Last update: 2013-10-24
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A

abort() - Method in interface org.proteios.core.AbortablePluginInterface
Set job command as aborted.
abort() - Method in class org.proteios.core.Job
Handles aborted job command.
AbortableJobQueueInterface - Interface in org.proteios.core
An interface for a job queue class that allows abortion of jobs.
AbortableJobQueueReadOnlyInterface - Interface in org.proteios.core
An interface for a job queue class that allows abortion of jobs, restricted to methods that do not modify the job queue when called.
AbortablePluginInterface - Interface in org.proteios.core
This interface defines methods to notify the plugin if the job command is aborted.
About - Interface in org.proteios.core.plugin
Get information, such as the name, version and authors, about a plugin.
AboutImpl - Class in org.proteios.core.plugin
A simple implementation of the About interface.
AboutImpl(String, String, String, String, String, String, String) - Constructor for class org.proteios.core.plugin.AboutImpl
Create a new About object.
AbsoluteProgressReporter - Interface in org.proteios.core
This is interface is an extension to the ProgressReporter interface.
AbstractBatcher - Class in org.proteios.core
This is an abstract class for batchers that are connected to a single DbControl object.
AbstractPlugin - Class in org.proteios.core.plugin
This is an abstract base class useful for developing plugins.
AbstractPlugin() - Constructor for class org.proteios.core.plugin.AbstractPlugin
Create a new AbstractPlugin.
AbstractReader<VALUE_TEMPLATE,OBJECT_TEMPLATE> - Class in org.proteios.props
Used as a proxy to control that objects are not null before reading their value.
AbstractReader() - Constructor for class org.proteios.props.AbstractReader
 
AbstractUpdateToSchemaVersion - Class in org.proteios.core
This abstract class contains methods to perform incremental update and adjustment of existing database items from a previous schema version to the version corresponding to this class.
AbstractUpdateToSchemaVersion() - Constructor for class org.proteios.core.AbstractUpdateToSchemaVersion
 
AccessControlled - Interface in org.proteios.core
This interface should be implemented by a class representing items which requires the logged in user to have permission to access them.
AccountExpiredException - Exception in org.proteios.core
This exception is thrown if you try to log in with an account that has expired.
AccountExpiredException(String, Date) - Constructor for exception org.proteios.core.AccountExpiredException
Creates a new AccountExpiredException.
Acquisition - Class in org.proteios.core
This class represent acquisition items.
AcquisitionData - Class in org.proteios.core.data
This represents an acquisition.
AcquisitionData() - Constructor for class org.proteios.core.data.AcquisitionData
 
acquisitionItem(PeakList) - Method in class org.proteios.io.mzdata.MzDataImpAcquisitionBlock
Creates an acquisition item.
activationItem(PeakList) - Method in class org.proteios.io.mzdata.MzDataImpActivationBlock
Creates an activation item.
add(FileNode) - Method in class org.proteios.core.FileNode
 
add(JobData) - Method in interface org.proteios.core.ManageableJobQueueInterface
Add job to the queue.
add(Expression, Expression) - Static method in class org.proteios.core.query.Expressions
Add two expressions: new expression = e1 + e2.
add(K, V) - Method in class org.proteios.util.Enumeration
 
add(E) - Method in class org.proteios.util.Tree
Not supported.
addAbortedJobId(int) - Method in interface org.proteios.core.AbortableJobQueueInterface
Add job id to the aborted job id list.
addAbortedJobId(int) - Static method in class org.proteios.core.JobQueueManager
Add job id to the aborted job id list.
addAddedParamAnnotation(Annotatable, String, String, Type, String, String, String) - Method in class org.proteios.core.Annotator
Stores variable values as addedParam annotation.
addAll(Collection<? extends E>) - Method in class org.proteios.util.Tree
Not supported.
addAnnotation(Annotatable, String, Type, Object) - Method in class org.proteios.core.Annotator
Add an annotation.
addBioMaterial(BioMaterial<?>) - Method in class org.proteios.core.File
Add a BioMaterial
addChild(XMLTag) - Method in class org.proteios.io.XMLTag
Add a child tag
addChild(E) - Method in class org.proteios.util.Tree.Entry
Add a child to the node.
addCreatedMeasuredBioMaterial(MeasuredBioMaterial) - Method in class org.proteios.core.CreationEvent
 
addDataProcessingStep(DataProcessingStep) - Method in class org.proteios.core.PeakListSet
Add a DataProcessingStep
addDigestParameter(DigestParameter) - Method in class org.proteios.core.SpectrumSearch
Add a DigestParameter
addExecutionTime(Job.ExecutionTime) - Method in interface org.proteios.core.ManageableJobQueueInterface
Add an execution time to list of execution times automatically handled by the job queue class.
AddExpression - Class in org.proteios.core.query
Add two expressions: e1 + e2.
addExtraData(StringPairInterface) - Method in class org.proteios.io.PrecursorSelectedIon
Add spectrum precursor selected ion extra data.
addExtraData(StringPairInterface) - Method in class org.proteios.io.SpectrumImpl
Add spectrum extra data.
addExtraData(StringPairInterface) - Method in class org.proteios.io.SpectrumPrecursor
Add spectrum precursor extra data.
addFile(File) - Method in class org.proteios.core.BioMaterial
Add a File
addGelScanEvent(GelScanEvent) - Method in class org.proteios.core.GelElectrophoresis
Add a GelScanEvent
addGroup(Group) - Method in class org.proteios.core.Group
Add a group as a member to this group.
addHit(Hit) - Method in class org.proteios.core.Feature
Add a Hit
addJob(JobData, ManageableJobQueueReadOnlyInterface) - Method in class org.proteios.core.JobQueueManager
Add a job to a specific job queue.
addObservedModification(ObservedModification) - Method in class org.proteios.core.PolyPeptide
Add a Modification
addPeak(Peak) - Method in class org.proteios.core.PeakList
 
addPeakList(PeakList) - Method in class org.proteios.core.PeakListSet
 
addPermissions(Group, Set<Permission>) - Method in class org.proteios.core.GroupPermissions
Grant permissions to a group, keeping those that have already been set.
addPermissions(User, Set<Permission>) - Method in class org.proteios.core.MultiPermissions
Grant permissions to a user, keeping those that have already been set.
addPermissions(Group, Set<Permission>) - Method in class org.proteios.core.MultiPermissions
Grant permissions to a group, keeping those that have already been set.
addPermissions(Project, Set<Permission>) - Method in class org.proteios.core.MultiPermissions
Grant permissions to a project, keeping those that have already been set.
addPermissions(Project, Set<Permission>) - Method in class org.proteios.core.ProjectPermissions
Grant permissions to a project, keeping those that have already been set.
addPermissions(User, Set<Permission>) - Method in class org.proteios.core.UserPermissions
Grant permissions to a user, keeping those that have already been set.
addPluginExecutionRequest(int, PluginExecutionRequest) - Method in interface org.proteios.core.AbortableJobQueueInterface
Add PluginExecutionRequest entry for job specified by id.
addPluginExecutionRequest(int, PluginExecutionRequest) - Method in class org.proteios.core.JobQueueManager
Add PluginExecutionRequest entry for job specified by id.
addPolyPeptide(PolyPeptide) - Method in class org.proteios.core.SearchResult
Add a PolyPeptide to the collection.
addPrecursor(SpectrumPrecursor) - Method in class org.proteios.io.SpectrumImpl
 
addReferencedResult(SearchResult) - Method in class org.proteios.core.SearchResult
Add a result to the list of referenced results.
address - Variable in class org.proteios.core.authentication.AuthenticationInformation
The postal address to the user.
addSearchDatabase(SearchDatabase) - Method in class org.proteios.core.SpectrumSearch
Add a SearchDatabase
addSearchModification(SearchModification) - Method in class org.proteios.core.SpectrumSearch
Add a SearchModification
addSearchResult(SearchResult) - Method in class org.proteios.core.SpectrumSearch
Add a SearchResult and set the association back to this SpectrumSearch
addSource(MeasuredBioMaterial, Float) - Method in class org.proteios.core.BioMaterialEvent
Add a source biomaterial to this event or update the used quantity of an existing source.
addStainingEvent(StainingEvent) - Method in class org.proteios.core.GelElectrophoresis
Add a StainingEvent
addThread(int, Thread) - Method in interface org.proteios.core.AbortableJobQueueInterface
Add Thread entry for job specified by id.
addThread(int, Thread) - Method in class org.proteios.core.JobQueueManager
Add Thread entry for job specified by id.
addUpdateComment(MeasuredBioMaterial, MeasuredBioMaterial) - Method in class org.proteios.core.UpdateEvent
Adds an update event comment with info on what properties (if any) that have had their values updated.
addUser(User) - Method in class org.proteios.core.Group
Add a user as a member to this group.
addUser(User) - Method in class org.proteios.core.Role
Assign this Role to a user.
addUserLoginTime(int) - Static method in class org.proteios.core.Application
Adds a user id to user login time map, if the user id is not already in map.
adjustExistingItems(Session) - Method in class org.proteios.core.AbstractUpdateToSchemaVersion
Adjust the existing items in the database to be compatible with the latest mappings corresponding to this class.
adjustExistingItems(boolean, ProgressReporter, String, String) - Static method in class org.proteios.core.Update
Adjust the existing items in the database to be compatible with the latest mappings.
adjustExistingItems(Session) - Method in interface org.proteios.core.UpdateToSchemaVersionInterface
Adjust the existing items in the database to be compatible with the latest mappings.
adjustItemsToNewSchemaVersion(Session) - Method in class org.proteios.core.AbstractUpdateToSchemaVersion
Adjust the existing items in the database to be compatible with the latest mappings corresponding to this class.
adjustItemsToNewSchemaVersion(Session) - Method in class org.proteios.core.UpdateToSchemaVersion10
Adjust the existing items in the database to be compatible with the latest mappings corresponding to this class.
adjustItemsToNewSchemaVersion(Session) - Method in class org.proteios.core.UpdateToSchemaVersion2
Does not do anything as hibernate takes care of it
adjustItemsToNewSchemaVersion(Session) - Method in class org.proteios.core.UpdateToSchemaVersion3
Does not do anything as hibernate takes care of it
adjustItemsToNewSchemaVersion(Session) - Method in class org.proteios.core.UpdateToSchemaVersion4
Adjust the existing items in the database to be compatible with the latest mappings corresponding to this class.
adjustItemsToNewSchemaVersion(Session) - Method in class org.proteios.core.UpdateToSchemaVersion5
Adjust the existing items in the database to be compatible with the latest mappings corresponding to this class.
adjustItemsToNewSchemaVersion(Session) - Method in class org.proteios.core.UpdateToSchemaVersion6
Adjust the existing items in the database to be compatible with the latest mappings corresponding to this class.
adjustItemsToNewSchemaVersion(Session) - Method in class org.proteios.core.UpdateToSchemaVersion7
Adjust the existing items in the database to be compatible with the latest mappings corresponding to this class.
adjustItemsToNewSchemaVersion(Session) - Method in class org.proteios.core.UpdateToSchemaVersion8
Adjust the existing items in the database to be compatible with the latest mappings corresponding to this class.
adjustItemsToNewSchemaVersion(Session) - Method in class org.proteios.core.UpdateToSchemaVersion9
Adjust the existing items in the database to be compatible with the latest mappings corresponding to this class.
adjustItemsToNewSchemaVersion(Session) - Method in class org.proteios.core.UpdateToSchemaVersionTmpl
Adjust the existing items in the database to be compatible with the latest mappings corresponding to this class.
ADMINISTRATOR - Static variable in class org.proteios.core.Role
The id for the Role item representing adminstrators.
aFloat(float) - Static method in class org.proteios.core.query.Expressions
Create a constant expression from a float.
Aggregations - Class in org.proteios.core.query
A factory class to create aggregate expressions.
Aggregations() - Constructor for class org.proteios.core.query.Aggregations
 
AHit - Class in org.proteios.io
 
AHit() - Constructor for class org.proteios.io.AHit
 
alias(String) - Static method in class org.proteios.core.query.Hql
Same as property(alias, null).
ALIAS_REGEXP - Static variable in class org.proteios.core.query.Hql
An alias can only contain the characters a-z, A-Z or 0-9.
ALIAS_REGEXP - Static variable in class org.proteios.core.query.Selects
An alias can only contain the characters a-z, A-Z or 0-9.
AliasKeyManager - Class in org.proteios.core
 
AliasKeyManager(KeyStore, String, String) - Constructor for class org.proteios.core.AliasKeyManager
 
allow(XMLTag...) - Method in class org.proteios.io.XMLTag
Adds one or more xml tags that are allowed as child tags.
allowed() - Method in class org.proteios.io.XMLTag
 
allQueuesEmpty() - Method in class org.proteios.core.JobQueueManager
Checks if all queues are empty.
allSame(Collection<Set<Permission>>) - Static method in class org.proteios.core.MultiPermissions
Check if a collection of Set:s all contain the same permissions.
aLong(long) - Static method in class org.proteios.core.query.Expressions
Create a constant expression from a long.
alphaToNumeric(String) - Static method in class org.proteios.util.Coordinate
Convert an alphanumeric coordinate to a numeric coordinate, case is unimportent.
AlreadyLoggedInException - Exception in org.proteios.core
This exception is thrown if you try to log in but are already logged in.
AlreadyLoggedInException(String) - Constructor for exception org.proteios.core.AlreadyLoggedInException
Creates a new AlreadyLoggedInException.
analyzerItem(PeakListSet, Hardware) - Method in class org.proteios.io.mzdata.MzDataImpAnalyzerBlock
Creates an analyzer item.
and(Restriction...) - Static method in class org.proteios.core.query.Restrictions
Combine one or more restrictions with AND: new restriction = r[0] AND r[1] AND ...
AndRestriction - Class in org.proteios.core.query
Combine one or more restrictions with AND: r[0] AND r[1] AND ...
anna - Variable in class org.proteios.io.mzdata.MzDataExpCommonDc
 
anna - Variable in class org.proteios.io.mzdata.MzDataImpCommonDc
 
Annotatable - Interface in org.proteios.core
This interface is implemented by all items which can be annotated.
AnnotatableData - Interface in org.proteios.core.data
An annotatable item is an item that can be annotated with name/value pairs.
AnnotatedData - Class in org.proteios.core.data
This class extends the CommonData class and implements the AnnotatableData interface.
AnnotatedData() - Constructor for class org.proteios.core.data.AnnotatedData
 
AnnotatedItem<D extends AnnotatedData> - Class in org.proteios.core
This is a helper class for items that need to implement the Annotatable interface.
Annotation - Class in org.proteios.core
This class represents an annotation.
AnnotationBetweenRestriction - Class in org.proteios.core
Restricts a query using annotation values between a low and high value.
AnnotationBetweenRestriction(AnnotationType, Object, Object, boolean) - Constructor for class org.proteios.core.AnnotationBetweenRestriction
Create a new annotation restriction.
AnnotationData - Class in org.proteios.core.data
This class holds information about an annotation
AnnotationData() - Constructor for class org.proteios.core.data.AnnotationData
 
AnnotationInRestriction - Class in org.proteios.core
Restricts a query using annotation values that exists in a set of given values.
AnnotationInRestriction(AnnotationType, boolean, Object...) - Constructor for class org.proteios.core.AnnotationInRestriction
Create a new annotation restriction.
Annotations - Class in org.proteios.core.query
A factory class to create restrictions based on annotation values.
Annotations() - Constructor for class org.proteios.core.query.Annotations
 
AnnotationSet - Class in org.proteios.core
An annotation set is the container for all annotations on an item.
AnnotationSetData - Class in org.proteios.core.data
This class holds information about a set of annotations.
AnnotationSetData() - Constructor for class org.proteios.core.data.AnnotationSetData
 
AnnotationSimpleRestriction - Class in org.proteios.core
Restricts a query using annotation values with a simple expression: annotation operator value.
AnnotationSimpleRestriction(AnnotationType, Operator, Object, boolean) - Constructor for class org.proteios.core.AnnotationSimpleRestriction
Create a new annotation restriction using a simple expression: annotation operator value.
AnnotationSimpleRestriction(int, Type, Operator, Object, boolean) - Constructor for class org.proteios.core.AnnotationSimpleRestriction
 
AnnotationType - Class in org.proteios.core
Objects of this class defines an annotation type.
AnnotationTypeData - Class in org.proteios.core.data
This class holds information about an annotation type.
AnnotationTypeData() - Constructor for class org.proteios.core.data.AnnotationTypeData
 
AnnotationTypeNameReader - Class in org.proteios.props
 
AnnotationTypeNameReader() - Constructor for class org.proteios.props.AnnotationTypeNameReader
 
AnnotationValueReader - Class in org.proteios.props
 
AnnotationValueReader() - Constructor for class org.proteios.props.AnnotationValueReader
 
Annotator - Class in org.proteios.core
Use this class whenever you want to add or list annotations of an Annotatable item.
Annotator(ItemFactory) - Constructor for class org.proteios.core.Annotator
Make sure the factory has a connected DbControl
aPeakListSet - Variable in class org.proteios.io.mzdata.MzDataImpCommonPeakListSet
 
append(String) - Method in interface org.proteios.core.ProgressReporter
Append a message to the previous one.
append(String) - Method in class org.proteios.core.SimpleProgressReporter
 
append(String) - Method in class org.proteios.util.ChainedProgressReporter
 
append(String) - Method in class org.proteios.util.ConsoleProgressReporter
 
Application - Class in org.proteios.core
This class represents the Proteios application and is the starting point for all client applications.
Application() - Constructor for class org.proteios.core.Application
 
ArrayIterator<E> - Class in org.proteios.util
This class implements the Iterator interface for an array of objects.
ArrayIterator(E[]) - Constructor for class org.proteios.util.ArrayIterator
Create a new ArrayIterator object.
asc(Expression) - Static method in class org.proteios.core.query.Orders
Sort the result of a query in ascending order by the expression.
AscOrder - Class in org.proteios.core.query
Sort the result of a query in ascending order by the expression.
asString() - Method in class org.proteios.io.XMLTag
 
AttributeDefinition - Class in org.proteios
An attribute is defined by it's set and get methods.
AttributeDefinition(Class, Class, String) - Constructor for class org.proteios.AttributeDefinition
Creates a method key where read prefix is 'get' and write prefix is 'set'
AttributeDefinition(Class, Class, String, AttributeReader) - Constructor for class org.proteios.AttributeDefinition
Creates a method key where read prefix is 'get' and write prefix is 'set' with an attribute reader that reads a value from this attribute type.
AttributeDefinition(Class, Class, String, String, String) - Constructor for class org.proteios.AttributeDefinition
 
AttributeFilter - Interface in org.proteios
Implement this filter when you want to describe a set of attributes as default or not and their sorting order.
AttributeReader<VALUETEMPLATE,OBJECT_TEMPLATE> - Interface in org.proteios.props
Used to read attributes of objects.
attributes() - Method in class org.proteios.io.TandemFactory.ModelGroup
 
attributes() - Method in class org.proteios.io.TandemFactory.Protein
 
attributes() - Method in class org.proteios.io.TandemFactory.SpectrumPathNote
 
attributes() - Method in class org.proteios.io.XMLTag
Override this method to create an attribute string
attributes() - Method in class org.proteios.util.SchemaFactory.Attribute
 
attributes() - Method in class org.proteios.util.SchemaFactory.ComplexType
 
attributes() - Method in class org.proteios.util.SchemaFactory.Element
 
attributes() - Method in class org.proteios.util.SchemaFactory.Schema
 
authenticate(String, String) - Method in interface org.proteios.core.authentication.Authenticator
Authenticates a user.
authenticate(String, String) - Method in class org.proteios.core.authentication.POP3Authenticator
Authenticates a user against the POP3 server.
authenticate(String, String) - Method in class org.proteios.core.authentication.SimpleAuthenticator
If login and password are equal the user is authenticated, otherwise an InvalidPasswordException is thrown.
AuthenticationException - Exception in org.proteios.core.authentication
This exception can be thrown when an error occurs during the authentication.
AuthenticationException(String) - Constructor for exception org.proteios.core.authentication.AuthenticationException
Create a new AuthenticationException object
AuthenticationException(Throwable) - Constructor for exception org.proteios.core.authentication.AuthenticationException
Create a new AuthenticationException object
AuthenticationInformation - Class in org.proteios.core.authentication
Objects of this class are returned by the Authenticator.authenticate(String,String) method and contains information about the authenticated user.
AuthenticationInformation(String, String) - Constructor for class org.proteios.core.authentication.AuthenticationInformation
Creates a new AuthenticationInformation object without extra information.
AuthenticationInformation(String, String, String, String, String, String, String, String, String, String) - Constructor for class org.proteios.core.authentication.AuthenticationInformation
Creates a new AuthenticationInformation object with extra information.
Authenticator - Interface in org.proteios.core.authentication
This interface defines the methods that needs to be implemented by a class to be able to use it for external authentication against another database or directory service.
AutoDetectingImporter - Interface in org.proteios.core.plugin
This interface should be implemented by an import plugin that supports auto-detection of the file format.
averageDeltaMass - Variable in class org.proteios.core.data.ModificationData
 
averageMass - Variable in class org.proteios.core.data.ModificationData
 

B

Base64Coder - Class in org.proteios.core
 
Base64Coder() - Constructor for class org.proteios.core.Base64Coder
 
Base64Util - Class in org.proteios.io
This class supports conversion to/from Base64-coded data.
Base64Util() - Constructor for class org.proteios.io.Base64Util
 
BaseException - Exception in org.proteios.core
This is the base class for exceptions in Proteios.
BaseException() - Constructor for exception org.proteios.core.BaseException
Create a new BaseException object.
BaseException(String) - Constructor for exception org.proteios.core.BaseException
Create a new BaseException object with the specified message
BaseException(String, Throwable) - Constructor for exception org.proteios.core.BaseException
Create a new BaseException object with the specified message
BaseException(Throwable) - Constructor for exception org.proteios.core.BaseException
Create a new BaseException object acting as a wrapper for another exception that caused the error.
BasicBatcher<D extends BatchableData> - Class in org.proteios.core
This is an abstract class for batching functionallity.
BasicData - Class in org.proteios.core.data
This is the root superclass of all data classes.
BasicData() - Constructor for class org.proteios.core.data.BasicData
 
BasicItem<D extends BasicData> - Class in org.proteios.core
This is the root superclass of all item classes.
BatchableData - Interface in org.proteios.core.data
This is a tagging interface only.
BatchedPropertyInfo - Class in org.proteios.core
Holds information about a batchable property.
Batcher - Interface in org.proteios.core
The basic interface which all batchers must implement.
between(AnnotationType, Object, Object, boolean) - Static method in class org.proteios.core.query.Annotations
Create a restriction that searches for annotations between two given values.
between(Expression, Expression, Expression) - Static method in class org.proteios.core.query.Restrictions
Compare if one expression falls between two other expressions: new expression = low <= e AND e < high.
BetweenRestriction - Class in org.proteios.core.query
Compare if one expression falls between to other expressions: e BETWEEN low AND high.
BioMaterial<D extends BioMaterialData> - Class in org.proteios.core
This is the base class for for the four types of biomaterials: BioSource, Sample, Extract and LabeledExtract.
BioMaterialData - Class in org.proteios.core.data
This class is the root class for biomaterials.
BioMaterialData() - Constructor for class org.proteios.core.data.BioMaterialData
 
BioMaterialEvent<D extends BioMaterialEventData> - Class in org.proteios.core
This class represents an event in the life of a MeasuredBioMaterial.
BioMaterialEventData - Class in org.proteios.core.data
This class is used to register events for measured biomaterials.
BioMaterialEventData() - Constructor for class org.proteios.core.data.BioMaterialEventData
 
BioSource - Class in org.proteios.core
This class represent biosource items.
BioSourceData - Class in org.proteios.core.data
This represents a biosoruce which is the starting point of all biomaterials.
BioSourceData() - Constructor for class org.proteios.core.data.BioSourceData
 
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpAcqSpecificationBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpAcquisitionBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpActivationBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpAnalyzerBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpAnalyzerListBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpCommon
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpDataBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpDataProcessingBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpDescriptionBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpDetectorBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpInstrumentNameBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpInstrumentSourceBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpIntenArrayBinaryBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpIonSelectionBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpMzArrayBinaryBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpMzDataBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpPrecursorBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpPrecursorListBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpSampleNameBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpSpectrumBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpSpectrumInstrumentBlock
Processes end of XML block processed by this class.
blockEnd(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpSpectrumListBlock
Processes end of XML block processed by this class.
blockStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpAcqSpecificationBlock
Processes start of XML block processed by this class.
blockStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpAcquisitionBlock
Processes start of XML block processed by this class.
blockStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpAnalyzerListBlock
Processes start of XML block processed by this class.
blockStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpCommon
Processes start of XML block processed by this class.
blockStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpDataBlock
Processes start of XML block processed by this class.
blockStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpMzDataBlock
Processes start of XML block processed by this class.
blockStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpPrecursorBlock
Processes start of XML block processed by this class.
blockStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpPrecursorListBlock
Processes start of XML block processed by this class.
blockStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpSoftwareBlock
Processes start of XML block processed by this class.
blockStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpSpectrumBlock
Processes start of XML block processed by this class.
blockStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpSpectrumInstrumentBlock
Processes start of XML block processed by this class.
blockStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpSpectrumListBlock
Processes start of XML block processed by this class.
BOOLEAN - Static variable in class org.proteios.core.hibernate.TypeWrapper
 
BooleanParameterType - Class in org.proteios.core
This class represent a parameter type that is a boolean.
BooleanParameterType() - Constructor for class org.proteios.core.BooleanParameterType
Create a new boolean parameter type, allowing null values.
BooleanParameterType(Boolean, boolean) - Constructor for class org.proteios.core.BooleanParameterType
Create a new boolean parameter type.
BooleanParameterValueData - Class in org.proteios.core.data
Boolean parameter value.
BooleanParameterValueData() - Constructor for class org.proteios.core.data.BooleanParameterValueData
 
BooleanParameterValueData(Boolean...) - Constructor for class org.proteios.core.data.BooleanParameterValueData
 
build(Object...) - Method in class org.proteios.io.XMLTag
Simplifies building of attribute strings

C

calculateLsid() - Method in class org.proteios.core.LsidElement
 
calculateTotalIntensity() - Method in class org.proteios.core.PeakList
Count the total intensity of all peaks in this peaklist
canEnumerate() - Method in enum org.proteios.core.Type
If it makes sense to use values of this type as an enumeration to choose from.
ChainedProgressReporter - Class in org.proteios.util
An implementation of the ProgressReporter interface that chains to another progress reporter while recalculating the percentage values.
ChainedProgressReporter(ProgressReporter) - Constructor for class org.proteios.util.ChainedProgressReporter
Create a new chained progress reporter.
channel(int) - Method in class org.proteios.util.jep.ChannelFunction
Get the value of the specified channel of the current sql result.
ChannelFunction - Class in org.proteios.util.jep
A JEP function class that adds a ch(int) function to a JEP expression parser.
ChannelFunction() - Constructor for class org.proteios.util.jep.ChannelFunction
Create a new instance of this function.
ChannelFunction(int[]) - Constructor for class org.proteios.util.jep.ChannelFunction
Create a new instance of this function which can be used to dynamically evaluate expressions.
checkAgainstStoredPassword(String) - Method in class org.proteios.core.User
Checks a string against the stored password.
checkMax(int, String, int) - Static method in class org.proteios.core.IntegerUtil
Check that an integer is equal or lower than a maximum value.
checkMin(int, String, int) - Static method in class org.proteios.core.IntegerUtil
Check that an integer is equal or greater than a minimum value.
checkMinMax(int, String, int, int) - Static method in class org.proteios.core.IntegerUtil
Check that an integer is equal or between a minimum and a maximum value.
checkPermission(Permission) - Method in interface org.proteios.core.AccessControlled
Check if the logged in user has the desired permission on the item, otherwise throw an exception.
checkPermission(Permission) - Method in class org.proteios.core.BasicBatcher
Checks if the logged in user has the specified permission on this item.
checkPermission(Permission) - Method in class org.proteios.core.BasicItem
Checks if the logged in user has the specified permission on this item.
children() - Method in class org.proteios.io.XMLTag
 
chooseClientAlias(String[], Principal[], Socket) - Method in class org.proteios.core.AliasKeyManager
 
chooseServerAlias(String, Principal[], Socket) - Method in class org.proteios.core.AliasKeyManager
 
ClassDescriptor - Class in org.proteios
Through the ClassDescriptor you can find methods by defined attributes.
ClassDescriptor(Class<?>) - Constructor for class org.proteios.ClassDescriptor
 
ClassLocal<E> - Class in org.proteios.util
This class is a similar to the JDK ThreadLocal class, but stores one object per class instead of one object per thread.
ClassLocal() - Constructor for class org.proteios.util.ClassLocal
Create a new ClassLocal object.
ClassMetadataExposed - Class in org.proteios.core
Exposes only get methods of the meta data.
ClassMetadataExposed(ClassMetadata) - Constructor for class org.proteios.core.ClassMetadataExposed
 
ClassUtil - Class in org.proteios.util
Utility class for Class objects.
ClassUtil() - Constructor for class org.proteios.util.ClassUtil
 
clear() - Method in class org.proteios.util.Tree
Clear all elements except the root element.
Client - Class in org.proteios.core
This class represents a registered client application.
ClientData - Class in org.proteios.core.data
This class holds information about a client.
ClientData() - Constructor for class org.proteios.core.data.ClientData
 
ClientDefaultSettingData - Class in org.proteios.core.data
 
ClientDefaultSettingData() - Constructor for class org.proteios.core.data.ClientDefaultSettingData
 
close() - Method in class org.proteios.core.AbstractBatcher
 
close() - Method in interface org.proteios.core.Batcher
Flush the batcher and close it.
close() - Method in class org.proteios.core.DataResultIterator
From the ResultIterator interface ---------------------------------
close() - Method in class org.proteios.core.DbControl
Close the connection to the database.
close() - Method in class org.proteios.core.DynamicResultIterator
From the ResultIterator interface ---------------------------------
close() - Method in class org.proteios.core.ItemResultIterator
From the ResultIterator interface ---------------------------------
close() - Method in interface org.proteios.core.query.ResultIterator
Close the iterator and immediately release all resources associated with it.
close() - Method in interface org.proteios.io.XMLCrudeWriter
Close (not) output stream.
close() - Method in class org.proteios.io.XMLCrudeWriter3Impl
Close (not) output stream.
close() - Method in class org.proteios.io.XMLCrudeWriterImpl
Close (not) output stream.
ColumnPreferences - Class in org.proteios.io
This class represents column preferences.
ColumnPreferences() - Constructor for class org.proteios.io.ColumnPreferences
Default constructor.
ColumnPreferences(String) - Constructor for class org.proteios.io.ColumnPreferences
Constructor with name argument.
columns() - Method in class org.proteios.util.FlatFileParser.Data
The number of columns as determined by the FlatFileParser.setDataSplitterRegexp(Pattern) regular expression.
COMMAND_CONFIGURE_JOB - Static variable in interface org.proteios.core.plugin.Request
This should be the first command to use when setting the plugin's job parameters.
COMMAND_CONFIGURE_PLUGIN - Static variable in interface org.proteios.core.plugin.Request
This should be the first command to use when setting the plugin's configuration.
COMMAND_EXECUTE - Static variable in interface org.proteios.core.plugin.Request
This command will tell the plugin to start its execution.
commit() - Method in class org.proteios.core.DbControl
Commit all changes made to items and close the connection to the database.
CommonData - Class in org.proteios.core.data
This is a convenience class that extends the SharedData class and implements the NameableData and RemovableData interfaces.
CommonData() - Constructor for class org.proteios.core.data.CommonData
 
CommonItem<D extends CommonData> - Class in org.proteios.core
 
compare(T, T) - Method in class org.proteios.util.ToStringComparator
 
compareTo(KeyPermission) - Method in class org.proteios.core.data.keyring.KeyPermission
Compare the keyId of this object to the keyId of another KeyPermission object.
compareTo(ProjectPermission) - Method in class org.proteios.core.data.keyring.ProjectPermission
Compare the projectId of this object to the projectId of another ProjectPermission object.
compareTo(SearchResultData) - Method in class org.proteios.core.data.SearchResultData
 
compareTo(Peak) - Method in class org.proteios.core.Peak
 
compareTo(PeakList) - Method in class org.proteios.core.PeakList
 
compareTo(SearchResult) - Method in class org.proteios.core.SearchResult
 
compileSchema(String) - Static method in class org.proteios.io.XMLValidator
Parses the XSD schema file and returns in-memory representation of the schema.
compress(ProgressReporter) - Method in class org.proteios.core.File
Compress the file if stored on an internal disk.
Config - Class in org.proteios.core
Use this class to access the configuration settings for Proteios.
Config() - Constructor for class org.proteios.core.Config
 
configuration - Variable in class org.proteios.core.plugin.AbstractPlugin
 
ConfigurationException - Exception in org.proteios.core
This exception is thrown by the Config class if there is a problem with finding or loading the configuration settings.
ConfigurationException(String) - Constructor for exception org.proteios.core.ConfigurationException
Creates a new ConfigurationException.
configure(GuiContext) - Method in class org.proteios.core.Job
Start the configuration sequence for a job.
configure(GuiContext, Request, Response) - Method in interface org.proteios.core.plugin.InteractivePlugin
Configure the plugin.
configure() - Method in class org.proteios.core.PluginConfiguration
Start the configuration sequence for a plugin.
ConnectionClosedException - Exception in org.proteios.core
This exception is thrown when trying to use a DbControl object that has been closed.
ConnectionClosedException() - Constructor for exception org.proteios.core.ConnectionClosedException
Creates a new ConnectionClosedException.
ConsoleProgressReporter - Class in org.proteios.util
An implementation of the ProgressReporter interface that writes all messages to the standard console.
ConsoleProgressReporter() - Constructor for class org.proteios.util.ConsoleProgressReporter
 
contains(Object) - Method in class org.proteios.core.ItemResultList
 
contains(JobData) - Method in interface org.proteios.core.ManageableJobQueueInterface
Checks if the queue contains a job item.
contains(JobData) - Method in interface org.proteios.core.ManageableJobQueueReadOnlyInterface
Checks if the queue contains a job item.
contains(Object) - Method in class org.proteios.util.Tree
 
containsAll(Collection<?>) - Method in class org.proteios.util.Tree
 
contentEquals(AnnotationSet) - Method in class org.proteios.core.AnnotationSet
Compare the AnnotationSet with another.
Controlled - Interface in org.proteios.core
This is the base tagging interface for items that needs special attention by the DbControl object when DbControl.commit() is called.
convertToLocalWellNotation(String, String) - Method in class org.proteios.io.FilenameParseUtil
Converts a well position of standard notation of type "A12" to local notation.
convertWellNotation(String) - Method in class org.proteios.io.FilenameParseUtil
Converts a well position to standard notation of type "A12", where the uppercase letter notates the column and the number the row.
Coordinate - Class in org.proteios.util
Util class for coordinate transformations in base.
Coordinate() - Constructor for class org.proteios.util.Coordinate
 
copy(Date) - Static method in class org.proteios.core.DateUtil
Get a copy of the date.
copy(InputStream, OutputStream) - Static method in class org.proteios.util.FileUtil
Copy from the input stream to the output stream until end of file is reached.
copy(InputStream, OutputStream, AbsoluteProgressReporter) - Static method in class org.proteios.util.FileUtil
Copy from the input stream to the output stream until end of file is reached.
copyFile(File, String, String, Directory, FileType) - Method in class org.proteios.io.FileExtraUtil
Copies contents of a file item to a new file item.
copyLocalFile(String, String, String, Directory, FileType) - Method in class org.proteios.io.FileExtraUtil
Copies contents of a local file to a new file item.
count(Expression, boolean) - Static method in class org.proteios.core.query.Aggregations
Calculates the number of values for an expression: new expression = COUNT(e)
count(DbControl) - Method in interface org.proteios.core.query.Query
Count the number of items/rows that are returned by the query.
CountExpression - Class in org.proteios.core.query
Count the number of values: COUNT(e)
countPlugins(DbControl, GuiContext) - Static method in class org.proteios.core.PluginDefinition
Count the number of plugins that can be used in a given context.
countUnreadMessages(DbControl, User) - Static method in class org.proteios.core.Message
Count the number of unread messages for the specified or logged in user.
create(Class<D>, Object...) - Method in class org.proteios.core.ItemFactory
Creates an instance of the given template class.
create(E) - Method in class org.proteios.io.TagFactory
This method tries to find a method in this factory named "newCLASS" where the CLASS is the classname of the template.
createAddedParamAnnotationType(Annotatable, String, Type, String, String, String) - Method in class org.proteios.core.Annotator
Creates added parameter annotation type for storing variable values as annotations.
createAddedParamAnnotationType(String, Type, Item, String, String, String) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Creates added parameter annotation type for storing variable values as annotations.
createAnnotationType(Annotatable, String, Type) - Method in class org.proteios.core.Annotator
 
createAnnotationType(String, Type, Item) - Method in class org.proteios.core.Annotator
Creates annotation type for storing variable values as annotations.
createAnnotationType(Type) - Method in class org.proteios.core.ItemFactory
Create a new AnnotationType item.
createAnnotationType(String, Type, Item) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Creates annotation type for storing variable values as annotations.
createCreationEvent(MeasuredBioMaterial<?>, MeasuredBioMaterial<?>, Float) - Method in class org.proteios.core.ItemFactory
Create a new BioMaterialEvent of the Type#OTHER type.
createCvLookupAnnotationType(String, Type, Item, String, String) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Creates cvLookup annotation type for storing variable values as annotations.
createCvParamAnnotationType(String, Type, Item, String, String) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Creates cvParam annotation type for storing variable values as annotations.
createDom(String, String) - Static method in class org.proteios.util.XMLUtil
Create a new Document with root element and System id declaration.
createGelImageAnalysisEvent(MeasuredBioMaterial<?>) - Method in class org.proteios.core.ItemFactory
Create a new GelImageAnalysisEvent of the Type#OTHER type.
createGelScanEvent(MeasuredBioMaterial<?>) - Method in class org.proteios.core.ItemFactory
Create a new GelScanEvent of the Type#OTHER type.
createGlobalDefaultSetting(String, String) - Method in class org.proteios.core.ItemFactory
Create a new GlobalDefaultSetting item.
createHomeDirectory(User) - Method in class org.proteios.core.ItemFactory
Creates and saves a home directory for the supplied user
createJob(PluginDefinition, PluginConfiguration) - Method in class org.proteios.core.ItemFactory
TODO this method does two things, create and configures a job to a starting state.
createLabeledExtract(Label) - Method in class org.proteios.core.ItemFactory
Create a new LabeledExtract with label.
createMessage(User, String, User, Job) - Method in class org.proteios.core.ItemFactory
Create a new Message item.
createSeparationEvent(MeasuredBioMaterial<?>, Float) - Method in class org.proteios.core.ItemFactory
Create a new SeparationEvent of the Type#OTHER type.
createSeparationMethod(String) - Method in class org.proteios.core.ItemFactory
Create a new SeparationMethod item.
createStainingEvent(MeasuredBioMaterial<?>) - Method in class org.proteios.core.ItemFactory
Create a new StainingEvent of the Type#OTHER type.
createTables(boolean, ProgressReporter) - Static method in class org.proteios.core.Install
 
createUpdateEvent(MeasuredBioMaterial<?>) - Method in class org.proteios.core.ItemFactory
Create a new UpdateEvent of the Type#OTHER type.
createUser(String, String) - Method in class org.proteios.core.ItemFactory
Create a new User item.
createUserParamAnnotationType(String, Type, Item) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Creates userParam annotation type for storing variable values as annotations.
CreationEvent - Class in org.proteios.core
This class is used for creation events like pooling of biomaterials
CreationEventData - Class in org.proteios.core.data
This class is used for creation events like pooling of biomaterials.
CreationEventData() - Constructor for class org.proteios.core.data.CreationEventData
 
CreationInterface - Interface in org.proteios.core.data
 
currentDateTime() - Method in class org.proteios.io.mzdata.MzDataImpMzDataBlock
Current date and time as a string.
CvLookup - Class in org.proteios.io.mzdata
This class processes a "cvLookup" XML block in an mzData file.
CvLookup() - Constructor for class org.proteios.io.mzdata.CvLookup
Default constructor.
CvLookup(String, String, String, String) - Constructor for class org.proteios.io.mzdata.CvLookup
Constructor with arguments for all attributes.
cvLookupElementStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpMzDataBlock
Processes start of cvLookup XML element.
CvParam - Class in org.proteios.io.mzdata
This class processes a "cvParam" XML block in an mzData file.
CvParam() - Constructor for class org.proteios.io.mzdata.CvParam
Default constructor.
CvParam(String, String, String, String) - Constructor for class org.proteios.io.mzdata.CvParam
Constructor with arguments for all attributes.
cvParamElementStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpActivationBlock
Processes start of cvParam XML element.
cvParamElementStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpAnalyzerBlock
Processes start of cvParam XML element.
cvParamElementStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpDetectorBlock
Processes start of cvParam XML element.
cvParamElementStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpInstrumentSourceBlock
Processes start of cvParam XML element.
cvParamElementStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpIonSelectionBlock
Processes start of cvParam XML element.
cvParamElementStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpProcessingMethodBlock
Processes start of cvParam XML element.
cvParamElementStart(XMLStreamReader) - Method in class org.proteios.io.mzdata.MzDataImpSpectrumInstrumentBlock
Processes start of cvParam XML element.

D

DatabaseException - Exception in org.proteios.core
Exceptions of this type are thrown when there is an error from the database.
DatabaseException() - Constructor for exception org.proteios.core.DatabaseException
Create a new DatabaseException object.
DatabaseException(String) - Constructor for exception org.proteios.core.DatabaseException
Create a new DatabaseException object with the specified message.
DatabaseException(String, Throwable) - Constructor for exception org.proteios.core.DatabaseException
Create a new DatabaseException object with the specified message
DatabaseException(Throwable) - Constructor for exception org.proteios.core.DatabaseException
Create a new DatabaseException object acting as a wrapper for another exception that caused the error.
dataItem(boolean, boolean, String) - Method in class org.proteios.io.mzdata.MzDataImpDataBlock
Creates a data item.
dataProcessingBlock(XMLCrudeWriter, DataProcessingStep) - Method in class org.proteios.io.mzdata.MzDataExpDataProcessingBlock
Creates a dataProcessing block.
dataProcessingItem(PeakListSet) - Method in class org.proteios.io.mzdata.MzDataImpDataProcessingBlock
Creates a dataProcessing item.
DataProcessingStep - Class in org.proteios.core
This class represent data processing steps items.
DataProcessingStepData - Class in org.proteios.core.data
This represents a data processing step of a peak list set.
DataProcessingStepData() - Constructor for class org.proteios.core.data.DataProcessingStepData
 
DataQuery<I extends BasicData> - Class in org.proteios.core
An implementation of the Query interface that returns data objects.
DataResultIterator<I extends BasicData> - Class in org.proteios.core
Return the results of a DataQuery as an iterator.
DATE - Static variable in class org.proteios.core.hibernate.TypeWrapper
 
DateParameterType - Class in org.proteios.core
This class represent a parameter type that is a date.
DateParameterType() - Constructor for class org.proteios.core.DateParameterType
Create a new date parameter type, allowing null values.
DateParameterType(Date, boolean) - Constructor for class org.proteios.core.DateParameterType
Create a new date parameter type.
DateParameterType(Date, boolean, int, int, int, List<Date>) - Constructor for class org.proteios.core.DateParameterType
 
DateParameterValueData - Class in org.proteios.core.data
Date parameter value.
DateParameterValueData() - Constructor for class org.proteios.core.data.DateParameterValueData
 
DateParameterValueData(Date...) - Constructor for class org.proteios.core.data.DateParameterValueData
 
DateReader - Class in org.proteios.props
 
DateReader() - Constructor for class org.proteios.props.DateReader
 
DateUtil - Class in org.proteios.core
Utility methods that will make it easier to handle date values.
DateUtil() - Constructor for class org.proteios.core.DateUtil
 
DbControl - Class in org.proteios.core
A DbControl object is the main object used for communicating with the database.
dc - Variable in class org.proteios.io.mzdata.MzDataExpCommonDc
 
dc - Variable in class org.proteios.io.mzdata.MzDataImpCommonDc
 
decode(String) - Static method in class org.proteios.core.Base64Coder
Decodes a Base64 string.
decode(char[]) - Static method in class org.proteios.core.Base64Coder
Decodes Base64 data.
decode(String) - Static method in class org.proteios.io.Base64Util
Decodes Base64 coded data String and returns a String containing the extracted data.
decode(boolean, boolean, String, String) - Static method in class org.proteios.io.Base64Util
Decodes Base64 coded data String and returns an ArrayList containing the extracted data.
decode(boolean, boolean, boolean, String, String) - Static method in class org.proteios.io.Base64Util
Decodes Base64 coded data String and returns an ArrayList containing the extracted data.
decompress(ProgressReporter) - Method in class org.proteios.core.File
Decompress the file if stored on an internal disk.
DECYDER_BVA_XML - Static variable in class org.proteios.core.FileType
 
DEFAULT - Static variable in class org.proteios.core.Quota
The ID for the system default quota, which is assigned to new users unless another quota is specified.
DEFAULT_MAX_UNKNOWN_LINES - Static variable in class org.proteios.util.FlatFileParser
The default value for the number of unknown lines in a row that may be encountered by the parseHeaders method before it gives up.
DefaultAttributeFilter - Class in org.proteios.core
A filter for basic item attributes.
DefaultAttributeFilter() - Constructor for class org.proteios.core.DefaultAttributeFilter
 
delete(D) - Method in class org.proteios.core.BasicBatcher
Delete a data object.
delete(int) - Method in class org.proteios.core.BasicBatcher
Delete a data object by id.
delete() - Method in class org.proteios.core.LockFile
Deletes user lock file if it exists.
delete(DbControl, Item, Set<Integer>) - Static method in class org.proteios.util.RemovableUtil
 
deleteAllFeatures(Project, File, SessionControl) - Static method in class org.proteios.core.Feature
Will delete all features for a specific file and commit to the database
deleteItem(BasicItem) - Method in class org.proteios.core.DbControl
Schedule an existing item to be deleted from the database.
deleteUnusedKeys() - Static method in class org.proteios.core.ItemKey
Delete all keys that are currently not used by any item.
deleteUnusedKeys() - Static method in class org.proteios.core.ProjectKey
Delete all keys that are currently not used by any item.
desc(Expression) - Static method in class org.proteios.core.query.Orders
Sort the result of a query in descending order by the expression.
DescOrder - Class in org.proteios.core.query
Sort the result of a query in descending order by the expression.
description - Variable in class org.proteios.core.authentication.AuthenticationInformation
A description of the user.
DetachedItemException - Exception in org.proteios.core
This exception is thrown when trying to use an item that has been detached from the DbControl that manages it.
DetachedItemException(String) - Constructor for exception org.proteios.core.DetachedItemException
Creates a new DetachedItemException.
detachItem(BasicItem) - Method in class org.proteios.core.DbControl
Detach an item from this DbControl.
detectorItem(PeakListSet, Hardware) - Method in class org.proteios.io.mzdata.MzDataImpDetectorBlock
Creates a detector item.
Diff3 - Class in org.proteios.util
This class is helpful when a client application needs to implement long-running transactions and still be able to update items with as few clashes as possible.
Diff3(BasicItem, BasicItem) - Constructor for class org.proteios.util.Diff3
Create a new Diff3 object to compare properties of the oldItem and newItem.
DigestParameter - Class in org.proteios.core
This class represent spectrumsearch.
DigestParameterData - Class in org.proteios.core.data
This represents a digestion parameter.
DigestParameterData() - Constructor for class org.proteios.core.data.DigestParameterData
 
Directory - Class in org.proteios.core
This is used to represent directory items.
DirectoryData - Class in org.proteios.core.data
This class holds information about directories.
DirectoryData() - Constructor for class org.proteios.core.data.DirectoryData
 
disableForItem(Item) - Method in class org.proteios.core.AnnotationType
Disable this annotation type to be used for items of the specified type.
disconnect() - Method in class org.proteios.core.DbControl
Temporarily disconnect from the database.
DiskConsumable - Interface in org.proteios.core
This interface is implemented by items that can use a lot of disk space.
DiskConsumableData - Interface in org.proteios.core.data
A diskconsumable item is an item that occupies a lot of diskspace and should be controlled by the quota system.
DiskUsage - Class in org.proteios.core
This class is used to represent the disk usage of DiskConsumable items.
DiskUsageData - Class in org.proteios.core.data
This class holds information about a users and/or groups disk usage.
DiskUsageData() - Constructor for class org.proteios.core.data.DiskUsageData
Creates a new DiskUsageData.
display(int, String) - Method in interface org.proteios.core.ProgressReporter
Display a progress message.
display(int, String) - Method in class org.proteios.core.SimpleProgressReporter
 
display(int, String) - Method in class org.proteios.util.ChainedProgressReporter
 
display(int, String) - Method in class org.proteios.util.ConsoleProgressReporter
 
displayAbsolute(long, String) - Method in interface org.proteios.core.AbsoluteProgressReporter
Display a progress message.
displayAbsolute(long, String) - Method in class org.proteios.core.SimpleAbsoluteProgressReporter
Display a progress message.
divide(Expression, Expression) - Static method in class org.proteios.core.query.Expressions
Divide one expression by another: new expression = e1 / e2.
DivideExpression - Class in org.proteios.core.query
Divide one expression by another: e1 / e2.
doImport(InputStream, ProgressReporter) - Method in interface org.proteios.core.plugin.AutoDetectingImporter
Import the data from the given InputStream.
done() - Method in class org.proteios.core.plugin.AbstractPlugin
Clears the variables set by the init method.
done() - Method in interface org.proteios.core.plugin.Plugin
This method is called when the core is finished with the plugin object.
done(E) - Method in class org.proteios.io.TagFactory
Tries to find the method done(E) and calls it with the supplied object.
doneAborted(String) - Method in class org.proteios.core.Job
Register the job as aborted.
doneError(String) - Method in class org.proteios.core.Job
Register the job as completed with an error.
doneOk(String) - Method in class org.proteios.core.Job
Register the job as successfully completed.
DOUBLE - Static variable in class org.proteios.core.hibernate.TypeWrapper
 
DoubleParameterType - Class in org.proteios.core
This class represent a parameter type that is a double.
DoubleParameterType() - Constructor for class org.proteios.core.DoubleParameterType
Create a new double parameter type, without any limits and allowing null values.
DoubleParameterType(Double, Double, Double, boolean) - Constructor for class org.proteios.core.DoubleParameterType
Create a new double parameter type.
DoubleParameterType(Double, Double, Double, boolean, int, int, int, List<Double>) - Constructor for class org.proteios.core.DoubleParameterType
 
DoubleParameterValueData - Class in org.proteios.core.data
Double parameter value.
DoubleParameterValueData() - Constructor for class org.proteios.core.data.DoubleParameterValueData
 
DoubleParameterValueData(Double...) - Constructor for class org.proteios.core.data.DoubleParameterValueData
 
download(OutputStream, long) - Method in class org.proteios.core.File
Download the physical file for this file item.
DTA_PEAK_LIST - Static variable in class org.proteios.core.FileType
 
DynamicResultIterator - Class in org.proteios.core
An iterator view of the result of an AbstractSqlQuery.

E

elements(String, String) - Static method in class org.proteios.core.query.Hql
Create an elements expression for a property that is a collection of values.
email - Variable in class org.proteios.core.authentication.AuthenticationInformation
The email address to the user.
enableAnnotator(DbControl) - Method in class org.proteios.io.mzdata.MzDataExpCommonDc
Make sure that Annotator exists, and that the DbControl is attached to it.
enableDbControl() - Method in class org.proteios.io.mzdata.MzDataExpCommonDc
Make sure that DbControl is running.
enableDbControl(BasicItem) - Method in class org.proteios.io.mzdata.MzDataExpCommonDc
Make sure that DbControl is running, and that the item is attached to it.
enableDbControl() - Method in class org.proteios.io.mzdata.MzDataExporter
Make sure that DbControl is running.
enableDbControl(BasicItem) - Method in class org.proteios.io.mzdata.MzDataExporter
Make sure that DbControl is running, and that the item is attached to it.
enableDbControl() - Method in class org.proteios.io.mzdata.MzDataImpCommonDc
Make sure that DbControl is running.
enableDbControl(BasicItem) - Method in class org.proteios.io.mzdata.MzDataImpCommonDc
Make sure that DbControl is running, and that the item is attached to it.
enableDbControl() - Method in class org.proteios.io.mzdata.MzDataImporter
Make sure that DbControl is running.
enableDbControl(BasicItem) - Method in class org.proteios.io.mzdata.MzDataImporter
Make sure that DbControl is running, and that the item is attached to it.
enableForItem(Item) - Method in class org.proteios.core.AnnotationType
Enable this annotation type to be used for items of the specified type.
encode(String) - Static method in class org.proteios.core.Base64Coder
Encodes a string into Base64 format.
encode(byte[]) - Static method in class org.proteios.core.Base64Coder
Encodes a byte array into Base64 format.
encode(String) - Static method in class org.proteios.io.Base64Util
Encodes Base64 coded data String and returns a String containing the encoded data.
encode(boolean, boolean, List<? extends Number>) - Static method in class org.proteios.io.Base64Util
Encodes Base64 coded data list and returns a containing the encoded data.
endPosition - Variable in class org.proteios.core.data.PeptideData
 
entity(BasicItem) - Static method in class org.proteios.core.query.Hql
Create an expression representing an item.
EntityQuery - Interface in org.proteios.core.query
This a HQL query that return enitities, ie. items.
entries - Variable in class org.proteios.util.Enumeration
 
EntryDateReader - Class in org.proteios.props
 
EntryDateReader() - Constructor for class org.proteios.props.EntryDateReader
 
entryIterator() - Method in class org.proteios.util.Tree
Create an iterator for the three that returns entry object.
Enumeration<K,V> - Class in org.proteios.util
 
Enumeration() - Constructor for class org.proteios.util.Enumeration
 
Enumeration.Entry<K,V> - Class in org.proteios.util
 
EnumReader - Class in org.proteios.props
 
EnumReader() - Constructor for class org.proteios.props.EnumReader
 
eq(AnnotationType, Object, boolean) - Static method in class org.proteios.core.query.Annotations
Create a restriction that searches for annotations equal to a given value.
eq(Expression, Expression) - Static method in class org.proteios.core.query.Restrictions
Compare if two expressions are equal: new restriction = e1 == e2.
EqRestriction - Class in org.proteios.core.query
Compare if two expressions are equal: e1 == e2, or e1 IS NULL
equals(Object) - Method in class org.proteios.AttributeDefinition
A defined attribute is equal to another if the keys are the same.
equals(Object) - Method in class org.proteios.core.BasicItem
Check if this item is equal to another item.
equals(Object) - Method in class org.proteios.core.data.BasicData
Check if this item is equal to another item.
equals(Object) - Method in class org.proteios.core.data.GuiContextData
Check if this object is equal to another GuiContext object.
equals(Object) - Method in class org.proteios.core.data.keyring.GroupGroups
Check if this object is equal to another GroupGroups object.
equals(Object) - Method in class org.proteios.core.data.keyring.GroupKeys
Check if this object is equal to another GroupKeys object.
equals(Object) - Method in class org.proteios.core.data.keyring.GroupProjects
Check if this object is equal to another GroupProjects object.
equals(Object) - Method in class org.proteios.core.data.keyring.ProjectKeys
Check if this object is equal to another ProjectKeys object.
equals(Object) - Method in class org.proteios.core.data.keyring.RoleKeys
Check if this object is equal to another RoleKeys object.
equals(Object) - Method in class org.proteios.core.data.keyring.UserGroups
Check if this object is equal to another UserGroups object.
equals(Object) - Method in class org.proteios.core.data.keyring.UserKeys
Check if this object is equal to another UserKeys object.
equals(Object) - Method in class org.proteios.core.data.keyring.UserProjects
Check if this object is equal to another UserProjects object.
equals(Object) - Method in class org.proteios.core.data.keyring.UserRoles
Check if this object is equal to another UserRoles object.
equals(Object) - Method in class org.proteios.core.data.MappingCoordinate
Check if this object is equal to another MappingCoordinate object.
equals(Object) - Method in class org.proteios.core.data.QuotaIndex
Check if this object is equal to another QuotaIndex object.
equals(Object) - Method in class org.proteios.core.data.UsedQuantity
Check if this object is equal to another UsedQuantity object.
equals(Object) - Method in class org.proteios.core.ItemResultList
 
equals(Object) - Method in class org.proteios.util.Tree
Equality only tests if the object is the same instance of this tree.
error(SAXParseException) - Method in class org.proteios.io.XMLValidatorErrorHandler
Handles validation non-fatal errors.
error(SAXParseException) - Method in class org.proteios.io.XMLValidatorLazyErrorHandler
Handles validation non-fatal errors.
EventCommentReader - Class in org.proteios.props
 
EventCommentReader() - Constructor for class org.proteios.props.EventCommentReader
 
EventTypeReader - Class in org.proteios.props
 
EventTypeReader() - Constructor for class org.proteios.props.EventTypeReader
 
EVERYONE - Static variable in class org.proteios.core.Group
The id of the Everyone group where all users are (virtual) members.
exclude(Include...) - Method in interface org.proteios.core.query.EntityQuery
Specify options for which items to exclude from the result.
execute(ProgressReporter, String) - Method in class org.proteios.core.Job
Start the execution sequence for a job.
exists(DbControl, Directory, String) - Static method in class org.proteios.core.Directory
Checks if a subdirectory with the specified name exists in a directory.
exists(DbControl, Directory, String) - Static method in class org.proteios.core.File
Checks if a file with the specified name exists in the directory.
exists() - Method in class org.proteios.core.LockFile
Checks if the lock file exists.
exists(String) - Static method in class org.proteios.util.JarClassLoader
Check if a class loader for the given JAR file exists.
expect - Variable in class org.proteios.io.TandemFactory.ModelGroup
 
expect - Variable in class org.proteios.io.TandemFactory.Protein
 
EXPERIMENT - Static variable in class org.proteios.core.QuotaType
The ID for experiments.
export(int, String) - Method in class org.proteios.io.mzdata.MzDataExporter
Exports mzData in Proteios to an mzData XML file.
export(PeakListSet, String) - Method in class org.proteios.io.mzdata.MzDataExporter
Exports mzData in Proteios to an mzData XML file.
export(PeakListSet, File) - Method in class org.proteios.io.mzdata.MzDataExporter
Exports mzData in Proteios to mzData XML data in a core file.
export(PeakListSet, OutputStream) - Method in class org.proteios.io.mzdata.MzDataExporter
Exports mzData in Proteios to an OutputStream.
exportMascotParameterSet(MascotParameterSet) - Method in class org.proteios.io.MascotParameterFileUtil
Export MascotParameterSet item to output stream.
exportOMSSAParameterSet(OMSSAParameterSet) - Method in class org.proteios.io.OMSSAParameterFileUtil
Export OMSSAParameterSet item to output stream.
exportXTandemParameterSet(XTandemParameterSet) - Method in class org.proteios.io.XTandemParameterFileUtil
Export XTandemParameterSet item to output stream.
Expression - Interface in org.proteios.core.query
An expression query element.
expression(Expression, String) - Static method in class org.proteios.core.query.Selects
Create a selection from an expression, optionally giving it an alias.
Expressions - Class in org.proteios.core.query
A factory class to create expressions.
Expressions() - Constructor for class org.proteios.core.query.Expressions
 
ExpressionSelect - Class in org.proteios.core.query
A selection query element that selects an expression, optionally giving it an alias.
ExtendableData - Interface in org.proteios.core.data
This class is inherited by data classes that supports per-server additions of columns to the underlying database table.
ExtendedProperties - Class in org.proteios.core
This class is used for reading XML files with information about extended properties.
ExtendedProperties() - Constructor for class org.proteios.core.ExtendedProperties
 
ExtendedProperty - Class in org.proteios.core
Holds information about an extended property for a class.
ExtendedPropertyAccessor - Class in org.proteios.core
This class is used to interface with Hibernate for extended properties.
ExtendedPropertyAccessor() - Constructor for class org.proteios.core.ExtendedPropertyAccessor
 
ExtensionDisableInterface - Interface in org.proteios.io
This interface is used to retrieve the disabled flag for an extension.
ExternalIdReader - Class in org.proteios.props
 
ExternalIdReader() - Constructor for class org.proteios.props.ExternalIdReader
 
Extract - Class in org.proteios.core
This class is used to represent extract items.
ExtractData - Class in org.proteios.core.data
This represents an extract.
ExtractData() - Constructor for class org.proteios.core.data.ExtractData
 
EXTRACTION - Static variable in class org.proteios.core.ProtocolType
The ID for the extraction protocol type, for example a protocol used when creating an Extract from a Sample.

F

factory - Variable in class org.proteios.io.mzdata.MzDataExpCommonDc
 
factory - Variable in class org.proteios.io.mzdata.MzDataImpCommonDc
 
fatalError(SAXParseException) - Method in class org.proteios.io.XMLValidatorErrorHandler
Handles validation fatal errors.
fatalError(SAXParseException) - Method in class org.proteios.io.XMLValidatorLazyErrorHandler
Handles validation fatal errors.
fax - Variable in class org.proteios.core.authentication.AuthenticationInformation
The fax number to the user.
Feature - Class in org.proteios.core
Represents information about features from an LC-MS run, as picked by a feature extraction algorithm.
FEATURE_EXTRACTION - Static variable in class org.proteios.core.ProtocolType
The ID for the feature extraction protocol type, for example a protocol used for analysing one or more images to create a raw data file.
FEATURE_EXTRACTION - Static variable in class org.proteios.core.SoftwareType
The id for the SoftwareType item representing the softwaretype "feature extraction software".
FeatureData - Class in org.proteios.core.data
Represents information about features from an LC-MS run.
FeatureData() - Constructor for class org.proteios.core.data.FeatureData
 
fetchAddedParamAnnotationType(String, Type, Item, String, String, String) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Fetches added parameter annotation type for storing variable values as annotations.
fetchAnalyzerAnnotations(HardwareConfiguration) - Method in class org.proteios.io.mzdata.MzDataExpAnalyzerBlock
Fetches variable values stored as annotations for analyzer.
fetchAnnotation(AnnotationSet, String, Type, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Fetches annotation value from annotation for given annotation type.
fetchAttribute(Hashtable<String, String>, String) - Method in class org.proteios.io.MascotParameterFileUtil
Convenience method to get an XML tag attribute for an XML tag value from a hash table.
fetchAttribute(Hashtable<String, String>, String) - Method in class org.proteios.io.OMSSAParameterFileUtil
Convenience method to get an XML tag attribute for an XML tag value from a hash table.
fetchBasename(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the basename from a filename, i.e. part of the filename before an optional file extension separated by a dot ".".
fetchBaseString(String, String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the base string from an input string given a separation string.
fetchConfiguration(User) - Method in class org.proteios.io.NotificationConfiguration
Fetches notification configurations that have not been explicitly set in this class from properties files and other sources.
fetchConfiguration(User) - Method in class org.proteios.io.TablePreferencesConfiguration
Fetches table preferences configurations that have not been explicitly set in this class from properties files and other sources.
fetchCounter(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the counter string from filename, i.e. part of the filename after the target id and date, excluding the position, e.g. filename "FL1_060306_2@A1.txt" will give counter "2".
fetchCvLookupAnnotation(AnnotationSet, String, Type, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Fetches annotation value from annotation for given cvLookup annotation type.
fetchCvLookupAnnotation(AnnotationSet, String, Type, DbControl) - Method in class org.proteios.io.mzdata.MzDataImpCommonAnnotation
Fetches annotation value from annotation for given cvLookup annotation type.
fetchCvLookupAnnotationList(AnnotationSet, Type, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Fetches list of cvLookup type annotations.
fetchCvLookupAnnotationList(AnnotationSet, Type, DbControl) - Method in class org.proteios.io.mzdata.MzDataImpCommonAnnotation
Fetches list of cvLookup type annotations.
fetchCvLookupAnnotationType(String, Type, Item, String, String) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Fetches cvLookup annotation type for storing variable values as annotations.
fetchCvParamAnnotation(AnnotationSet, String, Type, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Fetches annotation value from annotation for given cvParam annotation type.
fetchCvParamAnnotation(AnnotationSet, String, Type, DbControl) - Method in class org.proteios.io.mzdata.MzDataImpCommonAnnotation
Fetches annotation value from annotation for given cvParam annotation type.
fetchCvParamAnnotationList(AnnotationSet, Type, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Fetches list of cvParam type annotations.
fetchCvParamAnnotationList(AnnotationSet, Type, DbControl) - Method in class org.proteios.io.mzdata.MzDataImpCommonAnnotation
Fetches list of cvParam type annotations.
fetchDataFormatAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Data format alternatives list, key=
fetchDataFormatStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches data format string list with alternating key and value strings.
fetchDataProcessingStepAnnotations(DataProcessingStep) - Method in class org.proteios.io.mzdata.MzDataExpProcessingMethodBlock
Fetches variable values stored as annotations for dataProcessingStep.
fetchDataProcessingStepAnnotations(DataProcessingStep) - Method in class org.proteios.io.mzdata.MzDataExpSoftwareBlock
Fetches variable values stored as annotations for dataProcessingStep.
fetchDate(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the date from filename, i.e. part of the filename after the target id starting with a number character, e.g. filename "FL1_060306_2@A1.txt" will give date "060306".
fetchEnzymeAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Enzyme alternatives list, key=
fetchEnzymeAlternativesList() - Method in class org.proteios.io.OMSSAParameterFileUtil
Enxyme alternatives list, key=
fetchEnzymeAttributeHashtable() - Method in class org.proteios.io.OMSSAParameterFileUtil
Enzyme attribute hash table, key=, value=
fetchEnzymeStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches enzyme string list with alternating key and value strings.
fetchEnzymeStringList() - Method in class org.proteios.io.OMSSAParameterSetOptionsUtil
Fetches enzyme string list with alternating key and value strings.
fetchExperimenter(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the experimenter from filename, i.e. part of the target id before any number characters, e.g. filename "FL1_060306_2@A1.txt" will give experimenter "FL".
fetchExperimenterFromTarget(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the experimenter from a target id, i.e. part of the target id before any number characters, e.g. target id "FL1" will give experimenter "FL".
fetchExtensionDisabledFlag() - Method in interface org.proteios.io.ExtensionDisableInterface
 
fetchFileExtension(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the file extension from a filename, i.e. part of the filename after an optional separation dot ".".
fetchFileTypeStringList() - Method in class org.proteios.io.OMSSAParameterSetOptionsUtil
Fetches file type string list with alternating key and value strings.
fetchFirstNonNumCharIndex(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the position index of the first non-numerical character in a string.
fetchFirstNumCharIndex(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the position index of the first numerical character in a string.
fetchInstrumentAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Instrument alternatives list, key=
fetchInstrumentStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches instrument string list with alternating key and value strings.
fetchIonTypeAlternativesList() - Method in class org.proteios.io.OMSSAParameterFileUtil
Ion type alternatives list, key=
fetchIonTypeAttributeHashtable() - Method in class org.proteios.io.OMSSAParameterFileUtil
Ion type attribute hash table, key=, value=
fetchIonTypeStringList() - Method in class org.proteios.io.OMSSAParameterSetOptionsUtil
Fetches ion type string list with alternating key and value strings.
fetchLastNonNumCharIndex(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the position index of the last non-numerical character in a string.
fetchLastNumCharIndex(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the position index of the last numerical character in a string.
fetchListPathDefaultParametersStringList() - Method in class org.proteios.io.XTandemParameterSetOptionsUtil
Fetches list path default parameters string list with alternating key and value strings.
fetchLoggedInUserIdList() - Static method in class org.proteios.core.Application
Fetch a copy of the list of logged-in user id values.
fetchMascotParameterSet() - Method in class org.proteios.core.MascotParameterSetStorage
Fetch MascotParameterSet from existing parameter file item.
fetchMascotParameterSet() - Method in class org.proteios.io.MascotParameterFileUtil
Fetch MascotParameterSet item from input stream.
fetchMascotSearchProperties() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches Mascot search constants from Properties file.
fetchMascotStringListFromLocalInstallation(String) - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches Mascot string list with alternating key and value strings from locally installed search engine.
fetchMascotStringListFromWebInterface(String) - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches Mascot string list with alternating key and value strings.
fetchMassIonTypeAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Mass ion type alternatives list, key=
fetchMassIonTypeAttributeHashtable() - Method in class org.proteios.io.MascotParameterFileUtil
Mass ion type attribute hash table, key=, value=
fetchMassIonTypeStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches mass ion type string list with alternating key and value strings.
fetchMassTypeAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Mass type alternatives list, key=
fetchMassTypeStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches mass type string list with alternating key and value strings.
fetchMissedCleavagesAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Missed cleavages alternatives list, key=
fetchMissedCleavagesStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches missed cleavages string list with alternating key and value strings.
fetchModificationAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Modification alternatives list, key=
fetchModificationAlternativesList() - Method in class org.proteios.io.OMSSAParameterFileUtil
Modification alternatives list, key=
fetchModificationAttributeHashtable() - Method in class org.proteios.io.OMSSAParameterFileUtil
Modification attribute hash table, key=, value= Note that this hash table, that was obtained from the OMSSA web search HTML form, has the following gaps in the numerical key sequence up till key 165: 119-128, 142-161.
fetchModificationStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches modification string list with alternating key and value strings.
fetchModificationStringList() - Method in class org.proteios.io.OMSSAParameterSetOptionsUtil
Fetches modification string list with alternating key and value strings.
fetchMsMsTolUnitAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
MS-MS tolerance unit alternatives list, key=
fetchMsMsTolUnitStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches MS-MS tolerance unit string list with alternating key and value strings.
fetchNameAttribute(int, XMLStreamReader) - Static method in class org.proteios.io.XMLImportUtil
Fetches a specific "name" part from attributes, where the name attribute index is given (starting from 0).
fetchNameWithTimeStamp(String, String) - Method in class org.proteios.io.FileExtraUtil
Creates name with time stamp in format: prefix + yyyymmdd_hhmmss + suffix.
fetchNonPositionName(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the pure basename excluding plate position from a filename, i.e. part of the filename before any optional dot "." and "@" characters, e.g. filename "FL1_060306_2@A1.txt" will give "FL1_060306_1".
fetchOMSSAParameterSet() - Method in class org.proteios.core.OMSSAParameterSetStorage
Fetch OMSSAParameterSet from existing parameter file item.
fetchOMSSAParameterSet() - Method in class org.proteios.io.OMSSAParameterFileUtil
Fetch OMSSAParameterSet item from input stream.
fetchOMSSASearchProperties() - Method in class org.proteios.io.OMSSAParameterSetOptionsUtil
Fetches OMSSA search constants from Properties file.
fetchOMSSAStringListFromLocalInstallation(String) - Method in class org.proteios.io.OMSSAParameterSetOptionsUtil
Fetches OMSSA string list with alternating key and value strings from locally installed search engine.
fetchOMSSAStringListFromWebInterface(String) - Method in class org.proteios.io.OMSSAParameterSetOptionsUtil
Fetches OMSSA string list with alternating key and value strings.
fetchOptionalVersionMarker() - Static method in class org.proteios.core.Application
Fetch the optional version marker of Proteios.
fetchPartAfterEndCut(String, String, boolean, boolean) - Method in class org.proteios.io.FilenameParseUtil
Fetches the first or last part of an input string, after it has been cut in two pieces by the first or last occurrence of a separation string.
fetchPeakListAnnotations(PeakList, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpAcqSpecificationBlock
Fetches variable values stored as annotations for peakList.
fetchPeakListAnnotations(PeakList, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpSpectrumBlock
Fetches variable values stored as annotations for peakList.
fetchPeakListAnnotations(PeakList, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpSpectrumInstrumentBlock
Fetches variable values stored as annotations for peakList.
fetchPeakListAnnotations(PeakList, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpSpectrumSettingsBlock
Fetches variable values stored as annotations for peakList.
fetchPeakListSetAnnotations(PeakListSet) - Method in class org.proteios.io.mzdata.MzDataExpContactBlock
Fetches variable values stored as annotations for peakListSet.
fetchPeakListSetAnnotations(PeakListSet, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpDetectorBlock
Fetches variable values stored as annotations for detector.
fetchPeakListSetAnnotations(PeakListSet, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpMzDataBlock
Fetches variable values stored as annotations for peakListSet.
fetchPeakListSetAnnotations(PeakListSet, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpSourceBlock
Fetches variable values stored as annotations for ionisationSource.
fetchPeakListSetAnnotations(PeakListSet) - Method in class org.proteios.io.mzdata.MzDataExpSourceFileBlock
Fetches variable values stored as annotations for peakListSet.
fetchPeptideChargeAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Peptide charge alternatives list, key=
fetchPeptideChargeStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches peptide charge string list with alternating key and value strings.
fetchPeptideIsotopeErrorAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Peptide isotope error alternatives list, key=
fetchPeptideIsotopeErrorStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches peptide isotope error string list with alternating key and value strings.
fetchPeptideTolUnitAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Peptide tolerance unit alternatives list, key=
fetchPeptideTolUnitStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches peptide tolerance unit string list with alternating key and value strings.
fetchPlatePosition(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the plate position from filename, i.e. part of the basename after an "@" character, e.g. filename "FL1_060306_2@A1.txt" will give "A1".
fetchPrecursorAnnotations(Precursor, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpActivationBlock
Fetches variable values stored as annotations for precursor.
fetchPrecursorAnnotations(Precursor, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpIonSelectionBlock
Fetches variable values stored as annotations for precursor.
fetchProjectDirectoryId() - Method in class org.proteios.core.Project
Fetches the project directory id.
fetchProSpeciesStringList() - Method in class org.proteios.io.XTandemParameterSetOptionsUtil
Fetches Prokaryotes species string list with alternating key and value strings.
fetchProteinCleavageSiteStringList() - Method in class org.proteios.io.XTandemParameterSetOptionsUtil
Fetches protein cleavage site string list with alternating key and value strings.
fetchPureBasename(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the pure basename from a filename, i.e. part of the filename before any optional dots ".".
fetchPureBaseString(String, String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the pure base string from an input string given a separation string.
fetchPureFileExtension(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the pure file extension from a filename, i.e. part of the filename after any optional dots ".".
fetchPureResidueString(String, String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the pure residue string from an input string given a separation string.
fetchQuantitationAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Quantitation alternatives list, key=
fetchQuantitationStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches quantitation string list with alternating key and value strings.
fetchRefinePotentialModificationMass1StringList() - Method in class org.proteios.io.XTandemParameterSetOptionsUtil
Fetches refine potential modification mass 1 string list with alternating key and value strings.
fetchRefinePotentialModificationMassStringList() - Method in class org.proteios.io.XTandemParameterSetOptionsUtil
Fetches refine potential modification mass string list with alternating key and value strings.
fetchRegexResult(String, String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the resulting string after parsing an input string with an input regex pattern.
fetchReportTopAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Report top alternatives list, key=
fetchReportTopStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches report top string list with alternating key and value strings.
fetchResidueModificationMassStringList() - Method in class org.proteios.io.XTandemParameterSetOptionsUtil
Fetches residue modification mass string list with alternating key and value strings.
fetchResiduePotentialModificationMassStringList() - Method in class org.proteios.io.XTandemParameterSetOptionsUtil
Fetches residue potential modification mass string list with alternating key and value strings.
fetchResidueString(String, String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the residue string from an input string given a separation string.
fetchSampleNameFromPeakListSetAnnotations(PeakListSet) - Method in class org.proteios.io.mzdata.MzDataExpSampleNameBlock
Fetches variable values stored as annotations for peakListSet.
fetchSampleNameFromSampleItem(PeakListSet) - Method in class org.proteios.io.mzdata.MzDataExpSampleNameBlock
Fetches sample name from Sample item.
fetchSearchTypeAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Search type alternatives list, key=
fetchSearchTypeAlternativesList() - Method in class org.proteios.io.OMSSAParameterFileUtil
Search type alternatives list, key=
fetchSearchTypeAttributeHashtable() - Method in class org.proteios.io.MascotParameterFileUtil
Search type attribute hash table, key=, value=
fetchSearchTypeAttributeHashtable() - Method in class org.proteios.io.OMSSAParameterFileUtil
Search type attribute hash table, key=, value=
fetchSequenceLibraryAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Sequence library alternatives list, key=
fetchSequenceLibraryStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches sequence library (database) string list with alternating key and value strings.
fetchSequenceLibraryStringList() - Method in class org.proteios.io.OMSSAParameterSetOptionsUtil
Fetches sequence library (database) string list with alternating key and value strings.
fetchSpeciesAlternativesList() - Method in class org.proteios.io.MascotParameterFileUtil
Species alternatives list, key=
fetchSpeciesAlternativesList() - Method in class org.proteios.io.OMSSAParameterFileUtil
Species alternatives list, key=
fetchSpeciesAttributeHashtable() - Method in class org.proteios.io.OMSSAParameterFileUtil
Species attribute hash table, key=, value= This hash table was obtained from the OMSSA web search HTML form.
fetchSpeciesStringList() - Method in class org.proteios.io.MascotParameterSetOptionsUtil
Fetches species string list with alternating key and value strings.
fetchSpeciesStringList() - Method in class org.proteios.io.OMSSAParameterSetOptionsUtil
Fetches species string list with alternating key and value strings.
fetchSpeciesStringList() - Method in class org.proteios.io.XTandemParameterSetOptionsUtil
Fetches Eukaryotes species string list with alternating key and value strings.
fetchTargetId(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the target id from a filename, i.e. part of the filename before any optional underscore "_", dot "
fetchTargetIdFromSHWFilename(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the target id from a Spot Handling Worksatation (SHW) filename, i.e. part of the filename after string "18115042" and before any optional underscore "_", dot "
fetchTargetNumber(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the target number from filename, i.e. part of the target id starting with a number character, e.g. filename "FL1_060306_2@A1.txt" will give target number "1".
fetchTargetNumberFromTarget(String) - Method in class org.proteios.io.FilenameParseUtil
Fetches the target number from a target id, i.e. part of the target id starting with a number character, e.g. target id "FL1" will give target number "1".
fetchUserLoginTime(int) - Static method in class org.proteios.core.Application
Fetch user login time, or null if user not logged in.
fetchUserParamAnnotation(AnnotationSet, String, Type, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Fetches annotation value from annotation for given userParam annotation type.
fetchUserParamAnnotation(AnnotationSet, String, Type, DbControl) - Method in class org.proteios.io.mzdata.MzDataImpCommonAnnotation
Fetches annotation value from annotation for given userParam annotation type.
fetchUserParamAnnotationList(AnnotationSet, Type, DbControl) - Method in class org.proteios.io.mzdata.MzDataExpCommonAnnotation
Fetches list of userParam type annotations.
fetchUserParamAnnotationList(AnnotationSet, Type, DbControl) - Method in class org.proteios.io.mzdata.MzDataImpCommonAnnotation
Fetches list of userParam type annotations.
fetchUserTimeSinceLastAccessInMilliSeconds(int) - Static method in class org.proteios.core.Application
Fetch the time since last access for the user in milliseconds.
fetchVersionString() - Static method in class org.proteios.core.Application
Fetch the Proteios SE version string.
fetchXTandemParameterSet() - Method in class org.proteios.core.XTandemParameterSetStorage
Fetch XTandemParameterSet from existing parameter file item.
fetchXTandemParameterSet() - Method in class org.proteios.io.XTandemParameterFileUtil
Fetch XTandemParameterSet item from input stream.
fetchXTandemSearchProperties() - Method in class org.proteios.io.XTandemParameterSetOptionsUtil
Fetches X!
fetchZDependenceAlternativesList() - Method in class org.proteios.io.OMSSAParameterFileUtil
Z dependence alternatives list, key=
fetchZDependenceAttributeHashtable() - Method in class org.proteios.io.OMSSAParameterFileUtil
Z dependence attribute hash table, key=, value=
File - Class in org.proteios.core
This class is used to represent individual file items and information about them.
FILE - Static variable in class org.proteios.core.QuotaType
The ID for the file.
File.Action - Enum in org.proteios.core
A fileaction describes if a file should be moved to secondary storage or brought back from it.
FileAttachable - Interface in org.proteios.core
A FileAttachable item is an item that can have a File attached to it.
FileAttachableData - Interface in org.proteios.core.data
A fileattachable item is an item which can have a File attached to it.
FileAttributeFilter - Class in org.proteios.core
A filter for file item attributes.
FileAttributeFilter() - Constructor for class org.proteios.core.FileAttributeFilter
 
FileCrudeWriter - Interface in org.proteios.io
This interface defines crude file writing to a Proteios SE core file.
FileCrudeWriterImpl - Class in org.proteios.io
This class supports crude file writing.
FileCrudeWriterImpl(OutputStream) - Constructor for class org.proteios.io.FileCrudeWriterImpl
Constructor that takes an output stream as parameter.
FileData - Class in org.proteios.core.data
This class holds information about a file.
FileData() - Constructor for class org.proteios.core.data.FileData
 
FileExtraUtil - Class in org.proteios.io
 
FileExtraUtil() - Constructor for class org.proteios.io.FileExtraUtil
Default constructor.
FileExtraUtil(SessionControl) - Constructor for class org.proteios.io.FileExtraUtil
Constructor setting the SessionControl.
FilenameParseUtil - Class in org.proteios.io
This class supports simple extraction of data from filenames.
FilenameParseUtil() - Constructor for class org.proteios.io.FilenameParseUtil
Default constructor.
FileNode - Class in org.proteios.core
FileNode's are used to connect files in projects.
FileNode(String) - Constructor for class org.proteios.core.FileNode
 
FileNode(File) - Constructor for class org.proteios.core.FileNode
 
FileParameterType - Class in org.proteios.core
This class represent a parameter type that is a file.
FileParameterType() - Constructor for class org.proteios.core.FileParameterType
Create a new file parameter type, allowing null values.
FileParameterType(File, boolean, int) - Constructor for class org.proteios.core.FileParameterType
Create a new file parameter type.
FileParameterValueData - Class in org.proteios.core.data
File parameter value.
FileParameterValueData() - Constructor for class org.proteios.core.data.FileParameterValueData
 
FileParameterValueData(FileData...) - Constructor for class org.proteios.core.data.FileParameterValueData
 
FileType - Class in org.proteios.core
This class is used to represent the type of File items in Proteios.
FileTypeData - Class in org.proteios.core.data
This class hols information about the different filetyped
FileTypeData() - Constructor for class org.proteios.core.data.FileTypeData
 
FileTypeInterface - Interface in org.proteios.io
This interface is used to get the file type a class i working on
FileTypeNameReader - Class in org.proteios.props
 
FileTypeNameReader() - Constructor for class org.proteios.props.FileTypeNameReader
 
FileUtil - Class in org.proteios.util
This class collects some useful methods for file and stream handling.
FileUtil() - Constructor for class org.proteios.util.FileUtil
 
FileValidationInterface - Interface in org.proteios.io
 
finalize() - Method in class org.proteios.core.DbControl
Clean up if a bad client application forgot to close the connection.
finalize() - Method in class org.proteios.core.SessionControl
Clean up if a bad client application forgets to logout.
findBasePeakIntensity() - Method in class org.proteios.core.PeakList
Find the most intense peak in this peaklist and return the intensity
findClass(String) - Method in class org.proteios.util.JarClassLoader
 
findConstructor(Class<I>, Object[]) - Static method in class org.proteios.util.ClassUtil
Find a constructor for the specified class which takes parameters of the specified types taking superclasses and interfaces into account.
findResource(String) - Method in class org.proteios.util.JarClassLoader
 
FlatFileParser - Class in org.proteios.util
This class can be used to parse data from flat text files.
FlatFileParser() - Constructor for class org.proteios.util.FlatFileParser
Create a new FlatFileParser object.
FlatFileParser.Data - Class in org.proteios.util
This class holds data about a line parsed by the FlatFileParser.hasMoreData() method.
FlatFileParser.Line - Class in org.proteios.util
This class holds data about a line parsed by the FlatFileParser.parseHeaders() method.
FlatFileParser.LineType - Enum in org.proteios.util
 
FLOAT - Static variable in class org.proteios.core.hibernate.TypeWrapper
 
FloatExpression - Class in org.proteios.core.query
A constant float expression.
FloatParameterType - Class in org.proteios.core
This class represent a parameter type that is a float.
FloatParameterType() - Constructor for class org.proteios.core.FloatParameterType
Create a new float parameter type, without any limits and allowing null values.
FloatParameterType(Float, Float, Float, boolean) - Constructor for class org.proteios.core.FloatParameterType
Create a new float parameter type.
FloatParameterType(Float, Float, Float, boolean, int, int, int, List<Float>) - Constructor for class org.proteios.core.FloatParameterType
 
FloatParameterValueData - Class in org.proteios.core.data
Float parameter value.
FloatParameterValueData() - Constructor for class org.proteios.core.data.FloatParameterValueData
 
FloatParameterValueData(Float...) - Constructor for class org.proteios.core.data.FloatParameterValueData
 
flush() - Method in class org.proteios.core.BasicBatcher
 
flush() - Method in interface org.proteios.core.Batcher
Flush the batcher and send all remaining items in memory to the database.
flush() - Method in interface org.proteios.io.FileCrudeWriter
Flushes output stream.
flush() - Method in class org.proteios.io.FileCrudeWriterImpl
Flushes output stream.
flush() - Method in interface org.proteios.io.XMLCrudeWriter
Flushes output stream.
flush() - Method in class org.proteios.io.XMLCrudeWriter3Impl
Flushes output stream.
flush() - Method in class org.proteios.io.XMLCrudeWriterImpl
Flushes output stream.
flushDelete() - Method in class org.proteios.core.BasicBatcher
Flush the SQL delete command buffer.
flushInsert() - Method in class org.proteios.core.BasicBatcher
Flush the SQL insert command buffer.
flushUpdate() - Method in class org.proteios.core.BasicBatcher
Flush the SQL insert command buffer.
formatBytes(Long) - Static method in class org.proteios.util.Values
Formats a value using units of bytes, kilobytes, megabytes or gigabytes.
formatDate(Date) - Static method in class org.proteios.util.Values
Formats a date as four-digit year, two-digit month and two-digit day separated with a hyphen.
formatDateTime(Date) - Static method in class org.proteios.util.Values
Formats a date as four-digit year, two-digit month and two-digit day separated with a hyphen and a time as two-digit hour, minute and seconds separated with a colon.
formatMessage(String, Object...) - Static method in class org.proteios.util.Values
Insert the values of parameters into a template message.
formatNumber(Float, int) - Static method in class org.proteios.util.Values
Formats a decimal number with the specified number of decimals.
formatNumber(Float, int, String) - Static method in class org.proteios.util.Values
Formats a decimal number with the specified number of decimals and optionally adding a unit.
formatTime(Date) - Static method in class org.proteios.util.Values
Formats a time as two-digit hour, two-digit minute and two-digit seconds separated with a colon.
formatTime(long) - Static method in class org.proteios.util.Values
Formats a number of seconds to a more proper time format.
formulaToExpression(String, JepFunction...) - Static method in class org.proteios.util.jep.Jep
Convert JEP expression to a Query API Expression.
formulaToRestriction(String, JepFunction...) - Static method in class org.proteios.util.jep.Jep
Convert JEP expression to a Query API Restriction.
fromAbbreviation(String) - Static method in enum org.proteios.io.SpectrumPrecursor.FragmentationType
Get the SpectrumPrecursor.FragmentationType object when you know the abbreviation string.
fromClass(Class<?>) - Static method in enum org.proteios.core.Item
Get the Item object when you know either the item or data class.
fromDataClass(Class<? extends BasicData>) - Static method in enum org.proteios.core.Item
Get the Item object when you know the data class.
fromDataObject(BasicData) - Static method in enum org.proteios.core.Item
Get the Item object when you have a data layer object.
fromDisplayValue(String) - Static method in enum org.proteios.io.SpectrumPrecursor.FragmentationType
Get the SpectrumPrecursor.FragmentationType object when you know the displayValue string.
fromItemClass(Class<? extends BasicItem>) - Static method in enum org.proteios.core.Item
Get the Item object when you know the item class.
fromMsOntologyAccessionNumber(String) - Static method in enum org.proteios.io.SpectrumPrecursor.FragmentationType
Get the SpectrumPrecursor.FragmentationType object when you know the msOntologyAccessionNumber string.
fromValue(int) - Static method in enum org.proteios.core.File.Action
Get the File.Action object when you know the integer code.
fromValue(int) - Static method in enum org.proteios.core.Item
Get the Item object when you know the integer code.
fromValue(int) - Static method in enum org.proteios.core.Job.ExecutionTime
Get the Job.Status object when you know the integer code.
fromValue(int) - Static method in enum org.proteios.core.Job.Status
Get the Job.Status object when you know the integer code.
fromValue(int) - Static method in enum org.proteios.core.Job.Type
Get the Job.Status object when you know the integer code.
fromValue(int) - Static method in enum org.proteios.core.Location
Get the Location object when you know the integer code.
fromValue(int) - Static method in enum org.proteios.core.Operator
Get the Operator object when you know the integer code.
fromValue(int) - Static method in enum org.proteios.core.plugin.GuiContext.Type
Get the GuiContext.Type object when you know the integer code.
fromValue(int) - Static method in enum org.proteios.core.plugin.Plugin.MainType
 
fromValue(int) - Static method in enum org.proteios.core.Type
Get the Type object when you know the integer code.
fromValue(String) - Static method in enum org.proteios.core.Type
Get the Type object when you know the string value.
fromValue(int) - Static method in enum org.proteios.io.NotificationConfiguration.Mode
Get the NotificationConfiguration.Mode object when you know the integer code.
fromValue(int) - Static method in enum org.proteios.io.SpectrumPrecursor.FragmentationType
Get the SpectrumPrecursor.FragmentationType object when you know the integer value.
fromValue(int) - Static method in enum org.proteios.io.TablePreferencesConfiguration.Mode
Get the TablePreferencesConfiguration.Mode object when you know the integer code.

G

GelElectrophoresis - Class in org.proteios.core
This class represent gel electrophoresis items.
GelElectrophoresisData - Class in org.proteios.core.data
This represents a gel object which is generated by a separation event.
GelElectrophoresisData() - Constructor for class org.proteios.core.data.GelElectrophoresisData
 
GelImageAnalysisEvent - Class in org.proteios.core
This class represent GelImageAnalysisEvent items.
GelImageAnalysisEventData - Class in org.proteios.core.data
This represents a GelImageAnalysisEventData which is a starting point of a MeasuredItem.
GelImageAnalysisEventData() - Constructor for class org.proteios.core.data.GelImageAnalysisEventData
 
GelScanEvent - Class in org.proteios.core
This class represent GelScanEvent items.
GelScanEventData - Class in org.proteios.core.data
This class represent GelScanEvent items.
GelScanEventData() - Constructor for class org.proteios.core.data.GelScanEventData
 
generateRandomId(int) - Static method in class org.proteios.core.Application
Generate a random id.
get(int) - Method in class org.proteios.core.ItemResultList
Get a BasicItem derived object.
get(int, String) - Method in interface org.proteios.core.query.SqlResultList
 
get(int, int) - Method in interface org.proteios.core.query.SqlResultList
 
get(OBJECT_TEMPLATE) - Method in class org.proteios.props.AbstractReader
 
get(OBJECT_TEMPLATE) - Method in interface org.proteios.props.AttributeReader
 
get(Job) - Method in class org.proteios.props.JobStatusReader
 
get(Object) - Method in class org.proteios.util.ClassLocal
Get the object associated with the class of the specified instance.
get(int) - Method in class org.proteios.util.FlatFileParser.Data
Get the value in the specified column.
getAbbreviation() - Method in enum org.proteios.io.SpectrumPrecursor.FragmentationType
Get the abbreviation for a SpectrumPrecursor.FragmentationType.
getAbortableJobQueue() - Method in class org.proteios.core.Job
Get the abortable job queue used for the job.
getAbortableJobQueue(int) - Static method in class org.proteios.core.JobQueueManager
Get a read-only copy of the abortable job queue for a job with specific id.
getAbortedJobIdList() - Method in interface org.proteios.core.AbortableJobQueueReadOnlyInterface
Get the aborted job id list.
getAbout() - Method in interface org.proteios.core.plugin.Plugin
Get information about the plugin, such as name, version, authors, etc.
getAccession() - Method in class org.proteios.io.mzdata.CvParam
Get the accession.
getAccession_number() - Method in class org.proteios.core.LsidElement
hibernate.property column="`accession_number`"
getAccessionNumber() - Method in class org.proteios.core.data.PolyPeptideData
 
getAccessionNumber() - Method in class org.proteios.core.PolyPeptide
Get the accessionNumber of the polypeptide.
getAccessionNumber() - Method in class org.proteios.io.mzdata.MzDataImpAdminBlock
Get the source file accessionNumber.
getAccessionNumber() - Method in class org.proteios.io.mzdata.MzDataImpSourceFileBlock
Get the source file accessionNumber.
getAcqNumber() - Method in class org.proteios.core.Acquisition
Get the acquisition number.
getAcqNumber() - Method in class org.proteios.core.data.AcquisitionData
Get the acquisition number.
getAcquisitionInstrumentInfo() - Method in class org.proteios.core.Acquisition
Get the InstrumentConfiguration acquisitionInstrumentInfo.
getAcquisitionInstrumentInfo() - Method in class org.proteios.core.data.AcquisitionData
Get the acquisitionInstrumentInfo
getAcquisitionList() - Method in class org.proteios.core.data.PeakListData
Get the acquisitionList.
getAcquisitionList() - Method in class org.proteios.core.PeakList
Get the Acquisition acquisitionList.
getAcquisitionsQuery() - Method in class org.proteios.core.PeakList
Get a query that returns all Acquisition items created from this peaklist.
getAction() - Method in class org.proteios.core.data.FileData
Get the value of the action variable for this FileData object.
getAction() - Method in class org.proteios.core.File
Get the File.Action of this file.
getActivation() - Method in class org.proteios.core.data.PrecursorData
Get the activation
getActivation() - Method in class org.proteios.core.Precursor
Get the InstrumentConfiguration activation.
getActiveProjectId() - Method in class org.proteios.core.data.JobData
The ID of the project that should be made active when running this job.
getActiveProjectId() - Method in class org.proteios.core.Job
The ID of the project that should be made the active project while running this job.
getActiveProjectId() - Method in class org.proteios.core.SessionControl
Get the id of the active project, or 0 if no project is active.
getAddedParamAnnotationType(String, Type, Item, String, String, String) - Method in class org.proteios.core.Annotator
Fetches annotation type for storing variable values as annotations.
getAddedParameterName() - Method in class org.proteios.core.AnnotationType
Get the addedParameterName value.
getAddedParameterName() - Method in class org.proteios.core.data.AnnotationTypeData
Get the addedParameterName value.
getAddedParameterType() - Method in class org.proteios.core.AnnotationType
Get the addedParameterType value.
getAddedParameterType() - Method in class org.proteios.core.data.AnnotationTypeData
Get the addedParameterType value.
getAddedParameterValue() - Method in class org.proteios.core.AnnotationType
Get the addedParameterValue value.
getAddedParameterValue() - Method in class org.proteios.core.data.AnnotationTypeData
Get the addedParameterValue value.
getAdditional() - Method in class org.proteios.io.SpectrumFileInstrument
Get the spectrum instrument additional data.
getAdditional() - Method in interface org.proteios.io.SpectrumFileInstrumentInterface
Get the spectrum instrument additional data.
getAddress() - Method in class org.proteios.core.data.UserData
Get the address for the user, or null if unknown.
getAddress() - Method in class org.proteios.core.User
Get the address for the user, or null if unknown.
getAddress() - Method in class org.proteios.io.mzdata.CvLookup
Get the address.
getAddress() - Method in class org.proteios.io.SpectrumFileContact
Get the contact address.
getAddress() - Method in interface org.proteios.io.SpectrumFileContactInterface
Get the contact address.
getAlias() - Method in enum org.proteios.core.Item
Get the alias for this item, which is used in queries,
getAlias() - Method in class org.proteios.core.query.ExpressionSelect
 
getAlias() - Method in interface org.proteios.core.query.Select
Get the alias of the selected expression.
getAlias() - Method in class org.proteios.core.RealTable
Get the alias of this table.
getAminoAcidSpecificity() - Method in class org.proteios.core.data.SearchModificationData
 
getAminoAcidSpecificity() - Method in class org.proteios.core.SearchModification
Get the amino acid specificity of the modification.
getAnalysisTime() - Method in class org.proteios.core.data.SpectrumSearchData
 
getAnalysisTime() - Method in class org.proteios.core.SpectrumSearch
 
getAnalyzer() - Method in class org.proteios.io.SpectrumFileAnalyzer
Get the spectrum instrument analyzer.
getAnalyzer() - Method in interface org.proteios.io.SpectrumFileAnalyzerInterface
Get the spectrum instrument analyzer.
getAnalyzers() - Method in class org.proteios.core.data.PeakListSetData
Get the analyzers
getAnalyzers() - Method in class org.proteios.core.PeakListSet
Get the HardwareConfiguration analyzers list.
getAnalyzers() - Method in class org.proteios.io.SpectrumFileInstrument
Get the spectrum instrument analyzer list.
getAnalyzers() - Method in interface org.proteios.io.SpectrumFileInstrumentInterface
Get the spectrum instrument analyzer list.
getAnnotatableItems() - Static method in class org.proteios.core.Metadata
Get a set contining all Annotatable item types.
getAnnotatableParents() - Method in class org.proteios.core.BioSource
Always null.
getAnnotatableParents() - Method in class org.proteios.core.DataProcessingStep
Always null.
getAnnotatableParents() - Method in class org.proteios.core.DigestParameter
Always null.
getAnnotatableParents() - Method in class org.proteios.core.Extract
Get the sample or pooled extracts.
getAnnotatableParents() - Method in class org.proteios.core.GelElectrophoresis
Always null.
getAnnotatableParents() - Method in class org.proteios.core.GelImageAnalysisEvent
Always null.
getAnnotatableParents() - Method in class org.proteios.core.GelScanEvent
Always null.
getAnnotatableParents() - Method in class org.proteios.core.HardwareConfiguration
Always null.
getAnnotatableParents() - Method in class org.proteios.core.IPG
Always null.
getAnnotatableParents() - Method in class org.proteios.core.LabeledExtract
Get the extract or pooled labeled extracts.
getAnnotatableParents() - Method in class org.proteios.core.LiquidChromatography
Always null.
getAnnotatableParents() - Method in class org.proteios.core.MascotParameterSetStorage
Always null.
getAnnotatableParents() - Method in class org.proteios.core.ObservedModification
Always null.
getAnnotatableParents() - Method in class org.proteios.core.OMSSAParameterSetStorage
Always null.
getAnnotatableParents() - Method in class org.proteios.core.PeakList
Always null.
getAnnotatableParents() - Method in class org.proteios.core.PeakListSet
Always null.
getAnnotatableParents() - Method in class org.proteios.core.Peptide
Always null.
getAnnotatableParents() - Method in class org.proteios.core.Precursor
Always null.
getAnnotatableParents() - Method in class org.proteios.core.Protein
Always null.
getAnnotatableParents() - Method in class org.proteios.core.Sample
Get the biosource or pooled samples.
getAnnotatableParents() - Method in class org.proteios.core.SearchDatabase
Always null.
getAnnotatableParents() - Method in class org.proteios.core.SearchModification
Always null.
getAnnotatableParents() - Method in class org.proteios.core.SearchResult
Always null.
getAnnotatableParents() - Method in class org.proteios.core.SeparationEvent
Always null.
getAnnotatableParents() - Method in class org.proteios.core.SoftwareConfiguration
Always null.
getAnnotatableParents() - Method in class org.proteios.core.SpectrumSearch
Always null.
getAnnotatableParents() - Method in class org.proteios.core.StainingEvent
Always null.
getAnnotatableParents() - Method in class org.proteios.core.UpdateEvent
Always null.
getAnnotatableParents() - Method in class org.proteios.core.XTandemParameterSetStorage
Always null.
getAnnotatedFile() - Method in class org.proteios.core.data.GelImageAnalysisEventData
 
getAnnotatedFile() - Method in class org.proteios.core.GelImageAnalysisEvent
 
getAnnotation(Annotatable, AnnotationType) - Method in class org.proteios.core.Annotator
Get the Annotation object of the specified annotation type.
getAnnotations() - Method in class org.proteios.core.AnnotationSet
Get a query that reurns all direct annotations in this annotation set.
getAnnotations() - Method in class org.proteios.core.data.AnnotationSetData
The primary annotations in this annotation set.
getAnnotationSet() - Method in class org.proteios.core.Annotation
Get the annotation set this annotation belongs to.
getAnnotationSet(Annotatable) - Method in class org.proteios.core.Annotator
Get existing AnnotationSet or create a new one, and save it to the database.
getAnnotationSet() - Method in interface org.proteios.core.data.AnnotatableData
Get the annotation set that holds the annotations for an item.
getAnnotationSet() - Method in class org.proteios.core.data.AnnotatedData
 
getAnnotationSet() - Method in class org.proteios.core.data.AnnotationData
Get the annotation set this annotation primarily belongs to.
getAnnotationSet() - Method in class org.proteios.core.data.PeakData
 
getAnnotationSet() - Method in class org.proteios.core.Precursor
 
getAnnotationType() - Method in class org.proteios.core.Annotation
Get the annotation type of this annotation.
getAnnotationType(Annotatable, String, Type) - Method in class org.proteios.core.Annotator
 
getAnnotationType(String, Type, Item) - Method in class org.proteios.core.Annotator
Fetches annotation type for storing variable values as annotations.
getAnnotationType() - Method in class org.proteios.core.data.AnnotationData
Get the type of this annotation.
getApexIntensity() - Method in class org.proteios.core.data.FeatureData
 
getApexIntensity() - Method in class org.proteios.core.Feature
 
getApexRetentionTimeInMinutes() - Method in class org.proteios.core.data.FeatureData
 
getApexRetentionTimeInMinutes() - Method in class org.proteios.core.Feature
 
getApparentMass() - Method in class org.proteios.core.data.MeasuredAreaData
Get the apparent mass value.
getApparentMass() - Method in class org.proteios.core.MeasuredArea
Get the Float apparent mass value.
getApparentPI() - Method in class org.proteios.core.data.MeasuredAreaData
Get the apparent pI value.
getApparentPI() - Method in class org.proteios.core.MeasuredArea
Get the Float apparent pI value.
getApplicationBuild(Session) - Static method in class org.proteios.core.SchemaVersion
Get the current application build number as it is stored in the database.
getAttributes(AttributeFilter) - Method in class org.proteios.ClassDescriptor
 
getAttributes() - Method in class org.proteios.ClassDescriptor
Currently supports Primitive, Nameable and Enumerated attributes
getAttributeType() - Method in class org.proteios.AttributeDefinition
 
getAutoMassAdjust() - Method in class org.proteios.io.OMSSAParameterSet
 
getAverageDeltaMass() - Method in class org.proteios.core.data.ModificationData
 
getAverageDeltaMass() - Method in class org.proteios.core.Modification
 
getAverageMass() - Method in class org.proteios.core.data.ModificationData
 
getAverageMass() - Method in class org.proteios.core.Modification
 
getBasePeakIntensity() - Method in class org.proteios.core.data.PeakListData
Get the base peak intensity.
getBasePeakIntensity() - Method in class org.proteios.core.PeakList
Get the base peak intensity.
getBatchSize() - Method in class org.proteios.core.AbstractBatcher
 
getBatchSize() - Method in interface org.proteios.core.Batcher
Get the current batch size of the batcher.
getBioMaterial() - Method in class org.proteios.core.BioMaterialEvent
Get the single MeasuredBioMaterial that was used for this event.
getBioMaterial() - Method in class org.proteios.core.data.BioMaterialEventData
Get the single biomaterial used by this event.
getBioMaterialEvents() - Method in class org.proteios.core.data.SeparationMethodData
 
getBioMaterials() - Method in class org.proteios.core.data.FileData
 
getBioMaterials() - Method in class org.proteios.core.File
 
getBioSource() - Method in class org.proteios.core.Sample
Get the BioSource that is the parent of this sample.
getBlocker() - Method in class org.proteios.core.data.JobData
 
getBlocker() - Method in class org.proteios.core.Job
 
getBlockTagName() - Method in class org.proteios.io.mzdata.MzDataExpCommon
Get the blockTagName.
getBlockTagName() - Method in class org.proteios.io.mzdata.MzDataImpCommon
Get the blockTagName.
getBoolean(String) - Static method in class org.proteios.core.Config
Get the configuration setting specified by key as a boolean value.
getBoolean(String) - Static method in class org.proteios.util.Values
Convert a string to a boolean. '0', 'no', 'false', '' and the null string are converted to FALSE, all other values are converted to TRUE.
getBoolean(String, boolean) - Static method in class org.proteios.util.Values
Convert a string to a boolean.
getBooleanAttribute(Element, String, boolean) - Static method in class org.proteios.util.XMLUtil
Get the value of an attribute as a boolean.
getBuild() - Static method in class org.proteios.core.Application
Get the build number.
getBuild() - Method in class org.proteios.core.data.SchemaVersionData
Get the build number.
getByClassName(DbControl, String) - Static method in class org.proteios.core.PluginDefinition
Get a PluginDefinition item when you know the class name.
getByExtension(DbControl, String) - Static method in class org.proteios.core.MimeType
Get a MimeType item when you know the file extension.
getByExternalId(DbControl, String) - Static method in class org.proteios.core.Client
Get a Client item when you know the external ID.
getByExternalId(DbControl, String) - Static method in class org.proteios.core.GelElectrophoresis
Get a GelElectrophoresis item when you know the external ID.
getByExternalId(DbControl, String) - Static method in class org.proteios.core.IPG
Get an IPG item when you know the external ID.
getByExternalId(DbControl, String) - Static method in class org.proteios.core.LiquidChromatography
Get a LiquidChromatography item when you know the external ID.
getByExternalId(DbControl, String) - Static method in class org.proteios.core.SeparationMethod
Get a SeparationMethod item when you know the external ID.
getById(DbControl, int) - Method in enum org.proteios.core.Item
Get the item of the type represented by this enumeration constant with the specified id.
getById(Class<T>, Integer) - Method in class org.proteios.core.ItemFactory
 
getById(DbControl, int) - Static method in class org.proteios.core.ItemKey
Get an ItemKey item when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.Job
Get a Job item when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.Label
Get a Label item when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.Message
Get a Message item when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.MimeType
Get a MimeType object when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.News
Get a News item when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.ObservedModification
Get an ObservedModification item when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.Peak
Get a Peak item when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.PeakList
Get a PeakList item when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.PeakListSet
Get a PeakListSet item when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.Peptide
Get an Peptide item when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.PluginConfiguration
Get a PluginConfiguration item when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.PluginDefinition
Get a PluginDefinition item when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.PluginType
Get a PluginType object when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.Precursor
Get a Precursor item when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.Project
Get a Project item when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.ProjectKey
Get a ProjectKey item when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.Protein
Get an Protein item when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.Protocol
Get a Protocol item when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.ProtocolType
Get a ProtocolType object when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.Quota
Get a Quota item when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.QuotaType
Get a QuotaType object when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.Role
Get a Role item when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.RoleKey
Get a RoleKey item when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.Sample
Get an Sample item when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.Session
Get a Session item when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.Setting
Get a Setting item when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.Software
Get a Software item when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.SoftwareType
Get a SoftwareType object when you know the ID.
getById(DbControl, int) - Static method in class org.proteios.core.StainingEvent
Get a StainingEvent item when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.UpdateEvent
Get a UpdateEvent item when you know the id.
getById(DbControl, int) - Static method in class org.proteios.core.User
Get a User item when you know the ID.
getByInterfaceName(DbControl, String) - Static method in class org.proteios.core.PluginType
Get a PluginType object when you know the interface name it represents.
getByItemType(DbControl, Item) - Static method in class org.proteios.core.RoleKey
Get a RoleKey item when you know the Item type.
getByPath(Path, boolean) - Method in class org.proteios.core.ItemFactory
Get a File item when you know the path.
getByPath(Path) - Method in class org.proteios.core.ItemFactory
Get a Directory item when you know the path.
getBySystemId(Class<T>, String) - Method in class org.proteios.core.ItemFactory
 
getByteBufferSize() - Method in class org.proteios.io.FileCrudeWriterImpl
Get size of byte buffer for writing a String to an OutputStream.
getByteBufferSize() - Method in class org.proteios.io.XMLCrudeWriter3Impl
Get size of byte buffer for writing a String to an OutputStream.
getByteBufferSize() - Method in class org.proteios.io.XMLCrudeWriterImpl
Get size of byte buffer for writing a String to an OutputStream.
getBytes() - Method in class org.proteios.core.data.DiskUsageData
Get the number of bytes the DiskConsumable item is using.
getBytes() - Method in class org.proteios.core.DiskUsage
Get the number of bytes the DiskConsumable item is using.
getCertificateChain(String) - Method in class org.proteios.core.AliasKeyManager
 
getChallenge() - Method in class org.proteios.core.SessionControl
Generate a new random string to be used for password encryption in the login method.
getCharge() - Method in class org.proteios.core.data.HitData
The charge measured in Dalton.
getCharge() - Method in class org.proteios.core.Hit
 
getCharge() - Method in class org.proteios.io.AHit
 
getCharge() - Method in interface org.proteios.io.HitInterface
 
getCharge() - Method in class org.proteios.io.PrecursorSelectedIon
 
getCharge() - Method in class org.proteios.io.SpectrumPrecursor
 
getChargeDeconvolution() - Method in class org.proteios.io.mzdata.MzDataImpProcessingMethodBlock
Get the chargeDeconvolution.
getChargeState() - Method in class org.proteios.core.data.FeatureData
 
getChargeState() - Method in class org.proteios.core.data.PrecursorData
Get the chargeState value
getChargeState() - Method in class org.proteios.core.Feature
 
getChargeState() - Method in class org.proteios.core.Precursor
Get the chargeState
getChargeState() - Method in class org.proteios.io.mzdata.MzDataImpIonSelectionBlock
Get the chargeState.
getChildId() - Method in class org.proteios.core.data.keyring.GroupGroups
Get the id of the child group.
getChildren() - Method in class org.proteios.core.data.GroupData
Get the set that manages which other groups are members of this group.
getChildren() - Method in class org.proteios.core.FileNode
 
getChildren() - Method in class org.proteios.util.Tree.Entry
Get the list of entries for the children to this node.
getClasses() - Static method in class org.proteios.core.ExtendedProperties
Get a list with the name of all classes.
getClassName() - Method in class org.proteios.core.data.PluginDefinitionData
Get the class name of the Java class that implements this plugin.
getClassName() - Method in class org.proteios.core.PluginDefinition
Get the class name of the Java class that implements this plugin.
getClient() - Method in class org.proteios.core.data.ClientDefaultSettingData
Get the client application this setting is valid for.
getClient() - Method in class org.proteios.core.data.SessionData
Get the client application the user was using.
getClient() - Method in class org.proteios.core.data.UserClientSettingData
Get the client application this setting is valid for.
getClient() - Method in class org.proteios.core.Session
Get the client application the user was using in this session.
getClientAliases(String, Principal[]) - Method in class org.proteios.core.AliasKeyManager
 
getClientDefaultSetting(String) - Method in class org.proteios.core.SessionControl
Get the value of the ClientDefaultSetting with the specified name.
getClientId() - Method in class org.proteios.core.SessionControl
Get the id of the Client application in use.
getClusterId() - Method in class org.proteios.core.data.FeatureData
Features that have been matched between files should be assigned the same cluster id.
getClusterId() - Method in class org.proteios.core.Feature
Features that have been matched between files should be assigned the same cluster id.
getColumn() - Method in class org.proteios.core.data.MappingCoordinate
Get the column number.
getColumn() - Method in class org.proteios.core.ExtendedProperty
Get the database column of the extended property.
getColumnPreferencesList() - Method in class org.proteios.io.TablePreferences
Get the column preferences list.
getCombinationMethod() - Method in class org.proteios.core.data.PeakListData
Get the combinationMethod
getCombinationMethod() - Method in class org.proteios.core.PeakList
Get the combination method of this PeakList.
getCombinedFDR() - Method in class org.proteios.core.data.HitData
 
getCombinedFDR() - Method in class org.proteios.core.Hit
 
getCommand() - Method in interface org.proteios.core.plugin.Request
The command the plugin should execute.
getCommand() - Method in class org.proteios.core.RequestInformation
Get the command this request information object is valid for.
getComment() - Method in class org.proteios.core.BioMaterialEvent
Get the comment about this event.
getComment() - Method in class org.proteios.core.data.BioMaterialEventData
Get the comment about this event.
getCompleted() - Method in class org.proteios.core.SimpleAbsoluteProgressReporter
Get completed number of ticks of the task.
getCompletionTime() - Method in class org.proteios.core.data.DataProcessingStepData
Get the completionTime date
getCompletionTime() - Method in class org.proteios.core.DataProcessingStep
Get the completionTime date.
getCompressedSize() - Method in class org.proteios.core.data.FileData
Get the size in bytes that this FileData object uses after compression.
getCompressedSizeInBytes() - Method in class org.proteios.core.File
Get the compressed size in bytes of this file.
getConcentrationInGramsPerLiter() - Method in class org.proteios.core.data.MeasuredBioMaterialData
Get the concentration of the biomaterial.
getConcentrationInGramsPerLiter() - Method in class org.proteios.core.MeasuredBioMaterial
Get the concentration (in mg protein / ml) of the biomaterial.
getConfigFileName() - Static method in class org.proteios.core.Config
 
getConfigurationValues() - Method in class org.proteios.core.data.PluginConfigurationData
Used by Hibernate to link with configuration values.
getConsiderMult() - Method in class org.proteios.io.OMSSAParameterSet
Minimum charge to start using multiply charged products
getContact() - Method in class org.proteios.core.data.PluginDefinitionData
Get contact information for the plugin.
getContact() - Method in interface org.proteios.core.plugin.About
Contact information to get more information about the plugin.
getContact() - Method in class org.proteios.core.plugin.AboutImpl
 
getContact() - Method in class org.proteios.core.PluginDefinition
Get contact information for the plugin.
getContactInfo() - Method in class org.proteios.io.mzdata.MzDataExpContactBlock
Get the contactInfo.
getContactInfo() - Method in class org.proteios.io.mzdata.MzDataImpAdminBlock
Get the contactInfo.
getContactInfo() - Method in class org.proteios.io.mzdata.MzDataImpContactBlock
Get the contactInfo.
getContactInfo() - Method in class org.proteios.io.SpectrumFileContact
Get the contact info.
getContactInfo() - Method in interface org.proteios.io.SpectrumFileContactInterface
Get the contact info.
getContactInstitution() - Method in class org.proteios.io.mzdata.MzDataExpContactBlock
Get the contactInstitution.
getContactInstitution() - Method in class org.proteios.io.mzdata.MzDataImpAdminBlock
Get the contactInstitution.
getContactInstitution() - Method in class org.proteios.io.mzdata.MzDataImpContactBlock
Get the contactInstitution.
getContactName() - Method in class org.proteios.io.mzdata.MzDataExpContactBlock
Get the contactName.
getContactName() - Method in class org.proteios.io.mzdata.MzDataImpAdminBlock
Get the contactName.
getContactName() - Method in class org.proteios.io.mzdata.MzDataImpContactBlock
Get the contactName.
getContent() - Method in class org.proteios.core.LockFile
Get Lock file content.
getContextType() - Method in class org.proteios.core.data.GuiContextData
 
getCoordinate(String) - Method in interface org.proteios.io.PickFileInterface
 
getCoordinate(List<String>) - Method in interface org.proteios.io.PickFileInterface
 
getCopyright() - Method in class org.proteios.core.data.PluginDefinitionData
Get a copyright notice for the plugin.
getCopyright() - Method in interface org.proteios.core.plugin.About
A copyright notice.
getCopyright() - Method in class org.proteios.core.plugin.AboutImpl
 
getCopyright() - Method in class org.proteios.core.PluginDefinition
Get a copyright notice for the plugin.
getCoverage() - Method in class org.proteios.core.data.HitData
 
getCoverage() - Method in class org.proteios.core.Hit
 
getCoverage() - Method in class org.proteios.io.AHit
 
getCoverage() - Method in interface org.proteios.io.HitInterface
 
getCreated() - Method in interface org.proteios.core.data.CreationInterface
Get the creation date and time
getCreated() - Method in class org.proteios.core.data.DirectoryData
 
getCreated() - Method in class org.proteios.core.data.FileData
 
getCreated() - Method in class org.proteios.core.data.JobData
Get the date and time the job was created.
getCreated() - Method in class org.proteios.core.Directory
 
getCreated() - Method in class org.proteios.core.File
 
getCreated() - Method in class org.proteios.core.Job
Get the date and time the job was registered in the database.
getCreatedDate() - Method in class org.proteios.core.FileNode
 
getCreatedMeasuredBioMaterials() - Method in class org.proteios.core.CreationEvent
 
getCreatedMeasuredBioMaterials() - Method in class org.proteios.core.data.CreationEventData
 
getCreationEvent() - Method in class org.proteios.core.data.MeasuredBioMaterialData
 
getCreationEvent() - Method in class org.proteios.core.MeasuredBioMaterial
Get the event that represents the creation of this biomaterial.
getCurrentSection() - Method in class org.proteios.util.FlatFileParser
 
getCutHi() - Method in class org.proteios.io.OMSSAParameterSet
Peak high intensity cutoff (fraction of most intense)
getCutInc() - Method in class org.proteios.io.OMSSAParameterSet
 
getCutLo() - Method in class org.proteios.io.OMSSAParameterSet
Peak low intensity cutoff (fraction of most intense)
getCutoff() - Method in class org.proteios.io.OMSSAParameterSet
 
getCvId() - Method in class org.proteios.core.data.ModificationData
Get the CV ID
getCvId() - Method in class org.proteios.core.Modification
Get the controlled vocabulary ID of the modification.
getCvLabel() - Method in class org.proteios.io.mzdata.CvLookup
Get the cvLabel.
getCvLabel() - Method in class org.proteios.io.mzdata.CvParam
Get the cvLabel.
getCvParamList() - Method in class org.proteios.io.mzdata.MzDataImpProcessingMethodBlock
Get the cvParamList.
getDataClass() - Method in enum org.proteios.core.Item
Get the data object that is used to store information in the database for items of this type.
getDataFormat() - Method in class org.proteios.io.MascotParameterSet
Get data format.
getDataLength() - Method in class org.proteios.io.mzdata.MzDataImpDataBlock
Get the dataLength.
getDataLength() - Method in class org.proteios.io.mzdata.MzDataImpIntenArrayBinaryBlock
Get the dataLength.
getDataLength() - Method in class org.proteios.io.mzdata.MzDataImpMzArrayBinaryBlock
Get the dataLength.
getDataProcessingStepList() - Method in class org.proteios.core.data.PeakListSetData
Get the dataProcessingStepList
getDataProcessingStepList() - Method in class org.proteios.core.PeakListSet
Get the DataProcessingStep dataProcessingStepList.
getDate(String) - Static method in class org.proteios.util.Values
Convert a string to a date.
getDate(String, Date) - Static method in class org.proteios.util.Values
Convert a string to a date.
getDate(String[]) - Static method in class org.proteios.util.Values
Convert an array of strings to an array of Date:s.
getDateTime() - Method in class org.proteios.core.data.InstrumentConfigurationData
Get the dateTime string for the instrumentconfiguration
getDateTime() - Method in class org.proteios.core.InstrumentConfiguration
Get the dateTime string of the instrumentconfiguration.
getDb() - Method in class org.proteios.io.MascotParameterSet
 
getDb() - Method in class org.proteios.io.OMSSAParameterSet
 
getDbControl() - Method in class org.proteios.core.AbstractBatcher
Get the DbControl object that currently manages this batcher.
getDbControl() - Method in class org.proteios.core.BasicItem
Get the DbControl object that currently manages this item.
getDbControl() - Method in class org.proteios.core.LockFile
Get the DbControl.
getDbControl() - Method in class org.proteios.core.PreferencesFile
Get the DbControl.
getDbControl() - Method in class org.proteios.io.mzdata.MzDataExpCommonDc
Get the DbControl.
getDbControl() - Method in class org.proteios.io.mzdata.MzDataImpCommonDc
Get the DbControl.
getDc() - Method in class org.proteios.core.ItemFactory
 
getDecodedBase64List() - Method in class org.proteios.io.mzdata.MzDataImpDataBlock
Get the decodedBase64List.
getDecodedBase64List() - Method in class org.proteios.io.mzdata.MzDataImpIntenArrayBinaryBlock
Get the decodedBase64List.
getDecodedBase64List() - Method in class org.proteios.io.mzdata.MzDataImpMzArrayBinaryBlock
Get the decodedBase64List.
getDecoy() - Method in class org.proteios.io.MascotParameterSet
Get decoy.
getDefaultOrder() - Method in interface org.proteios.AttributeFilter
Get a list of overall order of all attributes.
getDefaultOrder() - Method in class org.proteios.core.DefaultAttributeFilter
Get a list of overall order of all attributes.
getDefaultOrder() - Method in class org.proteios.core.FileAttributeFilter
Get a list of overall order of all attributes.
getDefaultOrder() - Method in class org.proteios.core.HitsFilterForGelBasedProjects
Get a list of overall order of all attributes.
getDefaultOrder() - Method in class org.proteios.core.HitsFilterForNonGelBasedProjects
Get a list of overall order of all attributes.
getDefaultOrder() - Method in class org.proteios.core.MinimalAttributeFilter
Get a list of overall order of all attributes.
getDefaultOrder() - Method in class org.proteios.core.MinimalAttributeFilter2
Get a list of overall order of all attributes.
getDefaultPriority() - Method in enum org.proteios.core.Job.ExecutionTime
The default thread priority to use when executing jobs in with this execution time.
getDefaultSlots() - Method in enum org.proteios.core.Job.ExecutionTime
The default number of execution slots available for jobs with this execution time in the internal job queue.
getDefaultValue() - Method in class org.proteios.core.AnnotationType
Get the recommended default value for new annotations of this annotation type.
getDefaultValue() - Method in class org.proteios.core.data.AnnotationTypeData
The default value of new annotations.
getDefaultValue() - Method in class org.proteios.core.ParameterType
Get the default value.
getDefinedPermissions() - Method in enum org.proteios.core.Item
Get the permissions which are meaningful to assign to an item if this type.
getDeisotoping() - Method in class org.proteios.io.mzdata.MzDataImpProcessingMethodBlock
Get the deisotoping.
getDeltaMassInDaltons() - Method in class org.proteios.core.data.HitData
The delta mass of this item measured in Dalton.
getDeltaMassInDaltons() - Method in class org.proteios.core.Hit
 
getDeltaMassInDaltons() - Method in class org.proteios.io.AHit
 
getDeltaMassInDaltons() - Method in interface org.proteios.io.HitInterface
 
getDenaturatingAgent() - Method in class org.proteios.core.data.GelElectrophoresisData
Get the denaturatingAgent.
getDenaturatingAgent() - Method in class org.proteios.core.GelElectrophoresis
Get the denaturatingAgent of this GelElectrophoresis.
getDepth() - Method in class org.proteios.util.Tree.Entry
Get the depth of this entry within the tree.
getDescribedClass() - Method in class org.proteios.AttributeDefinition
 
getDescribedClass() - Method in class org.proteios.ClassDescriptor
 
getDescription() - Method in class org.proteios.core.CommonItem
 
getDescription() - Method in class org.proteios.core.data.CommonData
 
getDescription() - Method in class org.proteios.core.data.DataProcessingStepData
Get the description
getDescription() - Method in class org.proteios.core.data.FileTypeData
 
getDescription() - Method in class org.proteios.core.data.GroupData
 
getDescription() - Method in class org.proteios.core.data.HardwareTypeData
 
getDescription() - Method in class org.proteios.core.data.HitData
The description of a proteion or peptide that was identified.
getDescription() - Method in class org.proteios.core.data.JobData
 
getDescription() - Method in class org.proteios.core.data.MessageData
 
getDescription() - Method in class org.proteios.core.data.MimeTypeData
 
getDescription() - Method in interface org.proteios.core.data.NameableData
Get the description for the item.
getDescription() - Method in class org.proteios.core.data.NewsData
 
getDescription() - Method in class org.proteios.core.data.PeakListData
Get the description
getDescription() - Method in class org.proteios.core.data.PluginDefinitionData
Get a description of the plugin.
getDescription() - Method in class org.proteios.core.data.PluginTypeData
 
getDescription() - Method in class org.proteios.core.data.ProjectData
 
getDescription() - Method in class org.proteios.core.data.ProtocolTypeData
 
getDescription() - Method in class org.proteios.core.data.QuotaData
 
getDescription() - Method in class org.proteios.core.data.QuotaTypeData
 
getDescription() - Method in class org.proteios.core.data.RoleData
 
getDescription() - Method in class org.proteios.core.data.RoleKeyData
Get the description for the item.
getDescription() - Method in class org.proteios.core.data.SoftwareTypeData
 
getDescription() - Method in class org.proteios.core.data.UserData
 
getDescription() - Method in class org.proteios.core.DataProcessingStep
Get the description of this DataProcessingStep.
getDescription() - Method in class org.proteios.core.Directory
 
getDescription() - Method in class org.proteios.core.ExtendedProperty
Get a description of the extended property.
getDescription() - Method in class org.proteios.core.FileType
 
getDescription() - Method in class org.proteios.core.Group
 
getDescription() - Method in class org.proteios.core.HardwareType
 
getDescription() - Method in class org.proteios.core.Hit
 
getDescription() - Method in class org.proteios.core.Job
 
getDescription() - Method in interface org.proteios.core.ManageableJobQueueInterface
Get the job queue class description string.
getDescription() - Method in interface org.proteios.core.ManageableJobQueueReadOnlyInterface
Get the job queue class description string.
getDescription() - Method in class org.proteios.core.Message
 
getDescription() - Method in class org.proteios.core.MimeType
 
getDescription() - Method in interface org.proteios.core.Nameable
Get the description for the item.
getDescription() - Method in class org.proteios.core.News
 
getDescription() - Method in class org.proteios.core.PeakList
Get the description of this PeakList.
getDescription() - Method in interface org.proteios.core.plugin.About
A description of the plugin and what it does.
getDescription() - Method in class org.proteios.core.plugin.AboutImpl
 
getDescription() - Method in class org.proteios.core.PluginDefinition
Get a description of the plugin.
getDescription() - Method in class org.proteios.core.PluginParameter
Get a description of the parameter.
getDescription() - Method in class org.proteios.core.PluginType
 
getDescription() - Method in class org.proteios.core.Project
 
getDescription() - Method in class org.proteios.core.ProtocolType
 
getDescription() - Method in class org.proteios.core.Quota
 
getDescription() - Method in class org.proteios.core.QuotaType
 
getDescription() - Method in class org.proteios.core.RequestInformation
Get a description of the request.
getDescription() - Method in class org.proteios.core.Role
 
getDescription() - Method in class org.proteios.core.RoleKey
 
getDescription() - Method in class org.proteios.core.SoftwareType
 
getDescription() - Method in class org.proteios.core.User
 
getDescription() - Method in class org.proteios.io.AHit
 
getDescription() - Method in interface org.proteios.io.HitInterface
 
getDetector() - Method in class org.proteios.core.data.PeakListSetData
Get the detector
getDetector() - Method in class org.proteios.core.PeakListSet
Get the HardwareConfiguration detector.
getDetector() - Method in class org.proteios.io.SpectrumFileInstrument
Get the spectrum instrument detector.
getDetector() - Method in interface org.proteios.io.SpectrumFileInstrumentInterface
Get the spectrum instrument detector.
getDialect() - Static method in class org.proteios.core.HibernateUtil
Get the database dialect.
getDiffFormula() - Method in class org.proteios.core.data.ModificationData
Get the differential formula
getDiffFormula() - Method in class org.proteios.core.Modification
Get the differential chemical formula of the modification.
getDigestParameters() - Method in class org.proteios.core.data.SpectrumSearchData
Get the digestParameters.
getDigestParameters() - Method in class org.proteios.core.SpectrumSearch
 
getDirectory() - Method in class org.proteios.core.data.FileData
Get the associated DirectoryData item.
getDirectory() - Method in class org.proteios.core.File
Get the associated Directory item.
getDirectory(int) - Method in class org.proteios.core.Path
Get the name of the i:th directory on the path, starting with 0.
getDirectoryCount() - Method in class org.proteios.core.Path
Get the number of directories on the path.
getDirectoryTree(DbControl, Directory) - Static method in class org.proteios.util.FileUtil
Get the complete tree of subdirectories from a given directory.
getDiskUsage() - Method in interface org.proteios.core.data.DiskConsumableData
Get the DiskUsageData that this item use.
getDiskUsage() - Method in class org.proteios.core.data.FileData
 
getDiskUsage(QuotaType, Location) - Method in class org.proteios.core.Group
Get the used number of bytes for the specified quota type and location.
getDiskUsage(QuotaType, Location) - Method in class org.proteios.core.User
Get the used number of bytes for the specified quota type and location.
getDisplayAsList() - Method in class org.proteios.core.AnnotationType
Check if the enumeration values should be displayed as a selection list or as radio buttons/checkboxes by the client application.
getDisplayValue() - Method in enum org.proteios.io.SpectrumPrecursor.FragmentationType
Get the displayValue for a SpectrumPrecursor.FragmentationType.
getDouble(String) - Static method in class org.proteios.util.Values
Convert a string to a double.
getDouble(String, double) - Static method in class org.proteios.util.Values
Convert a string to a double.
getDouble(String, Double) - Static method in class org.proteios.util.Values
 
getDouble(String[]) - Static method in class org.proteios.util.Values
Convert an array of strings to an array of Double:s.
getDoubleNum() - Method in class org.proteios.io.OMSSAParameterSet
 
getDoubleWin() - Method in class org.proteios.io.OMSSAParameterSet
 
getDownloadStream(long) - Method in class org.proteios.core.File
Get an InputStream that can be used to download the physical file for this file item.
getEmail() - Method in class org.proteios.core.data.PluginDefinitionData
Get an email address that can be used to get more information about the plugin.
getEmail() - Method in class org.proteios.core.data.UserData
Get the email address to the user, or null if unknown.
getEmail() - Method in interface org.proteios.core.plugin.About
An email adress to get more information about the plugin.
getEmail() - Method in class org.proteios.core.plugin.AboutImpl
 
getEmail() - Method in class org.proteios.core.PluginDefinition
Get an email address that can be used to get more information about the plugin.
getEmail() - Method in class org.proteios.core.User
Get the email address to the user, or null if unknown.
getEmail() - Method in class org.proteios.io.SpectrumFileContact
Get the contact email.
getEmail() - Method in interface org.proteios.io.SpectrumFileContactInterface
Get the contact email.
getEnabledItems() - Method in class org.proteios.core.AnnotationType
Get the Item types this annotation type is enabled for.
getEndDate() - Method in class org.proteios.core.data.NewsData
Get the last day this news item should be shown.
getEndDate() - Method in class org.proteios.core.News
Get the end date and time for this news item to be published.
getEnded() - Method in class org.proteios.core.data.JobData
Get the date and time the job was ended or null if the job hasn't ended.
getEnded() - Method in class org.proteios.core.Job
Get the date and time the job ended.
getEndian() - Method in class org.proteios.io.mzdata.MzDataExpDataBlock
Get the endian.
getEndian() - Method in class org.proteios.io.mzdata.MzDataExpIntenArrayBinaryBlock
Get the endian.
getEndian() - Method in class org.proteios.io.mzdata.MzDataExpMzArrayBinaryBlock
Get the endian.
getEndian() - Method in class org.proteios.io.mzdata.MzDataImpDataBlock
Get the endian.
getEndian() - Method in class org.proteios.io.mzdata.MzDataImpIntenArrayBinaryBlock
Get the endian.
getEndian() - Method in class org.proteios.io.mzdata.MzDataImpMzArrayBinaryBlock
Get the endian.
getEndPosition() - Method in class org.proteios.core.data.PeptideData
 
getEndPosition() - Method in class org.proteios.core.Peptide
 
getEndRetentionTimeInMinutes() - Method in class org.proteios.core.data.FeatureData
 
getEndRetentionTimeInMinutes() - Method in class org.proteios.core.Feature
 
getEntityName() - Method in class org.proteios.core.ClassMetadataExposed
 
getEntry(int) - Method in class org.proteios.util.Enumeration
 
getEntry(E) - Method in class org.proteios.util.Tree
Get the entry for an arbitrary node.
getEntryDate() - Method in class org.proteios.core.BioMaterialEvent
Get the date this event was added to the database.
getEntryDate() - Method in class org.proteios.core.data.BioMaterialEventData
Get the date this event was added to the database.
getEnumerationValues() - Method in class org.proteios.core.data.AnnotationTypeData
The allowed values if this is an enumeration.
getEnzyme() - Method in class org.proteios.io.MascotParameterSet
 
getEnzyme() - Method in class org.proteios.io.OMSSAParameterSet
 
getErrorList() - Method in class org.proteios.core.PluginResponse
Get a list containing detailed error messages if the status is Response.Status.ERROR.
getErrorTolerant() - Method in class org.proteios.io.MascotParameterSet
Get error tolerant.
getEstimatedExecutionTime() - Method in class org.proteios.core.data.JobData
Get the estimated execution time of the job. 0 = < 1 minute, 1 = 1 - 10 minutes, 2 = < 1 hour, 3 = > 1 hour
getEstimatedExecutionTime() - Method in class org.proteios.core.Job
Get the estimated execution time of the job.
getEstimatedExecutionTime() - Method in class org.proteios.core.PluginResponse
Get the estimated execution time of the job.
getEValue() - Method in class org.proteios.io.AHit
 
getEValue() - Method in interface org.proteios.io.HitInterface
 
getEventDate() - Method in class org.proteios.core.BioMaterialEvent
Get the date this event was done in the lab.
getEventDate() - Method in class org.proteios.core.data.BioMaterialEventData
Get the date this event happened in the lab.
getEventQuery() - Method in class org.proteios.core.MeasuredBioMaterial
 
getEvents() - Method in class org.proteios.core.data.MeasuredBioMaterialData
These are the events that have used this biomaterial.
getEvents() - Method in class org.proteios.core.MeasuredBioMaterial
Get the events that have used this biomaterial.
getEventType() - Method in class org.proteios.core.BioMaterialEvent
Get the type of event.
getExactMass() - Method in class org.proteios.io.OMSSAParameterSet
 
getExecutionTimeList() - Method in interface org.proteios.core.ManageableJobQueueInterface
Get the execution time list.
getExecutionTimeList() - Method in interface org.proteios.core.ManageableJobQueueReadOnlyInterface
Get the execution time list.
getExistingAnnotation(Annotatable, AnnotationType) - Method in class org.proteios.core.Annotator
Get the Annotation object of the specified annotation type.
getExpectationValue() - Method in class org.proteios.core.data.HitData
 
getExpectationValue() - Method in class org.proteios.core.data.SearchResultData
 
getExpectationValue() - Method in class org.proteios.core.Hit
 
getExpectationValue() - Method in class org.proteios.core.SearchResult
 
getExperimentalMassInDaltons() - Method in class org.proteios.core.data.HitData
The experimental mass measured in Dalton.
getExperimentalMassInDaltons() - Method in class org.proteios.core.Hit
 
getExperimentalMassInDaltons() - Method in class org.proteios.io.AHit
 
getExperimentalMassInDaltons() - Method in interface org.proteios.io.HitInterface
 
getExpirationDate() - Method in class org.proteios.core.data.UserData
Get the expiration date for this user account, or null if no expiration date is set.
getExpirationDate() - Method in class org.proteios.core.User
Get the expire date of the account.
getExpression() - Method in class org.proteios.core.query.ExpressionSelect
 
getExpression() - Method in interface org.proteios.core.query.Select
Get the expression object representing the selected expression.
getExtended(String) - Method in interface org.proteios.core.data.ExtendableData
Get the value of an extended property.
getExtension() - Method in class org.proteios.core.data.MimeTypeData
Get the extension for this MimeType item.
getExtension() - Method in class org.proteios.core.MimeType
Get the extension for this MimeType item.
getExternalClientId() - Method in class org.proteios.core.SessionControl
Get the external id of the Client application in use.
getExternalId() - Method in class org.proteios.core.BioMaterial
Get the external id of the biomaterial.
getExternalId() - Method in class org.proteios.core.Client
Get the external id for this Client item.
getExternalId() - Method in class org.proteios.core.data.BioMaterialData
Get the external id for the biomaterial
getExternalId() - Method in class org.proteios.core.data.ClientData
Get the external id for this Client item.
getExternalId() - Method in class org.proteios.core.data.HitData
For proteins/peptides this is the Accession number.
getExternalId() - Method in class org.proteios.core.data.SeparationMethodData
Get the external id for the separation method
getExternalId() - Method in class org.proteios.core.data.UserData
Get the external ID for the user account.
getExternalId() - Method in class org.proteios.core.Hit
For proteins this is the accession number.
getExternalId() - Method in class org.proteios.core.SeparationMethod
Get the external id of the separation method.
getExternalId() - Method in class org.proteios.core.User
Get the external id for the user account.
getExternalId() - Method in class org.proteios.io.AHit
 
getExternalId() - Method in interface org.proteios.io.HitInterface
 
getExtract() - Method in class org.proteios.core.LabeledExtract
Get the Extract that is the parent of this labeled extract.
getExtracts() - Method in class org.proteios.core.Sample
Get a query that returns all extracts created from this sample.
getExtraDataList() - Method in class org.proteios.io.PrecursorSelectedIon
Get the spectrum precursor selected ion extra data list.
getExtraDataList() - Method in class org.proteios.io.SpectrumImpl
Get the spectrum extra data list.
getExtraDataList() - Method in interface org.proteios.io.SpectrumInterface
Get the spectrum extra data list.
getExtraDataList() - Method in class org.proteios.io.SpectrumPrecursor
Get the spectrum precursor extra data list.
getExtraString() - Method in class org.proteios.core.data.HitData
This field is used if the External id was to long.
getFax() - Method in class org.proteios.core.data.UserData
Get the fax number to the user, or null if unknown.
getFax() - Method in class org.proteios.core.User
Get the fax number to the user, or null if unknown.
getFeature() - Method in class org.proteios.core.data.HitData
Best matching feature
getFeature() - Method in class org.proteios.core.Hit
Best matching feature, source for precursor quantity
getFeatureExternalId() - Method in class org.proteios.core.data.FeatureData
 
getFeatureExternalId() - Method in class org.proteios.core.Feature
 
getFeatureFile() - Method in class org.proteios.core.data.FeatureData
feature file.
getFeatureFile() - Method in class org.proteios.core.Feature
feature file.
getFile() - Method in interface org.proteios.core.data.FileAttachableData
Get the file that is attached to the item.
getFile() - Method in class org.proteios.core.data.InputSpectraData
 
getFile() - Method in class org.proteios.core.data.InstrumentConfigurationData
Get the protocol file
getFile() - Method in class org.proteios.core.data.ProtocolData
 
getFile() - Method in interface org.proteios.core.FileAttachable
Get the file that is attached to the item.
getFile() - Method in class org.proteios.core.InstrumentConfiguration
Get the protocol File for the configuration.
getFile() - Method in class org.proteios.core.Protocol
 
getFileId() - Method in class org.proteios.core.FileNode
 
getFileName() - Method in class org.proteios.core.FileNode
 
getFilename() - Method in class org.proteios.core.Path
Get the filename part of the path.
getFileQuery() - Method in class org.proteios.core.Directory
 
getFiles() - Method in class org.proteios.core.BioMaterial
 
getFiles() - Method in class org.proteios.core.data.BioMaterialData
 
getFileType() - Method in class org.proteios.core.data.FileData
Get the associated FileTypeData item.
getFileType() - Method in class org.proteios.core.File
Get the associated FileType item.
getFileType() - Method in class org.proteios.core.FileNode
 
getFileType() - Method in interface org.proteios.io.FileTypeInterface
 
getFileType() - Method in class org.proteios.io.MascotFileReader
 
getFileType() - Method in class org.proteios.io.mzdata.MzDataExpSourceFileBlock
Get the source file fileType.
getFileType() - Method in class org.proteios.io.mzdata.MzDataImpAdminBlock
Get the source file fileType.
getFileType() - Method in class org.proteios.io.mzdata.MzDataImpSourceFileBlock
Get the source file fileType.
getFileWriter() - Method in class org.proteios.core.PreferencesFile
Get FileWriter instance to preferences file (Internal use only).
getFilterString() - Method in class org.proteios.io.ColumnPreferences
Get filter string value.
getFirstInCombination() - Method in class org.proteios.core.data.HitData
 
getFirstInCombination() - Method in class org.proteios.core.Hit
 
getFirstResult() - Method in interface org.proteios.core.query.Query
The number of the row the query should start returning.
getFixed() - Method in class org.proteios.io.MascotParameterSet
 
getFixed() - Method in class org.proteios.io.OMSSAParameterSet
 
getFixedMods(File, DbControl, ItemFactory) - Static method in class org.proteios.core.SearchModification
This function will return fixed search modifications for search results file (if it has been imported)
getFloat(int) - Method in interface org.proteios.core.query.SqlResult
Get the value of the specified column as a float.
getFloat(String) - Static method in class org.proteios.util.Values
Convert a string to an float.
getFloat(String, float) - Static method in class org.proteios.util.Values
Convert a string to an integer.
getFloat(String, Float) - Static method in class org.proteios.util.Values
 
getFloat(String[]) - Static method in class org.proteios.util.Values
Convert an array of strings to an array of Float:s.
getFractionId() - Method in class org.proteios.core.data.HitData
A fraction id, e.g. a serial number like 01.
getFractionId() - Method in class org.proteios.core.Hit
 
getFragmentationType() - Method in class org.proteios.io.SpectrumPrecursor
Get the fragmentation type.
getFriends() - Method in class org.proteios.core.SessionControl
Get the id of all friends to logged in user.
getFrom() - Method in class org.proteios.core.data.MessageData
The name of the user this message is from.
getFrom() - Method in class org.proteios.core.Message
Get the name of the sender of this message.
getFrom() - Method in class org.proteios.core.QueryFactory.QueryState
 
getFromAddress() - Method in class org.proteios.io.NotificationConfiguration
Get the "from" address to use for e-mail notification.
getFromId() - Method in class org.proteios.core.data.MessageData
The id of the user if this message was from a real user.
getFromName() - Method in class org.proteios.core.PreferencesFile
Get the "from" name to use for e-mail notification.
getFromName() - Method in class org.proteios.io.NotificationConfiguration
Get the "from" name to use for e-mail notification.
getFullName() - Method in class org.proteios.io.mzdata.CvLookup
Get the fullName.
getFunctionName() - Method in class org.proteios.util.jep.ChannelFunction
 
getFunctionName() - Method in interface org.proteios.util.jep.JepFunction
Get the name of this function.
getFunctionName() - Method in class org.proteios.util.jep.Log2Function
 
getFunctionName() - Method in class org.proteios.util.jep.MeanFunction
 
getGelElectrophoresis() - Method in class org.proteios.core.GelScanEvent
Get the GelElectrophoresis this GelScanEvent is associated with.
getGelElectrophoresis() - Method in class org.proteios.core.StainingEvent
Get the GelElectrophoresis this StainingEvent is associated with.
getGelExternalId() - Method in class org.proteios.core.data.HitData
 
getGelExternalId() - Method in class org.proteios.core.Hit
 
getGelIdFromMicroPlate(String, String) - Method in class org.proteios.io.RobotFileImpl
Get gel id for specified well and plate id.
getGelIdFromMicroPlate(List<String>, List<String>) - Method in class org.proteios.io.RobotFileImpl
Get list of gel ids for specified well and plate ids.
getGelIdFromMicroPlate(String, String) - Method in interface org.proteios.io.RobotFileInterface
Returns gel id that was put in wellId in plateId
getGelIdFromMicroPlate(List<String>, List<String>) - Method in interface org.proteios.io.RobotFileInterface
Returns gel ids that was put in wellId[i] in plateId[i]
getGelIdFromTargetPlate(String, String) - Method in class org.proteios.io.RobotFileImpl
Get target gel id for specified target id and target position (well) id.
getGelIdFromTargetPlate(List<String>, List<String>) - Method in class org.proteios.io.RobotFileImpl
Get list of target gel ids for specified target ids and target position (well) ids.
getGelIdFromTargetPlate(String, String) - Method in interface org.proteios.io.RobotFileInterface
Returns target gel id that was put in positionId in targetId
getGelIdFromTargetPlate(List<String>, List<String>) - Method in interface org.proteios.io.RobotFileInterface
Returns target gel ids that was put in positionId[i] in targetId[i]
getGelIdList() - Method in class org.proteios.io.RobotFileImpl
Get gel ids.
getGelIdList() - Method in interface org.proteios.io.RobotFileInterface
Get gel ids.
getGelScanEvents() - Method in class org.proteios.core.GelElectrophoresis
 
getGetter(Class, String) - Method in class org.proteios.core.ExtendedPropertyAccessor
Create a Getter object for the specified class and property.
getGroup() - Method in class org.proteios.core.data.DiskUsageData
Get the GroupData that owns the DiskConsumable item.
getGroup() - Method in class org.proteios.core.DiskUsage
Get the group that owns the DiskConsumable item or null if ther is none.
getGroupId() - Method in class org.proteios.core.data.keyring.GroupKeys
Get the id of the group.
getGroupId() - Method in class org.proteios.core.data.keyring.GroupProjects
Get the id of the group.
getGroupId() - Method in class org.proteios.core.data.keyring.UserGroups
Get the id of the group.
getGroups() - Method in class org.proteios.core.data.ItemKeyData
Get the map that manages which groups that have permissions for this key.
getGroups() - Method in class org.proteios.core.data.ProjectData
Get the map that manages which users are members of this project and their permissions.
getGroups() - Method in class org.proteios.core.Group
Get a query that returns the groups that are members of this group.
getGroups() - Method in class org.proteios.core.MultiPermissions
Get a query that returns all groups appearing in at least one of the item keys.
getGroups() - Method in class org.proteios.core.Project
Get a query that returns the groups that are members of this project.
getGroups() - Method in class org.proteios.core.SessionControl
Get the id of all groups where the logged in user is a member, directly or indirectly.
getGroups() - Method in class org.proteios.core.User
Get a query that returns the groups where this user is a member.
getGuiContext() - Method in class org.proteios.core.PluginConfigurationRequest
Get the context of the client application when this configuration request was created.
getGuiContexts() - Method in class org.proteios.core.data.PluginDefinitionData
The item code for all items where it makes sense to use the plugin in a client application.
getGuiContexts() - Method in interface org.proteios.core.plugin.InteractivePlugin
Get a set containing all items that the plugin handles.
getGuiContexts() - Method in class org.proteios.core.PluginDefinition
Get the Item types where it makes sense to use this plugin for a client application.
getHardware() - Method in class org.proteios.core.data.HardwareConfigurationData
Get the hardware
getHardware() - Method in class org.proteios.core.data.HardwareTypeData
This is the inverse end.
getHardware() - Method in class org.proteios.core.HardwareConfiguration
Get the Hardware that is configured.
getHardwareSettings() - Method in class org.proteios.core.data.GelImageAnalysisEventData
 
getHardwareSettings() - Method in class org.proteios.core.data.GelScanEventData
 
getHardwareSettings() - Method in class org.proteios.core.data.SeparationEventData
 
getHardwareSettings() - Method in class org.proteios.core.data.StainingEventData
 
getHardwareSettings() - Method in class org.proteios.core.GelImageAnalysisEvent
 
getHardwareSettings() - Method in class org.proteios.core.GelScanEvent
 
getHardwareSettings() - Method in class org.proteios.core.SeparationEvent
 
getHardwareSettings() - Method in class org.proteios.core.StainingEvent
 
getHardwareType() - Method in class org.proteios.core.data.HardwareData
 
getHardwareType() - Method in class org.proteios.core.Hardware
Get the associated HardwareType item.
getHashString(String) - Static method in class org.proteios.util.MD5
 
getHashString(MessageDigest) - Static method in class org.proteios.util.MD5
 
getHeader(String) - Method in class org.proteios.util.FlatFileParser
Get the value of the header with the specified name.
getHeaderNames() - Method in class org.proteios.util.FlatFileParser
Get the names of all headers found by the FlatFileParser.parseHeaders() method.
getHeight() - Method in class org.proteios.core.AnnotationType
Get the recommended height in characters a client application should use to render an input field for annotations of this annotation type.
getHeight() - Method in class org.proteios.core.data.AnnotationTypeData
The recommended height (lines) to display input fields for this annotation in client applications.
getHeight() - Method in class org.proteios.core.ParameterType
Get the height of the input field for the parameter in the GUI.
getHibernateType() - Method in class org.proteios.core.hibernate.TypeWrapper
Get the underlying Hibernate type.
getHibernateType() - Method in enum org.proteios.core.Type
Deprecated.
In 2.16. The NullableType class was deprecated in Hibernate 3.5.2. It will be removed in Hibernate 3.6. Since BASE probably will switch to newer Hibernate versions in the future this method will also be removed. The Type.getTypeWrapper() is intended to replace this method, but it may not provide the same information that a NullableType can. Problems are solved on a case-by-case basis. Please ask on the Proteios SE developers mailing list if you have any issues related to this.
getHitForFeatureMsFile(Project, File, DbControl) - Static method in class org.proteios.core.Hit
 
getHitListLen() - Method in class org.proteios.io.OMSSAParameterSet
 
getHits() - Method in class org.proteios.core.data.FeatureData
Get the Hits matched to this feature.
getHits() - Method in class org.proteios.core.Feature
 
getHomeDirectory() - Method in class org.proteios.core.data.UserData
Get the home directory for this user.
getHomeDirectory() - Method in class org.proteios.core.User
Get the home Directory for this user.
getHostName() - Static method in class org.proteios.core.Application
Get the host name of the server running Proteios 2.
GetHostName - Class in org.proteios.install
Usage: GetHostName Outputs a string with canonical name of local host.
GetHostName() - Constructor for class org.proteios.install.GetHostName
 
getId() - Method in class org.proteios.core.BasicItem
 
getId() - Method in class org.proteios.core.data.BasicData
Get the id of the item.
getId() - Method in interface org.proteios.core.data.IdentifiableData
Get the id for the item.
getId() - Method in class org.proteios.core.data.UserData
We must override this method because the id must be the same as the id for the password.
getId() - Method in interface org.proteios.core.Identifiable
Get the id for the item.
getId() - Method in interface org.proteios.core.ManageableJobQueueInterface
Get the job queue class id string.
getId() - Method in interface org.proteios.core.ManageableJobQueueReadOnlyInterface
Get the job queue class id string.
getId() - Method in interface org.proteios.core.plugin.ParameterValues
Get the ID of the job or configuration the parameters comes from.
getId() - Method in class org.proteios.core.SessionControl
Get the id of this SessionControl.
getId(String) - Static method in class org.proteios.core.SystemItems
Get the numeric id for an item when you know the system id.
getIdentificationResultFile() - Method in class org.proteios.core.data.HitData
identificationResultFile origin reference.
getIdentificationResultFile() - Method in class org.proteios.core.Hit
 
getIdentifier_name() - Method in class org.proteios.core.LsidElement
 
getIdsForSeparationMethodsWithSeaprationEvent(DbControl) - Static method in class org.proteios.core.SeparationMethod
 
getImageFile() - Method in class org.proteios.core.data.GelScanEventData
Using the source file column for the raw image file
getImageFile() - Method in class org.proteios.core.GelScanEvent
The raw image file
getImpersonated() - Method in class org.proteios.core.data.SessionData
Check if another user is acting as the user of this session.
getImpersonated() - Method in class org.proteios.core.Session
Check if another user was acting as the user of this session.
getIndentationLevel() - Method in interface org.proteios.io.XMLCrudeWriter3
Get indentation level.
getIndentationLevel() - Method in class org.proteios.io.XMLCrudeWriter3Impl
Get indentation level.
getIndex() - Method in class org.proteios.core.data.SearchResultData
 
getIndex(String) - Method in class org.proteios.core.DynamicResultIterator
 
getIndex(String) - Method in interface org.proteios.core.query.SqlResultIterator
Get the index number of a selected column.
getIndex() - Method in class org.proteios.core.SearchResult
 
getInherited() - Method in class org.proteios.core.data.AnnotationSetData
Annotations that are inherited from other annotation sets.
getInheritedAnnotations() - Method in class org.proteios.core.AnnotationSet
Get a query that returns all inherited annotations in this annotation set.
getInheritedAnnotationSets() - Method in class org.proteios.core.AnnotationSet
Get a query that returns all inherited annotation sets in this annotation set.
getInheritedSets() - Method in class org.proteios.core.data.AnnotationSetData
Annotation sets from which this set should inherit all annotations.
getInheritingAnnotationSets() - Method in class org.proteios.core.AnnotationSet
Get a query that returns all annotation sets inheriting from this annotation set.
getInputFileName() - Method in interface org.proteios.io.IdentificationFileInterface
 
getInputFileName() - Method in class org.proteios.io.MascotFileReader
 
getInputFileName() - Method in class org.proteios.io.TandemFileReader
 
getInputSpectra() - Method in class org.proteios.core.data.SpectrumSearchData
 
getInputSpectrumFileName() - Method in class org.proteios.core.data.SpectrumSearchData
 
getInputSpectrumFileName() - Method in class org.proteios.core.SpectrumSearch
Get the input filename of this SpectrumSearch.
getInputSpectrumId() - Method in class org.proteios.core.data.SearchResultData
 
getInputSpectrumId() - Method in class org.proteios.core.SearchResult
 
getInputStream() - Method in class org.proteios.io.MgfFileReader
Get MGF input stream.
getInputStream() - Method in class org.proteios.io.PklFileReader
Get PKL input stream.
getInputStream(File) - Static method in class org.proteios.util.FileUtil
Get a buffered InputStream object reading from the specified file.
getInstance(Class<I>) - Static method in class org.proteios.core.Metadata
Get the metadata instance for the specified type of item.
getInstance(Class<I>, String) - Static method in class org.proteios.core.Metadata
Get the metadata instance for the item with the specified entity name.
getInstance(String) - Static method in class org.proteios.util.JarClassLoader
Get a class loader for the specified JAR file.
getInstance() - Static method in class org.proteios.util.jep.Log2Function
Get the singleton instance of this function.
getInstitution() - Method in class org.proteios.io.SpectrumFileContact
Get the contact institution.
getInstitution() - Method in interface org.proteios.io.SpectrumFileContactInterface
Get the contact institution.
getInstrument() - Method in class org.proteios.core.data.PeakListSetData
Get the instrument
getInstrument() - Method in class org.proteios.core.PeakListSet
Get the Hardware instrument.
getInstrument() - Method in class org.proteios.io.MascotParameterSet
Get instrument.
getInstrumentName() - Method in class org.proteios.io.mzdata.MzDataImpInstrumentNameBlock
Get the instrumentName.
getInstrumentName() - Method in class org.proteios.io.SpectrumFileInstrument
Get the spectrum instrument name.
getInstrumentName() - Method in interface org.proteios.io.SpectrumFileInstrumentInterface
Get the spectrum instrument name.
getInstrumentSerialNo() - Method in class org.proteios.io.SpectrumFileInstrument
Get the spectrum instrument serial no.
getInstrumentSerialNo() - Method in interface org.proteios.io.SpectrumFileInstrumentInterface
Get the spectrum instrument serial no.
getInt(String) - Static method in class org.proteios.core.Config
Get the configuration setting specified by key as an integer value.
getInt(String, int) - Static method in class org.proteios.core.Config
Get the configuration setting specified by key as an integer value.
getInt(String) - Static method in class org.proteios.core.IntegerUtil
Get the int value of an String.
getInt(String, int) - Static method in class org.proteios.core.IntegerUtil
Get the int value of an String.
getInt(Integer) - Static method in class org.proteios.core.IntegerUtil
Get the value of an Integer.
getInt(Integer, int) - Static method in class org.proteios.core.IntegerUtil
Get the value of an Integer.
getInt(int) - Method in interface org.proteios.core.query.SqlResult
Get the value of the specified column as an integer.
getInt(String) - Static method in class org.proteios.util.Values
Convert a string to an integer.
getInt(String, int) - Static method in class org.proteios.util.Values
Convert a string to an integer.
getInt(String[]) - Static method in class org.proteios.util.Values
Convert an array of strings to an array of Integer:s.
getIntAttribute(Element, String, int) - Static method in class org.proteios.util.XMLUtil
Get the value of an attribute as an integer.
getInteger(String, Integer) - Static method in class org.proteios.util.Values
 
getIntegratedIntensity() - Method in class org.proteios.core.data.FeatureData
 
getIntegratedIntensity() - Method in class org.proteios.core.Feature
 
getIntensity() - Method in class org.proteios.core.data.MeasuredAreaData
Get the intensity.
getIntensity() - Method in class org.proteios.core.data.PeakData
Get the intensity.
getIntensity() - Method in class org.proteios.core.data.PrecursorData
Get the precursor intensity.
getIntensity() - Method in class org.proteios.core.MeasuredArea
Get the intensity.
getIntensity() - Method in class org.proteios.core.Peak
Get the intensity.
getIntensity() - Method in class org.proteios.core.Precursor
Get the precursor intensity.
getIntensity() - Method in class org.proteios.io.PrecursorSelectedIon
 
getIntensity() - Method in class org.proteios.io.SpectrumPrecursor
 
getInterfaceName() - Method in class org.proteios.core.data.PluginTypeData
Get the interface name a plugin must implement to be of this type.
getInterfaceName() - Method in class org.proteios.core.PluginType
Get the class name of the Java class that implements this plugin.
getInterfaces(Class) - Static method in class org.proteios.util.ClassUtil
Get all interfaces a class implements, including those implemented by superclasses.
getInternalName() - Method in class org.proteios.core.data.FileData
Get the internal name associated with this file.
getIonisationSource() - Method in class org.proteios.core.data.PeakListSetData
Get the ionisationSource
getIonisationSource() - Method in class org.proteios.core.PeakListSet
Get the HardwareConfiguration ionisationSource.
getIonSelection() - Method in class org.proteios.core.data.PrecursorData
Get the ionSelection
getIonSelection() - Method in class org.proteios.core.Precursor
Get the InstrumentConfiguration ionSelection.
getIonsToSearch1() - Method in class org.proteios.io.OMSSAParameterSet
 
getIonsToSearch2() - Method in class org.proteios.io.OMSSAParameterSet
 
getItem() - Method in class org.proteios.core.AnnotationSet
Get the item this annotation set belongs to.
getItem() - Method in class org.proteios.core.plugin.GuiContext
 
getItemClass() - Method in enum org.proteios.core.Item
Get the class object that is used to handle items of this type.
getItemKey() - Method in interface org.proteios.core.data.ShareableData
Get the ItemKeyData for the item.
getItemKey() - Method in class org.proteios.core.data.SharedData
 
getItemKey() - Method in interface org.proteios.core.Shareable
Get the ItemKey that is used to share this item to users and groups.
getItemKey() - Method in class org.proteios.core.SharedItem
 
getItemKeys() - Method in class org.proteios.core.SessionControl
Get the id of all item keys where the logged in user has a permission.
getItems() - Method in class org.proteios.core.ParameterType
Get the list of item data objects to choose from.
getItemType() - Method in class org.proteios.core.AnnotationSet
Get the Item type of the item this annotation set belongs to.
getItemType() - Method in class org.proteios.core.data.AnnotationSetData
Get the item type this annotation set is associated with.
getItemType() - Method in class org.proteios.core.data.GuiContextData
 
getItemType() - Method in class org.proteios.core.data.RoleKeyData
Get the code for the type of items this role key applies to.
getItemType() - Method in class org.proteios.core.DataResultIterator
Get the type of items contained in this list.
getItemType() - Method in class org.proteios.core.ItemResultIterator
Get the type of items contained in this list.
getItemType() - Method in class org.proteios.core.ItemResultList
Get the type of items contained in this list.
getItemType() - Method in interface org.proteios.core.query.EntityQuery
The type of items the query returns.
getItemType() - Method in class org.proteios.core.RoleKey
Get the Item type for the type of items this role key applies to.
getItemTypes() - Method in class org.proteios.core.data.AnnotationTypeData
The item code for all items this annotation type can be applied to.
getJarPath() - Method in class org.proteios.core.data.PluginDefinitionData
Get the path to the JAR file where the plugin class is located.
getJarPath() - Method in class org.proteios.core.data.PluginTypeData
Get the path to the JAR file where the interface class is located.
getJarPath() - Method in class org.proteios.core.PluginDefinition
Get the path to the JAR file that contains the plugin class file.
getJarPath() - Method in class org.proteios.core.PluginType
Get the path to the JAR file that contains the plugin class file.
getJob() - Method in class org.proteios.core.data.MessageData
If this message is a message about a job completion (or failure) this property contains a reference to that job.
getJob(int) - Method in interface org.proteios.core.ManageableJobQueueInterface
Get job specified by list index number in queue.
getJob(int) - Method in interface org.proteios.core.ManageableJobQueueReadOnlyInterface
Get job specified by list index number in queue.
getJob() - Method in class org.proteios.core.Message
Get the Job this message is about.
getJobQueue(int) - Static method in class org.proteios.core.JobQueueManager
Get a read-only copy of the job queue for a job with specific id.
getJobQueueList() - Static method in class org.proteios.core.JobQueueManager
Get a copy of the job queue list, with ManageableJobQueueReadOnlyInterface elements.
getJobQueueManager() - Static method in class org.proteios.core.JobQueueScheduler
Get the job queue manager.
getJobQueueScheduler() - Static method in class org.proteios.core.Application
Get the job queue scheduler.
getJobs() - Method in class org.proteios.core.PluginConfiguration
Get a query that returns the jobs using this plugin configuration.
getJobsStoppedByServerShutdownList() - Method in class org.proteios.core.JobQueueManager
Gets id values of Jobs with status EXECUTING or ABORTING that do not belong to a queue, and therefore are remnants left from a server shutdown.
getJobType() - Method in class org.proteios.core.Job
Get the type of job, ie. if it is a job executed by a plugin or not.
getJoinExpression() - Method in enum org.proteios.core.query.JoinType
 
getJspPage() - Method in class org.proteios.core.RequestInformation
The name of the jsp page to use for displaying the input form for requesting parameters.
getKey() - Method in class org.proteios.AttributeDefinition
 
getKey() - Method in class org.proteios.util.Enumeration.Entry
 
getKey(int) - Method in class org.proteios.util.Enumeration
 
getKeyId() - Method in class org.proteios.core.data.keyring.KeyPermission
Get the id of the key.
getLabel() - Method in class org.proteios.core.data.LabeledExtractData
The label compound used to label the extract.
getLabel() - Method in class org.proteios.core.LabeledExtract
Get the Label compound used for labeling the extract.
getLabel() - Method in class org.proteios.core.PluginParameter
Get the label of the parameter.
getLabeledExtracts() - Method in class org.proteios.core.Extract
Get a query that returns all labeled extracts created from this extract.
getLabeledExtracts() - Method in class org.proteios.core.Label
Get a query that returns all labeled extracts labeled with this label.
getLane() - Method in class org.proteios.core.data.MeasuredAreaData
Get the lane value.
getLane() - Method in class org.proteios.core.MeasuredArea
Get the int lane value.
getLaneIndex() - Method in class org.proteios.core.data.MeasuredAreaData
Get the laneIndex value.
getLaneIndex() - Method in class org.proteios.core.MeasuredArea
Get the int laneIndex value.
getLength() - Method in class org.proteios.core.ExtendedProperty
Get the maximum allowed length of the property value.
getLengthInCentiMeters() - Method in class org.proteios.core.data.IPGData
Get the Integer length value
getLengthInCentiMeters() - Method in class org.proteios.core.IPG
Get the int length value.
getLevel() - Method in class org.proteios.core.FileNode
 
getLimit() - Method in class org.proteios.core.QueryFactory.QueryState
 
getLine(int) - Method in class org.proteios.util.FlatFileParser
Get the line with the specified number.
getLineCount() - Method in class org.proteios.util.FlatFileParser
Get the number of lines that the FlatFileParser.parseHeaders() method parsed.
getLineSeparator() - Method in class org.proteios.core.LockFile
Get line separator string to use (Internal use only).
getListPathDefaultParameters() - Method in class org.proteios.io.XTandemParameterSet
 
getListPathTaxonomyInformation() - Method in class org.proteios.io.XTandemParameterSet
 
getLocal_background() - Method in class org.proteios.core.data.MeasuredAreaData
Get the local_background value.
getLocal_background() - Method in class org.proteios.core.MeasuredArea
Get the local_background.
getLocalSampleId() - Method in class org.proteios.core.data.HitData
An analysis sample's external id
getLocalSampleId() - Method in class org.proteios.core.Hit
 
getLocation() - Method in class org.proteios.core.data.DiskUsageData
Get the location of the DiskConsumable item.
getLocation() - Method in class org.proteios.core.data.FileData
Get the Location of this FileData
getLocation() - Method in class org.proteios.core.data.QuotaIndex
 
getLocation() - Method in interface org.proteios.core.DiskConsumable
Get the Location the items is stored at.
getLocation() - Method in class org.proteios.core.DiskUsage
Get the location of the DiskConsumable item.
getLocation() - Method in class org.proteios.core.File
 
getLockFilePath() - Method in class org.proteios.core.LockFile
Get Lock file path.
getLoggedInUserId() - Method in class org.proteios.core.SessionControl
Get the id of the logged in user, or 0 if no user is logged in.
getLoggedInUserIdAdminInfo() - Method in class org.proteios.core.SessionControl
Get the id of the logged in user, or 0 if no user is logged in.
getLogin() - Method in class org.proteios.core.data.UserData
Get the login for the user account.
getLogin() - Method in class org.proteios.core.User
Get the login for the user account.
getLoginComment() - Method in class org.proteios.core.data.SessionData
Get the login comment.
getLoginComment() - Method in class org.proteios.core.Session
Get the login comment.
getLoginTime() - Method in class org.proteios.core.data.SessionData
Get the date and time the user logged in.
getLoginTime() - Method in class org.proteios.core.Session
Get the date and time the user logged in.
getLogoutTime() - Method in class org.proteios.core.data.SessionData
Get the date and time the user logged out.
getLogoutTime() - Method in class org.proteios.core.Session
Get the date and time the user logged out.
getLong(String) - Static method in class org.proteios.util.Values
Convert a string to a long.
getLong(String, long) - Static method in class org.proteios.util.Values
Convert a string to an long.
getLong(String, Long) - Static method in class org.proteios.util.Values
Convert a string to an long.
getLong(String[]) - Static method in class org.proteios.util.Values
Convert an array of strings to an array of Long:s.
getLowerLimit() - Method in class org.proteios.core.DoubleParameterType
Get the lowst valid value of the parameter.
getLowerLimit() - Method in class org.proteios.core.FloatParameterType
Get the lowst valid value of the parameter.
getLowerLimit() - Method in class org.proteios.core.IntegerParameterType
Get the lowest valid value of the parameter.
getLowerLimit() - Method in class org.proteios.core.LongParameterType
Get the lowest valid value of the parameter.
getLsid() - Method in class org.proteios.core.data.PolyPeptideData
Get the external id for the biomaterial
getLsid() - Method in class org.proteios.core.LsidElement
hibernate.property column="`lsid`"
getLsid() - Method in class org.proteios.core.PolyPeptide
Get the lsid of the polypeptide.
getMainType() - Method in class org.proteios.core.data.PluginDefinitionData
Get the main type of plugin.
getMainType() - Method in interface org.proteios.core.plugin.Plugin
Get the type of the plugin.
getMainType() - Method in class org.proteios.core.PluginDefinition
Get the type of plugin.
getMajorVersion() - Static method in class org.proteios.core.Application
Get the major version of Proteios.
getMascotParameterFile() - Method in class org.proteios.io.MascotParameterFileUtil
Get the Mascot parameter file item.
getMascotParameterSet() - Method in class org.proteios.core.data.FileData
Get the mascotParameterSet.
getMascotParameterSet() - Method in class org.proteios.io.MascotParameterFileUtil
Get the Mascot parameter set item.
getMascotParameterSet() - Method in interface org.proteios.io.MascotParameterFileUtilInterface
 
getMascotQuery() - Method in class org.proteios.io.MascotParameterSet
Get Mascot query.
getMassEndInKiloDaltons() - Method in class org.proteios.core.data.GelElectrophoresisData
Get the massEnd value
getMassEndInKiloDaltons() - Method in class org.proteios.core.GelElectrophoresis
Get the integer massEnd value.
getMassIonType() - Method in class org.proteios.io.MascotParameterSet
Get mass ion type.
getMassStartInKiloDaltons() - Method in class org.proteios.core.data.GelElectrophoresisData
Get the massStart value
getMassStartInKiloDaltons() - Method in class org.proteios.core.GelElectrophoresis
Get the integer massStart value.
getMassToChargeRatio() - Method in class org.proteios.core.data.FeatureData
 
getMassToChargeRatio() - Method in class org.proteios.core.data.PeakData
Get the massToChargeRatio.
getMassToChargeRatio() - Method in class org.proteios.core.data.PrecursorData
Get the massToChargeRatio.
getMassToChargeRatio() - Method in class org.proteios.core.Feature
 
getMassToChargeRatio() - Method in class org.proteios.core.Peak
Get the massToChargeRatio.
getMassToChargeRatio() - Method in class org.proteios.core.Precursor
Get the mass to charge ratio.
getMassToChargeRatio() - Method in class org.proteios.io.mzdata.MzDataImpIonSelectionBlock
Get the massToChargeRatio.
getMassToChargeRatio() - Method in class org.proteios.io.PrecursorSelectedIon
 
getMassToChargeRatio() - Method in class org.proteios.io.SpectrumPrecursor
 
getMassType() - Method in class org.proteios.io.MascotParameterSet
Get mass type.
getMatchedPeaks() - Method in class org.proteios.core.data.HitData
 
getMatchedPeaks() - Method in class org.proteios.core.Hit
 
getMatchedPeaks() - Method in class org.proteios.io.AHit
 
getMatchedPeaks() - Method in interface org.proteios.io.HitInterface
 
getMaxCharge() - Method in class org.proteios.io.OMSSAParameterSet
Upper bound of precursor charge
getMaxLength() - Method in class org.proteios.core.AnnotationType
Get the maximum allowed string length for a Type.STRING annotation.
getMaxLength() - Method in class org.proteios.core.StringParameterType
Get the max length of the parameter.
getMaxMods() - Method in class org.proteios.io.OMSSAParameterSet
 
getMaxNoEnzyme() - Method in class org.proteios.io.OMSSAParameterSet
 
getMaxNumMissedCleavages() - Method in class org.proteios.core.data.DigestParameterData
 
getMaxNumMissedCleavages() - Method in class org.proteios.core.DigestParameter
 
getMaxProductCharge() - Method in class org.proteios.io.OMSSAParameterSet
 
getMaxProductions() - Method in class org.proteios.io.OMSSAParameterSet
 
getMaxResults() - Method in interface org.proteios.core.query.Query
The maximum number of rows returned by the query.
getMaxValueDouble() - Method in class org.proteios.core.AnnotationType
Get the maximum allowed value for a Type.FLOAT or Type.DOUBLE annotation.
getMaxValueLong() - Method in class org.proteios.core.AnnotationType
Get the maximum allowed value for an Type.INT or Type.LONG annotation.
getMd5() - Method in class org.proteios.core.data.FileData
Get the MD5 hash of the file contents.
getMd5() - Method in class org.proteios.core.File
Get the MD5 hash of the file contents, or null if not known.
getMd5Password() - Method in class org.proteios.core.data.PasswordData
Get the MD5 encrypted password.
getMessage() - Method in class org.proteios.core.PluginResponse
Get the return message from the plugin.
getMessage() - Method in class org.proteios.core.SimpleProgressReporter
Get the last progress message this progress reporter should display.
getMessages() - Method in class org.proteios.core.User
Get a query that returns all messages for the user.
getMetaData() - Method in exception org.proteios.core.DatabaseException
 
getMicroPlate() - Method in class org.proteios.core.data.HitData
 
getMicroVersion() - Static method in class org.proteios.core.Application
Get the micro version of Proteios.
getMimeType() - Method in class org.proteios.core.data.FileData
Get the mime type of this FileData item.
getMimeType() - Method in class org.proteios.core.File
The mimetype of this File.
getMimetype() - Method in class org.proteios.core.FileNode
 
getMimeTypeDataList(DbControl) - Static method in class org.proteios.core.MimeType
Get a list of MimeTypeData items.
getMimeTypeStringByExtension(DbControl, String) - Static method in class org.proteios.core.MimeType
Get a MimeType string when you know the file extension.
getMinCharge() - Method in class org.proteios.io.OMSSAParameterSet
Lower bound of precursor charge
getMinHit() - Method in class org.proteios.io.OMSSAParameterSet
 
getMinNoEnzyme() - Method in class org.proteios.io.OMSSAParameterSet
 
getMinorVersion() - Static method in class org.proteios.core.Application
Get the minor version of Proteios.
getMinSpectra() - Method in class org.proteios.io.OMSSAParameterSet
 
getMinValueDouble() - Method in class org.proteios.core.AnnotationType
Get the minumum allowed value for a Type.FLOAT or Type.DOUBLE annotation.
getMinValueLong() - Method in class org.proteios.core.AnnotationType
Get the minumum allowed value for an Type.INT or Type.LONG annotation.
getMissedCleavages() - Method in class org.proteios.io.MascotParameterSet
 
getMissedCleave() - Method in class org.proteios.io.OMSSAParameterSet
 
getMode() - Method in class org.proteios.io.NotificationConfiguration
Get the notification mode. 0 = "Never". 1 = "After every finished job". 2 = "After all jobs finished".
getMode() - Method in class org.proteios.io.TablePreferencesConfiguration
Get the table preferences mode. 0 = "Never". 1 = "Always". 2 = "Use current preferences but do not update them".
getModifiedAminoAcid() - Method in class org.proteios.core.data.ObservedModificationData
 
getModifiedAminoAcid() - Method in class org.proteios.core.ObservedModification
 
getModList(String, List<SearchModification>, ItemFactory) - Static method in class org.proteios.core.ObservedModification
This function will process a string formatted as a peptide hit description and return the modifications in the peptide sequence.
getModList(String, String, List<SearchModification>, ItemFactory) - Static method in class org.proteios.core.ObservedModification
This function will process a peptide sequence and a string formatted as the rest of a peptide hit description and return the modifications in the peptide sequence.
getModNameFromTandem(String) - Static method in class org.proteios.core.Modification
This function will return some common modifications in X!
getMonoisotopicDeltaMass() - Method in class org.proteios.core.data.ModificationData
 
getMonoisotopicDeltaMass() - Method in class org.proteios.core.Modification
 
getMonoisotopicMass() - Method in class org.proteios.core.data.ModificationData
 
getMonoisotopicMass() - Method in class org.proteios.core.Modification
 
getMsCalcCharge() - Method in class org.proteios.io.OMSSAParameterSet
 
getMsCalcPlusOne() - Method in class org.proteios.io.OMSSAParameterSet
 
getMsFile() - Method in class org.proteios.core.data.FeatureData
mzML / mzXML file.
getMsFile() - Method in class org.proteios.core.Feature
mzML / mzXML file.
getMsLevel() - Method in class org.proteios.core.data.PeakListData
Get the msLevel value
getMsLevel() - Method in class org.proteios.core.data.PrecursorData
Get the msLevel value
getMsLevel() - Method in class org.proteios.core.PeakList
Get the msLevel
getMsLevel() - Method in class org.proteios.core.Precursor
Get the msLevel
getMsLevel() - Method in class org.proteios.io.mzdata.MzDataImpSpectrumInstrumentBlock
Get the msLevel.
getMsMsTol() - Method in class org.proteios.io.MascotParameterSet
Get MS-MS mass tolerance.
getMsMsTol() - Method in class org.proteios.io.OMSSAParameterSet
Product mass tolerance (Da).
getMsMsTolUnit() - Method in class org.proteios.io.MascotParameterSet
Get MS-MS mass tolerance unit.
getMsOntologyAccessionNumber() - Method in enum org.proteios.io.SpectrumPrecursor.FragmentationType
Get the msOntologyAccessionNumber for a SpectrumPrecursor.FragmentationType.
getMultiPermissions(DbControl, Item, Set<Integer>) - Static method in class org.proteios.util.ShareableUtil
 
getMultiplicity() - Method in class org.proteios.core.AnnotationType
Get the multiplicity.
getMultiplicity() - Method in class org.proteios.core.data.AnnotationTypeData
How many values are allowed for this annotations of this type. 0 = no limit
getMultiplicity() - Method in class org.proteios.core.ParameterType
Get how many values that can be tied to this parameter. 0 is unlimited values and 1 is default.
getMwInDaltons() - Method in class org.proteios.core.data.HitData
 
getMwInDaltons() - Method in class org.proteios.core.Hit
 
getMwInDaltons() - Method in class org.proteios.io.AHit
 
getMwInDaltons() - Method in interface org.proteios.io.HitInterface
 
getMzDataAccessionNumber() - Method in class org.proteios.io.mzdata.MzDataImpDescriptionBlock
Get the mzData accessionNumber.
getMzDataAccessionNumber() - Method in class org.proteios.io.mzdata.MzDataImpMzDataBlock
Get the mzData accessionNumber.
getMzDataCvLookupList() - Method in class org.proteios.io.mzdata.MzDataImpDescriptionBlock
Get the mzData cvLookup list.
getMzDataNamespacePrefix() - Method in class org.proteios.io.mzdata.MzDataImpDescriptionBlock
Get the mzData namespace prefix.
getMzDataNamespacePrefix() - Method in class org.proteios.io.mzdata.MzDataImpMzDataBlock
Get the mzData namespace prefix.
getMzDataNamespaceURI() - Method in class org.proteios.io.mzdata.MzDataImpDescriptionBlock
Get the mzData namespace uri.
getMzDataNamespaceURI() - Method in class org.proteios.io.mzdata.MzDataImpMzDataBlock
Get the mzData namespace uri.
getMzDataVersion() - Method in class org.proteios.io.mzdata.MzDataImpDescriptionBlock
Get the mzData version.
getMzDataVersion() - Method in class org.proteios.io.mzdata.MzDataImpMzDataBlock
Get the mzData version.
getMzRangeStart() - Method in class org.proteios.core.data.PeakListData
Get the start of the mzRange.
getMzRangeStart() - Method in class org.proteios.core.PeakList
Get the start of the mzRange.
getMzRangeStart() - Method in class org.proteios.io.mzdata.MzDataImpSpectrumInstrumentBlock
Get the mzRangeStart.
getMzRangeStop() - Method in class org.proteios.core.data.PeakListData
Get the stop of the mzRange.
getMzRangeStop() - Method in class org.proteios.core.PeakList
Get the stop of the mzRange.
getMzRangeStop() - Method in class org.proteios.io.mzdata.MzDataImpSpectrumInstrumentBlock
Get the mzRangeStop.
getName() - Method in class org.proteios.core.BatchedPropertyInfo
Get the name of the property.
getName() - Method in class org.proteios.core.CommonItem
 
getName() - Method in class org.proteios.core.data.CommonData
 
getName() - Method in class org.proteios.core.data.DigestParameterData
 
getName() - Method in class org.proteios.core.data.DirectoryData
Get the name of the item.
getName() - Method in class org.proteios.core.data.FileData
Get the name of the item.
getName() - Method in class org.proteios.core.data.FileTypeData
 
getName() - Method in class org.proteios.core.data.GroupData
 
getName() - Method in class org.proteios.core.data.HardwareTypeData
 
getName() - Method in class org.proteios.core.data.JobData
 
getName() - Method in class org.proteios.core.data.MessageData
 
getName() - Method in class org.proteios.core.data.MimeTypeData
 
getName() - Method in interface org.proteios.core.data.NameableData
Get the name of the item.
getName() - Method in class org.proteios.core.data.NewsData
 
getName() - Method in class org.proteios.core.data.PluginDefinitionData
Get the name of the plugin.
getName() - Method in class org.proteios.core.data.PluginTypeData
 
getName() - Method in class org.proteios.core.data.ProjectData
 
getName() - Method in class org.proteios.core.data.ProtocolTypeData
 
getName() - Method in class org.proteios.core.data.QuotaData
 
getName() - Method in class org.proteios.core.data.QuotaTypeData
 
getName() - Method in class org.proteios.core.data.RoleData
 
getName() - Method in class org.proteios.core.data.RoleKeyData
Get the name of the role key.
getName() - Method in class org.proteios.core.data.SearchDatabaseData
 
getName() - Method in class org.proteios.core.data.SettingData
Used by Hibernate to link with setting name.
getName() - Method in class org.proteios.core.data.SoftwareTypeData
 
getName() - Method in class org.proteios.core.data.UserData
 
getName() - Method in class org.proteios.core.DigestParameter
Get the Name of this DigestParameter.
getName() - Method in class org.proteios.core.Directory
 
getName() - Method in class org.proteios.core.ExtendedProperty
Get the name of the extended property.
getName() - Method in class org.proteios.core.FileType
 
getName() - Method in class org.proteios.core.Group
 
getName() - Method in class org.proteios.core.HardwareType
 
getName() - Method in class org.proteios.core.Job
 
getName() - Method in class org.proteios.core.LsidElement
 
getName() - Method in class org.proteios.core.Message
 
getName() - Method in class org.proteios.core.MimeType
 
getName() - Method in interface org.proteios.core.Nameable
Get the name of the item.
getName() - Method in class org.proteios.core.News
 
getName() - Method in interface org.proteios.core.plugin.About
The name of the plugin.
getName() - Method in class org.proteios.core.plugin.AboutImpl
 
getName() - Method in class org.proteios.core.PluginDefinition
Get the name of the plugin.
getName() - Method in class org.proteios.core.PluginParameter
Get the parameter name.
getName() - Method in class org.proteios.core.PluginType
 
getName() - Method in class org.proteios.core.Project
 
getName() - Method in class org.proteios.core.ProtocolType
 
getName() - Method in class org.proteios.core.Quota
 
getName() - Method in class org.proteios.core.QuotaType
 
getName() - Method in class org.proteios.core.Role
 
getName() - Method in class org.proteios.core.RoleKey
 
getName() - Method in class org.proteios.core.SearchDatabase
Get the Name of this SearchDatabase.
getName() - Method in class org.proteios.core.Setting
Get the name of this setting.
getName() - Method in class org.proteios.core.SoftwareType
 
getName() - Method in class org.proteios.core.User
 
getName() - Method in class org.proteios.io.ColumnPreferences
Get column name.
getName() - Method in class org.proteios.io.mzdata.CvParam
Get the name.
getName() - Method in class org.proteios.io.mzdata.UserParam
Get the name.
getName() - Method in class org.proteios.io.SpectrumFileContact
Get the contact name.
getName() - Method in interface org.proteios.io.SpectrumFileContactInterface
Get the contact name.
getName() - Method in class org.proteios.io.StringPair
Get the name.
getName() - Method in interface org.proteios.io.StringPairInterface
Get the name.
getName() - Method in class org.proteios.io.TablePreferences
Get table name.
getNameOfFile() - Method in class org.proteios.io.mzdata.MzDataExpSourceFileBlock
Get the source file nameOfFile.
getNameOfFile() - Method in class org.proteios.io.mzdata.MzDataImpAdminBlock
Get the source file nameOfFile.
getNameOfFile() - Method in class org.proteios.io.mzdata.MzDataImpSourceFileBlock
Get the source file nameOfFile.
getNew(DbControl, PluginDefinition) - Static method in class org.proteios.core.PluginConfiguration
Create a new PluginConfiguration item.
getNew(DbControl, String) - Static method in class org.proteios.core.PluginDefinition
Create a new PluginDefinition item.
getNew(DbControl, String, File) - Static method in class org.proteios.core.PluginDefinition
 
getNew(DbControl, String, String) - Static method in class org.proteios.core.PluginType
Create a new PluginType item.
getNew(DbControl, long) - Static method in class org.proteios.core.Quota
Create a new Quota item.
getNewOrExisting(DbControl, UserPermissions, GroupPermissions) - Static method in class org.proteios.core.ItemKey
Create a new or load an existing ItemKey when you have a combination of user/group/permission values.
getNewOrExisting(DbControl, ProjectPermissions) - Static method in class org.proteios.core.ProjectKey
Create a new or load an existing ProjectKey when you have a combination of project/permission values.
getNewsDate() - Method in class org.proteios.core.data.NewsData
Get the news date of this news item.
getNewsDate() - Method in class org.proteios.core.News
Get the date that is shown in listings.
getNextJob() - Method in interface org.proteios.core.ManageableJobQueueInterface
Get next (first) job in queue, without modifying the queue.
getNextJob() - Method in interface org.proteios.core.ManageableJobQueueReadOnlyInterface
Get next (first) job in queue, without modifying the queue.
getNextRequest() - Method in class org.proteios.core.PluginResponse
Get a PluginRequest object that handles the next request, if status is Response.Status.CONTINUE.
getNMethionineAttribute() - Method in class org.proteios.io.OMSSAParameterSet
 
getNoCorrelationScore() - Method in class org.proteios.io.OMSSAParameterSet
 
getNode() - Method in class org.proteios.util.Tree.Entry
Get the node element object.
getNormalized_volume() - Method in class org.proteios.core.data.MeasuredAreaData
Get the normalized_volume value.
getNormalized_volume() - Method in class org.proteios.core.MeasuredArea
Get the Float normalized_volume value.
getNotificationMode() - Method in class org.proteios.core.PreferencesFile
Get the notification mode.
getNotNull() - Method in class org.proteios.core.ParameterType
Check if the parameter can be null.
getNumberOfEntries() - Method in class org.proteios.core.data.SearchDatabaseData
 
getNumberOfEntries() - Method in class org.proteios.core.SearchDatabase
 
getNumberOfEntriesAfterTaxonomy() - Method in class org.proteios.core.data.SearchDatabaseData
 
getNumberOfEntriesAfterTaxonomy() - Method in class org.proteios.core.SearchDatabase
 
getNumberOfParameters() - Method in class org.proteios.util.jep.ChannelFunction
 
getNumberOfParameters() - Method in class org.proteios.util.jep.Log2Function
 
getNumberOfParameters() - Method in class org.proteios.util.jep.MeanFunction
 
getNumberOfResidues() - Method in class org.proteios.core.data.SearchDatabaseData
 
getNumberOfResidues() - Method in class org.proteios.core.SearchDatabase
 
getNumChildren() - Method in class org.proteios.util.Tree.Entry
Get the number of children added to this node.
getNumInternalJobQueues() - Static method in class org.proteios.core.JobQueueManager
Get the number of internal job queues.
getObject(int) - Method in interface org.proteios.core.query.SqlResult
Get the value of the specified column as an object.
getObservedModifications() - Method in class org.proteios.core.data.PolyPeptideData
 
getObservedModifications() - Method in class org.proteios.core.PolyPeptide
 
getOMSSAParameterFile() - Method in class org.proteios.io.OMSSAParameterFileUtil
Get the OMSSA parameter file item.
getOMSSAParameterSet() - Method in class org.proteios.core.data.FileData
Get the OMSSAParameterSets.
getOMSSAParameterSet() - Method in class org.proteios.io.OMSSAParameterFileUtil
Get the OMSSA parameter set item.
getOMSSAParameterSet() - Method in interface org.proteios.io.OMSSAParameterFileUtilInterface
 
getOperator() - Method in class org.proteios.core.data.PropertyFilterData
Get the operator used for this filter.
getOperator() - Method in class org.proteios.core.PropertyFilter
Get the operator to use in the filter.
getOptions() - Method in class org.proteios.core.data.AnnotationTypeData
Additional options depending on the value type.
getOrganisation() - Method in class org.proteios.core.data.UserData
Get the organisation this user works for, or null if unknown.
getOrganisation() - Method in class org.proteios.core.User
Get the organisation this user works for, or null if unknown.
getOriginalQuantityInMicroLiters() - Method in class org.proteios.core.data.MeasuredBioMaterialData
Get the original quantity of the biomaterial measured in microliters.
getOriginalQuantityInMicroLiters() - Method in class org.proteios.core.MeasuredBioMaterial
Get the original quantity of the biomaterial measured in microliters.
getOtherInstrumentInfo() - Method in class org.proteios.core.data.PeakListSetData
Get the otherInstrumentInfo
getOtherInstrumentInfo() - Method in class org.proteios.core.PeakListSet
Get the InstrumentConfiguration otherInstrumentInfo.
getOutputHistogramColumnWidth() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputHistograms() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputLogPath() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputMaximumValidExpectationValue() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputMessage() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputOneSequenceCopy() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputParameters() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputPath() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputPathHashing() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputPerformance() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputProteins() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputResults() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputSequencePath() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputSequences() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputSortResultsBy() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputSpectra() - Method in class org.proteios.io.XTandemParameterSet
 
getOutputStream(File) - Static method in class org.proteios.util.FileUtil
Get a buffered OutputStream object writing to the specified file.
getOutputXslPath() - Method in class org.proteios.io.XTandemParameterSet
 
getOutStream() - Method in interface org.proteios.io.FileCrudeWriter
Get FileWriter output stream.
getOutStream() - Method in class org.proteios.io.FileCrudeWriterImpl
Get output stream.
getOutStream() - Method in interface org.proteios.io.XMLCrudeWriter
Get FileWriter output stream.
getOutStream() - Method in class org.proteios.io.XMLCrudeWriter3Impl
Get output stream.
getOutStream() - Method in class org.proteios.io.XMLCrudeWriterImpl
Get output stream.
getOwner() - Method in interface org.proteios.core.data.OwnableData
Get the UserData that is the owner of the item.
getOwner() - Method in class org.proteios.core.data.OwnedData
 
getOwner() - Method in interface org.proteios.core.Ownable
Get the User that is the owner of the item.
getOwner() - Method in class org.proteios.core.OwnedItem
 
getParameter(String) - Method in class org.proteios.core.RequestInformation
Get the plugin parameter with the specified name.
getParameterClass() - Method in class org.proteios.core.ParameterType
Get the class a value must have to match this parameter type.
getParameterFile() - Method in class org.proteios.core.data.MascotParameterSetStorageData
Get the Mascot parameter file that this Mascot Input was generated from
getParameterFile() - Method in class org.proteios.core.data.OMSSAParameterSetStorageData
Get the OMSSA parameter file that this OMSSA Input was generated from
getParameterFile() - Method in class org.proteios.core.data.XTandemParameterSetStorageData
Get the XTandem parameter file that this XTandem Input was generated from
getParameterFile() - Method in class org.proteios.core.MascotParameterSetStorage
Get the Mascot parameter file item coupled to this Mascot parameter set
getParameterFile() - Method in class org.proteios.core.OMSSAParameterSetStorage
Get the OMSSA parameter file item coupled to this OMSSA parameter set
getParameterFile() - Method in class org.proteios.core.XTandemParameterSetStorage
Get the XTandem parameter file item coupled to this XTandem parameter set
getParameterNames() - Method in class org.proteios.core.Job
Get the names of all parameters for the job.
getParameterNames() - Method in class org.proteios.core.PluginConfiguration
Get the names of all configuration values.
getParameters() - Method in class org.proteios.core.data.JobData
The parameters for this job.
getParameters() - Method in class org.proteios.core.RequestInformation
Get a list containing the information about the parameters needed for the current request.
getParameterType() - Method in class org.proteios.core.PluginParameter
Get the parameter type, which tells the client application the data type and allowed values for the parameter.
getParameterValue(String) - Method in interface org.proteios.core.plugin.Request
Get the value for the parameter with the specified name.
getParameterValues(String) - Method in class org.proteios.core.Job
Get the values of a named parameter.
getParameterValues(String) - Method in interface org.proteios.core.plugin.Request
Get the values for the parameter with the specified name.
getParameterValues(String) - Method in class org.proteios.core.PluginConfiguration
Get the values of a configuration parameter.
getParent() - Method in class org.proteios.core.data.DirectoryData
Get the parent directory of this directory.
getParent() - Method in class org.proteios.core.data.MeasuredBioMaterialData
Get the parent biomaterial.
getParent() - Method in class org.proteios.core.Directory
Get the parent directory of this directory.
getParent() - Method in class org.proteios.util.Tree.Entry
Get the entry for the parent node.
getParentId() - Method in class org.proteios.core.data.keyring.GroupGroups
Get the id of the parent group.
getParsedCharacters() - Method in class org.proteios.util.FlatFileParser
Get the number of parsed characters so far.
getParsedHTML(String) - Method in class org.proteios.io.MascotServerIO
Returns the mascot search_form.pl output with only input and select parameters.
getParsedLines() - Method in class org.proteios.util.FlatFileParser
Get the number of parsed lines so far.
getPassword() - Method in class org.proteios.core.data.UserData
Get the PasswordData object which allows you to change the password for the user.
getPath() - Method in class org.proteios.core.Directory
Get the complete path to this directory.
getPath() - Method in class org.proteios.core.File
Get the complete path of this file.
getPathToFile() - Method in class org.proteios.io.mzdata.MzDataExpSourceFileBlock
Get the source file pathToFile.
getPathToFile() - Method in class org.proteios.io.mzdata.MzDataImpAdminBlock
Get the source file pathToFile.
getPathToFile() - Method in class org.proteios.io.mzdata.MzDataImpSourceFileBlock
Get the source file pathToFile.
getPeakArrayList() - Method in class org.proteios.core.PeakList
Get the Peak peakArrayList.
getPeakList() - Method in class org.proteios.core.Acquisition
Get the PeakList this acquisition is created from.
getPeakList() - Method in class org.proteios.core.data.AcquisitionData
Get the PeakListData this acquisition is created from.
getPeakList() - Method in class org.proteios.core.data.PeakData
Get the PeakListData this peak is created from.
getPeakList() - Method in class org.proteios.core.data.PrecursorData
Get the PeakListData this precursor is created from.
getPeakList() - Method in class org.proteios.core.data.SearchResultData
 
getPeakList() - Method in class org.proteios.core.Peak
Get the PeakList this peak is created from.
getPeakList() - Method in class org.proteios.core.Precursor
Get the PeakList this precursor is created from.
getPeakList() - Method in class org.proteios.core.SearchResult
Get the PeakList this SearchResult is associated with.
getPeakList() - Method in class org.proteios.io.mzdata.MzDataExpCommonPeakList
Get the PeakList.
getPeakList() - Method in class org.proteios.io.mzdata.MzDataImpCommonPeakList
Get the PeakList.
getPeakList() - Method in class org.proteios.io.mzdata.MzDataImpMzDataBlock
Get the current PeakList for the mzData file.
getPeakList() - Method in class org.proteios.io.mzdata.MzDataImporter
Get the current PeakList for the mzData file.
getPeakListArrayList() - Method in class org.proteios.core.PeakListSet
Get the PeakList peakListArrayList.
getPeakListFile() - Method in class org.proteios.core.data.HitData
peakListFile origin reference.
getPeakListFile() - Method in class org.proteios.core.Hit
 
getPeaklists() - Method in class org.proteios.core.data.InputSpectraData
 
getPeakLists() - Method in class org.proteios.core.data.PeakListSetData
 
getPeakListSet() - Method in class org.proteios.core.data.PeakListData
Get the PeakListSetData this peakList is created from.
getPeakListSet() - Method in class org.proteios.core.data.SpectrumSearchData
 
getPeakListSet() - Method in class org.proteios.core.PeakList
Get the PeakListSet this peakList is created from.
getPeakListSet() - Method in class org.proteios.core.SpectrumSearch
Get the PeakListSet this SpectrumSearch is associated with.
getPeakListSet() - Method in class org.proteios.io.mzdata.MzDataExpCommonPeakListSet
Get the PeakListSet.
getPeakListSet() - Method in class org.proteios.io.mzdata.MzDataImpCommonPeakListSet
Get the PeakListSet.
getPeakListSet() - Method in class org.proteios.io.mzdata.MzDataImpMzDataBlock
Get the PeakListSet created from the imported mzData file.
getPeakListSet() - Method in class org.proteios.io.mzdata.MzDataImporter
Get the PeakListSet created from the imported mzData file.
getPeakListSet() - Method in class org.proteios.io.mzdata.MzDataImpSpectrumListBlock
Get the PeakListSet created from the imported mzData file.
getPeakListSets() - Method in class org.proteios.core.data.InputSpectraData
 
getPeakListsQuery() - Method in class org.proteios.core.PeakListSet
Get a query that returns all PeakList items created from this peaklistset.
getPeakProcessing() - Method in class org.proteios.io.mzdata.MzDataImpProcessingMethodBlock
Get the peakProcessing.
getPeaks() - Method in class org.proteios.core.data.PeakListData
Get the peaks.
getPeaksQuery() - Method in class org.proteios.core.PeakList
Get a query that returns all Peak items created from this peaklist.
getPendingJobsList() - Method in class org.proteios.core.JobQueueManager
Gets list of JobData for jobs with no end time set.
getPeptideCharge() - Method in class org.proteios.io.MascotParameterSet
Get peptide charge.
getPeptideIsotopeError() - Method in class org.proteios.io.MascotParameterSet
Get peptide isotope error.
getPeptides() - Method in class org.proteios.core.SearchResult
Get the Peptide polypeptides.
getPeptideSequence() - Method in class org.proteios.core.data.FeatureData
 
getPeptideSequence() - Method in class org.proteios.core.Feature
 
getPepTol() - Method in class org.proteios.io.MascotParameterSet
Get peptide mass tolerance.
getPepTol() - Method in class org.proteios.io.OMSSAParameterSet
Precursor mass tolerance (Da).
getPepTolUnit() - Method in class org.proteios.io.MascotParameterSet
Get peptide mass tolerance unit.
getPercent() - Method in class org.proteios.core.SimpleProgressReporter
Get the last percentage completed of the task.
getPercentAcrylamide() - Method in class org.proteios.core.data.GelElectrophoresisData
Get the percentAcrylamide value
getPercentAcrylamide() - Method in class org.proteios.core.GelElectrophoresis
Get the integer percentAcrylamide value.
getPercentComplete() - Method in class org.proteios.core.data.JobData
If the job is running, how many percent has been completed.
getPercentComplete() - Method in class org.proteios.core.Job
An estimate of the percentage of the work currently completed by an executing job.
getPermission() - Method in class org.proteios.core.data.keyring.KeyPermission
Get the permission.
getPermission() - Method in class org.proteios.core.data.keyring.ProjectPermission
Get the permission.
getPermissions() - Method in class org.proteios.core.BasicItem
 
getPermissions(Group) - Method in class org.proteios.core.GroupPermissions
Get the permissions for a group.
getPermissions(User) - Method in class org.proteios.core.ItemKey
Get the permissions for a user.
getPermissions(Group) - Method in class org.proteios.core.ItemKey
Get the permissions for a group.
getPermissions(User) - Method in class org.proteios.core.MultiPermissions
Get the permissions for a user.
getPermissions(Group) - Method in class org.proteios.core.MultiPermissions
Get the permissions for a group.
getPermissions(Project) - Method in class org.proteios.core.MultiPermissions
Get the permissions for a project.
getPermissions(User) - Method in class org.proteios.core.Project
Get the permissions for a user in this project.
getPermissions(Group) - Method in class org.proteios.core.Project
Get the permissions for a group in this project.
getPermissions(Project) - Method in class org.proteios.core.ProjectKey
Get the permissions for a project.
getPermissions(Project) - Method in class org.proteios.core.ProjectPermissions
Get the permissions for a project.
getPermissions(Role) - Method in class org.proteios.core.RoleKey
Get the permissions for a role.
getPermissions(User) - Method in class org.proteios.core.UserPermissions
Get the permissions for a user.
getPhone() - Method in class org.proteios.core.data.UserData
Get the phone number to the user, or null if unknown.
getPhone() - Method in class org.proteios.core.User
Get the phone number to the user, or null if unknown.
getPi() - Method in class org.proteios.core.data.HitData
 
getPi() - Method in class org.proteios.core.Hit
 
getPi() - Method in class org.proteios.io.AHit
 
getPi() - Method in interface org.proteios.io.HitInterface
 
getPiEnd() - Method in class org.proteios.core.data.IPGData
Get the int piEnd value
getPiEnd() - Method in class org.proteios.core.IPG
Get the int piEnd value.
getPiStart() - Method in class org.proteios.core.data.IPGData
Get the int piStart value
getPiStart() - Method in class org.proteios.core.IPG
Get the int piStart value.
getPixel_radius() - Method in class org.proteios.core.data.MeasuredAreaData
Get the pixel_radius value.
getPixel_radius() - Method in class org.proteios.core.MeasuredArea
Get the int pixel_radius value.
getPixel_x_coord() - Method in class org.proteios.core.data.MeasuredAreaData
Get the pixel_x_coord value.
getPixel_x_coord() - Method in class org.proteios.core.MeasuredArea
Get the int pixel_x_coord value.
getPixel_y_coord() - Method in class org.proteios.core.data.MeasuredAreaData
Get the pixel_y_coord value.
getPixel_y_coord() - Method in class org.proteios.core.MeasuredArea
Get the int pixel_y_coord value.
getPlate() - Method in class org.proteios.core.data.MappingCoordinate
Get the plate number.
getPlateId() - Method in class org.proteios.core.data.HitData
A plates external id
getPlateId() - Method in class org.proteios.core.Hit
 
getPlateId() - Method in class org.proteios.io.AHit
 
getPlateId() - Method in interface org.proteios.io.HitInterface
 
getPlateIdFromMicroPlate(String, String) - Method in class org.proteios.io.RobotFileImpl
Get plate id for specified spot id and gel id.
getPlateIdFromMicroPlate(List<String>, List<String>) - Method in class org.proteios.io.RobotFileImpl
Get list of plate ids for specified spot ids and gel ids.
getPlateIdFromMicroPlate(String, String) - Method in interface org.proteios.io.RobotFileInterface
 
getPlateIdFromMicroPlate(List<String>, List<String>) - Method in interface org.proteios.io.RobotFileInterface
 
getPlateIdFromTargetPlate(String, String) - Method in class org.proteios.io.RobotFileImpl
Get target plate id for a microtitre plate id and position.
getPlateIdListFromMicroPlate() - Method in class org.proteios.io.RobotFileImpl
Get plate ids.
getPlateIdListFromMicroPlate() - Method in interface org.proteios.io.RobotFileInterface
Get plate ids.
getPlatePosFromTargetPlate(String, String) - Method in class org.proteios.io.RobotFileImpl
Get target plate position for a microtitre plate id and position.
getPluginConfiguration() - Method in class org.proteios.core.data.JobData
The plugin configuration for the plugin.
getPluginConfiguration() - Method in class org.proteios.core.Job
Get the PluginConfiguration defining the plugin this job should execute.
getPluginConfigurations() - Method in class org.proteios.core.PluginDefinition
Get a query that returns the configurations for this plugin definition.
getPluginDefinition() - Method in class org.proteios.core.data.JobData
The plugin that executes the job.
getPluginDefinition() - Method in class org.proteios.core.data.PluginConfigurationData
Get the plugin definition for this configuration.
getPluginDefinition() - Method in class org.proteios.core.Job
Get the PluginConfiguration defining the plugin this job should execute.
getPluginDefinition() - Method in class org.proteios.core.PluginConfiguration
Get the plugin definition for this configuration.
getPluginExecutionRequest(int) - Method in interface org.proteios.core.AbortableJobQueueReadOnlyInterface
Get the PluginExecutionRequest for a job id.
getPluginExecutionRequest() - Method in class org.proteios.core.Job
Get the PluginExecutionRequest for the job.
getPlugins() - Method in class org.proteios.core.PluginType
Get a query that returns the plugin definitions which implements this type.
getPluginTypes() - Method in class org.proteios.core.data.PluginDefinitionData
The plugin types of this plugin, ie. all interfaces that it implements.
getPluginTypes() - Method in class org.proteios.core.PluginDefinition
Get a query that returns the plugin types for this plugin definition.
getPluginVersion() - Method in class org.proteios.core.data.PluginDefinitionData
Get the plugin version.
getPluginVersion() - Method in class org.proteios.core.PluginDefinition
Get the plugin version.
getPlusOne() - Method in class org.proteios.io.OMSSAParameterSet
Fraction of product peaks below precursor to determine +1 precursor
getPolyPeptides() - Method in class org.proteios.core.data.SearchResultData
 
getPolyPeptides() - Method in class org.proteios.core.SearchResult
 
getPosition() - Method in class org.proteios.core.data.ModificationData
 
getPosition() - Method in class org.proteios.core.Modification
 
getPositionIdFromTargetPlate(String, String) - Method in class org.proteios.io.RobotFileImpl
Get target position id for specified target spot id and gel id.
getPositionIdFromTargetPlate(List<String>, List<String>) - Method in class org.proteios.io.RobotFileImpl
Get list of target position ids for specified target spot ids and gel ids.
getPositionIdFromTargetPlate(String, String) - Method in interface org.proteios.io.RobotFileInterface
 
getPositionIdFromTargetPlate(List<String>, List<String>) - Method in interface org.proteios.io.RobotFileInterface
 
getPossibleFileTypes(DbControl) - Static method in class org.proteios.io.PeakListFileValidationFactory
 
getPossibleFileTypeSystemIds() - Static method in class org.proteios.io.PeakListFileValidationFactory
 
getPostSequence() - Method in class org.proteios.core.data.PeptideData
 
getPostSequence() - Method in class org.proteios.core.Peptide
Get the sequence before this peptide.
getPrecision() - Method in class org.proteios.io.mzdata.MzDataExpDataBlock
Get the precision.
getPrecision() - Method in class org.proteios.io.mzdata.MzDataExpIntenArrayBinaryBlock
Get the precision.
getPrecision() - Method in class org.proteios.io.mzdata.MzDataExpMzArrayBinaryBlock
Get the precision.
getPrecision() - Method in class org.proteios.io.mzdata.MzDataImpDataBlock
Get the precision.
getPrecursor() - Method in class org.proteios.io.MascotParameterSet
Get precursor.
getPrecursorCull() - Method in class org.proteios.io.OMSSAParameterSet
 
getPrecursorList() - Method in class org.proteios.core.data.PeakListData
Get the precursorList.
getPrecursorList() - Method in class org.proteios.core.PeakList
Get the Precursor precursorList.
getPrecursorQuantity() - Method in class org.proteios.core.data.HitData
 
getPrecursorQuantity() - Method in class org.proteios.core.Hit
 
getPrecursors() - Method in class org.proteios.io.SpectrumImpl
 
getPrecursors() - Method in interface org.proteios.io.SpectrumInterface
 
getPrecursorSearchType() - Method in class org.proteios.io.OMSSAParameterSet
 
getPrecursorsQuery() - Method in class org.proteios.core.PeakList
Get a query that returns all Precursor items created from this peaklist.
getPreferencesFilePath() - Method in class org.proteios.core.PreferencesFile
Get preferences file path.
getPreSequence() - Method in class org.proteios.core.data.PeptideData
 
getPreSequence() - Method in class org.proteios.core.Peptide
Get the sequence before this peptide.
getPreviousBioMaterialEvent() - Method in class org.proteios.core.BioMaterialEvent
This function returns the previous event that is directly linked to this event.
getPreviousBioMaterialEvent() - Method in class org.proteios.core.data.BioMaterialEventData
This function returns the previous event that is directly linked to this event.
getPrimaryCombined() - Method in class org.proteios.core.data.HitData
 
getPrimaryCombined() - Method in class org.proteios.core.Hit
 
getPriority() - Method in class org.proteios.core.data.JobData
The jobs priority.
getPriority() - Method in class org.proteios.core.Job
Get the priority of the job.
getPrivateKey(String) - Method in class org.proteios.core.AliasKeyManager
 
getProbFollowingIon() - Method in class org.proteios.io.OMSSAParameterSet
 
getProductSearchType() - Method in class org.proteios.io.OMSSAParameterSet
 
getProgressReporter() - Method in class org.proteios.io.mzdata.MzDataExporter
Get the ProgressReporter.
getProgressReporter() - Method in class org.proteios.io.mzdata.MzDataExpSpectrumListBlock
Get the ProgressReporter.
getProgressReporter() - Method in class org.proteios.io.mzdata.MzDataImpMzDataBlock
Get the ProgressReporter.
getProgressReporter() - Method in class org.proteios.io.mzdata.MzDataImporter
Get the ProgressReporter.
getProgressReporter() - Method in class org.proteios.io.mzdata.MzDataImpSpectrumListBlock
Get the ProgressReporter.
getProject() - Method in class org.proteios.core.data.FeatureData
Project origin reference.
getProject() - Method in class org.proteios.core.data.HitData
Project origin reference.
getProject() - Method in class org.proteios.core.Feature
The project.
getProject() - Method in class org.proteios.core.Hit
 
getProjectDirectory() - Method in class org.proteios.core.data.ProjectData
 
getProjectDirectory() - Method in class org.proteios.core.Project
 
getProjectDirectoryProject() - Method in class org.proteios.core.Directory
Returns the project if this directory is assigned to one, else null is returned.
getProjectId() - Method in class org.proteios.core.data.keyring.ProjectKeys
Get the id of the project.
getProjectId() - Method in class org.proteios.core.data.keyring.ProjectPermission
Get the id of the project.
getProjectKey() - Method in interface org.proteios.core.data.ShareableData
Get the ProjectKeyData for the item.
getProjectKey() - Method in class org.proteios.core.data.SharedData
 
getProjectKey() - Method in interface org.proteios.core.Shareable
Get the ProjectKey that is used to share this item to projects.
getProjectKey() - Method in class org.proteios.core.SharedItem
 
getProjectKeyId() - Method in class org.proteios.core.SessionControl
Get the id of the 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.
getProjectKeys() - Method in class org.proteios.core.SessionControl
Get the id of all project keys where the logged in user has a permission.
getProjects() - Method in class org.proteios.core.data.ProjectKeyData
Get the map that manages which projects that have permissions for this key.
getProjects() - Method in class org.proteios.core.Group
Get a query that returns the projects that this group is a member of.
getProjects() - Method in class org.proteios.core.MultiPermissions
Get a query that returns all projects appearing in at least one of the project keys.
getProjects() - Method in class org.proteios.core.SessionControl
Get the id of all projects where the logged in user is a member, directly or indirectly.
getProjects() - Method in class org.proteios.core.User
Get a query that returns the projects where this user is a member.
getProjectType() - Method in class org.proteios.core.data.ProjectData
0 - Undefined 1 - Gel based Project 2 - Non gel based, this should be more specific
getProjectType() - Method in class org.proteios.core.Project
 
getProperties(String) - Static method in class org.proteios.core.ExtendedProperties
Get a list of extended properties for the specified class.
getProperty() - Method in class org.proteios.core.PropertyFilter
Get the name of the property this filter is used on.
getPropertyNames() - Method in class org.proteios.core.ClassMetadataExposed
 
getPropertyValue(BasicItem, String) - Static method in class org.proteios.core.Metadata
Get the value of a property of an item.
getPropertyValue(DbControl, C, String) - Method in class org.proteios.core.Metadata
Get the value of a property of an item.
getProtein() - Method in class org.proteios.core.data.HitData
 
getProteinAssay() - Method in class org.proteios.core.data.GelElectrophoresisData
Get the proteinAssay.
getProteinAssay() - Method in class org.proteios.core.GelElectrophoresis
Get the proteinAssay of this GelElectrophoresis.
getProteinCleavageCTerminalMassChange() - Method in class org.proteios.io.XTandemParameterSet
 
getProteinCleavageNTerminalMassChange() - Method in class org.proteios.io.XTandemParameterSet
 
getProteinCleavageSite() - Method in class org.proteios.io.XTandemParameterSet
 
getProteinCTerminalResidueModificationMass() - Method in class org.proteios.io.XTandemParameterSet
 
getProteinHomologManagement() - Method in class org.proteios.io.XTandemParameterSet
 
getProteinMass() - Method in class org.proteios.io.MascotParameterSet
Get protein mass (kDa).
getProteinModifiedResidueMassFile() - Method in class org.proteios.io.XTandemParameterSet
 
getProteinNTerminalResidueModificationMass() - Method in class org.proteios.io.XTandemParameterSet
 
getProteins() - Method in class org.proteios.core.SearchResult
Get the Peptide polypeptides.
getProteinTaxon() - Method in class org.proteios.io.XTandemParameterSet
 
getProtocol() - Method in class org.proteios.core.BioMaterialEvent
Get the Protocol describing the procedure used in this event.
getProtocol() - Method in class org.proteios.core.data.BioMaterialEventData
Get the protocol used in this event.
getProtocols() - Method in class org.proteios.core.data.ProtocolTypeData
This is the inverse end.
getProtocolType() - Method in class org.proteios.core.data.ProtocolData
Get the associated ProtocolTypeData item.
getProtocolType() - Method in class org.proteios.core.Protocol
Get the associated ProtocolType item.
getPseudoCount() - Method in class org.proteios.io.OMSSAParameterSet
 
getPsiModList(String, List<SearchModification>, ItemFactory) - Static method in class org.proteios.core.ObservedModification
This function will process a string formatted as a peptide hit description and return the modifications in the peptide sequence.
getQualifiedTableName() - Method in class org.proteios.core.RealTable
Get the quoted table name of this table in the database.
getQuantitation() - Method in class org.proteios.io.MascotParameterSet
 
getQuantity() - Method in class org.proteios.io.AHit
 
getQuantity() - Method in interface org.proteios.io.HitInterface
 
getQuery() - Static method in class org.proteios.core.Acquisition
Get a query that returns acquisition items.
getQuery(Item) - Static method in class org.proteios.core.AnnotationType
Get a ItemQuery that returns annotation types.
getQuery(MeasuredBioMaterial) - Static method in class org.proteios.core.BioMaterialEvent
Get a query that returns events for a biomaterial.
getQuery() - Static method in class org.proteios.core.BioSource
Get a query that returns biosource items.
getQuery() - Static method in class org.proteios.core.Client
Get a new query object for this class.
getQuery() - Static method in class org.proteios.core.DataProcessingStep
Get a query that returns dataprocessingstep items.
getQuery() - Static method in class org.proteios.core.DigestParameter
Get a query that returns spectrumsearchset items.
getQuery() - Static method in class org.proteios.core.Directory
Get a query configured to retrieve directories.
getQuery(User) - Static method in class org.proteios.core.DiskUsage
Get a query configured to retrieve disk usage for the specified user.
getQuery() - Static method in class org.proteios.core.Extract
Get a query that returns extracts.
getQuery() - Static method in class org.proteios.core.File
Get a query configured to retrieve File items.
getQuery() - Static method in class org.proteios.core.FileType
Get a query configured to retrieve FileType items.
getQuery() - Static method in class org.proteios.core.GelElectrophoresis
Get a query that returns gelelectrophoresis items.
getQuery() - Static method in class org.proteios.core.GelImageAnalysisEvent
Get a query that returns GelImageAnalysisEvent items.
getQuery() - Static method in class org.proteios.core.GelScanEvent
Get a query that returns GelScanEvent items.
getQuery() - Static method in class org.proteios.core.GlobalDefaultSetting
Get a query configured to retrieve global default settings.
getQuery() - Static method in class org.proteios.core.Group
Get a query configured to retrieve groups.
getQuery() - Static method in class org.proteios.core.Hardware
Get a query configured to retrieve hardware.
getQuery() - Static method in class org.proteios.core.HardwareConfiguration
Get a query that returns hardwareconfiguration items.
getQuery() - Static method in class org.proteios.core.HardwareType
Get a query configured to retrieve hardware types.
getQuery() - Static method in class org.proteios.core.Hit
 
getQuery(Project) - Static method in class org.proteios.core.Hit
 
getQuery() - Static method in class org.proteios.core.IPG
Get a query that returns IPG items.
getQuery() - Static method in class org.proteios.core.Job
Get a query configured to retrieve
getQuery() - Static method in class org.proteios.core.Label
Get a query that returns labels.
getQuery() - Static method in class org.proteios.core.LabeledExtract
Get a query that returns labeled extracts.
getQuery() - Static method in class org.proteios.core.LiquidChromatography
Get a query that returns LiquidChromatography items.
getQuery() - Static method in class org.proteios.core.MascotParameterSetStorage
Get a query that returns MascotParameterSetStorage set items.
getQuery() - Static method in class org.proteios.core.MeasuredArea
Get a query that returns measuredArea items.
getQuery(User) - Static method in class org.proteios.core.Message
Get a query configured to retrieve messages for the specified user.
getQuery() - Static method in class org.proteios.core.MimeType
Get a query configured to retrieve MIME types.
getQuery() - Static method in class org.proteios.core.News
Get a query configured to retrieve news.
getQuery() - Static method in class org.proteios.core.ObservedModification
Get a query that returns observedModification items.
getQuery() - Static method in class org.proteios.core.OMSSAParameterSetStorage
Get a query that returns OMSSAParameterSetStorage set items.
getQuery() - Static method in class org.proteios.core.Peak
Get a query that returns peak items.
getQuery() - Static method in class org.proteios.core.PeakList
Get a query that returns peaklist items.
getQuery() - Static method in class org.proteios.core.PeakListSet
Get a query that returns peaklistset items.
getQuery() - Static method in class org.proteios.core.Peptide
Get a query that returns protein items.
getQuery() - Static method in class org.proteios.core.PluginConfiguration
Get a query configured to retrieve plugin configurations.
getQuery(GuiContext, String) - Static method in class org.proteios.core.PluginConfiguration
Get a query that returns all plugins configurations related to a specified GUI context and implementing a certain interface.
getQuery() - Static method in class org.proteios.core.PluginDefinition
Get a query that returns plugin definitions.
getQuery(GuiContext, String) - Static method in class org.proteios.core.PluginDefinition
Get a query that returns all plugins related to a specified GUI context and implementing a certain interface.
getQuery() - Static method in class org.proteios.core.PluginType
Get a query configured to retrieve plugin types.
getQuery() - Static method in class org.proteios.core.Precursor
Get a query that returns precursor items.
getQuery() - Static method in class org.proteios.core.Project
Get a query configured to retrieve projects.
getQuery() - Static method in class org.proteios.core.Protein
Get a query that returns protein items.
getQuery() - Static method in class org.proteios.core.Protocol
Get a query configured to retrieve protocols.
getQuery() - Static method in class org.proteios.core.ProtocolType
Get a query configured to retrieve protocol types.
getQuery() - Static method in class org.proteios.core.Quota
Get a query configured to retrieve quota.
getQuery() - Static method in class org.proteios.core.QuotaType
Get a query configured to retrieve QuotaType.
getQuery() - Static method in class org.proteios.core.Role
Get a ItemQuery object configured to retrieve Role items.
getQuery() - Static method in class org.proteios.core.RoleKey
Get a query object configured to retrieve role keys.
getQuery() - Static method in class org.proteios.core.Sample
Get a query that returns samples.
getQuery() - Static method in class org.proteios.core.SearchDatabase
Get a query that returns spectrumsearchset items.
getQuery() - Static method in class org.proteios.core.SearchModification
Get a query that returns searchModification items.
getQuery() - Static method in class org.proteios.core.SearchResult
Get a query that returns spectrumsearchset items.
getQuery(User) - Static method in class org.proteios.core.Session
Get a query configured to retrieve sessions for the specified user.
getQuery() - Static method in class org.proteios.core.Software
Get a query configured to retrieve software.
getQuery() - Static method in class org.proteios.core.SoftwareConfiguration
Get a query that returns softwareconfiguration items.
getQuery() - Static method in class org.proteios.core.SoftwareType
Get a query configured to retrieve software types.
getQuery() - Static method in class org.proteios.core.SpectrumSearch
Get a query that returns spectrumsearchset items.
getQuery() - Static method in class org.proteios.core.StainingEvent
Get a query that returns StainingEvent items.
getQuery() - Static method in class org.proteios.core.UpdateEvent
Get a query that returns UpdateEvent items.
getQuery() - Static method in class org.proteios.core.User
Get a query configured to retrieve users.
getQuery() - Static method in class org.proteios.core.XTandemParameterSetStorage
Get a query that returns XTandemParameterSetStorage set items.
getQueryType() - Method in interface org.proteios.core.query.Query
Get the type of query.
getQuota() - Method in class org.proteios.core.data.GroupData
Get the quota object which holds quota information for this group.
getQuota() - Method in class org.proteios.core.data.UserData
Get the quota object which holds quota information for this user.
getQuota() - Method in class org.proteios.core.Group
Get the Quota that applies to the group.
getQuota() - Method in class org.proteios.core.User
Get the Quota that applies to the user.
getQuotaGroup() - Method in class org.proteios.core.data.UserData
Get the group this user is sharing quota with, or null if this user only has it's own quota.
getQuotaGroup() - Method in class org.proteios.core.User
Get the Group whose Quota also applies to the user.
getQuotaType() - Method in class org.proteios.core.data.DiskUsageData
Get the QuotaTypeData for this DiskUsageData.
getQuotaType() - Method in class org.proteios.core.data.QuotaIndex
 
getQuotaType() - Method in class org.proteios.core.DiskUsage
Get the QuotaType the DiskConsumable item is using.
getQuotaTypeSystemId() - Method in interface org.proteios.core.DiskConsumable
Get the QuotaType system id of this item.
getQuotaTypeSystemId() - Method in class org.proteios.core.File
 
getQuotaValue(QuotaType, Location) - Method in class org.proteios.core.Quota
Get the quota for the specified type and location.
getQuotaValues() - Method in class org.proteios.core.data.QuotaData
 
getRawDownloadStream(long) - Method in class org.proteios.core.File
Get an InputStream that can be used to download the physical file for this file item.
getRawFile() - Method in class org.proteios.core.data.GelImageAnalysisEventData
Using the source file column for the raw image file
getRawFile() - Method in class org.proteios.core.GelImageAnalysisEvent
The raw image file
getReader() - Method in class org.proteios.AttributeDefinition
 
getReadMethod(AttributeDefinition) - Method in class org.proteios.ClassDescriptor
 
getReadMethodName() - Method in class org.proteios.AttributeDefinition
 
getReferencedResults() - Method in class org.proteios.core.data.SearchResultData
 
getReferencedResults() - Method in class org.proteios.core.SearchResult
Get the SearchResult referenced results.
getRefine() - Method in class org.proteios.io.XTandemParameterSet
 
getRefineMaximumValidExpectationValue() - Method in class org.proteios.io.XTandemParameterSet
 
getRefineModificationMass() - Method in class org.proteios.io.XTandemParameterSet
 
getRefinePointMutations() - Method in class org.proteios.io.XTandemParameterSet
 
getRefinePotentialCTerminusModifications() - Method in class org.proteios.io.XTandemParameterSet
 
getRefinePotentialModificationMass() - Method in class org.proteios.io.XTandemParameterSet
 
getRefinePotentialModificationMotif() - Method in class org.proteios.io.XTandemParameterSet
 
getRefinePotentialNTerminusModifications() - Method in class org.proteios.io.XTandemParameterSet
 
getRefineSequencePath() - Method in class org.proteios.io.XTandemParameterSet
 
getRefineSpectrumSynthesis() - Method in class org.proteios.io.XTandemParameterSet
 
getRefineTicPercent() - Method in class org.proteios.io.XTandemParameterSet
 
getRefineUnanticipatedCleavage() - Method in class org.proteios.io.XTandemParameterSet
 
getRefineUsePotentialModificationsForFullRefinement() - Method in class org.proteios.io.XTandemParameterSet
 
getReleaseDate() - Method in class org.proteios.core.data.SearchDatabaseData
 
getReleaseDate() - Method in class org.proteios.core.SearchDatabase
 
getRemainingQuantityInMicroLiters() - Method in class org.proteios.core.data.MeasuredBioMaterialData
Get the remaining quantity of the biomaterial measured in microliters.
getRemainingQuantityInMicroLiters() - Method in class org.proteios.core.MeasuredBioMaterial
Get the remaining quantity of the biomaterial measured in microliters.
getRemoteId() - Method in class org.proteios.core.data.SessionData
Get the login comment.
getRemoteId() - Method in class org.proteios.core.Session
Get the remote ID of the host the user used for this session.
getRemovableItems() - Static method in class org.proteios.core.Metadata
Get a set contining all Removable item types.
getReplaceThresh() - Method in class org.proteios.io.OMSSAParameterSet
 
getReplicateId() - Method in class org.proteios.core.data.HitData
A replicate id, e.g. a serial number like 01.
getReplicateId() - Method in class org.proteios.core.Hit
 
getReportTop() - Method in class org.proteios.io.MascotParameterSet
Get report top.
getRequestInformation(GuiContext, String) - Method in interface org.proteios.core.plugin.InteractivePlugin
This method will return the RequestInformation for a given command, i.e.
getRequestInformation() - Method in class org.proteios.core.PluginConfigurationRequest
Get the request information object containing information about the parameters needed for the plugin.
getResearchThresh() - Method in class org.proteios.io.OMSSAParameterSet
 
getResidueModificationMass() - Method in class org.proteios.io.XTandemParameterSet
 
getResiduePotentialModificationMass() - Method in class org.proteios.io.XTandemParameterSet
 
getResiduePotentialModificationMotif() - Method in class org.proteios.io.XTandemParameterSet
 
getRestriction(Expression, Expression) - Method in enum org.proteios.core.Operator
 
getRestriction() - Method in class org.proteios.core.PropertyFilter
Create a restriction from the filter.
getResultFile() - Method in class org.proteios.core.data.SpectrumSearchData
Get the result file that this spectrumsearch was generated from
getResultFile() - Method in class org.proteios.core.SpectrumSearch
Get the result file that this spectrumsearch was generated from
getRetentionTimeInMinutes() - Method in class org.proteios.core.data.HitData
 
getRetentionTimeInMinutes() - Method in class org.proteios.core.Hit
 
getRetentionTimeInMinutes() - Method in class org.proteios.io.AHit
 
getRetentionTimeInMinutes() - Method in interface org.proteios.io.HitInterface
 
getRetentionTimeInMinutes() - Method in class org.proteios.io.SpectrumImpl
Get the retention time in minutes.
getRetentionTimeInMinutes() - Method in interface org.proteios.io.SpectrumInterface
 
getRMSError() - Method in class org.proteios.io.AHit
 
getRMSError() - Method in interface org.proteios.io.HitInterface
 
getRoleId() - Method in class org.proteios.core.data.keyring.RoleKeys
Get the id of the role.
getRoleId() - Method in class org.proteios.core.data.keyring.UserRoles
Get the id of the role.
getRoleKeyId(Item) - Static method in class org.proteios.core.SystemItems
Get the numeric id for a RoleKey when you know the Item type of the RoleKey.
getRoles() - Method in class org.proteios.core.data.RoleKeyData
Get the map that manages which roles that have permissions for this key.
getRoles() - Method in class org.proteios.core.SessionControl
Get the id of all roles where the logged in user is a member.
getRoles() - Method in class org.proteios.core.User
Get a query that returns the roles where this user is a member.
getRootAlias() - Method in interface org.proteios.core.query.Query
The alias of the root-entity in the FROM part.
getRootEntry() - Method in class org.proteios.util.Tree
Get the entry for the root node.
getRootMeanSquareError() - Method in class org.proteios.core.data.HitData
 
getRootMeanSquareError() - Method in class org.proteios.core.Hit
 
getRow() - Method in class org.proteios.core.data.MappingCoordinate
Get the row number.
getSample() - Method in class org.proteios.core.data.PeakListSetData
Get the sample
getSample() - Method in class org.proteios.core.Extract
Get the Sample that is the parent of this extract.
getSample() - Method in class org.proteios.core.PeakListSet
Get the Sample /** Get the Sample
getSampleName() - Method in class org.proteios.io.mzdata.MzDataExpSampleNameBlock
Get the sample name.
getSampleName() - Method in class org.proteios.io.mzdata.MzDataImpAdminBlock
Get the sample name.
getSampleName() - Method in class org.proteios.io.mzdata.MzDataImpSampleNameBlock
Get the sample name.
getSamples() - Method in class org.proteios.core.BioSource
Get a query that returns all samples created from this biosource.
getScale() - Method in class org.proteios.io.OMSSAParameterSet
 
getSchemaTemplate() - Method in class org.proteios.util.SchemaFactory
 
getSchemaVersion() - Method in class org.proteios.core.data.SchemaVersionData
Get the schema version.
getSchemaVersion(Session) - Static method in class org.proteios.core.SchemaVersion
Get the current schema version number as it is stored in the database.
getSchemaVersion() - Static method in class org.proteios.core.SchemaVersion
 
getScore() - Method in class org.proteios.core.data.HitData
 
getScore() - Method in class org.proteios.core.data.SearchResultData
 
getScore() - Method in class org.proteios.core.Hit
 
getScore() - Method in class org.proteios.core.SearchResult
 
getScore() - Method in class org.proteios.io.AHit
 
getScore() - Method in interface org.proteios.io.HitInterface
 
getScoreType() - Method in class org.proteios.core.data.HitData
 
getScoreType() - Method in class org.proteios.core.data.SearchResultData
 
getScoreType() - Method in class org.proteios.core.Hit
 
getScoreType() - Method in class org.proteios.core.SearchResult
Get the input filename of this SearchResult.
getScoreType() - Method in class org.proteios.io.AHit
 
getScoreType() - Method in interface org.proteios.io.HitInterface
 
getScoringAIons() - Method in class org.proteios.io.XTandemParameterSet
 
getScoringAlgorithm() - Method in class org.proteios.io.XTandemParameterSet
 
getScoringBIons() - Method in class org.proteios.io.XTandemParameterSet
 
getScoringCIons() - Method in class org.proteios.io.XTandemParameterSet
 
getScoringCyclicPermutation() - Method in class org.proteios.io.XTandemParameterSet
 
getScoringIncludeReverse() - Method in class org.proteios.io.XTandemParameterSet
 
getScoringMaximumMissedCleavageSites() - Method in class org.proteios.io.XTandemParameterSet
 
getScoringMinimumIonCount() - Method in class org.proteios.io.XTandemParameterSet
 
getScoringXIons() - Method in class org.proteios.io.XTandemParameterSet
 
getScoringYIons() - Method in class org.proteios.io.XTandemParameterSet
 
getScoringZIons() - Method in class org.proteios.io.XTandemParameterSet
 
getSearchB1() - Method in class org.proteios.io.OMSSAParameterSet
 
getSearchCTermProduct() - Method in class org.proteios.io.OMSSAParameterSet
 
getSearchDatabases() - Method in class org.proteios.core.data.SpectrumSearchData
Get the searchDatabases.
getSearchDatabases() - Method in class org.proteios.core.SpectrumSearch
 
getSearchDate() - Method in class org.proteios.core.data.HitData
Date when the identification search was performed
getSearchDate() - Method in class org.proteios.core.Hit
 
getSearchDate() - Method in class org.proteios.io.AHit
 
getSearchDate() - Method in interface org.proteios.io.HitInterface
 
getSearchEngine() - Method in class org.proteios.core.data.SpectrumSearchData
Get the software
getSearchEngine() - Method in class org.proteios.core.SpectrumSearch
Get the earch engine Software this SpectrumSearch is associated with.
getSearchModifications() - Method in class org.proteios.core.data.SpectrumSearchData
Get the searchModifications.
getSearchModifications() - Method in class org.proteios.core.SpectrumSearch
 
getSearchResult() - Method in class org.proteios.core.data.PolyPeptideData
 
getSearchResult() - Method in class org.proteios.core.PolyPeptide
Get the SearchResult this PolyPeptide is associated with.
getSearchResults() - Method in class org.proteios.core.data.SpectrumSearchData
 
getSearchResults() - Method in class org.proteios.core.SpectrumSearch
 
getSearchSpectrumType() - Method in class org.proteios.io.OMSSAParameterSet
 
getSearchTitle() - Method in class org.proteios.io.MascotParameterSet
 
getSearchType() - Method in class org.proteios.io.MascotParameterSet
Get search type.
getSecondaryLocation() - Method in class org.proteios.core.data.QuotaTypeData
If this quota type can use disk quota in the secondary location or not.
getSelectedIonList() - Method in class org.proteios.io.SpectrumPrecursor
Get the spectrum precursor selected ion list.
getSender() - Method in class org.proteios.core.Message
Get the user that sent this message.
getSeparationEvents() - Method in class org.proteios.core.SeparationMethod
 
getSeparationMethod() - Method in class org.proteios.core.data.BioMaterialEventData
 
getSeparationMethod() - Method in class org.proteios.core.SeparationEvent
Get the separation method object.
getSequence() - Method in class org.proteios.core.data.PolyPeptideData
Get the sequence
getSequence() - Method in class org.proteios.core.PolyPeptide
Get the sequence of the polypeptide.
getServer() - Method in class org.proteios.core.data.JobData
The name of the server where the job is executing.
getServer() - Method in class org.proteios.core.Job
Get the name of the server where the job is executing.
getServerAliases(String, Principal[]) - Method in class org.proteios.core.AliasKeyManager
 
getSessionControl() - Method in class org.proteios.core.AbstractBatcher
Get the SessionControl object that manages this item.
getSessionControl(String, String) - Static method in class org.proteios.core.Application
Get an existing SessionControl object if you know the id.
getSessionControl() - Method in class org.proteios.core.BasicItem
Get the SessionControl object that manages this item.
getSessionControl() - Method in class org.proteios.core.DbControl
Get the SessionControl object that owns this DbControl object.
getSessionControl() - Method in class org.proteios.io.FileExtraUtil
Get SessionControl
getSessionControl() - Method in class org.proteios.io.mzdata.MzDataExpCommonDc
 
getSessionControl() - Method in class org.proteios.io.mzdata.MzDataImpCommonDc
 
getSessionSetting(String) - Method in class org.proteios.core.SessionControl
Get the value of a session setting with the specified name.
getSetter(Class, String) - Method in class org.proteios.core.ExtendedPropertyAccessor
Create a Setter object for the specified class and property.
getSettingId() - Method in class org.proteios.io.OMSSAParameterSet
 
getShareableItems() - Static method in class org.proteios.core.Metadata
Get a set contining all Shareable item types.
getShort(int) - Method in interface org.proteios.core.query.SqlResult
Get the value of the specified column as a short.
getSignalToNoiseRatio() - Method in class org.proteios.core.data.FeatureData
 
getSignalToNoiseRatio() - Method in class org.proteios.core.Feature
 
getSingleNum() - Method in class org.proteios.io.OMSSAParameterSet
 
getSingleWin() - Method in class org.proteios.io.OMSSAParameterSet
 
getSize() - Method in class org.proteios.core.data.FileData
Get the size in bytes for this FileData object.
getSize() - Method in class org.proteios.core.File
Get the size of this file.
getSizeInBytes() - Method in interface org.proteios.core.DiskConsumable
Get the number of bytes this item uses.
getSizeInBytes() - Method in class org.proteios.core.File
Get the (uncompressed) size in bytes of this file.
getSizeXInCentiMeters() - Method in class org.proteios.core.data.GelElectrophoresisData
Get the sizeX value
getSizeXInCentiMeters() - Method in class org.proteios.core.GelElectrophoresis
Get the Integer sizeX value.
getSizeYInCentiMeters() - Method in class org.proteios.core.data.GelElectrophoresisData
Get the sizeY value
getSizeYInCentiMeters() - Method in class org.proteios.core.GelElectrophoresis
Get the Integer sizeY value.
getSmtpHost() - Method in class org.proteios.core.PreferencesFile
Get the SMTP host to use for e-mail notification.
getSmtpHost() - Method in class org.proteios.io.NotificationConfiguration
Get the SMTP host to use for e-mail notification.
getSoftware() - Method in class org.proteios.core.data.DataProcessingStepData
Get the software
getSoftware() - Method in class org.proteios.core.data.SoftwareConfigurationData
Get the software
getSoftware() - Method in class org.proteios.core.data.SoftwareTypeData
This is the inverse end.
getSoftware() - Method in class org.proteios.core.DataProcessingStep
Get the Software software.
getSoftware() - Method in class org.proteios.core.SoftwareConfiguration
Get the Software that is configured.
getSoftwareComment() - Method in class org.proteios.io.mzdata.MzDataExpSoftwareBlock
Get the softwareComment.
getSoftwareComment() - Method in class org.proteios.io.mzdata.MzDataImpSoftwareBlock
Get the softwareComment.
getSoftwareCompletionTime() - Method in class org.proteios.io.mzdata.MzDataExpSoftwareBlock
Get the softwareCompletionTime.
getSoftwareCompletionTime() - Method in class org.proteios.io.mzdata.MzDataImpSoftwareBlock
Get the softwareCompletionTime.
getSoftwareName() - Method in class org.proteios.io.mzdata.MzDataImpSoftwareBlock
Get the softwareName.
getSoftwareSettings() - Method in class org.proteios.core.data.GelImageAnalysisEventData
 
getSoftwareSettings() - Method in class org.proteios.core.GelImageAnalysisEvent
 
getSoftwareType() - Method in class org.proteios.core.data.SoftwareData
 
getSoftwareType() - Method in class org.proteios.core.Software
Get the associated SoftwareType item.
getSoftwareVersion() - Method in class org.proteios.io.mzdata.MzDataExpSoftwareBlock
Get the softwareVersion.
getSoftwareVersion() - Method in class org.proteios.io.mzdata.MzDataImpSoftwareBlock
Get the softwareVersion.
getSolubilizationBuffer() - Method in class org.proteios.core.data.GelElectrophoresisData
Get the solubilizationBuffer.
getSolubilizationBuffer() - Method in class org.proteios.core.GelElectrophoresis
Get the solubilizationBuffer of this GelElectrophoresis.
getSortOrder() - Method in class org.proteios.io.ColumnPreferences
Get sorting order value.
getSortPriority() - Method in class org.proteios.io.ColumnPreferences
Get sort priority value.
getSource() - Method in class org.proteios.io.SpectrumFileInstrument
Get the spectrum instrument source.
getSource() - Method in interface org.proteios.io.SpectrumFileInstrumentInterface
Get the spectrum instrument source.
getSourceBioMaterials() - Method in class org.proteios.core.BioMaterialEvent
Get all source biomaterials
getSourceFile() - Method in class org.proteios.core.data.PeakListSetData
Get the source file
getSourceFile() - Method in class org.proteios.core.data.SeparationEventData
 
getSourceFile() - Method in class org.proteios.core.PeakListSet
Get the File sourceFile.
getSourceFile() - Method in class org.proteios.core.SeparationEvent
 
getSourceFile() - Method in class org.proteios.io.mzdata.MzDataImpMzDataBlock
Get source core file with mzData.
getSourceFile() - Method in class org.proteios.io.mzdata.MzDataImporter
Get source core file with mzData.
getSources() - Method in class org.proteios.core.BioMaterialEvent
Get a query that return all biomaterials used as sources for this event.
getSources() - Method in class org.proteios.core.data.BioMaterialEventData
Get a map containing the source biomaterials and the used quantity for this event.
getSpecies() - Method in class org.proteios.io.MascotParameterSet
 
getSpecies() - Method in class org.proteios.io.OMSSAParameterSet
 
getSpecificity() - Method in class org.proteios.core.data.DigestParameterData
 
getSpecificity() - Method in class org.proteios.core.DigestParameter
Get the description of this DigestParameter.
getSpectrum(String) - Method in class org.proteios.io.MgfFileReader
Get the spectrum data for specified spectrum id.
getSpectrum(List<String>) - Method in class org.proteios.io.MgfFileReader
Get an iterator for spectra with specified spectrum id values.
getSpectrum(String) - Method in class org.proteios.io.MzMLFileReader
Get the spectrum data for specified spectrum id.
getSpectrum(List<String>) - Method in class org.proteios.io.MzMLFileReader
Get an iterator for spectra with specified spectrum id values.
getSpectrum(String) - Method in class org.proteios.io.PeakListFileImpl
Get the spectrum data for specified spectrum id.
getSpectrum(List<String>) - Method in class org.proteios.io.PeakListFileImpl
Get an iterator for spectra with specified spectrum ids.
getSpectrum(String) - Method in interface org.proteios.io.PeakListFileInterface
Get spectrum with specified spectrum id value.
getSpectrum(List<String>) - Method in interface org.proteios.io.PeakListFileInterface
Get an iterator for spectra with specified spectrum id values.
getSpectrum(String) - Method in class org.proteios.io.PklFileReader
Get the spectrum data for specified spectrum id.
getSpectrum(List<String>) - Method in class org.proteios.io.PklFileReader
Get an iterator for spectra with specified spectrum id values.
getSpectrumContact() - Method in class org.proteios.io.MzMLFileReader
Get the spectrum contact data.
getSpectrumContact() - Method in class org.proteios.io.PeakListFileImpl
Get the spectrum contact data.
getSpectrumContact() - Method in interface org.proteios.io.SpectrumFileContactReaderInterface
Get the spectrum file contact data.
getSpectrumDescComment() - Method in class org.proteios.io.mzdata.MzDataExpSpectrumDescBlock
Get the spectrumDescComment.
getSpectrumDescComment() - Method in class org.proteios.io.mzdata.MzDataImpSpectrumDescBlock
Get the spectrumDescComment.
getSpectrumDynamicRange() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumFileInstrumentList() - Method in class org.proteios.io.MzMLFileReader
Get the spectrum file instrument list.
getSpectrumFileInstrumentList() - Method in class org.proteios.io.PeakListFileImpl
Get the spectrum file instrument list.
getSpectrumFileInstrumentList() - Method in interface org.proteios.io.SpectrumFileInstrumentReaderInterface
Get the spectrum file instrument list.
getSpectrumFragmentMassType() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumFragmentMonoisotopicMassError() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumFragmentMonoisotopicMassErrorUnits() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumId() - Method in class org.proteios.core.data.HitData
Spectrum identifier
getSpectrumId() - Method in class org.proteios.core.data.PeakListData
Get the spectrumId value Note: No underscore is used in the database column name, i.e.
getSpectrumId() - Method in class org.proteios.core.Hit
 
getSpectrumId() - Method in class org.proteios.core.PeakList
Get the spectrumId
getSpectrumId() - Method in class org.proteios.io.AHit
 
getSpectrumId() - Method in interface org.proteios.io.HitInterface
 
getSpectrumIdList() - Method in class org.proteios.io.MgfFileReader
Get spectrum id list.
getSpectrumIdList() - Method in class org.proteios.io.MzMLFileReader
Get spectrum id list.
getSpectrumIdList() - Method in class org.proteios.io.PeakListFileImpl
Get list of all mzData spectrum ids from input stream. the function will read through the entire file.
getSpectrumIdList() - Method in class org.proteios.io.PklFileReader
Get spectrum id list.
getSpectrumIdList() - Method in interface org.proteios.io.SpectrumIdReaderInterface
Get a list of spectrum id values.
getSpectrumInstrument() - Method in class org.proteios.core.data.PeakListData
Get the spectrumInstrument
getSpectrumInstrument() - Method in class org.proteios.core.PeakList
Get the InstrumentConfiguration spectrumInstrument.
getSpectrumMaximumParentCharge() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumMaximumParentMPlusH() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumMinimumFragmentMz() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumMinimumParentMPlusH() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumMinimumPeaks() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumParentMonoisotopicMassErrorMinus() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumParentMonoisotopicMassErrorPlus() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumParentMonoisotopicMassErrorUnits() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumParentMonoisotopicMassIsotopeError() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumPath() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumRef() - Method in class org.proteios.core.data.PrecursorData
Get the spectrumRef value
getSpectrumRef() - Method in class org.proteios.core.Precursor
Get the spectrumRef
getSpectrumSearch() - Method in class org.proteios.core.data.DigestParameterData
Get the SpectrumSearchData this SearchDatabase is created from.
getSpectrumSearch() - Method in class org.proteios.core.data.SearchDatabaseData
Get the SpectrumSearchData this SearchDatabase is created from.
getSpectrumSearch() - Method in class org.proteios.core.data.SearchModificationData
Get the SpectrumSearchData this SearchDatabase is created from.
getSpectrumSearch() - Method in class org.proteios.core.data.SearchResultData
 
getSpectrumSearch() - Method in class org.proteios.core.DigestParameter
Get the SpectrumSearch this digestParameter is associated with.
getSpectrumSearch() - Method in class org.proteios.core.SearchDatabase
Get the SpectrumSearch this SearchDatabase is associated with.
getSpectrumSearch() - Method in class org.proteios.core.SearchModification
Get the SpectrumSearch this SearchModification is associated with.
getSpectrumSearch() - Method in class org.proteios.core.SearchResult
Get the SpectrumSearch this SearchResult is associated with.
getSpectrumSearches() - Method in class org.proteios.core.data.InputSpectraData
 
getSpectrumSearches() - Method in class org.proteios.core.data.PeakListSetData
 
getSpectrumSearches() - Method in class org.proteios.core.PeakListSet
 
getSpectrumSequenceBatchSize() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumStringId() - Method in class org.proteios.core.data.HitData
 
getSpectrumStringId() - Method in class org.proteios.core.data.SearchResultData
 
getSpectrumStringId() - Method in class org.proteios.core.Hit
 
getSpectrumStringId() - Method in class org.proteios.core.SearchResult
 
getSpectrumStringId() - Method in class org.proteios.io.AHit
 
getSpectrumStringId() - Method in interface org.proteios.io.HitInterface
 
getSpectrumThreads() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumTotalPeaks() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumType() - Method in class org.proteios.io.mzdata.MzDataExpAcqSpecificationBlock
Get the spectrumType.
getSpectrumType() - Method in class org.proteios.io.mzdata.MzDataExpSpectrumSettingsBlock
Get the spectrumType.
getSpectrumType() - Method in class org.proteios.io.mzdata.MzDataImpAcqSpecificationBlock
Get the spectrumType.
getSpectrumType() - Method in class org.proteios.io.mzdata.MzDataImpSpectrumDescBlock
Get the spectrumType.
getSpectrumType() - Method in class org.proteios.io.mzdata.MzDataImpSpectrumSettingsBlock
Get the spectrumType.
getSpectrumUseConditioning() - Method in class org.proteios.io.XTandemParameterSet
 
getSpectrumUseNoiseSuppression() - Method in class org.proteios.io.XTandemParameterSet
 
getSpotId() - Method in class org.proteios.core.data.HitData
 
getSpotId() - Method in class org.proteios.core.Hit
 
getSpotId() - Method in class org.proteios.io.AHit
 
getSpotId() - Method in interface org.proteios.io.HitInterface
 
getSpotId(XYCoordinate) - Method in interface org.proteios.io.PickFileInterface
 
getSpotId(List<XYCoordinate>) - Method in interface org.proteios.io.PickFileInterface
 
getSpotIdFromMicroPlate(String, String) - Method in class org.proteios.io.RobotFileImpl
Get spot id for specified well and plate id.
getSpotIdFromMicroPlate(List<String>, List<String>) - Method in class org.proteios.io.RobotFileImpl
Get list of spot ids for specified well and plate ids.
getSpotIdFromMicroPlate(String, String) - Method in interface org.proteios.io.RobotFileInterface
Returns spot id that was put in wellId in plateId
getSpotIdFromMicroPlate(List<String>, List<String>) - Method in interface org.proteios.io.RobotFileInterface
Returns spot ids that was put in wellId[i] in plateId[i]
getSpotIdFromTargetPlate(String, String) - Method in class org.proteios.io.RobotFileImpl
Get target spot id for specified target id and target position (well) id.
getSpotIdFromTargetPlate(List<String>, List<String>) - Method in class org.proteios.io.RobotFileImpl
Get list of target spot ids for specified target ids and target position (well) ids.
getSpotIdFromTargetPlate(String, String) - Method in interface org.proteios.io.RobotFileInterface
Returns target spot id that was put in positionId in targetId
getSpotIdFromTargetPlate(List<String>, List<String>) - Method in interface org.proteios.io.RobotFileInterface
Returns target spot ids that was put in positionId[i] in targetId[i]
getSpotIdListFromMicroPlate(String) - Method in class org.proteios.io.RobotFileImpl
Get spot ids for given gel id.
getSpotIdListFromMicroPlate(String) - Method in interface org.proteios.io.RobotFileInterface
Get spot ids for given gel id.
getSpotXPixel() - Method in class org.proteios.core.data.HitData
X coordinate of gel spot
getSpotXPixel() - Method in class org.proteios.core.Hit
X coordinate of gel spot
getSpotXs(List<String>, List<String>) - Method in class org.proteios.io.RobotFileSpotXY
Get list of spot x coordinates for lists of spot ids and gel ids.
getSpotYPixel() - Method in class org.proteios.core.data.HitData
Y coordinate of gel spot
getSpotYPixel() - Method in class org.proteios.core.Hit
Y coordinate of gel spot
getSpotYs(List<String>, List<String>) - Method in class org.proteios.io.RobotFileSpotXY
Get list of spot Y coordinates for lists of spot ids and gel ids.
getSqlSymbol() - Method in enum org.proteios.core.Operator
Get the SQL symbol for this operator.
getSQLType() - Method in class org.proteios.core.hibernate.TypeWrapper
Get the SQL code for database columns that can store this type.
getSQLType() - Method in enum org.proteios.core.Type
Get the type of this parameter as specified by the java.sql.Types class.
getSqlTypeCode() - Method in class org.proteios.core.BatchedPropertyInfo
Get the sql type code as defined by Types.
getSSLSocketFactory() - Static method in class org.proteios.core.Application
 
getStain() - Method in class org.proteios.core.data.StainingEventData
 
getStain() - Method in class org.proteios.core.StainingEvent
 
getStainingEvents() - Method in class org.proteios.core.GelElectrophoresis
 
getStartDate() - Method in class org.proteios.core.data.NewsData
Get the first day this news item should be shown.
getStartDate() - Method in class org.proteios.core.News
Get the start date and time for this news item to be published.
getStarted() - Method in class org.proteios.core.data.JobData
Get the date and time the job was started or null if the job hasn't been started.
getStarted() - Method in class org.proteios.core.Job
Get the date and time the job was started.
getStartPosition() - Method in class org.proteios.core.data.PeptideData
 
getStartPosition() - Method in class org.proteios.core.Peptide
 
getStartRetentionTimeInMinutes() - Method in class org.proteios.core.data.FeatureData
 
getStartRetentionTimeInMinutes() - Method in class org.proteios.core.Feature
 
getState(Class<D>) - Method in class org.proteios.core.QueryFactory
 
getStatus() - Method in class org.proteios.core.data.JobData
Get the status of the job. 1 = waiting, 2 = running, 3 = completed ok, 4 = error
getStatus() - Method in class org.proteios.core.Job
Get the status of the job.
getStatus() - Method in class org.proteios.core.PluginResponse
Get the status of the response.
getStatusMessage() - Method in class org.proteios.core.data.JobData
Get a status message.
getStatusMessage() - Method in class org.proteios.core.Job
Get a message about the current status of the job.
getStorageLocation() - Method in class org.proteios.core.BioMaterial
Get the storage location of the biomaterial.
getStorageLocation() - Method in class org.proteios.core.data.BioMaterialData
Get the storage location for the biomaterial
getString(String) - Static method in class org.proteios.core.Config
Get the configuration setting specified by key as a String value.
getString(String, String) - Static method in class org.proteios.core.Config
Get the configuration setting specified by key as a String value.
getString(int) - Method in interface org.proteios.core.query.SqlResult
Get the value of the specified column as a string.
getString(String) - Static method in class org.proteios.util.Values
Convert a string to a string, and map NULL to the empty string.
getString(String, String) - Static method in class org.proteios.util.Values
Convert a string to a string.
getString(Collection<?>, String, boolean) - Static method in class org.proteios.util.Values
 
getStringOrNull(String) - Static method in class org.proteios.util.Values
Convert the empty string ("") to null after removing leading and trailing whitespace.
getStringValue() - Method in enum org.proteios.core.Type
Get the string value representation of this type.
getSubDirectories() - Method in class org.proteios.core.Directory
Get a query that return subdirectories of this directory.
getSubHitsInCombination() - Method in class org.proteios.core.Hit
This function will return a list of combined hits that have this hit as their primary hit.
getSubsetThresh() - Method in class org.proteios.io.OMSSAParameterSet
 
getSymbol() - Method in enum org.proteios.core.Operator
Get the symbol for this operator, useful for display in client applications.
getSystemId() - Method in class org.proteios.core.data.DirectoryData
 
getSystemId() - Method in class org.proteios.core.data.FileTypeData
 
getSystemId() - Method in class org.proteios.core.data.GroupData
 
getSystemId() - Method in class org.proteios.core.data.HardwareTypeData
 
getSystemId() - Method in class org.proteios.core.data.ProtocolTypeData
 
getSystemId() - Method in class org.proteios.core.data.QuotaData
 
getSystemId() - Method in class org.proteios.core.data.QuotaTypeData
 
getSystemId() - Method in class org.proteios.core.data.RoleData
 
getSystemId() - Method in class org.proteios.core.data.SoftwareTypeData
 
getSystemId() - Method in interface org.proteios.core.data.SystemData
Get the system id for the item.
getSystemId() - Method in class org.proteios.core.data.UserData
 
getSystemId() - Method in class org.proteios.core.Directory
 
getSystemId() - Method in class org.proteios.core.FileType
 
getSystemId() - Method in class org.proteios.core.Group
 
getSystemId() - Method in class org.proteios.core.HardwareType
 
getSystemId() - Method in class org.proteios.core.ProtocolType
 
getSystemId() - Method in class org.proteios.core.Quota
 
getSystemId() - Method in class org.proteios.core.QuotaType
 
getSystemId() - Method in class org.proteios.core.Role
 
getSystemId() - Method in class org.proteios.core.SoftwareType
 
getSystemId() - Method in interface org.proteios.core.SystemItem
Get the system id for the item.
getSystemId() - Method in class org.proteios.core.User
 
getTableName() - Method in class org.proteios.core.RealTable
Get the unquoted table name of this table in the database.
getTablePreferencesList() - Method in class org.proteios.core.PreferencesFile
Get the table preferences list.
getTablePreferencesMode() - Method in class org.proteios.core.PreferencesFile
Get the table preferences mode.
getTargetIdFromTargetPlate(String, String) - Method in class org.proteios.io.RobotFileImpl
Get target id for specified target spot id and gel id.
getTargetIdFromTargetPlate(List<String>, List<String>) - Method in class org.proteios.io.RobotFileImpl
Get list of target ids for specified target spot ids and gel ids.
getTargetIdFromTargetPlate(String, String) - Method in interface org.proteios.io.RobotFileInterface
 
getTargetIdFromTargetPlate(List<String>, List<String>) - Method in interface org.proteios.io.RobotFileInterface
 
getTargetIdListFromTargetPlate() - Method in class org.proteios.io.RobotFileImpl
Get target ids.
getTargetIdListFromTargetPlate() - Method in interface org.proteios.io.RobotFileInterface
Get target ids.
getTargetPlateIdFromTargetPlate(String, String) - Method in class org.proteios.io.RobotFileImpl
Get target plate id for specified target id and target position (well) id.
getTargetPlateIdFromTargetPlate(List<String>, List<String>) - Method in class org.proteios.io.RobotFileImpl
Get list of target plate ids for specified target ids and target position (well) ids.
getTargetPlateIdFromTargetPlate(String, String) - Method in interface org.proteios.io.RobotFileInterface
Returns target plate id that was put in positionId in targetId
getTargetPlateIdFromTargetPlate(List<String>, List<String>) - Method in interface org.proteios.io.RobotFileInterface
Returns target plate ids that was put in positionId[i] in targetId[i]
getTargetPositionExampleFromTargetPlate() - Method in class org.proteios.io.RobotFileImpl
Get target position example from input stream.
getTaxonomy() - Method in class org.proteios.core.data.SearchDatabaseData
 
getTaxonomy() - Method in class org.proteios.core.SearchDatabase
Get the taxonomy of this SearchDatabase.
getTempStrBuf() - Method in class org.proteios.io.mzdata.MzDataImpCommon
Get the StringBuffer tempStrBuf value.
getTerminalSpecificity() - Method in class org.proteios.core.data.SearchModificationData
 
getTerminalSpecificity() - Method in class org.proteios.core.SearchModification
The enum representation of the int value in the database is returned.
getThetaJoin(Query, DbControl) - Method in class org.proteios.core.query.HqlInnerJoin
 
getThetaJoin(Query, DbControl) - Method in class org.proteios.core.query.HqlLeftJoin
 
getThetaJoin(Query, DbControl) - Method in class org.proteios.core.query.HqlRightJoin
 
getThetaJoin(Query, DbControl) - Method in interface org.proteios.core.query.Join
 
getThetaJoinCondition(Query, DbControl) - Method in class org.proteios.core.query.HqlInnerJoin
 
getThetaJoinCondition(Query, DbControl) - Method in class org.proteios.core.query.HqlLeftJoin
 
getThetaJoinCondition(Query, DbControl) - Method in class org.proteios.core.query.HqlRightJoin
 
getThetaJoinCondition(Query, DbControl) - Method in interface org.proteios.core.query.Join
 
getThread(int) - Method in interface org.proteios.core.AbortableJobQueueReadOnlyInterface
Get the thread for a job id.
getThread() - Method in class org.proteios.core.Job
Get the Thread for the job.
getTimeInMinutes() - Method in class org.proteios.core.data.PeakListData
Get the time in minutes.
getTimeInMinutes() - Method in class org.proteios.core.PeakList
Get the time in minutes.
getTimeInMinutes() - Method in class org.proteios.io.mzdata.MzDataExpSpectrumInstrumentBlock
Get the timeInMinutes.
getTimeInMinutes() - Method in class org.proteios.io.mzdata.MzDataImpSpectrumInstrumentBlock
Get the timeInMinutes.
getTimeSent() - Method in class org.proteios.core.data.MessageData
Get the date and time this message was sent.
getTimeSent() - Method in class org.proteios.core.Message
Get the date and time the message was sent.
getTitle() - Method in class org.proteios.core.ExtendedProperty
Get the title of the extended property.
getTitle() - Method in class org.proteios.core.RequestInformation
Get the title of the request.
getTo() - Method in class org.proteios.core.data.MessageData
The user this message is to.
getTo() - Method in class org.proteios.core.Message
Get the User this message was sent to.
getToAddress() - Method in class org.proteios.core.PreferencesFile
Get the "to" address to use for e-mail notification.
getToAddress() - Method in class org.proteios.io.NotificationConfiguration
Get the "to" address to use for e-mail notification.
getTopHitNum() - Method in class org.proteios.io.OMSSAParameterSet
Number of top intensity peaks in first pass
getTotal() - Method in class org.proteios.core.SimpleAbsoluteProgressReporter
Get the end point of the task.
getTotalCount() - Method in class org.proteios.core.DataResultIterator
From the QueryResult interface ---------------------------------
getTotalCount() - Method in class org.proteios.core.DynamicResultIterator
From the QueryResult interface ---------------------------------
getTotalCount() - Method in class org.proteios.core.ItemResultIterator
From the QueryResult interface ---------------------------------
getTotalCount() - Method in interface org.proteios.core.query.QueryResult
Get the total number of items returned by the query, ignoring any limits set by Query.setFirstResult(int) and Query.setMaxResults(int).
getTotalInsertCount() - Method in class org.proteios.core.BasicBatcher
 
getTotalIntensity() - Method in class org.proteios.core.data.HitData
The total intensity of a spot
getTotalIntensity() - Method in class org.proteios.core.data.PeakListData
Get the total peak intensity.
getTotalIntensity() - Method in class org.proteios.core.Hit
 
getTotalIntensity() - Method in class org.proteios.core.PeakList
Get the total peak intensity.
getTotalIntensity() - Method in class org.proteios.io.AHit
 
getTotalIntensity() - Method in interface org.proteios.io.HitInterface
 
getTotalPeaks() - Method in class org.proteios.core.data.HitData
 
getTotalPeaks() - Method in class org.proteios.core.Hit
 
getTotalPeaks() - Method in class org.proteios.io.AHit
 
getTotalPeaks() - Method in interface org.proteios.io.HitInterface
 
getType() - Method in class org.proteios.core.Acquisition
 
getType() - Method in class org.proteios.core.Annotation
 
getType() - Method in class org.proteios.core.AnnotationSet
 
getType() - Method in class org.proteios.core.AnnotationType
 
getType(Annotatable) - Method in class org.proteios.core.Annotator
 
getType() - Method in class org.proteios.core.BasicBatcher
Get the type of item supported by the batcher.
getType() - Method in class org.proteios.core.BioMaterialEvent
 
getType() - Method in class org.proteios.core.BioSource
 
getType() - Method in class org.proteios.core.Client
 
getType() - Method in class org.proteios.core.data.JobData
The type of job: 1 = run plugin, 2 = other
getType() - Method in class org.proteios.core.DataProcessingStep
 
getType() - Method in class org.proteios.core.DigestParameter
 
getType() - Method in class org.proteios.core.Directory
 
getType() - Method in class org.proteios.core.DiskUsage
 
getType() - Method in class org.proteios.core.ExtendedProperty
Get the type of the extended property.
getType() - Method in class org.proteios.core.Extract
 
getType() - Method in class org.proteios.core.Feature
 
getType() - Method in class org.proteios.core.File
 
getType() - Method in class org.proteios.core.FileType
 
getType() - Method in class org.proteios.core.GelElectrophoresis
 
getType() - Method in class org.proteios.core.GelImageAnalysisEvent
 
getType() - Method in class org.proteios.core.GelScanEvent
 
getType() - Method in class org.proteios.core.GlobalDefaultSetting
 
getType() - Method in class org.proteios.core.Group
 
getType() - Method in class org.proteios.core.Hardware
 
getType() - Method in class org.proteios.core.HardwareConfiguration
 
getType() - Method in class org.proteios.core.HardwareType
 
getType() - Method in class org.proteios.core.Hit
 
getType() - Method in interface org.proteios.core.Identifiable
Get the type of item represented by the object.
getType() - Method in class org.proteios.core.IPG
 
getType() - Method in class org.proteios.core.ItemKey
 
getType() - Method in class org.proteios.core.Job
 
getType() - Method in class org.proteios.core.Label
 
getType() - Method in class org.proteios.core.LabeledExtract
 
getType() - Method in class org.proteios.core.LiquidChromatography
 
getType() - Method in class org.proteios.core.MascotParameterSetStorage
 
getType() - Method in class org.proteios.core.MeasuredArea
 
getType() - Method in class org.proteios.core.Message
 
getType() - Method in class org.proteios.core.MimeType
 
getType() - Method in class org.proteios.core.News
 
getType() - Method in class org.proteios.core.ObservedModification
 
getType() - Method in class org.proteios.core.OMSSAParameterSetStorage
 
getType() - Method in class org.proteios.core.Path
Get the type of the path.
getType() - Method in class org.proteios.core.Peak
 
getType() - Method in class org.proteios.core.PeakBatcher
 
getType() - Method in class org.proteios.core.PeakList
 
getType() - Method in class org.proteios.core.PeakListBatcher
 
getType() - Method in class org.proteios.core.PeakListSet
 
getType() - Method in class org.proteios.core.Peptide
 
getType() - Method in class org.proteios.core.plugin.GuiContext
 
getType() - Method in class org.proteios.core.PluginConfiguration
 
getType() - Method in class org.proteios.core.PluginDefinition
 
getType() - Method in class org.proteios.core.PluginType
 
getType() - Method in class org.proteios.core.Precursor
 
getType() - Method in class org.proteios.core.Project
 
getType() - Method in class org.proteios.core.ProjectKey
 
getType() - Method in class org.proteios.core.Protein
 
getType() - Method in class org.proteios.core.Protocol
 
getType() - Method in class org.proteios.core.ProtocolType
 
getType() - Method in class org.proteios.core.Quota
 
getType() - Method in class org.proteios.core.QuotaType
 
getType() - Method in class org.proteios.core.Role
 
getType() - Method in class org.proteios.core.RoleKey
 
getType() - Method in class org.proteios.core.Sample
 
getType() - Method in class org.proteios.core.SearchDatabase
 
getType() - Method in class org.proteios.core.SearchModification
 
getType() - Method in class org.proteios.core.SearchResult
 
getType() - Method in class org.proteios.core.SeparationEvent
 
getType() - Method in class org.proteios.core.SeparationMethod
 
getType() - Method in class org.proteios.core.Session
 
getType() - Method in class org.proteios.core.Software
 
getType() - Method in class org.proteios.core.SoftwareConfiguration
 
getType() - Method in class org.proteios.core.SoftwareType
 
getType() - Method in class org.proteios.core.SpectrumSearch
 
getType() - Method in class org.proteios.core.StainingEvent
 
getType() - Method in class org.proteios.core.UpdateEvent
 
getType() - Method in class org.proteios.core.User
 
getType() - Method in class org.proteios.core.XTandemParameterSetStorage
 
getType(Class<?>) - Method in class org.proteios.TypeUtil
 
getTypeWrapper() - Method in enum org.proteios.core.Type
Get a wrapper for accessing underlying type information from Hibernate.
getUniformResourceIdentifier() - Method in class org.proteios.core.data.FileData
Get the URI of this file.
getUniformResourceIdentifier() - Method in class org.proteios.core.File
 
getUniqueCharges(Project, DbControl) - Static method in class org.proteios.core.Hit
 
getUniqueExternalIds(Project, DbControl) - Static method in class org.proteios.core.Hit
 
getUniqueFeatureFiles(Project, DbControl) - Static method in class org.proteios.core.Feature
 
getUniqueFeatureFilesForMsFile(Project, File, DbControl) - Static method in class org.proteios.core.Feature
 
getUniqueFractionIds(Project, DbControl) - Static method in class org.proteios.core.Hit
 
getUniqueGelIds(Project, DbControl) - Static method in class org.proteios.core.Hit
 
getUniqueIdentificationResultFiles(Project, DbControl) - Static method in class org.proteios.core.Hit
 
getUniqueIdentificationResultFilesForPeakListFile(Project, File, DbControl) - Static method in class org.proteios.core.Hit
 
getUniqueLocalSampleIds(Project, DbControl) - Static method in class org.proteios.core.Hit
 
getUniqueMsFiles(Project, DbControl) - Static method in class org.proteios.core.Feature
 
getUniqueMsFilesForFeatureFile(Project, File, DbControl) - Static method in class org.proteios.core.Feature
 
getUniquePeakListFiles(Project, DbControl) - Static method in class org.proteios.core.Hit
 
getUniquePeakListFilesForIdentificationResultFile(Project, File, DbControl) - Static method in class org.proteios.core.Hit
 
getUniquePeptideSequences(Project, DbControl) - Static method in class org.proteios.core.Hit
 
getUniquePlateIds(Project, DbControl) - Static method in class org.proteios.core.Hit
 
getUniqueReplicateIds(Project, DbControl) - Static method in class org.proteios.core.Hit
 
getUniqueReplicateIdsForLocalSampleId(Project, String, DbControl) - Static method in class org.proteios.core.Hit
 
getUniqueScoreTypes(Project, DbControl) - Static method in class org.proteios.core.Hit
 
getUniqueScoreTypesWithCombinedFDR(Project, DbControl) - Static method in class org.proteios.core.Hit
 
getUpdates(int, int) - Method in class org.proteios.core.UpdatesFactory
Update the database by modifying existing items to follow new requirements.
getUpdateSchemaVersion() - Method in class org.proteios.core.AbstractUpdateToSchemaVersion
Get the update schema version.
getUpdateSchemaVersion() - Method in class org.proteios.core.UpdateToSchemaVersion10
Get the update schema version.
getUpdateSchemaVersion() - Method in class org.proteios.core.UpdateToSchemaVersion2
Get the update schema version.
getUpdateSchemaVersion() - Method in class org.proteios.core.UpdateToSchemaVersion3
Get the update schema version.
getUpdateSchemaVersion() - Method in class org.proteios.core.UpdateToSchemaVersion4
Get the update schema version.
getUpdateSchemaVersion() - Method in class org.proteios.core.UpdateToSchemaVersion5
Get the update schema version.
getUpdateSchemaVersion() - Method in class org.proteios.core.UpdateToSchemaVersion6
Get the update schema version.
getUpdateSchemaVersion() - Method in class org.proteios.core.UpdateToSchemaVersion7
Get the update schema version.
getUpdateSchemaVersion() - Method in class org.proteios.core.UpdateToSchemaVersion8
Get the update schema version.
getUpdateSchemaVersion() - Method in class org.proteios.core.UpdateToSchemaVersion9
Get the update schema version.
getUpdateSchemaVersion() - Method in class org.proteios.core.UpdateToSchemaVersionTmpl
Get the update schema version.
getUploadStream(boolean) - Method in class org.proteios.core.File
Get an OutputStream that can be used to upload a physical file for this file item.
getUploadStream(boolean, Boolean) - Method in class org.proteios.core.File
Get an OutputStream that can be used to upload a physical file for this file item.
getUploadStream(boolean, Boolean, boolean) - Method in class org.proteios.core.File
Get an OutputStream that can be used to upload a physical file for this file item.
getUpperLimit() - Method in class org.proteios.core.DoubleParameterType
Get the highest valid value of the parameter.
getUpperLimit() - Method in class org.proteios.core.FloatParameterType
Get the highest valid value of the parameter.
getUpperLimit() - Method in class org.proteios.core.IntegerParameterType
Get the highest valid value of the parameter.
getUpperLimit() - Method in class org.proteios.core.LongParameterType
Get the highest valid value of the parameter.
getUrl() - Method in class org.proteios.core.data.PluginDefinitionData
Get a URL with more information about the plugin.
getUrl() - Method in class org.proteios.core.data.UserData
Get the URL to the user's homepage, or null if unknown.
getURL() - Method in class org.proteios.core.LsidElement
Will return a URL to an online resource where more info on the protein can be found.
getUrl() - Method in interface org.proteios.core.plugin.About
An URL to get more information about the plugin.
getUrl() - Method in class org.proteios.core.plugin.AboutImpl
 
getUrl() - Method in class org.proteios.core.PluginDefinition
Get a URL with more information about the plugin.
getUrl() - Method in class org.proteios.core.User
Get the URL to the user's homepage, or null if unknown.
getUrl() - Method in class org.proteios.io.SpectrumFileContact
Get the contact url.
getUrl() - Method in interface org.proteios.io.SpectrumFileContactInterface
Get the contact url.
getUsedQuantityInMicroLiters() - Method in class org.proteios.core.BioMaterialEvent
Get the quantity that was used from the biomaterial by this event.
getUsedQuantityInMicroLiters(MeasuredBioMaterial) - Method in class org.proteios.core.BioMaterialEvent
Get the quantity in microliters that was used by this event for the specified biomaterial.
getUsedQuantityInMicroLiters() - Method in class org.proteios.core.data.BioMaterialEventData
Get the used quantity of the biomaterial affected by this event, measured in microliters.
getUsedQuantityInMicroLiters() - Method in class org.proteios.core.data.UsedQuantity
Get the used quantity.
getUser() - Method in class org.proteios.core.BioMaterialEvent
Get the User that is responsible for this event.
getUser() - Method in class org.proteios.core.data.BioMaterialEventData
Get the user that is responsible for this event, typically this is the user that entered the information in the database.
getUser() - Method in class org.proteios.core.data.DiskUsageData
Get the user that owns the DiskConsumable item.
getUser() - Method in class org.proteios.core.data.PasswordData
Get the user this password is referring to.
getUser() - Method in class org.proteios.core.data.SessionData
Get the user that logged in with this session.
getUser() - Method in class org.proteios.core.data.UserClientSettingData
Get the user this setting is valid for.
getUser() - Method in class org.proteios.core.data.UserDefaultSettingData
Get the user this setting is valid for.
getUser() - Method in class org.proteios.core.DiskUsage
Get the user that owns the DiskConsumable item.
getUser() - Method in class org.proteios.core.LockFile
Get the user the Lock file is intended for.
getUser() - Method in class org.proteios.core.PreferencesFile
Get the user the preferences file is intended for.
getUser() - Method in class org.proteios.core.Session
Get the user that logged in with this session.
getUserClientSetting(String) - Method in class org.proteios.core.SessionControl
Get the value of the UserClientSetting with the specified name.
getUserDefaultSetting(String) - Method in class org.proteios.core.SessionControl
Get the value of the UserDefaultSetting with the specified name.
getUserId() - Method in class org.proteios.core.data.keyring.UserGroups
Get the id of the user.
getUserId() - Method in class org.proteios.core.data.keyring.UserKeys
Get the id of the user.
getUserId() - Method in class org.proteios.core.data.keyring.UserProjects
Get the id of the user.
getUserId() - Method in class org.proteios.core.data.keyring.UserRoles
Get the id of the user.
getUserLogin() - Method in class org.proteios.core.Path
Get the userlogin part of the path.
getUserParamList() - Method in class org.proteios.io.mzdata.MzDataImpProcessingMethodBlock
Get the userParamList.
getUsers() - Method in class org.proteios.core.data.GroupData
Get the set that manages which users are members of this group.
getUsers() - Method in class org.proteios.core.data.ItemKeyData
Get the map that manages which users that have permissions for this key.
getUsers() - Method in class org.proteios.core.data.ProjectData
Get the map that manages which users are members of this project and their permissions.
getUsers() - Method in class org.proteios.core.data.RoleData
Get the set that manages which users are members of this role.
getUsers() - Method in class org.proteios.core.Group
Get a query that returns the users that are members of this group.
getUsers() - Method in class org.proteios.core.MultiPermissions
Get a query that returns all users appearing in at least one of the item keys.
getUsers() - Method in class org.proteios.core.Project
Get a query that returns the users that are members of this project.
getUsers() - Method in class org.proteios.core.Role
Get a query that returns the users that are members of this role.
getValidatedXml(URL, URL) - Static method in class org.proteios.util.XMLUtil
Load and validate an XML file against a DTD, and return it as a Document object.
getValidatedXml(String, URL) - Static method in class org.proteios.util.XMLUtil
Parse and validate a string containing XML against a DTD, and return it as a Document object.
getValue() - Method in class org.proteios.core.data.PropertyFilterData
Get the value used in this filter.
getValue() - Method in class org.proteios.core.data.SettingData
Get the value of this setting.
getValue() - Method in enum org.proteios.core.File.Action
Get the integer value that is used when storing an File.Action to the database.
getValue() - Method in enum org.proteios.core.Item
Get the integer value that is used when storing an item to the database.
getValue() - Method in enum org.proteios.core.Job.ExecutionTime
Get the integer value that is used when storing a Job.ExecutionTime in the database.
getValue() - Method in enum org.proteios.core.Job.Status
Get the integer value that is used when storing a Job.Status to the database.
getValue() - Method in enum org.proteios.core.Job.Type
Get the integer value that is used when storing a Job.Status to the database.
getValue() - Method in enum org.proteios.core.Location
Get the integer value that is used when storing an location to the database.
getValue() - Method in enum org.proteios.core.Operator
Get the integer value that is used when storing an operator in the database.
getValue() - Method in enum org.proteios.core.plugin.GuiContext.Type
Get the integer value that is used when storing a GuiContext.Type to the database.
getValue(String) - Method in interface org.proteios.core.plugin.ParameterValues
Get a single value for a specific parameter.
getValue() - Method in enum org.proteios.core.plugin.Plugin.MainType
 
getValue() - Method in class org.proteios.core.PropertyFilter
Get the value to use in the filter.
getValue() - Method in class org.proteios.core.Setting
Get the value of this setting.
getValue() - Method in enum org.proteios.core.Type
Get the integer value that is used when storing a type in the database.
getValue() - Method in class org.proteios.io.mzdata.CvParam
Get the value.
getValue() - Method in class org.proteios.io.mzdata.UserParam
Get the value.
getValue() - Method in enum org.proteios.io.NotificationConfiguration.Mode
Get the integer value that is used when storing a NotificationConfiguration.Mode to the database.
getValue() - Method in enum org.proteios.io.SpectrumPrecursor.FragmentationType
Get the integer value for a SpectrumPrecursor.FragmentationType.
getValue() - Method in class org.proteios.io.StringPair
Get the value.
getValue() - Method in interface org.proteios.io.StringPairInterface
Get the value.
getValue() - Method in enum org.proteios.io.TablePreferencesConfiguration.Mode
Get the integer value that is used when storing a TablePreferencesConfiguration.Mode to the database.
getValue(OBJECT_TEMPLATE) - Method in class org.proteios.props.AbstractReader
 
getValue(Annotation) - Method in class org.proteios.props.AnnotationTypeNameReader
 
getValue(Annotation) - Method in class org.proteios.props.AnnotationValueReader
 
getValue(Date) - Method in class org.proteios.props.DateReader
 
getValue(BioMaterialEvent) - Method in class org.proteios.props.EntryDateReader
 
getValue(Enum) - Method in class org.proteios.props.EnumReader
 
getValue(BioMaterialEvent) - Method in class org.proteios.props.EventCommentReader
 
getValue(BioMaterialEvent) - Method in class org.proteios.props.EventTypeReader
 
getValue(BioMaterial) - Method in class org.proteios.props.ExternalIdReader
 
getValue(File) - Method in class org.proteios.props.FileTypeNameReader
 
getValue(Hit) - Method in class org.proteios.props.IdentificationResultFileNameReader
 
getValue(Identifiable) - Method in class org.proteios.props.IdReader
 
getValue(LabeledExtract) - Method in class org.proteios.props.LabelNameReader
 
getValue(MascotParameterSetStorage) - Method in class org.proteios.props.MascotParameterFileNameReader
 
getValue(MascotParameterSetStorage) - Method in class org.proteios.props.MascotParameterFileSearchTypeReader
 
getValue(Nameable) - Method in class org.proteios.props.NameReader
 
getValue(OMSSAParameterSetStorage) - Method in class org.proteios.props.OMSSAParameterFileNameReader
 
getValue(MeasuredBioMaterial) - Method in class org.proteios.props.OriginalQuantityReader
 
getValue(Hit) - Method in class org.proteios.props.PeakListFileNameReader
 
getValue(Protocol) - Method in class org.proteios.props.ProtocolFileNameReader
 
getValue(Protocol) - Method in class org.proteios.props.ProtocolTypeNameReader
 
getValue(XTandemParameterSetStorage) - Method in class org.proteios.props.XTandemParameterFileNameReader
 
getValue(T, T, T) - Method in class org.proteios.util.Diff3
Get the correct value to set on the newItem object.
getValue() - Method in class org.proteios.util.Enumeration.Entry
 
getValue(int) - Method in class org.proteios.util.Enumeration
 
getValueAsObject() - Method in class org.proteios.core.PropertyFilter
Get the value as an object of the correct type.
getValueClass() - Method in enum org.proteios.core.Type
Get the class of objects that can be used as values for this type.
getValueOf(String) - Method in class org.proteios.io.AHit
 
getValueOf(List<String>) - Method in class org.proteios.io.AHit
 
getValueOf(String) - Method in interface org.proteios.io.HitInterface
Implementation specific method to get an arbitrary value not defined by the methods in this interface.
getValueOf(List<String>) - Method in interface org.proteios.io.HitInterface
Implementation specific method to get an arbitrary values not defined by the methods in this interface.
getValues() - Method in class org.proteios.core.Annotation
Get the values this annotation contains.
getValues() - Method in class org.proteios.core.AnnotationType
Get the list of allowed values if this annotation type is an enumeration.
getValues() - Method in class org.proteios.core.data.AnnotationData
The values of this annotation.
getValues() - Method in class org.proteios.core.data.BooleanParameterValueData
 
getValues() - Method in class org.proteios.core.data.DateParameterValueData
 
getValues() - Method in class org.proteios.core.data.DoubleParameterValueData
 
getValues() - Method in class org.proteios.core.data.FileParameterValueData
 
getValues() - Method in class org.proteios.core.data.FloatParameterValueData
 
getValues() - Method in class org.proteios.core.data.IntegerParameterValueData
 
getValues() - Method in class org.proteios.core.data.ItemParameterValueData
 
getValues() - Method in class org.proteios.core.data.LongParameterValueData
 
getValues() - Method in class org.proteios.core.data.ParameterValueData
Get values of this parameter.
getValues() - Method in class org.proteios.core.data.StringParameterValueData
 
getValues() - Method in class org.proteios.core.data.TextParameterValueData
 
getValues(String) - Method in interface org.proteios.core.plugin.ParameterValues
Get a List of values for a specific parameter.
getValuesVersion() - Method in class org.proteios.core.Annotation
Get the version number of the item keeping the values.
getValueType() - Method in class org.proteios.core.AnnotationType
Get the value type for this annotation type.
getValueType() - Method in class org.proteios.core.data.AnnotationTypeData
The code for the value type.
getValueType() - Method in class org.proteios.core.data.PropertyFilterData
Get the type of value user for this filter.
getValueType() - Method in class org.proteios.core.PropertyFilter
Get the type of the property.
getVariable() - Method in class org.proteios.io.MascotParameterSet
 
getVariable() - Method in class org.proteios.io.OMSSAParameterSet
 
getVersion() - Method in class org.proteios.core.BasicItem
 
getVersion() - Method in class org.proteios.core.data.BasicData
Get the version of the item.
getVersion() - Method in interface org.proteios.core.data.IdentifiableData
Get the version of this item.
getVersion() - Method in interface org.proteios.core.Identifiable
Get the version number of the item.
getVersion() - Method in interface org.proteios.core.plugin.About
The version of the plugin software.
getVersion() - Method in class org.proteios.core.plugin.AboutImpl
 
getVersion() - Method in class org.proteios.io.mzdata.CvLookup
Get the version.
getVersionIdentifier() - Method in class org.proteios.core.data.SearchDatabaseData
 
getVersionIdentifier() - Method in class org.proteios.core.SearchDatabase
 
getVersionMarker() - Static method in class org.proteios.core.Application
Get the version marker of Proteios.
getVersionString() - Method in class org.proteios.core.data.HardwareData
 
getVersionString() - Method in class org.proteios.core.data.SoftwareData
 
getVersionString() - Method in class org.proteios.core.Hardware
Get the versionstring of this Hardware item.
getVersionString() - Method in class org.proteios.core.Software
Get the versionstring of this Software item.
getVolume() - Method in class org.proteios.core.data.MeasuredAreaData
Get the volume value.
getVolume() - Method in class org.proteios.core.MeasuredArea
Get the Float volume value.
getWellIdExampleFromMicroPlate() - Method in class org.proteios.io.RobotFileImpl
Get well id example from input stream.
getWellIdFromMicroPlate(String, String) - Method in class org.proteios.io.RobotFileImpl
Get well id for specified spot id and gel id.
getWellIdFromMicroPlate(List<String>, List<String>) - Method in class org.proteios.io.RobotFileImpl
Get list of well ids for specified spot ids and gel ids.
getWellIdFromMicroPlate(String, String) - Method in interface org.proteios.io.RobotFileInterface
 
getWellIdFromMicroPlate(List<String>, List<String>) - Method in interface org.proteios.io.RobotFileInterface
 
getWellPosition() - Method in class org.proteios.core.data.HitData
A well position, e.g.
getWellPosition() - Method in class org.proteios.core.Hit
 
getWellPosition() - Method in class org.proteios.io.AHit
 
getWellPosition() - Method in interface org.proteios.io.HitInterface
 
getWidth() - Method in class org.proteios.core.AnnotationType
Get the recommended width in characters a client application should use to render an input field for annotations of this annotation type.
getWidth() - Method in class org.proteios.core.data.AnnotationTypeData
The recommended width (characters) to display input fields for this annotation in client applications.
getWidth() - Method in class org.proteios.core.ParameterType
Get the width of the input field in the GUI.
getWriteMethod(AttributeDefinition) - Method in class org.proteios.ClassDescriptor
 
getWriteMethodName() - Method in class org.proteios.AttributeDefinition
 
getX() - Method in class org.proteios.XYCoordinate
 
getXMLCrudeWriter() - Method in class org.proteios.io.XMLExportUtil
Get XMLCrudeWriter implementation.
getXMLFilePath() - Method in class org.proteios.io.MascotParameterFileUtil
Get Mascot input XML file path.
getXMLFilePath() - Method in class org.proteios.io.mzdata.MzDataExporter
Get mzData XML file path.
getXMLFilePath() - Method in class org.proteios.io.mzdata.MzDataImpCommonPeakListSet
Get mzData XML file path.
getXMLFilePath() - Method in class org.proteios.io.mzdata.MzDataImpMzDataBlock
Get mzData XML file path.
getXMLFilePath() - Method in class org.proteios.io.mzdata.MzDataImporter
Get mzData XML file path.
getXMLFilePath() - Method in class org.proteios.io.mzdata.MzDataImportTest
Get mzData XML file path.
getXMLFilePath() - Method in class org.proteios.io.OMSSAParameterFileUtil
Get OMSSA input XML file path.
getXMLFilePath() - Method in class org.proteios.io.XTandemParameterFileUtil
Get XTandem input XML file path.
getXMLInputStream() - Method in class org.proteios.io.MascotParameterFileUtil
Get Mascot input XML input stream.
getXMLInputStream() - Method in class org.proteios.io.MzMLFileReader
Get mzML XML input stream.
getXMLInputStream() - Method in class org.proteios.io.OMSSAParameterFileUtil
Get OMSSA input XML input stream.
getXMLInputStream() - Method in class org.proteios.io.PeakListFileImpl
Get mzData XML input stream.
getXMLInputStream() - Method in class org.proteios.io.RobotFileImpl
Get robot XML input stream.
getXMLInputStream() - Method in class org.proteios.io.XTandemParameterFileUtil
Get XTandem input XML input stream.
getXMLOutputStream() - Method in class org.proteios.io.MascotParameterFileUtil
Get Mascot input XML output stream.
getXMLOutputStream() - Method in class org.proteios.io.OMSSAParameterFileUtil
Get OMSSA input XML output stream.
getXMLOutputStream() - Method in class org.proteios.io.XTandemParameterFileUtil
Get XTandem input XML output stream.
getXsdFilePath() - Method in class org.proteios.io.MascotParameterFileUtil
Get XSD schema file to validate against.
getXsdFilePath() - Method in class org.proteios.io.mzdata.MzDataExporter
Get XSD schema file to validate against.
getXsdFilePath() - Method in class org.proteios.io.mzdata.MzDataImporter
Get XSD schema file to validate against.
getXsdFilePath() - Method in class org.proteios.io.mzdata.MzDataImportTest
Get XSD schema file to validate against.
getXsdFilePath() - Method in class org.proteios.io.MzMLFileReader
Get XSD schema file to validate against.
getXsdFilePath() - Method in class org.proteios.io.OMSSAParameterFileUtil
Get XSD schema file to validate against.
getXsdFilePath() - Method in class org.proteios.io.PeakListFileImpl
Get XSD schema file to validate against.
getXsdFilePath() - Method in class org.proteios.io.RobotFileImpl
Get XSD schema file to validate against.
getXsdFilePath() - Method in class org.proteios.io.RobotFileSpotXY
Get XSD schema file to validate against.
getXsdFilePath() - Method in class org.proteios.io.XTandemParameterFileUtil
Get XSD schema file to validate against.
getXTandemParameterFile() - Method in class org.proteios.io.XTandemParameterFileUtil
Get the XTandem parameter file item.
getXTandemParameterSet() - Method in class org.proteios.core.data.FileData
Get the xTandemParameterSets.
getXTandemParameterSet() - Method in class org.proteios.io.XTandemParameterFileUtil
Get the XTandem parameter set item.
getXTandemParameterSet() - Method in interface org.proteios.io.XTandemParameterFileUtilInterface
 
getY() - Method in class org.proteios.XYCoordinate
 
getZDep() - Method in class org.proteios.io.OMSSAParameterSet
 
GlobalDefaultSetting - Class in org.proteios.core
This class is used to represent a global default setting.
GlobalDefaultSettingData - Class in org.proteios.core.data
 
GlobalDefaultSettingData() - Constructor for class org.proteios.core.data.GlobalDefaultSettingData
 
gotoTag(XMLStreamReader, XMLTag) - Method in class org.proteios.io.XMLReaderUtil
Positions the parser to start tag matching the given template.
gotoTag(XMLStreamReader, String) - Method in class org.proteios.io.XMLReaderUtil
Positions the parser to the tag named tagName.
gotoTag(XMLStreamReader, String, Integer, String) - Method in class org.proteios.io.XMLReaderUtil
If attrIndex and attrValue are both null only the tagName will be searched for
gotoTag(XMLStreamReader, String, String, String) - Method in class org.proteios.io.XMLReaderUtil
 
Group - Class in org.proteios.core
This class is used to represent groups.
group(Expression) - Method in interface org.proteios.core.query.Query
Add an expression query element to the group list.
GroupData - Class in org.proteios.core.data
This class holds information about a group.
GroupData() - Constructor for class org.proteios.core.data.GroupData
 
GroupGroups - Class in org.proteios.core.data.keyring
Class for mapping the GroupGroups table.
GroupGroups() - Constructor for class org.proteios.core.data.keyring.GroupGroups
Create a new GroupGroups object.
GroupKeys - Class in org.proteios.core.data.keyring
Class for mapping the GroupKeys table.
GroupKeys() - Constructor for class org.proteios.core.data.keyring.GroupKeys
Create a new GroupKeys object.
groupPermanent(Expression) - Method in interface org.proteios.core.query.Query
Permanently add an expression query element to the group list.
GroupPermissions - Class in org.proteios.core
This class is used to specify permissions to share an item to groups.
GroupPermissions() - Constructor for class org.proteios.core.GroupPermissions
Create a new empty object.
GroupPermissions(ItemKey) - Constructor for class org.proteios.core.GroupPermissions
Create a new object, and initialise it with the permissions from a ItemKey.
GroupProjects - Class in org.proteios.core.data.keyring
Class for mapping the GroupProjects table.
GroupProjects() - Constructor for class org.proteios.core.data.keyring.GroupProjects
Create a new GroupProjects object.
gt(AnnotationType, Object, boolean) - Static method in class org.proteios.core.query.Annotations
Create a restriction that searches for annotations greater than a given value.