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.
Helpers for the math (ASTNode) of SBML elements.
Getting and setting the attributes (columns) of the nodes, edges and networks in the
default tables of a network.
The details of a BioModels model from the model endpoint of the BioModels REST API.
The HTML texts of the BioModels dialog, each with the BioModels logo as header.
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 of the cy3sbml panel: a JavaFX
WebView showing the rendered HTML and the
bundled pages, embedded in Swing with a JFXPanel.Handles the links clicked in the cy3sbml panel.
The symbolic name and version of the cy3sbml bundle at runtime.
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).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.
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.
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.
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.
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.
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 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.
The result of a fetch: its
FetchStatus and the value, if found.Outcome of a single
HttpJson fetch, distinguishing "not found" (e.g.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.Actions of the info panel links: loading the examples and opening the SBML, the panel HTML
or a URL in the system browser.
Shows the help page in the cy3sbml panel.
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.
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
<!-- NAME --> and <!-- /NAME -->.Escaping of text for HTML.
Small JSON-over-HTTP helper for the REST web services (OLS, ChEBI, UniProt, BioModels).
Constants of the web resources that resolve the annotations of the models.
Imports SBML files and COMBINE archives chosen in a file dialog.
The panel that shows the SBML information, see
WebViewPanel.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.
A data collection (namespace) of the MIRIAM registry, e.g.
The split cofactor nodes of the networks, per (sub)network SUID.
Mapping between CyNetworks and SBMLDocuments.
Helpers for the networks of a collection: the root network, the subnetworks, and the
selection of nodes.
Small client for the OLS4 (Ontology Lookup Service) REST API.
An OLS4 ontology term: its IRI, label, ontology, synonyms and descriptions.
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).
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.Renders one previously-resolved render target (see
PanelUpdater.resolveTarget(org.cytoscape.model.CyNetwork, org.cy3sbml.SBMLManager)) into the
panel.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.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.
Extracts the bundled GUI resources into the app directory, so the JavaFX WebView can
load them via file URIs (it cannot load bundle: URIs).
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.
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>.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".
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).
Use identical fields to the SBMLCore.
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).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.
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).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.
Saves the cy3sbml data of a Cytoscape session and restores it when the session is loaded.
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.
Generates the style files of cy3sbml from a template, which defines the default values,
and the mappings of a
StyleInfo.Parent class of all StyleInfo.
Definition of mappings for style.
Dark style.
Loads the visual styles of cy3sbml and their layout styles, at start and after a
session is loaded.
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).The keys of the UniProt HTML fragments in
GUIConstants.htmlFragments and their
placeholders, and the base URL of the UniProt entry pages.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.
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.Reading and writing XML with parsers hardened against XML external entity (XXE) attacks,
and formatting XML as indented text or HTML.