Index (cy3sbml 0.9.0 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 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: Shows the results panel with this panel selected, and the information of the current selection, which was not updated while the panel was hidden.
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 the document of a root network with the mapping of the cyIds of its SBases to the node SUIDs.
addSBMLForNetwork(SBMLDocument, CyNetwork, One2ManyMapping<String, Long>) - Method in class org.cy3sbml.SBMLManager: Adds the document of a network with the mapping of the cyIds of its SBases to the node SUIDs.
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
api() - Method in class org.cy3sbml.sbml4humans.Sbml4HumansClient: The address of the api.
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: Helpers for the math (ASTNode) of SBML elements.
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: Getting and setting the attributes (columns) of the nodes, edges and networks in the default tables of a network.
AttributeUtil() - Constructor for class org.cy3sbml.util.AttributeUtil
authors() - Method in record class org.cy3sbml.biomodel.Biomodel: Returns the value of the authors record component.

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: The details of a BioModels model from the model endpoint of the BioModels REST API.
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: The HTML texts of the BioModels dialog, each with the BioModels logo as header.
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: Creates the toolbar action.
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 of the cy3sbml panel: a JavaFX WebView showing the rendered HTML and the bundled pages, embedded in Swing with a JFXPanel.
Browser(File, BrowserHyperlinkListener) - Constructor for class org.cy3sbml.gui.Browser
BrowserHyperlinkListener - Class in org.cy3sbml.gui: Handles the links clicked in the cy3sbml panel.
BrowserHyperlinkListener(ServiceAdapter, WebViewPanel, SBMLManager, CofactorManager, BiomodelsDialog) - Constructor for class org.cy3sbml.gui.BrowserHyperlinkListener: Creates the listener, which runs the actions of the links on the Swing event dispatch thread and opens the web links in the system browser.
buildCyNetworkView(CyNetwork) - Method in class org.cy3sbml.archive.CombineArchiveReaderTask: The view of the network by the reader that read it.
buildCyNetworkView(CyNetwork) - Method in class org.cy3sbml.reader.FailedReaderTask
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 symbolic name and version of the cy3sbml bundle at runtime.
BundleInformation(BundleContext) - Constructor for class org.cy3sbml.BundleInformation: Reads the name and version of the bundle of the context.

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: Hides the panel if it is shown, else shows it.
ChangeStateAction - Class in org.cy3sbml.actions: Activate or deactivate the cy3sbml panel.
ChangeStateAction(WebViewPanel) - Constructor for class org.cy3sbml.actions.ChangeStateAction: Creates the toolbar action.
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: Removes all cached results.
CLONE_DISTANCE - Static variable in class org.cy3sbml.cofactors.CofactorManager: Distance of a clone from its neighbor in the network view.
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: A COMBINE archive that cannot be imported: no zip file or COMBINE archive, an entry outside the archive, too large, or without a readable manifest or an SBML file.
CombineArchiveException(String) - Constructor for exception org.cy3sbml.archive.CombineArchiveException: Creates the exception with the message for the user.
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: Creates the filter of the COMBINE extensions and the zip media types.
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
CombineArchiveWriter - Class in org.cy3sbml.archive: Writes an SBML document into a COMBINE archive (OMEX), with the files of its comp external model definitions, so that a tool which reads the archive (sbml4humans) resolves the external models inside the archive as cy3sbml resolved them.
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
confirm() - Method in class org.cy3sbml.sbml4humans.Sbml4HumansConsent: Stores that uploads are confirmed.
CONNECT_AND - Static variable in class org.cy3sbml.biomodel.SearchContent: The search mode in which all terms must match.
CONNECT_OR - Static variable in class org.cy3sbml.biomodel.SearchContent: The search mode in which any term must match.
ConnectionProxy - Class in org.cy3sbml: Sets the Java system proxy properties for the web services (OLS, UniProt, ChEBI, identifiers.org, BioModels) from the proxy settings in the Cytoscape properties, when the app starts.
ConnectionProxy(CyProperty<Properties>) - Constructor for class org.cy3sbml.ConnectionProxy: Creates the proxy settings from the Cytoscape properties.
containsDocument(Long) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: Whether a SBMLDocument is stored for the root network.
containsKey(T1) - Method in class org.cy3sbml.mapping.One2ManyMapping: Whether the key has values.
CONTENT_MODE - Static variable in class org.cy3sbml.biomodel.SearchContent: The key of the search mode in the form fields.
CONTENT_NAME - Static variable in class org.cy3sbml.biomodel.SearchContent: The key of the search text in the form fields.
CONTINOUS - Enum constant in enum class org.cy3sbml.styles.Mapping.MappingType
copyEdgeAttributes(CyNetwork, CyEdge, CyEdge) - Static method in class org.cy3sbml.util.AttributeUtil: Copies the attributes of the default edge table from the source to the target edge, except the SUID.
copyInputStream(InputStream) - Static method in class org.cy3sbml.util.IOUtil: Reads the stream into memory and closes it, e.g. to read a stream twice.
copyNodeAttributes(CyNetwork, CyNode, CyNode) - Static method in class org.cy3sbml.util.AttributeUtil: Copies the attributes of the default node table from the source to the target node, except the SUID.
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_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: A new mapping of every value to the keys that have it.
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: Writes the style file of the style information: its template with the name and the mappings of the style.
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: A file in the directory with the name and extension that does not exist yet: the name with a suffix _0, _1, ... if the file exists.
createUniqueMetaId(SBMLDocument, String) - Static method in class org.cy3sbml.util.MappingUtil: The metaId, with a number appended if the document has it already.
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.
cy3sbmlDirectory - Variable in class org.cy3sbml.ServiceAdapter: The app directory in the Cytoscape configuration directory.
cy3sbmlProperties - Variable in class org.cy3sbml.ServiceAdapter: The cy3sbml properties (cy3sbml.props).
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: Hides the results panel, unless it has other components.
DEFAULT_NOT_FOUND_TTL - Static variable in class org.cy3sbml.cache.MemoryCache: Default TTL for a cached "not found" result.
DEFAULT_URL - Static variable in class org.cy3sbml.sbml4humans.Sbml4HumansClient: The address of sbml4humans.
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.
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_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
dispose() - Method in class org.cy3sbml.SessionData: Deletes the temporary files of the last saved session, called when the app stops.
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: A transient error, e.g. a timeout, which is not cached.
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: Creates the toolbar action.
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.
FailedReaderTask - Class in org.cy3sbml.reader: The reader of an input that could not be read before the reader was created, e.g. a URL whose connection dropped: running it reports the error, as the reader of a broken file does.
FailedReaderTask(String, Throwable) - Constructor for class org.cy3sbml.reader.FailedReaderTask
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 a deterministic failure (e.g.
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 (e.g. an SVG image), distinguishing a deterministic failure (e.g.
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).
findReferencedNamedSBases(ASTNode) - Static method in class org.cy3sbml.util.ASTNodeUtil: The NamedSBases the math references by name or as function, each once.
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.
fromProperties(Properties) - Static method in class org.cy3sbml.sbml4humans.Sbml4HumansClient: The client of the addresses of the cy3sbml properties, with the defaults for missing ones.
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(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: The attribute of the node, edge or network.
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
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
getCurrentCyNode2SBaseMapping() - Method in class org.cy3sbml.SBMLManager: The mapping of the node SUIDs to the cyIds (metaIds) of the current document.
getCurrentModel() - Method in class org.cy3sbml.SBMLManager: The model of the current network collection, see SBMLManager.getModel(Long).
getCurrentSBase2CyNodeMapping() - Method in class org.cy3sbml.SBMLManager: The mapping of the cyIds (metaIds) to the node SUIDs of the current document.
getCurrentSBMLDocument() - Method in class org.cy3sbml.SBMLManager: The current document, of the collection of the current network.
getCurrentSUID() - Method in class org.cy3sbml.SBMLManager: The root network SUID of the current document.
getCyIdsFromSUIDs(List<Long>) - Method in class org.cy3sbml.SBMLManager: The cyIds (metaIds) of the SBases of the nodes in the current document.
getCyNode2SBaseMapping(Long) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: The mapping of node SUIDs to the cyIds (metaIds) of their SBases.
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
getDescription() - Method in class org.cy3sbml.miriam.Resource: The description of the resource, empty if it has none.
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: The documents by root network SUID.
getError() - Method in class org.cy3sbml.reader.SBMLReaderTask: Returns true if reading failed.
getHeaderString() - Static method in class org.cy3sbml.biomodel.BioModelDialogText: The BioModels logo, linked to BioModels.
getHtml() - Method in class org.cy3sbml.gui.WebViewPanel: The HTML text shown last, or null if no rendered text has been shown yet.
getIcon() - Method in class org.cy3sbml.gui.WebViewPanel
getId() - Method in class org.cy3sbml.miriam.Namespace: The id of the data collection in the registry.
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: The help of the dialog, shown when it opens.
getInfo() - Method in class org.cy3sbml.BundleInformation: {name}-v{version} of bundle.
getInfo() - Method in class org.cy3sbml.gui.SBaseHTMLThread: Get the created information.
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: The mapping of the cyIds (metaIds) of the SBases to the node SUIDs of the root network.
getMapping(CyNetwork) - Method in class org.cy3sbml.SBMLManager: The mapping of the cyIds (metaIds) of the SBases to the node SUIDs of the collection of the network.
getMappings() - Method in class org.cy3sbml.styles.StyleInfo
getMappingType() - Method in class org.cy3sbml.styles.Mapping
getModel(Long) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: The model the root network was created from, null if none is stored.
getModel(Long) - Method in class org.cy3sbml.SBMLManager: The model the network collection of the root network was created from: the main model, a comp model definition, the model of an external model definition or the flat model.
getModelMap() - Method in class org.cy3sbml.mapping.Network2SBMLMapper: The models of the root networks; a defensive copy.
getName() - Method in class org.cy3sbml.BundleInformation: Name of bundle.
getName() - Method in class org.cy3sbml.miriam.Namespace: The name of the data collection, e.g.
getName() - Method in class org.cy3sbml.styles.StyleInfo
getNames() - Method in class org.cy3sbml.biomodel.SearchContent: The search terms, in the order of the search text.
getNamespaceEmbeddedInLui() - Method in class org.cy3sbml.miriam.Namespace: Whether the identifiers of the data collection start with its prefix, e.g.
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: The mapper of the root networks to their documents and node mappings.
getNetworks() - Method in class org.cy3sbml.archive.CombineArchiveReaderTask
getNetworks() - Method in class org.cy3sbml.reader.FailedReaderTask
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: The first node with the value of the attribute in the default node table.
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: The regular expression of the identifiers of the data collection, or null.
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: The prefix of the data collection, e.g.
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).
getProxyHost() - Method in class org.cy3sbml.ConnectionProxy: The proxy host of the Cytoscape settings.
getProxyPort() - Method in class org.cy3sbml.ConnectionProxy: The proxy port of the Cytoscape settings.
getProxyType() - Method in class org.cy3sbml.ConnectionProxy: The proxy type of the Cytoscape settings: direct, http or socks.
getResourceHomeUrl() - Method in class org.cy3sbml.miriam.Resource: The home page of the resource, empty if it has none.
getResources() - Method in class org.cy3sbml.miriam.Namespace: The resources of the data collection, unmodifiable.
getRootNetwork(CyNetwork) - Static method in class org.cy3sbml.util.NetworkUtil: The root network of the network.
getRootNetworkSUID(CyNetwork) - Static method in class org.cy3sbml.util.NetworkUtil: The SUID of the root network of the network.
getSBase2CyNodeMapping(Long) - Method in class org.cy3sbml.mapping.Network2SBMLMapper: The mapping of the cyIds (metaIds) of the SBases to their node SUIDs.
getSBaseByCyId(String) - Method in class org.cy3sbml.SBMLManager: The SBase of the current document with the cyId (the metaId the reader sets on every SBase).
getSBaseByCyId(String, Long) - Method in class org.cy3sbml.SBMLManager: The SBase of the document of the root network with the cyId (metaId).
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: The document of the root network.
getSBMLDocument(CyNetwork) - Method in class org.cy3sbml.SBMLManager: The document of the collection of the network.
getSearchMode() - Method in class org.cy3sbml.biomodel.SearchContent: The search mode, null if not set.
getString(String) - Static method in class org.cy3sbml.biomodel.BioModelDialogText: The given HTML below the header.
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
getTitle() - Method in class org.cy3sbml.gui.WebViewPanel
getUnqualifiedClassName(Object) - Static method in class org.cy3sbml.util.SBMLUtil: The class name of the object without the package, with . for the $ of a nested class, e.g.
getUrlPattern() - Method in class org.cy3sbml.miriam.Resource: The URL of an entry, with the placeholder {$id} for its identifier.
getValues(Collection<T1>) - Method in class org.cy3sbml.mapping.One2ManyMapping: The values of all the keys; a copy.
getValues(T1) - Method in class org.cy3sbml.mapping.One2ManyMapping: The values of the key, empty if it has none; a copy.
getVariableFromRule(Rule) - Static method in class org.cy3sbml.util.SBMLUtil: The variable of an AssignmentRule or 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: The message that BioModels could not be reached.
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 of the GUI: the resources, icons, toolbar positions and descriptions of the actions, and the HTML fragments of the info panel from gui/linktemplate.html.
GUIUtil - Class in org.cy3sbml.util: Actions of the info panel links: loading the examples and opening the SBML, the panel HTML or a URL in the system browser.
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: Makes the SBML document of the new current network the current document and shows its information.
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: Removes the document when the last network of its collection is destroyed, also when a session is closed (all networks are destroyed).
handleEvent(RowsSetEvent) - Method in class org.cy3sbml.gui.WebViewPanel: Shows the information of the selected node when the selection in the node table of the current network changes.
handleEvent(SessionAboutToBeSavedEvent) - Method in class org.cy3sbml.SessionData: Adds the cy3sbml files to the session that is about to be saved.
handleEvent(SessionLoadedEvent) - Method in class org.cy3sbml.SessionData: Restores the cy3sbml data of the loaded session.
handleEvent(SessionLoadedEvent) - Method in class org.cy3sbml.styles.StyleManager: Loads the styles missing in the loaded session.
handleEvent(NetworkViewAboutToBeDestroyedEvent) - Method in class org.cy3sbml.gui.WebViewPanel: Shows the help page when the view of the current network is closed; the view of another network leaves the information of the current network.
handleEvent(NetworkViewAddedEvent) - Method in class org.cy3sbml.gui.WebViewPanel: Shows the information of the current network once it has a view.
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: Whether the search has a search term.
height() - Method in record class org.cy3sbml.layout.CyBoundingBox: Returns the value of the height record component.
HelpAction - Class in org.cy3sbml.actions: Shows the help page in the cy3sbml panel.
HelpAction(WebViewPanel) - Constructor for class org.cy3sbml.actions.HelpAction: Creates the toolbar action.
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: the chemical data and the structure image (embedded as image, so the SVG cannot run scripts in the 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: The HTML fragments of gui/linktemplate.html by section name.
HtmlSanitizer - Class in org.cy3sbml.util: Reduces the XHTML of the notes of a model to formatting markup before it is shown in the info panel, with an allowlist of elements, attributes and link schemes.
HtmlTemplateParser - Class in org.cy3sbml: Reads the HTML fragments of the info panel from the bundled template gui/linktemplate.html, in which every fragment is enclosed in a pair of comments  and .
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, ChEBI, UniProt, BioModels).
HttpJson(HttpClient, ObjectMapper) - Constructor for class org.cy3sbml.util.HttpJson: Creates the helper for the given client, with the default response timeout and size limit; see HttpJson.createDefault() for the client the app uses.

I

ICON_BIOMODELS - 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_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.
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
IdentifiersConstants - Class in org.cy3sbml: Constants of the web resources that resolve the annotations of the models.
ImportAction - Class in org.cy3sbml.actions: Imports SBML files and COMBINE archives chosen in a file dialog.
ImportAction(ServiceAdapter) - Constructor for class org.cy3sbml.actions.ImportAction: Creates the toolbar action.
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: The panel that shows the SBML information, see WebViewPanel.
initialize() - Static method in class org.cy3sbml.reader.JsbmlSetup: Creates the JSBML parser manager.
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: Whether the results panel is shown, so the information is updated.
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.
isConfirmed() - Method in class org.cy3sbml.sbml4humans.Sbml4HumansConsent: Whether uploads are confirmed, so no dialog is shown.
isDeprecated() - Method in class org.cy3sbml.miriam.Resource: Whether the resource is deprecated, i.e. its links only lead to a deprecation page.
isExternalLink(String) - Static method in class org.cy3sbml.util.HtmlSanitizer: Whether the link opens in the system browser: a web, ftp or mailto link.
isIdentifiersURI(String) - Static method in class org.cy3sbml.miriam.RegistryUtil: Whether the given resource URI is an identifiers.org URI (http or https, host identifiers.org or www.identifiers.org) or a urn:miriam URN, the forms that MiriamRegistry.resolve(String) resolves against the registry.
isOfficial() - Method in class org.cy3sbml.miriam.Resource: Whether this is the official resource of the data collection.
isOlsResource(Resource) - Static method in class org.cy3sbml.ols.OlsClient: Whether the given resource of a data collection is 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.
isReady() - Method in class org.cy3sbml.actions.SBMLEnableTaskFactory
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.
isSBML(InputStream) - Static method in class org.cy3sbml.util.SBMLUtil: Checks if the stream is an SBML file: XML whose root element is an sbml element in an SBML core namespace.
isSBMLNetwork(CyNetwork) - Static method in class org.cy3sbml.util.NetworkUtil: Whether the network was created by cy3sbml: its network table has the SBML network type column.

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: The keys; a copy.
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, CofactorManager) - 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: Reads the bundled template.
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, LayoutTools) - Constructor for class org.cy3sbml.actions.LoadLayoutAction: Creates the toolbar action.
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.
loadPageFromResource(String) - Method in class org.cy3sbml.gui.Browser: Loads a page extracted from the bundle into the app directory, e.g.
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: Shows the HTML text.
localParameterId(LocalParameter) - Static method in class org.cy3sbml.util.MappingUtil: The id of the node of a local parameter, unique in the model: <reaction id>_<parameter id>.
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.
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.
masterLocation(SBMLDocument, Optional<ArchiveImport>) - Static method in class org.cy3sbml.archive.CombineArchiveWriter: The location of the document in an archive: for a document of an archive import its entry in that archive (the import of every collection of an archive is the one of the master entry, so the entry is found by the location of the document, the unpacked file), else the file name of its location, else "model.xml".
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.
MAX_UPLOAD_BYTES - Static variable in class org.cy3sbml.sbml4humans.Sbml4HumansClient: The largest upload sbml4humans takes.
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: Creates a cache with the default TTL of a "not found" result.
MemoryCache(int, Duration, Clock) - Constructor for class org.cy3sbml.cache.MemoryCache: Creates a cache with the TTL and clock of the "not found" results, for tests.
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
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_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 class org.cy3sbml.styles.StyleInfo_cy3sbml
NAME - Static variable in class org.cy3sbml.styles.StyleInfo_cy3sbmlDark
Namespace - Class in org.cy3sbml.miriam: A data collection (namespace) of the MIRIAM registry, e.g.
NAMESPACE - Static variable in class org.cy3sbml.commands.Commands: The command namespace.
namesToString(String) - Method in class org.cy3sbml.biomodel.SearchContent: The search terms joined by the separator.
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: Creates an empty mapper.
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: Helpers for the networks of a collection: the root network, the subnetworks, and the selection of nodes.
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.
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: A deterministic "not found", e.g. an HTTP 404, which may be cached for a short time.

O

OLS_BASE_URL - Static variable in class org.cy3sbml.IdentifiersConstants: The base URL of the ontology pages of the Ontology Lookup Service (OLS).
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: its IRI, label, ontology, synonyms and descriptions.
OlsTerm(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: A mapping of keys to sets of values, e.g. of the cyIds of SBases to the SUIDs of their nodes (one SBase can have several nodes).
One2ManyMapping() - Constructor for class org.cy3sbml.mapping.One2ManyMapping: Creates an empty mapping.
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: Opens URLs in the system browser: with Desktop.browse(java.net.URI), else with the first browser command that starts, else it shows the URL in a dialog to copy.
OpenBrowser() - Constructor for class org.cy3sbml.util.OpenBrowser
openCurrentSBMLInBrowser(SBMLManager) - Static method in class org.cy3sbml.util.GUIUtil: Opens the SBML of the current document in the browser: writes it to a temporary file, deleted on exit.
openFileInBrowser(File) - Static method in class org.cy3sbml.util.GUIUtil: Opens the file in the system browser, on the Swing event dispatch thread.
openHTMLInBrowser(String) - Static method in class org.cy3sbml.util.GUIUtil: Opens the HTML in the system browser: writes it to a temporary file, deleted on exit.
openSBaseHTMLInBrowser(String) - Static method in class org.cy3sbml.util.GUIUtil: Opens the HTML of the info panel in the system browser, without its export button.
openURL(String) - Static method in class org.cy3sbml.util.OpenBrowser: Opens the URL in the system default web browser.
openURLinExternalBrowser(String) - Static method in class org.cy3sbml.util.GUIUtil: Opens the URL in the system browser, on the Swing event dispatch thread.
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.sbml4humans - package org.cy3sbml.sbml4humans: Opening the model of a network in sbml4humans, the human readable report of SBML models (#473): the model is uploaded as a COMBINE archive and its report opened in the system browser.
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.
parseCVTerms(SBase) - Static method in class org.cy3sbml.util.AnnotationUtil: The identifiers of the resources of the CV terms by the namespace of their data collection, e.g.
PARSED_IDS - Static variable in class org.cy3sbml.biomodel.SearchContent: The mode of model ids parsed from text, not searched.
parseNotes(SBase) - Static method in class org.cy3sbml.util.SBMLUtil: The XHTML content of the <notes> of the SBase, without an enclosing <body> element, one top level element per line, sanitized with HtmlSanitizer.
parseTemplateSections(String) - Static method in class org.cy3sbml.HtmlTemplateParser: Extracts the template sections of the HTML, in the order of the template.
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.
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: The message of a running search.
placeClones(CyNetwork, CyNetworkView) - Method in class org.cy3sbml.cofactors.CofactorManager: Places the clones of all split nodes of the network next to their neighbors, e.g.
postMultipart(URI, String, String, byte[]) - Method in class org.cy3sbml.util.HttpJson: Posts the content as a file in the field of a multipart/form-data request and parses the JSON answer, e.g. an upload of a model to a web service.
PREFIX_ALGEBRAIC_RULE - Static variable in class org.cy3sbml.util.MappingUtil
PREFIX_CONSTRAINT - 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_API - Static variable in class org.cy3sbml.sbml4humans.Sbml4HumansClient: The property of the address of the api, by default <url>api/.
PROPERTY_CONFIRMED - Static variable in class org.cy3sbml.sbml4humans.Sbml4HumansConsent: The property of the consent, true after "Don't ask again".
PROPERTY_URL - Static variable in class org.cy3sbml.sbml4humans.Sbml4HumansClient: The property of the address of the reports.
PROPERTY_VISUAL_STYLE - Static variable in class org.cy3sbml.SBML
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: Adds a value to the key.
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: The classpath resource of the app.
readSBMLDocument(String) - Static method in class org.cy3sbml.util.SBMLUtil: Reads the SBMLDocument of a classpath resource.
readXMLString(String) - Static method in class org.cy3sbml.util.XMLUtil: Parses the XML with the hardened XMLUtil.documentBuilder().
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: Reading the MIRIAM registry of identifiers.org (the JSON of its resolution API) and parsing identifiers.org resource URIs (http(s)://identifiers.org/... and urn:miriam:...) without a registry lookup.
remove(T1) - Method in class org.cy3sbml.mapping.One2ManyMapping: Removes the key with all its values.
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: Removes the document of the network if it is the last network of its collection: the root network has no other subnetwork.
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.
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: A resource (provider) of a data collection in the MIRIAM registry: a web site that shows the entries of the collection, e.g. the ChEBI or OLS page of a ChEBI identifier.
ResourceExtractor - Class in org.cy3sbml: Extracts the bundled GUI resources into the app directory, so the JavaFX WebView can load them via file URIs (it cannot load bundle: URIs).
ResourceExtractor(BundleContext, File) - Constructor for class org.cy3sbml.ResourceExtractor
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.FailedReaderTask
run(TaskMonitor) - Method in class org.cy3sbml.reader.SBMLReaderTask: Reads the SBML and creates the networks for its models.
run(TaskMonitor) - Method in class org.cy3sbml.sbml4humans.Sbml4HumansTask

S

sanitizeChildren(Element) - Static method in class org.cy3sbml.util.HtmlSanitizer: Sanitizes the children of the element, the element itself is kept.
sanitizeMarkup(String) - Static method in class org.cy3sbml.util.HtmlSanitizer: A text of a web service that is either XHTML (e.g.
sanitizeXhtml(String) - Static method in class org.cy3sbml.util.HtmlSanitizer: The XHTML content of the root element of the XML, e.g.
SaveLayoutAction - Class in org.cy3sbml.actions: Save node positions to file.
SaveLayoutAction(ServiceAdapter, LayoutTools) - Constructor for class org.cy3sbml.actions.SaveLayoutAction: Creates the toolbar action.
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: Writes the cy3sbml data into a temporary directory and adds the files to the session.
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
Sbml4HumansClient - Class in org.cy3sbml.sbml4humans: The upload of a model to sbml4humans: POST <api>upload keeps the model (an SBML file or COMBINE archive) for 24 hours and answers its id, whose report is at <url>report?upload=<id>.
Sbml4HumansClient(HttpJson, URI, URI) - Constructor for class org.cy3sbml.sbml4humans.Sbml4HumansClient
Sbml4HumansConsent - Class in org.cy3sbml.sbml4humans: Whether the user agreed to upload models to sbml4humans without being asked: the upload is public (anyone with the link can open the report for 24 hours), so cy3sbml asks before the first upload, and the answer "Don't ask again" is stored in the cy3sbml properties as "cy3sbml.sbml4humans.confirmed".
Sbml4HumansConsent(CyProperty<Properties>) - Constructor for class org.cy3sbml.sbml4humans.Sbml4HumansConsent
Sbml4HumansTask - Class in org.cy3sbml.sbml4humans: Opens the model of a network in sbml4humans: writes the document of the collection of the network with the files of its external model definitions into a COMBINE archive, uploads it and opens the report in the system browser, at the model of the collection (the main model, a comp model definition, an external model or the flat model).
Sbml4HumansTask(SBMLManager, CyNetwork, Supplier<Sbml4HumansClient>, Consumer<String>) - Constructor for class org.cy3sbml.sbml4humans.Sbml4HumansTask
SBMLCore - Class in org.cy3sbml: Use identical fields to the SBMLCore.
SBMLEnableTaskFactory - Class in org.cy3sbml.actions: The enable state of an action, as a task factory without tasks: the action is enabled while the factory is ready (see AbstractCyAction with an enable task factory).
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: Creates an empty manager.
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_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: Creates the search with the given BioModels queries.
SearchBioModel.Result - Record Class in org.cy3sbml.biomodel: The models of a search or of parsed ids.
searchContent() - Method in record class org.cy3sbml.biomodel.SearchBioModel.Result: Returns the value of the searchContent record component.
SearchContent - Class in org.cy3sbml.biomodel: The search of the BioModels dialog: the search terms of the name field and the search mode, which combines them (SearchContent.CONNECT_AND, SearchContent.CONNECT_OR) or marks ids parsed from text (SearchContent.PARSED_IDS).
SearchContent(Map<String, String>) - Constructor for class org.cy3sbml.biomodel.SearchContent: Creates the search from the form fields.
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: Selects this panel in the results panel.
selectById(CyNetwork, String) - Static method in class org.cy3sbml.util.NetworkUtil: Selects the node with the SBML id, unselecting all other nodes.
selectByMetaId(CyNetwork, String) - Static method in class org.cy3sbml.util.NetworkUtil: Selects the node with the cyId (metaId), unselecting all other nodes.
selectNodeInNetwork(CyNetwork, CyNode) - Static method in class org.cy3sbml.util.NetworkUtil: Selects the node in the network, unselecting all other nodes.
SEPARATOR - Static variable in class org.cy3sbml.util.MappingUtil
ServiceAdapter - Class in org.cy3sbml: The Cytoscape services and app settings that the actions, readers and the info panel need, so that they do not each take a long list of constructor arguments.
ServiceAdapter(CySwingApplication, CyApplicationManager, CyNetworkManager, CyNetworkViewManager, VisualMappingManager, CyLayoutAlgorithmManager, DialogTaskManager, CyNetworkFactory, CyGroupFactory, CyNetworkViewFactory, CyProperty<Properties>, File, OpenBrowser, LoadNetworkFileTaskFactory, FileUtil) - Constructor for class org.cy3sbml.ServiceAdapter: Creates the adapter; a service a test does not need may be null.
SessionData - Class in org.cy3sbml: Saves the cy3sbml data of a Cytoscape session and restores it when the session is loaded.
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: Sets the attribute of the node, edge or network, creating the column if needed.
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: Sets the list attribute of the node, edge or network, creating the list column if needed.
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: Sets whether the action is enabled.
setSBaseMetaId(SBMLDocument, SBase) - Static method in class org.cy3sbml.util.MappingUtil: Sets a metaId, unique in the document, on the SBase if it has none: the cyId of its node.
setSBML2NetworkMapper(Network2SBMLMapper) - Method in class org.cy3sbml.SBMLManager: Replaces the documents and mappings with the ones of the mapper, when a session is restored, and updates the current document for the current network.
setSystemProxy(String, String, String) - Method in class org.cy3sbml.ConnectionProxy: Sets the HTTP and HTTPS system proxy: none for direct, the host and port for http.
setSystemProxyFromCyProperties() - Method in class org.cy3sbml.ConnectionProxy: Sets the system proxy from the Cytoscape proxy settings.
setText(String) - Method in interface org.cy3sbml.gui.InfoPanel: Shows the HTML 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: Shows the information of the SBase.
showSBaseInfo(Object) - Method in class org.cy3sbml.gui.WebViewPanel: Shows the information of the SBase, see WebViewPanel.showSBaseInfo(Set).
showSBaseInfo(Set<Object>) - Method in interface org.cy3sbml.gui.InfoPanel: Shows the information of the SBases.
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) and deletes the temporary directories of the COMBINE archives and of the last saved session, before AbstractCyActivator unregisters the OSGi services.
size() - Method in class org.cy3sbml.cache.MemoryCache: The number of cached found values.
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.
string - Enum constant in enum class org.cy3sbml.styles.Mapping.DataType
string2InputStream(String) - Static method in class org.cy3sbml.util.IOUtil: The UTF-8 bytes of the string as stream.
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: Generates the style files of cy3sbml from a template, which defines the default values, and the mappings of a StyleInfo.
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: Loads the visual styles of cy3sbml and their layout styles, at start and after a session is loaded.
StyleManager(LoadVizmapFileTaskFactory, VisualMappingManager, String[], LayoutStyleFactory) - Constructor for class org.cy3sbml.styles.StyleManager
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.
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: The search terms and the search mode as an HTML table.
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: The root network SUIDs with their documents, one per line.
toString() - Method in class org.cy3sbml.mapping.One2ManyMapping: The keys with their values, one per line.
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: The documents by root network SUID.
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.
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: The keys of the UniProt HTML fragments in GUIConstants.htmlFragments and their placeholders, and the base URL of the UniProt entry pages.
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: Sets the current document to the one of the root network; no current document if the root network has none.
updateCurrent(CyNetwork) - Method in class org.cy3sbml.SBMLManager: Sets the current document to the one of the collection of the network.
updateInformation() - Method in class org.cy3sbml.gui.WebViewPanel: Updates the panel information on the render executor.
upload(byte[], String, String) - Method in class org.cy3sbml.sbml4humans.Sbml4HumansClient: Uploads the archive and returns the address of its report, opened at the entry and the model.
url() - Method in class org.cy3sbml.sbml4humans.Sbml4HumansClient: The address of the reports.
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: The registry JSON of the identifiers.org resolution API.
URL_SAVELAYOUT - Static variable in class org.cy3sbml.gui.BrowserHyperlinkListener
URL_SBML4HUMANS - 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: The cy3sbml panel in the Cytoscape results panel (east): a JavaFX Browser that shows the SBML information of the current network and the selected node, or the help and examples pages.
WebViewPanel(ServiceAdapter, SBMLManager, SBaseHTMLFactory, CofactorManager, BiomodelsDialog) - Constructor for class org.cy3sbml.gui.WebViewPanel: Creates the panel, which shows the help page until the first render.
width() - Method in record class org.cy3sbml.layout.CyBoundingBox: Returns the value of the width record component.
write(SBMLDocument, String, CompModels, OutputStream) - Static method in class org.cy3sbml.archive.CombineArchiveWriter: Writes the archive of the document.
writeNodeToTidyFile(Node, File) - Static method in class org.cy3sbml.util.XMLUtil: Writes the node as indented XML to the file; the error is logged.
writeNodeToTidyString(Node) - Static method in class org.cy3sbml.util.XMLUtil: The node as indented XML, without XML declaration.
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: The XML as HTML text: indented if it is well-formed, escaped, with the line breaks and the indentation kept.
XMLInterface - Class in org.cy3sbml.layout
XMLInterface() - Constructor for class org.cy3sbml.layout.XMLInterface
XMLUtil - Class in org.cy3sbml.util: Reading and writing XML with parsers hardened against XML external entity (XXE) attacks, and formatting XML as indented text or HTML.
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.

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