Index (cy3sbml 0.8.0 API)

A B C D E F G H I J K L M N O P R S T U V W X Y
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

accepts(InputStream, DataCategory) - Method in class org.cy3sbml.archive.CombineArchiveFileFilter: A stream that starts like a zip file.
accepts(InputStream, DataCategory) - Method in class org.cy3sbml.SBMLFileFilter: Indicates which streams the SBMLFileFilter accepts.
accepts(Object) - Method in class org.cy3sbml.util.filter.SBaseFilter
accepts(URI, DataCategory) - Method in class org.cy3sbml.archive.CombineArchiveFileFilter: An archive file: a COMBINE extension and the content of a zip file.
accepts(URI, DataCategory) - Method in class org.cy3sbml.SBMLFileFilter: Indicates which URI the SBMLFileFilter accepts.
ACCESSION - Static variable in record class org.cy3sbml.biomodel.Biomodel
ACCESSION - Static variable in interface org.cy3sbml.uniprot.UniprotHTMLFields
actionPerformed(ActionEvent) - Method in class org.cy3sbml.actions.SplitCofactorsAction
actionPerformed(ActionEvent) - Method in class org.cy3sbml.actions.BiomodelsAction
actionPerformed(ActionEvent) - Method in class org.cy3sbml.actions.ChangeStateAction
actionPerformed(ActionEvent) - Method in class org.cy3sbml.actions.ExamplesAction
actionPerformed(ActionEvent) - Method in class org.cy3sbml.actions.HelpAction
actionPerformed(ActionEvent) - Method in class org.cy3sbml.actions.ImportAction
actionPerformed(ActionEvent) - Method in class org.cy3sbml.actions.LoadLayoutAction
actionPerformed(ActionEvent) - Method in class org.cy3sbml.actions.SaveLayoutAction
activate() - Method in class org.cy3sbml.gui.WebViewPanel
addArchive(Long, ArchiveImport) - Method in class org.cy3sbml.SBMLManager: Registers the COMBINE archive the document of the root network was imported from.
addModelForNetwork(CyNetwork, Model) - Method in class org.cy3sbml.SBMLManager: Stores the model the network collection of the network was created from.
addNodeMapping(CyNetwork, CyNode) - Method in class org.cy3sbml.SBMLManager: Maps a node added to the network after the import (a cofactor clone) to the SBase of its cyId, so that the node shows the information of the SBase.
addSBaseRefResolver(SBaseRefResolver) - Method in class org.cy3sbml.SBMLManager: Adds the resolver the reader resolved the comp references of a document with, so that the info panel finds the same targets, with the same metaids.
addSBMLForNetwork(SBMLDocument, Long, One2ManyMapping<String, Long>) - Method in class org.cy3sbml.SBMLManager: Adds an SBMLDocument - network entry to the SBMLManager.
addSBMLForNetwork(SBMLDocument, CyNetwork, One2ManyMapping<String, Long>) - Method in class org.cy3sbml.SBMLManager: Adds an SBMLDocument - network entry to the SBMLManager.
addSessionRestoredListener(Runnable) - Method in class org.cy3sbml.SBMLManager: Adds a listener that is notified when a session is restored: the mapping and the archives of the session are set.
alternativeNames() - Method in record class org.cy3sbml.uniprot.UniprotEntry: Returns the value of the alternativeNames record component.
AnnotationUtil - Class in org.cy3sbml.util: Tools for working with annotations.
AnnotationUtil() - Constructor for class org.cy3sbml.util.AnnotationUtil
applicationManager() - Method in record class org.cy3sbml.commands.CommandServices: Returns the value of the applicationManager record component.
ArchiveDirectories - Class in org.cy3sbml.archive: The directories COMBINE archives are unpacked into: one new directory per import below a root, so that the SBML files of an archive can reference each other by their relative paths.
ArchiveDirectories(Path) - Constructor for class org.cy3sbml.archive.ArchiveDirectories
ArchiveHtml - Class in org.cy3sbml.gui: The HTML of the COMBINE archive a document was imported from: the archive name and title, its description and creators, and its files (location, format, master), the imported SBML file in bold.
ArchiveImport - Record Class in org.cy3sbml.archive: The archive an SBML document was imported from.
ArchiveImport(ArchiveInfo, String) - Constructor for record class org.cy3sbml.archive.ArchiveImport: Creates an instance of a ArchiveImport record class.
ArchiveInfo - Record Class in org.cy3sbml.archive: The content of a COMBINE archive (OMEX): its manifest entries and the metadata of the archive from metadata.rdf.
ArchiveInfo(String, String, String, List<ArchiveInfo.Creator>, List<ArchiveInfo.Entry>) - Constructor for record class org.cy3sbml.archive.ArchiveInfo: Creates an instance of a ArchiveInfo record class.
ArchiveInfo.Creator - Record Class in org.cy3sbml.archive: A creator of the archive; the parts that are not set are empty.
ArchiveInfo.Entry - Record Class in org.cy3sbml.archive: A file of the archive.
ASTNodeUtil - Class in org.cy3sbml.util
ASTNodeUtil() - Constructor for class org.cy3sbml.util.ASTNodeUtil
ATTR_ARCHIVE - Static variable in class org.cy3sbml.SBML
ATTR_AREA_UNITS - Static variable in class org.cy3sbml.SBML
ATTR_BOUNDARY_CONDITION - Static variable in class org.cy3sbml.SBML
ATTR_CHARGE - Static variable in class org.cy3sbml.SBML
ATTR_CHARGE - Static variable in class org.cy3sbml.util.SBMLUtil
ATTR_COFACTOR_CLONE - Static variable in class org.cy3sbml.SBML
ATTR_COMP_CONVERSION_FACTOR - Static variable in class org.cy3sbml.SBML
ATTR_COMP_DELETION - Static variable in class org.cy3sbml.SBML
ATTR_COMP_EXTENT_CONVERSION_FACTOR - Static variable in class org.cy3sbml.SBML
ATTR_COMP_IDREF - Static variable in class org.cy3sbml.SBML
ATTR_COMP_METAIDREF - Static variable in class org.cy3sbml.SBML
ATTR_COMP_MODELREF - Static variable in class org.cy3sbml.SBML
ATTR_COMP_PORTREF - Static variable in class org.cy3sbml.SBML
ATTR_COMP_RESOLUTION - Static variable in class org.cy3sbml.SBML
ATTR_COMP_SBASEREF - Static variable in class org.cy3sbml.SBML
ATTR_COMP_SUBMODELREF - Static variable in class org.cy3sbml.SBML
ATTR_COMP_TARGET_ID - Static variable in class org.cy3sbml.SBML
ATTR_COMP_TARGET_METAID - Static variable in class org.cy3sbml.SBML
ATTR_COMP_TARGET_MODEL - Static variable in class org.cy3sbml.SBML
ATTR_COMP_TARGET_TYPE - Static variable in class org.cy3sbml.SBML
ATTR_COMP_TIME_CONVERSION_FACTOR - Static variable in class org.cy3sbml.SBML
ATTR_COMP_UNITREF - Static variable in class org.cy3sbml.SBML
ATTR_COMPARTMENT - Static variable in class org.cy3sbml.SBML
ATTR_COMPARTMENT - Static variable in class org.cy3sbml.util.SBMLUtil
ATTR_COMPARTMENT_CODE - Static variable in class org.cy3sbml.SBML
ATTR_CONSTANT - Static variable in class org.cy3sbml.SBML
ATTR_CONVERSION_FACTOR - Static variable in class org.cy3sbml.SBML
ATTR_CYID - Static variable in class org.cy3sbml.SBML
ATTR_DERIVED_UNITS - Static variable in class org.cy3sbml.SBML
ATTR_DISTRIB_UNCERTAINTY - Static variable in class org.cy3sbml.SBML
ATTR_DISTRIB_UNCERTAINTY_COUNT - Static variable in class org.cy3sbml.SBML
ATTR_EQUATION - Static variable in class org.cy3sbml.SBML
ATTR_EXTENT_UNITS - Static variable in class org.cy3sbml.SBML
ATTR_FAST - Static variable in class org.cy3sbml.SBML
ATTR_FBC_CHARGE - Static variable in class org.cy3sbml.SBML
ATTR_FBC_CHEMICAL_FORMULA - Static variable in class org.cy3sbml.SBML
ATTR_FBC_COEFFICIENT - Static variable in class org.cy3sbml.SBML
ATTR_FBC_LOWER_BOUND - Static variable in class org.cy3sbml.SBML
ATTR_FBC_LOWER_FLUX_BOUND - Static variable in class org.cy3sbml.SBML
ATTR_FBC_OBJECTIVE_TEMPLATE - Static variable in class org.cy3sbml.SBML
ATTR_FBC_OBJECTIVE_VARIABLE_TYPE_TEMPLATE - Static variable in class org.cy3sbml.SBML
ATTR_FBC_STRICT - Static variable in class org.cy3sbml.SBML
ATTR_FBC_UPPER_BOUND - Static variable in class org.cy3sbml.SBML
ATTR_FBC_UPPER_FLUX_BOUND - Static variable in class org.cy3sbml.SBML
ATTR_FBC_VARIABLE_TYPE - Static variable in class org.cy3sbml.SBML
ATTR_HAS_ONLY_SUBSTANCE_UNITS - Static variable in class org.cy3sbml.SBML
ATTR_ID - Static variable in class org.cy3sbml.SBML
ATTR_INITIAL_AMOUNT - Static variable in class org.cy3sbml.SBML
ATTR_INITIAL_AMOUNT - Static variable in class org.cy3sbml.util.SBMLUtil
ATTR_INITIAL_ASSIGNMENT - Static variable in class org.cy3sbml.SBML
ATTR_INITIAL_CONCENTRATION - Static variable in class org.cy3sbml.SBML
ATTR_INITIAL_CONCENTRATION - Static variable in class org.cy3sbml.util.SBMLUtil
ATTR_KINETIC_LAW - Static variable in class org.cy3sbml.SBML
ATTR_LAYOUT_GLYPH - Static variable in class org.cy3sbml.SBML
ATTR_LAYOUT_GLYPH_TYPE - Static variable in class org.cy3sbml.SBML
ATTR_LAYOUT_HEIGHT - Static variable in class org.cy3sbml.SBML
ATTR_LAYOUT_ID - Static variable in class org.cy3sbml.SBML
ATTR_LAYOUT_ROLE - Static variable in class org.cy3sbml.SBML
ATTR_LAYOUT_WIDTH - Static variable in class org.cy3sbml.SBML
ATTR_LAYOUT_X - Static variable in class org.cy3sbml.SBML
ATTR_LAYOUT_Y - Static variable in class org.cy3sbml.SBML
ATTR_LENGTH_UNITS - Static variable in class org.cy3sbml.SBML
ATTR_MATH - Static variable in class org.cy3sbml.SBML
ATTR_MESSAGE - Static variable in class org.cy3sbml.SBML
ATTR_METAID - Static variable in class org.cy3sbml.SBML
ATTR_NAME - Static variable in class org.cy3sbml.SBML
ATTR_PORT_SID - Static variable in class org.cy3sbml.SBML
ATTR_QUAL_INITIAL_LEVEL - Static variable in class org.cy3sbml.SBML
ATTR_QUAL_MAX_LEVEL - Static variable in class org.cy3sbml.SBML
ATTR_QUAL_OUTPUT_LEVEL - Static variable in class org.cy3sbml.SBML
ATTR_QUAL_QUALITATIVE_SPECIES - Static variable in class org.cy3sbml.SBML
ATTR_QUAL_RESULT_LEVELS - Static variable in class org.cy3sbml.SBML
ATTR_QUAL_SIGN - Static variable in class org.cy3sbml.SBML
ATTR_QUAL_THRESHOLD_LEVEL - Static variable in class org.cy3sbml.SBML
ATTR_QUAL_TRANSITION_EFFECT - Static variable in class org.cy3sbml.SBML
ATTR_REVERSIBLE - Static variable in class org.cy3sbml.SBML
ATTR_SBOTERM - Static variable in class org.cy3sbml.SBML
ATTR_SIZE - Static variable in class org.cy3sbml.SBML
ATTR_SPATIAL_DIMENSIONS - Static variable in class org.cy3sbml.SBML
ATTR_STOICHIOMETRY - Static variable in class org.cy3sbml.SBML
ATTR_SUBSTANCE_UNITS - Static variable in class org.cy3sbml.SBML
ATTR_TIME_UNITS - Static variable in class org.cy3sbml.SBML
ATTR_UNIT_EXPONENT - Static variable in class org.cy3sbml.SBML
ATTR_UNIT_KIND - Static variable in class org.cy3sbml.SBML
ATTR_UNIT_MULTIPLIER - Static variable in class org.cy3sbml.SBML
ATTR_UNIT_SCALE - Static variable in class org.cy3sbml.SBML
ATTR_UNIT_SID - Static variable in class org.cy3sbml.SBML
ATTR_UNITS - Static variable in class org.cy3sbml.SBML
ATTR_USE_VALUES_FROM_TRIGGER_TIME - Static variable in class org.cy3sbml.SBML
ATTR_VALUE - Static variable in class org.cy3sbml.SBML
ATTR_VARIABLE - Static variable in class org.cy3sbml.SBML
ATTR_VOLUME_UNITS - Static variable in class org.cy3sbml.SBML
attributeType() - Method in enum class org.cy3sbml.styles.Mapping.DataType: The attributeType of the mapping in the style file.
AttributeUtil - Class in org.cy3sbml.util: Helper class for getting and setting attribute.
AttributeUtil() - Constructor for class org.cy3sbml.util.AttributeUtil
AUTH_HELP_DESCRIPTION - Static variable in interface org.cy3sbml.miriam.Fields
AUTH_HELP_URL - Static variable in interface org.cy3sbml.miriam.Fields
authors() - Method in record class org.cy3sbml.biomodel.Biomodel: Returns the value of the authors record component.
AUTHORS - Static variable in record class org.cy3sbml.biomodel.Biomodel

B

BASE_URL - Static variable in interface org.cy3sbml.uniprot.UniprotHTMLFields
baseDirFromAppDir(File) - Static method in class org.cy3sbml.gui.SBaseHTMLFactory: Returns the base URL of the gui resources in the given application directory.
Biomodel - Record Class in org.cy3sbml.biomodel: Stores information for a given biomodel.
Biomodel(String, String, String, String, String, String) - Constructor for record class org.cy3sbml.biomodel.Biomodel: Creates an instance of a Biomodel record class.
BioModelDialogText - Class in org.cy3sbml.biomodel
BioModelDialogText() - Constructor for class org.cy3sbml.biomodel.BioModelDialogText
biomodelLoader() - Method in record class org.cy3sbml.commands.CommandServices: Returns the value of the biomodelLoader record component.
BiomodelLoader - Class in org.cy3sbml.biomodel: Loads BioModels: downloads the SBML of each model into the biomodels folder of the cy3sbml directory, <id>.xml, and loads it with the Cytoscape network file loader.
BiomodelLoader(BiomodelsQuery, Path, LoadNetworkFileTaskFactory) - Constructor for class org.cy3sbml.biomodel.BiomodelLoader
BIOMODELS_URL - Static variable in class org.cy3sbml.biomodel.BiomodelsQuery: Base URL of the BioModels REST API.
BiomodelsAction - Class in org.cy3sbml.actions: Open the BioModel GUI for importing BioModels via search terms.
BiomodelsAction(BiomodelsDialog) - Constructor for class org.cy3sbml.actions.BiomodelsAction: Constructor.
BiomodelsDialog - Class in org.cy3sbml.biomodel: The dialog to search BioModels and load models from it.
BiomodelsDialog(Frame, SearchBioModel, Consumer<String>, Consumer<List<String>>) - Constructor for class org.cy3sbml.biomodel.BiomodelsDialog
BiomodelsHtml - Class in org.cy3sbml.biomodel: The HTML of the BioModels dialog for a search result: one entry per model with the information of the search response, and the details of the models that were looked up.
biomodelsQuery() - Method in record class org.cy3sbml.commands.CommandServices: Returns the value of the biomodelsQuery record component.
BiomodelsQuery - Class in org.cy3sbml.biomodel: Queries of the BioModels REST API (https://www.biomodels.org/docs/).
BiomodelsQuery(HttpJson, URI) - Constructor for class org.cy3sbml.biomodel.BiomodelsQuery: Creates the queries against the BioModels REST API at the given base URL, which must end with a slash.
BiomodelsSearchResult - Record Class in org.cy3sbml.biomodel: The result of a BioModels search: the number of matching models and the models read, in the order of the search response.
BiomodelsSearchResult(int, List<BiomodelSummary>) - Constructor for record class org.cy3sbml.biomodel.BiomodelsSearchResult: Creates an instance of a BiomodelsSearchResult record class.
BiomodelSummary - Record Class in org.cy3sbml.biomodel: A model found by a BioModels search, with the information of the search response.
BiomodelSummary(String, String, String, String) - Constructor for record class org.cy3sbml.biomodel.BiomodelSummary: Creates an instance of a BiomodelSummary record class.
bool - Enum constant in enum class org.cy3sbml.styles.Mapping.DataType
booleanHTML(boolean) - Static method in class org.cy3sbml.gui.SBaseHTMLFactory: Creates true or false HTML depending on boolean.
BOX - Static variable in class org.cy3sbml.layout.XMLInterface
BOX_CYID - Static variable in class org.cy3sbml.layout.XMLInterface
BOX_GLYPH - Static variable in class org.cy3sbml.layout.XMLInterface
BOX_HEIGHT - Static variable in class org.cy3sbml.layout.XMLInterface
BOX_ID - Static variable in class org.cy3sbml.layout.XMLInterface
BOX_LIST - Static variable in class org.cy3sbml.layout.XMLInterface
BOX_WIDTH - Static variable in class org.cy3sbml.layout.XMLInterface
BOX_X - Static variable in class org.cy3sbml.layout.XMLInterface
BOX_Y - Static variable in class org.cy3sbml.layout.XMLInterface
Browser - Class in org.cy3sbml.gui: Browser for displaying HTML within a JavaFX Webview.
Browser(File, BrowserHyperlinkListener) - Constructor for class org.cy3sbml.gui.Browser
BrowserHyperlinkListener - Class in org.cy3sbml.gui: Handle hyperlink events in WebView.
BrowserHyperlinkListener(ServiceAdapter, WebViewPanel, SBMLManager, CofactorManager, BiomodelsDialog) - Constructor for class org.cy3sbml.gui.BrowserHyperlinkListener
buildCyNetworkView(CyNetwork) - Method in class org.cy3sbml.archive.CombineArchiveReaderTask: The view of the network by the reader that read it; registers the archive of the network.
buildCyNetworkView(CyNetwork) - Method in class org.cy3sbml.reader.SBMLReaderTask: Build NetworkViews for given network.
bundled() - Static method in class org.cy3sbml.miriam.MiriamRegistry: Creates the registry from the copy bundled with the app.
BundleInformation - Class in org.cy3sbml: The BundleInformation provides runtime information on the bundle.
BundleInformation(BundleContext) - Constructor for class org.cy3sbml.BundleInformation: Constructor.

C

cancel() - Method in class org.cy3sbml.archive.CombineArchiveReaderTask
canSplit(CyNetwork, CyNode) - Method in class org.cy3sbml.cofactors.CofactorManager: Whether the node can be split: a node of the network with at least two edges that is neither a clone nor a group node.
CATALYTIC_ACTIVITY - Static variable in interface org.cy3sbml.uniprot.UniprotHTMLFields
catalyticActivities() - Method in record class org.cy3sbml.uniprot.UniprotEntry: Returns the value of the catalyticActivities record component.
changeState() - Method in class org.cy3sbml.gui.WebViewPanel
ChangeStateAction - Class in org.cy3sbml.actions: Activate or deactivate the cy3sbml panel.
ChangeStateAction(WebViewPanel) - Constructor for class org.cy3sbml.actions.ChangeStateAction: Constructor.
charge() - Method in record class org.cy3sbml.chebi.ChebiCompound: Returns the value of the charge record component.
ChebiAccess - Class in org.cy3sbml.chebi: Client for the ChEBI public backend REST API.
ChebiAccess(HttpJson) - Constructor for class org.cy3sbml.chebi.ChebiAccess
ChebiCompound - Record Class in org.cy3sbml.chebi: A ChEBI compound, parsed from the ChEBI public backend REST JSON (https://www.ebi.ac.uk/chebi/backend/api/public/compound/<id>/).
ChebiCompound(String, String, String, String, String) - Constructor for record class org.cy3sbml.chebi.ChebiCompound: Creates an instance of a ChebiCompound record class.
chebiId() - Method in record class org.cy3sbml.chebi.ChebiCompound: Returns the value of the chebiId record component.
checkRegexp(String, String) - Static method in class org.cy3sbml.miriam.RegistryUtil: Returns true if the identifier matches the given regular expression pattern.
cleanEmptyTextNodes(Node) - Static method in class org.cy3sbml.util.XMLUtil: Removes text nodes that only contains whitespace.
clear() - Method in class org.cy3sbml.cache.MemoryCache
close() - Method in class org.cy3sbml.gui.LatestTaskExecutor: Stops the current task (interrupting it if it is running) and shuts down the executor thread.
close() - Method in class org.cy3sbml.gui.WebViewPanel: Stops the render executor.
cofactorManager - Variable in class org.cy3sbml.actions.SplitCofactorsAction
cofactorManager() - Method in record class org.cy3sbml.commands.CommandServices: Returns the value of the cofactorManager record component.
CofactorManager - Class in org.cy3sbml.cofactors: Splits cofactor nodes into clones and merges the clones back.
CofactorManager(SBMLManager, CyEventHelper) - Constructor for class org.cy3sbml.cofactors.CofactorManager
CofactorViews - Class in org.cy3sbml.cofactors: The view update after a split or merge of cofactor nodes.
CombineArchive - Class in org.cy3sbml.archive: Reads a COMBINE archive (OMEX): unpacks it into a directory and reads its manifest (manifest.xml) and the metadata of the archive (metadata.rdf).
CombineArchiveException - Exception in org.cy3sbml.archive
CombineArchiveException(String) - Constructor for exception org.cy3sbml.archive.CombineArchiveException
CombineArchiveFileFilter - Class in org.cy3sbml.archive: The COMBINE archives (OMEX) the archive reader imports: zip files with one of the file extensions of the COMBINE specification.
CombineArchiveFileFilter(StreamUtil) - Constructor for class org.cy3sbml.archive.CombineArchiveFileFilter
CombineArchiveReaderTask - Class in org.cy3sbml.archive: Reads the SBML models of a COMBINE archive (OMEX): the archive is unpacked, and every SBML file to import (ArchiveInfo.modelsToImport()) is read by an SBMLReaderTask with the unpacked file as its location, so that the SBML files of the archive can reference each other (comp external model definitions).
CombineArchiveReaderTask(InputStream, String, ArchiveDirectories, CombineArchiveReaderTask.SBMLReaders, SBMLManager) - Constructor for class org.cy3sbml.archive.CombineArchiveReaderTask
CombineArchiveReaderTask.SBMLReaders - Interface in org.cy3sbml.archive: Creates the reader of an SBML file of the archive.
CombineArchiveReaderTaskFactory - Class in org.cy3sbml.archive: Creates the task that reads the SBML models of a COMBINE archive.
CombineArchiveReaderTaskFactory(CombineArchiveFileFilter, ServiceAdapter, SBMLManager, ArchiveDirectories) - Constructor for class org.cy3sbml.archive.CombineArchiveReaderTaskFactory
Command(String, String, String, String, TaskFactory) - Constructor for record class org.cy3sbml.commands.Commands.Command: Creates an instance of a Command record class.
Commands - Class in org.cy3sbml.commands: The automation commands of cy3sbml in the command namespace "cy3sbml": available in the Cytoscape command line, in automation scripts and in CyREST as POST /v1/commands/cy3sbml/<command>.
Commands.Command - Record Class in org.cy3sbml.commands: A command: its name in the namespace, descriptions, an example of its JSON result, and the task factory.
CommandServices - Record Class in org.cy3sbml.commands: The Cytoscape and cy3sbml services the automation commands use.
CommandServices(CyApplicationManager, CyNetworkManager, CyNetworkViewManager, VisualMappingManager, LoadNetworkFileTaskFactory, LoadNetworkURLTaskFactory, SynchronousTaskManager<?>, SBMLManager, CofactorManager, BiomodelsQuery, BiomodelLoader, LayoutTools) - Constructor for record class org.cy3sbml.commands.CommandServices: Creates an instance of a CommandServices record class.
COMMENT_TEXT - Static variable in interface org.cy3sbml.uniprot.UniprotHTMLFields
commonName() - Method in record class org.cy3sbml.uniprot.UniprotEntry: Returns the value of the commonName record component.
COMP_RESOLVED - Static variable in class org.cy3sbml.SBML
compile(double, int, String) - Method in class org.cy3sbml.util.UnitsFormulaCompiler
compile(double, String) - Method in class org.cy3sbml.util.UnitsFormulaCompiler
compile(int, String) - Method in class org.cy3sbml.util.UnitsFormulaCompiler
CompModels - Class in org.cy3sbml.comp: Resolves the model references of the comp package for one document: the model a Submodel instantiates, which is the main model, a ModelDefinition or the model of an ExternalModelDefinition.
CompModels(SBMLDocument) - Constructor for class org.cy3sbml.comp.CompModels: Resolver for the model references of the document and the documents it loads.
CompModels(SBMLDocument, Map<URI, SBMLDocument>) - Constructor for class org.cy3sbml.comp.CompModels: Resolver that uses the given open documents for their locations instead of reading the files again, e.g. the documents of a restored session.
CompModels.External - Record Class in org.cy3sbml.comp: An external model definition with the resolution of its model.
compound(String) - Method in class org.cy3sbml.chebi.ChebiAccess: Gets the ChEBI compound for a given id, e.g.
CompTargets - Interface in org.cy3sbml.comp: The comp references of the open documents: the resolver of the document of an element, and the network collection of a model, to link a target to its node.
computePrefHeight(double) - Method in class org.cy3sbml.gui.Browser
computePrefWidth(double) - Method in class org.cy3sbml.gui.Browser
CONDITIONAL_LINK - Static variable in class org.cy3sbml.gui.GUIConstants
CONNECT_AND - Static variable in class org.cy3sbml.biomodel.SearchContent
CONNECT_OR - Static variable in class org.cy3sbml.biomodel.SearchContent
connectionProxy - Variable in class org.cy3sbml.ServiceAdapter
ConnectionProxy - Class in org.cy3sbml: Handling the system proxy settings required to use the web services (SOAP, REST).
ConnectionProxy(CyProperty<Properties>) - Constructor for class org.cy3sbml.ConnectionProxy: Constructor.
containsDocument(Long) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: Exists a SBMLDocument for the given rootNetwork.
containsKey(T1) - Method in class org.cy3sbml.mapping.One2ManyMapping
CONTENT_MODE - Static variable in class org.cy3sbml.biomodel.SearchContent
CONTENT_NAME - Static variable in class org.cy3sbml.biomodel.SearchContent
CONTINOUS - Enum constant in enum class org.cy3sbml.styles.Mapping.MappingType
copyEdgeAttributes(CyNetwork, CyEdge, CyEdge) - Static method in class org.cy3sbml.util.AttributeUtil: Copy edge attributes.
copyInputStream(InputStream) - Static method in class org.cy3sbml.util.IOUtil: Copy InputStream.
copyNodeAttributes(CyNetwork, CyNode, CyNode) - Static method in class org.cy3sbml.util.AttributeUtil: Copy node attributes.
coreEdgeTypes - Static variable in class org.cy3sbml.SBML
coreNodeTypes - Static variable in class org.cy3sbml.SBML
create(InputStream, String, URI) - Method in interface org.cy3sbml.archive.CombineArchiveReaderTask.SBMLReaders
create(ArchiveImport) - Static method in class org.cy3sbml.gui.ArchiveHtml
create(CommandServices) - Static method in class org.cy3sbml.commands.Commands: All commands, with their task factories using the given services.
create(VisualStyle) - Method in class org.cy3sbml.styles.LayoutStyleFactory: Creates the layout style of the base style.
create(SBase) - Static method in class org.cy3sbml.gui.KeyValuePairHtml: The HTML of the key-value pairs of the SBase, empty if it has none.
create(SBase, CompTargets) - Static method in class org.cy3sbml.gui.UncertaintyHtml: The HTML of the uncertainties of the SBase, empty if it has none.
createAbstractMathContainerNodeMap(AbstractMathContainer) - Static method in class org.cy3sbml.util.SBMLUtil
createAbstractMathContainerNodeMap(AbstractMathContainer, Variable) - Static method in class org.cy3sbml.util.SBMLUtil: Map for AbstractMathContainer.
createCompartmentMap(Compartment) - Static method in class org.cy3sbml.util.SBMLUtil: Compartment map.
createCompDocumentMap(SBMLDocument, CompTargets) - Static method in class org.cy3sbml.util.SBMLUtil: The model definitions and external model definitions of the document, with the model of each external model definition or why it could not be read.
createConstraintMap(Constraint) - Static method in class org.cy3sbml.util.SBMLUtil: Constraint map.
CREATED - Static variable in interface org.cy3sbml.miriam.Fields
CREATED_DATE1 - Static variable in class org.cy3sbml.gui.GUIConstants
createDefault() - Static method in class org.cy3sbml.biomodel.BiomodelsQuery: Creates the queries against the public BioModels REST API.
createDefault() - Static method in class org.cy3sbml.util.HttpJson: Creates a default instance that honors the Cytoscape system proxy settings (set as system properties by ConnectionProxy).
createEventAssignmentMap(EventAssignment) - Static method in class org.cy3sbml.util.SBMLUtil: EventAssignment map.
createEventMap(Event) - Static method in class org.cy3sbml.util.SBMLUtil: Event map.
createFunctionDefinitionMap(FunctionDefinition) - Static method in class org.cy3sbml.util.SBMLUtil: FunctionDefinition map.
createGeneProductMap(GeneProduct) - Static method in class org.cy3sbml.util.SBMLUtil: GeneProduct map.
createGroupMap(Group) - Static method in class org.cy3sbml.util.SBMLUtil: Group map.
createHTMLText(String) - Method in class org.cy3sbml.gui.SBaseHTMLFactory: Creates HTML text.
createHTMLText(String, String) - Method in class org.cy3sbml.gui.SBaseHTMLFactory: Creates HTML for given text String.
createInfo(SBase) - Method in class org.cy3sbml.gui.SBaseHTMLFactory: Creates the HTML information for the given SBase.
createInitialAssignmentMap(InitialAssignment) - Static method in class org.cy3sbml.util.SBMLUtil: InitialAssignment map.
createInputMap(Input) - Static method in class org.cy3sbml.util.SBMLUtil: Input map.
createKineticLawMap(KineticLaw) - Static method in class org.cy3sbml.util.SBMLUtil: KineticLaw map.
createLocalParameterMap(LocalParameter) - Static method in class org.cy3sbml.util.SBMLUtil: LocalParameter map.
createMappings() - Method in class org.cy3sbml.styles.StyleInfo_cy3sbml: Create the mappings for the given style.
createMappings() - Method in class org.cy3sbml.styles.StyleInfo_cy3sbmlDark: Create the mappings for the given style.
createMappings() - Method in class org.cy3sbml.styles.StyleInfo: Creates the mappings for all styles.
createModelMap(Model) - Static method in class org.cy3sbml.util.SBMLUtil: Model map.
createNamedSBaseMap(NamedSBase) - Static method in class org.cy3sbml.util.SBMLUtil: Map for NamedSBase.
createNamedSBaseWithDerivedUnitMap(NamedSBaseWithDerivedUnit) - Static method in class org.cy3sbml.util.SBMLUtil: Map for NamedSBaseWithDerivedUnit.
createOutputMap(Output) - Static method in class org.cy3sbml.util.SBMLUtil: Output map.
createParameterMap(Parameter) - Static method in class org.cy3sbml.util.SBMLUtil: Parameter map.
createQualitativeSpeciesMap(QualitativeSpecies) - Static method in class org.cy3sbml.util.SBMLUtil: QualitativeSpecies map.
createQuantityWithUnitNodeMap(QuantityWithUnit) - Static method in class org.cy3sbml.util.SBMLUtil: Map for QuantityWithUnit.
createReactionMap(Reaction) - Static method in class org.cy3sbml.util.SBMLUtil: Reaction map.
createReverseMapping() - Method in class org.cy3sbml.mapping.One2ManyMapping
createRuleMap(Rule) - Static method in class org.cy3sbml.util.SBMLUtil: Rule map.
createSBaseMap(SBase) - Static method in class org.cy3sbml.util.SBMLUtil: Map for SBase.
createSBaseRefMap(SBaseRef, CompTargets) - Static method in class org.cy3sbml.util.SBMLUtil: Map of a port, deletion, replaced element or replaced by: the attributes that are set, the chain of the reference, and its target with a link to the node in the network of the target model.
createSBMLDocumentMap(SBMLDocument) - Static method in class org.cy3sbml.util.SBMLUtil: SBMLDocument map.
createSecondaryInformation(Namespace, String) - Method in class org.cy3sbml.gui.SBaseHTMLFactory: Resolves secondary resourses and returns the HTML.
createSpeciesMap(Species) - Static method in class org.cy3sbml.util.SBMLUtil: Species map.
createStyle(StyleInfo, File) - Static method in class org.cy3sbml.styles.StyleFactory: Creates VisualStyle from StyleInfo
createSubmodelMap(Submodel, CompTargets) - Static method in class org.cy3sbml.util.SBMLUtil: Submodel map: the referenced model, with a link to its network, and the conversion factors.
createSymbolMap(Symbol) - Static method in class org.cy3sbml.util.SBMLUtil: Map for Symbol.
createTaskIterator() - Method in class org.cy3sbml.actions.SBMLEnableTaskFactory
createTaskIterator(InputStream, String) - Method in class org.cy3sbml.archive.CombineArchiveReaderTaskFactory
createTaskIterator(InputStream, String) - Method in class org.cy3sbml.SBMLReaderTaskFactory
createTaskIterator(Collection<String>) - Method in class org.cy3sbml.biomodel.BiomodelLoader: Creates the tasks that download and load the given BioModels, one after another.
createTransitionMap(Transition) - Static method in class org.cy3sbml.util.SBMLUtil: Transition map.
createUniqueFile(File, String, String) - Static method in class org.cy3sbml.util.IOUtil: Creates a unique file with a given filename and a given extension in a given directory.
createUniqueMetaId(SBMLDocument, String) - Static method in class org.cy3sbml.util.MappingUtil: Creates unique metaId in the model.
createUnitDefinitionMap(UnitDefinition) - Static method in class org.cy3sbml.util.SBMLUtil: UnitDefinition map.
createUnitMap(Unit) - Static method in class org.cy3sbml.util.SBMLUtil: Unit map.
createUserDefinedConstraintComponentMap(UserDefinedConstraintComponent) - Static method in class org.cy3sbml.util.SBMLUtil: UserDefinedConstraintComponent map (fbc v3).
createUserDefinedConstraintMap(UserDefinedConstraint) - Static method in class org.cy3sbml.util.SBMLUtil: UserDefinedConstraint map (fbc v3): the bound parameters, the constraint lowerBound <= sum of the components <= upperBound and a row per component.
Creator(String, String, String, String) - Constructor for record class org.cy3sbml.archive.ArchiveInfo.Creator: Creates an instance of a Creator record class.
creators() - Method in record class org.cy3sbml.archive.ArchiveInfo: Returns the value of the creators record component.
CY3SBML - Static variable in class org.cy3sbml.gui.SBaseHTMLFactory
cy3sbmlDirectory - Variable in class org.cy3sbml.ServiceAdapter
cy3sbmlProperties - Variable in class org.cy3sbml.ServiceAdapter
CyActivator - Class in org.cy3sbml: Entry point to cy3sbml.
CyActivator() - Constructor for class org.cy3sbml.CyActivator
cyApplicationManager - Variable in class org.cy3sbml.ServiceAdapter
CyBoundingBox - Record Class in org.cy3sbml.layout: Position and size of a node in a layout file.
CyBoundingBox(String, String, String, double, double, double, double) - Constructor for record class org.cy3sbml.layout.CyBoundingBox: Creates an instance of a CyBoundingBox record class.
cyGroupFactory - Variable in class org.cy3sbml.ServiceAdapter
cyId() - Method in record class org.cy3sbml.layout.CyBoundingBox: Returns the value of the cyId record component.
cyLayoutAlgorithmManager - Variable in class org.cy3sbml.ServiceAdapter
cyNetworkFactory - Variable in class org.cy3sbml.ServiceAdapter
cyNetworkManager - Variable in class org.cy3sbml.ServiceAdapter
cyNetworkViewFactory - Variable in class org.cy3sbml.ServiceAdapter
cyNetworkViewManager - Variable in class org.cy3sbml.ServiceAdapter
cySwingApplication - Variable in class org.cy3sbml.ServiceAdapter

D

dataCollection() - Method in record class org.cy3sbml.miriam.MiriamRegistry.ResolvedURI: Returns the value of the dataCollection record component.
deactivate() - Method in class org.cy3sbml.gui.WebViewPanel
DEFAULT_NOT_FOUND_TTL - Static variable in class org.cy3sbml.cache.MemoryCache: Default TTL for a cached "not found" result.
definition() - Method in record class org.cy3sbml.comp.CompModels.External: Returns the value of the definition record component.
delete(Path) - Method in class org.cy3sbml.archive.ArchiveDirectories: Deletes the directory of an archive with its files.
deleteAll() - Method in class org.cy3sbml.archive.ArchiveDirectories: Deletes the root with all unpacked archives.
delim - Static variable in class org.cy3sbml.gui.SBaseHTMLFactory
DEPRECATED - Static variable in interface org.cy3sbml.miriam.Fields
DEPRECATION_DATE - Static variable in interface org.cy3sbml.miriam.Fields
DEPRECATION_OFFLINE_DATE - Static variable in interface org.cy3sbml.miriam.Fields
DEPRECATION_STATEMENT - Static variable in interface org.cy3sbml.miriam.Fields
describe(SBaseRef) - Static method in class org.cy3sbml.comp.SBaseRefResolver: The chain of the reference, e.g.
description() - Method in record class org.cy3sbml.archive.ArchiveInfo: Returns the value of the description record component.
description() - Method in record class org.cy3sbml.biomodel.Biomodel: Returns the value of the description record component.
description() - Method in record class org.cy3sbml.commands.Commands.Command: Returns the value of the description record component.
DESCRIPTION - Static variable in record class org.cy3sbml.biomodel.Biomodel
DESCRIPTION - Static variable in interface org.cy3sbml.miriam.Fields
DESCRIPTION_BIOMODELS - Static variable in class org.cy3sbml.gui.GUIConstants
DESCRIPTION_CHANGESTATE - Static variable in class org.cy3sbml.gui.GUIConstants
DESCRIPTION_COFACTOR_MERGE - Static variable in class org.cy3sbml.gui.GUIConstants
DESCRIPTION_COFACTOR_SPLIT - Static variable in class org.cy3sbml.gui.GUIConstants
DESCRIPTION_EXAMPLES - Static variable in class org.cy3sbml.gui.GUIConstants
DESCRIPTION_HELP - Static variable in class org.cy3sbml.gui.GUIConstants
DESCRIPTION_IMPORT - Static variable in class org.cy3sbml.gui.GUIConstants
DESCRIPTION_LABEL - Static variable in class org.cy3sbml.gui.GUIConstants
DESCRIPTION_LOADLAYOUT - Static variable in class org.cy3sbml.gui.GUIConstants
DESCRIPTION_SAVELAYOUT - Static variable in class org.cy3sbml.gui.GUIConstants
descriptions() - Method in record class org.cy3sbml.ols.OlsTerm: Returns the value of the descriptions record component.
dialogTaskManager - Variable in class org.cy3sbml.ServiceAdapter
DISCRETE - Enum constant in enum class org.cy3sbml.styles.Mapping.MappingType
DistribUtil - Class in org.cy3sbml.util: The uncertainties of the SBML distrib package (version 1): every SBase can have a list of uncertainties, each with uncertainty parameters and spans (mean, standard deviation, confidence interval, a distribution, ...).
document() - Method in class org.cy3sbml.comp.CompModels: The document whose model references are resolved.
document() - Method in record class org.cy3sbml.comp.ModelResolution.Resolved: Returns the value of the document record component.
documentBuilder() - Static method in class org.cy3sbml.util.XMLUtil: Creates a document builder from the hardened XMLUtil.documentBuilderFactory() that reports parse errors only through its exceptions.
documentBuilderFactory() - Static method in class org.cy3sbml.util.XMLUtil: Creates a DocumentBuilderFactory hardened against XML external entity (XXE) attacks.
doLayout - Variable in class org.cy3sbml.reader.SBMLReaderTask
download(URI, Path) - Method in class org.cy3sbml.util.HttpJson: Downloads the body at the given URI into the given file, streaming it.
download(URI, Duration) - Static method in class org.cy3sbml.miriam.RegistryUtil: Downloads and parses the registry.
DOWNLOAD_TIMEOUT - Static variable in class org.cy3sbml.miriam.MiriamRegistry: Connect and read timeout of the registry download.
downloadSBML(String, Path) - Method in class org.cy3sbml.biomodel.BiomodelsQuery: Downloads the SBML file of the given BioModel into the given file.

E

ecNumbers() - Method in record class org.cy3sbml.uniprot.UniprotEntry: Returns the value of the ecNumbers record component.
EDGE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_BEND - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_LABEL - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_LABEL_COLOR - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_LABEL_FONT_FACE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_LABEL_FONT_SIZE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_LABEL_TRANSPARENCY - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_LABEL_WIDTH - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_LINE_TYPE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_PAINT - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_SELECTED - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_SELECTED_PAINT - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_SOURCE_ARROW_SHAPE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_SOURCE_ARROW_UNSELECTED_PAINT - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_STROKE_SELECTED_PAINT - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_STROKE_UNSELECTED_PAINT - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_TARGET_ARROW_SHAPE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_TARGET_ARROW_UNSELECTED_PAINT - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_TOOLTIP - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_TRANSPARENCY - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_UNSELECTED_PAINT - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_VISIBLE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
EDGE_WIDTH - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
email() - Method in record class org.cy3sbml.archive.ArchiveInfo.Creator: Returns the value of the email record component.
EMAIL_LINK - Static variable in class org.cy3sbml.gui.GUIConstants
entries() - Method in record class org.cy3sbml.archive.ArchiveInfo: Returns the value of the entries record component.
entry(String) - Method in class org.cy3sbml.uniprot.UniprotAccess: Gets the UniProt entry for a given accession, e.g.
Entry(String, String, boolean) - Constructor for record class org.cy3sbml.archive.ArchiveInfo.Entry: Creates an instance of a Entry record class.
equals(Object) - Method in record class org.cy3sbml.archive.ArchiveImport: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.archive.ArchiveInfo.Creator: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.archive.ArchiveInfo.Entry: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.archive.ArchiveInfo: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.biomodel.Biomodel: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.biomodel.BiomodelsSearchResult: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.biomodel.BiomodelSummary: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.biomodel.SearchBioModel.Result: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.chebi.ChebiCompound: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.commands.Commands.Command: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.commands.CommandServices: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.comp.CompModels.External: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.comp.ModelResolution.Failed: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.comp.ModelResolution.Resolved: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.comp.SBaseRefResolution.Resolved: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.comp.SBaseRefResolution.Unresolved: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.layout.CyBoundingBox: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.miriam.MiriamRegistry.ResolvedURI: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.ols.OlsTerm: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.uniprot.UniprotEntry: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.cy3sbml.util.FetchResult: Indicates whether some other object is "equal to" this one.
error() - Static method in record class org.cy3sbml.util.FetchResult
ERROR - Enum constant in enum class org.cy3sbml.util.FetchStatus
escape(String) - Static method in class org.cy3sbml.util.HtmlUtil: Escapes the characters with a meaning in HTML (& < > "), so the text shows as is in an element or an attribute value.
EXAMPLE_SBML - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
exampleJson() - Method in record class org.cy3sbml.commands.Commands.Command: Returns the value of the exampleJson record component.
ExamplesAction - Class in org.cy3sbml.actions: Loads the example HTML page.
ExamplesAction(WebViewPanel) - Constructor for class org.cy3sbml.actions.ExamplesAction: Constructor.
EXPORT_HTML - Static variable in class org.cy3sbml.gui.GUIConstants
EXTENSIONS - Static variable in class org.cy3sbml.archive.CombineArchiveFileFilter: The file extensions of COMBINE archives.
External(ExternalModelDefinition, ModelResolution) - Constructor for record class org.cy3sbml.comp.CompModels.External: Creates an instance of a External record class.
externalModels() - Method in class org.cy3sbml.comp.CompModels: Every external model definition of the document and of the documents it loads, each once, in document order, with the resolution of its model.
extract() - Method in class org.cy3sbml.ResourceExtractor: Extracts the bundle resources from the BundleContext in the application directory, replacing the previously extracted resources.
extract(InputStream, String, Path) - Static method in class org.cy3sbml.archive.CombineArchive: Unpacks the archive into the directory and reads its content.

F

factory() - Method in record class org.cy3sbml.commands.Commands.Command: Returns the value of the factory record component.
Failed(String) - Constructor for record class org.cy3sbml.comp.ModelResolution.Failed: Creates an instance of a Failed record class.
familyName() - Method in record class org.cy3sbml.archive.ArchiveInfo.Creator: Returns the value of the familyName record component.
fetch(URI) - Method in class org.cy3sbml.util.HttpJson: Fetches and parses the JSON body at the given URI, distinguishing "not found" (HTTP 404) from a transport or parse error.
fetchAsync(URI) - Method in class org.cy3sbml.util.HttpJson: Fetches and parses the JSON body at the given URI asynchronously, see HttpJson.fetch(java.net.URI).
FetchResult<T> - Record Class in org.cy3sbml.util: The result of a fetch: its FetchStatus and the value, if found.
FetchResult(FetchStatus, Optional<T>) - Constructor for record class org.cy3sbml.util.FetchResult: Creates an instance of a FetchResult record class.
FetchStatus - Enum Class in org.cy3sbml.util: Outcome of a single HttpJson fetch, distinguishing "not found" (e.g.
fetchText(URI) - Method in class org.cy3sbml.util.HttpJson: Fetches the raw text body at the given URI, distinguishing "not found" (HTTP 404) from a transport error.
Fields - Interface in org.cy3sbml.miriam
FILENAME_NAMESPACE - Static variable in class org.cy3sbml.gui.SBaseHTMLFactory
fileURIforResource(String) - Method in class org.cy3sbml.ResourceExtractor: Returns the file URI in the application folder for given resource string.
fileUtil - Variable in class org.cy3sbml.ServiceAdapter
findBaseNetwork(Collection<CyNetwork>, Long) - Static method in class org.cy3sbml.util.NetworkUtil: The base network of the collection with the root network SUID.
findByURI(String) - Method in class org.cy3sbml.miriam.MiriamRegistry: The data collection of the given identifiers.org resource URI or urn:miriam URN, or null, see MiriamRegistry.resolve(String).
findReferencedGlobalParameters(ASTNode) - Static method in class org.cy3sbml.util.ASTNodeUtil
findReferencedNamedSBases(ASTNode) - Static method in class org.cy3sbml.util.ASTNodeUtil
findRootNetwork(Model) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: The root network created from the model object; by identity, as JSBML's equals compares the content.
findTargetNetwork(Collection<CyNetwork>, Long, String) - Static method in class org.cy3sbml.util.NetworkUtil: The network of the collection with the root network SUID that has a node for the element with the cyId: the base network if it has the node, else the kinetic or the all network.
format() - Method in record class org.cy3sbml.archive.ArchiveInfo.Entry: Returns the value of the format record component.
formatLabel(String) - Static method in record class org.cy3sbml.archive.ArchiveInfo: A short name of the format, e.g.
formula() - Method in record class org.cy3sbml.chebi.ChebiCompound: Returns the value of the formula record component.
found(T) - Static method in record class org.cy3sbml.util.FetchResult: A found value.
FOUND - Enum constant in enum class org.cy3sbml.util.FetchStatus
fromIds(Collection<String>) - Static method in class org.cy3sbml.biomodel.SearchBioModel: Returns the result for the given model ids, e.g. parsed from text.
fromJson(JsonNode) - Static method in record class org.cy3sbml.biomodel.Biomodel: Creates the biomodel from the JSON of the BioModels model endpoint.
fromMap(Map<?, ?>) - Static method in class org.cy3sbml.miriam.Resource
fullName() - Method in record class org.cy3sbml.uniprot.UniprotEntry: Returns the value of the fullName record component.
FUNCTION_COMMENT - Static variable in interface org.cy3sbml.uniprot.UniprotHTMLFields
functionComments() - Method in record class org.cy3sbml.uniprot.UniprotEntry: Returns the value of the functionComments record component.

G

geneNames() - Method in record class org.cy3sbml.uniprot.UniprotEntry: Returns the value of the geneNames record component.
get(String) - Method in class org.cy3sbml.miriam.MiriamRegistry: The data collection with the given prefix, or null.
get(URI) - Method in class org.cy3sbml.util.HttpJson: Fetches and parses the JSON body at the given URI.
get(K, Function<K, FetchResult<V>>) - Method in class org.cy3sbml.cache.MemoryCache: Returns the cached value or loads it with the given loader.
get(CyNetwork, CyIdentifiable, String, Class<? extends T>) - Static method in class org.cy3sbml.util.AttributeUtil: Get attribute for CyIdentifiable.
getArchive(Long) - Method in class org.cy3sbml.SBMLManager: The COMBINE archive the document of the root network was imported from.
getArchive(SBMLDocument) - Method in class org.cy3sbml.SBMLManager: The COMBINE archive the document was imported from.
getArchiveInfo() - Method in class org.cy3sbml.archive.CombineArchiveReaderTask: The content of the archive, null before the task ran.
getArchives() - Method in class org.cy3sbml.SBMLManager: The archives by root network SUID, for the session.
getAttributeName() - Method in class org.cy3sbml.styles.Mapping
getAuthHelpDescription() - Method in class org.cy3sbml.miriam.Resource
getAuthHelpUrl() - Method in class org.cy3sbml.miriam.Resource
getCloneEdges(Long) - Method in class org.cy3sbml.cofactors.Network2CofactorMapper: The clone edges of the network with their original edges.
getClones(Long, Long) - Method in class org.cy3sbml.cofactors.Network2CofactorMapper: The clones of the cofactor node, empty if it is not split.
getCofactor(Long, Long) - Method in class org.cy3sbml.cofactors.Network2CofactorMapper: The cofactor node of the clone, or null if the node is no clone.
getCofactors(Long) - Method in class org.cy3sbml.cofactors.Network2CofactorMapper: The split cofactor nodes of the network.
getComponent() - Method in class org.cy3sbml.gui.WebViewPanel
getCountryCode() - Method in class org.cy3sbml.miriam.Resource.Location
getCountryName() - Method in class org.cy3sbml.miriam.Resource.Location
getCreated() - Method in class org.cy3sbml.miriam.Namespace
getCurrentCyNode2SBaseMapping() - Method in class org.cy3sbml.SBMLManager
getCurrentSBase2CyNodeMapping() - Method in class org.cy3sbml.SBMLManager
getCurrentSBMLDocument() - Method in class org.cy3sbml.SBMLManager: Get current SBMLDocument.
getCurrentSUID() - Method in class org.cy3sbml.SBMLManager: Get current network SUID.
getCyIdsFromSUIDs(List<Long>) - Method in class org.cy3sbml.SBMLManager: Lookup the list of cyIds of SBase objects for the given suids.
getCyNode2SBaseMapping(Long) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: Mapping
getCytoPanelName() - Method in class org.cy3sbml.gui.WebViewPanel
getDataCollectionPartFromURI(String) - Static method in class org.cy3sbml.miriam.RegistryUtil: Extracts the data collection part from an identifiers.org resource URI, e.g.
getDataType() - Method in class org.cy3sbml.styles.Mapping
getDefaultValue() - Method in class org.cy3sbml.styles.Mapping
getDeprecated() - Method in class org.cy3sbml.miriam.Namespace
getDeprecationDate() - Method in class org.cy3sbml.miriam.Namespace
getDeprecationDate() - Method in class org.cy3sbml.miriam.Resource
getDeprecationOfflineDate() - Method in class org.cy3sbml.miriam.Resource
getDeprecationStatetement() - Method in class org.cy3sbml.miriam.Resource
getDescription() - Method in class org.cy3sbml.miriam.Namespace
getDescription() - Method in class org.cy3sbml.miriam.Resource
getDescription() - Method in class org.cy3sbml.miriam.Resource.Institution
getDetails(Collection<String>) - Method in class org.cy3sbml.biomodel.SearchBioModel: Returns the details of the given models by id, in the order of the ids.
getDocument(Long) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: Get SBMLDocument for given rootNetworkSUID.
getDocumentMap() - Method in class org.cy3sbml.mapping.Network2SBMLMapper: Get DocumentMap.
getError() - Method in class org.cy3sbml.reader.SBMLReaderTask: Returns true if reading failed.
getHeaderString() - Static method in class org.cy3sbml.biomodel.BioModelDialogText
getHomeUrl() - Method in class org.cy3sbml.miriam.Resource.Institution
getHtml() - Method in class org.cy3sbml.gui.WebViewPanel
getIcon() - Method in class org.cy3sbml.gui.WebViewPanel
getId() - Method in class org.cy3sbml.miriam.Namespace
getId() - Method in class org.cy3sbml.miriam.Resource
getId() - Method in class org.cy3sbml.miriam.Resource.Institution
getIdentifier() - Method in class org.cy3sbml.gui.WebViewPanel
getIdentifierFromURI(String) - Static method in class org.cy3sbml.miriam.RegistryUtil: Extracts the identifier (accession) part from an identifiers.org resource URI, e.g.
getInfo() - Static method in class org.cy3sbml.biomodel.BioModelDialogText
getInfo() - Method in class org.cy3sbml.BundleInformation: {name}-v{version} of bundle.
getInfo() - Method in class org.cy3sbml.gui.SBaseHTMLThread: Get the created information.
getInstitution() - Method in class org.cy3sbml.miriam.Resource
getListOfSelectedModelIds() - Method in class org.cy3sbml.biomodel.BiomodelsDialog
getLocation() - Method in class org.cy3sbml.miriam.Resource
getLocation() - Method in class org.cy3sbml.miriam.Resource.Institution
getLocation() - Method in class org.cy3sbml.reader.SBMLReaderTask: The location of the file, if known.
getMap() - Method in class org.cy3sbml.styles.MappingDiscrete
getMapping(Long) - Method in class org.cy3sbml.SBMLManager: Returns mapping or null if no mapping exists.
getMapping(CyNetwork) - Method in class org.cy3sbml.SBMLManager: Returns mapping or null if no mapping exists.
getMappings() - Method in class org.cy3sbml.styles.StyleInfo
getMappingType() - Method in class org.cy3sbml.styles.Mapping
getMirId() - Method in class org.cy3sbml.miriam.Namespace
getMirId() - Method in class org.cy3sbml.miriam.Resource
getModelMap() - Method in class org.cy3sbml.mapping.Network2SBMLMapper: The models of the root networks; a defensive copy.
getModified() - Method in class org.cy3sbml.miriam.Namespace
getName() - Method in class org.cy3sbml.BundleInformation: Name of bundle.
getName() - Method in class org.cy3sbml.miriam.Namespace
getName() - Method in class org.cy3sbml.miriam.Resource
getName() - Method in class org.cy3sbml.miriam.Resource.Institution
getName() - Method in class org.cy3sbml.styles.StyleInfo
getNames() - Method in class org.cy3sbml.biomodel.SearchContent
getNamespaceEmbeddedInLui() - Method in class org.cy3sbml.miriam.Namespace
getNamespaceFromURI(String) - Static method in class org.cy3sbml.miriam.RegistryUtil: Extracts the short namespace prefix from an identifiers.org resource URI, e.g.
getNetwork2CofactorMapper() - Method in class org.cy3sbml.cofactors.CofactorManager: The mapper, for the serialization in sessions.
getNetwork2SBMLMapper() - Method in class org.cy3sbml.SBMLManager: Access to the SBML to network mapper.
getNetworks() - Method in class org.cy3sbml.archive.CombineArchiveReaderTask
getNetworks() - Method in class org.cy3sbml.reader.SBMLReaderTask: Get created networks from the reader.
getNodeByAttribute(CyNetwork, String, String) - Static method in class org.cy3sbml.util.AttributeUtil: Returns the first matching node.
getOriginalEdge(Long, Long) - Method in class org.cy3sbml.cofactors.Network2CofactorMapper: The original edge of a clone edge, or null if the edge is no clone edge.
getPattern() - Method in class org.cy3sbml.miriam.Namespace
getPosition(Long, Long) - Method in class org.cy3sbml.cofactors.Network2CofactorMapper: The position of the cofactor node before the split, or null if unknown.
getPrefix() - Method in class org.cy3sbml.miriam.Namespace
getPrefixValue(String) - Static method in class org.cy3sbml.gui.SBaseHTMLFactory
getPrimaryResource() - Method in class org.cy3sbml.miriam.Namespace: The resource to link to: the official resource if it is not deprecated, else the first resource that is not deprecated, else the first resource (a deprecated resource only leads to a deprecation page).
getProviderCode() - Method in class org.cy3sbml.miriam.Resource
getProxyHost() - Method in class org.cy3sbml.ConnectionProxy
getProxyPort() - Method in class org.cy3sbml.ConnectionProxy
getProxyType() - Method in class org.cy3sbml.ConnectionProxy
getRenderDeprecatedLanding() - Method in class org.cy3sbml.miriam.Resource
getResource(String) - Method in class org.cy3sbml.ResourceExtractor: Returns the file URI in the application folder for given resource string.
getResourceHomeUrl() - Method in class org.cy3sbml.miriam.Resource
getResources() - Method in class org.cy3sbml.miriam.Namespace
getRootNetwork(CyNetwork) - Static method in class org.cy3sbml.util.NetworkUtil: Get rootNetwork for given network.
getRootNetworkSUID(CyNetwork) - Static method in class org.cy3sbml.util.NetworkUtil: Get SUID of root network.
getRorId() - Method in class org.cy3sbml.miriam.Resource.Institution
getSampleId() - Method in class org.cy3sbml.miriam.Namespace
getSampleId() - Method in class org.cy3sbml.miriam.Resource
getSBase2CyNodeMapping(Long) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: Mapping
getSBaseByCyId(String) - Method in class org.cy3sbml.SBMLManager: Lookup a SBase object via id.
getSBaseByCyId(String, Long) - Method in class org.cy3sbml.SBMLManager
getSBaseRefResolver(SBase) - Method in class org.cy3sbml.SBMLManager: The resolver of the comp references of the document of the element: the one of the reader that read the document, else a new one (e.g. for a document of a session).
getSBMLDocument(Long) - Method in class org.cy3sbml.SBMLManager: Get SBMLDocument.
getSBMLDocument(CyNetwork) - Method in class org.cy3sbml.SBMLManager: Get SBMLDocument for given network.
getSearchContent() - Method in class org.cy3sbml.biomodel.BiomodelsDialog
getSearchMode() - Method in class org.cy3sbml.biomodel.SearchContent
getString(String) - Static method in class org.cy3sbml.biomodel.BioModelDialogText
getSubnetwork(CyNetwork[], String) - Static method in class org.cy3sbml.util.NetworkUtil: Returns the subnetwork with the given suffix, e.g.
getTemplate() - Method in class org.cy3sbml.styles.StyleInfo
getText(URI) - Method in class org.cy3sbml.util.HttpJson: Fetches the raw text body at the given URI (e.g. an SVG image response).
getTitle() - Method in class org.cy3sbml.gui.WebViewPanel
getTokensFromSearchText(String) - Method in class org.cy3sbml.biomodel.SearchContent
getUnqualifiedClassName(Object) - Static method in class org.cy3sbml.util.SBMLUtil: Returns unqualified class name of a given object.
getUrlPattern() - Method in class org.cy3sbml.miriam.Resource
getValues(Collection<T1>) - Method in class org.cy3sbml.mapping.One2ManyMapping
getValues(T1) - Method in class org.cy3sbml.mapping.One2ManyMapping
getVariableFromRule(Rule) - Static method in class org.cy3sbml.util.SBMLUtil: Get the variable from AssignmentRule and RateRule.
getVersion() - Method in class org.cy3sbml.BundleInformation: Version of bundle.
getVisualProperty() - Method in class org.cy3sbml.styles.Mapping
getVisualStyleByName(VisualMappingManager, String) - Static method in class org.cy3sbml.styles.StyleManager: Get the visual style by name.
getWebserviceError() - Static method in class org.cy3sbml.biomodel.BioModelDialogText
getWebserviceSBMLRequest() - Static method in class org.cy3sbml.biomodel.BioModelDialogText
givenName() - Method in record class org.cy3sbml.archive.ArchiveInfo.Creator: Returns the value of the givenName record component.
glyph() - Method in record class org.cy3sbml.layout.CyBoundingBox: Returns the value of the glyph record component.
GRAVITY_BIOMODELS - Static variable in class org.cy3sbml.gui.GUIConstants
GRAVITY_CHANGESTATE - Static variable in class org.cy3sbml.gui.GUIConstants
GRAVITY_COFACTOR_MERGE - Static variable in class org.cy3sbml.gui.GUIConstants
GRAVITY_COFACTOR_SPLIT - Static variable in class org.cy3sbml.gui.GUIConstants
GRAVITY_EXAMPLES - Static variable in class org.cy3sbml.gui.GUIConstants
GRAVITY_HELP - Static variable in class org.cy3sbml.gui.GUIConstants
GRAVITY_IMPORT - Static variable in class org.cy3sbml.gui.GUIConstants
GRAVITY_LOADLAYOUT - Static variable in class org.cy3sbml.gui.GUIConstants
GRAVITY_SAVELAYOUT - Static variable in class org.cy3sbml.gui.GUIConstants
GUI_RESOURCES - Static variable in class org.cy3sbml.ResourceExtractor
GUIConstants - Class in org.cy3sbml.gui: Constants used in GUI.
GUIUtil - Class in org.cy3sbml.util
GUIUtil() - Constructor for class org.cy3sbml.util.GUIUtil

H

handleEvent(SetCurrentNetworkEvent) - Method in class org.cy3sbml.actions.SplitCofactorsAction
handleEvent(SetCurrentNetworkEvent) - Method in class org.cy3sbml.gui.WebViewPanel: Listening to changes in Networks and NetworkViews.
handleEvent(NetworkAboutToBeDestroyedEvent) - Method in class org.cy3sbml.cofactors.CofactorManager: Removes the split cofactors of a destroyed network.
handleEvent(NetworkAboutToBeDestroyedEvent) - Method in class org.cy3sbml.SBMLManager: Remove the mappings if networks are destroyed.
handleEvent(RowsSetEvent) - Method in class org.cy3sbml.gui.WebViewPanel
handleEvent(PropertyUpdatedEvent) - Method in class org.cy3sbml.ConnectionProxy
handleEvent(SessionAboutToBeSavedEvent) - Method in class org.cy3sbml.SessionData: Save session.
handleEvent(SessionLoadedEvent) - Method in class org.cy3sbml.SessionData: Load Session.
handleEvent(SessionLoadedEvent) - Method in class org.cy3sbml.styles.StyleManager
handleEvent(NetworkViewAboutToBeDestroyedEvent) - Method in class org.cy3sbml.gui.WebViewPanel
handleEvent(NetworkViewAddedEvent) - Method in class org.cy3sbml.gui.WebViewPanel
hasClones(CyNetwork) - Method in class org.cy3sbml.cofactors.CofactorManager: Whether the network has split cofactor nodes.
hashCode() - Method in record class org.cy3sbml.archive.ArchiveImport: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.archive.ArchiveInfo.Creator: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.archive.ArchiveInfo.Entry: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.archive.ArchiveInfo: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.biomodel.Biomodel: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.biomodel.BiomodelsSearchResult: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.biomodel.BiomodelSummary: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.biomodel.SearchBioModel.Result: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.chebi.ChebiCompound: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.commands.Commands.Command: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.commands.CommandServices: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.comp.CompModels.External: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.comp.ModelResolution.Failed: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.comp.ModelResolution.Resolved: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.comp.SBaseRefResolution.Resolved: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.comp.SBaseRefResolution.Unresolved: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.layout.CyBoundingBox: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.miriam.MiriamRegistry.ResolvedURI: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.ols.OlsTerm: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.uniprot.UniprotEntry: Returns a hash code value for this object.
hashCode() - Method in record class org.cy3sbml.util.FetchResult: Returns a hash code value for this object.
hasNames() - Method in class org.cy3sbml.biomodel.SearchContent
height() - Method in record class org.cy3sbml.layout.CyBoundingBox: Returns the value of the height record component.
HelpAction - Class in org.cy3sbml.actions: Set help information in ResultsPanel.
HelpAction(WebViewPanel) - Constructor for class org.cy3sbml.actions.HelpAction: Constructor.
html(String) - Method in class org.cy3sbml.chebi.ChebiAccess: Creates the secondary-information HTML fragment for a ChEBI id, for display in the SBase details panel.
html(String) - Method in class org.cy3sbml.uniprot.UniprotAccess: Creates the secondary-information HTML fragment for a UniProt accession, for display in the SBase details panel.
HTML_EXAMPLE_RESOURCE - Static variable in class org.cy3sbml.gui.GUIConstants
HTML_HELP_RESOURCE - Static variable in class org.cy3sbml.gui.GUIConstants
HTML_INDENT - Static variable in class org.cy3sbml.util.XMLUtil
HTML_START_TEMPLATE - Static variable in class org.cy3sbml.gui.GUIConstants
HTML_STOP_TEMPLATE - Static variable in class org.cy3sbml.gui.GUIConstants
htmlFragments - Static variable in class org.cy3sbml.gui.GUIConstants
htmlTemplate - Static variable in class org.cy3sbml.gui.GUIConstants
HtmlTemplateParser - Class in org.cy3sbml
HtmlTemplateParser() - Constructor for class org.cy3sbml.HtmlTemplateParser
HtmlUtil - Class in org.cy3sbml.util: Escaping of text for HTML.
HttpJson - Class in org.cy3sbml.util: Small JSON-over-HTTP helper for the REST web services (OLS, ...).
HttpJson(HttpClient, ObjectMapper) - Constructor for class org.cy3sbml.util.HttpJson

I

ICON_BIOMODELS - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_BIOMODELS_DEPRECATED - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_CHANGESTATE - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_COFACTOR_MERGE - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_COFACTOR_SPLIT - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_CY3SBML - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_EXAMPLES - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_FALSE - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_HELP - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_IMPORT - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_INVISIBLE - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_LINK - Static variable in class org.cy3sbml.gui.GUIConstants: Link icon, with its tooltip in the placeholder {title}.
ICON_LOADLAYOUT - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_SAVELAYOUT - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_SPINNER - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_TRUE - Static variable in class org.cy3sbml.gui.GUIConstants
ICON_WARNING - Static variable in class org.cy3sbml.gui.GUIConstants
id() - Method in record class org.cy3sbml.biomodel.Biomodel: Returns the value of the id record component.
id() - Method in record class org.cy3sbml.biomodel.BiomodelSummary: Returns the value of the id record component.
ID - Static variable in interface org.cy3sbml.miriam.Fields
ID1 - Static variable in interface org.cy3sbml.miriam.Fields
ID2 - Static variable in interface org.cy3sbml.miriam.Fields
identifier() - Method in record class org.cy3sbml.miriam.MiriamRegistry.ResolvedURI: Returns the value of the identifier record component.
IDENTIFIER_LINK - Static variable in class org.cy3sbml.gui.GUIConstants
IDENTIFIER_PATTERN_MISMATCH - Static variable in class org.cy3sbml.gui.GUIConstants
IDENTIFIERS_BASE - Static variable in class org.cy3sbml.gui.SBaseHTMLFactory
IdentifiersConstants - Class in org.cy3sbml
IdentifiersConstants() - Constructor for class org.cy3sbml.IdentifiersConstants
ImportAction - Class in org.cy3sbml.actions: Importing SBML networks..
ImportAction(ServiceAdapter) - Constructor for class org.cy3sbml.actions.ImportAction
INDENT_AMOUNT - Static variable in class org.cy3sbml.util.XMLUtil
info() - Method in record class org.cy3sbml.archive.ArchiveImport: Returns the value of the info record component.
InfoPanel - Interface in org.cy3sbml.gui
initialize() - Static method in class org.cy3sbml.reader.JsbmlSetup: Creates the JSBML parser manager.
Institution(Integer, String, String, String, String, Resource.Location) - Constructor for class org.cy3sbml.miriam.Resource.Institution
INSTITUTION - Static variable in interface org.cy3sbml.miriam.Fields
integer - Enum constant in enum class org.cy3sbml.styles.Mapping.DataType
INTERACTION_ATTR - Static variable in class org.cy3sbml.SBML
INTERACTION_ATTR_EXTENDED - Static variable in class org.cy3sbml.SBML
INTERACTION_COMP_SBASE_DELETION - Static variable in class org.cy3sbml.SBML
INTERACTION_COMP_SBASE_REPLACED_BY - Static variable in class org.cy3sbml.SBML
INTERACTION_COMP_SBASE_REPLACED_ELEMENT - Static variable in class org.cy3sbml.SBML
INTERACTION_COMP_SBASEREF_ID - Static variable in class org.cy3sbml.SBML
INTERACTION_COMP_SBASEREF_METAID - Static variable in class org.cy3sbml.SBML
INTERACTION_COMP_SBASEREF_PORT - Static variable in class org.cy3sbml.SBML
INTERACTION_COMP_SBASEREF_SUBMODEL - Static variable in class org.cy3sbml.SBML
INTERACTION_COMP_SBASEREF_UNIT - Static variable in class org.cy3sbml.SBML
INTERACTION_DELAY_EVENT - Static variable in class org.cy3sbml.SBML
INTERACTION_EVENT_EVENT_ASSIGNMENT - Static variable in class org.cy3sbml.SBML
INTERACTION_FBC_ASSOCIATION_ASSOCIATION - Static variable in class org.cy3sbml.SBML
INTERACTION_FBC_ASSOCIATION_REACTION - Static variable in class org.cy3sbml.SBML
INTERACTION_FBC_GENEPRODUCT_SPECIES - Static variable in class org.cy3sbml.SBML
INTERACTION_FBC_PARAMETER_USER_DEFINED_CONSTRAINT - Static variable in class org.cy3sbml.SBML
INTERACTION_FBC_VARIABLE_USER_DEFINED_CONSTRAINT - Static variable in class org.cy3sbml.SBML
INTERACTION_LAYOUT_REFERENCE - Static variable in class org.cy3sbml.SBML
INTERACTION_LOCALPARAMETER_KINETICLAW - Static variable in class org.cy3sbml.SBML
INTERACTION_PARAMETER_REACTION - Static variable in class org.cy3sbml.SBML
INTERACTION_PRIORITY_EVENT - Static variable in class org.cy3sbml.SBML
INTERACTION_QUAL_TRANSITION_INPUT - Static variable in class org.cy3sbml.SBML
INTERACTION_QUAL_TRANSITION_OUTPUT - Static variable in class org.cy3sbml.SBML
INTERACTION_REACTION_ACTIVATOR - Static variable in class org.cy3sbml.SBML
INTERACTION_REACTION_COMPARTMENT - Static variable in class org.cy3sbml.SBML
INTERACTION_REACTION_INHIBITOR - Static variable in class org.cy3sbml.SBML
INTERACTION_REACTION_KINETICLAW - Static variable in class org.cy3sbml.SBML
INTERACTION_REACTION_MODIFIER - Static variable in class org.cy3sbml.SBML
INTERACTION_REACTION_PRODUCT - Static variable in class org.cy3sbml.SBML
INTERACTION_REACTION_REACTANT - Static variable in class org.cy3sbml.SBML
INTERACTION_REFERENCE_EVENT_ASSIGNMENT - Static variable in class org.cy3sbml.SBML
INTERACTION_REFERENCE_FUNCTIONDEFINITION - Static variable in class org.cy3sbml.SBML
INTERACTION_REFERENCE_INITIAL_ASSIGNMENT - Static variable in class org.cy3sbml.SBML
INTERACTION_REFERENCE_KINETICLAW - Static variable in class org.cy3sbml.SBML
INTERACTION_REFERENCE_RULE - Static variable in class org.cy3sbml.SBML
INTERACTION_SBASE_UNITDEFINITION - Static variable in class org.cy3sbml.SBML
INTERACTION_SPECIES_COMPARTMENT - Static variable in class org.cy3sbml.SBML
INTERACTION_TRIGGER_EVENT - Static variable in class org.cy3sbml.SBML
INTERACTION_TYPE_ATTR - Static variable in class org.cy3sbml.SBMLCore
INTERACTION_TYPE_REACTION_MODIFIER - Static variable in class org.cy3sbml.SBMLCore
INTERACTION_TYPE_REACTION_PRODUCT - Static variable in class org.cy3sbml.SBMLCore
INTERACTION_TYPE_REACTION_REACTANT - Static variable in class org.cy3sbml.SBMLCore
INTERACTION_UNIT_UNITDEFINITION - Static variable in class org.cy3sbml.SBML
INTERACTION_VARIABLE_EVENT_ASSIGNMENT - Static variable in class org.cy3sbml.SBML
INTERACTION_VARIABLE_INITIAL_ASSIGNMENT - Static variable in class org.cy3sbml.SBML
INTERACTION_VARIABLE_RULE - Static variable in class org.cy3sbml.SBML
INVISIBLE_RESOURCE_LINK - Static variable in class org.cy3sbml.gui.GUIConstants
IOUtil - Class in org.cy3sbml.util: Helper functions for input and output.
IOUtil() - Constructor for class org.cy3sbml.util.IOUtil
iri() - Method in record class org.cy3sbml.ols.OlsTerm: Returns the value of the iri record component.
isActive() - Method in class org.cy3sbml.gui.WebViewPanel
isClone(CyNetwork, CyNode) - Method in class org.cy3sbml.cofactors.CofactorManager: Whether the node is a clone of a split cofactor node in the network.
isComplete() - Method in record class org.cy3sbml.biomodel.BiomodelsSearchResult: Returns true if all matching models were read.
isDeprecated() - Method in class org.cy3sbml.miriam.Resource
isIdentifiersURI(String) - Static method in class org.cy3sbml.miriam.RegistryUtil: Whether the given resource URI is an identifiers.org URI or a urn:miriam URN, the forms that MiriamRegistry.resolve(String) resolves against the registry.
isOfficial() - Method in class org.cy3sbml.miriam.Resource
isOlsResource(Resource) - Static method in class org.cy3sbml.ols.OlsClient: Is a given resource physically located at OLS, i.e. an ontology in OLS.
isParsed() - Method in record class org.cy3sbml.biomodel.SearchBioModel.Result: Returns true if the models were parsed from text, not searched.
isProtectedUrls() - Method in class org.cy3sbml.miriam.Resource
isReady() - Method in class org.cy3sbml.actions.SBMLEnableTaskFactory
isRenderProtectedLanding() - Method in class org.cy3sbml.miriam.Resource
isSbml(String) - Static method in record class org.cy3sbml.archive.ArchiveInfo: Whether the format is SBML: a COMBINE specification URI of SBML (any level and version) or the media type application/sbml+xml.
isSBMLNetwork(CyNetwork) - Static method in class org.cy3sbml.util.NetworkUtil: Check if network is an SBMLNetwork.

J

JsbmlSetup - Class in org.cy3sbml.reader: One-time setup of JSBML before SBML files are read or written on several threads.

K

keySet() - Method in class org.cy3sbml.cofactors.Network2CofactorMapper: The networks with split cofactors.
keySet() - Method in class org.cy3sbml.mapping.Network2SBMLMapper: Get all rootNetwork SUIDs which have an association SBMLDocument.
keySet() - Method in class org.cy3sbml.mapping.One2ManyMapping
KeyValuePairHtml - Class in org.cy3sbml.gui: The HTML of the key-value pairs of an SBase (fbc v3, a listOfKeyValuePairs in the annotation): a table with a row per pair, the key (with id and name, if set), and the value with the uri defining the key, as a link if it is a URL.
KINETIC_LAW_ATTR_TEMPLATE - Static variable in class org.cy3sbml.SBMLCore
KINETIC_LAW_UNITS_ATTR_TEMPLATE - Static variable in class org.cy3sbml.SBMLCore
kineticEdgeTypes - Static variable in class org.cy3sbml.SBML
kineticNodeTypes - Static variable in class org.cy3sbml.SBML

L

label() - Method in record class org.cy3sbml.ols.OlsTerm: Returns the value of the label record component.
label(UncertParameter) - Static method in class org.cy3sbml.util.DistribUtil: The type, for an external parameter its name if it is set.
LABEL - Static variable in class org.cy3sbml.SBML
lastModified() - Method in record class org.cy3sbml.biomodel.BiomodelSummary: Returns the value of the lastModified record component.
LatestTaskExecutor - Class in org.cy3sbml.gui: Runs render tasks one at a time on a single daemon thread, keeping only the most recently submitted task alive, and coalescing a resubmission of the task that is already pending or running.
LatestTaskExecutor() - Constructor for class org.cy3sbml.gui.LatestTaskExecutor
LAYOUT - Static variable in class org.cy3sbml.layout.XMLInterface
layoutChildren() - Method in class org.cy3sbml.gui.Browser
LayoutStyleFactory - Class in org.cy3sbml.styles: Creates the style of the layout networks (#71) from a cy3sbml style: a copy named <style>SBML.STYLE_SUFFIX_LAYOUT with the node sizes of the glyphs.
LayoutStyleFactory(VisualStyleFactory, VisualMappingFunctionFactory, VisualMappingFunctionFactory) - Constructor for class org.cy3sbml.styles.LayoutStyleFactory
layoutStyleName(String) - Static method in class org.cy3sbml.styles.LayoutStyleFactory: Name of the layout style of the style.
layoutTools() - Method in record class org.cy3sbml.commands.CommandServices: Returns the value of the layoutTools record component.
LayoutTools - Class in org.cy3sbml.layout: Utilities for working with layouts.
LayoutTools(ServiceAdapter) - Constructor for class org.cy3sbml.layout.LayoutTools
LEVEL_VERSION - Static variable in class org.cy3sbml.SBML
linkActivated(URL) - Method in class org.cy3sbml.gui.BrowserHyperlinkListener: Called on the JavaFX thread when a link is clicked.
load() - Static method in class org.cy3sbml.HtmlTemplateParser
loadBioModelByIdsAndDisposeDialog() - Method in class org.cy3sbml.biomodel.BiomodelsDialog
loadBundledRegistry() - Static method in class org.cy3sbml.miriam.RegistryUtil: Load the offline copy of the registry bundled with the app.
loadExampleFromResource(ServiceAdapter, String) - Static method in class org.cy3sbml.util.GUIUtil: Loads an SBML example file from the given resource: copies it into a temporary file, named like the resource, and loads the file in a Cytoscape task.
LoadLayoutAction - Class in org.cy3sbml.actions: Load node positions from file.
LoadLayoutAction(ServiceAdapter) - Constructor for class org.cy3sbml.actions.LoadLayoutAction: Constructor.
loadLayoutForViewFromFile(CyNetworkView, File) - Method in class org.cy3sbml.layout.LayoutTools: Moves every node of the view with a position in the file to that position.
loadLayoutOfCurrentViewFromFile(File) - Method in class org.cy3sbml.layout.LayoutTools: Load layout of current view from file.
loadNetworkFile() - Method in record class org.cy3sbml.commands.CommandServices: Returns the value of the loadNetworkFile record component.
loadNetworkFileTaskFactory - Variable in class org.cy3sbml.ServiceAdapter
loadNetworkURL() - Method in record class org.cy3sbml.commands.CommandServices: Returns the value of the loadNetworkURL record component.
loadPage(String) - Method in class org.cy3sbml.gui.Browser: Load page in webView;
loadPageFromResource(String) - Method in class org.cy3sbml.gui.Browser: Load local resource;
loadRegistry(File) - Static method in class org.cy3sbml.miriam.RegistryUtil: Load the registry from a MIRIAM json file.
loadSelectedBioModelsAndDisposeDialog() - Method in class org.cy3sbml.biomodel.BiomodelsDialog
loadStyles() - Method in class org.cy3sbml.styles.StyleManager: Load the visual styles of the app and add the layout style of every style (#71), if they do not exist yet (e.g. from a session).
loadText(String) - Method in class org.cy3sbml.gui.Browser: Load HTML text in the webEngine.
localParameterId(LocalParameter) - Static method in class org.cy3sbml.util.MappingUtil
location() - Method in record class org.cy3sbml.archive.ArchiveImport: Returns the value of the location record component.
location() - Method in record class org.cy3sbml.archive.ArchiveInfo.Entry: Returns the value of the location record component.
Location(String, String) - Constructor for class org.cy3sbml.miriam.Resource.Location
LOCATION - Static variable in interface org.cy3sbml.miriam.Fields
LOGO_BIOMODELS - Static variable in class org.cy3sbml.gui.GUIConstants
longDescription() - Method in record class org.cy3sbml.commands.Commands.Command: Returns the value of the longDescription record component.

M

Mapping - Class in org.cy3sbml.styles: Parent class of mappings.
Mapping(Mapping.MappingType, Mapping.DataType, VisualPropertyKey, String, String) - Constructor for class org.cy3sbml.styles.Mapping
Mapping.DataType - Enum Class in org.cy3sbml.styles
Mapping.MappingType - Enum Class in org.cy3sbml.styles
MappingDiscrete - Class in org.cy3sbml.styles: Information storage for DiscreteMapping
MappingDiscrete(Mapping.DataType, VisualPropertyKey, String, String, Map<String, String>) - Constructor for class org.cy3sbml.styles.MappingDiscrete
mappingFromNetwork(CyNetwork, One2ManyMapping<String, Long>) - Static method in class org.cy3sbml.reader.SBMLReaderTask: Create mapping between cyIds and cytoscape nodes.
MappingPassthrough - Class in org.cy3sbml.styles: Information storage for PassthroughMapping.
MappingPassthrough(Mapping.DataType, VisualPropertyKey, String, String) - Constructor for class org.cy3sbml.styles.MappingPassthrough
MappingUtil - Class in org.cy3sbml.util: Helper for mapping between Cytoscape and SBML objects.
MappingUtil() - Constructor for class org.cy3sbml.util.MappingUtil
mass() - Method in record class org.cy3sbml.chebi.ChebiCompound: Returns the value of the mass record component.
master() - Method in record class org.cy3sbml.archive.ArchiveInfo.Entry: Returns the value of the master record component.
matches() - Method in record class org.cy3sbml.biomodel.BiomodelsSearchResult: Returns the value of the matches record component.
matches() - Method in record class org.cy3sbml.biomodel.SearchBioModel.Result: Returns the value of the matches record component.
MAX_RESULTS - Static variable in class org.cy3sbml.biomodel.BiomodelsQuery: Maximum number of models read for a search.
MemoryCache<K,V> - Class in org.cy3sbml.cache: Thread-safe, size-bounded least-recently-used cache for web service lookups.
MemoryCache(int) - Constructor for class org.cy3sbml.cache.MemoryCache
MemoryCache(int, Duration, Clock) - Constructor for class org.cy3sbml.cache.MemoryCache: For tests: an injectable TTL and clock for the "not found" entries.
merge(CyNetwork, CyNetworkView, Collection<CyNode>) - Method in class org.cy3sbml.cofactors.CofactorManager: Merges the cofactor nodes of the given clones; nodes that are no clones are skipped.
mergeAll(CyNetwork, CyNetworkView) - Method in class org.cy3sbml.cofactors.CofactorManager: Merges all split cofactor nodes of the network.
MergeCofactorsAction - Class in org.cy3sbml.actions: Merges the clones of split nodes back into the nodes: the nodes of the selected clones, or all split nodes of the current network if no clone is selected.
MergeCofactorsAction(ServiceAdapter, SBMLManager, CofactorManager) - Constructor for class org.cy3sbml.actions.MergeCofactorsAction
MIR_ID - Static variable in interface org.cy3sbml.miriam.Fields
MIRIAM_COLLECTION_LINK - Static variable in class org.cy3sbml.gui.GUIConstants
MiriamRegistry - Class in org.cy3sbml.miriam: The MIRIAM registry of data collections used to resolve annotation URIs.
MiriamRegistry.ResolvedURI - Record Class in org.cy3sbml.miriam: An identifiers.org resource URI resolved against the registry: its data collection (null if the registry has none for it) and its identifier.
model() - Method in record class org.cy3sbml.comp.ModelResolution.Resolved: Returns the value of the model record component.
model() - Method in record class org.cy3sbml.comp.SBaseRefResolution.Resolved: Returns the value of the model record component.
modelIds() - Method in record class org.cy3sbml.biomodel.SearchBioModel.Result: Returns the value of the modelIds record component.
ModelResolution - Interface in org.cy3sbml.comp: The result of resolving a model reference of the comp package: the model, or why it could not be resolved.
ModelResolution.Failed - Record Class in org.cy3sbml.comp: The model could not be resolved, with the reason for the user.
ModelResolution.Resolved - Record Class in org.cy3sbml.comp: The referenced model and the document it is defined in, which is another document for an external model definition.
models() - Method in record class org.cy3sbml.biomodel.BiomodelsSearchResult: Returns the value of the models record component.
models() - Method in class org.cy3sbml.comp.SBaseRefResolver: The resolver of the model references the SBaseRefs are resolved with.
modelsToImport() - Method in record class org.cy3sbml.archive.ArchiveInfo: The SBML files to import: the master SBML files if there is one, else all SBML files.
MODIFIED - Static variable in interface org.cy3sbml.miriam.Fields
MODIFIED_DATE - Static variable in class org.cy3sbml.gui.GUIConstants

N

name() - Method in record class org.cy3sbml.archive.ArchiveInfo: Returns the value of the name record component.
name() - Method in record class org.cy3sbml.biomodel.Biomodel: Returns the value of the name record component.
name() - Method in record class org.cy3sbml.biomodel.BiomodelSummary: Returns the value of the name record component.
name() - Method in record class org.cy3sbml.chebi.ChebiCompound: Returns the value of the name record component.
name() - Method in record class org.cy3sbml.commands.Commands.Command: Returns the value of the name record component.
NAME - Static variable in record class org.cy3sbml.biomodel.Biomodel
NAME - Static variable in interface org.cy3sbml.miriam.Fields
NAME - Static variable in class org.cy3sbml.styles.StyleInfo_cy3sbml
NAME - Static variable in class org.cy3sbml.styles.StyleInfo_cy3sbmlDark
Namespace - Class in org.cy3sbml.miriam
Namespace(List<Resource>) - Constructor for class org.cy3sbml.miriam.Namespace
Namespace(Map<Object, Object>) - Constructor for class org.cy3sbml.miriam.Namespace
NAMESPACE - Static variable in class org.cy3sbml.commands.Commands: The command namespace.
NAMESPACE_EMBEDDED_IN_LUI - Static variable in interface org.cy3sbml.miriam.Fields
NAMESPACES - Static variable in interface org.cy3sbml.miriam.Fields
NAMESPACES - Static variable in class org.cy3sbml.miriam.RegistryUtil
namesToString(String) - Method in class org.cy3sbml.biomodel.SearchContent
NETWORK - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NETWORK_BACKGROUND_PAINT - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NETWORK_CENTER_X_LOCATION - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NETWORK_CENTER_Y_LOCATION - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NETWORK_CENTER_Z_LOCATION - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NETWORK_DEPTH - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NETWORK_HEIGHT - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NETWORK_SCALE_FACTOR - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NETWORK_SIZE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NETWORK_TITLE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NETWORK_WIDTH - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
Network2CofactorMapper - Class in org.cy3sbml.cofactors: The split cofactor nodes of the networks, per (sub)network SUID.
Network2CofactorMapper() - Constructor for class org.cy3sbml.cofactors.Network2CofactorMapper
Network2SBMLMapper - Class in org.cy3sbml.mapping: Mapping between CyNetworks and SBMLDocuments.
Network2SBMLMapper() - Constructor for class org.cy3sbml.mapping.Network2SBMLMapper
networkManager() - Method in record class org.cy3sbml.commands.CommandServices: Returns the value of the networkManager record component.
NETWORKTYPE_ATTR - Static variable in class org.cy3sbml.SBML
NETWORKTYPE_LAYOUT - Static variable in class org.cy3sbml.SBML
NETWORKTYPE_SBML - Static variable in class org.cy3sbml.SBML
NetworkUtil - Class in org.cy3sbml.util: Utils for working with networks.
NetworkUtil() - Constructor for class org.cy3sbml.util.NetworkUtil
networkViewManager() - Method in record class org.cy3sbml.commands.CommandServices: Returns the value of the networkViewManager record component.
newDirectory(String) - Method in class org.cy3sbml.archive.ArchiveDirectories: A new, empty directory for the archive with the given file name.
NO_DESCRIPTION_AVAILABLE - Static variable in interface org.cy3sbml.miriam.Fields
NODE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_BORDER_LINE_TYPE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_BORDER_PAINT - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_BORDER_STROKE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_BORDER_TRANSPARENCY - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_BORDER_WIDTH - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_DEPTH - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_FILL_COLOR - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_HEIGHT - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_LABEL - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_LABEL_COLOR - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_LABEL_FONT_FACE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_LABEL_FONT_SIZE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_LABEL_POSITION - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_LABEL_TRANSPARENCY - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_LABEL_WIDTH - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_NAME_ATTR_LABEL - Static variable in class org.cy3sbml.SBMLCore
NODE_NESTED_NETWORK_IMAGE_VISIBLE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_PAINT - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_SELECTED - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_SELECTED_PAINT - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_SHAPE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_SIZE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_TOOLTIP - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_TRANSPARENCY - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_VISIBLE - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_WIDTH - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_X_LOCATION - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_Y_LOCATION - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
NODE_Z_LOCATION - Enum constant in enum class org.cy3sbml.styles.VisualPropertyKey
nodeLink(Model, String, CompTargets) - Static method in class org.cy3sbml.util.SBMLUtil: The link to the node with the metaid in the network collection of the model, empty if the model has no network collection.
NODETYPE_ALGEBRAIC_RULE - Static variable in class org.cy3sbml.SBML
NODETYPE_ASSIGNMENT_RULE - Static variable in class org.cy3sbml.SBML
NODETYPE_ATTR - Static variable in class org.cy3sbml.SBML
NODETYPE_ATTR_EXTENDED - Static variable in class org.cy3sbml.SBML
NODETYPE_COMP_DELETION - Static variable in class org.cy3sbml.SBML
NODETYPE_COMP_PORT - Static variable in class org.cy3sbml.SBML
NODETYPE_COMP_REPLACED_BY - Static variable in class org.cy3sbml.SBML
NODETYPE_COMP_REPLACED_ELEMENT - Static variable in class org.cy3sbml.SBML
NODETYPE_COMP_SUBMODEL - Static variable in class org.cy3sbml.SBML
NODETYPE_COMPARTMENT - Static variable in class org.cy3sbml.SBML
NODETYPE_CONSTRAINT - Static variable in class org.cy3sbml.SBML
NODETYPE_EVENT - Static variable in class org.cy3sbml.SBML
NODETYPE_EVENT_ASSIGNMENT - Static variable in class org.cy3sbml.SBML
NODETYPE_FBC_AND - Static variable in class org.cy3sbml.SBML
NODETYPE_FBC_GENEPRODUCT - Static variable in class org.cy3sbml.SBML
NODETYPE_FBC_OR - Static variable in class org.cy3sbml.SBML
NODETYPE_FBC_USER_DEFINED_CONSTRAINT - Static variable in class org.cy3sbml.SBML
NODETYPE_FUNCTION_DEFINITION - Static variable in class org.cy3sbml.SBML
NODETYPE_GROUP - Static variable in class org.cy3sbml.SBML
NODETYPE_INITIAL_ASSIGNMENT - Static variable in class org.cy3sbml.SBML
NODETYPE_KINETIC_LAW - Static variable in class org.cy3sbml.SBML
NODETYPE_LAYOUT_COMPARTMENTGLYPH - Static variable in class org.cy3sbml.SBML
NODETYPE_LAYOUT_GENERALGLYPH - Static variable in class org.cy3sbml.SBML
NODETYPE_LAYOUT_GENERATED - Static variable in class org.cy3sbml.SBML
NODETYPE_LAYOUT_GRAPHICALOBJECT - Static variable in class org.cy3sbml.SBML
NODETYPE_LAYOUT_REACTIONGLYPH - Static variable in class org.cy3sbml.SBML
NODETYPE_LAYOUT_SPECIESGLYPH - Static variable in class org.cy3sbml.SBML
NODETYPE_LOCAL_PARAMETER - Static variable in class org.cy3sbml.SBML
NODETYPE_PARAMETER - Static variable in class org.cy3sbml.SBML
NODETYPE_QUAL_SPECIES - Static variable in class org.cy3sbml.SBML
NODETYPE_QUAL_TRANSITION - Static variable in class org.cy3sbml.SBML
NODETYPE_RATE_RULE - Static variable in class org.cy3sbml.SBML
NODETYPE_REACTION - Static variable in class org.cy3sbml.SBML
NODETYPE_REACTION_IRREVERSIBLE - Static variable in class org.cy3sbml.SBML
NODETYPE_REACTION_REVERSIBLE - Static variable in class org.cy3sbml.SBML
NODETYPE_SPECIES - Static variable in class org.cy3sbml.SBML
NODETYPE_UNIT - Static variable in class org.cy3sbml.SBML
NODETYPE_UNIT_DEFINITION - Static variable in class org.cy3sbml.SBML
NOT_FOUND - Enum constant in enum class org.cy3sbml.util.FetchStatus
notFound() - Static method in record class org.cy3sbml.util.FetchResult

O

oboId() - Method in record class org.cy3sbml.ols.OlsTerm: Returns the value of the oboId record component.
OFFICIAL - Static variable in interface org.cy3sbml.miriam.Fields
OLS_BASE_URL - Static variable in class org.cy3sbml.IdentifiersConstants
OLS_TERM_ERROR - Static variable in class org.cy3sbml.gui.GUIConstants
OlsClient - Class in org.cy3sbml.ols: Small client for the OLS4 (Ontology Lookup Service) REST API.
OlsClient(HttpJson) - Constructor for class org.cy3sbml.ols.OlsClient
OlsTerm - Record Class in org.cy3sbml.ols: An OLS4 ontology term.
OlsTerm(String, String, String, String, List<String>, List<String>) - Constructor for record class org.cy3sbml.ols.OlsTerm: Creates an instance of a OlsTerm record class.
One2ManyMapping<T1,T2> - Class in org.cy3sbml.mapping: One to many mapping class.
One2ManyMapping() - Constructor for class org.cy3sbml.mapping.One2ManyMapping
ONLINE_REGISTRY - Static variable in class org.cy3sbml.miriam.MiriamRegistry: The current registry at identifiers.org.
ONTOLOGY_TERM_LINK - Static variable in class org.cy3sbml.gui.GUIConstants
ontologyName() - Method in record class org.cy3sbml.ols.OlsTerm: Returns the value of the ontologyName record component.
openBrowser - Variable in class org.cy3sbml.ServiceAdapter
OpenBrowser - Class in org.cy3sbml.util: Static OpenBrower helper class.
OpenBrowser() - Constructor for class org.cy3sbml.util.OpenBrowser
openCurrentSBMLInBrowser(SBMLManager) - Static method in class org.cy3sbml.util.GUIUtil: Open current SBML in browser.
openFileInBrowser(File) - Static method in class org.cy3sbml.util.GUIUtil: Open a given file in browser.
openHTMLInBrowser(String) - Static method in class org.cy3sbml.util.GUIUtil: Open validation HTML in external Browser.
openSBaseHTMLInBrowser(String) - Static method in class org.cy3sbml.util.GUIUtil: Open the given SBase HTML information in external Browser.
openURL(String) - Static method in class org.cy3sbml.util.OpenBrowser: Opens the specified URL in the system default web browser.
openURLinExternalBrowser(String) - Static method in class org.cy3sbml.util.GUIUtil: Open url in external webView.
org.cy3sbml - package org.cy3sbml
org.cy3sbml.actions - package org.cy3sbml.actions
org.cy3sbml.archive - package org.cy3sbml.archive
org.cy3sbml.biomodel - package org.cy3sbml.biomodel
org.cy3sbml.cache - package org.cy3sbml.cache
org.cy3sbml.chebi - package org.cy3sbml.chebi
org.cy3sbml.cofactors - package org.cy3sbml.cofactors
org.cy3sbml.commands - package org.cy3sbml.commands
org.cy3sbml.comp - package org.cy3sbml.comp
org.cy3sbml.gui - package org.cy3sbml.gui
org.cy3sbml.layout - package org.cy3sbml.layout
org.cy3sbml.mapping - package org.cy3sbml.mapping
org.cy3sbml.miriam - package org.cy3sbml.miriam
org.cy3sbml.ols - package org.cy3sbml.ols
org.cy3sbml.reader - package org.cy3sbml.reader
org.cy3sbml.styles - package org.cy3sbml.styles
org.cy3sbml.uniprot - package org.cy3sbml.uniprot
org.cy3sbml.util - package org.cy3sbml.util
org.cy3sbml.util.filter - package org.cy3sbml.util.filter
organization() - Method in record class org.cy3sbml.archive.ArchiveInfo.Creator: Returns the value of the organization record component.
owns(SBMLDocument) - Method in class org.cy3sbml.comp.CompModels: True if the document is the document of this resolver or one it read.

P

PanelUpdater - Class in org.cy3sbml.gui: Renders one previously-resolved render target (see PanelUpdater.resolveTarget(org.cytoscape.model.CyNetwork, org.cy3sbml.SBMLManager)) into the panel.
PanelUpdater(InfoPanel, Object, SBaseHTMLFactory) - Constructor for class org.cy3sbml.gui.PanelUpdater
parameter(UncertParameter) - Static method in class org.cy3sbml.util.DistribUtil: The uncertainty parameter as label=value, e.g.
parseBioModelByIds() - Method in class org.cy3sbml.biomodel.BiomodelsDialog: Lists the BioModel ids parsed from the text and looks up their details.
parseBioModelIdsFromString(String) - Static method in class org.cy3sbml.biomodel.BiomodelsDialog: Returns set of BioModel identifiers from given text.
parseCVTerms(SBase) - Static method in class org.cy3sbml.util.AnnotationUtil: Parses the CV-terms into properties.
PARSED_IDS - Static variable in class org.cy3sbml.biomodel.SearchContent
parseNotes(SBase) - Static method in class org.cy3sbml.util.SBMLUtil: Parses the notes xml from the <notes> element.
parseTemplateSections(String) - Static method in class org.cy3sbml.HtmlTemplateParser: Extracts template sections from HTML into a map preserving insertion order
PASSTHROUGH - Enum constant in enum class org.cy3sbml.styles.Mapping.MappingType
path() - Method in record class org.cy3sbml.comp.SBaseRefResolution.Resolved: Returns the value of the path record component.
PATHWAY - Static variable in interface org.cy3sbml.uniprot.UniprotHTMLFields
PATHWAY_NAME - Static variable in interface org.cy3sbml.uniprot.UniprotHTMLFields
pathways() - Method in record class org.cy3sbml.uniprot.UniprotEntry: Returns the value of the pathways record component.
PATTERN - Static variable in interface org.cy3sbml.miriam.Fields
PAYLOAD - Static variable in class org.cy3sbml.miriam.RegistryUtil
performBiomodelQuery(String) - Method in class org.cy3sbml.biomodel.BiomodelsQuery: Gets the information for the given BioModel.
performBioModelSearch() - Static method in class org.cy3sbml.biomodel.BioModelDialogText
PREFIX - Static variable in interface org.cy3sbml.miriam.Fields
PREFIX - Static variable in class org.cy3sbml.miriam.RegistryUtil
PREFIX_ALGEBRAIC_RULE - Static variable in class org.cy3sbml.util.MappingUtil
PREFIX_CONSTRAINT - Static variable in class org.cy3sbml.util.MappingUtil
PREFIX_EVENT - Static variable in class org.cy3sbml.util.MappingUtil
PREFIX_EVENT_ASSIGNMENT - Static variable in class org.cy3sbml.util.MappingUtil
PREFIX_INITIAL_ASSIGNMENT - Static variable in class org.cy3sbml.util.MappingUtil
PREFIX_KINETIC_LAW - Static variable in class org.cy3sbml.util.MappingUtil
PREFIX_NETWORK_FLAT - Static variable in class org.cy3sbml.SBML
PREFIX_RULE - Static variable in class org.cy3sbml.util.MappingUtil
PREFIX_UNITSID - Static variable in class org.cy3sbml.util.MappingUtil
primaryAccession() - Method in record class org.cy3sbml.uniprot.UniprotEntry: Returns the value of the primaryAccession record component.
properties() - Method in record class org.cy3sbml.commands.Commands.Command: The service properties that register the task factory as the command.
PROPERTIES_FILE - Static variable in class org.cy3sbml.CyActivator
PROPERTY_VISUAL_STYLE - Static variable in class org.cy3sbml.SBML
PROTECTED_URLS - Static variable in interface org.cy3sbml.miriam.Fields
PROVIDER_CODE - Static variable in interface org.cy3sbml.miriam.Fields
PUBLICATION - Static variable in record class org.cy3sbml.biomodel.Biomodel
PUBLICATION_ID - Static variable in record class org.cy3sbml.biomodel.Biomodel
publicationIdentifier() - Method in record class org.cy3sbml.biomodel.Biomodel: Returns the value of the publicationIdentifier record component.
publishIfCurrent(Runnable) - Method in class org.cy3sbml.gui.LatestTaskExecutor: Runs publication if, and only if, the calling thread is running a task of this executor that is still the current one: no task under a different key (and no later task under an earlier key) has been submitted since, and the executor is not closed.
put(T1, T2) - Method in class org.cy3sbml.mapping.One2ManyMapping
putClone(Long, Long, Long) - Method in class org.cy3sbml.cofactors.Network2CofactorMapper: Stores a clone of the cofactor node.
putCloneEdge(Long, Long, Long) - Method in class org.cy3sbml.cofactors.Network2CofactorMapper: Stores the original edge a clone edge stands for.
putDocument(Long, SBMLDocument, One2ManyMapping<String, Long>) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: The SBMLDocument is stored with the SBML id to SUID (CyNode) mapping.
putModel(Long, Model) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: Stores the model the root network was created from.
putNode(Long, String, Long) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: Maps a node created after the import (a cofactor clone) to the SBase of its cyId.
putPosition(Long, Long, double, double) - Method in class org.cy3sbml.cofactors.Network2CofactorMapper: Stores the position of the cofactor node before the split.

R

REACTION_NAME - Static variable in interface org.cy3sbml.uniprot.UniprotHTMLFields
readLayoutFromXML(File) - Static method in class org.cy3sbml.layout.XMLInterface: Reads the bounding boxes of the layout file, or returns an empty list if the file cannot be read.
readResource(String) - Static method in class org.cy3sbml.util.IOUtil: Read resource to InputStream
readSBMLDocument(String) - Static method in class org.cy3sbml.util.SBMLUtil: Read the SBMLDocument from given SBML file resource.
readXMLString(String) - Static method in class org.cy3sbml.util.XMLUtil: Read XML Document from String.
reason() - Method in record class org.cy3sbml.comp.ModelResolution.Failed: Returns the value of the reason record component.
reason() - Method in record class org.cy3sbml.comp.SBaseRefResolution.Unresolved: Returns the value of the reason record component.
refresh(URI, Duration) - Method in class org.cy3sbml.miriam.MiriamRegistry: Replaces the registry with the one downloaded from the source.
refreshInBackground(URI) - Method in class org.cy3sbml.miriam.MiriamRegistry: Refreshes the registry from the source on a background thread, so the caller (e.g. the bundle start) is not blocked by the network.
RegistryUtil - Class in org.cy3sbml.miriam: Tools for working with Miriam registry.
RegistryUtil() - Constructor for class org.cy3sbml.miriam.RegistryUtil
remove(T1) - Method in class org.cy3sbml.mapping.One2ManyMapping
removeCloneEdge(Long, Long) - Method in class org.cy3sbml.cofactors.Network2CofactorMapper
removeCofactor(Long, Long) - Method in class org.cy3sbml.cofactors.Network2CofactorMapper: Removes the cofactor node with its clones and position; its clone edges are removed one by one.
removeDocument(Long) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: Removes the document for a given root network SUID.
removeNetwork(Long) - Method in class org.cy3sbml.cofactors.Network2CofactorMapper: Removes all entries of the network, e.g. when it is destroyed.
removeNode(Long, Long) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: Removes the mapping of a node, e.g. of a cofactor clone that is merged.
removeNodeMapping(CyNetwork, CyNode) - Method in class org.cy3sbml.SBMLManager: Removes the mapping of a node added with SBMLManager.addNodeMapping(org.cytoscape.model.CyNetwork, org.cytoscape.model.CyNode).
removeSBMLForNetwork(CyNetwork) - Method in class org.cy3sbml.SBMLManager: Remove the SBMLDocument for network.
removeValue(T1, T2) - Method in class org.cy3sbml.mapping.One2ManyMapping: Removes one value of the key, and the key if it has no values left.
RENDER_DEPRECATED_LANDING - Static variable in interface org.cy3sbml.miriam.Fields
RENDER_PROTECTED_LANDING - Static variable in interface org.cy3sbml.miriam.Fields
resetFields() - Method in class org.cy3sbml.biomodel.BiomodelsDialog
resolution() - Method in record class org.cy3sbml.comp.CompModels.External: Returns the value of the resolution record component.
resolve(String) - Method in class org.cy3sbml.miriam.MiriamRegistry: Resolves the given identifiers.org resource URI or urn:miriam URN to its data collection and identifier, or null if the URI cannot be parsed.
resolve(SBaseRef) - Method in class org.cy3sbml.comp.SBaseRefResolver: The element the reference points to.
resolve(Submodel) - Method in class org.cy3sbml.comp.CompModels: The model the submodel instantiates.
resolve(SBMLDocument, String) - Method in class org.cy3sbml.comp.CompModels: The model with the id in the scope document: its main model, a model definition or the model of an external model definition.
Resolved(Model, SBase, List<Submodel>) - Constructor for record class org.cy3sbml.comp.SBaseRefResolution.Resolved: Creates an instance of a Resolved record class.
Resolved(Model, SBMLDocument) - Constructor for record class org.cy3sbml.comp.ModelResolution.Resolved: Creates an instance of a Resolved record class.
ResolvedURI(Namespace, String) - Constructor for record class org.cy3sbml.miriam.MiriamRegistry.ResolvedURI: Creates an instance of a ResolvedURI record class.
resolver(SBase) - Method in interface org.cy3sbml.comp.CompTargets: The resolver of the comp references of the document of the element, null if there is none.
resolver(SBase) - Method in class org.cy3sbml.SBMLManager
Resource - Class in org.cy3sbml.miriam
Resource() - Constructor for class org.cy3sbml.miriam.Resource
RESOURCE_HOME_URL - Static variable in interface org.cy3sbml.miriam.Fields
Resource.Institution - Class in org.cy3sbml.miriam
Resource.Location - Class in org.cy3sbml.miriam
ResourceExtractor - Class in org.cy3sbml: This class extracts bundled resources to a local directory.
ResourceExtractor(BundleContext, File) - Constructor for class org.cy3sbml.ResourceExtractor: Constructor.
RESOURCES - Static variable in interface org.cy3sbml.miriam.Fields
RESOURCES - Static variable in class org.cy3sbml.ResourceExtractor: Bundle directories extracted into the app directory.
Result(SearchContent, int, List<String>, Map<String, BiomodelSummary>) - Constructor for record class org.cy3sbml.biomodel.SearchBioModel.Result: Creates an instance of a Result record class.
rootNetwork(Model) - Method in interface org.cy3sbml.comp.CompTargets: The SUID of the root network created from the model, empty if there is none.
rootNetwork(Model) - Method in class org.cy3sbml.SBMLManager
run() - Method in class org.cy3sbml.gui.PanelUpdater: Renders PanelUpdater.target.
run() - Method in class org.cy3sbml.gui.SBaseHTMLThread: Creates information for all objects within a single thread.
run(TaskMonitor) - Method in class org.cy3sbml.archive.CombineArchiveReaderTask
run(TaskMonitor) - Method in class org.cy3sbml.reader.SBMLReaderTask: Reads the SBML and creates the networks for its models.

S

SAMPLE_ID - Static variable in interface org.cy3sbml.miriam.Fields
SaveLayoutAction - Class in org.cy3sbml.actions: Save node positions to file.
SaveLayoutAction(ServiceAdapter) - Constructor for class org.cy3sbml.actions.SaveLayoutAction: Constructor.
saveLayoutOfCurrentViewInFile(File) - Method in class org.cy3sbml.layout.LayoutTools: Save layout of current view in file.
saveLayoutOfViewInFile(CyNetworkView, File) - Method in class org.cy3sbml.layout.LayoutTools: Save layout of given view in file.
saveSessionData(SessionAboutToBeSavedEvent) - Method in class org.cy3sbml.SessionData: Save the session data from cy3sbml.
SBaseFilter - Class in org.cy3sbml.util.filter: Filter testing if object is SBase.
SBaseFilter() - Constructor for class org.cy3sbml.util.filter.SBaseFilter
SBaseHTMLFactory - Class in org.cy3sbml.gui: Creates HTML information for given SBase.
SBaseHTMLFactory(String, MiriamRegistry, OlsClient, UniprotAccess, ChebiAccess) - Constructor for class org.cy3sbml.gui.SBaseHTMLFactory: Creates the factory.
SBaseHTMLFactory(String, MiriamRegistry, OlsClient, UniprotAccess, ChebiAccess, CompTargets) - Constructor for class org.cy3sbml.gui.SBaseHTMLFactory: Creates the factory, which shows the targets of the comp references.
SBaseHTMLFactory(String, MiriamRegistry, OlsClient, UniprotAccess, ChebiAccess, CompTargets, Function<SBMLDocument, Optional<ArchiveImport>>) - Constructor for class org.cy3sbml.gui.SBaseHTMLFactory: Creates the factory, which shows the targets of the comp references and the COMBINE archive a document was imported from.
SBaseHTMLThread - Class in org.cy3sbml.gui: Builds the HTML information for a set of SBase objects, via web-service lookups (OLS, UniProt, ChEBI), and posts it to a panel.
SBaseHTMLThread(Collection<Object>, InfoPanel, SBaseHTMLFactory) - Constructor for class org.cy3sbml.gui.SBaseHTMLThread: Constructor.
SBaseRefResolution - Interface in org.cy3sbml.comp: The result of resolving an SBaseRef: the element it points to, or why it could not be resolved.
SBaseRefResolution.Resolved - Record Class in org.cy3sbml.comp: The target element in its model.
SBaseRefResolution.Unresolved - Record Class in org.cy3sbml.comp: The reference could not be resolved, with the reason for the user.
SBaseRefResolver - Class in org.cy3sbml.comp: Resolves the element an SBaseRef of the comp package points to.
SBaseRefResolver(CompModels) - Constructor for class org.cy3sbml.comp.SBaseRefResolver
SBML - Class in org.cy3sbml: Definition of cy3sbml constants.
SBML_CHARGE_ATTR - Static variable in class org.cy3sbml.SBMLCore
SBML_COMPARTMENT_ATTR - Static variable in class org.cy3sbml.SBMLCore
SBML_ID_ATTR - Static variable in class org.cy3sbml.SBMLCore
SBML_INITIAL_AMOUNT_ATTR - Static variable in class org.cy3sbml.SBMLCore
SBML_INITIAL_CONCENTRATION_ATTR - Static variable in class org.cy3sbml.SBMLCore
SBML_LAYOUT - Static variable in class org.cy3sbml.SBML
SBML_TYPE_ATTR - Static variable in class org.cy3sbml.SBMLCore
SBML_TYPE_REACTION - Static variable in class org.cy3sbml.SBMLCore
SBML_TYPE_SPECIES - Static variable in class org.cy3sbml.SBMLCore
SBMLCore - Class in org.cy3sbml: Use identical fields to the SBMLCore.
SBMLEnableTaskFactory - Class in org.cy3sbml.actions: Use a TaskFactory to set the ready state.
SBMLEnableTaskFactory() - Constructor for class org.cy3sbml.actions.SBMLEnableTaskFactory
sbmlEntries() - Method in record class org.cy3sbml.archive.ArchiveInfo: The SBML files of the archive.
SBMLFileFilter - Class in org.cy3sbml: SBML Filter class.
SBMLFileFilter(StreamUtil) - Constructor for class org.cy3sbml.SBMLFileFilter: Constructor.
sbmlId() - Method in record class org.cy3sbml.layout.CyBoundingBox: Returns the value of the sbmlId record component.
sbmlManager() - Method in record class org.cy3sbml.commands.CommandServices: Returns the value of the sbmlManager record component.
SBMLManager - Class in org.cy3sbml: The SBMLManager class manages mappings between SBMLDocuments and CyNetworks.
SBMLManager(CyApplicationManager) - Constructor for class org.cy3sbml.SBMLManager
SBMLReaderError - Exception in org.cy3sbml: Error thrown by the SBMLReaderTask if an SBML file cannot be read.
SBMLReaderError(String) - Constructor for exception org.cy3sbml.SBMLReaderError
SBMLReaderError(String, Throwable) - Constructor for exception org.cy3sbml.SBMLReaderError
SBMLReaderTask - Class in org.cy3sbml.reader: The SBMLReaderTask creates CyNetworks from SBMLDocuments.
SBMLReaderTask(InputStream, String, URI, CyNetworkFactory, CyGroupFactory) - Constructor for class org.cy3sbml.reader.SBMLReaderTask: Creates the reader for the file at the location without view, style, layout and SBMLManager support, e.g. for tests.
SBMLReaderTask(InputStream, String, URI, CyNetworkFactory, CyGroupFactory, CyNetworkViewFactory, VisualMappingManager, CyLayoutAlgorithmManager, CyProperty<Properties>, SBMLManager) - Constructor for class org.cy3sbml.reader.SBMLReaderTask: Creates the reader for the SBML in the stream.
SBMLReaderTask(InputStream, String, CyNetworkFactory, CyGroupFactory) - Constructor for class org.cy3sbml.reader.SBMLReaderTask: Creates the reader without view, style, layout and SBMLManager support, e.g. for tests.
SBMLReaderTaskFactory - Class in org.cy3sbml: SBMLReaderTaskFactory class TaskFactory for the SBMLReaderTask.
SBMLReaderTaskFactory(SBMLFileFilter, ServiceAdapter, SBMLManager) - Constructor for class org.cy3sbml.SBMLReaderTaskFactory: Constructor.
SBMLUtil - Class in org.cy3sbml.util: Some utils to work with SBML and SBML naming.
SBMLUtil() - Constructor for class org.cy3sbml.util.SBMLUtil
SBO - Static variable in class org.cy3sbml.gui.SBaseHTMLFactory
SBO_ACTIVATORS - Static variable in class org.cy3sbml.SBML
SBO_INHIBITORS - Static variable in class org.cy3sbml.SBML
SBO_MODIFIERS - Static variable in class org.cy3sbml.SBML
scientificName() - Method in record class org.cy3sbml.uniprot.UniprotEntry: Returns the value of the scientificName record component.
search(String) - Method in class org.cy3sbml.biomodel.BiomodelsQuery: Runs a BioModels search and reads the matching models, page by page, up to BiomodelsQuery.MAX_RESULTS models.
search(SearchContent) - Method in class org.cy3sbml.biomodel.SearchBioModel: Searches BioModels with the search terms of the given content, combined with its search mode (AND, OR).
SearchBioModel - Class in org.cy3sbml.biomodel: The BioModels search of the dialog: the models found by a search or parsed from text, and their details.
SearchBioModel(BiomodelsQuery) - Constructor for class org.cy3sbml.biomodel.SearchBioModel
SearchBioModel.Result - Record Class in org.cy3sbml.biomodel: The models of a search or of parsed ids.
searchBioModels() - Method in class org.cy3sbml.biomodel.BiomodelsDialog
searchContent() - Method in record class org.cy3sbml.biomodel.SearchBioModel.Result: Returns the value of the searchContent record component.
SearchContent - Class in org.cy3sbml.biomodel: Parsing of the form fields into usable SearchContent instance.
SearchContent(Map<String, String>) - Constructor for class org.cy3sbml.biomodel.SearchContent
searchResult(SearchBioModel.Result, Map<String, Biomodel>, Collection<String>, Collection<String>) - Static method in class org.cy3sbml.biomodel.BiomodelsHtml: Returns the HTML of the given search result.
select() - Method in class org.cy3sbml.gui.WebViewPanel
selectById(CyNetwork, String) - Static method in class org.cy3sbml.util.NetworkUtil: Select node by id.
selectByMetaId(CyNetwork, String) - Static method in class org.cy3sbml.util.NetworkUtil: Select node by metaId.
selectNodeInNetwork(CyNetwork, CyNode) - Static method in class org.cy3sbml.util.NetworkUtil: Selects given node in network.
SEPARATOR - Static variable in class org.cy3sbml.util.MappingUtil
ServiceAdapter - Class in org.cy3sbml: Adapter for working with services.
ServiceAdapter(CySwingApplication, CyApplicationManager, CyNetworkManager, CyNetworkViewManager, VisualMappingManager, CyLayoutAlgorithmManager, DialogTaskManager, TaskManager, CyNetworkFactory, CyGroupFactory, CyNetworkViewFactory, CyProperty<Properties>, File, StreamUtil, OpenBrowser, ConnectionProxy, LoadNetworkFileTaskFactory, FileUtil) - Constructor for class org.cy3sbml.ServiceAdapter
SessionData - Class in org.cy3sbml: This class implements the saving of cy3sbml session data and the restoring of the saved data.
SessionData(SBMLManager, CofactorManager) - Constructor for class org.cy3sbml.SessionData: Saves the mappers of the SBMLManager and the CofactorManager and restores the loaded mappers in them.
set(CyNetwork, CyIdentifiable, String, Object, Class<?>) - Static method in class org.cy3sbml.util.AttributeUtil: Set attribute for CyIdentifiable.
setArchives(Map<Long, ArchiveImport>) - Method in class org.cy3sbml.SBMLManager: Replaces the archives, on session restore.
setExamples() - Method in class org.cy3sbml.gui.WebViewPanel: Shows the static examples page.
setHelp() - Method in class org.cy3sbml.gui.WebViewPanel: Shows the static help page.
setList(CyNetwork, CyIdentifiable, String, Object, Class<?>) - Static method in class org.cy3sbml.util.AttributeUtil: Set attribute list for CyIdentifiable.
setMappings(List<Mapping>) - Method in class org.cy3sbml.styles.StyleInfo
setNetwork2CofactorMapper(Network2CofactorMapper) - Method in class org.cy3sbml.cofactors.CofactorManager: Sets the mapper of a restored session.
setReady(boolean) - Method in class org.cy3sbml.actions.SBMLEnableTaskFactory
setSBaseMetaId(SBMLDocument, SBase) - Static method in class org.cy3sbml.util.MappingUtil: Set the unique metaId for the given sbase.
setSBML2NetworkMapper(Network2SBMLMapper) - Method in class org.cy3sbml.SBMLManager: Set all information in SBMLManager from given Network2SBMLMapper.
setSystemProxy(String, String, String) - Method in class org.cy3sbml.ConnectionProxy
setSystemProxyFromCyProperties() - Method in class org.cy3sbml.ConnectionProxy: Sets Cytoscape proxy settings.
setText(String) - Method in interface org.cy3sbml.gui.InfoPanel: Set text.
setText(String) - Method in class org.cy3sbml.gui.WebViewPanel: Shows the given HTML text.
setUIHelper(TunableUIHelper) - Method in class org.cy3sbml.reader.SBMLReaderTask: The reader has no custom UI.
showSBaseInfo(Object) - Method in interface org.cy3sbml.gui.InfoPanel: Display SBase information
showSBaseInfo(Object) - Method in class org.cy3sbml.gui.WebViewPanel: Create information string for SBML Node and display.
showSBaseInfo(Set<Object>) - Method in interface org.cy3sbml.gui.InfoPanel: Display information for set of nodes.
showSBaseInfo(Set<Object>) - Method in class org.cy3sbml.gui.WebViewPanel: Display information for set of nodes.
shutDown() - Method in class org.cy3sbml.CyActivator: Stops the WebViewPanel's render executor (its daemon thread and any in-flight web-service call) before AbstractCyActivator unregisters the OSGi services.
size() - Method in class org.cy3sbml.cache.MemoryCache
snapshot() - Method in class org.cy3sbml.miriam.MiriamRegistry: The current content, an unmodifiable map from prefix to data collection.
split(CyNetwork, CyNetworkView, Collection<CyNode>) - Method in class org.cy3sbml.cofactors.CofactorManager: Splits the given nodes into clones, one per edge; nodes that cannot be split (CofactorManager.canSplit(org.cytoscape.model.CyNetwork, org.cytoscape.model.CyNode)) are skipped.
SplitCofactorsAction - Class in org.cy3sbml.actions: Splits the selected nodes of the current network into one clone per edge, e.g. the nodes of cofactors like ATP or water that take part in many reactions.
SplitCofactorsAction(ServiceAdapter, SBMLManager, CofactorManager) - Constructor for class org.cy3sbml.actions.SplitCofactorsAction
start(BundleContext) - Method in class org.cy3sbml.CyActivator: Starts the cy3sbml OSGI bundle.
status() - Method in record class org.cy3sbml.util.FetchResult: Returns the value of the status record component.
streamUtil - Variable in class org.cy3sbml.ServiceAdapter
string - Enum constant in enum class org.cy3sbml.styles.Mapping.DataType
string2InputStream(String) - Static method in class org.cy3sbml.util.IOUtil: Create InputStream from String.
STYLE_CY3SBML - Static variable in class org.cy3sbml.SBML
STYLE_CY3SBML_DARK - Static variable in class org.cy3sbml.SBML
STYLE_SUFFIX_LAYOUT - Static variable in class org.cy3sbml.SBML
StyleFactory - Class in org.cy3sbml.styles: Factory for creating visual styles depending on the current SBML attributes and values.
StyleFactory() - Constructor for class org.cy3sbml.styles.StyleFactory
StyleInfo - Class in org.cy3sbml.styles: Parent class of all StyleInfo.
StyleInfo(String, String) - Constructor for class org.cy3sbml.styles.StyleInfo: Constructor.
StyleInfo_cy3sbml - Class in org.cy3sbml.styles: Definition of mappings for style.
StyleInfo_cy3sbml() - Constructor for class org.cy3sbml.styles.StyleInfo_cy3sbml
StyleInfo_cy3sbmlDark - Class in org.cy3sbml.styles: Dark style.
StyleInfo_cy3sbmlDark() - Constructor for class org.cy3sbml.styles.StyleInfo_cy3sbmlDark: Constructor.
StyleManager - Class in org.cy3sbml.styles: Class to manage the loading of the visual styles.
StyleManager(LoadVizmapFileTaskFactory, VisualMappingManager, String[], LayoutStyleFactory) - Constructor for class org.cy3sbml.styles.StyleManager
SUBMISSION_ID - Static variable in record class org.cy3sbml.biomodel.Biomodel
submissionDate() - Method in record class org.cy3sbml.biomodel.BiomodelSummary: Returns the value of the submissionDate record component.
submissionIdentifier() - Method in record class org.cy3sbml.biomodel.Biomodel: Returns the value of the submissionIdentifier record component.
submit(Object, Runnable) - Method in class org.cy3sbml.gui.LatestTaskExecutor: Submits task under key.
SUBNETWORK_ALL - Static variable in class org.cy3sbml.SBML
SUBNETWORK_ATTR - Static variable in class org.cy3sbml.SBML
SUBNETWORK_BASE - Static variable in class org.cy3sbml.SBML
SUBNETWORK_KINETIC - Static variable in class org.cy3sbml.SBML
SUBNETWORK_LAYOUT - Static variable in class org.cy3sbml.SBML
SUFFIX - Static variable in class org.cy3sbml.biomodel.BiomodelLoader: Suffix of the downloaded files, has to match the SBML reader.
SUFFIX_SUBNETWORK_ALL - Static variable in class org.cy3sbml.SBML
SUFFIX_SUBNETWORK_BASE - Static variable in class org.cy3sbml.SBML
SUFFIX_SUBNETWORK_KINETIC - Static variable in class org.cy3sbml.SBML
SUFFIX_SUBNETWORK_LAYOUT - Static variable in class org.cy3sbml.SBML
summaries() - Method in record class org.cy3sbml.biomodel.SearchBioModel.Result: Returns the value of the summaries record component.
summary(List<Uncertainty>) - Static method in class org.cy3sbml.util.DistribUtil: One line text of the uncertainties: the parameters of an uncertainty are separated by "; ", the uncertainties by " | ", each prefixed by its id if set, e.g.
synchronousTaskManager() - Method in record class org.cy3sbml.commands.CommandServices: Returns the value of the synchronousTaskManager record component.
synonyms() - Method in record class org.cy3sbml.ols.OlsTerm: Returns the value of the synonyms record component.
SYNONYMS_LABEL - Static variable in class org.cy3sbml.gui.GUIConstants

T

TABLE_END - Static variable in class org.cy3sbml.gui.GUIConstants
TABLE_START - Static variable in class org.cy3sbml.gui.GUIConstants
takeAcceptedUri(String) - Method in class org.cy3sbml.SBMLFileFilter: Returns the URI this filter accepted last on the calling thread if its file name is the given input name, and forgets it.
target() - Method in record class org.cy3sbml.comp.SBaseRefResolution.Resolved: Returns the value of the target record component.
taskManager - Variable in class org.cy3sbml.ServiceAdapter
TE - Static variable in class org.cy3sbml.gui.GUIConstants
TEMPLATE - Static variable in class org.cy3sbml.styles.StyleInfo_cy3sbml
TEMPLATE - Static variable in class org.cy3sbml.styles.StyleInfo_cy3sbmlDark
TEMPLATE_ALGEBRAIC_RULE - Static variable in class org.cy3sbml.util.SBMLUtil
TEMPLATE_ASSIGNMENT_RULE - Static variable in class org.cy3sbml.util.SBMLUtil
TEMPLATE_RATE_RULE - Static variable in class org.cy3sbml.util.SBMLUtil
temporary() - Static method in class org.cy3sbml.archive.ArchiveDirectories: The directories below a root in the temporary directory of the system, one per process.
termForPage(String) - Method in class org.cy3sbml.ols.OlsClient: Gets the OLS term shown by the given OLS term page URL.
title() - Method in record class org.cy3sbml.archive.ArchiveInfo: Returns the value of the title record component.
TM - Static variable in class org.cy3sbml.gui.GUIConstants
toFormula(ASTNode) - Static method in class org.cy3sbml.util.ASTNodeUtil: Infix formula of the math, with the inline units of numbers (UnitsFormulaCompiler).
toHTML() - Method in class org.cy3sbml.biomodel.SearchContent
toString() - Method in record class org.cy3sbml.archive.ArchiveImport: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.archive.ArchiveInfo.Creator: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.archive.ArchiveInfo.Entry: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.archive.ArchiveInfo: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.biomodel.Biomodel: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.biomodel.BiomodelsSearchResult: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.biomodel.BiomodelSummary: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.biomodel.SearchBioModel.Result: Returns a string representation of this record class.
toString() - Method in class org.cy3sbml.biomodel.SearchContent
toString() - Method in record class org.cy3sbml.chebi.ChebiCompound: Returns a string representation of this record class.
toString() - Method in class org.cy3sbml.cofactors.CofactorManager
toString() - Method in class org.cy3sbml.cofactors.Network2CofactorMapper
toString() - Method in record class org.cy3sbml.commands.Commands.Command: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.commands.CommandServices: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.comp.CompModels.External: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.comp.ModelResolution.Failed: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.comp.ModelResolution.Resolved: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.comp.SBaseRefResolution.Resolved: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.comp.SBaseRefResolution.Unresolved: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.layout.CyBoundingBox: Returns a string representation of this record class.
toString() - Method in class org.cy3sbml.mapping.Network2SBMLMapper: Creates information string.
toString() - Method in class org.cy3sbml.mapping.One2ManyMapping
toString() - Method in record class org.cy3sbml.miriam.MiriamRegistry.ResolvedURI: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.ols.OlsTerm: Returns a string representation of this record class.
toString() - Method in class org.cy3sbml.SBMLManager: String information.
toString() - Method in record class org.cy3sbml.uniprot.UniprotEntry: Returns a string representation of this record class.
toString() - Method in record class org.cy3sbml.util.FetchResult: Returns a string representation of this record class.
transformer() - Static method in class org.cy3sbml.util.XMLUtil: Creates a Transformer (identity transform) that never fetches external DTDs or stylesheets.
TRUE - Static variable in interface org.cy3sbml.miriam.Fields
TS - Static variable in class org.cy3sbml.gui.GUIConstants

U

uncertainties(SBase) - Static method in class org.cy3sbml.util.DistribUtil: The uncertainties of the SBase, empty if it has none.
UncertaintyHtml - Class in org.cy3sbml.gui: The HTML of the uncertainties of an SBase (distrib package): per uncertainty its id and name and a table of its uncertainty parameters and spans (type and value, like the attribute table), with the nested parameters after their parent.
uncertParameters(Uncertainty) - Static method in class org.cy3sbml.util.DistribUtil: The uncertainty parameters and spans of the uncertainty.
UNIPROT_ID - Static variable in interface org.cy3sbml.uniprot.UniprotHTMLFields
UNIPROT_LINK - Static variable in interface org.cy3sbml.uniprot.UniprotHTMLFields
UNIPROT_URL - Static variable in interface org.cy3sbml.uniprot.UniprotHTMLFields
UniprotAccess - Class in org.cy3sbml.uniprot: Client for the UniProtKB REST API.
UniprotAccess(HttpJson) - Constructor for class org.cy3sbml.uniprot.UniprotAccess
UniprotEntry - Record Class in org.cy3sbml.uniprot: A UniProt entry, parsed from the UniProtKB REST JSON (https://rest.uniprot.org/uniprotkb/<accession>.json).
UniprotEntry(String, String, String, List<String>, List<String>, String, String, List<String>, List<String>, List<String>, List<String>) - Constructor for record class org.cy3sbml.uniprot.UniprotEntry: Creates an instance of a UniprotEntry record class.
UniprotHTMLFields - Interface in org.cy3sbml.uniprot
uniProtId() - Method in record class org.cy3sbml.uniprot.UniprotEntry: Returns the value of the uniProtId record component.
UnitsFormulaCompiler - Class in org.cy3sbml.util: Infix formula of the math with the inline units of numbers (SBML L3 sbml:units on cn), written after the number like libSBML's formulaToL3String, e.g.
UnitsFormulaCompiler() - Constructor for class org.cy3sbml.util.UnitsFormulaCompiler
UNKNOWN_DATA_COLLECTION - Static variable in class org.cy3sbml.gui.GUIConstants
Unresolved(String) - Constructor for record class org.cy3sbml.comp.SBaseRefResolution.Unresolved: Creates an instance of a Unresolved record class.
update(VisualMappingManager, CyNetworkView) - Static method in class org.cy3sbml.cofactors.CofactorViews: Applies the style of the view again, so the new nodes and edges get the mappings of the style, and updates the view.
updateCurrent(Long) - Method in class org.cy3sbml.SBMLManager: Update current SBML via rootNetworkSUID.
updateCurrent(CyNetwork) - Method in class org.cy3sbml.SBMLManager: Update current SBML for network.
updateInformation() - Method in class org.cy3sbml.gui.WebViewPanel: Updates panel information within a separate thread.
updateModelListInDialog(List<String>) - Method in class org.cy3sbml.biomodel.BiomodelsDialog
URL_BIOMODELS - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_CHANGESTATE - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_COFACTOR_MERGE - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_COFACTOR_SPLIT - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_EXAMPLES - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_HELP - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_HTML_SBASE - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_IMPORT - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_LOADLAYOUT - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_MIRIAM_JSON - Static variable in class org.cy3sbml.miriam.RegistryUtil
URL_PATTERN - Static variable in interface org.cy3sbml.miriam.Fields
URL_SAVELAYOUT - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_SBMLFILE - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_SELECT_ID - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_SELECT_METAID - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_SELECT_TARGET - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URLS_ACTION - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener

V

value() - Method in record class org.cy3sbml.util.FetchResult: Returns the value of the value record component.
value(UncertParameter) - Static method in class org.cy3sbml.util.DistribUtil: The value of the parameter: the value, else the var, followed by the units if set; the bounds of a span; else the formula of the math, else the definition URL; null if none is set.
valueOf(String) - Static method in enum class org.cy3sbml.styles.Mapping.DataType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.cy3sbml.styles.Mapping.MappingType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.cy3sbml.styles.VisualPropertyKey: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.cy3sbml.util.FetchStatus: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.cy3sbml.styles.Mapping.DataType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.cy3sbml.styles.Mapping.MappingType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.cy3sbml.styles.VisualPropertyKey: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.cy3sbml.util.FetchStatus: Returns an array containing the constants of this enum class, in the order they are declared.
visualMappingManager - Variable in class org.cy3sbml.ServiceAdapter
visualMappingManager() - Method in record class org.cy3sbml.commands.CommandServices: Returns the value of the visualMappingManager record component.
VisualPropertyKey - Enum Class in org.cy3sbml.styles: Allowed keys for mapping.

W

WebViewPanel - Class in org.cy3sbml.gui: WebView panel based on javafx.
WebViewPanel(ServiceAdapter, SBMLManager, SBaseHTMLFactory, CofactorManager, BiomodelsDialog) - Constructor for class org.cy3sbml.gui.WebViewPanel: Constructor
width() - Method in record class org.cy3sbml.layout.CyBoundingBox: Returns the value of the width record component.
writeNodeToTidyFile(Node, File) - Static method in class org.cy3sbml.util.XMLUtil: Write XML Document to file.
writeNodeToTidyString(Node) - Static method in class org.cy3sbml.util.XMLUtil: Write XML Document to string.
writeXMLFileForLayout(File, Collection<CyBoundingBox>) - Static method in class org.cy3sbml.layout.XMLInterface: Writes the bounding boxes to the layout file.

X

x() - Method in record class org.cy3sbml.layout.CyBoundingBox: Returns the value of the x record component.
XML_INDENT - Static variable in class org.cy3sbml.util.XMLUtil
xml2Html(String) - Static method in class org.cy3sbml.util.XMLUtil: Convert XML String to html string.
xml2xml(String) - Static method in class org.cy3sbml.util.XMLUtil: Create tidy xml string from xml string.
XMLInterface - Class in org.cy3sbml.layout
XMLInterface() - Constructor for class org.cy3sbml.layout.XMLInterface
XMLUtil - Class in org.cy3sbml.util
XMLUtil() - Constructor for class org.cy3sbml.util.XMLUtil

Y

y() - Method in record class org.cy3sbml.layout.CyBoundingBox: Returns the value of the y record component.

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