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## Uses of Class
ru.biosoft.access.DataCollection

Packages that use DataCollection
biouml.model |
biouml.model.dynamics |
biouml.model.util |
biouml.plugins.cellml |
biouml.plugins.gxl |
biouml.plugins.sbml |
biouml.plugins.sbw |
biouml.plugins.simulation |
biouml.plugins.simulation.access |
biouml.plugins.simulation.plot |
biouml.plugins.simulation.plot.access |
biouml.standard.type |
biouml.standard.type.access |
biouml.workbench.diagram |
ru.biosoft.access |
ru.biosoft.access.repository |
ru.biosoft.access.search |
ru.biosoft.access.support |
ru.biosoft.gui.wizard |
ru.biosoft.plugins |
ru.biosoft.plugins.javascript |

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)`

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