All Classes and Interfaces
Class
Description
Tools for working with annotations.
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.
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.
The archive an SBML document was imported from.
The content of a COMBINE archive (OMEX): its manifest entries and the metadata of the
archive from
metadata.rdf.A creator of the archive; the parts that are not set are empty.
A file of the archive.
Helper class for getting and setting attribute.
Stores information for a given 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.Open the BioModel GUI for importing BioModels via search terms.
The dialog to search BioModels and load models from it.
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.
Queries of the BioModels REST API (https://www.biomodels.org/docs/).
The result of a BioModels search: the number of matching models and the models read,
in the order of the search response.
A model found by a BioModels search, with the information of the search response.
Browser for displaying HTML within a JavaFX Webview.
Handle hyperlink events in WebView.
The BundleInformation provides runtime information on the bundle.
Activate or deactivate the cy3sbml panel.
Client for the ChEBI public backend REST API.
A ChEBI compound, parsed from the ChEBI public backend REST JSON
(
https://www.ebi.ac.uk/chebi/backend/api/public/compound/<id>/).Splits cofactor nodes into clones and merges the clones back.
The view update after a split or merge of cofactor nodes.
Reads a COMBINE archive (OMEX): unpacks it into a directory and reads its manifest
(
manifest.xml) and the metadata of the archive (metadata.rdf).The COMBINE archives (OMEX) the archive reader imports: zip files with one of the file
extensions of the COMBINE specification.
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).Creates the reader of an SBML file of the archive.
Creates the task that reads the SBML models of a COMBINE archive.
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>.A command: its name in the namespace, descriptions, an example of its JSON result, and
the task factory.
The Cytoscape and cy3sbml services the automation commands use.
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.An external model definition with the resolution of its model.
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.
Handling the system proxy settings required to use the web services (SOAP, REST).
Entry point to cy3sbml.
Position and size of a node in a layout file.
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, ...).
Loads the example HTML page.
The result of a fetch: its
FetchStatus and the value, if found.Outcome of a single
HttpJson fetch, distinguishing "not found" (e.g.Constants used in GUI.
Set help information in ResultsPanel.
Escaping of text for HTML.
Small JSON-over-HTTP helper for the REST web services (OLS, ...).
Importing SBML networks..
Helper functions for input and output.
One-time setup of JSBML before SBML files are read or written on several threads.
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.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.
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.Utilities for working with layouts.
Load node positions from file.
Parent class of mappings.
Information storage for DiscreteMapping
Information storage for PassthroughMapping.
Helper for mapping between Cytoscape and SBML objects.
Thread-safe, size-bounded least-recently-used cache for web service lookups.
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.
The MIRIAM registry of data collections used to resolve annotation URIs.
An identifiers.org resource URI resolved against the registry: its data collection (null
if the registry has none for it) and its identifier.
The result of resolving a model reference of the comp package: the model, or why
it could not be resolved.
The model could not be resolved, with the reason for the user.
The referenced model and the document it is defined in, which is another
document for an external model definition.
The split cofactor nodes of the networks, per (sub)network SUID.
Mapping between CyNetworks and SBMLDocuments.
Utils for working with networks.
Small client for the OLS4 (Ontology Lookup Service) REST API.
An OLS4 ontology term.
One to many mapping class.
Static OpenBrower helper class.
Renders one previously-resolved render target (see
PanelUpdater.resolveTarget(org.cytoscape.model.CyNetwork, org.cy3sbml.SBMLManager)) into the
panel.Tools for working with Miriam registry.
This class extracts bundled resources to a local directory.
Save node positions to file.
Filter testing if object is SBase.
Creates HTML information for given SBase.
Builds the HTML information for a set of SBase objects, via web-service lookups
(OLS, UniProt, ChEBI), and posts it to a panel.
The result of resolving an
SBaseRef: the element it
points to, or why it could not be resolved.The target element in its model.
The reference could not be resolved, with the reason for the user.
Resolves the element an
SBaseRef of the comp package points to.Definition of cy3sbml constants.
Use identical fields to the SBMLCore.
Use a TaskFactory to set the ready state.
SBML Filter class.
The SBMLManager class manages mappings between SBMLDocuments and CyNetworks.
Error thrown by the SBMLReaderTask if an SBML file cannot be read.
The SBMLReaderTask creates CyNetworks from SBMLDocuments.
SBMLReaderTaskFactory class
TaskFactory for the SBMLReaderTask.
Some utils to work with SBML and SBML naming.
The BioModels search of the dialog: the models found by a search or parsed from text,
and their details.
The models of a search or of parsed ids.
Parsing of the form fields into usable SearchContent instance.
Adapter for working with services.
This class implements the saving of cy3sbml session data and
the restoring of the saved data.
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.
Factory for creating visual styles depending on the current
SBML attributes and values.
Parent class of all StyleInfo.
Definition of mappings for style.
Dark style.
Class to manage the loading of the visual styles.
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.
Client for the UniProtKB REST API.
A UniProt entry, parsed from the UniProtKB REST JSON
(
https://rest.uniprot.org/uniprotkb/<accession>.json).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.Allowed keys for mapping.
WebView panel based on javafx.