean)
, or
ExtensionsControl.enableAllInFile(String, boolean)
.
DbControl
and a RawDataBatcher
.
DbControl
and a FeatureBatcher
.
DbControl
and a ReporterBatcher
.
DbControl
and a FeatureBatcher
.
Mapper
:s.
DbControl
and a new PlateMapping
.
Mapper
:s.
Mapper
:s.
Mapper
:s.
Annotations.between(String, AnnotationType, Object, Object, boolean)
instead with alias=null
ExperimentExplorer.getBioAssay(DbControl, short)
method.
Transformation
has been applied to it.SerialBaseFileExporter
or MatrixBaseFileExporter
for BASEfile export and the extension package at http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev
for MeV exportBioAssaySet
.BioAssaySet
.BioAssaySet.getSpotCount(int)
.
BioSource
, Sample
, Extract
and LabeledExtract
.MeasuredBioMaterial
.MeasuredBioMaterialData.getSourceEvents()
and still be able
to filter in the used quantity or the source group property.BioPlate
and contains a MeasuredBioMaterial
.BlockInfo
object is used to represent the uniqe identifiers of an
ArrayDesignBlock
.ButtonAction
interface.TarFilePacker
in a BZIP2 stream, creating
a tar.bz2 file.Session.cancelQuery()
.
Quantity
object representing capacitance.
CASE WHEN r1 THEN e1 WHEN r2 THEN e2 ...
CASE-WHEN
expression:
CASE WHEN r1 THEN e1 WHEN r2 THEN e2 ...
DataFileType.AFFYMETRIX_CDF
DataFileType.AFFYMETRIX_CEL
VirtualColumn.channelIntensity(int)
or
VirtualColumn.channelRaw(int)
instead. This method is forwarded
to VirtualColumn.channelIntensity(int)
for maximum backwards
compatibility.
ch(int)
function to a
JEP expression parser.ChannelFunction.ChannelFunction(int[], IntensityTransform)
instead. Using this constructor will disable the untransformation
of transformed values when JEP dynamic evalution is used.
Quantity
object representing electrical charge.
Parameters.CHARSET_PARAMETER
Parameters.charsetParameter(String, String, String)
Parameters.charsetParameter(String, String, String)
line
matches the boundary
.
InteractivePlugin.isInContext(GuiContext, Object)
method
for all plug-ins returned by the queries.
SignalReceivedException
is thrown.
SignalReceivedException
is thrown.
ThreadSignalHandler.checkInterrupted()
instead
ThreadSignalHandler.checkInterrupted()
instead
ThreadSignalHandler.checkInterrupted()
instead
ThreadSignalHandler.checkInterrupted()
instead
ThreadSignalHandler.checkInterrupted()
instead
Parameters.childDescriptionParameter(String, String, String)
Parameters.childNameParameter(String, String, String)
Shareable
parent item.DataFileType
name
attribute of all classes found in
the xml file.
ThreadLocal
class,
but stores one object per class instead of one object per thread.ClassLocal
object.
Throwable
.ClassMapErrorHandler
.
Class
objects.class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute.
class
attribute.
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
class
attribute
SessionControl
objects.
ClientDefaultSettingData
.
ClientData
. 0 = no client
Writer
without throwing any exceptions.
Reader
without throwing any exceptions.
InputStream
without throwing any exceptions.
AbstractPlugin.createLogFile(String)
.
col()
function to Jep.colspan
attribute
ColumnMapper.ColumnMapper(int, String, NumberFormat, boolean)
<tbl:header>
tags.FlatFileParser.setDataSplitterRegexp(Pattern)
regular expression.
InteractivePlugin.getRequestInformation(GuiContext, String)
and InteractivePlugin.configure(GuiContext, Request, Response)
InteractivePlugin.getRequestInformation(GuiContext, String)
and InteractivePlugin.configure(GuiContext, Request, Response)
Plugin.run(Request, Response, ProgressReporter)
SharedData
class
and implements the NameableData
and RemovableData
interfaces.CompactButtonRenderer
objects
for rendering ButtonAction
:s.KeyPermission
object.
PluginKeys
object.
ProjectPermission
object.
jsp_precompile=true
therby compiling all JSP files into servlets.CompoundMapper.CompoundMapper(List, NumberFormat, boolean)
Options
object.Config
class
if there is a problem with finding or loading the configuration
settings.ConfigurationException
.
ConfigurationException
with a cause.
Request.COMMAND_CONFIGURE_PLUGIN
,
and Request.COMMAND_CONFIGURE_JOB
.
Request.COMMAND_CONFIGURE_PLUGIN
and Request.COMMAND_CONFIGURE_JOB
.
Request.COMMAND_CONFIGURE_PLUGIN
and
Request.COMMAND_CONFIGURE_JOB
.
Request.COMMAND_CONFIGURE_PLUGIN
and
Request.COMMAND_CONFIGURE_JOB
.
Request.COMMAND_CONFIGURE_JOB
.
Request.COMMAND_CONFIGURE_PLUGIN
and Request.COMMAND_CONFIGURE_JOB
.
Request.COMMAND_CONFIGURE_PLUGIN
,
RawDataFlatFileImporter.COMMAND_CONFIGURE_PARSER
and Request.COMMAND_CONFIGURE_JOB
.
Request.COMMAND_CONFIGURE_PLUGIN
and
Request.COMMAND_CONFIGURE_JOB
.
Request.COMMAND_CONFIGURE_PLUGIN
and
Request.COMMAND_CONFIGURE_JOB
.
FlatFileParser
and wants easier configuration
of the regular expressions used to parse the file.ItemContext.configureQuery(DbControl, EntityQuery, boolean)
instead
DbControl
object that has been closed.ConnectionClosedException
.
ConstantMapper.ConstantMapper(String, NumberFormat, boolean)
style
attribute for the content section
style
attribute for the content section
Item
and it's subcontext.
InteractivePlugin.isInContext(GuiContext, Object)
method.ContextUtil.ContextResult
:s and return only those
that return true from ContextUtil.ContextResult.isInContext()
.UnsupportedFileFormatException
.
DbControl
object when DbControl.commit()
is called.JepConversionFunction
objects for converting built-in
JEP object to Query API Expression
or Restriction
objects.plugins.dir
setting in base.config
.
About
object
to this one.
InputStreamSplitter.skip(long)
method should copy
to the output streams or no.
LabeledExtract
that are create from this item.
AnnotationType
.
BioPlateEventType
.
BioPlateType
.
Client
.
ffp
FlatFileParser
.
JspContext
object without an active DbControl.
JspContext
object with an active DbControl.
JspContext
object with an active DbControl
and a current GuiContext
and item.
DataFileType
.
ItemContext
with settings for default
visible columns and sort property.
Directory
.
Document
with root element and System id
declaration.
DbEngine
object.
FileType
.
Formula
.
Group
.
HardwareData
.
HardwareType
.
ItemKey
.
ArrayBatch.getQuery()
.
Hybridization.getQuery()
.
ArraySlide.getQuery()
.
BioPlate.getQuery()
.
BioSource.getQuery()
.
Extract.getQuery()
.
Hybridization.getQuery()
.
Extract.getQuery()
.
RawBioAssay.getQuery()
.
Sample.getQuery()
.
Scan.getQuery()
.
BioAssaySetUtil.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)
BioAssaySetUtil.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)
Label
.
MimeType
.
News
.
RequestInformation.getParameter(String)
method doesn't have
to look in the list.
PlateGeometry
.
PlateMapping
.
Platform
.
PluginConfiguration
s from a XML file.
PluginDefinition
.
PluginType
.
ProtocolType
.
Quantity
.
Quota
.
QuotaType
.
Role
.
RoleKey
.
RPCServiceClient
object.
Software
.
SoftwareType
.
sourceItem
:s into a collection with destinationItem
:s
by following parent/child paths.
Unit
.
User
.
ExtensionsDirectory.variableConverter
and ExtensionsDirectory.pathConverter
with it.
Quantity
object representing electric current.
DatabaseException
object.
DatabaseException
object with the
specified message
.
DatabaseException
object with the
specified message
DatabaseException
object acting as a
wrapper for another exception that caused the error.
DataFileType
.DataFileType
.DataFileType
.SimpleExport
to get data
that in some way are associated with an item.dataNo()
function to Jep.Query
interface that returns data
objects.DataQuery
:s.DataQuery
as an iterator.Parameters.dateFormatError(String, String, String, String...)
.
Parameters.dateFormatParameter(String, String, String)
DateFormatException
.
DateFormatException
.
DbControl
object is the main object used for communicating
with the database.DbControl
object, so we can close
them if the user logs out.
Dialect
objects.Parameters.DECIMAL_SEPARATOR_PARAMETER
Parameters.decimalSeparatorParameter(String, String, String)
Parameters.decimalSeparatorParameter(String, String, String)
Parameters.defaultError(String, String, String, String...)
.
Registry.useExtensions(ClientContext, ExtensionsFilter, String...)
parseHeaders
method before it
gives up.
FallbackIdMethod
class. This array is now empty.
LoggableData
interface.Extension.getIndex()
values.PermissionDeniedException
, since a feature cannot
be modifed once it has been created.
AnyToAny.deleteStrayLinks(ProgressReporter)
instead.
ItemKey.deleteUnusedItemKeys()
instead which returns the number of
deleted keys
ProjectKey.deleteUnusedProjectKeys()
instead which returns the number of
deleted keys
Quantity
object representing density.