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## Uses of Package
ru.biosoft.access

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

Classes in ru.biosoft.access used by biouml.model
Compartment General definition of the compartment as a container for nodes and edges between them.
Diagram
DiagramElement Common definition of diagram element.
Edge Edge is directed relation between two diagram nodes, called "input" and "output".
EquivalentNodeGroup Group of equivalent nodes.
Module The module data is hierarchically organised in following manner: Diagrams `DataCollection` of `Diagram`s.
ModuleType
Node Diagram node element

Classes in ru.biosoft.access used by biouml.model.dynamics
EModel Genrally this role should be assotiated with Diagram.
EModel.VariableFilter
Variable Model parameter.
VariableRole General variable definition.
VariablesDataCollection

Classes in ru.biosoft.access used by biouml.model.util
DiagramXmlReader
DiagramXmlTransformer
Framework
ModuleActivator This class is used to activate the module during the process of module instalation.
ModulePackager

Classes in ru.biosoft.access used by biouml.plugins.cellml
CellMLDiagramTransformer
CellMLModelReader
CellMLModuleType Module type that process CellML 1.0 and 1.1 biochemical models.
Reaction
Species This is a wrapper class to handle RDF elemenet assotiated with CellML component.

Classes in ru.biosoft.access used by biouml.plugins.ginsim
GinSimTransformer

Classes in ru.biosoft.access used by biouml.plugins.gxl
GxlReader
GxlTransformer

Classes in ru.biosoft.access used by biouml.plugins.jgraph
DiagramToJGraphTransformer Converts BioUML diagram or its part into org.jgraph.graph for usage by graph layout algorithm.

Classes in ru.biosoft.access used by biouml.plugins.sbml
SbmlDiagramTransformer
SbmlModelFactory Utility class to read/write diagrams in SBML format.
SbmlModelReader
SbmlModuleType Module type that process SBML diagrams.
Specie

Classes in ru.biosoft.access used by biouml.plugins.sbw
SbwModule
SbwService
SbwServiceCategory
SbwServiceMethod
SbwVisiblePlugin Wrapper class to get access to SBW modules from BioUML.

Classes in ru.biosoft.access used by biouml.plugins.simulation
SimulationResult

Classes in ru.biosoft.access used by biouml.plugins.simulation.access
SimulationResultSqlTransformer
SimulationResultTransformer

Classes in ru.biosoft.access used by biouml.plugins.simulation.plot
Plot
PlotEx It supports extened views of plot in property inspector.
PlotPane

Classes in ru.biosoft.access used by biouml.plugins.simulation.plot.access
PlotSqlTransformer
PlotTransformer

Classes in ru.biosoft.access used by biouml.standard
StandardModuleActivator
StandardModuleType Definition of standard BioUML module.

Classes in ru.biosoft.access used by biouml.standard.filter
BiopolimerDiagramFilter.CellTypeFilter
BiopolimerDiagramFilter.InducerFilter
BiopolimerDiagramFilter.SpeciesFilter
ValueActionFilter Filter condition is specified as a set of ActionValuess.

Classes in ru.biosoft.access used by biouml.standard.type
Base General interface to be implemented by all classes to be used as BioUML diagram elements.
BaseSupport Base class for all data element types.
Cell Stub
Compartment Stub
Concept
Constant Some constant that can be used in kinetic or other equations.
DatabaseInfo Many data elements can refer to other databases through its database references field.
DiagramInfo Defines common properties for diagram description.
DiagramReference
Function Molecular function is an activity or task performed by a gene product or other biological entity.
Gene Stub
KineticType Definition of KinetReactionType defines: - meta information about reaction
LiteratureReference Defines coomon properties of literature reference.
Process Biological process is a biological goal that requires more than one function.
Protein Stub
Reaction
ReferrerBeanInfo.LiteratureReferencesEditor
RelationType Unit to specify kinetic constat, parameter or variable units.
RNA Stub
SemanticRelation SemanticRelatio specified semantic relationships between concepts (kernels) assotiated with two nodes on the diagram.
SpecieReference SpecieReference specifies role of molecule involved in the Reaction.
Species General definition for 'Species' concept.
State State, stage or variant of biological system or its subunits.
Stub
Substance Stub
Unit Unit to specify kinetic constat, parameter or variable units.

Classes in ru.biosoft.access used by biouml.standard.type.access
BiopolymerSqlTransformer
CellSqlTransformer
CompartmentSqlTransformer
ConceptSqlTransformer
DatabaseInfoSqlTransformer
DiagramSqlTransformer
GeneSqlTransformer
ProteinSqlTransformer
ReactionSqlTransformer
ReactionTransformer
ReferrerSqlTransformer
RelationSqlTransformer
RelationTypeSqlTransformer
RNASqlTransformer
SpeciesSqlTransformer
SubstanceSqlTransformer
TitleSqlIndex TitleSqlIndex is map where key is Base#title and value Base#name.
UnitSqlTransformer

Classes in ru.biosoft.access used by biouml.workbench
RepositoryDocument.RepositoryUndoListener Special listener to undo/redo changes in repository document.

Classes in ru.biosoft.access used by biouml.workbench.diagram
NewDiagramDialog

Classes in ru.biosoft.access used by ru.biosoft.access
AbstractDataCollection This abstract class provides default implementations for most of the methods in the `DataCollection` interface.
AbstractTransformer Transform data element of one type to other type.
BTreeIndex Maps keys to entries.
BTreeIndex.IntKey
BTreeRangeIndex Index for search keys by custom algorithm.
CollectionFactory
CollectionUnion Collection that is union of several collections.
CompositeFilter
CreateDataCollectionDefaultController Default implementation of creating data collection.
DataCollection DataCollection is a set of homogeneous DataElements.
DataCollectionAddUndo
DataCollectionEvent Implements event change in a collection .
DataCollectionInfo
DataCollectionListener Interface for listen data collection events.
DataCollectionListenerSupport Utility class that implements stub for DataCollectionListener.
DataCollectionRemoveUndo
DataCollectionUndoListener These class listen all changes inn DataCollection, converts them to UndoableEdit and add them to UndoManager.
DataCollectionUnion Collection that is union of several collections.
DataCollectionUnion2
DataElement Minimal interface for storing object in the data collection.
DataElementRef
DataElementSupport Implements DataElement interface by common way.
DefaultQuerySystem DefaultQuerySystem loads indexes based on information from DataCollectionInfo.
DerivedDataCollection General class for derived data collection.
Entry DataElement that store his data in text-based format.
EntryCollection
FileCollection FileCollection is DataCollection for storing FileDataElement objects .
FileDataElement FileDataElement is DataElement which wraps the File object.
FileEntryCollection Implements simple access procedures to databases in EMBL-like format.
FileEntryCollection2
Filter Used for filtering data elements.
Filter.IncludeAllFilter Implementation of filter that accept any data element.
Filter.IncludeNoneFilter Implementation of filter that accept nothing.
FilteredDataCollection
Index Interface for storing/extracting indexes.
Index.StringIndexEntry
IndexTable IndexTable extention of hash table for work with database indexes.
LocalRepository LocalRepository creates hierarchical DataCollection.
LocalRepositoryBeanInfo
MemIndex
MutableDataElement
MutableDataElementSupport
MutableFilter `MutableFilter` is a filter whose selection condition can be changed in runtime.
PatternFilter Abstract filter to check some `DataElement` property to correspond regular expression.
QueryFilter
QuerySystem ...
Repository
SqlDataCollection DataCollection which store all information in SQL DBMS.
SqlDataCollectionBeanInfo
SqlTransformer Adapter for storing/extracting data elements to/from SQL DBMS.
SqlTransformerSupport
TransformedDataCollection Implemnation note: we are not propagate DataCollectionEvents, because this work is done by primary DataCollection (it has the same parent).
TransformedDataCollectionBeanInfo
Transformer Transforms DataElement from one type to another.
VectorDataCollection DataCollection based on Vector ( DataElement's is stored in Vector ).
XMLTransformer Converts FileDataElement to the Object and back This transformer is used for Embl file format converting

Classes in ru.biosoft.access used by ru.biosoft.access.repository
DataCollectionTreeModelAdapter
RepositoryListener
RepositoryPane

Classes in ru.biosoft.access used by ru.biosoft.access.search
ArrayPropertyValueFilter
BeanValueFilter
DataSearch
FilteringSettings
PropertyValueFilter

Classes in ru.biosoft.access used by ru.biosoft.access.support
AbstractImportDialog Abstract dialog for import
BeanInfoEntryTransformer
DatabaseEntry General class allowing to present (wrap) the database Entry as DynamicPropertySetSupport
DatabaseEntryTransformer
DataCollectionMultyChoiceDialog
DataCollectionMultyChoicePane This pane allows a user to select several DataElement names from DataCollection name list.
DataCollectionMultyChoicePropertyEditor
DataCollectionRowModelAdapter
EntryParser Parse the field value from database Entry.
IdGenerator Utility class to generate unique name for the specified database using pattern # specified by decimal format.
NameListToComboBoxModelAdapter
NameListToListModelAdapter
NewDataElementDialog Creates new DataElement for the specified DataCollection.
TagEntryTransformer

Classes in ru.biosoft.access used by ru.biosoft.gui
RepositoryDocument

Classes in ru.biosoft.access used by ru.biosoft.gui.wizard
WizardTarget

Classes in ru.biosoft.access used by ru.biosoft.plugins
Plugins This class is used to show 'visible' plugins in plugins tab of repository pane.
VisiblePlugin Superclass for all 'visible' plugins.

Classes in ru.biosoft.access used by ru.biosoft.plugins.javascript
ClassInfo
FunctionInfo Provides JavaScript function description, and description for its arguments, throwable exception and returned value.
HostObjectInfo Provides description of JavaScript host object.
JScriptContext
JScriptVisiblePlugin Utility class used as root tree for JavaScript functions and host objects.
JScriptVisiblePluginBeanInfo
PropertyInfo Provides description for property of JavaScript class or host object.

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