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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.
PluginConfigurations 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.