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| 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 Diagrams. | |
| 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.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 | |
MutableFilterMutableFilter 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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