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 Diagrams.

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