Package org.cy3sbml.util

package org.cy3sbml.util
  • Class
    Description
    AnnotationUtil
    Tools for working with annotations.
    ASTNodeUtil
    Helpers for the math (ASTNode) of SBML elements.
    AttributeUtil
    Getting and setting the attributes (columns) of the nodes, edges and networks in the default tables of a network.
    DistribUtil
    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, ...).
    FetchResult<T>
    The result of a fetch: its FetchStatus and the value, if found.
    FetchStatus
    Outcome of a single HttpJson fetch, distinguishing "not found" (e.g.
    GUIUtil
    Actions of the info panel links: loading the examples and opening the SBML, the panel HTML or a URL in the system browser.
    HtmlSanitizer
    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.
    HtmlUtil
    Escaping of text for HTML.
    HttpJson
    Small JSON-over-HTTP helper for the REST web services (OLS, ChEBI, UniProt, BioModels).
    IOUtil
    Helper functions for input and output.
    MappingUtil
    Helper for mapping between Cytoscape and SBML objects.
    NetworkUtil
    Helpers for the networks of a collection: the root network, the subnetworks, and the selection of nodes.
    OpenBrowser
    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.
    SBMLUtil
    Some utils to work with SBML and SBML naming.
    UnitsFormulaCompiler
    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.
    XMLUtil
    Reading and writing XML with parsers hardened against XML external entity (XXE) attacks, and formatting XML as indented text or HTML.