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Last update: 2011-06-23 | |||||||||
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About interface.About object.
ProgressReporter
interface.DbControl object.AbstractPlugin.
AccountExpiredException.
Role to a user.
Role item representing adminstrators.
property(alias, null).
Set:s all contain
the same permissions.
AlreadyLoggedInException.
CommonData class and implements the
AnnotatableData interface.Annotatable interface.annotation operator value.annotation operator value.
Iterator interface
for an array of objects.ArrayIterator object.
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.
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.
BioSource, Sample, Extract
and LabeledExtract.MeasuredBioMaterial.ch(int) function to a
JEP expression parser.ThreadLocal class,
but stores one object per class instead of one object per thread.ClassLocal object.
Class objects.FlatFileParser.setDataSplitterRegexp(Pattern)
regular expression.
SharedData class
and implements the NameableData and RemovableData
interfaces.KeyPermission object.
ProjectPermission object.
Config class
if there is a problem with finding or loading the configuration
settings.ConfigurationException.
DbControl object that has been closed.ConnectionClosedException.
DbControl object when DbControl.commit()
is called.AnnotationType item.
BioMaterialEvent of the Type#OTHER
type.
Document with root element and System id
declaration.
GelImageAnalysisEvent of the Type#OTHER type.
GelScanEvent of the Type#OTHER type.
GlobalDefaultSetting item.
LabeledExtract with label.
Message item.
SeparationEvent of the Type#OTHER type.
SeparationMethod item.
StainingEvent of the Type#OTHER type.
UpdateEvent of the Type#OTHER type.
User item.
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.
Query interface that returns data
objects.DataQuery as an iterator.DbControl object is the main object used for communicating
with the database.parseHeaders method before it
gives up.
DbControl that
manages it.DetachedItemException.
DbControl.
Diff3 object to compare properties
of the oldItem and newItem.
DiskConsumable items.InputStream.
init method.
GuiContext
object.
GroupGroups
object.
GroupKeys
object.
GroupProjects
object.
ProjectKeys
object.
RoleKeys
object.
UserGroups
object.
UserKeys
object.
UserProjects
object.
UserRoles
object.
MappingCoordinate
object.
QuotaIndex
object.
UsedQuantity
object.
Extract from a Sample.
SoftwareType item representing the
softwaretype "feature extraction software".
FileAttachable item is an item that can have
a File attached to it.File
attached to it.File items in Proteios.FlatFileParser object.
FlatFileParser.hasMoreData() method.FlatFileParser.parseHeaders() method.Expression.
Restriction.
SpectrumPrecursor.FragmentationType object
when you know the abbreviation string.
Item object when you know either the item or data
class.
Item object when you know the data class.
Item object when you have a data layer object.
SpectrumPrecursor.FragmentationType object
when you know the displayValue string.
Item object when you know the item class.
SpectrumPrecursor.FragmentationType object
when you know the msOntologyAccessionNumber string.
File.Action object when you know the integer
code.
Item object when you know the integer code.
Job.Status object when you know the integer
code.
Job.Status object when you know the integer
code.
Job.Status object when you know the integer
code.
Location object when you know the integer code.
Operator object when you know the integer code.
GuiContext.Type object when you know the integer code.
Type object when you know the integer code.
Type object when you know the string value.
NotificationConfiguration.Mode object when you know the integer
code.
SpectrumPrecursor.FragmentationType object when you know the integer
value.
TablePreferencesConfiguration.Mode object when you know the integer
code.
SpectrumPrecursor.FragmentationType.
InstrumentConfiguration acquisitionInstrumentInfo.
Acquisition acquisitionList.
FileData
object.
File.Action of this file.
InstrumentConfiguration activation.
HardwareConfiguration analyzers list.
Annotatable item types.
Annotation object of the specified annotation type.
MeasuredBioMaterial that was used for this event.
BioSource that is the parent of this sample.
key as a
boolean value.
PluginDefinition item when you know the class name.
MimeType item when you know the file extension.
Client item when you know the external ID.
GelElectrophoresis item when you know the external ID.
IPG item when you know the external ID.
LiquidChromatography item when you know the external ID.
SeparationMethod item when you know the external ID.
ItemKey item when you know the ID.
Job item when you know the id.
Label item when you know the id.
Message item when you know the id.
MimeType object when you know the ID.
News item when you know the ID.
ObservedModification item when you know the id.
Peak item when you know the id.
PeakList item when you know the id.
PeakListSet item when you know the id.
Peptide item when you know the id.
PluginConfiguration item when you know the ID.
PluginDefinition item when you know the ID.
PluginType object when you know the ID.
Precursor item when you know the id.
Project item when you know the ID.
ProjectKey item when you know the ID.
Protein item when you know the id.
Protocol item when you know the ID.
ProtocolType object when you know the ID.
Quota item when you know the ID.
QuotaType object when you know the id.
Role item when you know the ID.
RoleKey item when you know the ID.
Sample item when you know the id.
Session item when you know the ID.
Setting item when you know the ID.
Software item when you know the ID.
SoftwareType object when you know the ID.
StainingEvent item when you know the id.
UpdateEvent item when you know the id.
User item when you know the ID.
PluginType object when you know the interface
name it represents.
RoleKey item when you know the Item type.
File item when you know the path.
Directory item when you know the path.
DiskConsumable item is using.
DiskConsumable
item is using.
Client application in use.
PeakList.
FileData object
uses after compression.
DataProcessingStep dataProcessingStepList.
DbControl object that currently manages this batcher.
DbControl object that currently manages this item.
GelElectrophoresis.
DataProcessingStep.
PeakList.
HardwareConfiguration detector.
DirectoryData item.
Directory item.
DiskUsageData that this item use.
SpectrumPrecursor.FragmentationType.
InputStream that can be used to download the
physical file for this file item.
Item types this annotation type is enabled for.
Response.Status.ERROR.
MimeType item.
MimeType item.
Client application in use.
Client item.
Client item.
Extract that is the parent of this labeled extract.
File for the configuration.
FileTypeData item.
FileType item.
GelElectrophoresis this GelScanEvent is associated with.
GelElectrophoresis this StainingEvent is associated with.
Getter object for the specified class and
property.
GroupData that owns the DiskConsumable item.
DiskConsumable item or null
if ther is none.
Item types where it makes sense to use this plugin for a
client application.
Hardware that is configured.
HardwareType item.
FlatFileParser.parseHeaders()
method.
Directory for this user.
SessionControl.
SpectrumSearch.
InputStream object reading from
the specified file.
Hardware instrument.
key as an
integer value.
key as an
integer value.
String.
String.
Integer.
Integer.
HardwareConfiguration ionisationSource.
InstrumentConfiguration ionSelection.
ItemKeyData for the item.
ItemKey that is used to share this item to users
and groups.
Item type of the item this annotation set belongs to.
Item type for the type of items this role key applies to.
Job this message is about.
Label compound used for labeling the extract.
FlatFileParser.parseHeaders()
method parsed.
DiskConsumable item.
Location of this FileData
Location the items is stored at.
DiskConsumable item.
Type.STRING
annotation.
Type.FLOAT or
Type.DOUBLE annotation.
Type.INT or
Type.LONG annotation.
FileData item.
File.
MimeTypeData items.
MimeType string when you know the file extension.
Type.FLOAT or
Type.DOUBLE annotation.
Type.INT or
Type.LONG annotation.
SpectrumPrecursor.FragmentationType.
DigestParameter.
SearchDatabase.
PluginConfiguration item.
PluginDefinition item.
PluginType item.
Quota item.
ItemKey when you
have a combination of user/group/permission values.
ProjectKey when you
have a combination of project/permission values.
PluginRequest object that handles the next request,
if status is Response.Status.CONTINUE.
InstrumentConfiguration otherInstrumentInfo.
OutputStream object writing to
the specified file.
UserData that is the owner of the item.
User that is the owner of the item.
PasswordData object which allows you to change the
password for the user.
Peak peakArrayList.
PeakList this acquisition is created from.
PeakListData this acquisition is created from.
PeakListData this peak is created from.
PeakListData this precursor is created from.
PeakList this peak is created from.
PeakList this precursor is created from.
PeakList this SearchResult is associated with.
PeakList peakListArrayList.
PeakListSetData this peakList is created from.
PeakListSet this peakList is created from.
PeakListSet this SpectrumSearch is associated with.
Peptide polypeptides.
PluginConfiguration defining the plugin this job should
execute.
PluginConfiguration defining the plugin this job should
execute.
Precursor precursorList.
ProjectKeyData for the item.
ProjectKey that is used to share this item to projects.
ProjectKey that can be used to share an item to
the active project with full permission, or 0 if no project is active or
the logged in user only has read permission to the active project.
GelElectrophoresis.
Peptide polypeptides.
Protocol describing the procedure used in this event.
ProtocolTypeData item.
ProtocolType item.
ItemQuery that returns annotation types.
File items.
FileType items.
QuotaType.
ItemQuery object configured to retrieve Role
items.
Quota that applies to the group.
Quota that applies to the user.
Group whose Quota also applies to the user.
QuotaTypeData for this DiskUsageData.
QuotaType the DiskConsumable item is using.
QuotaType system id of this item.
InputStream that can be used to download the
physical file for this file item.
SearchResult referenced results.
Removable item types.
RequestInformation for a given command, i.e.
RoleKey when you know the Item
type of the RoleKey.
root-entity in the FROM part.
Sample that is the parent of this extract.
Sample /** Get the Sample
SearchResult.
Software this SpectrumSearch is associated
with.
SearchResult this PolyPeptide is associated with.
SessionControl object that manages this item.
SessionControl object if you know the id.
SessionControl object that manages this item.
SessionControl object that owns this
DbControl object.
Setter object for the specified class and
property.
Shareable item types.
FileData object.
Software software.
Software that is configured.
SoftwareType item.
GelElectrophoresis.
File sourceFile.
DigestParameter.
InstrumentConfiguration spectrumInstrument.
SpectrumSearchData this SearchDatabase is created from.
SpectrumSearchData this SearchDatabase is created from.
SpectrumSearchData this SearchDatabase is created from.
SpectrumSearch this digestParameter is associated with.
SpectrumSearch this SearchDatabase is associated with.
SpectrumSearch this SearchModification is associated with.
SpectrumSearch this SearchResult is associated with.
java.sql.Types class.
Types.
key as a String
value.
key as a String
value.
SearchDatabase.
User this message was sent to.
Query.setFirstResult(int) and
Query.setMaxResults(int).
OutputStream that can be used to upload a physical
file for this file item.
OutputStream that can be used to upload a physical
file for this file item.
OutputStream that can be used to upload a physical
file for this file item.
User that is responsible for this event.
DiskConsumable item.
DiskConsumable item.
Document object.
Document object.
Job.ExecutionTime in the database.
Job.Status to the database.
Job.Status to the database.
GuiContext.Type
to the database.
NotificationConfiguration.Mode to the database.
SpectrumPrecursor.FragmentationType.
TablePreferencesConfiguration.Mode to the database.
newItem object.
List of values for a specific parameter.
Hardware item.
Software item.
GroupGroups table.GroupGroups object.
GroupKeys table.GroupKeys object.
ItemKey.
GroupProjects table.GroupProjects object.
Role item representing guests.
PluginDefinitionData item to
store the contexts where a plugin can be used in a client application.Hardware items
in Proteios.System.identityHashCode() method.
Directory item representing the home
directory.
UnsupportedOperationException if
Query.getQueryType() isn't QueryType.HQL.JOIN <alias.property> <joinedAlias>
to the query.LEFT JOIN <alias.property> <joinedAlias>
to the query.RIGHT JOIN <alias.property> <joinedAlias>
to the query.Identifiable item is an item which has an
id a type and a version.id and
a version.FileType item representing an image file.
innerJoin(null, propert, joinedAlias)
HardwareConfiguration and SoftwareConfiguration.Plugin that supports interactive
configuration in a user session.InvalidAnnotationException object.
InvalidAnnotationException object with the
specified message.
InvalidAnnotationException object when
the annotation type cannot be used for the specified item type.
InvalidDataException object.
InvalidDataException object.
InvalidDataException object with the
specified message.
InvalidPasswordException object
InvalidPasswordException object
InvalidPasswordException object with
the specified message
InvalidPathException object.
InvalidUseOfNullException object.
InvalidUseOfNullException object.
DbControl object or not.
Object.equals(Object) method.
Directory.HOME.
InputStream can be imported by this
plugin.
MeasuredArea.
Sample has been created from this biosource
LabeledExtract:s has been created from this item
no Extract:s has been created from this item
FileAttachable item is using this key.
Shareable item is using this key.
LabeledExtract:s are labeled with this label
LabeledExtract:s has been created from this item
Sample has been created from this observedModification
Sample has been created from this protein
Job is using this plugin configuration
PluginConfiguration is using this definition.
Shareable item is using this key.
Sample has been created from this protein
BioMaterialEvent
Protocol of this type exists
Group has been assigned this quota
a User has been assigned this quota
Extract:s has been created from this item
no Sample:s has been created from this item
Sample has been created from this searchModification
Software using this type
Ownable item is owned by this user
A user can also be referenced from groups, roles, projects, item keys,
sessions and settings, but those references are automatically deleted if
the user is deleted and aren't inclued in this check.
Path.INVALID_CHARACTERS.
ItemAlreadyExistsException.
ItemInUseException.
Shareable item has been shared to.ItemModifiedException.
ItemModifiedException trying to find the item
information from the Hibernate exception.
ItemNotFoundException.
BasicData.Query interface that returns item
objects.ItemQuery as an iterator.ItemQuery as a list.Expression that
can be used in queries.JEP expression.Expression.
Restriction.
KeyPermission object.
LabeledExtract from an Extract.
leftJoin(null, propert, joinedAlias, null)
log2(expression) function to a
JEP expression parser.MappingCoordinate with the specified plate, row and column.
HardwareType object representing a robot.
mean(string) function to a
JEP expression parser.ObservedModification and
SearchModification.Shareable items and want to modify some permissions on
all of them without affecting the rest of the permissions.MultiPermissions object and feed it the
collection of Shareable items that you want to modify.
Nameable item is an item that has
a name and description.name
and, optionally, a description.Nameable interface, including data validation.DbControl object for this session.
PluginConfiguration for this plugin.
SessionControl object.
NotLoggedInException.
NumberOutOfRangeException object.
NumberOutOfRangeException object when the
parameter is less than a minimum or greater than a maximum value.
NumberOutOfRangeException object when the
parameter is outside both a minimum and a maximum allowed value.
NumberOutOfRangeException object when the
parameter is less than a minimum or greater than a maximum value.
NumberOutOfRangeException object when the
parameter is outside both a minimum and a maximum allowed value.
Keyring class.Ownable item is an item which has a User as its owner.Ownable interface, including data validation.BasicData class and implements the
OwnableData interface.BasicItem
class and implements the Ownable interface.ParameterType and
ParameterValueData.ParameterException.
Directory
or File item.Path object by parsing the given string.
PermissionDeniedException.
PermissionDeniedException.
PermissionDeniedException.
FileType item representing a plate mapping
file.
Protein
and Peptide.Sample, Extract or
LabeledExtract) from a set of other biomaterial items.
Authenticator
interface that authenticates a user against a POP3 server.POP3Authenticator object.
Role item representing power users.
FileType item representing a print map
file.
Shareable item has been shared to.ProjectKeys table.ProjectKeys object.
ProjectPermission object.
ProjectKey.
property(null, property).
FileType item representing a protocol.
Protocol items in
Proteios.Query to
build the structure of the query.DiskConsumable item cannot be saved.QuotaException object.
QuotaException object.
QuotaData item to
help with the Hibernate mapping between quota and
quota type/location/max bytes.FileType item representing a raw data file.
DbControl.
DbControl.disconnect().
Removable item is an item that can be flagged
as removed.Role from a user.
FileType item representing a reporter map
file.
rightJoin(null, propert, joinedAlias, null)
HardwareType object representing a robot.
RoleKeys table.RoleKeys object.
Directory item representing the root.
User representing the root account.
Sample from a BioSource.
HardwareType object representing a scanner.
InstrumentConfiguration acquisitionInstrumentInfo.
Acquisition acquisitionList.
File item.
InstrumentConfiguration activation.
HardwareConfiguration analyzers.
BioMaterial bioMaterials set.
BioSource item that is the the parent of this sample.
PeakList item.
DataProcessingStep dataProcessingStepList.
GelElectrophoresis
item.
DataProcessingStep item.
NameableData object.
PeakList item.
HardwareConfiguration detector.
DigestParameter digestParameters set.
File item.
MimeType item.
Client item.
SeparationMethod item.
Extract item that is the the parent
of this labeled extract.
File for the configuration.
File files set.
File item.
GelElectrophoresis this GelScanEvent is associated with.
GelElectrophoresis this StainingEvent is associated with.
Hardware that is configured.
HardwareType of this Hardware item.
Hit hits set.
SpectrumSearch
item.
Hardware instrument.
HardwareConfiguration ionisationSource.
InstrumentConfiguration ionSelection.
ItemKeyData for the item.
ItemKey for this item.
ShareableData object.
Label that was used to label the extract.
File item.
Type.STRING
annotation.
parseHeaders method before it gives
up.
Type.FLOAT or
Type.DOUBLE annotation.
Type.INT or
Type.LONG annotation.
File item.
Type.FLOAT or
Type.DOUBLE annotation.
Type.INT or
Type.LONG annotation.
DigrestParameter item.
NameableData object.
DigrestParameter item.
MeasuredArea item.
Date object.
Date object.
ObservedModification modifications set.
InstrumentConfiguration otherInstrumentInfo.
OwnableData object.
Peak peakArrayList.
PeakList this acquisition is created from.
PeakListData this acquisition is created from.
PeakListData this peak is created from.
PeakListData this precursor is created from. param
PeakList this peak is created from.
PeakList this precursor is created from.
PeakList this SearchResult is associated with.
PeakList peakListArrayList.
PeakListSetData this peakList is created from.
PeakListSet this peakList is created from.
PeakListSet this SpectrumSearch is associated with.
PolyPeptide polypeptides
SearchResult item.
Precursor precursorList.
SearchResult item.
ProjectKeyData for the item.
ProjectKey for this item.
ShareableData object.
GelElectrophoresis item.
Protocol that describes the procedure used in this event.
Protocol item.
SearchResult referenced results.
Query.setFirstResult(int)
and Query.setMaxResults(int) had been disabled, or if the results are
loaded by an iterator where the number of rows not are known beforehand.
Sample item that is the the parent of this extract.
Sample
SearchResult item.
SearchDatabase searchDatabases set.
Software this SpectrumSearch is associated
with.
SearchModification searchModifications set.
SearchResult this PolyPeptide is associated with.
SearchResult searchResults set.
Software software.
Software that is configured.
SoftwareType of this Software item.
GelElectrophoresis
item.
File sourceFile.
DigrestParameter item.
InstrumentConfiguration spectrumInstrument.
SpectrumSearchData this peakList is created from.
SpectrumSearchData this peakList is created from.
SpectrumSearchData this peakList is created from.
SpectrumSearch this DigestParameter is associated with.
SpectrumSearch this SearchDatabase is associated with.
SpectrumSearch this SearchModification is associated with.
SpectrumSearch this SearchResult is associated with.
SpectrumSearch spectrumSearches set.
SearchResult item.
SearchResult item.
SqlResult object that will be used the next time the
JEP expression is evaluated.
SearchDatabase item.
File item.
User that is responsible for this event.
Hardware item.
Software item.
Shareable item is an item which can be shared to
other User:s, Group:s and Project:s.Shareable interface, including data validation.OwnedData class and implements the
ShareableData interface.OwnedItem
class and implements the Shareable interface.AbsoluteProgressReporter interface,
which simply remembers that last values.Authenticator
interface that authenticates everyone as long as the login is the same
as the password.SimpleAuthenticator object.
ProgressReporter interface,
which simply remembers that last values.Software items
in Proteios.FileType item representing a spot images
file.
SqlQuery.SqlQuery as an iterator.Request to a ParameterValues
object.
Request to a ParameterValues
object.
StringTooLongException object.
StringTooLongException object.
Role item representing supervisors.
SystemItem is an item which has an
additional systemwide unique id in the form of string.SystemData items to the numerical internal
id in the current installation.Directory item representing the template
directory.
Expression that can be used
in a query.
Expressions.log2(Expression) method to create an
expression taking the 2-based logarithm of the argument.
ClassName[id=55] or
ClassName[new].
Comparator interface which uses
the result of the toString method to compare the objects.Document to xml.
FlatFileParser.parseHeaders() method.
UnknownLoginException object
UnknownLoginException object
BioMaterialEventData.getSources()
where the element is null, so we have to use a composite element instead.Role item representing regular users.
UserGroups table.UserGroups object.
UserKeys table.UserKeys object.
ItemKey.
UserProjects table.UserProjects object.
UserRoles table.UserRoles object.
|
Last update: 2011-06-23 | |||||||||
| PREV NEXT | FRAMES NO FRAMES | |||||||||