Uses of DataCollection in biouml.model

 

Classes in biouml.model that implement DataCollection
class	Compartment           General definition of the compartment as a container for nodes and edges between them.

 

Constructors in biouml.model with parameters of type DataCollection

Compartment.Compartment(DataCollection parent, Base kernel)

Compartment.Compartment(DataCollection parent, String id, Base kernel)

Diagram.Diagram(DataCollection origin, Base kernel, DiagramType type)           Creates the diagram of the specified type.

DiagramElement.DiagramElement(DataCollection parent, Base kernel)           Constructs the diagram element.

DiagramElement.DiagramElement(DataCollection parent, String name, Base kernel)           Constructs the diagram element.

Edge.Edge(DataCollection parent, Base kernel, Node input, Node output)

Edge.Edge(DataCollection parent, String id, Base kernel, Node input, Node output)

EquivalentNodeGroup.EquivalentNodeGroup(DataCollection parent, String name)

Module.Module(DataCollection primaryCollection, Properties properties)           Constructs derived data collection with primary collection.

Node.Node(DataCollection parent, Base kernel)

Node.Node(DataCollection parent, String name, Base kernel)

 

Methods in biouml.model that return DataCollection
DataCollection	Module.getCategory(Class c)
DataCollection	Module.getDiagrams()
static DataCollection	Node.findCommonOrigin(DataCollection first, DataCollection second)

 

Methods in biouml.model with parameters of type DataCollection
void	Compartment.propagateElementChanged(DataCollection source, DataCollectionEvent primaryEvent)
void	Compartment.propagateElementWillChange(DataCollection source, DataCollectionEvent primaryEvent)
DiagramElement	Diagram.clone(DataCollection origin, String newName)
static Diagram	Diagram.createDiagram(DiagramType type, String diagramName, DataCollection origin)
static DataCollection	Node.findCommonOrigin(DataCollection first, DataCollection second)

 

Uses of DataCollection in biouml.model.dynamics

 

Constructors in biouml.model.dynamics with parameters of type DataCollection

Variable.Variable(String name, EModel model, DataCollection origin)

VariableRole.VariableRole(String name, DataCollection origin, double initialValue)           For internal usage.

VariableRole.VariableRole(DataCollection origin, DiagramElement diagramElement, double initialValue)

VariablesDataCollection.VariablesDataCollection(DataCollection parent, Diagram diagram)

 

Methods in biouml.model.dynamics that return DataCollection
DataCollection	EModel.getParameters()
DataCollection	EModel.getVariableRoles()
DataCollection	EModel.getVariables()

 

Uses of DataCollection in biouml.model.util

 

Methods in biouml.model.util that return DataCollection
static DataCollection	Framework.getModules()

 

Methods in biouml.model.util with parameters of type DataCollection
Diagram	DiagramXmlReader.read(DataCollection origin, Module module)

 

Uses of DataCollection in biouml.plugins.cellml

 

Constructors in biouml.plugins.cellml with parameters of type DataCollection

Reaction.Reaction(DataCollection origin, String name)

Species.Species(String name, DataCollection parent, String type)

Species.Species(String name, DataCollection parent)

 

Methods in biouml.plugins.cellml with parameters of type DataCollection
Diagram	CellMLModelReader.read(DataCollection origin, Module module)

 

Uses of DataCollection in biouml.plugins.gxl

 

Methods in biouml.plugins.gxl with parameters of type DataCollection
Diagram	GxlReader.readDiagram(File file, DataCollection origin)

 

Uses of DataCollection in biouml.plugins.sbml

 

Constructors in biouml.plugins.sbml with parameters of type DataCollection

Specie.Specie(String name, DataCollection parent, String type)

Specie.Specie(String name, DataCollection parent)

 

Methods in biouml.plugins.sbml with parameters of type DataCollection
static Diagram	SbmlModelFactory.readDiagram(File file, DataCollection origin, String diagramName)
Diagram	SbmlModelReader.read(Document document, String name, DataCollection origin)

 

Uses of DataCollection in biouml.plugins.sbw

 

Constructors in biouml.plugins.sbw with parameters of type DataCollection

SbwModule.SbwModule(DataCollection parent, ModuleDescriptor descriptor)

SbwServiceCategory.SbwServiceCategory(DataCollection parent, String name)

SbwVisiblePlugin.SbwVisiblePlugin(DataCollection parent, Properties properties)           Constructor to be used by CollectionFactory to create a Plugin.

 

Methods in biouml.plugins.sbw that return DataCollection
DataCollection	SbwServiceMethod.getOrigin()

 

Uses of DataCollection in biouml.plugins.simulation

 

Constructors in biouml.plugins.simulation with parameters of type DataCollection

SimulationResult.SimulationResult(DataCollection origin, String name)

 

Uses of DataCollection in biouml.plugins.simulation.access

 

Methods in biouml.plugins.simulation.access with parameters of type DataCollection
void	SimulationResultTransformer.init(DataCollection primaryCollection, DataCollection transformedCollection)

 

Uses of DataCollection in biouml.plugins.simulation.plot

 

Constructors in biouml.plugins.simulation.plot with parameters of type DataCollection

Plot.Plot(String name, DataCollection origin, List series)

Plot.Plot(String name, DataCollection origin)

 

Methods in biouml.plugins.simulation.plot that return DataCollection
DataCollection	PlotEx.getPlotCollection()
DataCollection	PlotEx.getSimulationResultCollection()
DataCollection	PlotPane.getResultCollection()

 

Methods in biouml.plugins.simulation.plot with parameters of type DataCollection
static Plot	Plot.createDefaultPlot(DataCollection plotCollection)
void	PlotPane.setResultCollection(DataCollection resultCollection)

 

Uses of DataCollection in biouml.plugins.simulation.plot.access

 

Methods in biouml.plugins.simulation.plot.access with parameters of type DataCollection
void	PlotTransformer.init(DataCollection primaryCollection, DataCollection transformedCollection)

 

Uses of DataCollection in biouml.standard.type

 

Classes in biouml.standard.type that implement DataCollection
class	Reaction

 

Constructors in biouml.standard.type with parameters of type DataCollection

BaseSupport.BaseSupport(String name, DataCollection parent, String type)

Cell.Cell(DataCollection parent, String name)

Compartment.Compartment(DataCollection origin, String name)

Concept.Concept(DataCollection origin, String name)

Constant.Constant(DataCollection parent, String name)

DatabaseInfo.DatabaseInfo(DataCollection parent, String name)

DiagramInfo.DiagramInfo(DataCollection parent, String name)

DiagramReference.DiagramReference(DataCollection origin, String name)

Function.Function(DataCollection parent, String name)

Gene.Gene(DataCollection origin, String name)

KineticType.KineticType(DataCollection origin, String name, String title, String description, boolean reversible, String function, Element[] elements)

KineticType.KineticType(DataCollection origin, String name)

LiteratureReference.LiteratureReference(DataCollection parent, String name)

Process.Process(DataCollection parent, String name)

Protein.Protein(DataCollection origin, String name)

Reaction.Reaction(DataCollection origin, String name)

RelationType.RelationType(DataCollection parent, String name)

RNA.RNA(DataCollection origin, String name)

SemanticRelation.SemanticRelation(DataCollection origin, String name, String relationType)

SemanticRelation.SemanticRelation(DataCollection origin, String name)

SpecieReference.SpecieReference(DataCollection origin, String name, String role)

SpecieReference.SpecieReference(DataCollection origin, String name)

Species.Species(DataCollection parent, String name)

State.State(DataCollection parent, String name)

Stub.Stub(String name, DataCollection parent, String type)

Stub.Stub(String name, DataCollection parent)

Substance.Substance(DataCollection origin, String name)

Unit.Unit(DataCollection parent, String name)

 

Methods in biouml.standard.type that return DataCollection
DataCollection	ReferrerBeanInfo.LiteratureReferencesEditor.getDataCollection()

 

Methods in biouml.standard.type with parameters of type DataCollection
void	Reaction.propagateElementChanged(DataCollection source, DataCollectionEvent primaryEvent)
void	Reaction.propagateElementWillChange(DataCollection source, DataCollectionEvent primaryEvent)
SpecieReference	SpecieReference.clone(DataCollection origin, String name)

 

Uses of DataCollection in biouml.standard.type.access

 

Constructors in biouml.standard.type.access with parameters of type DataCollection

TitleSqlIndex.TitleSqlIndex(DataCollection dc)

 

Methods in biouml.standard.type.access with parameters of type DataCollection
boolean	CellSqlTransformer.init(DataCollection owner)
boolean	CompartmentSqlTransformer.init(DataCollection owner)
boolean	ConceptSqlTransformer.init(DataCollection owner)
boolean	DatabaseInfoSqlTransformer.init(DataCollection owner)
boolean	DiagramSqlTransformer.init(DataCollection owner)
boolean	GeneSqlTransformer.init(DataCollection owner)
boolean	ProteinSqlTransformer.init(DataCollection owner)
boolean	ReactionSqlTransformer.init(DataCollection owner)
void	ReactionTransformer.init(DataCollection primaryCollection, DataCollection transformedCollection)
boolean	RelationSqlTransformer.init(DataCollection owner)
boolean	RNASqlTransformer.init(DataCollection owner)
boolean	SubstanceSqlTransformer.init(DataCollection owner)

 

Uses of DataCollection in biouml.workbench.diagram

 

Constructors in biouml.workbench.diagram with parameters of type DataCollection

NewDiagramDialog.NewDiagramDialog(JFrame frame, String title, DataCollection repository, Module module)

 

Uses of DataCollection in ru.biosoft.access

 

Subinterfaces of DataCollection in ru.biosoft.access
interface	CollectionUnion           Collection that is union of several collections.

 

Classes in ru.biosoft.access that implement DataCollection
class	AbstractDataCollection           This abstract class provides default implementations for most of the methods in the DataCollection interface.

 

Constructors in ru.biosoft.access with parameters of type DataCollection

AbstractDataCollection.AbstractDataCollection(DataCollection parent, Properties properties)           Constructor to be used by CollectionFactory to creata DataCollection.

DataCollectionAddUndo.DataCollectionAddUndo(DataElement elementWillAdd, DataCollection parent)

DataCollectionEvent.DataCollectionEvent(Object source, int type, DataCollection owner, String name, DataCollectionEvent primaryEvent)           Constructs the DataCollectionEvent object.

DataCollectionInfo.DataCollectionInfo(DataCollection dc, Properties properties, Category cat)

DataCollectionRemoveUndo.DataCollectionRemoveUndo(DataElement elementWillRemove, DataCollection parent)

DataCollectionUnion.DataCollectionUnion(DataCollection dc, Properties properties)           Make union of all collections contained in specified data collection.

DataCollectionUnion2.DataCollectionUnion2(DataCollection dc, Properties properties)

DataCollectionUnion2.DataCollectionUnion2(DataCollection[] collections, Properties properties)

DataElementRef.DataElementRef(String name, DataCollection origin, String elementName)

DataElementSupport.DataElementSupport(String name, DataCollection origin)           Construct data element.

DefaultQuerySystem.DefaultQuerySystem(DataCollection dc)

DerivedDataCollection.DerivedDataCollection(DataCollection parent, String name, DataCollection primaryDC, Properties properties)           Constructs DerivedDataCollection with the parent, name and primary data collection.

DerivedDataCollection.DerivedDataCollection(DataCollection parent, Properties properties)           Constructor to be used by CollectionFactory.

Entry.Entry(DataCollection parent, String name, File pFile, long pOffset, long pSize)           Construct big data element with TEXT_FORMAT.

Entry.Entry(DataCollection pParent, String pName, String pData, String pFormat)           Construct data element.

Entry.Entry(DataCollection pParent, String pName, String pData)           Construct data element with TEXT_FORMAT.

EntryCollection.EntryCollection(DataCollection parent, Properties properties)           Standard data collection constructor.

FileCollection.FileCollection(DataCollection parent, Properties properties)           Constructs data collection with parent.

FileDataElement.FileDataElement(String name, DataCollection origin, File parent)           Constructs FileDataElement with specified name,parent DataCollection,and parent subdirectory

FileDataElement.FileDataElement(String name, DataCollection origin, String parent)           Constructs FileDataElement with specified name,parent DataCollection,and name of parent subdirectory

FileEntryCollection.FileEntryCollection(DataCollection parent, Properties properties)           Loads the data collection and its indexes (currently only for id).

FileEntryCollection2.FileEntryCollection2(DataCollection parent, Properties properties)

FilteredDataCollection.FilteredDataCollection(DataCollection parent, String name, DataCollection primaryCollection, Filter filter, FunctionJobControl jobControl, Properties properties)           Creates FilteredDataCollection with the specified parent, name, primary data collection and filter.

FilteredDataCollection.FilteredDataCollection(DataCollection parent, Properties properties)           Constructor to be used by CollectionFactory.

LocalRepository.LocalRepository(DataCollection parent, Properties properties)           Constructs LocalRepository.

MutableDataElementSupport.MutableDataElementSupport(String name, DataCollection origin)

SqlDataCollection.SqlDataCollection(DataCollection parent, Properties properties)           Standart constructor for creating data collection.

TransformedDataCollection.TransformedDataCollection(DataCollection parent, Properties properties)           Constructs transformed data collection with parent.

VectorDataCollection.VectorDataCollection(String name, DataCollection parent, Properties properties)           Constructs data collection with specified name and parent.

VectorDataCollection.VectorDataCollection(DataCollection parent, Properties properties)           Constructor to be used by CollectionFactory to create VectorDataCollection.

 

Methods in ru.biosoft.access that return DataCollection
DataCollection	AbstractTransformer.getPrimaryCollection()           Gets primary data collection connected with transformer.
DataCollection	AbstractTransformer.getTransformedCollection()           Gets transformed data collection connected with transformer.
static DataCollection	CollectionFactory.createCollection(DataCollection parent, Properties properties)           Creates DataCollection with the specified parent and properties.
static DataCollection	CollectionFactory.createDerivedCollection(Repository parent, String name, Properties primary, Properties derived, String subDir)
static DataCollection	CollectionFactory.createRepository(String path)
static DataCollection	CollectionFactory.createTempMemoryCollection()
static DataCollection	CollectionFactory.createTransformedCollection(Repository parent, String name, Class transformerClass, Class dataElementType, String imgName, String childrenImage, String fileFilter, String startTag, String idTag, String endTag, String subDir)
static DataCollection	CollectionFactory.createTransformedFileCollection(LocalRepository parent, String name, String filter, Class transformerClass)
static DataCollection	CollectionFactory.getDataCollection(String completeName)           Returns the data collection with the speicified complete name relative of one of the data collection from data collections registered in root hash map.
DataCollection	DataCollectionEvent.getOwner()
DataCollection	DataElement.getOrigin()           Returns the collection this element belongs to.
DataCollection	DataElementSupport.getOrigin()           Return origin data collection for this data element.
DataCollection	DerivedDataCollection.getPrimaryCollection()
DataCollection	LocalRepository.createDataCollection(String name, Properties properties, String subDir, String configName, File[] files, boolean copy, CreateDataCollectionController controller)           Creates new DataCollection with specified subdir (if not null) and config file name.
DataCollection	MutableDataElementSupport.getOrigin()
DataCollection	Repository.createDataCollection(String name, Properties properties, String subDir, String configName, File[] files, boolean copy, CreateDataCollectionController controller)           Creates new DataCollection.
DataCollection	Transformer.getPrimaryCollection()           Return data collection which contain output data element.
DataCollection	Transformer.getTransformedCollection()           Return data collection which contain input data element.

 

Methods in ru.biosoft.access with parameters of type DataCollection
void	AbstractDataCollection.propagateElementChanged(DataCollection source, DataCollectionEvent primaryEvent)
void	AbstractDataCollection.propagateElementWillChange(DataCollection source, DataCollectionEvent primaryEvent)
void	AbstractTransformer.init(DataCollection primaryCollection, DataCollection transformedCollection)           Initialize transformer for support optional methods.
static void	CollectionFactory.copyDataCollection(DataCollection source, DataCollection dest, FunctionJobControl jc, String successMessage)
static DataCollection	CollectionFactory.createCollection(DataCollection parent, Properties properties)           Creates DataCollection with the specified parent and properties.
static DataElement	CollectionFactory.getDataElement(String relativeName, DataCollection ancestor)           Returns the DataElement with the specified name.
static String	CollectionFactory.getRelativeName(DataElement child, DataCollection ancestor)           Returns complete name of DataElement relative its ancestor.
static void	CollectionFactory.registerRoot(DataCollection dc)           Register DataCollection in root HashMap.
static void	CollectionFactory.releaseCollection(DataCollection dataCollection)           Releases all element of DataCollection DataCollection.
static void	CollectionFactory.unregisterRoot(DataCollection dataCollection)           Unegister DataCollection in root HashMap.
void	CollectionUnion.addCollection(DataCollection dc)           Add all elements from specified collection to union.
void	DataCollection.propagateElementChanged(DataCollection source, DataCollectionEvent primaryEvent)
void	DataCollection.propagateElementWillChange(DataCollection source, DataCollectionEvent primaryEvent)
void	DataCollectionUnion.addCollection(DataCollection dc)
void	DataCollectionUnion2.addCollection(DataCollection child)
List	QueryFilter.doQuery(DataCollection dc)
boolean	SqlTransformer.init(DataCollection owner)           Initialize transformer.
boolean	SqlTransformerSupport.init(DataCollection owner)
void	Transformer.init(DataCollection dcInput, DataCollection dcOutput)           Initialize transformer for support optional methods.

 

Uses of DataCollection in ru.biosoft.access.repository

 

Constructors in ru.biosoft.access.repository with parameters of type DataCollection

RepositoryPane.RepositoryPane(DataCollection repository)

 

Methods in ru.biosoft.access.repository that return DataCollection
DataCollection	RepositoryPane.getRootDataCollection()

 

Uses of DataCollection in ru.biosoft.access.search

 

Constructors in ru.biosoft.access.search with parameters of type DataCollection

DataSearch.DataSearch(String title, DataCollection collection)

 

Uses of DataCollection in ru.biosoft.access.support

 

Constructors in ru.biosoft.access.support with parameters of type DataCollection

DatabaseEntry.DatabaseEntry(DataCollection origin, String name, Entry entry)

DataCollectionMultyChoiceDialog.DataCollectionMultyChoiceDialog(Component parent, String title, DataCollection dc, String[] selectedValues, boolean isSorted)

DataCollectionMultyChoicePane.DataCollectionMultyChoicePane(DataCollection dc, String[] selectedValues, boolean isSorted)

DataCollectionRowModelAdapter.DataCollectionRowModelAdapter(DataCollection dc)

NameListToComboBoxModelAdapter.NameListToComboBoxModelAdapter(DataCollection dataCollection)

NameListToListModelAdapter.NameListToListModelAdapter(DataCollection dataCollection)

NewDataElementDialog.NewDataElementDialog(Component parent, String title, DataCollection dc)

 

Methods in ru.biosoft.access.support that return DataCollection
DataCollection	DatabaseEntry.getOrigin()
abstract DataCollection	DataCollectionMultyChoicePropertyEditor.getDataCollection()           Should return the DataCollection containing possible values.

 

Methods in ru.biosoft.access.support with parameters of type DataCollection
void	BeanInfoEntryTransformer.init(DataCollection primaryCollection, DataCollection transformedCollection)           Initialize transformer.
static String	IdGenerator.generateUniqueName(DataCollection dc, DecimalFormat formatter)

 

Uses of DataCollection in ru.biosoft.gui.wizard

 

Methods in ru.biosoft.gui.wizard that return DataCollection
DataCollection	WizardTarget.getProfiles()
DataCollection	WizardTarget.getSequences()

 

Uses of DataCollection in ru.biosoft.plugins

 

Constructors in ru.biosoft.plugins with parameters of type DataCollection

VisiblePlugin.VisiblePlugin(DataCollection parent, Properties properties)           Constructor to be used by CollectionFactory to create a Plugin.

 

Methods in ru.biosoft.plugins that return DataCollection
static DataCollection	Plugins.getPlugins()

 

Uses of DataCollection in ru.biosoft.plugins.javascript

 

Constructors in ru.biosoft.plugins.javascript with parameters of type DataCollection

ClassInfo.ClassInfo(String name, DataCollection parent)           Creates info for the specified Java class.

FunctionInfo.FunctionInfo(String name, DataCollection parent)           Creates info for the specified JavaScript function.

HostObjectInfo.HostObjectInfo(String name, DataCollection parent)           Creates info for the specified host object.

JScriptVisiblePlugin.JScriptVisiblePlugin(DataCollection parent, Properties properties)           Constructor to be used by CollectionFactory to create a Plugin.

PropertyInfo.PropertyInfo(String name, DataCollection parent)           Creates info for the specified property.

 

Methods in ru.biosoft.plugins.javascript that return DataCollection
DataCollection	JScriptVisiblePlugin.getFunctions()
DataCollection	JScriptVisiblePlugin.getHostObjects()

 

Methods in ru.biosoft.plugins.javascript with parameters of type DataCollection
static void	JScriptContext.defineFunction(IConfigurationElement element, Context context, ScriptableObject scope, DataCollection functions)
static void	JScriptContext.defineHostObject(IConfigurationElement element, Context context, ScriptableObject scope, DataCollection hostObjects)
static void	JScriptContext.loadFunctionExtensions(String extensionPointId, DataCollection functions)           Load all executable extensions for the specified extension point.
static void	JScriptContext.loadHostObjectExtensions(String extensionPointId, DataCollection hostObjects)