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## Uses of Package
ru.biosoft.access

Packages that use ru.biosoft.access
biouml.editor |
biouml.model |
biouml.model.dynamics |
biouml.model.util |
biouml.modules.genenet |
biouml.modules.genenet.access |
biouml.modules.genenet.type |
biouml.modules.kegg |
biouml.modules.kegg.type |
biouml.modules.kegg.type.access |
biouml.modules.transpath |
biouml.modules.transpath.type |
biouml.modules.transpath.type.access |
biouml.standard |
biouml.standard.diagram.pathway |
biouml.standard.filter |
biouml.standard.type |
biouml.standard.type.access |
ru.biosoft.access |
ru.biosoft.access.repository |
ru.biosoft.access.support |

Classes in ru.biosoft.access used by biouml.editor
CreateReactionDialog
DataCollectionAddUndo
DataCollectionRemoveUndo
DiagramListener These class listen all diagram changes event and convert them to UndoableEdit.
FilteringSettings
NewDiagramDialog
NewDiagramElementDialog
SearchOptions
ViewerDiagramFilter

Classes in ru.biosoft.access used by biouml.model
Compartment General definition of the compartment as a container for nodes and edges between them.
DefaultDiagramViewBuilder Default implementation of `DiagramViewBuilder`.
Diagram
DiagramElement Common definition of diagram element.
DiagramFilter This interface is needed to take into account difference between hiding and highlighting modes.
DiagramType Formalyze the diagram attributes.
DiagramViewBuilder
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
Constant
EModel Genrally this role should be assotiated with Diagram.
EModelDiagramType Type for executable model diagram.
MatlabOdeModel
Variable General variable definition.
VariablesDataCollection

Classes in ru.biosoft.access used by biouml.model.util
DiagramXMLReader
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.modules.genenet
GeneNetDiagramType
GeneNetModuleActivator Definition of GeneNet module creator.
GeneNetModuleType Definition of GeneNet module.

Classes in ru.biosoft.access used by biouml.modules.genenet.access
DiagramFilter
DiagramTransformer The definition of compartment for the GeneNet database.
ExpertTransformer
LiteratureReferenceTransformer
MglDataCollection Data collection to access to GeneNet server

Classes in ru.biosoft.access used by biouml.modules.genenet.type
Cell Definition of entry for GeneNet 'Cell' table.
Compartment Definition of entry for GeneNet 'Compartment' table.
DiagramDescription Definition of entry for GeneNet 'Scheme' table.
Expert Definition of entry for GeneNet 'Expert' table.
Gene Definition of entry for GeneNet 'Gene' table.
Proces Definition of entry for GeneNet 'Process' table.
Protein Definition of entry for GeneNet 'Protein' table.
Reaction Definition of entry for GeneNet 'Relation' table.
RNA Definition of entry for GeneNet 'RNA' table.
Substance Definition of entry for GeneNet 'Substance' table.

Classes in ru.biosoft.access used by biouml.modules.kegg
KeggPathwayModuleActivator
KeggPathwayModuleType Definition of KEGG Pathways module.

Classes in ru.biosoft.access used by biouml.modules.kegg.type
Compound Stub
Enzyme Stub

Classes in ru.biosoft.access used by biouml.modules.kegg.type.access
CompoundTransformer
DiagramReader
DiagramTransformer
EnzymeTransformer
ReactionTransformer

Classes in ru.biosoft.access used by biouml.modules.transpath
TranspathModuleActivator Definition of Transpath module.
TranspathModuleType Definition of Transpath module.

Classes in ru.biosoft.access used by biouml.modules.transpath.type
Molecule Stub
Reaction

Classes in ru.biosoft.access used by biouml.modules.transpath.type.access
DummyRelationDataCollection
ReactionTransformer

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.diagram.pathway
PathwayDiagramType

Classes in ru.biosoft.access used by biouml.standard.filter
BiopolimerDiagramFilter Common purpose diagram filter allowing to filter Biopolimers by species, cell types and inducers.
BiopolimerDiagramFilter.CellTypeFilter
BiopolimerDiagramFilter.InducerFilter
BiopolimerDiagramFilter.SpeciesFilter
ValueListFilter
ValueListFilter.ValueFilter

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
DiagramDescription Defines coomon properties for diagram description.
Gene Stub
LiteratureReference Defines coomon properties of literature reference.
Protein Stub
Reaction
ReferrerBeanInfo.LiteratureReferencesEditor
Relation Intermediary class to generalize what is common for all relations/edges.
RNA Stub
Species General definition for 'Species' concept.
Substance Stub

Classes in ru.biosoft.access used by biouml.standard.type.access
DiagramXMLTransformer
GenericEntityTransformer

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.
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.
DataCollectionEvent Implements event change in a collection .
DataCollectionInfoParser Parse data collection description file.
DataCollectionListener Interface for listen data collection events.
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.
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
IndexTable IndexTable extention of hash table for work with database indexes.
LocalRepository LocalRepository creates hierarchical DataCollection.
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 pattern defined by Perl5 regular expression.
QuerySystem
Repository
SQLDataCollection DataCollection which store all information in SQL DBMS.
SQLTransformer Adapter for storing/extracting data elements to/from SQL DBMS.
TransformedDataCollection Implemnation note: we are not propagate DataCollectionEvents, because this work is done by primary DataCollection (it has the same parent).
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
DataCollectionTreeModelAdapter2
RepositoryListener
RepositoryPane
RepositoryPane2

Classes in ru.biosoft.access used by ru.biosoft.access.support
ArrayPropertyValueFilter
BeanValueFilter
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
EntryParser Parse the field value from database Entry.
NameListToListModelAdapter
NewDataElementDialog Creates new DataElement for the specified DataCollection.
PropertyValueFilter
TagEntryTransformer

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